From 0840e3afb546c83ed03df1273c93c7eb644ab813 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 8 Apr 2015 22:13:05 -0700
Subject: [PATCH 001/347] first commit

---
 .gitignore                   |   1 +
 ConjunctiveQueryParser.scala | 342 +++++++++++++++++++++++++++++++++++
 test.scala                   |  55 ++++++
 3 files changed, 398 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 ConjunctiveQueryParser.scala
 create mode 100644 test.scala

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 000000000..6b468b62a
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+*.class
diff --git a/ConjunctiveQueryParser.scala b/ConjunctiveQueryParser.scala
new file mode 100644
index 000000000..ea6f5bcfe
--- /dev/null
+++ b/ConjunctiveQueryParser.scala
@@ -0,0 +1,342 @@
+import scala.util.parsing.combinator._
+import scala.collection.immutable.HashMap
+/*
+ This file parses an extended form of datalog like sugar.
+
+ It allows schema declarations
+
+ SomeOther(realname, otherattribute)
+
+ And queries
+
+ Q(x,y) :- R(x,y), SomeOther(y, z)
+ 
+ Using the schema can SQLized as
+ 
+ SELECT R1.x,R2.y
+ FROM   R as R1,SomeOther as R2
+ WHERE  R1.y = R2.realname
+
+ We translate by introducing aliases R1, R2 , etc. to deal with
+ repeated symbols.
+ 
+ TODO: 
+ =================
+
+ Our schema needs to know whether a symbol is this a query table (and
+ so should contain an _id) field or is a regular table from the
+ user. 
+
+ If a head term is not mentioned in the schema, its assumed it is a
+ query table that this code must create. 
+
+ If one wants to explicilty mention a query table in the schema, they
+ do so with a trailing exclamation point as follows
+
+ Q(x,y)!;
+
+Consider
+
+ Q(x) :- R(x,f) weight=f 
+
+ ... R is likely *not* a variable table ... we record its translation below.
+ 
+ In contrast, Q(x) :- R(x),S(x) ... coule be treated as variable tables. Hence, the schema has:
+
+ R(x,f) // regular table
+ R(x,f)! // variable table.
+
+ */
+
+/* TODOs:
+
+ Refactor schema object and introduce error checking (unsafe queries,
+ unordered attributes, etc.).
+*/
+
+// ***************************************
+// * The union types for for the parser. *
+// ***************************************
+trait Statement
+case class Variable(varName : String, relName: String, index : Int ) 
+case class Atom(name : String, terms : List[Variable]) 
+case class ConjunctiveQuery(head: Atom, body: List[Atom])
+
+case class WeightedRule(q : ConjunctiveQuery, weights : Option[List[String]]) extends Statement // Weighted rule
+case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
+
+
+// Parser
+class ConjunctiveQueryParser extends JavaTokenParsers {   
+  // Odd definitions, but we'll keep them.
+  def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
+  def stringliteral2: Parser[String] = """[a-zA-Z_0-9\.]*""".r ^^ {case (x) => x}
+  def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
+
+  // relation names and columns are just strings.
+  def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
+  def col : Parser[String] = stringliteral  ^^ { case(x) => x }
+
+  def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
+    case (r ~ "(" ~ cols ~ ")") => {
+      val vars = cols.zipWithIndex map { case(name,i) => Variable(name, r, i) }
+      Atom(r,vars)
+    }
+  }
+
+  def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
+    case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
+  }
+
+  def schema_element : Parser[SchemaElement] = atom ~ opt("!") ^^ {
+    case (a ~ None) => SchemaElement(a,true)
+    case (a ~ Some(_)) =>  SchemaElement(a,false)
+  }
+
+
+  def rule : Parser[WeightedRule] = query ~ opt( "weight=" ~ rep1sep(col, ",")) ^^ {
+    case (q ~ Some("weight=" ~ weights)) => WeightedRule(q,Some(weights))
+    case (q ~ None)                      => WeightedRule(q,None)
+  }
+
+  // rules or schema elements in aribitrary order
+  def statement : Parser[Statement] = (rule | schema_element) ^^ {case(x) => x}
+
+  def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
+}
+
+
+// This handles the schema statements.
+// It can tell you if a predicate is a "query" predicate or a "ground prediate"
+// and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
+class StatementSchema( statements : List[Statement] )  {
+    // TODO: refactor the schema into a class that constructs and
+    // manages these maps. Also it should have appropriate
+    // abstractions and error handling for missing values.
+    // ** Start refactor.
+  var schema : Map[ Tuple2[String,Int], String ] = new HashMap[ Tuple2[String,Int], String ]()
+
+  var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
+
+  def init() = {    
+    // generate the statements.
+    statements.foreach {
+      case SchemaElement(Atom(r, terms),query) =>
+        terms.foreach {
+          case Variable(n,r,i) =>
+            schema           += { (r,i) -> n }
+            ground_relations += { r -> query } // record whether a query or a ground term.
+        }
+      case WeightedRule(_,_) => ()
+    }
+    println(schema)
+    println(ground_relations)
+  }
+
+  init()
+
+  // Given a variable, resolve it.  TODO: This should give a warning,
+  // if we encouter a variable that is not in this map, then something
+  // odd has happened.
+  def resolveName( v : Variable ) : String = {
+    v match { case Variable(v,relName,i) =>
+      if(schema contains (relName,i)) {
+        schema(relName,i)
+      } else {
+        return v // I do not like this default, as it allows some errors. TOOD: MAKE MORE PRECISE!
+      }
+    }
+  }
+
+  // The default is query term.
+  def isQueryTerm( relName : String ): Boolean = {
+    if( ground_relations contains relName ) !ground_relations(relName) else true
+  }
+}
+
+// This is responsible for schema elements within a given query, e.g.,
+// what is the canonical version of x? (i.e., the first time it is
+// mentioned in the body. This is useful to translate to SQL (join
+// conditions, select, etc.)
+class QuerySchema(q : ConjunctiveQuery) {
+    var query_schema = new HashMap[ String, Tuple2[Int,Variable] ]()
+  
+  // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
+  // index is the index of the subgoal/atom this variable is found in the body.
+  // variable is the complete Variable type for the found variable.
+  def generateCanonicalVar()  = {
+    q.body.zipWithIndex.foreach {
+      case (Atom(relName,terms),index) =>  {
+        terms.foreach {
+          case Variable(v, r, i) =>
+            if( ! (query_schema contains v) )
+              query_schema += { v -> (index, Variable(v,r,i) ) }
+        }
+      }
+    }
+  }
+  generateCanonicalVar() // initialize
+
+  // accessors
+  def getBodyIndex( varName : String ) : Int = { query_schema(varName)._1 }
+  def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
+
+}
+object ConjunctiveQueryParser extends ConjunctiveQueryParser  {
+
+  // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
+  // and the corresponding WHERE clause (equating all variables)
+  def generateSQLBody(ss : StatementSchema, z : ConjunctiveQuery) : String = {
+    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} as R${i}"}).mkString(",")
+    // Simple logic for the where clause, first find every first occurence of a
+    // and stick it in a map.
+    val qs = new QuerySchema(z)
+
+    val whereClause = z.body.zipWithIndex flatMap {
+      case (Atom(relName, terms),body_index) =>
+        terms flatMap {
+          case Variable(varName, relName, index) =>
+            val canonical_body_index = qs.getBodyIndex(varName)
+
+            if (canonical_body_index != body_index) {
+              val real_attr_name1 = ss.resolveName( Variable(varName, relName, index) )
+              val real_attr_name2 = ss.resolveName( qs.getVar(varName))
+              Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+            } else { None }
+        }
+    }
+    val whereClauseStr = whereClause match {
+      case Nil => ""
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
+    }
+
+    s"""FROM ${ bodyNames } ${ whereClauseStr }"""
+  }
+  // generate the node portion (V) of the factor graph
+  def nodeRule(ss : StatementSchema, z : ConjunctiveQuery) : String = {
+    val headTerms = z.head.terms map {
+      case Variable(v,r,i) => s"R${i}.${ss.resolveName(Variable(v,r,i)) }"
+    }
+    val headTermsStr = ( "0 as _id"  :: headTerms ).mkString(",")
+    s"""CREATE TABLE ${ z.head.name } AS
+    SELECT DISTINCT ${ headTermsStr }
+    ${ generateSQLBody(ss,z) }
+     """
+  }
+
+
+  // The input is a weighted rule and our goal is to generate both the
+  // node query and the (hyper) edge query. The node query is
+  // straightforward using our previous code.
+
+  // The edge query has three parts.
+
+  // The FROM and WHERE clause contain the same terms from node rule, with two extras.
+  // (1) We add the head atom into the FROM clause.
+  // (2) We add the join conditions to the WHERE clause between the head atom and the body.
+  // In the code below, we create a "fake CQ" and generate its body (ignoring the head)
+
+  // The SELECT clause of the query is a bit interesting. 
+  // (1) The SELECT clause contains the id of the head relation (if it is a query term)
+  // (2) The SELECT clause should also contain the weight attributes (resolved properly)
+  // (2) There should be an array_agg( tuple(id1,id2,..) ) of the all query relations in the body.
+
+  // GROUP BY
+  // We should have a group that contains the head variable and the weight attributes.
+  def weightedRule( ss: StatementSchema, r : WeightedRule ) : Tuple2[Option[String], Option[String] ] = {
+    val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,r.q)) else None  
+    val edge_query = {
+      // in the code below, we rely on the head being the last atom for indexing (since we index R{index})
+      val fakeBody        = r.q.body :+ r.q.head
+      val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
+
+      // Generate the body of the query.
+      val qs              = new QuerySchema( r.q )
+      val body_attributes = r.q.body.zipWithIndex flatMap {
+        // check if relName is a ground term, if so skip it.
+        // if not, generate the id column.
+        case (Atom(r,_),i) =>
+          if(ss.isQueryTerm(r)) Some(s"R${i}._id") else None
+      } // we know have all variables in the body
+
+      // Construct the various terms for the select and group by
+      val factor_id_select = Some("0 as _fid")
+      val factor_id        = Some("_fid")
+      val head_id          = if (ss.isQueryTerm(r.q.head.name)) Some(s"R${ r.q.body.length }._id") else None
+
+      // does array agg need a tuple constructor?
+      val array_agg        = if (body_attributes.length > 0) Some(s"array_agg(${ body_attributes.mkString(", ") })") else None
+
+      val uw_str =
+        r.weights match {
+          case None => None
+          case Some(w) =>
+            val uw = w map {
+              case(s) =>
+                s"R${ qs.getBodyIndex(s) }.${ ss.resolveName( qs.getVar(s) ) }"
+            }
+            Some(s"${ uw.mkString(", ") }")
+        }
+
+      val select_str = (List(factor_id_select, head_id, array_agg, uw_str) flatMap { case(u) => u }).mkString(", ")
+      val group_str  = (List(factor_id, head_id, uw_str) flatMap { case(u) => (u) }).mkString(", ")
+
+      val u = s"""
+        SELECT ${select_str} 
+        ${ generateSQLBody(ss, fakeCQ) } 
+        GROUP BY ${group_str} """
+      // if no random variables in the query then don't emit a factor term
+      if (ss.isQueryTerm(r.q.head.name) || body_attributes.length > 0) Some(u) else None
+    }
+    (node_query, edge_query)
+  }
+
+  /*
+   T(base_attr);
+   S(a1,a2)
+   Q(x) :- S(x,y),T(y) 
+   Should generate.
+
+   Node query:
+   CREATE TABLE Q AS
+   SELECT 0 as _id, R0.a1
+   FROM S as R0,T as R1 
+   WHERE R0.a2 = R1.base_attr
+   
+   Edge Query (if S and T are probabilistic)
+   SELECT Q._id, array_agg( (S._id, T_.id) )
+   FROM Q as R0,S as R1,T as R2 
+   WHERE S.y = T.base_attr AND 
+         Q.x = S.x AND Q.z = S.z  
+   
+   Factor Function: OR
+
+   =======
+   R(x,y) (assume non probabilistic)
+
+   Q(x) :- R(x,f) weight=f
+
+   Node Query:
+   CREATE TABLE Q AS
+   SELECT DISTINCT 0 as _id, x FROM R
+   
+   Edge Query:
+   SELECT 0 as _fid, Q.id, R.f as w
+   FROM Q, R
+   WHERE Q.x = R.x
+
+   =======
+   
+   */
+  def main(args: Array[String]) = {
+    val q      = parse(statements, "S(a1,a2); R(pk,f); Q(x) :- R(x,f) weight=f; Q(x) :- S(x,y),T(y); T(base_attr)!; R(x,y) :- U(x,y); S(x,y) :- R(x,y);")
+    val schema = new StatementSchema( q.get )
+
+    val queries = q.get flatMap {
+      case _ : SchemaElement => None
+      case w : WeightedRule =>
+        Some(weightedRule(schema,w))
+    }
+    queries.foreach { case(query) => println(query) }
+  }
+}
diff --git a/test.scala b/test.scala
new file mode 100644
index 000000000..e8917dff9
--- /dev/null
+++ b/test.scala
@@ -0,0 +1,55 @@
+import scala.util.parsing.combinator._
+import scala.collection.immutable.HashMap
+
+trait Statement
+case class Variable(varName : String, relName: String, index : Int ) 
+case class Atom(name : String, terms : List[Variable]) 
+case class ConjunctiveQuery(head: Atom, body: List[Atom])
+
+case class WeightedRule(q : ConjunctiveQuery, weights : Option[List[String]]) extends Statement // Weighted rule
+case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
+
+
+// Parser
+class ConjunctiveQueryParser extends JavaTokenParsers {   
+  def stringliteral: Parser[String] = """[\w]+""".r
+
+  // relation names and columns are just strings.
+  def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
+  def col : Parser[String] = stringliteral  ^^ { case(x) => x }
+
+  def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
+    case (r ~ "(" ~ cols ~ ")") => {
+      val vars = cols.zipWithIndex map { case(name,i) => Variable(name, r, i) }
+      Atom(r,vars)
+    }
+  }
+
+  def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
+    case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
+  }
+
+  def schema_element : Parser[SchemaElement] = atom ~ opt("!") ^^ {
+    case (a ~ None) => SchemaElement(a,true)
+    case (a ~ Some(_)) =>  SchemaElement(a,false)
+  }
+
+
+  def rule : Parser[WeightedRule] = query ~ opt( "weight=" ~ rep1sep(col, ",")) ^^ {
+    case (q ~ Some("weight=" ~ weights)) => WeightedRule(q,Some(weights))
+    case (q ~ None)                      => WeightedRule(q,None)
+  }
+
+  // rules or schema elements in aribitrary order
+  def statement : Parser[Statement] = (rule | schema_element) ^^ {case(x) => x}
+
+  def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
+}
+
+object ConjunctiveQueryParser extends ConjunctiveQueryParser  {
+
+  def main(args: Array[String]) = {
+    val q = parse(statements, args(0))
+    println(q.get)
+  }
+}

From ccbc9881f74e5f1d29c1701368ac9481ecb99a2e Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 8 Apr 2015 22:21:09 -0700
Subject: [PATCH 002/347] minor change

---
 test.scala => Test.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename test.scala => Test.scala (96%)

diff --git a/test.scala b/Test.scala
similarity index 96%
rename from test.scala
rename to Test.scala
index e8917dff9..facf6831b 100644
--- a/test.scala
+++ b/Test.scala
@@ -46,7 +46,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
 }
 
-object ConjunctiveQueryParser extends ConjunctiveQueryParser  {
+object Test extends ConjunctiveQueryParser  {
 
   def main(args: Array[String]) = {
     val q = parse(statements, args(0))

From 779244f1b8feea8b7a5c2f6596a1e002b5c04dae Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 10 Apr 2015 15:55:13 -0700
Subject: [PATCH 003/347] add extraction rule

---
 Test.scala | 212 +++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 204 insertions(+), 8 deletions(-)

diff --git a/Test.scala b/Test.scala
index facf6831b..eec636334 100644
--- a/Test.scala
+++ b/Test.scala
@@ -6,13 +6,18 @@ case class Variable(varName : String, relName: String, index : Int )
 case class Atom(name : String, terms : List[Variable]) 
 case class ConjunctiveQuery(head: Atom, body: List[Atom])
 
-case class WeightedRule(q : ConjunctiveQuery, weights : Option[List[String]]) extends Statement // Weighted rule
 case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
+case class ExtractionRule(q : ConjunctiveQuery, udfs : Option[String]) extends Statement // Extraction rule
+case class InferenceRule(q : ConjunctiveQuery, weights : Option[List[String]]) extends Statement // Inference rule
 
 
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {   
-  def stringliteral: Parser[String] = """[\w]+""".r
+
+  // Odd definitions, but we'll keep them.
+  def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
+  def stringliteral2: Parser[String] = """[a-zA-Z_0-9\.]*""".r ^^ {case (x) => x}
+  def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
 
   // relation names and columns are just strings.
   def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
@@ -25,6 +30,8 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     }
   }
 
+  def udf : Parser[String] = stringliteral ^^ {case (x) => x}
+
   def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
     case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
   }
@@ -34,22 +41,211 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     case (a ~ Some(_)) =>  SchemaElement(a,false)
   }
 
+  def extraction_rule : Parser[ExtractionRule] = query ~ opt( "udf=" ~ udf) ^^ {
+    case (q ~ Some("udf=" ~ udfs)) => ExtractionRule(q,Some(udfs))
+    case (q ~ None)                => ExtractionRule(q,None)
+  }
 
-  def rule : Parser[WeightedRule] = query ~ opt( "weight=" ~ rep1sep(col, ",")) ^^ {
-    case (q ~ Some("weight=" ~ weights)) => WeightedRule(q,Some(weights))
-    case (q ~ None)                      => WeightedRule(q,None)
+  def inference_rule : Parser[InferenceRule] = query ~ opt( "weight=" ~ rep1sep(col, ",")) ^^ {
+    case (q ~ Some("weight=" ~ weights)) => InferenceRule(q,Some(weights))
+    case (q ~ None)                      => InferenceRule(q,None)
   }
 
+
   // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = (rule | schema_element) ^^ {case(x) => x}
+  def statement : Parser[Statement] = (extraction_rule | inference_rule | schema_element) ^^ {case(x) => x}
 
   def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
 }
 
+// This handles the schema statements.
+// It can tell you if a predicate is a "query" predicate or a "ground prediate"
+// and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
+class StatementSchema( statements : List[Statement] )  {
+    // TODO: refactor the schema into a class that constructs and
+    // manages these maps. Also it should have appropriate
+    // abstractions and error handling for missing values.
+    // ** Start refactor.
+  var schema : Map[ Tuple2[String,Int], String ] = new HashMap[ Tuple2[String,Int], String ]()
+
+  var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
+
+  def init() = {    
+    // generate the statements.
+    statements.foreach {
+      case SchemaElement(Atom(r, terms),query) =>
+        terms.foreach {
+          case Variable(n,r,i) =>
+            schema           += { (r,i) -> n }
+            ground_relations += { r -> query } // record whether a query or a ground term.
+        }
+      case ExtractionRule(_,_) => ()
+      case InferenceRule(_,_) => ()
+    }
+    println(schema)
+    println(ground_relations)
+  }
+
+  init()
+
+  // Given a variable, resolve it.  TODO: This should give a warning,
+  // if we encouter a variable that is not in this map, then something
+  // odd has happened.
+  def resolveName( v : Variable ) : String = {
+    v match { case Variable(v,relName,i) =>
+      if(schema contains (relName,i)) {
+        schema(relName,i)
+      } else {
+        return v // I do not like this default, as it allows some errors. TOOD: MAKE MORE PRECISE!
+      }
+    }
+  }
+
+  // The default is query term.
+  def isQueryTerm( relName : String ): Boolean = {
+    if( ground_relations contains relName ) !ground_relations(relName) else true
+  }
+}
+
+// This is responsible for schema elements within a given query, e.g.,
+// what is the canonical version of x? (i.e., the first time it is
+// mentioned in the body. This is useful to translate to SQL (join
+// conditions, select, etc.)
+class QuerySchema(q : ConjunctiveQuery) {
+    var query_schema = new HashMap[ String, Tuple2[Int,Variable] ]()
+  
+  // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
+  // index is the index of the subgoal/atom this variable is found in the body.
+  // variable is the complete Variable type for the found variable.
+  def generateCanonicalVar()  = {
+    q.body.zipWithIndex.foreach {
+      case (Atom(relName,terms),index) =>  {
+        terms.foreach {
+          case Variable(v, r, i) =>
+            if( ! (query_schema contains v) )
+              query_schema += { v -> (index, Variable(v,r,i) ) }
+        }
+      }
+    }
+  }
+  generateCanonicalVar() // initialize
+
+  // accessors
+  def getBodyIndex( varName : String ) : Int = { query_schema(varName)._1 }
+  def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
+
+}
 object Test extends ConjunctiveQueryParser  {
 
+  // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
+  // and the corresponding WHERE clause (equating all variables)
+  def generateSQLBody(ss : StatementSchema, z : ConjunctiveQuery) : String = {
+    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} as R${i}"}).mkString(",")
+    // Simple logic for the where clause, first find every first occurence of a
+    // and stick it in a map.
+    val qs = new QuerySchema(z)
+
+    val whereClause = z.body.zipWithIndex flatMap {
+      case (Atom(relName, terms),body_index) =>
+        terms flatMap {
+          case Variable(varName, relName, index) =>
+            val canonical_body_index = qs.getBodyIndex(varName)
+
+            if (canonical_body_index != body_index) {
+              val real_attr_name1 = ss.resolveName( Variable(varName, relName, index) )
+              val real_attr_name2 = ss.resolveName( qs.getVar(varName))
+              Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+            } else { None }
+        }
+    }
+    val whereClauseStr = whereClause match {
+      case Nil => ""
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
+    }
+
+    s"""FROM ${ bodyNames } ${ whereClauseStr }"""
+  }
+  // generate the node portion (V) of the factor graph
+  def nodeRule(ss : StatementSchema, z : ConjunctiveQuery) : String = {
+    val headTerms = z.head.terms map {
+      case Variable(v,r,i) => s"R${i}.${ss.resolveName(Variable(v,r,i)) }"
+    }
+    val headTermsStr = ( "0 as _id"  :: headTerms ).mkString(",")
+    s"""CREATE TABLE ${ z.head.name } AS
+    SELECT DISTINCT ${ headTermsStr }
+    ${ generateSQLBody(ss,z) }
+     """
+  }
+
+  // Generate extraction rule part for deepdive
+  def extractionRule( ss: StatementSchema, r : ExtractionRule ) : String = {
+    println(r.udfs.get)
+    // Generate the body of the query.
+    val qs              = new QuerySchema( r.q )
+    // variable columns
+    val variableCols = r.q.head.terms flatMap {
+      case(Variable(v,rr,i)) => {
+        val index = qs.getBodyIndex(v)
+        val name  = ss.resolveName(qs.getVar(v))
+        val relation = r.q.body(index).name
+        Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
+      }
+    }
+
+    val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
+    
+    val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
+    
+    println(s"${selectStr}")
+    val inputQuery = s"""
+      SELECT ${selectStr} 
+      ${ generateSQLBody(ss, r.q) }"""
+
+    
+    val extractor = s"""
+      e_${r.udfs.get} {
+        input : \"\"\" ${inputQuery}
+        \"\"\"
+        output_relation : \"${r.q.head.name}\"
+        udf : \"/udf/${r.udfs.get}.py\"
+        style : \"tsv_extractor\"
+      }
+    """
+    extractor
+  }
+
   def main(args: Array[String]) = {
-    val q = parse(statements, args(0))
-    println(q.get)
+    var input = """
+      articles(article_id, text);
+      sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
+      people_mentions(sentence_id, start_position, length, text, mention_id);
+      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id, id);
+      has_spouse_features(relation_id, feature);
+      people_mentions(sentence_id, words, ner_tags):- 
+        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)
+      udf=ext_people;
+      has_spouse(sentence_id, p1.mention_id, p1.text, p2.mention_id, p2.text):-
+        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, p1.mention_id),
+        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, p2.mention_id)
+      udf=ext_has_spouse;
+      has_spouse_features(words, relation_id, p1.start_position, p1.length, p2.start_position, p2.length):-
+        sentences(s.document_id, s.sentence, words, s.lemma, s.pos_tags, s.dependencies, s.ner_tags, s.sentence_offset, sentence_id),
+        has_spouse(person1_id, person2_id, sentence_id, h.description, h.is_true, relation_id, h.id),
+        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, person1_id),
+        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
+      udf=ext_has_spouse_features;
+    """
+    // val q = parse(statements, args(0))
+    val q = parse(statements, input)
+    val schema = new StatementSchema( q.get )
+    val queries = q.get flatMap {
+      case _ : SchemaElement => None
+      case e : ExtractionRule =>
+        Some(extractionRule(schema, e))
+      // case w : InferenceRule =>
+      //   Some(inferenceRule(schema,w))
+    }
+    for (query <- queries)
+      println(query)
   }
 }

From 49a5386ac79e277680b9d7b01dee248648b29a06 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 10 Apr 2015 16:14:55 -0700
Subject: [PATCH 004/347] MERGEDgit commit -m !

---
 Test.scala | 250 ++++++++++++++++++++++++++++++++++++++++++++++++-----
 run.sh     |   7 ++
 2 files changed, 235 insertions(+), 22 deletions(-)
 create mode 100644 run.sh

diff --git a/Test.scala b/Test.scala
index eec636334..43cbd718b 100644
--- a/Test.scala
+++ b/Test.scala
@@ -1,19 +1,82 @@
 import scala.util.parsing.combinator._
 import scala.collection.immutable.HashMap
+/*
+ This file parses an extended form of datalog like sugar.
 
+ It allows schema declarations
+
+ SomeOther(realname, otherattribute)
+
+ And queries
+
+ Q(x,y) :- R(x,y), SomeOther(y, z)
+ 
+ Using the schema can SQLized as
+ 
+ SELECT R1.x,R2.y
+ FROM   R as R1,SomeOther as R2
+ WHERE  R1.y = R2.realname
+
+ We translate by introducing aliases R1, R2 , etc. to deal with
+ repeated symbols.
+ 
+ TODO: 
+ =================
+
+ Our schema needs to know whether a symbol is this a query table (and
+ so should contain an _id) field or is a regular table from the
+ user. 
+
+ If a head term is not mentioned in the schema, its assumed it is a
+ query table that this code must create. 
+
+ If one wants to explicilty mention a query table in the schema, they
+ do so with a trailing exclamation point as follows
+
+ Q(x,y)!;
+
+Consider
+
+ Q(x) :- R(x,f) weight=f 
+
+ ... R is likely *not* a variable table ... we record its translation below.
+ 
+ In contrast, Q(x) :- R(x),S(x) ... coule be treated as variable tables. Hence, the schema has:
+
+ R(x,f) // regular table
+ R(x,f)! // variable table.
+
+ */
+
+/* TODOs:
+
+ Refactor schema object and introduce error checking (unsafe queries,
+ unordered attributes, etc.).
+*/
+
+// ***************************************
+// * The union types for for the parser. *
+// ***************************************
 trait Statement
 case class Variable(varName : String, relName: String, index : Int ) 
 case class Atom(name : String, terms : List[Variable]) 
 case class ConjunctiveQuery(head: Atom, body: List[Atom])
 
+sealed trait FactorWeight {
+  def variables : List[String]
+}
+case class KnownFactorWeight(value: Double) extends FactorWeight {
+  def variables = Nil
+}
+case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
+
 case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
 case class ExtractionRule(q : ConjunctiveQuery, udfs : Option[String]) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : Option[List[String]]) extends Statement // Inference rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight) extends Statement // Weighted rule
 
 
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {   
-
   // Odd definitions, but we'll keep them.
   def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
   def stringliteral2: Parser[String] = """[a-zA-Z_0-9\.]*""".r ^^ {case (x) => x}
@@ -36,24 +99,29 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
   }
 
-  def schema_element : Parser[SchemaElement] = atom ~ opt("!") ^^ {
+  def schemaElement : Parser[SchemaElement] = atom ~ opt("!") ^^ {
     case (a ~ None) => SchemaElement(a,true)
     case (a ~ Some(_)) =>  SchemaElement(a,false)
   }
 
-  def extraction_rule : Parser[ExtractionRule] = query ~ opt( "udf=" ~ udf) ^^ {
-    case (q ~ Some("udf=" ~ udfs)) => ExtractionRule(q,Some(udfs))
-    case (q ~ None)                => ExtractionRule(q,None)
+  def extractionRule : Parser[ExtractionRule] = query ~  "udf" ~ "=" ~ opt(udf) ^^ {
+    case (q ~ "udf" ~ "=" ~ Some(udfs)) => ExtractionRule(q,Some(udfs))
+    case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
   }
 
-  def inference_rule : Parser[InferenceRule] = query ~ opt( "weight=" ~ rep1sep(col, ",")) ^^ {
-    case (q ~ Some("weight=" ~ weights)) => InferenceRule(q,Some(weights))
-    case (q ~ None)                      => InferenceRule(q,None)
+  def constantWeight = "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ { x => KnownFactorWeight(x.toDouble) }
+  def unknwonWeight = "weight" ~> "=" ~> opt(rep1sep(col, ",")) ^^ {
+    case Some(varList) => UnknownFactorWeight(varList.toList)
+    case _ => UnknownFactorWeight(List())
   }
+  def factorWeight = constantWeight | unknwonWeight
 
+  def inferenceRule : Parser[InferenceRule] = query ~ factorWeight ^^ {
+    case (q ~ weight) => InferenceRule(q, weight)
+  }
 
   // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = (extraction_rule | inference_rule | schema_element) ^^ {case(x) => x}
+  def statement : Parser[Statement] = (extractionRule | inferenceRule | schemaElement) ^^ {case(x) => x}
 
   def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
 }
@@ -140,7 +208,7 @@ object Test extends ConjunctiveQueryParser  {
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
   def generateSQLBody(ss : StatementSchema, z : ConjunctiveQuery) : String = {
-    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} as R${i}"}).mkString(",")
+    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
     // Simple logic for the where clause, first find every first occurence of a
     // and stick it in a map.
     val qs = new QuerySchema(z)
@@ -163,7 +231,8 @@ object Test extends ConjunctiveQueryParser  {
       case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
     }
 
-    s"""FROM ${ bodyNames } ${ whereClauseStr }"""
+    s"""FROM ${ bodyNames }
+        ${ whereClauseStr }"""
   }
   // generate the node portion (V) of the factor graph
   def nodeRule(ss : StatementSchema, z : ConjunctiveQuery) : String = {
@@ -211,11 +280,149 @@ object Test extends ConjunctiveQueryParser  {
         style : \"tsv_extractor\"
       }
     """
+    println(extractor)
     extractor
   }
 
+
+  // resolve a column name with alias
+  def resolveColumn(s: String, ss: StatementSchema, qs: QuerySchema, r : InferenceRule,
+   alias: Boolean) : Option[String] = {
+    val index = qs.getBodyIndex(s)
+    val name  = ss.resolveName(qs.getVar(s))
+    val relation = r.q.body(index).name
+    if (alias)
+      Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
+    else
+      Some(s"${relation}.R${index}.${name}")
+  }
+
+  // generate inference rule part for deepdive
+  def inferenceRule(ss : StatementSchema, r : InferenceRule) : String = {
+    // Generate the body of the query.
+    val qs = new QuerySchema( r.q )
+    // check if relName is a ground term, if so skip it.
+    // if not, generate the id column.
+    val variableIds = r.q.body.zipWithIndex flatMap {
+      case (Atom(r,_),i) =>
+        if(ss.isQueryTerm(r)) Some(s"""R${i}.id AS "${r}.R${i}.id" """) else None
+    } // we know have all variables in the body
+
+    val variableIdsStr = if (variableIds.length > 0) Some(variableIds.mkString(", ")) else None
+
+    // variable columns
+    val variableCols = r.q.head.terms flatMap {
+      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r, true)
+    }
+    val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
+
+    // weight string
+    val uwStr = r.weights match {
+      case KnownFactorWeight(x) => None
+      case UnknownFactorWeight(w) => Some(w.flatMap(s => resolveColumn(s, ss, qs, r, true)).mkString(", "))
+    }
+
+    val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
+
+    // factor input query
+    val inputQuery = s"""
+      SELECT ${selectStr} 
+      ${ generateSQLBody(ss, r.q) }"""
+
+    // variable columns using alias (for factor function)
+    val variableColsAlias = r.q.head.terms flatMap {
+      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r, false)
+    }
+    val variableColsAliasStr = if (variableColsAlias.length > 0) Some(variableColsAlias.mkString(", ")) else None
+
+    // factor function
+    val func = s"""Imply(${variableColsAliasStr.get})"""
+
+    // weight
+    val weight = r.weights match {
+      case KnownFactorWeight(x) => s"${x}"
+      case UnknownFactorWeight(w) => {
+        s"""?(${w.flatMap(s => resolveColumn(s, ss, qs, r, false)).mkString(", ")})"""
+      }
+    }
+    
+    val rule = s"""
+      factor_${r.q.head.name} {
+        input_query: \"\"\"${inputQuery}\"\"\"
+        function: "${func}"
+        weight: "${weight}"
+      }
+    """
+    println(rule)
+
+    return inputQuery
+  }
+  /*
+   T(base_attr);
+   S(a1,a2)
+   Q(x) :- S(x,y),T(y) 
+   Should generate.
+
+   Node query:
+   CREATE TABLE Q AS
+   SELECT 0 as _id, R0.a1
+   FROM S as R0,T as R1 
+   WHERE R0.a2 = R1.base_attr
+   
+   Edge Query (if S and T are probabilistic)
+   SELECT Q._id, array_agg( (S._id, T_.id) )
+   FROM Q as R0,S as R1,T as R2 
+   WHERE S.y = T.base_attr AND 
+         Q.x = S.x AND Q.z = S.z  
+   
+   Factor Function: OR
+
+   =======
+   R(x,y) (assume non probabilistic)
+
+   Q(x) :- R(x,f) weight=f
+
+   Node Query:
+   CREATE TABLE Q AS
+   SELECT DISTINCT 0 as _id, x FROM R
+   
+   Edge Query:
+   SELECT 0 as _fid, Q.id, R.f as w
+   FROM Q, R
+   WHERE Q.x = R.x
+
+   =======
+   
+   */
   def main(args: Array[String]) = {
-    var input = """
+    val test1 = """
+      S(a1,a2); 
+      R(pk,f)!; 
+      Q(x) :- R(x,f) weight=f;
+      Q2(x) :- R(x, f), S(x, y) weight = f"""
+    val test2 = """
+      S(a1,a2); 
+      R(pk,f); 
+      Q(x) :- R(x,f) weight=f; 
+      Q(x) :- S(x,y),T(y); 
+      T(base_attr)!; 
+      R(y,x) :- U(x,y); 
+      S(x,y) :- R(x,y);"""
+    val test3 = """
+      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id, id)!;
+      has_spouse_features(relation_id, feature);
+
+      f_has_spouse_features(x) :-
+        has_spouse(a, b, c, d, x, y, e),
+        has_spouse_features(y, f)
+        weight = f;
+
+      f_has_spouse_symmetry(x, y) :-
+        has_spouse(a1, a2, a3, a4, x, a6, a7),
+        has_spouse(a2, a1, b3, b4, y, b6, b7)
+        weight = 1;
+    """
+    val test4 = """
       articles(article_id, text);
       sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
       people_mentions(sentence_id, start_position, length, text, mention_id);
@@ -235,17 +442,16 @@ object Test extends ConjunctiveQueryParser  {
         people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
       udf=ext_has_spouse_features;
     """
-    // val q = parse(statements, args(0))
-    val q = parse(statements, input)
+    val q      = parse(statements, test4)
     val schema = new StatementSchema( q.get )
+
+    println(test4)
+    println()
+
     val queries = q.get flatMap {
-      case _ : SchemaElement => None
-      case e : ExtractionRule =>
-        Some(extractionRule(schema, e))
-      // case w : InferenceRule =>
-      //   Some(inferenceRule(schema,w))
+      case _ : SchemaElement  => None
+      case e : ExtractionRule => Some(extractionRule(schema, e))
+      case w : InferenceRule  => Some(inferenceRule(schema, w))
     }
-    for (query <- queries)
-      println(query)
   }
 }
diff --git a/run.sh b/run.sh
new file mode 100644
index 000000000..ab1252885
--- /dev/null
+++ b/run.sh
@@ -0,0 +1,7 @@
+# scalac ConjunctiveQueryParser.scala
+# scala ConjunctiveQueryParser
+
+
+scalac Test.scala
+scala Test
+

From c6cfcd99621a1ae5fe4e489f800df5d14f2caf5f Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Fri, 10 Apr 2015 16:25:55 -0700
Subject: [PATCH 005/347] refactoring

---
 Test.scala | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/Test.scala b/Test.scala
index 43cbd718b..68c0641df 100644
--- a/Test.scala
+++ b/Test.scala
@@ -248,17 +248,11 @@ object Test extends ConjunctiveQueryParser  {
 
   // Generate extraction rule part for deepdive
   def extractionRule( ss: StatementSchema, r : ExtractionRule ) : String = {
-    println(r.udfs.get)
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
     val variableCols = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => {
-        val index = qs.getBodyIndex(v)
-        val name  = ss.resolveName(qs.getVar(v))
-        val relation = r.q.body(index).name
-        Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
-      }
+      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
     }
 
     val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
@@ -286,11 +280,11 @@ object Test extends ConjunctiveQueryParser  {
 
 
   // resolve a column name with alias
-  def resolveColumn(s: String, ss: StatementSchema, qs: QuerySchema, r : InferenceRule,
+  def resolveColumn(s: String, ss: StatementSchema, qs: QuerySchema, q : ConjunctiveQuery,
    alias: Boolean) : Option[String] = {
     val index = qs.getBodyIndex(s)
     val name  = ss.resolveName(qs.getVar(s))
-    val relation = r.q.body(index).name
+    val relation = q.body(index).name
     if (alias)
       Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
     else
@@ -312,14 +306,14 @@ object Test extends ConjunctiveQueryParser  {
 
     // variable columns
     val variableCols = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r, true)
+      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
     }
     val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
 
     // weight string
     val uwStr = r.weights match {
       case KnownFactorWeight(x) => None
-      case UnknownFactorWeight(w) => Some(w.flatMap(s => resolveColumn(s, ss, qs, r, true)).mkString(", "))
+      case UnknownFactorWeight(w) => Some(w.flatMap(s => resolveColumn(s, ss, qs, r.q, true)).mkString(", "))
     }
 
     val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
@@ -331,7 +325,7 @@ object Test extends ConjunctiveQueryParser  {
 
     // variable columns using alias (for factor function)
     val variableColsAlias = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r, false)
+      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, false)
     }
     val variableColsAliasStr = if (variableColsAlias.length > 0) Some(variableColsAlias.mkString(", ")) else None
 
@@ -342,7 +336,7 @@ object Test extends ConjunctiveQueryParser  {
     val weight = r.weights match {
       case KnownFactorWeight(x) => s"${x}"
       case UnknownFactorWeight(w) => {
-        s"""?(${w.flatMap(s => resolveColumn(s, ss, qs, r, false)).mkString(", ")})"""
+        s"""?(${w.flatMap(s => resolveColumn(s, ss, qs, r.q, false)).mkString(", ")})"""
       }
     }
     

From 15b9a198c84e9d8909c2b2edf1dd46612483fd98 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Fri, 10 Apr 2015 17:12:33 -0700
Subject: [PATCH 006/347] resolve variable schema

---
 Test.scala | 39 ++++++++++++++++++++++++++++++---------
 1 file changed, 30 insertions(+), 9 deletions(-)

diff --git a/Test.scala b/Test.scala
index 68c0641df..f75ec5728 100644
--- a/Test.scala
+++ b/Test.scala
@@ -246,6 +246,29 @@ object Test extends ConjunctiveQueryParser  {
      """
   }
 
+  // generate variable schema statements
+  def variableSchema(statements : List[Statement], ss: StatementSchema) : String = {
+    var schema = Set[String]() 
+    // generate the statements.
+    statements.foreach {
+      case InferenceRule(q, weights) =>
+        val qs = new QuerySchema(q)
+        q.head.terms.foreach {
+          case Variable(n,r,i) => {
+            println(n)
+            val index = qs.getBodyIndex(n)
+            val name  = ss.resolveName(qs.getVar(n))
+            val relation = q.body(index).name
+            schema += s"${relation}.${name} : Boolean"
+          }
+        }
+      case _ => ()
+    }
+    val ddSchema = schema.mkString("\n")
+    println(ddSchema)
+    ddSchema
+  }
+
   // Generate extraction rule part for deepdive
   def extractionRule( ss: StatementSchema, r : ExtractionRule ) : String = {
     // Generate the body of the query.
@@ -436,16 +459,14 @@ object Test extends ConjunctiveQueryParser  {
         people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
       udf=ext_has_spouse_features;
     """
-    val q      = parse(statements, test4)
+    val q      = parse(statements, test3)
     val schema = new StatementSchema( q.get )
+    val variables = variableSchema(q.get, schema)
 
-    println(test4)
-    println()
-
-    val queries = q.get flatMap {
-      case _ : SchemaElement  => None
-      case e : ExtractionRule => Some(extractionRule(schema, e))
-      case w : InferenceRule  => Some(inferenceRule(schema, w))
-    }
+    // val queries = q.get flatMap {
+    //   case _ : SchemaElement  => None
+    //   case e : ExtractionRule => Some(extractionRule(schema, e))
+    //   case w : InferenceRule  => Some(inferenceRule(schema, w))
+    // }
   }
 }

From 7ac3cb11e424cc5873da23eb033ed30024c2f136 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 10 Apr 2015 17:35:05 -0700
Subject: [PATCH 007/347] add dependency in extraction rule

---
 Test.scala | 46 +++++++++++++++++++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 9 deletions(-)

diff --git a/Test.scala b/Test.scala
index 68c0641df..7405c03f9 100644
--- a/Test.scala
+++ b/Test.scala
@@ -58,7 +58,7 @@ Consider
 // * The union types for for the parser. *
 // ***************************************
 trait Statement
-case class Variable(varName : String, relName: String, index : Int ) 
+case class Variable(varName : String, relName : String, index : Int ) 
 case class Atom(name : String, terms : List[Variable]) 
 case class ConjunctiveQuery(head: Atom, body: List[Atom])
 
@@ -247,7 +247,7 @@ object Test extends ConjunctiveQueryParser  {
   }
 
   // Generate extraction rule part for deepdive
-  def extractionRule( ss: StatementSchema, r : ExtractionRule ) : String = {
+  def extractionRule( ss: StatementSchema, em: List[(Int, String)], r : ExtractionRule, index : Int ) : String = {
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
@@ -259,19 +259,27 @@ object Test extends ConjunctiveQueryParser  {
     
     val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
     
-    println(s"${selectStr}")
+    // println(s"${selectStr}")
     val inputQuery = s"""
       SELECT ${selectStr} 
       ${ generateSQLBody(ss, r.q) }"""
 
+    val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
+    var dependencies = List[String]()
+    for (e <- em) {
+      if (dependencyRelation contains e._2) 
+        dependencies ::= s""" "extraction_rule_${e._1}" """
+    }
+    val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
     
     val extractor = s"""
-      e_${r.udfs.get} {
+      extraction_rule_${index} {
         input : \"\"\" ${inputQuery}
         \"\"\"
         output_relation : \"${r.q.head.name}\"
         udf : \"/udf/${r.udfs.get}.py\"
         style : \"tsv_extractor\"
+        ${dependencyStr}
       }
     """
     println(extractor)
@@ -439,13 +447,33 @@ object Test extends ConjunctiveQueryParser  {
     val q      = parse(statements, test4)
     val schema = new StatementSchema( q.get )
 
-    println(test4)
-    println()
+    // println(test4)
+    // println()
 
-    val queries = q.get flatMap {
+    val extracions = q.get flatMap {
       case _ : SchemaElement  => None
-      case e : ExtractionRule => Some(extractionRule(schema, e))
-      case w : InferenceRule  => Some(inferenceRule(schema, w))
+      case e : ExtractionRule => Some(e)
+      case w : InferenceRule  => None
+    }
+    val extractionsWithIndex = extracions.zipWithIndex
+    val extractionMap = extractionsWithIndex map {
+      case (e) => (e._2, e._1.q.head.name)
+    }
+    // for (extractor <- extractionsWithIndex) {
+    //   extractionMap += (extractor.get(1), extractor.get(0).q.head)
+    // }
+
+    println(extractionMap)
+
+    val queries = extractionsWithIndex flatMap {
+      case (e) => Some(extractionRule(schema, extractionMap, e._1, e._2))
     }
+    // println(extractionsWithIndex)
+    // println(extracions)
+    // val queries = q.get flatMap {
+    //   case _ : SchemaElement  => None
+    //   case e : ExtractionRule => Some(extractionRule(schema, extractionMap, e))
+    //   case w : InferenceRule  => Some(inferenceRule(schema, w))
+    // }
   }
 }

From 2ea05d54401b8a8ba727ac86010bcb650820d59b Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Thu, 16 Apr 2015 15:24:55 -0700
Subject: [PATCH 008/347] try new semantics

---
 Test.scala | 106 +++++++++++++++++++++++++++++++++--------------------
 1 file changed, 67 insertions(+), 39 deletions(-)

diff --git a/Test.scala b/Test.scala
index 89aac39dd..b55956ea4 100644
--- a/Test.scala
+++ b/Test.scala
@@ -72,7 +72,7 @@ case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
 
 case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
 case class ExtractionRule(q : ConjunctiveQuery, udfs : Option[String]) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight) extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
 
 
 // Parser
@@ -116,8 +116,10 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   }
   def factorWeight = constantWeight | unknwonWeight
 
-  def inferenceRule : Parser[InferenceRule] = query ~ factorWeight ^^ {
-    case (q ~ weight) => InferenceRule(q, weight)
+  def supervision = "label" ~> "=" ~> col
+
+  def inferenceRule : Parser[InferenceRule] = query ~ factorWeight ~ supervision ^^ {
+    case (q ~ weight ~ supervision) => InferenceRule(q, weight, supervision)
   }
 
   // rules or schema elements in aribitrary order
@@ -148,7 +150,7 @@ class StatementSchema( statements : List[Statement] )  {
             ground_relations += { r -> query } // record whether a query or a ground term.
         }
       case ExtractionRule(_,_) => ()
-      case InferenceRule(_,_) => ()
+      case InferenceRule(_,_,_) => ()
     }
     println(schema)
     println(ground_relations)
@@ -235,14 +237,17 @@ object Test extends ConjunctiveQueryParser  {
         ${ whereClauseStr }"""
   }
   // generate the node portion (V) of the factor graph
-  def nodeRule(ss : StatementSchema, z : ConjunctiveQuery) : String = {
-    val headTerms = z.head.terms map {
-      case Variable(v,r,i) => s"R${i}.${ss.resolveName(Variable(v,r,i)) }"
+  def nodeRule(ss : StatementSchema, qs: QuerySchema, z : InferenceRule) : String = {
+    val headTerms = z.q.head.terms map {
+      case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
     }
-    val headTermsStr = ( "0 as _id"  :: headTerms ).mkString(",")
-    s"""CREATE TABLE ${ z.head.name } AS
-    SELECT DISTINCT ${ headTermsStr }
-    ${ generateSQLBody(ss,z) }
+    val index = qs.getBodyIndex(z.supervision)
+    val name  = ss.resolveName(qs.getVar(z.supervision))
+    val labelCol = s"R${index}.${name}"
+    val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
+    s"""CREATE TABLE ${ z.q.head.name } AS
+    SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
+    ${ generateSQLBody(ss,z.q) }
      """
   }
 
@@ -251,7 +256,7 @@ object Test extends ConjunctiveQueryParser  {
     var schema = Set[String]() 
     // generate the statements.
     statements.foreach {
-      case InferenceRule(q, weights) =>
+      case InferenceRule(q, weights, supervision) =>
         val qs = new QuerySchema(q)
         q.head.terms.foreach {
           case Variable(n,r,i) => {
@@ -324,22 +329,36 @@ object Test extends ConjunctiveQueryParser  {
 
   // generate inference rule part for deepdive
   def inferenceRule(ss : StatementSchema, r : InferenceRule) : String = {
-    // Generate the body of the query.
+    println("==================")
     val qs = new QuerySchema( r.q )
+
+    // node query
+    val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,qs,r)) else None  
+    println(node_query)
+
+    // edge query
+    val fakeBody        = r.q.head +: r.q.body 
+    println(fakeBody)
+    val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
+
+    // Generate the body of the query.
     // check if relName is a ground term, if so skip it.
     // if not, generate the id column.
-    val variableIds = r.q.body.zipWithIndex flatMap {
-      case (Atom(r,_),i) =>
-        if(ss.isQueryTerm(r)) Some(s"""R${i}.id AS "${r}.R${i}.id" """) else None
-    } // we know have all variables in the body
+    // val variableIds = r.q.body.zipWithIndex flatMap {
+    //   case (Atom(r,_),i) =>
+    //     if(ss.isQueryTerm(r)) Some(s"""R${i}.id AS "${r}.R${i}.id" """) else None
+    // } // we know have all variables in the body
 
-    val variableIdsStr = if (variableIds.length > 0) Some(variableIds.mkString(", ")) else None
+    // val variableIdsStr = if (variableIds.length > 0) Some(variableIds.mkString(", ")) else None
 
     // variable columns
-    val variableCols = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
-    }
-    val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
+    // val variableCols = r.q.head.terms flatMap {
+    //   case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
+    // }
+    // val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
+    
+    val variableIdsStr = Some(s"""R0.id AS "${r.q.head.name}.R0.id" """)
+    val variableColsStr = Some(s"""R0.label AS "${r.q.head.name}.R0.label" """)
 
     // weight string
     val uwStr = r.weights match {
@@ -352,16 +371,16 @@ object Test extends ConjunctiveQueryParser  {
     // factor input query
     val inputQuery = s"""
       SELECT ${selectStr} 
-      ${ generateSQLBody(ss, r.q) }"""
+      ${ generateSQLBody(ss, fakeCQ) }"""
 
     // variable columns using alias (for factor function)
-    val variableColsAlias = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, false)
-    }
-    val variableColsAliasStr = if (variableColsAlias.length > 0) Some(variableColsAlias.mkString(", ")) else None
+    // val variableColsAlias = r.q.head.terms flatMap {
+    //   case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, false)
+    // }
+    // val variableColsAliasStr = if (variableColsAlias.length > 0) Some(variableColsAlias.mkString(", ")) else None
 
     // factor function
-    val func = s"""Imply(${variableColsAliasStr.get})"""
+    val func = s"""Imply(${r.q.head.name}.R0.label)"""
 
     // weight
     val weight = r.weights match {
@@ -419,7 +438,7 @@ object Test extends ConjunctiveQueryParser  {
    =======
    
    */
-  def main(args: Array[String]) = {
+  def main(args: Array[String]) {
     val test1 = """
       S(a1,a2); 
       R(pk,f)!; 
@@ -434,19 +453,22 @@ object Test extends ConjunctiveQueryParser  {
       R(y,x) :- U(x,y); 
       S(x,y) :- R(x,y);"""
     val test3 = """
-      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id, id)!;
+      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id);
       has_spouse_features(relation_id, feature);
+      q(rid)!;
 
-      f_has_spouse_features(x) :-
-        has_spouse(a, b, c, d, x, y, e),
+      q(y) :-
+        has_spouse(a, b, c, d, x, y),
         has_spouse_features(y, f)
-        weight = f;
-
-      f_has_spouse_symmetry(x, y) :-
-        has_spouse(a1, a2, a3, a4, x, a6, a7),
-        has_spouse(a2, a1, b3, b4, y, b6, b7)
-        weight = 1;
-    """
+        weight = f
+        label = x;
+        """
+
+    //   f_has_spouse_symmetry(x, y) :-
+    //     has_spouse(a1, a2, a3, a4, x, a6),
+    //     has_spouse(a2, a1, b3, b4, y, b6)
+    //     weight = 1;
+    // """
     val test4 = """
       articles(article_id, text);
       sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
@@ -489,6 +511,12 @@ object Test extends ConjunctiveQueryParser  {
     val queries = extractionsWithIndex flatMap {
       case (e) => Some(extractionRule(schema, extractionMap, e._1, e._2))
     }
+
+    q.get flatMap {
+      case w : InferenceRule  => Some(inferenceRule(schema, w))
+      case _ => None
+    }
+
     // println(extractionsWithIndex)
     // println(extracions)
     // val queries = q.get flatMap {

From e86d99e8c2f8325f65c4d7514202c5e72746d72e Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Mon, 20 Apr 2015 16:16:54 -0700
Subject: [PATCH 009/347] fix issues to fit new syntax

---
 Test.scala | 145 ++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 111 insertions(+), 34 deletions(-)

diff --git a/Test.scala b/Test.scala
index 89aac39dd..7b317b2f0 100644
--- a/Test.scala
+++ b/Test.scala
@@ -71,7 +71,9 @@ case class KnownFactorWeight(value: Double) extends FactorWeight {
 case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
 
 case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
-case class ExtractionRule(q : ConjunctiveQuery, udfs : Option[String]) extends Statement // Extraction rule
+case class FunctionElement( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
+case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
+case class FunctionRule(input : String, output : String, function : String) extends Statement // Extraction rule
 case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight) extends Statement // Weighted rule
 
 
@@ -79,7 +81,7 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight) extends S
 class ConjunctiveQueryParser extends JavaTokenParsers {   
   // Odd definitions, but we'll keep them.
   def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
-  def stringliteral2: Parser[String] = """[a-zA-Z_0-9\.]*""".r ^^ {case (x) => x}
+  def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
   def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
 
   // relation names and columns are just strings.
@@ -104,9 +106,19 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     case (a ~ Some(_)) =>  SchemaElement(a,false)
   }
 
-  def extractionRule : Parser[ExtractionRule] = query ~  "udf" ~ "=" ~ opt(udf) ^^ {
-    case (q ~ "udf" ~ "=" ~ Some(udfs)) => ExtractionRule(q,Some(udfs))
-    case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
+
+  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~ "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ stringliteral ~ "handles" ~ stringliteral ~ "lines" ^^ {
+    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
+  }
+
+
+  def extractionRule : Parser[ExtractionRule] = query  ^^ {
+    case (q) => ExtractionRule(q)
+    // case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
+  }
+
+  def functionRule : Parser[FunctionRule] = stringliteral ~ ":-" ~ "!" ~ stringliteral ~ "(" ~ stringliteral ~ ")" ^^ {
+    case (a ~ ":-" ~ "!" ~ b ~ "(" ~ c ~ ")") => FunctionRule(c, a, b)
   }
 
   def constantWeight = "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ { x => KnownFactorWeight(x.toDouble) }
@@ -121,9 +133,9 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   }
 
   // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = (extractionRule | inferenceRule | schemaElement) ^^ {case(x) => x}
+  def statement : Parser[Statement] = (functionElement | extractionRule | functionRule | inferenceRule | schemaElement) ^^ {case(x) => x}
 
-  def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
+  def statements : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
 }
 
 // This handles the schema statements.
@@ -138,6 +150,8 @@ class StatementSchema( statements : List[Statement] )  {
 
   var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
 
+  var function_schema : Map[String, FunctionElement] = new HashMap[ String, FunctionElement]()
+
   def init() = {    
     // generate the statements.
     statements.foreach {
@@ -147,8 +161,10 @@ class StatementSchema( statements : List[Statement] )  {
             schema           += { (r,i) -> n }
             ground_relations += { r -> query } // record whether a query or a ground term.
         }
-      case ExtractionRule(_,_) => ()
+      case ExtractionRule(_) => ()
       case InferenceRule(_,_) => ()
+      case FunctionElement(a, b, c, d, e) => function_schema += {a -> FunctionElement(a, b, c, d, e)}
+      case FunctionRule(_,_,_) => ()
     }
     println(schema)
     println(ground_relations)
@@ -169,6 +185,15 @@ class StatementSchema( statements : List[Statement] )  {
     }
   }
 
+  def resolveFunctionName( v : String ) : FunctionElement = {
+    if (function_schema contains v) {
+      function_schema(v)
+    } else {
+      return FunctionElement("0","0","0","0","0")
+    }
+
+  } 
+
   // The default is query term.
   def isQueryTerm( relName : String ): Boolean = {
     if( ground_relations contains relName ) !ground_relations(relName) else true
@@ -203,6 +228,8 @@ class QuerySchema(q : ConjunctiveQuery) {
   def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
 
 }
+
+
 object Test extends ConjunctiveQueryParser  {
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
@@ -294,14 +321,56 @@ object Test extends ConjunctiveQueryParser  {
         dependencies ::= s""" "extraction_rule_${e._1}" """
     }
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
+
+    val extractor = s"""
+      extraction_rule_${index} {
+        input : \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
+        \"\"\"
+        style : \"sql_extractor\"
+        ${dependencyStr}
+      }
+    """
+    
+    // val extractor = s"""
+    //   extraction_rule_${index} {
+    //     input : \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
+    //     \"\"\"
+    //     output_relation : \"${r.q.head.name}\"
+    //     udf : \"/udf/${r.udfs.get}.py\"
+    //     style : \"tsv_extractor\"
+    //     ${dependencyStr}
+    //   }
+    // """
+    println(extractor)
+    extractor
+  }
+
+  def functionRule( ss: StatementSchema, dependencies: List[(Int, String)], r : FunctionRule, index : Int) : String = {
+    
+    val inputQuery = s"""
+    SELECT * FROM ${r.input}
+    """
+
+    val function = ss.resolveFunctionName(r.function)    
+
+    // val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
+    var dependency = List[String]()
+    for (d <- dependencies) {
+      if (r.input == d._2) {
+        dependency ::= s""" "extraction_rule_${d._1}" """
+      }
+    }
+    val dependencyStr = if (dependency.length > 0) s"dependencies: [${dependency.mkString(", ")}]" else ""
+
+
     
     val extractor = s"""
       extraction_rule_${index} {
-        input : \"\"\" ${inputQuery}
+        input : \"\"\" SELECT * FROM ${r.input}
         \"\"\"
-        output_relation : \"${r.q.head.name}\"
-        udf : \"/udf/${r.udfs.get}.py\"
-        style : \"tsv_extractor\"
+        output_relation : \"${r.output}\"
+        udf : \"${function.implementation}\"
+        style : \"${function.mode}_extractor\"
         ${dependencyStr}
       }
     """
@@ -467,32 +536,40 @@ object Test extends ConjunctiveQueryParser  {
         people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
       udf=ext_has_spouse_features;
     """
-    val q      = parse(statements, test3)
+
+    val test5 = """
+      ext_people_input(
+        sentence_id,
+        words,
+        ner_tags).
+      function ext_has_spouse_features over like ext_has_spouse_features_input
+                                  returns like has_spouse_features
+      implementation udf/ext_has_spouse_features.py handles tsv lines.
+      function ext_people over like ext_people_input
+                     returns like people_mentions
+      implementation udf/ext_people.py handles tsv lines.
+      ext_people_input(sentence_id, words, ner_tags):- 
+        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
+      people_mentions :-
+      !ext_people(ext_people_input).
+      people_mentions_1 :-
+      !ext_people(people_mentions).
+    """
+    val q      = parse(statements, test5)
+    println(q)
     val schema = new StatementSchema( q.get )
     val variables = variableSchema(q.get, schema)
 
-    val extracions = q.get flatMap {
-      case _ : SchemaElement  => None
-      case e : ExtractionRule => Some(e)
-      case w : InferenceRule  => None
-    }
-    val extractionsWithIndex = extracions.zipWithIndex
-    val extractionMap = extractionsWithIndex map {
-      case (e) => (e._2, e._1.q.head.name)
+    var dependencies = q.get.zipWithIndex map {
+      case (e : ExtractionRule, i) => (i, e.q.head.name)
+      case (f : FunctionRule, i) => (i, f.output)
+      case (_,_) => (-1, "-1")
     }
-    // for (extractor <- extractionsWithIndex) {
-    //   extractionMap += (extractor.get(1), extractor.get(0).q.head)
-    // }
-
-    println(extractionMap)
-
-    val queries = extractionsWithIndex flatMap {
-      case (e) => Some(extractionRule(schema, extractionMap, e._1, e._2))
+    val extracions = q.get.zipWithIndex flatMap {
+      case (e : ExtractionRule, i) => Some(extractionRule(schema, dependencies, e, i))
+      // case (w : InferenceRule, i)  => None
+      case (f : FunctionRule, i) => Some(functionRule(schema, dependencies, f, i))
+      case (_,_) => None
     }
-    // println(extractionsWithIndex)
-    // println(extracions)
-    // val queries = q.get flatMap {
-    //   case _ : SchemaElement  => None
-    //   case e : ExtractionRule => Some(extractionRule(schema, extractionMap, e))
   }
 }

From 8afbcf0fef7b9f046ec80c325a65e69b61d1b33b Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Mon, 20 Apr 2015 18:09:09 -0700
Subject: [PATCH 010/347] add spouse example as test case -- need feiran to add
 inference rule

---
 Test.scala | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 84 insertions(+), 1 deletion(-)

diff --git a/Test.scala b/Test.scala
index 846c2fe0c..be3ef92d7 100644
--- a/Test.scala
+++ b/Test.scala
@@ -583,7 +583,90 @@ object Test extends ConjunctiveQueryParser  {
       people_mentions_1 :-
       !ext_people(people_mentions).
     """
-    val q      = parse(statements, test3)
+
+    val test6 = """
+    articles(
+      article_id,
+      text);
+    sentences(
+      document_id,
+      sentence,
+      words,
+      lemma,
+      pos_tags,
+      dependencies,
+      ner_tags,
+      sentence_offset,
+      sentence_id);
+    people_mentions(
+      sentence_id,
+      start_position,
+      length,
+      text,
+      mention_id);
+    has_spouse_candidates(
+      person1_id,
+      person2_id,
+      sentence_id,
+      description,
+      relation_id);
+    has_spouse_features(
+      relation_id,
+      feature);
+
+    has_spouse(relation_id)!;
+
+    people_mentions :-
+      !ext_people(ext_people_input);
+    ext_people_input(
+      sentence_id,
+      words,
+      ner_tags);
+    ext_people_input(s, words, ner_tags) :-
+      sentences(a, b, words, c, d, e, ner_tags, f, s);
+    function ext_people over like ext_people_input
+                     returns like people_mentions
+      implementation udf/ext_people.py handles tsv lines;
+
+    has_spouse_candidates :-
+      !ext_has_spouse(ext_has_spouse_input);
+    ext_has_spouse_input(
+      sentence_id,
+      p1_id,
+      p1_text,
+      p2_id,
+      p2_text);
+    ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+      people_mentions(s, a, b, p1_text, p1_id),
+      people_mentions(s, c, d, p2_text, p2_id);
+    function ext_has_spouse over like ext_has_spouse_input
+                         returns like has_spouse_candidates
+      implementation udf/ext_has_spouse.py handles tsv lines;
+
+    has_spouse_features :-
+      !ext_has_spouse_features(ext_has_spouse_features_input);
+    ext_has_spouse_features_input(
+      words,
+      relation_id,
+      p1_start_position,
+      p1_length,
+      p2_start_position,
+      p2_length);
+    ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+      sentences(a, b, words, c, d, e, f, g, s),
+      has_spouse_candidates(person1_id, person2_id, s, h, i, rid),
+      people_mentions(s, p1idx, p1len, k, person1_id),
+      people_mentions(s, p2idx, p2len, l, person2_id);
+    function ext_has_spouse_features over like ext_has_spouse_features_input
+                                  returns like has_spouse_features
+      implementation udf/ext_has_spouse_features.py handles tsv lines;
+    """
+    // has_spouse(rid) :-
+    //   has_spouse_candidates(a, b, c, d, rid),
+    //   has_spouse_features(rid, f)
+    // weight = f;
+    // """
+    val q      = parse(statements, test6)
     println(q)
     val schema = new StatementSchema( q.get )
     val variables = variableSchema(q.get, schema)

From 0c2db4bd3e48b02d9001ab9d32997972b857c783 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Mon, 20 Apr 2015 22:03:02 -0700
Subject: [PATCH 011/347] put node query into sql extractor

---
 Test.scala | 50 ++++++++++++++++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 18 deletions(-)

diff --git a/Test.scala b/Test.scala
index 846c2fe0c..77d0bde98 100644
--- a/Test.scala
+++ b/Test.scala
@@ -265,7 +265,7 @@ object Test extends ConjunctiveQueryParser  {
         ${ whereClauseStr }"""
   }
   // generate the node portion (V) of the factor graph
-  def nodeRule(ss : StatementSchema, qs: QuerySchema, z : InferenceRule) : String = {
+  def nodeRule(ss : StatementSchema, qs: QuerySchema, z : InferenceRule, dep: List[(Int, String)]) : String = {
     val headTerms = z.q.head.terms map {
       case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
     }
@@ -273,10 +273,31 @@ object Test extends ConjunctiveQueryParser  {
     val name  = ss.resolveName(qs.getVar(z.supervision))
     val labelCol = s"R${index}.${name}"
     val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-    s"""CREATE TABLE ${ z.q.head.name } AS
-    SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
-    ${ generateSQLBody(ss,z.q) }
-     """
+    val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
+    ${ generateSQLBody(ss,z.q) }"""
+    
+    val dependencyRelation = z.q.body map { case(x) => s"${x.name}"}
+    var dependencies = List[String]()
+    for (e <- dep) {
+      if (dependencyRelation contains e._2) 
+        dependencies ::= s""" "extraction_rule_${e._1}" """
+    }
+    val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
+
+
+    // s"""CREATE TABLE ${ z.q.head.name } AS
+    // SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
+    // ${ generateSQLBody(ss,z.q) }
+    //  """
+    s"""
+      extraction_rule_${z.q.head.name} {
+        input : \"\"\" CREATE TABLE ${z.q.head.name} AS 
+        ${query}
+        \"\"\"
+        style : \"sql_extractor\"
+        ${dependencyStr}
+      }
+    """
   }
 
   // generate variable schema statements
@@ -286,15 +307,7 @@ object Test extends ConjunctiveQueryParser  {
     statements.foreach {
       case InferenceRule(q, weights, supervision) =>
         val qs = new QuerySchema(q)
-        q.head.terms.foreach {
-          case Variable(n,r,i) => {
-            println(n)
-            val index = qs.getBodyIndex(n)
-            val name  = ss.resolveName(qs.getVar(n))
-            val relation = q.body(index).name
-            schema += s"${relation}.${name} : Boolean"
-          }
-        }
+        schema += s"${q.head.name}.label : Boolean"
       case _ => ()
     }
     val ddSchema = schema.mkString("\n")
@@ -303,7 +316,7 @@ object Test extends ConjunctiveQueryParser  {
   }
 
   // Generate extraction rule part for deepdive
-  def extractionRule( ss: StatementSchema, em: List[(Int, String)], r : ExtractionRule, index : Int ) : String = {
+  def extractionRule( ss: StatementSchema, em: List[(Int, String)], r : ExtractionRule, index : Int) : String = {
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
@@ -398,12 +411,12 @@ object Test extends ConjunctiveQueryParser  {
   }
 
   // generate inference rule part for deepdive
-  def inferenceRule(ss : StatementSchema, r : InferenceRule) : String = {
+  def inferenceRule(ss : StatementSchema, r : InferenceRule, dep : List[(Int, String)]) : String = {
     println("==================")
     val qs = new QuerySchema( r.q )
 
     // node query
-    val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,qs,r)) else None  
+    val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,qs,r, dep)) else None  
     println(node_query)
 
     // edge query
@@ -591,11 +604,12 @@ object Test extends ConjunctiveQueryParser  {
     var dependencies = q.get.zipWithIndex map {
       case (e : ExtractionRule, i) => (i, e.q.head.name)
       case (f : FunctionRule, i) => (i, f.output)
+      case (w : InferenceRule, i) => (i, w.q.head.name)
       case (_,_) => (-1, "-1")
     }
     val queries = q.get.zipWithIndex flatMap {
       case (e : ExtractionRule, i) => Some(extractionRule(schema, dependencies, e, i))
-      case (w : InferenceRule, i)  => Some(inferenceRule(schema, w))
+      case (w : InferenceRule, i)  => Some(inferenceRule(schema, w, dependencies))
       case (f : FunctionRule, i) => Some(functionRule(schema, dependencies, f, i))
       case (_,_) => None
     }

From a95f053ea61128a3d6afcf802865a6c98b95b27e Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Mon, 20 Apr 2015 22:07:09 -0700
Subject: [PATCH 012/347] add inference rule to example

---
 Test.scala | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/Test.scala b/Test.scala
index 5177c4c4e..1289fee3d 100644
--- a/Test.scala
+++ b/Test.scala
@@ -622,7 +622,8 @@ object Test extends ConjunctiveQueryParser  {
       person2_id,
       sentence_id,
       description,
-      relation_id);
+      relation_id,
+      is_correct);
     has_spouse_features(
       relation_id,
       feature);
@@ -673,6 +674,12 @@ object Test extends ConjunctiveQueryParser  {
     function ext_has_spouse_features over like ext_has_spouse_features_input
                                   returns like has_spouse_features
       implementation udf/ext_has_spouse_features.py handles tsv lines;
+
+    has_spouse(rid) :-
+      has_spouse_candidates(a, b, c, d, rid, l),
+      has_spouse_features(rid, f)
+    weight = f
+    label = l;
     """
     // has_spouse(rid) :-
     //   has_spouse_candidates(a, b, c, d, rid),

From fadab97376321122c0260e4ac49d37b9ce9d5127 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Mon, 20 Apr 2015 22:11:11 -0700
Subject: [PATCH 013/347] small fix

---
 Test.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Test.scala b/Test.scala
index 1289fee3d..3330518c7 100644
--- a/Test.scala
+++ b/Test.scala
@@ -668,7 +668,7 @@ object Test extends ConjunctiveQueryParser  {
       p2_length);
     ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
       sentences(a, b, words, c, d, e, f, g, s),
-      has_spouse_candidates(person1_id, person2_id, s, h, i, rid),
+      has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
       people_mentions(s, p1idx, p1len, k, person1_id),
       people_mentions(s, p2idx, p2len, l, person2_id);
     function ext_has_spouse_features over like ext_has_spouse_features_input

From bdb2a8809dea58de56ba98562344b68797a1777b Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Tue, 21 Apr 2015 14:25:45 -0700
Subject: [PATCH 014/347] generate full application.conf

---
 Test.scala | 45 ++++++++++++++++++++++++++-------------------
 1 file changed, 26 insertions(+), 19 deletions(-)

diff --git a/Test.scala b/Test.scala
index 3330518c7..9c44f81bf 100644
--- a/Test.scala
+++ b/Test.scala
@@ -169,8 +169,8 @@ class StatementSchema( statements : List[Statement] )  {
       case FunctionElement(a, b, c, d, e) => function_schema += {a -> FunctionElement(a, b, c, d, e)}
       case FunctionRule(_,_,_) => ()
     }
-    println(schema)
-    println(ground_relations)
+    // println(schema)
+    // println(ground_relations)
   }
 
   init()
@@ -284,13 +284,8 @@ object Test extends ConjunctiveQueryParser  {
     }
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
 
-
-    // s"""CREATE TABLE ${ z.q.head.name } AS
-    // SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
-    // ${ generateSQLBody(ss,z.q) }
-    //  """
-    s"""
-      extraction_rule_${z.q.head.name} {
+    val ext = s"""
+      extraction.extractors.extraction_rule_${z.q.head.name} {
         input : \"\"\" CREATE TABLE ${z.q.head.name} AS 
         ${query}
         \"\"\"
@@ -298,6 +293,8 @@ object Test extends ConjunctiveQueryParser  {
         ${dependencyStr}
       }
     """
+    println(ext)
+    ext
   }
 
   // generate variable schema statements
@@ -310,7 +307,11 @@ object Test extends ConjunctiveQueryParser  {
         schema += s"${q.head.name}.label : Boolean"
       case _ => ()
     }
-    val ddSchema = schema.mkString("\n")
+    val ddSchema = s"""
+      deepdive.schema.variables {
+        ${schema.mkString("\n")}
+      }
+    """
     println(ddSchema)
     ddSchema
   }
@@ -328,7 +329,6 @@ object Test extends ConjunctiveQueryParser  {
     
     val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
     
-    // println(s"${selectStr}")
     val inputQuery = s"""
       SELECT ${selectStr} 
       ${ generateSQLBody(ss, r.q) }"""
@@ -342,7 +342,7 @@ object Test extends ConjunctiveQueryParser  {
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
 
     val extractor = s"""
-      extraction_rule_${index} {
+      extraction.extractors.extraction_rule_${index} {
         input : \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
         \"\"\"
         style : \"sql_extractor\"
@@ -384,7 +384,7 @@ object Test extends ConjunctiveQueryParser  {
 
     
     val extractor = s"""
-      extraction_rule_${index} {
+      extraction.extractors.extraction_rule_${index} {
         input : \"\"\" SELECT * FROM ${r.input}
         \"\"\"
         output_relation : \"${r.output}\"
@@ -412,16 +412,13 @@ object Test extends ConjunctiveQueryParser  {
 
   // generate inference rule part for deepdive
   def inferenceRule(ss : StatementSchema, r : InferenceRule, dep : List[(Int, String)]) : String = {
-    println("==================")
     val qs = new QuerySchema( r.q )
 
     // node query
     val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,qs,r, dep)) else None  
-    println(node_query)
 
     // edge query
     val fakeBody        = r.q.head +: r.q.body 
-    println(fakeBody)
     val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
 
     // Generate the body of the query.
@@ -474,7 +471,7 @@ object Test extends ConjunctiveQueryParser  {
     }
     
     val rule = s"""
-      factor_${r.q.head.name} {
+      inference.factors.factor_${r.q.head.name} {
         input_query: \"\"\"${inputQuery}\"\"\"
         function: "${func}"
         weight: "${weight}"
@@ -484,6 +481,18 @@ object Test extends ConjunctiveQueryParser  {
 
     return inputQuery
   }
+
+  def dbSettings() : String = """
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  """
   /*
    T(base_attr);
    S(a1,a2)
@@ -687,10 +696,8 @@ object Test extends ConjunctiveQueryParser  {
     // weight = f;
     // """
     val q      = parse(statements, test6)
-    println(q)
     val schema = new StatementSchema( q.get )
     val variables = variableSchema(q.get, schema)
-    println(variables)
     var dependencies = q.get.zipWithIndex map {
       case (e : ExtractionRule, i) => (i, e.q.head.name)
       case (f : FunctionRule, i) => (i, f.output)

From b9289eab1176c867b348a5e7d21e7c9d6832ae5a Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Tue, 21 Apr 2015 16:31:32 -0700
Subject: [PATCH 015/347] minor change

---
 Test.scala | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/Test.scala b/Test.scala
index 9c44f81bf..f23adcf72 100644
--- a/Test.scala
+++ b/Test.scala
@@ -108,7 +108,8 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   }
 
 
-  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~ "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ stringliteral ~ "handles" ~ stringliteral ~ "lines" ^^ {
+  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral 
+  ~ "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ stringliteral ~ "handles" ~ stringliteral ~ "lines" ^^ {
     case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
   }
 
@@ -286,10 +287,10 @@ object Test extends ConjunctiveQueryParser  {
 
     val ext = s"""
       extraction.extractors.extraction_rule_${z.q.head.name} {
-        input : \"\"\" CREATE TABLE ${z.q.head.name} AS 
+        input: \"\"\" CREATE TABLE ${z.q.head.name} AS 
         ${query}
         \"\"\"
-        style : \"sql_extractor\"
+        style: "sql_extractor"
         ${dependencyStr}
       }
     """
@@ -304,7 +305,7 @@ object Test extends ConjunctiveQueryParser  {
     statements.foreach {
       case InferenceRule(q, weights, supervision) =>
         val qs = new QuerySchema(q)
-        schema += s"${q.head.name}.label : Boolean"
+        schema += s"${q.head.name}.label: Boolean"
       case _ => ()
     }
     val ddSchema = s"""
@@ -343,9 +344,9 @@ object Test extends ConjunctiveQueryParser  {
 
     val extractor = s"""
       extraction.extractors.extraction_rule_${index} {
-        input : \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
+        input: \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
         \"\"\"
-        style : \"sql_extractor\"
+        style: \"sql_extractor\"
         ${dependencyStr}
       }
     """
@@ -385,11 +386,11 @@ object Test extends ConjunctiveQueryParser  {
     
     val extractor = s"""
       extraction.extractors.extraction_rule_${index} {
-        input : \"\"\" SELECT * FROM ${r.input}
+        input: \"\"\" SELECT * FROM ${r.input}
         \"\"\"
-        output_relation : \"${r.output}\"
-        udf : \"${function.implementation}\"
-        style : \"${function.mode}_extractor\"
+        output_relation: \"${r.output}\"
+        udf: \"${function.implementation}\"
+        style: \"${function.mode}_extractor\"
         ${dependencyStr}
       }
     """
@@ -695,6 +696,7 @@ object Test extends ConjunctiveQueryParser  {
     //   has_spouse_features(rid, f)
     // weight = f;
     // """
+    println(dbSettings())
     val q      = parse(statements, test6)
     val schema = new StatementSchema( q.get )
     val variables = variableSchema(q.get, schema)

From 3cf3506ea8e04fae3f2454bfd3e5bf506a6f99fd Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Tue, 21 Apr 2015 16:38:31 -0700
Subject: [PATCH 016/347] small fix

---
 Test.scala | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/Test.scala b/Test.scala
index f23adcf72..73b50ed7d 100644
--- a/Test.scala
+++ b/Test.scala
@@ -108,8 +108,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   }
 
 
-  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral 
-  ~ "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ stringliteral ~ "handles" ~ stringliteral ~ "lines" ^^ {
+  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~ "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ stringliteral ~ "handles" ~ stringliteral ~ "lines" ^^ {
     case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
   }
 
@@ -286,7 +285,7 @@ object Test extends ConjunctiveQueryParser  {
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
 
     val ext = s"""
-      extraction.extractors.extraction_rule_${z.q.head.name} {
+      deepdive.extraction.extractors.extraction_rule_${z.q.head.name} {
         input: \"\"\" CREATE TABLE ${z.q.head.name} AS 
         ${query}
         \"\"\"
@@ -343,7 +342,7 @@ object Test extends ConjunctiveQueryParser  {
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
 
     val extractor = s"""
-      extraction.extractors.extraction_rule_${index} {
+      deepdive.extraction.extractors.extraction_rule_${index} {
         input: \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
         \"\"\"
         style: \"sql_extractor\"
@@ -385,7 +384,7 @@ object Test extends ConjunctiveQueryParser  {
 
     
     val extractor = s"""
-      extraction.extractors.extraction_rule_${index} {
+      deepdive.extraction.extractors.extraction_rule_${index} {
         input: \"\"\" SELECT * FROM ${r.input}
         \"\"\"
         output_relation: \"${r.output}\"
@@ -472,7 +471,7 @@ object Test extends ConjunctiveQueryParser  {
     }
     
     val rule = s"""
-      inference.factors.factor_${r.q.head.name} {
+      deepdive.inference.factors.factor_${r.q.head.name} {
         input_query: \"\"\"${inputQuery}\"\"\"
         function: "${func}"
         weight: "${weight}"

From 50b9067b99725061d6a0f0702151887dbfe13026 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Tue, 21 Apr 2015 17:48:14 -0700
Subject: [PATCH 017/347] fix inference rule alias

---
 Test.scala | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/Test.scala b/Test.scala
index 73b50ed7d..141a0ba35 100644
--- a/Test.scala
+++ b/Test.scala
@@ -286,7 +286,8 @@ object Test extends ConjunctiveQueryParser  {
 
     val ext = s"""
       deepdive.extraction.extractors.extraction_rule_${z.q.head.name} {
-        input: \"\"\" CREATE TABLE ${z.q.head.name} AS 
+        sql: \"\"\" DROP TABLE IF EXISTS ${z.q.head.name};
+        CREATE TABLE ${z.q.head.name} AS 
         ${query}
         \"\"\"
         style: "sql_extractor"
@@ -343,9 +344,10 @@ object Test extends ConjunctiveQueryParser  {
 
     val extractor = s"""
       deepdive.extraction.extractors.extraction_rule_${index} {
-        input: \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
+        sql: \"\"\" DROP VIEW IF EXISTS ${r.q.head.name};
+        CREATE VIEW ${r.q.head.name} AS ${inputQuery}
         \"\"\"
-        style: \"sql_extractor\"
+        style: "sql_extractor"
         ${dependencyStr}
       }
     """
@@ -436,14 +438,15 @@ object Test extends ConjunctiveQueryParser  {
     //   case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
     // }
     // val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
-    
+    val index = r.q.body.length + 1
+    val qs2 = new QuerySchema( fakeCQ )
     val variableIdsStr = Some(s"""R0.id AS "${r.q.head.name}.R0.id" """)
     val variableColsStr = Some(s"""R0.label AS "${r.q.head.name}.R0.label" """)
 
     // weight string
     val uwStr = r.weights match {
       case KnownFactorWeight(x) => None
-      case UnknownFactorWeight(w) => Some(w.flatMap(s => resolveColumn(s, ss, qs, r.q, true)).mkString(", "))
+      case UnknownFactorWeight(w) => Some(w.flatMap(s => resolveColumn(s, ss, qs2, fakeCQ, true)).mkString(", "))
     }
 
     val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
@@ -466,7 +469,7 @@ object Test extends ConjunctiveQueryParser  {
     val weight = r.weights match {
       case KnownFactorWeight(x) => s"${x}"
       case UnknownFactorWeight(w) => {
-        s"""?(${w.flatMap(s => resolveColumn(s, ss, qs, r.q, false)).mkString(", ")})"""
+        s"""?(${w.flatMap(s => resolveColumn(s, ss, qs2, fakeCQ, false)).mkString(", ")})"""
       }
     }
     
@@ -649,7 +652,7 @@ object Test extends ConjunctiveQueryParser  {
       sentences(a, b, words, c, d, e, ner_tags, f, s);
     function ext_people over like ext_people_input
                      returns like people_mentions
-      implementation udf/ext_people.py handles tsv lines;
+      implementation /Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py handles tsv lines;
 
     has_spouse_candidates :-
       !ext_has_spouse(ext_has_spouse_input);
@@ -664,7 +667,7 @@ object Test extends ConjunctiveQueryParser  {
       people_mentions(s, c, d, p2_text, p2_id);
     function ext_has_spouse over like ext_has_spouse_input
                          returns like has_spouse_candidates
-      implementation udf/ext_has_spouse.py handles tsv lines;
+      implementation /Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py handles tsv lines;
 
     has_spouse_features :-
       !ext_has_spouse_features(ext_has_spouse_features_input);
@@ -682,7 +685,7 @@ object Test extends ConjunctiveQueryParser  {
       people_mentions(s, p2idx, p2len, l, person2_id);
     function ext_has_spouse_features over like ext_has_spouse_features_input
                                   returns like has_spouse_features
-      implementation udf/ext_has_spouse_features.py handles tsv lines;
+      implementation /Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py handles tsv lines;
 
     has_spouse(rid) :-
       has_spouse_candidates(a, b, c, d, rid, l),

From 9247777f645d98dcd6a9e72c39a69804bcbe6855 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Tue, 21 Apr 2015 21:23:52 -0700
Subject: [PATCH 018/347] small fix

---
 Test.scala | 37 -------------------------------------
 1 file changed, 37 deletions(-)

diff --git a/Test.scala b/Test.scala
index 141a0ba35..309858285 100644
--- a/Test.scala
+++ b/Test.scala
@@ -351,17 +351,6 @@ object Test extends ConjunctiveQueryParser  {
         ${dependencyStr}
       }
     """
-    
-    // val extractor = s"""
-    //   extraction_rule_${index} {
-    //     input : \"\"\" CREATE VIEW ${r.q.head.name} AS ${inputQuery}
-    //     \"\"\"
-    //     output_relation : \"${r.q.head.name}\"
-    //     udf : \"/udf/${r.udfs.get}.py\"
-    //     style : \"tsv_extractor\"
-    //     ${dependencyStr}
-    //   }
-    // """
     println(extractor)
     extractor
   }
@@ -423,21 +412,6 @@ object Test extends ConjunctiveQueryParser  {
     val fakeBody        = r.q.head +: r.q.body 
     val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
 
-    // Generate the body of the query.
-    // check if relName is a ground term, if so skip it.
-    // if not, generate the id column.
-    // val variableIds = r.q.body.zipWithIndex flatMap {
-    //   case (Atom(r,_),i) =>
-    //     if(ss.isQueryTerm(r)) Some(s"""R${i}.id AS "${r}.R${i}.id" """) else None
-    // } // we know have all variables in the body
-
-    // val variableIdsStr = if (variableIds.length > 0) Some(variableIds.mkString(", ")) else None
-
-    // variable columns
-    // val variableCols = r.q.head.terms flatMap {
-    //   case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
-    // }
-    // val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
     val index = r.q.body.length + 1
     val qs2 = new QuerySchema( fakeCQ )
     val variableIdsStr = Some(s"""R0.id AS "${r.q.head.name}.R0.id" """)
@@ -456,12 +430,6 @@ object Test extends ConjunctiveQueryParser  {
       SELECT ${selectStr} 
       ${ generateSQLBody(ss, fakeCQ) }"""
 
-    // variable columns using alias (for factor function)
-    // val variableColsAlias = r.q.head.terms flatMap {
-    //   case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, false)
-    // }
-    // val variableColsAliasStr = if (variableColsAlias.length > 0) Some(variableColsAlias.mkString(", ")) else None
-
     // factor function
     val func = s"""Imply(${r.q.head.name}.R0.label)"""
 
@@ -693,11 +661,6 @@ object Test extends ConjunctiveQueryParser  {
     weight = f
     label = l;
     """
-    // has_spouse(rid) :-
-    //   has_spouse_candidates(a, b, c, d, rid),
-    //   has_spouse_features(rid, f)
-    // weight = f;
-    // """
     println(dbSettings())
     val q      = parse(statements, test6)
     val schema = new StatementSchema( q.get )

From f9531e21426d3fb56ad737c986a026499114a29d Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Tue, 21 Apr 2015 21:38:26 -0700
Subject: [PATCH 019/347] use . as delimiter, quote function implementation

---
 Test.scala | 60 ++++++++++++++++++++++++++++++++----------------------
 1 file changed, 36 insertions(+), 24 deletions(-)

diff --git a/Test.scala b/Test.scala
index 309858285..5aa2756ce 100644
--- a/Test.scala
+++ b/Test.scala
@@ -83,7 +83,8 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
   // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
   // def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
-  def stringliteral: Parser[String] = """[a-zA-Z0-9\./_]+""".r
+  def stringliteral: Parser[String] = """[a-zA-Z0-9_]+""".r
+  def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
 
   // relation names and columns are just strings.
   def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
@@ -102,14 +103,17 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
   }
 
-  def schemaElement : Parser[SchemaElement] = atom ~ opt("!") ^^ {
+  def schemaElement : Parser[SchemaElement] = atom ~ opt("?") ^^ {
     case (a ~ None) => SchemaElement(a,true)
     case (a ~ Some(_)) =>  SchemaElement(a,false)
   }
 
 
-  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~ "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ stringliteral ~ "handles" ~ stringliteral ~ "lines" ^^ {
-    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
+  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~ 
+  "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ 
+  "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines" ^^ {
+    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~ 
+      "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
   }
 
 
@@ -138,7 +142,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   // rules or schema elements in aribitrary order
   def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
 
-  def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
+  def statements : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
 }
 
 // This handles the schema statements.
@@ -580,7 +584,7 @@ object Test extends ConjunctiveQueryParser  {
     val test6 = """
     articles(
       article_id,
-      text);
+      text).
     sentences(
       document_id,
       sentence,
@@ -590,76 +594,84 @@ object Test extends ConjunctiveQueryParser  {
       dependencies,
       ner_tags,
       sentence_offset,
-      sentence_id);
+      sentence_id).
     people_mentions(
       sentence_id,
       start_position,
       length,
       text,
-      mention_id);
+      mention_id).
     has_spouse_candidates(
       person1_id,
       person2_id,
       sentence_id,
       description,
       relation_id,
-      is_correct);
+      is_correct).
     has_spouse_features(
       relation_id,
-      feature);
+      feature).
 
-    has_spouse(relation_id)!;
+    has_spouse(relation_id)?.
 
     people_mentions :-
-      !ext_people(ext_people_input);
+      !ext_people(ext_people_input).
     ext_people_input(
       sentence_id,
       words,
-      ner_tags);
+      ner_tags).
+
     ext_people_input(s, words, ner_tags) :-
-      sentences(a, b, words, c, d, e, ner_tags, f, s);
+      sentences(a, b, words, c, d, e, ner_tags, f, s).
+
     function ext_people over like ext_people_input
                      returns like people_mentions
-      implementation /Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py handles tsv lines;
+      implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
 
     has_spouse_candidates :-
-      !ext_has_spouse(ext_has_spouse_input);
+      !ext_has_spouse(ext_has_spouse_input).
+
     ext_has_spouse_input(
       sentence_id,
       p1_id,
       p1_text,
       p2_id,
-      p2_text);
+      p2_text).
+
     ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
       people_mentions(s, a, b, p1_text, p1_id),
-      people_mentions(s, c, d, p2_text, p2_id);
+      people_mentions(s, c, d, p2_text, p2_id).
+
     function ext_has_spouse over like ext_has_spouse_input
                          returns like has_spouse_candidates
-      implementation /Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py handles tsv lines;
+      implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
 
     has_spouse_features :-
-      !ext_has_spouse_features(ext_has_spouse_features_input);
+      !ext_has_spouse_features(ext_has_spouse_features_input).
+
     ext_has_spouse_features_input(
       words,
       relation_id,
       p1_start_position,
       p1_length,
       p2_start_position,
-      p2_length);
+      p2_length).
+
     ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
       sentences(a, b, words, c, d, e, f, g, s),
       has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
       people_mentions(s, p1idx, p1len, k, person1_id),
-      people_mentions(s, p2idx, p2len, l, person2_id);
+      people_mentions(s, p2idx, p2len, l, person2_id).
+      
     function ext_has_spouse_features over like ext_has_spouse_features_input
                                   returns like has_spouse_features
-      implementation /Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py handles tsv lines;
+      implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
 
     has_spouse(rid) :-
       has_spouse_candidates(a, b, c, d, rid, l),
       has_spouse_features(rid, f)
     weight = f
-    label = l;
+    label = l.
     """
     println(dbSettings())
     val q      = parse(statements, test6)

From 78f40720217ae0a5e8eaa1252ac70f50e2312e82 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 21 Apr 2015 23:15:23 -0700
Subject: [PATCH 020/347] add attribute type in schema

---
 Test.scala | 105 ++++++++++++++++++++++++++++++-----------------------
 1 file changed, 60 insertions(+), 45 deletions(-)

diff --git a/Test.scala b/Test.scala
index 5aa2756ce..2696147a7 100644
--- a/Test.scala
+++ b/Test.scala
@@ -60,17 +60,21 @@ Consider
 trait Statement
 case class Variable(varName : String, relName : String, index : Int ) 
 case class Atom(name : String, terms : List[Variable]) 
+case class Attribute(name : String, terms : List[Variable], types : List[String]) 
 case class ConjunctiveQuery(head: Atom, body: List[Atom])
+case class Column(name : String, t : String)
 
 sealed trait FactorWeight {
   def variables : List[String]
 }
+
 case class KnownFactorWeight(value: Double) extends FactorWeight {
   def variables = Nil
 }
+
 case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
 
-case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
+case class SchemaElement( a : Attribute , query : Boolean ) extends Statement // atom and whether this is a query relation.
 case class FunctionElement( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 case class FunctionRule(input : String, output : String, function : String) extends Statement // Extraction rule
@@ -83,12 +87,15 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
   // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
   // def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
-  def stringliteral: Parser[String] = """[a-zA-Z0-9_]+""".r
+  def stringliteral: Parser[String] = """[a-zA-Z0-9_\[\]]+""".r
   def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
 
   // relation names and columns are just strings.
   def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
   def col : Parser[String] = stringliteral  ^^ { case(x) => x }
+  def attr : Parser[Column] = stringliteral ~ stringliteral ^^ {
+    case(x ~ y) => Column(x, y)
+  }
 
   def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
     case (r ~ "(" ~ cols ~ ")") => {
@@ -97,13 +104,21 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     }
   }
 
+  def attribute: Parser[Attribute] = relation_name ~ "(" ~ rep1sep(attr, ",") ~ ")" ^^ {
+    case (r ~ "(" ~ attrs ~ ")") => {
+      val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
+      var types = attrs map { case(x) => x.t }
+      Attribute(r,vars, types)
+    }
+  }
+
   def udf : Parser[String] = stringliteral ^^ {case (x) => x}
 
   def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
     case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
   }
 
-  def schemaElement : Parser[SchemaElement] = atom ~ opt("?") ^^ {
+  def schemaElement : Parser[SchemaElement] = attribute ~ opt("?") ^^ {
     case (a ~ None) => SchemaElement(a,true)
     case (a ~ Some(_)) =>  SchemaElement(a,false)
   }
@@ -116,7 +131,6 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
       "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
   }
 
-
   def extractionRule : Parser[ExtractionRule] = query  ^^ {
     case (q) => ExtractionRule(q)
     // case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
@@ -162,7 +176,7 @@ class StatementSchema( statements : List[Statement] )  {
   def init() = {    
     // generate the statements.
     statements.foreach {
-      case SchemaElement(Atom(r, terms),query) =>
+      case SchemaElement(Attribute(r, terms, types),query) =>
         terms.foreach {
           case Variable(n,r,i) =>
             schema           += { (r,i) -> n }
@@ -583,43 +597,44 @@ object Test extends ConjunctiveQueryParser  {
 
     val test6 = """
     articles(
-      article_id,
-      text).
+      article_id text,
+      text       text).
     sentences(
-      document_id,
-      sentence,
-      words,
-      lemma,
-      pos_tags,
-      dependencies,
-      ner_tags,
-      sentence_offset,
-      sentence_id).
+      document_id     text,
+      sentence        text,
+      words           text[],
+      lemma           text[],
+      pos_tags        text[],
+      dependencies    text[],
+      ner_tags        text[],
+      sentence_offset int,
+      sentence_id     text).
     people_mentions(
-      sentence_id,
-      start_position,
-      length,
-      text,
-      mention_id).
+      sentence_id    text,
+      start_position int,
+      length         int,
+      text           text,
+      mention_id     text).
+
     has_spouse_candidates(
-      person1_id,
-      person2_id,
-      sentence_id,
-      description,
-      relation_id,
-      is_correct).
+      person1_id  text,
+      person2_id  text,
+      sentence_id text,
+      description text,
+      relation_id text).
     has_spouse_features(
-      relation_id,
-      feature).
-
-    has_spouse(relation_id)?.
+      relation_id text,
+      feature     text).
 
+    has_spouse(relation_id text)?.
+    
     people_mentions :-
       !ext_people(ext_people_input).
+
     ext_people_input(
-      sentence_id,
-      words,
-      ner_tags).
+      sentence_id text,
+      words       text[],
+      ner_tags    text[]).
 
     ext_people_input(s, words, ner_tags) :-
       sentences(a, b, words, c, d, e, ner_tags, f, s).
@@ -632,11 +647,11 @@ object Test extends ConjunctiveQueryParser  {
       !ext_has_spouse(ext_has_spouse_input).
 
     ext_has_spouse_input(
-      sentence_id,
-      p1_id,
-      p1_text,
-      p2_id,
-      p2_text).
+      sentence_id text,
+      p1_id       text,
+      p1_text     text,
+      p2_id       text,
+      p2_text     text).
 
     ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
       people_mentions(s, a, b, p1_text, p1_id),
@@ -650,12 +665,12 @@ object Test extends ConjunctiveQueryParser  {
       !ext_has_spouse_features(ext_has_spouse_features_input).
 
     ext_has_spouse_features_input(
-      words,
-      relation_id,
-      p1_start_position,
-      p1_length,
-      p2_start_position,
-      p2_length).
+      words             text[],
+      relation_id       text,
+      p1_start_position int,
+      p1_length         int,
+      p2_start_position int,
+      p2_length         int).
 
     ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
       sentences(a, b, words, c, d, e, f, g, s),

From eefd47d99296c6d36d5ac2d82bd8f25054da74ed Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 22 Apr 2015 23:25:41 -0700
Subject: [PATCH 021/347] Renames to DeepDiveLogCompiler.scala

Uses sbt instead of scalac/scala
---
 .gitignore                              |   2 +-
 ConjunctiveQueryParser.scala            | 342 ------------------------
 Test.scala => DeepDiveLogCompiler.scala |   2 +-
 run.sh                                  |   8 +-
 4 files changed, 3 insertions(+), 351 deletions(-)
 delete mode 100644 ConjunctiveQueryParser.scala
 rename Test.scala => DeepDiveLogCompiler.scala (99%)

diff --git a/.gitignore b/.gitignore
index 6b468b62a..ea8c4bf7f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1 @@
-*.class
+/target
diff --git a/ConjunctiveQueryParser.scala b/ConjunctiveQueryParser.scala
deleted file mode 100644
index ea6f5bcfe..000000000
--- a/ConjunctiveQueryParser.scala
+++ /dev/null
@@ -1,342 +0,0 @@
-import scala.util.parsing.combinator._
-import scala.collection.immutable.HashMap
-/*
- This file parses an extended form of datalog like sugar.
-
- It allows schema declarations
-
- SomeOther(realname, otherattribute)
-
- And queries
-
- Q(x,y) :- R(x,y), SomeOther(y, z)
- 
- Using the schema can SQLized as
- 
- SELECT R1.x,R2.y
- FROM   R as R1,SomeOther as R2
- WHERE  R1.y = R2.realname
-
- We translate by introducing aliases R1, R2 , etc. to deal with
- repeated symbols.
- 
- TODO: 
- =================
-
- Our schema needs to know whether a symbol is this a query table (and
- so should contain an _id) field or is a regular table from the
- user. 
-
- If a head term is not mentioned in the schema, its assumed it is a
- query table that this code must create. 
-
- If one wants to explicilty mention a query table in the schema, they
- do so with a trailing exclamation point as follows
-
- Q(x,y)!;
-
-Consider
-
- Q(x) :- R(x,f) weight=f 
-
- ... R is likely *not* a variable table ... we record its translation below.
- 
- In contrast, Q(x) :- R(x),S(x) ... coule be treated as variable tables. Hence, the schema has:
-
- R(x,f) // regular table
- R(x,f)! // variable table.
-
- */
-
-/* TODOs:
-
- Refactor schema object and introduce error checking (unsafe queries,
- unordered attributes, etc.).
-*/
-
-// ***************************************
-// * The union types for for the parser. *
-// ***************************************
-trait Statement
-case class Variable(varName : String, relName: String, index : Int ) 
-case class Atom(name : String, terms : List[Variable]) 
-case class ConjunctiveQuery(head: Atom, body: List[Atom])
-
-case class WeightedRule(q : ConjunctiveQuery, weights : Option[List[String]]) extends Statement // Weighted rule
-case class SchemaElement( a : Atom , query : Boolean ) extends Statement // atom and whether this is a query relation.
-
-
-// Parser
-class ConjunctiveQueryParser extends JavaTokenParsers {   
-  // Odd definitions, but we'll keep them.
-  def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
-  def stringliteral2: Parser[String] = """[a-zA-Z_0-9\.]*""".r ^^ {case (x) => x}
-  def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
-
-  // relation names and columns are just strings.
-  def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
-  def col : Parser[String] = stringliteral  ^^ { case(x) => x }
-
-  def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ cols ~ ")") => {
-      val vars = cols.zipWithIndex map { case(name,i) => Variable(name, r, i) }
-      Atom(r,vars)
-    }
-  }
-
-  def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
-    case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
-  }
-
-  def schema_element : Parser[SchemaElement] = atom ~ opt("!") ^^ {
-    case (a ~ None) => SchemaElement(a,true)
-    case (a ~ Some(_)) =>  SchemaElement(a,false)
-  }
-
-
-  def rule : Parser[WeightedRule] = query ~ opt( "weight=" ~ rep1sep(col, ",")) ^^ {
-    case (q ~ Some("weight=" ~ weights)) => WeightedRule(q,Some(weights))
-    case (q ~ None)                      => WeightedRule(q,None)
-  }
-
-  // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = (rule | schema_element) ^^ {case(x) => x}
-
-  def statements : Parser[List[Statement]] = rep1sep(statement, ";") ^^ { case(x) => x }
-}
-
-
-// This handles the schema statements.
-// It can tell you if a predicate is a "query" predicate or a "ground prediate"
-// and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
-class StatementSchema( statements : List[Statement] )  {
-    // TODO: refactor the schema into a class that constructs and
-    // manages these maps. Also it should have appropriate
-    // abstractions and error handling for missing values.
-    // ** Start refactor.
-  var schema : Map[ Tuple2[String,Int], String ] = new HashMap[ Tuple2[String,Int], String ]()
-
-  var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
-
-  def init() = {    
-    // generate the statements.
-    statements.foreach {
-      case SchemaElement(Atom(r, terms),query) =>
-        terms.foreach {
-          case Variable(n,r,i) =>
-            schema           += { (r,i) -> n }
-            ground_relations += { r -> query } // record whether a query or a ground term.
-        }
-      case WeightedRule(_,_) => ()
-    }
-    println(schema)
-    println(ground_relations)
-  }
-
-  init()
-
-  // Given a variable, resolve it.  TODO: This should give a warning,
-  // if we encouter a variable that is not in this map, then something
-  // odd has happened.
-  def resolveName( v : Variable ) : String = {
-    v match { case Variable(v,relName,i) =>
-      if(schema contains (relName,i)) {
-        schema(relName,i)
-      } else {
-        return v // I do not like this default, as it allows some errors. TOOD: MAKE MORE PRECISE!
-      }
-    }
-  }
-
-  // The default is query term.
-  def isQueryTerm( relName : String ): Boolean = {
-    if( ground_relations contains relName ) !ground_relations(relName) else true
-  }
-}
-
-// This is responsible for schema elements within a given query, e.g.,
-// what is the canonical version of x? (i.e., the first time it is
-// mentioned in the body. This is useful to translate to SQL (join
-// conditions, select, etc.)
-class QuerySchema(q : ConjunctiveQuery) {
-    var query_schema = new HashMap[ String, Tuple2[Int,Variable] ]()
-  
-  // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
-  // index is the index of the subgoal/atom this variable is found in the body.
-  // variable is the complete Variable type for the found variable.
-  def generateCanonicalVar()  = {
-    q.body.zipWithIndex.foreach {
-      case (Atom(relName,terms),index) =>  {
-        terms.foreach {
-          case Variable(v, r, i) =>
-            if( ! (query_schema contains v) )
-              query_schema += { v -> (index, Variable(v,r,i) ) }
-        }
-      }
-    }
-  }
-  generateCanonicalVar() // initialize
-
-  // accessors
-  def getBodyIndex( varName : String ) : Int = { query_schema(varName)._1 }
-  def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
-
-}
-object ConjunctiveQueryParser extends ConjunctiveQueryParser  {
-
-  // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
-  // and the corresponding WHERE clause (equating all variables)
-  def generateSQLBody(ss : StatementSchema, z : ConjunctiveQuery) : String = {
-    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} as R${i}"}).mkString(",")
-    // Simple logic for the where clause, first find every first occurence of a
-    // and stick it in a map.
-    val qs = new QuerySchema(z)
-
-    val whereClause = z.body.zipWithIndex flatMap {
-      case (Atom(relName, terms),body_index) =>
-        terms flatMap {
-          case Variable(varName, relName, index) =>
-            val canonical_body_index = qs.getBodyIndex(varName)
-
-            if (canonical_body_index != body_index) {
-              val real_attr_name1 = ss.resolveName( Variable(varName, relName, index) )
-              val real_attr_name2 = ss.resolveName( qs.getVar(varName))
-              Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
-            } else { None }
-        }
-    }
-    val whereClauseStr = whereClause match {
-      case Nil => ""
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
-    }
-
-    s"""FROM ${ bodyNames } ${ whereClauseStr }"""
-  }
-  // generate the node portion (V) of the factor graph
-  def nodeRule(ss : StatementSchema, z : ConjunctiveQuery) : String = {
-    val headTerms = z.head.terms map {
-      case Variable(v,r,i) => s"R${i}.${ss.resolveName(Variable(v,r,i)) }"
-    }
-    val headTermsStr = ( "0 as _id"  :: headTerms ).mkString(",")
-    s"""CREATE TABLE ${ z.head.name } AS
-    SELECT DISTINCT ${ headTermsStr }
-    ${ generateSQLBody(ss,z) }
-     """
-  }
-
-
-  // The input is a weighted rule and our goal is to generate both the
-  // node query and the (hyper) edge query. The node query is
-  // straightforward using our previous code.
-
-  // The edge query has three parts.
-
-  // The FROM and WHERE clause contain the same terms from node rule, with two extras.
-  // (1) We add the head atom into the FROM clause.
-  // (2) We add the join conditions to the WHERE clause between the head atom and the body.
-  // In the code below, we create a "fake CQ" and generate its body (ignoring the head)
-
-  // The SELECT clause of the query is a bit interesting. 
-  // (1) The SELECT clause contains the id of the head relation (if it is a query term)
-  // (2) The SELECT clause should also contain the weight attributes (resolved properly)
-  // (2) There should be an array_agg( tuple(id1,id2,..) ) of the all query relations in the body.
-
-  // GROUP BY
-  // We should have a group that contains the head variable and the weight attributes.
-  def weightedRule( ss: StatementSchema, r : WeightedRule ) : Tuple2[Option[String], Option[String] ] = {
-    val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,r.q)) else None  
-    val edge_query = {
-      // in the code below, we rely on the head being the last atom for indexing (since we index R{index})
-      val fakeBody        = r.q.body :+ r.q.head
-      val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
-
-      // Generate the body of the query.
-      val qs              = new QuerySchema( r.q )
-      val body_attributes = r.q.body.zipWithIndex flatMap {
-        // check if relName is a ground term, if so skip it.
-        // if not, generate the id column.
-        case (Atom(r,_),i) =>
-          if(ss.isQueryTerm(r)) Some(s"R${i}._id") else None
-      } // we know have all variables in the body
-
-      // Construct the various terms for the select and group by
-      val factor_id_select = Some("0 as _fid")
-      val factor_id        = Some("_fid")
-      val head_id          = if (ss.isQueryTerm(r.q.head.name)) Some(s"R${ r.q.body.length }._id") else None
-
-      // does array agg need a tuple constructor?
-      val array_agg        = if (body_attributes.length > 0) Some(s"array_agg(${ body_attributes.mkString(", ") })") else None
-
-      val uw_str =
-        r.weights match {
-          case None => None
-          case Some(w) =>
-            val uw = w map {
-              case(s) =>
-                s"R${ qs.getBodyIndex(s) }.${ ss.resolveName( qs.getVar(s) ) }"
-            }
-            Some(s"${ uw.mkString(", ") }")
-        }
-
-      val select_str = (List(factor_id_select, head_id, array_agg, uw_str) flatMap { case(u) => u }).mkString(", ")
-      val group_str  = (List(factor_id, head_id, uw_str) flatMap { case(u) => (u) }).mkString(", ")
-
-      val u = s"""
-        SELECT ${select_str} 
-        ${ generateSQLBody(ss, fakeCQ) } 
-        GROUP BY ${group_str} """
-      // if no random variables in the query then don't emit a factor term
-      if (ss.isQueryTerm(r.q.head.name) || body_attributes.length > 0) Some(u) else None
-    }
-    (node_query, edge_query)
-  }
-
-  /*
-   T(base_attr);
-   S(a1,a2)
-   Q(x) :- S(x,y),T(y) 
-   Should generate.
-
-   Node query:
-   CREATE TABLE Q AS
-   SELECT 0 as _id, R0.a1
-   FROM S as R0,T as R1 
-   WHERE R0.a2 = R1.base_attr
-   
-   Edge Query (if S and T are probabilistic)
-   SELECT Q._id, array_agg( (S._id, T_.id) )
-   FROM Q as R0,S as R1,T as R2 
-   WHERE S.y = T.base_attr AND 
-         Q.x = S.x AND Q.z = S.z  
-   
-   Factor Function: OR
-
-   =======
-   R(x,y) (assume non probabilistic)
-
-   Q(x) :- R(x,f) weight=f
-
-   Node Query:
-   CREATE TABLE Q AS
-   SELECT DISTINCT 0 as _id, x FROM R
-   
-   Edge Query:
-   SELECT 0 as _fid, Q.id, R.f as w
-   FROM Q, R
-   WHERE Q.x = R.x
-
-   =======
-   
-   */
-  def main(args: Array[String]) = {
-    val q      = parse(statements, "S(a1,a2); R(pk,f); Q(x) :- R(x,f) weight=f; Q(x) :- S(x,y),T(y); T(base_attr)!; R(x,y) :- U(x,y); S(x,y) :- R(x,y);")
-    val schema = new StatementSchema( q.get )
-
-    val queries = q.get flatMap {
-      case _ : SchemaElement => None
-      case w : WeightedRule =>
-        Some(weightedRule(schema,w))
-    }
-    queries.foreach { case(query) => println(query) }
-  }
-}
diff --git a/Test.scala b/DeepDiveLogCompiler.scala
similarity index 99%
rename from Test.scala
rename to DeepDiveLogCompiler.scala
index 2696147a7..01a56a02b 100644
--- a/Test.scala
+++ b/DeepDiveLogCompiler.scala
@@ -251,7 +251,7 @@ class QuerySchema(q : ConjunctiveQuery) {
 }
 
 
-object Test extends ConjunctiveQueryParser  {
+object ddlc extends ConjunctiveQueryParser  {
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
diff --git a/run.sh b/run.sh
index ab1252885..7c9cf44ca 100644
--- a/run.sh
+++ b/run.sh
@@ -1,7 +1 @@
-# scalac ConjunctiveQueryParser.scala
-# scala ConjunctiveQueryParser
-
-
-scalac Test.scala
-scala Test
-
+sbt run

From e8d68fde3f57a031be7de7729099cc8cc88f62cb Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 22 Apr 2015 23:32:31 -0700
Subject: [PATCH 022/347] Moves test input programs to separate files

---
 DeepDiveLogCompiler.scala | 177 ++------------------------------------
 examples/test1.ddl        |   4 +
 examples/test2.ddl        |   7 ++
 examples/test3.ddl        |  19 ++++
 examples/test4.ddl        |  18 ++++
 examples/test5.ddl        |  16 ++++
 examples/test6.ddl        |  91 ++++++++++++++++++++
 run.sh                    |   2 +-
 8 files changed, 165 insertions(+), 169 deletions(-)
 create mode 100644 examples/test1.ddl
 create mode 100644 examples/test2.ddl
 create mode 100644 examples/test3.ddl
 create mode 100644 examples/test4.ddl
 create mode 100644 examples/test5.ddl
 create mode 100644 examples/test6.ddl

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 01a56a02b..81b7540b4 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -520,176 +520,17 @@ object ddlc extends ConjunctiveQueryParser  {
    
    */
   def main(args: Array[String]) {
-    val test1 = """
-      S(a1,a2); 
-      R(pk,f)!; 
-      Q(x) :- R(x,f) weight=f;
-      Q2(x) :- R(x, f), S(x, y) weight = f"""
-    val test2 = """
-      S(a1,a2); 
-      R(pk,f); 
-      Q(x) :- R(x,f) weight=f; 
-      Q(x) :- S(x,y),T(y); 
-      T(base_attr)!; 
-      R(y,x) :- U(x,y); 
-      S(x,y) :- R(x,y);"""
-    val test3 = """
-      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id);
-      has_spouse_features(relation_id, feature);
-      q(rid)!;
-
-      q(y) :-
-        has_spouse(a, b, c, d, x, y),
-        has_spouse_features(y, f)
-        weight = f
-        label = x;
-      q(y) :-
-        has_spouse(a, b, c, d, x, y),
-        has_spouse_features(y, f)
-        weight = f
-        label = x;
-        """
-
-    //   f_has_spouse_symmetry(x, y) :-
-    //     has_spouse(a1, a2, a3, a4, x, a6),
-    //     has_spouse(a2, a1, b3, b4, y, b6)
-    //     weight = 1;
-    // """
-    val test4 = """
-      articles(article_id, text);
-      sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
-      people_mentions(sentence_id, start_position, length, text, mention_id);
-      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id, id);
-      has_spouse_features(relation_id, feature);
-      people_mentions(sentence_id, words, ner_tags):- 
-        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)
-      udf=ext_people;
-      has_spouse(sentence_id, p1.mention_id, p1.text, p2.mention_id, p2.text):-
-        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, p1.mention_id),
-        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, p2.mention_id)
-      udf=ext_has_spouse;
-      has_spouse_features(words, relation_id, p1.start_position, p1.length, p2.start_position, p2.length):-
-        sentences(s.document_id, s.sentence, words, s.lemma, s.pos_tags, s.dependencies, s.ner_tags, s.sentence_offset, sentence_id),
-        has_spouse(person1_id, person2_id, sentence_id, h.description, h.is_true, relation_id, h.id),
-        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, person1_id),
-        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
-      udf=ext_has_spouse_features;
-    """
-
-    val test5 = """
-      ext_people_input(
-        sentence_id,
-        words,
-        ner_tags).
-      function ext_has_spouse_features over like ext_has_spouse_features_input
-                                  returns like has_spouse_features
-      implementation udf/ext_has_spouse_features.py handles tsv lines.
-      function ext_people over like ext_people_input
-                     returns like people_mentions
-      implementation udf/ext_people.py handles tsv lines.
-      ext_people_input(sentence_id, words, ner_tags):- 
-        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
-      people_mentions :-
-      !ext_people(ext_people_input).
-      people_mentions_1 :-
-      !ext_people(people_mentions).
-    """
+    // get contents of all given files as one flat input program
+    val getContents = (filename: String) => {
+      val source = scala.io.Source.fromFile(filename)
+      try source.getLines mkString "\n" finally source.close()
+    }
+    val inputProgram = args.map(getContents).reduce(_ ++ _)
 
-    val test6 = """
-    articles(
-      article_id text,
-      text       text).
-    sentences(
-      document_id     text,
-      sentence        text,
-      words           text[],
-      lemma           text[],
-      pos_tags        text[],
-      dependencies    text[],
-      ner_tags        text[],
-      sentence_offset int,
-      sentence_id     text).
-    people_mentions(
-      sentence_id    text,
-      start_position int,
-      length         int,
-      text           text,
-      mention_id     text).
-
-    has_spouse_candidates(
-      person1_id  text,
-      person2_id  text,
-      sentence_id text,
-      description text,
-      relation_id text).
-    has_spouse_features(
-      relation_id text,
-      feature     text).
-
-    has_spouse(relation_id text)?.
-    
-    people_mentions :-
-      !ext_people(ext_people_input).
-
-    ext_people_input(
-      sentence_id text,
-      words       text[],
-      ner_tags    text[]).
-
-    ext_people_input(s, words, ner_tags) :-
-      sentences(a, b, words, c, d, e, ner_tags, f, s).
-
-    function ext_people over like ext_people_input
-                     returns like people_mentions
-      implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
-
-    has_spouse_candidates :-
-      !ext_has_spouse(ext_has_spouse_input).
-
-    ext_has_spouse_input(
-      sentence_id text,
-      p1_id       text,
-      p1_text     text,
-      p2_id       text,
-      p2_text     text).
-
-    ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
-      people_mentions(s, a, b, p1_text, p1_id),
-      people_mentions(s, c, d, p2_text, p2_id).
-
-    function ext_has_spouse over like ext_has_spouse_input
-                         returns like has_spouse_candidates
-      implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
-
-    has_spouse_features :-
-      !ext_has_spouse_features(ext_has_spouse_features_input).
-
-    ext_has_spouse_features_input(
-      words             text[],
-      relation_id       text,
-      p1_start_position int,
-      p1_length         int,
-      p2_start_position int,
-      p2_length         int).
-
-    ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-      sentences(a, b, words, c, d, e, f, g, s),
-      has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-      people_mentions(s, p1idx, p1len, k, person1_id),
-      people_mentions(s, p2idx, p2len, l, person2_id).
-      
-    function ext_has_spouse_features over like ext_has_spouse_features_input
-                                  returns like has_spouse_features
-      implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
-
-    has_spouse(rid) :-
-      has_spouse_candidates(a, b, c, d, rid, l),
-      has_spouse_features(rid, f)
-    weight = f
-    label = l.
-    """
+    // TODO refactor side effects out of the codegen functions
+    // TODO print the generated code all at once at the end
     println(dbSettings())
-    val q      = parse(statements, test6)
+    val q      = parse(statements, inputProgram)
     val schema = new StatementSchema( q.get )
     val variables = variableSchema(q.get, schema)
     var dependencies = q.get.zipWithIndex map {
diff --git a/examples/test1.ddl b/examples/test1.ddl
new file mode 100644
index 000000000..2e0e20fdc
--- /dev/null
+++ b/examples/test1.ddl
@@ -0,0 +1,4 @@
+      S(a1,a2); 
+      R(pk,f)!; 
+      Q(x) :- R(x,f) weight=f;
+      Q2(x) :- R(x, f), S(x, y) weight = f
diff --git a/examples/test2.ddl b/examples/test2.ddl
new file mode 100644
index 000000000..6add95d11
--- /dev/null
+++ b/examples/test2.ddl
@@ -0,0 +1,7 @@
+      S(a1,a2); 
+      R(pk,f); 
+      Q(x) :- R(x,f) weight=f; 
+      Q(x) :- S(x,y),T(y); 
+      T(base_attr)!; 
+      R(y,x) :- U(x,y); 
+      S(x,y) :- R(x,y);
diff --git a/examples/test3.ddl b/examples/test3.ddl
new file mode 100644
index 000000000..a5fdbc227
--- /dev/null
+++ b/examples/test3.ddl
@@ -0,0 +1,19 @@
+      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id);
+      has_spouse_features(relation_id, feature);
+      q(rid)!;
+
+      q(y) :-
+        has_spouse(a, b, c, d, x, y),
+        has_spouse_features(y, f)
+        weight = f
+        label = x;
+      q(y) :-
+        has_spouse(a, b, c, d, x, y),
+        has_spouse_features(y, f)
+        weight = f
+        label = x;
+
+    //   f_has_spouse_symmetry(x, y) :-
+    //     has_spouse(a1, a2, a3, a4, x, a6),
+    //     has_spouse(a2, a1, b3, b4, y, b6)
+    //     weight = 1;
diff --git a/examples/test4.ddl b/examples/test4.ddl
new file mode 100644
index 000000000..47989f676
--- /dev/null
+++ b/examples/test4.ddl
@@ -0,0 +1,18 @@
+      articles(article_id, text);
+      sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
+      people_mentions(sentence_id, start_position, length, text, mention_id);
+      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id, id);
+      has_spouse_features(relation_id, feature);
+      people_mentions(sentence_id, words, ner_tags):- 
+        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)
+      udf=ext_people;
+      has_spouse(sentence_id, p1.mention_id, p1.text, p2.mention_id, p2.text):-
+        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, p1.mention_id),
+        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, p2.mention_id)
+      udf=ext_has_spouse;
+      has_spouse_features(words, relation_id, p1.start_position, p1.length, p2.start_position, p2.length):-
+        sentences(s.document_id, s.sentence, words, s.lemma, s.pos_tags, s.dependencies, s.ner_tags, s.sentence_offset, sentence_id),
+        has_spouse(person1_id, person2_id, sentence_id, h.description, h.is_true, relation_id, h.id),
+        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, person1_id),
+        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
+      udf=ext_has_spouse_features;
diff --git a/examples/test5.ddl b/examples/test5.ddl
new file mode 100644
index 000000000..55144dda4
--- /dev/null
+++ b/examples/test5.ddl
@@ -0,0 +1,16 @@
+      ext_people_input(
+        sentence_id,
+        words,
+        ner_tags).
+      function ext_has_spouse_features over like ext_has_spouse_features_input
+                                  returns like has_spouse_features
+      implementation udf/ext_has_spouse_features.py handles tsv lines.
+      function ext_people over like ext_people_input
+                     returns like people_mentions
+      implementation udf/ext_people.py handles tsv lines.
+      ext_people_input(sentence_id, words, ner_tags):- 
+        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
+      people_mentions :-
+      !ext_people(ext_people_input).
+      people_mentions_1 :-
+      !ext_people(people_mentions).
diff --git a/examples/test6.ddl b/examples/test6.ddl
new file mode 100644
index 000000000..753bea2e5
--- /dev/null
+++ b/examples/test6.ddl
@@ -0,0 +1,91 @@
+articles(
+  article_id text,
+  text       text).
+sentences(
+  document_id     text,
+  sentence        text,
+  words           text[],
+  lemma           text[],
+  pos_tags        text[],
+  dependencies    text[],
+  ner_tags        text[],
+  sentence_offset int,
+  sentence_id     text).
+people_mentions(
+  sentence_id    text,
+  start_position int,
+  length         int,
+  text           text,
+  mention_id     text).
+
+has_spouse_candidates(
+  person1_id  text,
+  person2_id  text,
+  sentence_id text,
+  description text,
+  relation_id text).
+has_spouse_features(
+  relation_id text,
+  feature     text).
+
+has_spouse(relation_id text)?.
+
+people_mentions :-
+  !ext_people(ext_people_input).
+
+ext_people_input(
+  sentence_id text,
+  words       text[],
+  ner_tags    text[]).
+
+ext_people_input(s, words, ner_tags) :-
+  sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people over like ext_people_input
+                 returns like people_mentions
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
+
+has_spouse_candidates :-
+  !ext_has_spouse(ext_has_spouse_input).
+
+ext_has_spouse_input(
+  sentence_id text,
+  p1_id       text,
+  p1_text     text,
+  p2_id       text,
+  p2_text     text).
+
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, a, b, p1_text, p1_id),
+  people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse over like ext_has_spouse_input
+                     returns like has_spouse_candidates
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
+
+has_spouse_features :-
+  !ext_has_spouse_features(ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(
+  words             text[],
+  relation_id       text,
+  p1_start_position int,
+  p1_length         int,
+  p2_start_position int,
+  p2_length         int).
+
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(a, b, words, c, d, e, f, g, s),
+  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+  people_mentions(s, p1idx, p1len, k, person1_id),
+  people_mentions(s, p2idx, p2len, l, person2_id).
+  
+function ext_has_spouse_features over like ext_has_spouse_features_input
+                              returns like has_spouse_features
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
+
+has_spouse(rid) :-
+  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_features(rid, f)
+weight = f
+label = l.
diff --git a/run.sh b/run.sh
index 7c9cf44ca..fece1865a 100644
--- a/run.sh
+++ b/run.sh
@@ -1 +1 @@
-sbt run
+sbt "run examples/test6.ddl"

From 055345a30cb02ef7b7fbd3eaa9ac3fbd58b30cdf Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 22 Apr 2015 23:34:00 -0700
Subject: [PATCH 023/347] Runs a packaged jar instead of doing sbt run

---
 .gitignore | 1 +
 run.sh     | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index ea8c4bf7f..e6525fdb8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
+/ddlc.jar
 /target
diff --git a/run.sh b/run.sh
index fece1865a..6a4748fd8 100644
--- a/run.sh
+++ b/run.sh
@@ -1 +1,2 @@
-sbt "run examples/test6.ddl"
+sbt package
+scala target/scala-*/*.jar examples/test6.ddl

From b5f81d8db7f5eb28a88812f66bac874b9a75124d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 22 Apr 2015 23:45:45 -0700
Subject: [PATCH 024/347] Turns run.sh into a Makefile with README

---
 Makefile  | 12 ++++++++++++
 README.md | 16 ++++++++++++++++
 run.sh    |  2 --
 3 files changed, 28 insertions(+), 2 deletions(-)
 create mode 100644 Makefile
 create mode 100644 README.md
 delete mode 100644 run.sh

diff --git a/Makefile b/Makefile
new file mode 100644
index 000000000..b498c074e
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,12 @@
+# Makefile for DeepDiveLogCompiler
+
+JAR = ddlc.jar
+
+test: $(JAR)
+	scala $(JAR) examples/test6.ddl
+
+$(JAR): $(wildcard *.scala)
+	sbt package
+	jar=(target/scala-*/*.jar); ln -sfn $${jar[0]} $(JAR)
+	touch $(JAR)
+
diff --git a/README.md b/README.md
new file mode 100644
index 000000000..87f79a46d
--- /dev/null
+++ b/README.md
@@ -0,0 +1,16 @@
+DeepDiveLogCompiler
+===================
+
+A compiler that enables writing DeepDive apps in a Datalog-like syntax.
+
+## Building
+
+```bash
+make
+```
+
+## Running
+The following will generate an application.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
+```bash
+scala ddlc.jar examples/spouse_example.ddl >application.conf
+```
diff --git a/run.sh b/run.sh
deleted file mode 100644
index 6a4748fd8..000000000
--- a/run.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-sbt package
-scala target/scala-*/*.jar examples/test6.ddl

From 8ebad42f3834f6499c57e64b6d1a3979a251aa9e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 02:07:57 -0700
Subject: [PATCH 025/347] Adds an expected output that will guide refactor

---
 Makefile                |   2 +-
 examples/test6.expected | 104 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+), 1 deletion(-)
 create mode 100644 examples/test6.expected

diff --git a/Makefile b/Makefile
index b498c074e..adf97c16c 100644
--- a/Makefile
+++ b/Makefile
@@ -3,7 +3,7 @@
 JAR = ddlc.jar
 
 test: $(JAR)
-	scala $(JAR) examples/test6.ddl
+	scala $(JAR) examples/test6.ddl | diff -u examples/test6.expected -
 
 $(JAR): $(wildcard *.scala)
 	sbt package
diff --git a/examples/test6.expected b/examples/test6.expected
new file mode 100644
index 000000000..6429ede0e
--- /dev/null
+++ b/examples/test6.expected
@@ -0,0 +1,104 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  
+
+      deepdive.schema.variables {
+        has_spouse.label: Boolean
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        input: """ SELECT * FROM ext_people_input
+        """
+        output_relation: "people_mentions"
+        udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+        style: "tsv_extractor"
+        dependencies: [ "extraction_rule_8" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_8 {
+        sql: """ DROP VIEW IF EXISTS ext_people_input;
+        CREATE VIEW ext_people_input AS 
+      SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags"  
+      FROM sentences R0
+        
+        """
+        style: "sql_extractor"
+        
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_10 {
+        input: """ SELECT * FROM ext_has_spouse_input
+        """
+        output_relation: "has_spouse_candidates"
+        udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+        style: "tsv_extractor"
+        dependencies: [ "extraction_rule_12" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_12 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
+        CREATE VIEW ext_has_spouse_input AS 
+      SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text"  
+      FROM people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        """
+        style: "sql_extractor"
+        dependencies: [ "extraction_rule_6" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_14 {
+        input: """ SELECT * FROM ext_has_spouse_features_input
+        """
+        output_relation: "has_spouse_features"
+        udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+        style: "tsv_extractor"
+        dependencies: [ "extraction_rule_16" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_16 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
+        CREATE VIEW ext_has_spouse_features_input AS 
+      SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length"  
+      FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+        dependencies: [ "extraction_rule_10" ,  "extraction_rule_6" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_has_spouse {
+        sql: """ DROP TABLE IF EXISTS has_spouse;
+        CREATE TABLE has_spouse AS 
+        SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label
+    FROM has_spouse_candidates R0, has_spouse_features R1
+        WHERE R1.relation_id = R0.relation_id 
+        """
+        style: "sql_extractor"
+        dependencies: [ "extraction_rule_14" ,  "extraction_rule_10" ]
+      }
+    
+
+      deepdive.inference.factors.factor_has_spouse {
+        input_query: """
+      SELECT R0.id AS "has_spouse.R0.id" , R0.label AS "has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  
+      FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        function: "Imply(has_spouse.R0.label)"
+        weight: "?(has_spouse_features.R2.feature)"
+      }
+    

From c733cafcd914736168f91a808fe79154f36e3853 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 24 Apr 2015 00:32:51 -0700
Subject: [PATCH 026/347] Separates make rules for ddlc-test.jar and ddlc.jar

---
 .gitignore |  3 ++-
 Makefile   | 24 ++++++++++++++++++------
 2 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index e6525fdb8..a57fd1549 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 /ddlc.jar
-/target
+/ddlc-test.jar
+target
diff --git a/Makefile b/Makefile
index adf97c16c..5a36a213a 100644
--- a/Makefile
+++ b/Makefile
@@ -1,12 +1,24 @@
 # Makefile for DeepDiveLogCompiler
 
-JAR = ddlc.jar
+TESTJAR = ddlc-test.jar
+TEST = examples/test6.ddl
 
-test: $(JAR)
-	scala $(JAR) examples/test6.ddl | diff -u examples/test6.expected -
+test: $(TESTJAR)
+	CLASSPATH=$(shell sbt "export compile:dependency-classpath" | tail -1) \
+	scala $< $(TEST) | diff -u $(TEST:.ddl=.expected) -
+$(TESTJAR): $(wildcard *.scala)
+	sbt package
+	ln -sfn $(shell ls -t target/scala-*/*_*.jar | head -1) $@
+	touch $@
 
+# standalone jar
+JAR = ddlc.jar
+test-package: $(JAR)
+	scala $< $(TEST) | diff -u $(TEST:.ddl=.expected) -
 $(JAR): $(wildcard *.scala)
-	sbt package
-	jar=(target/scala-*/*.jar); ln -sfn $${jar[0]} $(JAR)
-	touch $(JAR)
+	sbt assembly
+	ln -sfn $(shell ls -t target/scala-*/*-assembly-*.jar | head -1) $@
+	touch $@
 
+clean:
+	sbt clean

From 1a3aeb01f9c215ecd6e1be0d66d9cd53f353d3ed Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 01:50:00 -0700
Subject: [PATCH 027/347] Makes compilation side effect free

by moving all println()s to the end of main(), and making their type
uniform to produce a list of application.conf blocks (List[String]).
---
 DeepDiveLogCompiler.scala | 105 ++++++++++++++++++++++++--------------
 1 file changed, 66 insertions(+), 39 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 81b7540b4..690207bec 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -187,8 +187,6 @@ class StatementSchema( statements : List[Statement] )  {
       case FunctionElement(a, b, c, d, e) => function_schema += {a -> FunctionElement(a, b, c, d, e)}
       case FunctionRule(_,_,_) => ()
     }
-    // println(schema)
-    // println(ground_relations)
   }
 
   init()
@@ -250,8 +248,28 @@ class QuerySchema(q : ConjunctiveQuery) {
 
 }
 
+// The compiler
+object DeepDiveLogCompiler {
 
-object ddlc extends ConjunctiveQueryParser  {
+  def parseArgs(args: Array[String]) = {
+    val getContents = (filename: String) => {
+      val source = scala.io.Source.fromFile(filename)
+      try source.getLines mkString "\n" finally source.close()
+    }
+    args.map(getContents).reduce(_ ++ _)
+  }
+
+  val parser = new ConjunctiveQueryParser
+  def parseProgram(inputProgram: String) = parser.parse(parser.statements, inputProgram)
+
+  type CompiledBlocks = List[String]
+  class CompilationState(
+    // schema derived from all statements
+    ss: Option[StatementSchema],
+    // all head names
+    headNames: List[String],
+    // a handy counter for generating unique names
+    numRules: Int)
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
@@ -283,7 +301,7 @@ object ddlc extends ConjunctiveQueryParser  {
         ${ whereClauseStr }"""
   }
   // generate the node portion (V) of the factor graph
-  def nodeRule(ss : StatementSchema, qs: QuerySchema, z : InferenceRule, dep: List[(Int, String)]) : String = {
+  def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: StatementSchema, dep: List[(Int, String)]) : CompiledBlocks = {
     val headTerms = z.q.head.terms map {
       case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
     }
@@ -312,12 +330,11 @@ object ddlc extends ConjunctiveQueryParser  {
         ${dependencyStr}
       }
     """
-    println(ext)
-    ext
+    List(ext)
   }
 
   // generate variable schema statements
-  def variableSchema(statements : List[Statement], ss: StatementSchema) : String = {
+  def compileVariableSchema(statements: List[Statement], ss: StatementSchema): CompiledBlocks = {
     var schema = Set[String]() 
     // generate the statements.
     statements.foreach {
@@ -331,12 +348,11 @@ object ddlc extends ConjunctiveQueryParser  {
         ${schema.mkString("\n")}
       }
     """
-    println(ddSchema)
-    ddSchema
+    List(ddSchema)
   }
 
   // Generate extraction rule part for deepdive
-  def extractionRule( ss: StatementSchema, em: List[(Int, String)], r : ExtractionRule, index : Int) : String = {
+  def compile(r: ExtractionRule, index: Int, ss: StatementSchema, em: List[(Int, String)]): CompiledBlocks = {
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
@@ -369,11 +385,10 @@ object ddlc extends ConjunctiveQueryParser  {
         ${dependencyStr}
       }
     """
-    println(extractor)
-    extractor
+    List(extractor)
   }
 
-  def functionRule( ss: StatementSchema, dependencies: List[(Int, String)], r : FunctionRule, index : Int) : String = {
+  def compile(r: FunctionRule, index: Int, ss: StatementSchema, dependencies: List[(Int, String)]): CompiledBlocks = {
     
     val inputQuery = s"""
     SELECT * FROM ${r.input}
@@ -402,8 +417,7 @@ object ddlc extends ConjunctiveQueryParser  {
         ${dependencyStr}
       }
     """
-    println(extractor)
-    extractor
+    List(extractor)
   }
 
 
@@ -420,11 +434,13 @@ object ddlc extends ConjunctiveQueryParser  {
   }
 
   // generate inference rule part for deepdive
-  def inferenceRule(ss : StatementSchema, r : InferenceRule, dep : List[(Int, String)]) : String = {
+  def compile(r: InferenceRule, i: Int, ss: StatementSchema, dep: List[(Int, String)]): CompiledBlocks = {
+    var blocks = List[String]()
     val qs = new QuerySchema( r.q )
 
     // node query
-    val node_query = if (ss.isQueryTerm(r.q.head.name)) Some(nodeRule(ss,qs,r, dep)) else None  
+    if (ss.isQueryTerm(r.q.head.name))
+      blocks :::= compileNodeRule(r, qs, ss, dep)
 
     // edge query
     val fakeBody        = r.q.head +: r.q.body 
@@ -459,16 +475,15 @@ object ddlc extends ConjunctiveQueryParser  {
       }
     }
     
-    val rule = s"""
+    blocks ::= s"""
       deepdive.inference.factors.factor_${r.q.head.name} {
         input_query: \"\"\"${inputQuery}\"\"\"
         function: "${func}"
         weight: "${weight}"
       }
     """
-    println(rule)
 
-    return inputQuery
+    blocks.reverse
   }
 
   def dbSettings() : String = """
@@ -521,29 +536,41 @@ object ddlc extends ConjunctiveQueryParser  {
    */
   def main(args: Array[String]) {
     // get contents of all given files as one flat input program
-    val getContents = (filename: String) => {
-      val source = scala.io.Source.fromFile(filename)
-      try source.getLines mkString "\n" finally source.close()
-    }
-    val inputProgram = args.map(getContents).reduce(_ ++ _)
-
-    // TODO refactor side effects out of the codegen functions
-    // TODO print the generated code all at once at the end
-    println(dbSettings())
-    val q      = parse(statements, inputProgram)
-    val schema = new StatementSchema( q.get )
-    val variables = variableSchema(q.get, schema)
-    var dependencies = q.get.zipWithIndex map {
+    val inputProgram = parseArgs(args)
+    val parsedProgram = parseProgram(inputProgram)
+
+    // take an initial pass to analyze the parsed program
+    val schema = new StatementSchema( parsedProgram.get )
+    // TODO analyze the real dependency (Map[headname, List[headname]]) here
+    var dependencies = parsedProgram.get.zipWithIndex map {
       case (e : ExtractionRule, i) => (i, e.q.head.name)
       case (f : FunctionRule, i) => (i, f.output)
       case (w : InferenceRule, i) => (i, w.q.head.name)
       case (_,_) => (-1, "-1")
     }
-    val queries = q.get.zipWithIndex flatMap {
-      case (e : ExtractionRule, i) => Some(extractionRule(schema, dependencies, e, i))
-      case (w : InferenceRule, i)  => Some(inferenceRule(schema, w, dependencies))
-      case (f : FunctionRule, i) => Some(functionRule(schema, dependencies, f, i))
-      case (_,_) => None
-    }
+
+    // compile the program into blocks of application.conf
+    val compiledBlocks = (
+      compileVariableSchema(parsedProgram.get, schema)
+      :::
+      (
+      parsedProgram.get.zipWithIndex flatMap {
+        // XXX Ideally, a single compile call should handle all the polymorphic
+        // cases, but Scala/Java's ad-hoc polymorphism doesn't work that way.
+        // Instead, we need to use the visitor pattern, adding compile(...)
+        // methods to all case classes of Statement.
+        // TODO move schema, dependencies args into a composite field of type CompilationState
+        // TODO get rid of zipWithIndex by keeping a counter in the CompilationState
+        case (s:InferenceRule , i:Int) => compile(s, i, schema, dependencies)
+        case (s:ExtractionRule, i:Int) => compile(s, i, schema, dependencies)
+        case (s:FunctionRule  , i:Int) => compile(s, i, schema, dependencies)
+        case _ => List()
+      }
+      )
+    )
+
+    // emit the generated code
+    println(dbSettings())  // TODO read user's proto-application.conf and augment it
+    compiledBlocks foreach println
   }
 }

From 951437ca244a7d86e41d8b468ca0ee32932e3aa1 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 01:52:20 -0700
Subject: [PATCH 028/347] Cleans trailing white spaces

---
 DeepDiveLogCompiler.scala | 82 +++++++++++++++++++--------------------
 examples/test6.expected   | 10 ++---
 2 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 690207bec..56df143d5 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -10,25 +10,25 @@ import scala.collection.immutable.HashMap
  And queries
 
  Q(x,y) :- R(x,y), SomeOther(y, z)
- 
+
  Using the schema can SQLized as
- 
+
  SELECT R1.x,R2.y
  FROM   R as R1,SomeOther as R2
  WHERE  R1.y = R2.realname
 
  We translate by introducing aliases R1, R2 , etc. to deal with
  repeated symbols.
- 
- TODO: 
+
+ TODO:
  =================
 
  Our schema needs to know whether a symbol is this a query table (and
  so should contain an _id) field or is a regular table from the
- user. 
+ user.
 
  If a head term is not mentioned in the schema, its assumed it is a
- query table that this code must create. 
+ query table that this code must create.
 
  If one wants to explicilty mention a query table in the schema, they
  do so with a trailing exclamation point as follows
@@ -37,10 +37,10 @@ import scala.collection.immutable.HashMap
 
 Consider
 
- Q(x) :- R(x,f) weight=f 
+ Q(x) :- R(x,f) weight=f
 
  ... R is likely *not* a variable table ... we record its translation below.
- 
+
  In contrast, Q(x) :- R(x),S(x) ... coule be treated as variable tables. Hence, the schema has:
 
  R(x,f) // regular table
@@ -58,9 +58,9 @@ Consider
 // * The union types for for the parser. *
 // ***************************************
 trait Statement
-case class Variable(varName : String, relName : String, index : Int ) 
-case class Atom(name : String, terms : List[Variable]) 
-case class Attribute(name : String, terms : List[Variable], types : List[String]) 
+case class Variable(varName : String, relName : String, index : Int )
+case class Atom(name : String, terms : List[Variable])
+case class Attribute(name : String, terms : List[Variable], types : List[String])
 case class ConjunctiveQuery(head: Atom, body: List[Atom])
 case class Column(name : String, t : String)
 
@@ -82,7 +82,7 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
 
 
 // Parser
-class ConjunctiveQueryParser extends JavaTokenParsers {   
+class ConjunctiveQueryParser extends JavaTokenParsers {
   // Odd definitions, but we'll keep them.
   // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
   // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
@@ -124,10 +124,10 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   }
 
 
-  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~ 
-  "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~ 
+  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~
+  "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~
   "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines" ^^ {
-    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~ 
+    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~
       "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
   }
 
@@ -173,7 +173,7 @@ class StatementSchema( statements : List[Statement] )  {
 
   var function_schema : Map[String, FunctionElement] = new HashMap[ String, FunctionElement]()
 
-  def init() = {    
+  def init() = {
     // generate the statements.
     statements.foreach {
       case SchemaElement(Attribute(r, terms, types),query) =>
@@ -211,7 +211,7 @@ class StatementSchema( statements : List[Statement] )  {
       return FunctionElement("0","0","0","0","0")
     }
 
-  } 
+  }
 
   // The default is query term.
   def isQueryTerm( relName : String ): Boolean = {
@@ -225,7 +225,7 @@ class StatementSchema( statements : List[Statement] )  {
 // conditions, select, etc.)
 class QuerySchema(q : ConjunctiveQuery) {
     var query_schema = new HashMap[ String, Tuple2[Int,Variable] ]()
-  
+
   // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
@@ -311,11 +311,11 @@ object DeepDiveLogCompiler {
     val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
     val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
     ${ generateSQLBody(ss,z.q) }"""
-    
+
     val dependencyRelation = z.q.body map { case(x) => s"${x.name}"}
     var dependencies = List[String]()
     for (e <- dep) {
-      if (dependencyRelation contains e._2) 
+      if (dependencyRelation contains e._2)
         dependencies ::= s""" "extraction_rule_${e._1}" """
     }
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
@@ -323,7 +323,7 @@ object DeepDiveLogCompiler {
     val ext = s"""
       deepdive.extraction.extractors.extraction_rule_${z.q.head.name} {
         sql: \"\"\" DROP TABLE IF EXISTS ${z.q.head.name};
-        CREATE TABLE ${z.q.head.name} AS 
+        CREATE TABLE ${z.q.head.name} AS
         ${query}
         \"\"\"
         style: "sql_extractor"
@@ -335,7 +335,7 @@ object DeepDiveLogCompiler {
 
   // generate variable schema statements
   def compileVariableSchema(statements: List[Statement], ss: StatementSchema): CompiledBlocks = {
-    var schema = Set[String]() 
+    var schema = Set[String]()
     // generate the statements.
     statements.foreach {
       case InferenceRule(q, weights, supervision) =>
@@ -361,17 +361,17 @@ object DeepDiveLogCompiler {
     }
 
     val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
-    
+
     val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
-    
+
     val inputQuery = s"""
-      SELECT ${selectStr} 
+      SELECT ${selectStr}
       ${ generateSQLBody(ss, r.q) }"""
 
     val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
     var dependencies = List[String]()
     for (e <- em) {
-      if (dependencyRelation contains e._2) 
+      if (dependencyRelation contains e._2)
         dependencies ::= s""" "extraction_rule_${e._1}" """
     }
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
@@ -389,12 +389,12 @@ object DeepDiveLogCompiler {
   }
 
   def compile(r: FunctionRule, index: Int, ss: StatementSchema, dependencies: List[(Int, String)]): CompiledBlocks = {
-    
+
     val inputQuery = s"""
     SELECT * FROM ${r.input}
     """
 
-    val function = ss.resolveFunctionName(r.function)    
+    val function = ss.resolveFunctionName(r.function)
 
     // val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
     var dependency = List[String]()
@@ -406,7 +406,7 @@ object DeepDiveLogCompiler {
     val dependencyStr = if (dependency.length > 0) s"dependencies: [${dependency.mkString(", ")}]" else ""
 
 
-    
+
     val extractor = s"""
       deepdive.extraction.extractors.extraction_rule_${index} {
         input: \"\"\" SELECT * FROM ${r.input}
@@ -443,7 +443,7 @@ object DeepDiveLogCompiler {
       blocks :::= compileNodeRule(r, qs, ss, dep)
 
     // edge query
-    val fakeBody        = r.q.head +: r.q.body 
+    val fakeBody        = r.q.head +: r.q.body
     val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
 
     val index = r.q.body.length + 1
@@ -461,7 +461,7 @@ object DeepDiveLogCompiler {
 
     // factor input query
     val inputQuery = s"""
-      SELECT ${selectStr} 
+      SELECT ${selectStr}
       ${ generateSQLBody(ss, fakeCQ) }"""
 
     // factor function
@@ -474,7 +474,7 @@ object DeepDiveLogCompiler {
         s"""?(${w.flatMap(s => resolveColumn(s, ss, qs2, fakeCQ, false)).mkString(", ")})"""
       }
     }
-    
+
     blocks ::= s"""
       deepdive.inference.factors.factor_${r.q.head.name} {
         input_query: \"\"\"${inputQuery}\"\"\"
@@ -500,21 +500,21 @@ object DeepDiveLogCompiler {
   /*
    T(base_attr);
    S(a1,a2)
-   Q(x) :- S(x,y),T(y) 
+   Q(x) :- S(x,y),T(y)
    Should generate.
 
    Node query:
    CREATE TABLE Q AS
    SELECT 0 as _id, R0.a1
-   FROM S as R0,T as R1 
+   FROM S as R0,T as R1
    WHERE R0.a2 = R1.base_attr
-   
+
    Edge Query (if S and T are probabilistic)
    SELECT Q._id, array_agg( (S._id, T_.id) )
-   FROM Q as R0,S as R1,T as R2 
-   WHERE S.y = T.base_attr AND 
-         Q.x = S.x AND Q.z = S.z  
-   
+   FROM Q as R0,S as R1,T as R2
+   WHERE S.y = T.base_attr AND
+         Q.x = S.x AND Q.z = S.z
+
    Factor Function: OR
 
    =======
@@ -525,14 +525,14 @@ object DeepDiveLogCompiler {
    Node Query:
    CREATE TABLE Q AS
    SELECT DISTINCT 0 as _id, x FROM R
-   
+
    Edge Query:
    SELECT 0 as _fid, Q.id, R.f as w
    FROM Q, R
    WHERE Q.x = R.x
 
    =======
-   
+
    */
   def main(args: Array[String]) {
     // get contents of all given files as one flat input program
diff --git a/examples/test6.expected b/examples/test6.expected
index 6429ede0e..984ad5e6c 100644
--- a/examples/test6.expected
+++ b/examples/test6.expected
@@ -28,7 +28,7 @@
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-      SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags"  
+      SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
       FROM sentences R0
         
         """
@@ -50,7 +50,7 @@
       deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-      SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text"  
+      SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
       FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
@@ -72,7 +72,7 @@
       deepdive.extraction.extractors.extraction_rule_16 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-      SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length"  
+      SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
       FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
@@ -83,7 +83,7 @@
 
       deepdive.extraction.extractors.extraction_rule_has_spouse {
         sql: """ DROP TABLE IF EXISTS has_spouse;
-        CREATE TABLE has_spouse AS 
+        CREATE TABLE has_spouse AS
         SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label
     FROM has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
@@ -95,7 +95,7 @@
 
       deepdive.inference.factors.factor_has_spouse {
         input_query: """
-      SELECT R0.id AS "has_spouse.R0.id" , R0.label AS "has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  
+      SELECT R0.id AS "has_spouse.R0.id" , R0.label AS "has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature" 
       FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
         function: "Imply(has_spouse.R0.label)"

From a62c1e9518d2d11886844d1b58998dd9aff48e48 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 02:04:54 -0700
Subject: [PATCH 029/347] Renames StatementSchema to CompilationState

---
 DeepDiveLogCompiler.scala | 38 ++++++++++++++++----------------------
 1 file changed, 16 insertions(+), 22 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 56df143d5..a25b47f27 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -156,13 +156,14 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   // rules or schema elements in aribitrary order
   def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
 
-  def statements : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
+  type Program = List[Statement]
+  def statements : Parser[Program] = rep1sep(statement, ".") ^^ { case(x) => x }
 }
 
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
-class StatementSchema( statements : List[Statement] )  {
+class CompilationState( statements : List[Statement] )  {
     // TODO: refactor the schema into a class that constructs and
     // manages these maps. Also it should have appropriate
     // abstractions and error handling for missing values.
@@ -263,17 +264,10 @@ object DeepDiveLogCompiler {
   def parseProgram(inputProgram: String) = parser.parse(parser.statements, inputProgram)
 
   type CompiledBlocks = List[String]
-  class CompilationState(
-    // schema derived from all statements
-    ss: Option[StatementSchema],
-    // all head names
-    headNames: List[String],
-    // a handy counter for generating unique names
-    numRules: Int)
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
-  def generateSQLBody(ss : StatementSchema, z : ConjunctiveQuery) : String = {
+  def generateSQLBody(ss : CompilationState, z : ConjunctiveQuery) : String = {
     val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
     // Simple logic for the where clause, first find every first occurence of a
     // and stick it in a map.
@@ -301,7 +295,7 @@ object DeepDiveLogCompiler {
         ${ whereClauseStr }"""
   }
   // generate the node portion (V) of the factor graph
-  def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: StatementSchema, dep: List[(Int, String)]) : CompiledBlocks = {
+  def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: CompilationState, dep: List[(Int, String)]) : CompiledBlocks = {
     val headTerms = z.q.head.terms map {
       case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
     }
@@ -334,7 +328,7 @@ object DeepDiveLogCompiler {
   }
 
   // generate variable schema statements
-  def compileVariableSchema(statements: List[Statement], ss: StatementSchema): CompiledBlocks = {
+  def compileVariableSchema(statements: List[Statement], ss: CompilationState): CompiledBlocks = {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
@@ -352,7 +346,7 @@ object DeepDiveLogCompiler {
   }
 
   // Generate extraction rule part for deepdive
-  def compile(r: ExtractionRule, index: Int, ss: StatementSchema, em: List[(Int, String)]): CompiledBlocks = {
+  def compile(r: ExtractionRule, index: Int, ss: CompilationState, em: List[(Int, String)]): CompiledBlocks = {
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
@@ -388,7 +382,7 @@ object DeepDiveLogCompiler {
     List(extractor)
   }
 
-  def compile(r: FunctionRule, index: Int, ss: StatementSchema, dependencies: List[(Int, String)]): CompiledBlocks = {
+  def compile(r: FunctionRule, index: Int, ss: CompilationState, dependencies: List[(Int, String)]): CompiledBlocks = {
 
     val inputQuery = s"""
     SELECT * FROM ${r.input}
@@ -422,7 +416,7 @@ object DeepDiveLogCompiler {
 
 
   // resolve a column name with alias
-  def resolveColumn(s: String, ss: StatementSchema, qs: QuerySchema, q : ConjunctiveQuery,
+  def resolveColumn(s: String, ss: CompilationState, qs: QuerySchema, q : ConjunctiveQuery,
    alias: Boolean) : Option[String] = {
     val index = qs.getBodyIndex(s)
     val name  = ss.resolveName(qs.getVar(s))
@@ -434,7 +428,7 @@ object DeepDiveLogCompiler {
   }
 
   // generate inference rule part for deepdive
-  def compile(r: InferenceRule, i: Int, ss: StatementSchema, dep: List[(Int, String)]): CompiledBlocks = {
+  def compile(r: InferenceRule, i: Int, ss: CompilationState, dep: List[(Int, String)]): CompiledBlocks = {
     var blocks = List[String]()
     val qs = new QuerySchema( r.q )
 
@@ -540,7 +534,7 @@ object DeepDiveLogCompiler {
     val parsedProgram = parseProgram(inputProgram)
 
     // take an initial pass to analyze the parsed program
-    val schema = new StatementSchema( parsedProgram.get )
+    val state = new CompilationState( parsedProgram.get )
     // TODO analyze the real dependency (Map[headname, List[headname]]) here
     var dependencies = parsedProgram.get.zipWithIndex map {
       case (e : ExtractionRule, i) => (i, e.q.head.name)
@@ -551,7 +545,7 @@ object DeepDiveLogCompiler {
 
     // compile the program into blocks of application.conf
     val compiledBlocks = (
-      compileVariableSchema(parsedProgram.get, schema)
+      compileVariableSchema(parsedProgram.get, state)
       :::
       (
       parsedProgram.get.zipWithIndex flatMap {
@@ -559,11 +553,11 @@ object DeepDiveLogCompiler {
         // cases, but Scala/Java's ad-hoc polymorphism doesn't work that way.
         // Instead, we need to use the visitor pattern, adding compile(...)
         // methods to all case classes of Statement.
-        // TODO move schema, dependencies args into a composite field of type CompilationState
+        // TODO move state, dependencies args into a composite field of type CompilationState
         // TODO get rid of zipWithIndex by keeping a counter in the CompilationState
-        case (s:InferenceRule , i:Int) => compile(s, i, schema, dependencies)
-        case (s:ExtractionRule, i:Int) => compile(s, i, schema, dependencies)
-        case (s:FunctionRule  , i:Int) => compile(s, i, schema, dependencies)
+        case (s:InferenceRule , i:Int) => compile(s, i, state, dependencies)
+        case (s:ExtractionRule, i:Int) => compile(s, i, state, dependencies)
+        case (s:FunctionRule  , i:Int) => compile(s, i, state, dependencies)
         case _ => List()
       }
       )

From 5a37d06ec3c7d61950124dc6c1f533aa2b13df69 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 02:08:40 -0700
Subject: [PATCH 030/347] Moves resolveColumn to CompilationState

---
 DeepDiveLogCompiler.scala | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index a25b47f27..677e5a114 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -218,6 +218,18 @@ class CompilationState( statements : List[Statement] )  {
   def isQueryTerm( relName : String ): Boolean = {
     if( ground_relations contains relName ) !ground_relations(relName) else true
   }
+
+  // resolve a column name with alias
+  def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: Boolean) : Option[String] = {
+    val index = qs.getBodyIndex(s)
+    val name  = resolveName(qs.getVar(s))
+    val relation = q.body(index).name
+    if (alias)
+      Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
+    else
+      Some(s"${relation}.R${index}.${name}")
+  }
+
 }
 
 // This is responsible for schema elements within a given query, e.g.,
@@ -351,7 +363,7 @@ object DeepDiveLogCompiler {
     val qs              = new QuerySchema( r.q )
     // variable columns
     val variableCols = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => resolveColumn(v, ss, qs, r.q, true)
+      case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, r.q, true)
     }
 
     val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
@@ -415,18 +427,6 @@ object DeepDiveLogCompiler {
   }
 
 
-  // resolve a column name with alias
-  def resolveColumn(s: String, ss: CompilationState, qs: QuerySchema, q : ConjunctiveQuery,
-   alias: Boolean) : Option[String] = {
-    val index = qs.getBodyIndex(s)
-    val name  = ss.resolveName(qs.getVar(s))
-    val relation = q.body(index).name
-    if (alias)
-      Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
-    else
-      Some(s"${relation}.R${index}.${name}")
-  }
-
   // generate inference rule part for deepdive
   def compile(r: InferenceRule, i: Int, ss: CompilationState, dep: List[(Int, String)]): CompiledBlocks = {
     var blocks = List[String]()
@@ -448,7 +448,7 @@ object DeepDiveLogCompiler {
     // weight string
     val uwStr = r.weights match {
       case KnownFactorWeight(x) => None
-      case UnknownFactorWeight(w) => Some(w.flatMap(s => resolveColumn(s, ss, qs2, fakeCQ, true)).mkString(", "))
+      case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
     }
 
     val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
@@ -465,7 +465,7 @@ object DeepDiveLogCompiler {
     val weight = r.weights match {
       case KnownFactorWeight(x) => s"${x}"
       case UnknownFactorWeight(w) => {
-        s"""?(${w.flatMap(s => resolveColumn(s, ss, qs2, fakeCQ, false)).mkString(", ")})"""
+        s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, false)).mkString(", ")})"""
       }
     }
 

From bcb994cc1d5807fb0b4e6f05c81fd807b2d8efbc Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 02:26:33 -0700
Subject: [PATCH 031/347] Reorders pieces of codes around

- Renames dbSettings to compileUserSettings.
- Folds compileNodeRule into compile(InferenceRule, ...)
---
 DeepDiveLogCompiler.scala | 189 ++++++++++++++++----------------------
 1 file changed, 77 insertions(+), 112 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 677e5a114..151451198 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -230,6 +230,35 @@ class CompilationState( statements : List[Statement] )  {
       Some(s"${relation}.R${index}.${name}")
   }
 
+  // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
+  // and the corresponding WHERE clause (equating all variables)
+  def generateSQLBody(z : ConjunctiveQuery) : String = {
+    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
+    // Simple logic for the where clause, first find every first occurence of a
+    // and stick it in a map.
+    val qs = new QuerySchema(z)
+
+    val whereClause = z.body.zipWithIndex flatMap {
+      case (Atom(relName, terms),body_index) =>
+        terms flatMap {
+          case Variable(varName, relName, index) =>
+            val canonical_body_index = qs.getBodyIndex(varName)
+
+            if (canonical_body_index != body_index) {
+              val real_attr_name1 = resolveName( Variable(varName, relName, index) )
+              val real_attr_name2 = resolveName( qs.getVar(varName))
+              Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+            } else { None }
+        }
+    }
+    val whereClauseStr = whereClause match {
+      case Nil => ""
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
+    }
+
+    s"""FROM ${ bodyNames }
+        ${ whereClauseStr }"""
+  }
 }
 
 // This is responsible for schema elements within a given query, e.g.,
@@ -277,66 +306,19 @@ object DeepDiveLogCompiler {
 
   type CompiledBlocks = List[String]
 
-  // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
-  // and the corresponding WHERE clause (equating all variables)
-  def generateSQLBody(ss : CompilationState, z : ConjunctiveQuery) : String = {
-    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
-    // Simple logic for the where clause, first find every first occurence of a
-    // and stick it in a map.
-    val qs = new QuerySchema(z)
-
-    val whereClause = z.body.zipWithIndex flatMap {
-      case (Atom(relName, terms),body_index) =>
-        terms flatMap {
-          case Variable(varName, relName, index) =>
-            val canonical_body_index = qs.getBodyIndex(varName)
-
-            if (canonical_body_index != body_index) {
-              val real_attr_name1 = ss.resolveName( Variable(varName, relName, index) )
-              val real_attr_name2 = ss.resolveName( qs.getVar(varName))
-              Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
-            } else { None }
-        }
-    }
-    val whereClauseStr = whereClause match {
-      case Nil => ""
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
-    }
-
-    s"""FROM ${ bodyNames }
-        ${ whereClauseStr }"""
+  def compileUserSettings(): CompiledBlocks = {
+    // TODO read user's proto-application.conf and augment it
+    List("""
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
   }
-  // generate the node portion (V) of the factor graph
-  def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: CompilationState, dep: List[(Int, String)]) : CompiledBlocks = {
-    val headTerms = z.q.head.terms map {
-      case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
-    }
-    val index = qs.getBodyIndex(z.supervision)
-    val name  = ss.resolveName(qs.getVar(z.supervision))
-    val labelCol = s"R${index}.${name}"
-    val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-    val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
-    ${ generateSQLBody(ss,z.q) }"""
-
-    val dependencyRelation = z.q.body map { case(x) => s"${x.name}"}
-    var dependencies = List[String]()
-    for (e <- dep) {
-      if (dependencyRelation contains e._2)
-        dependencies ::= s""" "extraction_rule_${e._1}" """
-    }
-    val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
-
-    val ext = s"""
-      deepdive.extraction.extractors.extraction_rule_${z.q.head.name} {
-        sql: \"\"\" DROP TABLE IF EXISTS ${z.q.head.name};
-        CREATE TABLE ${z.q.head.name} AS
-        ${query}
-        \"\"\"
-        style: "sql_extractor"
-        ${dependencyStr}
-      }
-    """
-    List(ext)
+  """)
   }
 
   // generate variable schema statements
@@ -372,7 +354,7 @@ object DeepDiveLogCompiler {
 
     val inputQuery = s"""
       SELECT ${selectStr}
-      ${ generateSQLBody(ss, r.q) }"""
+      ${ ss.generateSQLBody(r.q) }"""
 
     val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
     var dependencies = List[String]()
@@ -395,7 +377,6 @@ object DeepDiveLogCompiler {
   }
 
   def compile(r: FunctionRule, index: Int, ss: CompilationState, dependencies: List[(Int, String)]): CompiledBlocks = {
-
     val inputQuery = s"""
     SELECT * FROM ${r.input}
     """
@@ -426,13 +407,44 @@ object DeepDiveLogCompiler {
     List(extractor)
   }
 
-
   // generate inference rule part for deepdive
   def compile(r: InferenceRule, i: Int, ss: CompilationState, dep: List[(Int, String)]): CompiledBlocks = {
     var blocks = List[String]()
     val qs = new QuerySchema( r.q )
 
     // node query
+    // generate the node portion (V) of the factor graph
+    def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: CompilationState, dep: List[(Int, String)]) : CompiledBlocks = {
+      val headTerms = z.q.head.terms map {
+        case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+      }
+      val index = qs.getBodyIndex(z.supervision)
+      val name  = ss.resolveName(qs.getVar(z.supervision))
+      val labelCol = s"R${index}.${name}"
+      val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
+      val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
+    ${ ss.generateSQLBody(z.q) }"""
+
+      val dependencyRelation = z.q.body map { case(x) => s"${x.name}"}
+      var dependencies = List[String]()
+      for (e <- dep) {
+        if (dependencyRelation contains e._2)
+          dependencies ::= s""" "extraction_rule_${e._1}" """
+      }
+      val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
+
+      val ext = s"""
+      deepdive.extraction.extractors.extraction_rule_${z.q.head.name} {
+        sql: \"\"\" DROP TABLE IF EXISTS ${z.q.head.name};
+        CREATE TABLE ${z.q.head.name} AS
+        ${query}
+        \"\"\"
+        style: "sql_extractor"
+        ${dependencyStr}
+      }
+    """
+      List(ext)
+    }
     if (ss.isQueryTerm(r.q.head.name))
       blocks :::= compileNodeRule(r, qs, ss, dep)
 
@@ -456,7 +468,7 @@ object DeepDiveLogCompiler {
     // factor input query
     val inputQuery = s"""
       SELECT ${selectStr}
-      ${ generateSQLBody(ss, fakeCQ) }"""
+      ${ ss.generateSQLBody(fakeCQ) }"""
 
     // factor function
     val func = s"""Imply(${r.q.head.name}.R0.label)"""
@@ -480,54 +492,6 @@ object DeepDiveLogCompiler {
     blocks.reverse
   }
 
-  def dbSettings() : String = """
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-  }
-  """
-  /*
-   T(base_attr);
-   S(a1,a2)
-   Q(x) :- S(x,y),T(y)
-   Should generate.
-
-   Node query:
-   CREATE TABLE Q AS
-   SELECT 0 as _id, R0.a1
-   FROM S as R0,T as R1
-   WHERE R0.a2 = R1.base_attr
-
-   Edge Query (if S and T are probabilistic)
-   SELECT Q._id, array_agg( (S._id, T_.id) )
-   FROM Q as R0,S as R1,T as R2
-   WHERE S.y = T.base_attr AND
-         Q.x = S.x AND Q.z = S.z
-
-   Factor Function: OR
-
-   =======
-   R(x,y) (assume non probabilistic)
-
-   Q(x) :- R(x,f) weight=f
-
-   Node Query:
-   CREATE TABLE Q AS
-   SELECT DISTINCT 0 as _id, x FROM R
-
-   Edge Query:
-   SELECT 0 as _fid, Q.id, R.f as w
-   FROM Q, R
-   WHERE Q.x = R.x
-
-   =======
-
-   */
   def main(args: Array[String]) {
     // get contents of all given files as one flat input program
     val inputProgram = parseArgs(args)
@@ -545,6 +509,8 @@ object DeepDiveLogCompiler {
 
     // compile the program into blocks of application.conf
     val compiledBlocks = (
+      compileUserSettings
+      :::
       compileVariableSchema(parsedProgram.get, state)
       :::
       (
@@ -564,7 +530,6 @@ object DeepDiveLogCompiler {
     )
 
     // emit the generated code
-    println(dbSettings())  // TODO read user's proto-application.conf and augment it
     compiledBlocks foreach println
   }
 }

From abc2f17aad53f9a1cbeff81c0ab19ed5fb9cd349 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 02:47:58 -0700
Subject: [PATCH 032/347] Moves dependencies to CompilationState.headNames

---
 DeepDiveLogCompiler.scala | 37 ++++++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 151451198..7b08f4987 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -174,6 +174,8 @@ class CompilationState( statements : List[Statement] )  {
 
   var function_schema : Map[String, FunctionElement] = new HashMap[ String, FunctionElement]()
 
+  var headNames : List[(Int, String)] = List()
+
   def init() = {
     // generate the statements.
     statements.foreach {
@@ -188,6 +190,15 @@ class CompilationState( statements : List[Statement] )  {
       case FunctionElement(a, b, c, d, e) => function_schema += {a -> FunctionElement(a, b, c, d, e)}
       case FunctionRule(_,_,_) => ()
     }
+
+    // TODO analyze the real dependency (Map[headname, List[headname]]) here
+    headNames = statements.zipWithIndex flatMap {
+      case (e : ExtractionRule, i) => Some(i, e.q.head.name)
+      case (f : FunctionRule  , i) => Some(i, f.output     )
+      case (w : InferenceRule , i) => Some(i, w.q.head.name)
+      case _ => None
+    }
+
   }
 
   init()
@@ -340,7 +351,7 @@ object DeepDiveLogCompiler {
   }
 
   // Generate extraction rule part for deepdive
-  def compile(r: ExtractionRule, index: Int, ss: CompilationState, em: List[(Int, String)]): CompiledBlocks = {
+  def compile(r: ExtractionRule, index: Int, ss: CompilationState): CompiledBlocks = {
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
@@ -356,6 +367,7 @@ object DeepDiveLogCompiler {
       SELECT ${selectStr}
       ${ ss.generateSQLBody(r.q) }"""
 
+    val em = ss.headNames // TODO move this dependency analysis to a separate method
     val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
     var dependencies = List[String]()
     for (e <- em) {
@@ -376,13 +388,14 @@ object DeepDiveLogCompiler {
     List(extractor)
   }
 
-  def compile(r: FunctionRule, index: Int, ss: CompilationState, dependencies: List[(Int, String)]): CompiledBlocks = {
+  def compile(r: FunctionRule, index: Int, ss: CompilationState): CompiledBlocks = {
     val inputQuery = s"""
     SELECT * FROM ${r.input}
     """
 
     val function = ss.resolveFunctionName(r.function)
 
+    val dependencies = ss.headNames // TODO move this dependency analysis to a separate method
     // val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
     var dependency = List[String]()
     for (d <- dependencies) {
@@ -408,13 +421,13 @@ object DeepDiveLogCompiler {
   }
 
   // generate inference rule part for deepdive
-  def compile(r: InferenceRule, i: Int, ss: CompilationState, dep: List[(Int, String)]): CompiledBlocks = {
+  def compile(r: InferenceRule, i: Int, ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
     val qs = new QuerySchema( r.q )
 
     // node query
     // generate the node portion (V) of the factor graph
-    def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: CompilationState, dep: List[(Int, String)]) : CompiledBlocks = {
+    def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: CompilationState) : CompiledBlocks = {
       val headTerms = z.q.head.terms map {
         case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
       }
@@ -425,6 +438,7 @@ object DeepDiveLogCompiler {
       val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
     ${ ss.generateSQLBody(z.q) }"""
 
+      val dep = ss.headNames
       val dependencyRelation = z.q.body map { case(x) => s"${x.name}"}
       var dependencies = List[String]()
       for (e <- dep) {
@@ -446,7 +460,7 @@ object DeepDiveLogCompiler {
       List(ext)
     }
     if (ss.isQueryTerm(r.q.head.name))
-      blocks :::= compileNodeRule(r, qs, ss, dep)
+      blocks :::= compileNodeRule(r, qs, ss)
 
     // edge query
     val fakeBody        = r.q.head +: r.q.body
@@ -499,13 +513,6 @@ object DeepDiveLogCompiler {
 
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( parsedProgram.get )
-    // TODO analyze the real dependency (Map[headname, List[headname]]) here
-    var dependencies = parsedProgram.get.zipWithIndex map {
-      case (e : ExtractionRule, i) => (i, e.q.head.name)
-      case (f : FunctionRule, i) => (i, f.output)
-      case (w : InferenceRule, i) => (i, w.q.head.name)
-      case (_,_) => (-1, "-1")
-    }
 
     // compile the program into blocks of application.conf
     val compiledBlocks = (
@@ -521,9 +528,9 @@ object DeepDiveLogCompiler {
         // methods to all case classes of Statement.
         // TODO move state, dependencies args into a composite field of type CompilationState
         // TODO get rid of zipWithIndex by keeping a counter in the CompilationState
-        case (s:InferenceRule , i:Int) => compile(s, i, state, dependencies)
-        case (s:ExtractionRule, i:Int) => compile(s, i, state, dependencies)
-        case (s:FunctionRule  , i:Int) => compile(s, i, state, dependencies)
+        case (s:InferenceRule , i:Int) => compile(s, i, state)
+        case (s:ExtractionRule, i:Int) => compile(s, i, state)
+        case (s:FunctionRule  , i:Int) => compile(s, i, state)
         case _ => List()
       }
       )

From 2cfabcc43c29849662e7753487928088d5b42544 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 03:04:53 -0700
Subject: [PATCH 033/347] Gets rid of the Int argument for compile() methods

by defining a (extractor) block name resolving function in the
CompilationState
---
 DeepDiveLogCompiler.scala | 32 ++++++++++++++++++++------------
 1 file changed, 20 insertions(+), 12 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 7b08f4987..9571e9f5b 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -203,6 +203,13 @@ class CompilationState( statements : List[Statement] )  {
 
   init()
 
+  // Given a statement, resolve its name for the compiled extractor block.
+  def resolveExtractorBlockName(s: Statement): String = s match {
+    case s: ExtractionRule => s"extraction_rule_${statements indexOf s}"
+    case s: FunctionRule   => s"extraction_rule_${statements indexOf s}"
+    case s: InferenceRule  => s"extraction_rule_${s.q.head.name}"
+  }
+
   // Given a variable, resolve it.  TODO: This should give a warning,
   // if we encouter a variable that is not in this map, then something
   // odd has happened.
@@ -351,7 +358,7 @@ object DeepDiveLogCompiler {
   }
 
   // Generate extraction rule part for deepdive
-  def compile(r: ExtractionRule, index: Int, ss: CompilationState): CompiledBlocks = {
+  def compile(r: ExtractionRule, ss: CompilationState): CompiledBlocks = {
     // Generate the body of the query.
     val qs              = new QuerySchema( r.q )
     // variable columns
@@ -376,8 +383,9 @@ object DeepDiveLogCompiler {
     }
     val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
 
+    val blockName = ss.resolveExtractorBlockName(r)
     val extractor = s"""
-      deepdive.extraction.extractors.extraction_rule_${index} {
+      deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" DROP VIEW IF EXISTS ${r.q.head.name};
         CREATE VIEW ${r.q.head.name} AS ${inputQuery}
         \"\"\"
@@ -388,7 +396,7 @@ object DeepDiveLogCompiler {
     List(extractor)
   }
 
-  def compile(r: FunctionRule, index: Int, ss: CompilationState): CompiledBlocks = {
+  def compile(r: FunctionRule, ss: CompilationState): CompiledBlocks = {
     val inputQuery = s"""
     SELECT * FROM ${r.input}
     """
@@ -407,8 +415,9 @@ object DeepDiveLogCompiler {
 
 
 
+    val blockName = ss.resolveExtractorBlockName(r)
     val extractor = s"""
-      deepdive.extraction.extractors.extraction_rule_${index} {
+      deepdive.extraction.extractors.${blockName} {
         input: \"\"\" SELECT * FROM ${r.input}
         \"\"\"
         output_relation: \"${r.output}\"
@@ -421,7 +430,7 @@ object DeepDiveLogCompiler {
   }
 
   // generate inference rule part for deepdive
-  def compile(r: InferenceRule, i: Int, ss: CompilationState): CompiledBlocks = {
+  def compile(r: InferenceRule, ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
     val qs = new QuerySchema( r.q )
 
@@ -447,8 +456,9 @@ object DeepDiveLogCompiler {
       }
       val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
 
+      val blockName = ss.resolveExtractorBlockName(z)
       val ext = s"""
-      deepdive.extraction.extractors.extraction_rule_${z.q.head.name} {
+      deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" DROP TABLE IF EXISTS ${z.q.head.name};
         CREATE TABLE ${z.q.head.name} AS
         ${query}
@@ -521,16 +531,14 @@ object DeepDiveLogCompiler {
       compileVariableSchema(parsedProgram.get, state)
       :::
       (
-      parsedProgram.get.zipWithIndex flatMap {
+      parsedProgram.get flatMap {
         // XXX Ideally, a single compile call should handle all the polymorphic
         // cases, but Scala/Java's ad-hoc polymorphism doesn't work that way.
         // Instead, we need to use the visitor pattern, adding compile(...)
         // methods to all case classes of Statement.
-        // TODO move state, dependencies args into a composite field of type CompilationState
-        // TODO get rid of zipWithIndex by keeping a counter in the CompilationState
-        case (s:InferenceRule , i:Int) => compile(s, i, state)
-        case (s:ExtractionRule, i:Int) => compile(s, i, state)
-        case (s:FunctionRule  , i:Int) => compile(s, i, state)
+        case s:InferenceRule  => compile(s, state)
+        case s:ExtractionRule => compile(s, state)
+        case s:FunctionRule   => compile(s, state)
         case _ => List()
       }
       )

From 85015a907dcbe4c5a2351d508886e14b61cc5b67 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 03:34:14 -0700
Subject: [PATCH 034/347] Refactors dependencies generation

---
 DeepDiveLogCompiler.scala | 77 ++++++++++++++++++---------------------
 examples/test6.expected   |  2 +-
 2 files changed, 36 insertions(+), 43 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 9571e9f5b..4feb3a1ce 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -174,7 +174,8 @@ class CompilationState( statements : List[Statement] )  {
 
   var function_schema : Map[String, FunctionElement] = new HashMap[ String, FunctionElement]()
 
-  var headNames : List[(Int, String)] = List()
+  // The dependency graph between statements.
+  var dependencies : Map[Statement, Set[Statement]] = new HashMap()
 
   def init() = {
     // generate the statements.
@@ -191,14 +192,7 @@ class CompilationState( statements : List[Statement] )  {
       case FunctionRule(_,_,_) => ()
     }
 
-    // TODO analyze the real dependency (Map[headname, List[headname]]) here
-    headNames = statements.zipWithIndex flatMap {
-      case (e : ExtractionRule, i) => Some(i, e.q.head.name)
-      case (f : FunctionRule  , i) => Some(i, f.output     )
-      case (w : InferenceRule , i) => Some(i, w.q.head.name)
-      case _ => None
-    }
-
+    analyzeDependency(statements)
   }
 
   init()
@@ -277,6 +271,35 @@ class CompilationState( statements : List[Statement] )  {
     s"""FROM ${ bodyNames }
         ${ whereClauseStr }"""
   }
+
+
+  // Analyze the dependency between statements and construct a graph.
+  def analyzeDependency(statements: List[Statement]) = {
+    // first map head names to the actual statement
+    var stmtByHeadName = new HashMap[String, Statement]()
+    statements foreach {
+      case e : ExtractionRule => stmtByHeadName += { e.q.head.name -> e }
+      case f : FunctionRule   => stmtByHeadName += { f.output      -> f }
+      case w : InferenceRule  => stmtByHeadName += { w.q.head.name -> w }
+      case _ =>
+    }
+    // then, look at the body of each statement to construct a dependency graph
+    statements foreach {
+      case f : FunctionRule   => dependencies += { f -> (        Some(f.input) flatMap (stmtByHeadName get _)).toSet }
+      case e : ExtractionRule => dependencies += { e -> (e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
+      case w : InferenceRule  => dependencies += { w -> (w.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
+      case _ =>
+    }
+  }
+  // Generates a "dependencies" value for a compiled block of given statement.
+  def generateDependenciesOfCompiledBlockFor(statement: Statement): String = {
+    val dependentExtractorBlockNames =
+      dependencies getOrElse (statement, Set()) map resolveExtractorBlockName
+    if (dependentExtractorBlockNames.size == 0) "" else {
+      val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")
+      s"dependencies: [${depStr}]"
+    }
+  }
 }
 
 // This is responsible for schema elements within a given query, e.g.,
@@ -374,15 +397,6 @@ object DeepDiveLogCompiler {
       SELECT ${selectStr}
       ${ ss.generateSQLBody(r.q) }"""
 
-    val em = ss.headNames // TODO move this dependency analysis to a separate method
-    val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
-    var dependencies = List[String]()
-    for (e <- em) {
-      if (dependencyRelation contains e._2)
-        dependencies ::= s""" "extraction_rule_${e._1}" """
-    }
-    val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
-
     val blockName = ss.resolveExtractorBlockName(r)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
@@ -390,7 +404,7 @@ object DeepDiveLogCompiler {
         CREATE VIEW ${r.q.head.name} AS ${inputQuery}
         \"\"\"
         style: "sql_extractor"
-        ${dependencyStr}
+        ${ss.generateDependenciesOfCompiledBlockFor(r)}
       }
     """
     List(extractor)
@@ -403,18 +417,6 @@ object DeepDiveLogCompiler {
 
     val function = ss.resolveFunctionName(r.function)
 
-    val dependencies = ss.headNames // TODO move this dependency analysis to a separate method
-    // val dependencyRelation = r.q.body map { case(x) => s"${x.name}"}
-    var dependency = List[String]()
-    for (d <- dependencies) {
-      if (r.input == d._2) {
-        dependency ::= s""" "extraction_rule_${d._1}" """
-      }
-    }
-    val dependencyStr = if (dependency.length > 0) s"dependencies: [${dependency.mkString(", ")}]" else ""
-
-
-
     val blockName = ss.resolveExtractorBlockName(r)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
@@ -423,7 +425,7 @@ object DeepDiveLogCompiler {
         output_relation: \"${r.output}\"
         udf: \"${function.implementation}\"
         style: \"${function.mode}_extractor\"
-        ${dependencyStr}
+        ${ss.generateDependenciesOfCompiledBlockFor(r)}
       }
     """
     List(extractor)
@@ -447,15 +449,6 @@ object DeepDiveLogCompiler {
       val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
     ${ ss.generateSQLBody(z.q) }"""
 
-      val dep = ss.headNames
-      val dependencyRelation = z.q.body map { case(x) => s"${x.name}"}
-      var dependencies = List[String]()
-      for (e <- dep) {
-        if (dependencyRelation contains e._2)
-          dependencies ::= s""" "extraction_rule_${e._1}" """
-      }
-      val dependencyStr = if (dependencies.length > 0) s"dependencies: [${dependencies.mkString(", ")}]" else ""
-
       val blockName = ss.resolveExtractorBlockName(z)
       val ext = s"""
       deepdive.extraction.extractors.${blockName} {
@@ -464,7 +457,7 @@ object DeepDiveLogCompiler {
         ${query}
         \"\"\"
         style: "sql_extractor"
-        ${dependencyStr}
+        ${ss.generateDependenciesOfCompiledBlockFor(z)}
       }
     """
       List(ext)
diff --git a/examples/test6.expected b/examples/test6.expected
index 984ad5e6c..cb5252ee9 100644
--- a/examples/test6.expected
+++ b/examples/test6.expected
@@ -89,7 +89,7 @@
         WHERE R1.relation_id = R0.relation_id 
         """
         style: "sql_extractor"
-        dependencies: [ "extraction_rule_14" ,  "extraction_rule_10" ]
+        dependencies: [ "extraction_rule_10" ,  "extraction_rule_14" ]
       }
     
 

From 8d1491795f1ca4201848662fb483a95e47bcebde Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 03:40:13 -0700
Subject: [PATCH 035/347] Cleans up redundant .get

---
 DeepDiveLogCompiler.scala | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 4feb3a1ce..ff1904a28 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -512,19 +512,19 @@ object DeepDiveLogCompiler {
   def main(args: Array[String]) {
     // get contents of all given files as one flat input program
     val inputProgram = parseArgs(args)
-    val parsedProgram = parseProgram(inputProgram)
+    val parsedProgram = parseProgram(inputProgram).get
 
     // take an initial pass to analyze the parsed program
-    val state = new CompilationState( parsedProgram.get )
+    val state = new CompilationState( parsedProgram )
 
     // compile the program into blocks of application.conf
     val compiledBlocks = (
       compileUserSettings
       :::
-      compileVariableSchema(parsedProgram.get, state)
+      compileVariableSchema(parsedProgram, state)
       :::
       (
-      parsedProgram.get flatMap {
+      parsedProgram flatMap {
         // XXX Ideally, a single compile call should handle all the polymorphic
         // cases, but Scala/Java's ad-hoc polymorphism doesn't work that way.
         // Instead, we need to use the visitor pattern, adding compile(...)

From 0b7296834436e37a36cc7541d3c9ec9c2b4d75d8 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 03:57:39 -0700
Subject: [PATCH 036/347] Turns compile() functions into methods (Visitor
 pattern)

---
 DeepDiveLogCompiler.scala | 195 +++++++++++++++++++-------------------
 1 file changed, 96 insertions(+), 99 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index ff1904a28..3f8ef00f9 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -57,7 +57,6 @@ Consider
 // ***************************************
 // * The union types for for the parser. *
 // ***************************************
-trait Statement
 case class Variable(varName : String, relName : String, index : Int )
 case class Atom(name : String, terms : List[Variable])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
@@ -74,13 +73,6 @@ case class KnownFactorWeight(value: Double) extends FactorWeight {
 
 case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
 
-case class SchemaElement( a : Attribute , query : Boolean ) extends Statement // atom and whether this is a query relation.
-case class FunctionElement( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
-case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
-case class FunctionRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
-
-
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {
   // Odd definitions, but we'll keep them.
@@ -331,62 +323,23 @@ class QuerySchema(q : ConjunctiveQuery) {
 
 }
 
-// The compiler
-object DeepDiveLogCompiler {
-
-  def parseArgs(args: Array[String]) = {
-    val getContents = (filename: String) => {
-      val source = scala.io.Source.fromFile(filename)
-      try source.getLines mkString "\n" finally source.close()
-    }
-    args.map(getContents).reduce(_ ++ _)
-  }
-
-  val parser = new ConjunctiveQueryParser
-  def parseProgram(inputProgram: String) = parser.parse(parser.statements, inputProgram)
-
-  type CompiledBlocks = List[String]
-
-  def compileUserSettings(): CompiledBlocks = {
-    // TODO read user's proto-application.conf and augment it
-    List("""
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-  }
-  """)
-  }
-
-  // generate variable schema statements
-  def compileVariableSchema(statements: List[Statement], ss: CompilationState): CompiledBlocks = {
-    var schema = Set[String]()
-    // generate the statements.
-    statements.foreach {
-      case InferenceRule(q, weights, supervision) =>
-        val qs = new QuerySchema(q)
-        schema += s"${q.head.name}.label: Boolean"
-      case _ => ()
-    }
-    val ddSchema = s"""
-      deepdive.schema.variables {
-        ${schema.mkString("\n")}
-      }
-    """
-    List(ddSchema)
-  }
 
+// Statements that will be parsed and compiled
+trait Statement {
+  type CompiledBlocks = DeepDiveLogCompiler.CompiledBlocks
+  def compile(state: CompilationState): CompiledBlocks = List()
+}
+case class SchemaElement( a : Attribute , query : Boolean ) extends Statement // atom and whether this is a query relation.
+case class FunctionElement( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
+case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
+{
   // Generate extraction rule part for deepdive
-  def compile(r: ExtractionRule, ss: CompilationState): CompiledBlocks = {
+  override def compile(ss: CompilationState): CompiledBlocks = {
     // Generate the body of the query.
-    val qs              = new QuerySchema( r.q )
+    val qs              = new QuerySchema( q )
     // variable columns
-    val variableCols = r.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, r.q, true)
+    val variableCols = q.head.terms flatMap {
+      case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, q, true)
     }
 
     val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
@@ -395,46 +348,50 @@ object DeepDiveLogCompiler {
 
     val inputQuery = s"""
       SELECT ${selectStr}
-      ${ ss.generateSQLBody(r.q) }"""
+      ${ ss.generateSQLBody(q) }"""
 
-    val blockName = ss.resolveExtractorBlockName(r)
+    val blockName = ss.resolveExtractorBlockName(this)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" DROP VIEW IF EXISTS ${r.q.head.name};
-        CREATE VIEW ${r.q.head.name} AS ${inputQuery}
+        sql: \"\"\" DROP VIEW IF EXISTS ${q.head.name};
+        CREATE VIEW ${q.head.name} AS ${inputQuery}
         \"\"\"
         style: "sql_extractor"
-        ${ss.generateDependenciesOfCompiledBlockFor(r)}
+        ${ss.generateDependenciesOfCompiledBlockFor(this)}
       }
     """
     List(extractor)
   }
-
-  def compile(r: FunctionRule, ss: CompilationState): CompiledBlocks = {
+}
+case class FunctionRule(input : String, output : String, function : String) extends Statement // Extraction rule
+{
+  override def compile(ss: CompilationState): CompiledBlocks = {
     val inputQuery = s"""
-    SELECT * FROM ${r.input}
+    SELECT * FROM ${input}
     """
 
-    val function = ss.resolveFunctionName(r.function)
+    val function = ss.resolveFunctionName(this.function)
 
-    val blockName = ss.resolveExtractorBlockName(r)
+    val blockName = ss.resolveExtractorBlockName(this)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        input: \"\"\" SELECT * FROM ${r.input}
+        input: \"\"\" SELECT * FROM ${input}
         \"\"\"
-        output_relation: \"${r.output}\"
+        output_relation: \"${output}\"
         udf: \"${function.implementation}\"
         style: \"${function.mode}_extractor\"
-        ${ss.generateDependenciesOfCompiledBlockFor(r)}
+        ${ss.generateDependenciesOfCompiledBlockFor(this)}
       }
     """
     List(extractor)
   }
-
+}
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
+{
   // generate inference rule part for deepdive
-  def compile(r: InferenceRule, ss: CompilationState): CompiledBlocks = {
+  override def compile(ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
-    val qs = new QuerySchema( r.q )
+    val qs = new QuerySchema( q )
 
     // node query
     // generate the node portion (V) of the factor graph
@@ -462,20 +419,20 @@ object DeepDiveLogCompiler {
     """
       List(ext)
     }
-    if (ss.isQueryTerm(r.q.head.name))
-      blocks :::= compileNodeRule(r, qs, ss)
+    if (ss.isQueryTerm(q.head.name))
+      blocks :::= compileNodeRule(this, qs, ss)
 
     // edge query
-    val fakeBody        = r.q.head +: r.q.body
-    val fakeCQ          = ConjunctiveQuery(r.q.head, fakeBody) // we will just use the fakeBody below.
+    val fakeBody        = q.head +: q.body
+    val fakeCQ          = ConjunctiveQuery(q.head, fakeBody) // we will just use the fakeBody below.
 
-    val index = r.q.body.length + 1
+    val index = q.body.length + 1
     val qs2 = new QuerySchema( fakeCQ )
-    val variableIdsStr = Some(s"""R0.id AS "${r.q.head.name}.R0.id" """)
-    val variableColsStr = Some(s"""R0.label AS "${r.q.head.name}.R0.label" """)
+    val variableIdsStr = Some(s"""R0.id AS "${q.head.name}.R0.id" """)
+    val variableColsStr = Some(s"""R0.label AS "${q.head.name}.R0.label" """)
 
     // weight string
-    val uwStr = r.weights match {
+    val uwStr = weights match {
       case KnownFactorWeight(x) => None
       case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
     }
@@ -488,10 +445,10 @@ object DeepDiveLogCompiler {
       ${ ss.generateSQLBody(fakeCQ) }"""
 
     // factor function
-    val func = s"""Imply(${r.q.head.name}.R0.label)"""
+    val func = s"""Imply(${q.head.name}.R0.label)"""
 
     // weight
-    val weight = r.weights match {
+    val weight = weights match {
       case KnownFactorWeight(x) => s"${x}"
       case UnknownFactorWeight(w) => {
         s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, false)).mkString(", ")})"""
@@ -499,7 +456,7 @@ object DeepDiveLogCompiler {
     }
 
     blocks ::= s"""
-      deepdive.inference.factors.factor_${r.q.head.name} {
+      deepdive.inference.factors.factor_${q.head.name} {
         input_query: \"\"\"${inputQuery}\"\"\"
         function: "${func}"
         weight: "${weight}"
@@ -508,6 +465,57 @@ object DeepDiveLogCompiler {
 
     blocks.reverse
   }
+}
+
+
+// Compiler object that wires up everything together
+object DeepDiveLogCompiler {
+
+  def parseArgs(args: Array[String]) = {
+    val getContents = (filename: String) => {
+      val source = scala.io.Source.fromFile(filename)
+      try source.getLines mkString "\n" finally source.close()
+    }
+    args.map(getContents).reduce(_ ++ _)
+  }
+
+  val parser = new ConjunctiveQueryParser
+  def parseProgram(inputProgram: String) = parser.parse(parser.statements, inputProgram)
+
+  type CompiledBlocks = List[String]
+
+  def compileUserSettings(): CompiledBlocks = {
+    // TODO read user's proto-application.conf and augment it
+    List("""
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  """)
+  }
+
+  // generate variable schema statements
+  def compileVariableSchema(statements: List[Statement], ss: CompilationState): CompiledBlocks = {
+    var schema = Set[String]()
+    // generate the statements.
+    statements.foreach {
+      case InferenceRule(q, weights, supervision) =>
+        val qs = new QuerySchema(q)
+        schema += s"${q.head.name}.label: Boolean"
+      case _ => ()
+    }
+    val ddSchema = s"""
+      deepdive.schema.variables {
+        ${schema.mkString("\n")}
+      }
+    """
+    List(ddSchema)
+  }
 
   def main(args: Array[String]) {
     // get contents of all given files as one flat input program
@@ -523,18 +531,7 @@ object DeepDiveLogCompiler {
       :::
       compileVariableSchema(parsedProgram, state)
       :::
-      (
-      parsedProgram flatMap {
-        // XXX Ideally, a single compile call should handle all the polymorphic
-        // cases, but Scala/Java's ad-hoc polymorphism doesn't work that way.
-        // Instead, we need to use the visitor pattern, adding compile(...)
-        // methods to all case classes of Statement.
-        case s:InferenceRule  => compile(s, state)
-        case s:ExtractionRule => compile(s, state)
-        case s:FunctionRule   => compile(s, state)
-        case _ => List()
-      }
-      )
+      (parsedProgram flatMap (_.compile(state)))
     )
 
     // emit the generated code

From b20236e143fcc780642764caee151771d6721ab4 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 04:09:14 -0700
Subject: [PATCH 037/347] minor cleanup

---
 DeepDiveLogCompiler.scala | 34 +++++++++++++++++++++++-----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 3f8ef00f9..cede0c360 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -1,5 +1,7 @@
-import scala.util.parsing.combinator._
-import scala.collection.immutable.HashMap
+// DeepDiveLog compiler
+// See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
+
+// TODO update the following comment to new syntax.
 /*
  This file parses an extended form of datalog like sugar.
 
@@ -54,6 +56,9 @@ Consider
  unordered attributes, etc.).
 */
 
+import scala.util.parsing.combinator._
+import scala.collection.immutable.HashMap
+
 // ***************************************
 // * The union types for for the parser. *
 // ***************************************
@@ -148,14 +153,14 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   // rules or schema elements in aribitrary order
   def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
 
-  type Program = List[Statement]
-  def statements : Parser[Program] = rep1sep(statement, ".") ^^ { case(x) => x }
+  def program : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
 }
 
+
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
-class CompilationState( statements : List[Statement] )  {
+class CompilationState( statements : DeepDiveLogCompiler.Program )  {
     // TODO: refactor the schema into a class that constructs and
     // manages these maps. Also it should have appropriate
     // abstractions and error handling for missing values.
@@ -325,6 +330,8 @@ class QuerySchema(q : ConjunctiveQuery) {
 
 
 // Statements that will be parsed and compiled
+// Statement-local compilation logic is kept in each case class' compile() method.
+// Any global compilation logic should be kept in DeepDiveLogCompiler object.
 trait Statement {
   type CompiledBlocks = DeepDiveLogCompiler.CompiledBlocks
   def compile(state: CompilationState): CompiledBlocks = List()
@@ -471,6 +478,10 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
 // Compiler object that wires up everything together
 object DeepDiveLogCompiler {
 
+  type Program = List[Statement]
+  type CompiledBlock = String
+  type CompiledBlocks = List[CompiledBlock]
+
   def parseArgs(args: Array[String]) = {
     val getContents = (filename: String) => {
       val source = scala.io.Source.fromFile(filename)
@@ -480,9 +491,9 @@ object DeepDiveLogCompiler {
   }
 
   val parser = new ConjunctiveQueryParser
-  def parseProgram(inputProgram: String) = parser.parse(parser.statements, inputProgram)
-
-  type CompiledBlocks = List[String]
+  def parseProgram(inputProgram: String) = {
+    parser.parse(parser.program, inputProgram)
+  }
 
   def compileUserSettings(): CompiledBlocks = {
     // TODO read user's proto-application.conf and augment it
@@ -500,7 +511,7 @@ object DeepDiveLogCompiler {
   }
 
   // generate variable schema statements
-  def compileVariableSchema(statements: List[Statement], ss: CompilationState): CompiledBlocks = {
+  def compileVariableSchema(statements: Program, ss: CompilationState): CompiledBlocks = {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
@@ -517,6 +528,7 @@ object DeepDiveLogCompiler {
     List(ddSchema)
   }
 
+  // entry point for command-line interface
   def main(args: Array[String]) {
     // get contents of all given files as one flat input program
     val inputProgram = parseArgs(args)
@@ -526,7 +538,7 @@ object DeepDiveLogCompiler {
     val state = new CompilationState( parsedProgram )
 
     // compile the program into blocks of application.conf
-    val compiledBlocks = (
+    val blocks = (
       compileUserSettings
       :::
       compileVariableSchema(parsedProgram, state)
@@ -535,6 +547,6 @@ object DeepDiveLogCompiler {
     )
 
     // emit the generated code
-    compiledBlocks foreach println
+    blocks foreach println
   }
 }

From 116b210ea9c97d6d51cb374063b5ebcb240deba1 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 04:12:58 -0700
Subject: [PATCH 038/347] Separates parser defining syntax from the compiler

---
 DeepDiveLogCompiler.scala | 101 --------------------------------------
 DeepDiveLogParser.scala   | 100 +++++++++++++++++++++++++++++++++++++
 2 files changed, 100 insertions(+), 101 deletions(-)
 create mode 100644 DeepDiveLogParser.scala

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index cede0c360..dd0f44a8b 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -56,107 +56,8 @@ Consider
  unordered attributes, etc.).
 */
 
-import scala.util.parsing.combinator._
 import scala.collection.immutable.HashMap
 
-// ***************************************
-// * The union types for for the parser. *
-// ***************************************
-case class Variable(varName : String, relName : String, index : Int )
-case class Atom(name : String, terms : List[Variable])
-case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, body: List[Atom])
-case class Column(name : String, t : String)
-
-sealed trait FactorWeight {
-  def variables : List[String]
-}
-
-case class KnownFactorWeight(value: Double) extends FactorWeight {
-  def variables = Nil
-}
-
-case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
-
-// Parser
-class ConjunctiveQueryParser extends JavaTokenParsers {
-  // Odd definitions, but we'll keep them.
-  // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
-  // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
-  // def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
-  def stringliteral: Parser[String] = """[a-zA-Z0-9_\[\]]+""".r
-  def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
-
-  // relation names and columns are just strings.
-  def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
-  def col : Parser[String] = stringliteral  ^^ { case(x) => x }
-  def attr : Parser[Column] = stringliteral ~ stringliteral ^^ {
-    case(x ~ y) => Column(x, y)
-  }
-
-  def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ cols ~ ")") => {
-      val vars = cols.zipWithIndex map { case(name,i) => Variable(name, r, i) }
-      Atom(r,vars)
-    }
-  }
-
-  def attribute: Parser[Attribute] = relation_name ~ "(" ~ rep1sep(attr, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ attrs ~ ")") => {
-      val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
-      var types = attrs map { case(x) => x.t }
-      Attribute(r,vars, types)
-    }
-  }
-
-  def udf : Parser[String] = stringliteral ^^ {case (x) => x}
-
-  def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
-    case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
-  }
-
-  def schemaElement : Parser[SchemaElement] = attribute ~ opt("?") ^^ {
-    case (a ~ None) => SchemaElement(a,true)
-    case (a ~ Some(_)) =>  SchemaElement(a,false)
-  }
-
-
-  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~
-  "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~
-  "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines" ^^ {
-    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~
-      "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
-  }
-
-  def extractionRule : Parser[ExtractionRule] = query  ^^ {
-    case (q) => ExtractionRule(q)
-    // case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
-  }
-
-  def functionRule : Parser[FunctionRule] = stringliteral ~ ":-" ~ "!" ~ stringliteral ~ "(" ~ stringliteral ~ ")" ^^ {
-    case (a ~ ":-" ~ "!" ~ b ~ "(" ~ c ~ ")") => FunctionRule(c, a, b)
-  }
-
-  def constantWeight = "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ { x => KnownFactorWeight(x.toDouble) }
-  def unknwonWeight = "weight" ~> "=" ~> opt(rep1sep(col, ",")) ^^ {
-    case Some(varList) => UnknownFactorWeight(varList.toList)
-    case _ => UnknownFactorWeight(List())
-  }
-  def factorWeight = constantWeight | unknwonWeight
-
-  def supervision = "label" ~> "=" ~> col
-
-  def inferenceRule : Parser[InferenceRule] = query ~ factorWeight ~ supervision ^^ {
-    case (q ~ weight ~ supervision) => InferenceRule(q, weight, supervision)
-  }
-
-  // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
-
-  def program : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
-}
-
-
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
@@ -325,7 +226,6 @@ class QuerySchema(q : ConjunctiveQuery) {
   // accessors
   def getBodyIndex( varName : String ) : Int = { query_schema(varName)._1 }
   def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
-
 }
 
 
@@ -477,7 +377,6 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
 
 // Compiler object that wires up everything together
 object DeepDiveLogCompiler {
-
   type Program = List[Statement]
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
new file mode 100644
index 000000000..a8d788a8c
--- /dev/null
+++ b/DeepDiveLogParser.scala
@@ -0,0 +1,100 @@
+// DeepDiveLog syntax
+
+import scala.util.parsing.combinator._
+
+// ***************************************
+// * The union types for for the parser. *
+// ***************************************
+case class Variable(varName : String, relName : String, index : Int )
+case class Atom(name : String, terms : List[Variable])
+case class Attribute(name : String, terms : List[Variable], types : List[String])
+case class ConjunctiveQuery(head: Atom, body: List[Atom])
+case class Column(name : String, t : String)
+
+sealed trait FactorWeight {
+  def variables : List[String]
+}
+
+case class KnownFactorWeight(value: Double) extends FactorWeight {
+  def variables = Nil
+}
+
+case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
+
+// Parser
+class ConjunctiveQueryParser extends JavaTokenParsers {
+  // Odd definitions, but we'll keep them.
+  // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
+  // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
+  // def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
+  def stringliteral: Parser[String] = """[a-zA-Z0-9_\[\]]+""".r
+  def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
+
+  // relation names and columns are just strings.
+  def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
+  def col : Parser[String] = stringliteral  ^^ { case(x) => x }
+  def attr : Parser[Column] = stringliteral ~ stringliteral ^^ {
+    case(x ~ y) => Column(x, y)
+  }
+
+  def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
+    case (r ~ "(" ~ cols ~ ")") => {
+      val vars = cols.zipWithIndex map { case(name,i) => Variable(name, r, i) }
+      Atom(r,vars)
+    }
+  }
+
+  def attribute: Parser[Attribute] = relation_name ~ "(" ~ rep1sep(attr, ",") ~ ")" ^^ {
+    case (r ~ "(" ~ attrs ~ ")") => {
+      val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
+      var types = attrs map { case(x) => x.t }
+      Attribute(r,vars, types)
+    }
+  }
+
+  def udf : Parser[String] = stringliteral ^^ {case (x) => x}
+
+  def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
+    case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
+  }
+
+  def schemaElement : Parser[SchemaElement] = attribute ~ opt("?") ^^ {
+    case (a ~ None) => SchemaElement(a,true)
+    case (a ~ Some(_)) =>  SchemaElement(a,false)
+  }
+
+
+  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~
+  "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~
+  "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines" ^^ {
+    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~
+      "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
+  }
+
+  def extractionRule : Parser[ExtractionRule] = query  ^^ {
+    case (q) => ExtractionRule(q)
+    // case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
+  }
+
+  def functionRule : Parser[FunctionRule] = stringliteral ~ ":-" ~ "!" ~ stringliteral ~ "(" ~ stringliteral ~ ")" ^^ {
+    case (a ~ ":-" ~ "!" ~ b ~ "(" ~ c ~ ")") => FunctionRule(c, a, b)
+  }
+
+  def constantWeight = "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ { x => KnownFactorWeight(x.toDouble) }
+  def unknwonWeight = "weight" ~> "=" ~> opt(rep1sep(col, ",")) ^^ {
+    case Some(varList) => UnknownFactorWeight(varList.toList)
+    case _ => UnknownFactorWeight(List())
+  }
+  def factorWeight = constantWeight | unknwonWeight
+
+  def supervision = "label" ~> "=" ~> col
+
+  def inferenceRule : Parser[InferenceRule] = query ~ factorWeight ~ supervision ^^ {
+    case (q ~ weight ~ supervision) => InferenceRule(q, weight, supervision)
+  }
+
+  // rules or schema elements in aribitrary order
+  def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
+
+  def program : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
+}

From 8094421ae97d160a8eff686880de5bbd665f6d80 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 23:09:06 -0700
Subject: [PATCH 039/347] Prints parse error

---
 DeepDiveLogCompiler.scala | 24 +++++++++++-------------
 DeepDiveLogParser.scala   | 13 +++++++++++++
 2 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index dd0f44a8b..a8e0a8639 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -381,17 +381,16 @@ object DeepDiveLogCompiler {
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
 
-  def parseArgs(args: Array[String]) = {
-    val getContents = (filename: String) => {
-      val source = scala.io.Source.fromFile(filename)
-      try source.getLines mkString "\n" finally source.close()
-    }
-    args.map(getContents).reduce(_ ++ _)
-  }
-
   val parser = new ConjunctiveQueryParser
-  def parseProgram(inputProgram: String) = {
-    parser.parse(parser.program, inputProgram)
+  def parseFilesOrExit(fileNames: Array[String]): Program = {
+    try {
+      fileNames.toList flatMap { parser.parseProgramFile(_) }
+    } catch {
+      case e: RuntimeException =>
+        System.err.println("[error] " + e.getMessage)
+        System.exit(1)
+        null
+    }
   }
 
   def compileUserSettings(): CompiledBlocks = {
@@ -429,9 +428,8 @@ object DeepDiveLogCompiler {
 
   // entry point for command-line interface
   def main(args: Array[String]) {
-    // get contents of all given files as one flat input program
-    val inputProgram = parseArgs(args)
-    val parsedProgram = parseProgram(inputProgram).get
+    // parse each file into a single program
+    val parsedProgram = parseFilesOrExit(args)
 
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( parsedProgram )
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index a8d788a8c..6f7bcc9a5 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -97,4 +97,17 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
 
   def program : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
+
+  def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
+    parse(program, inputProgram) match {
+      case result: Success[_] => result.get
+      case error:  NoSuccess  => throw new RuntimeException(fileName.getOrElse("") + error.toString())
+    }
+  }
+
+  def parseProgramFile(fileName: String): List[Statement] = {
+    val source = scala.io.Source.fromFile(fileName)
+    try parseProgram(source.getLines mkString "\n", Some(fileName))
+    finally source.close()
+  }
 }

From 0035ce96d709a944599cf4c6a6ad260bbae1cb39 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 04:43:52 -0700
Subject: [PATCH 040/347] Formats the grammar to appear prettier

(mostly only white space changes)
---
 DeepDiveLogParser.scala | 120 ++++++++++++++++++++++++----------------
 1 file changed, 71 insertions(+), 49 deletions(-)

diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 6f7bcc9a5..00478f4ce 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -31,72 +31,94 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
 
   // relation names and columns are just strings.
-  def relation_name: Parser[String] = stringliteral ^^ {case (x) => x}
-  def col : Parser[String] = stringliteral  ^^ { case(x) => x }
-  def attr : Parser[Column] = stringliteral ~ stringliteral ^^ {
-    case(x ~ y) => Column(x, y)
-  }
-
-  def atom: Parser[Atom] = relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ cols ~ ")") => {
-      val vars = cols.zipWithIndex map { case(name,i) => Variable(name, r, i) }
-      Atom(r,vars)
+  def relation_name: Parser[String] = stringliteral
+  def col : Parser[String] = stringliteral
+  def attr : Parser[Column] =
+    stringliteral ~ stringliteral ^^ {
+      case(x ~ y) => Column(x, y)
     }
-  }
 
-  def attribute: Parser[Attribute] = relation_name ~ "(" ~ rep1sep(attr, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ attrs ~ ")") => {
-      val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
-      var types = attrs map { case(x) => x.t }
-      Attribute(r,vars, types)
+  def atom: Parser[Atom] =
+    relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
+      case (r ~ "(" ~ cols ~ ")") =>
+        Atom(r, cols.zipWithIndex map { case(name,i) => Variable(name, r, i) })
     }
-  }
 
-  def udf : Parser[String] = stringliteral ^^ {case (x) => x}
+  def attribute: Parser[Attribute] =
+    relation_name ~ "(" ~ rep1sep(attr, ",") ~ ")" ^^ {
+      case (r ~ "(" ~ attrs ~ ")") => {
+        val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
+        var types = attrs map { case(x) => x.t }
+        Attribute(r, vars, types)
+      }
+    }
 
-  def query : Parser[ConjunctiveQuery] = atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
-    case (headatom ~ ":-" ~ bodyatoms) => ConjunctiveQuery(headatom, bodyatoms.toList)
-  }
+  def query : Parser[ConjunctiveQuery] =
+    atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
+      case (headatom ~ ":-" ~ bodyatoms) =>
+        ConjunctiveQuery(headatom, bodyatoms.toList)
+    }
 
-  def schemaElement : Parser[SchemaElement] = attribute ~ opt("?") ^^ {
-    case (a ~ None) => SchemaElement(a,true)
-    case (a ~ Some(_)) =>  SchemaElement(a,false)
-  }
+  def schemaElement : Parser[SchemaElement] =
+    attribute ~ opt("?") ^^ {
+      case (a ~ None   ) => SchemaElement(a,true)
+      case (a ~ Some(_)) => SchemaElement(a,false)
+    }
 
 
-  def functionElement : Parser[FunctionElement] = "function" ~ stringliteral ~
-  "over like" ~ stringliteral ~ "returns like" ~ stringliteral ~ "implementation" ~
-  "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines" ^^ {
-    case ("function" ~ a ~ "over like" ~ b ~ "returns like" ~ c ~ "implementation" ~
-      "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") => FunctionElement(a, b, c, d, e)
-  }
+  def functionElement : Parser[FunctionElement] =
+    ( "function" ~ stringliteral
+    ~ "over" ~ "like" ~ stringliteral
+    ~ "returns" ~ "like" ~ stringliteral
+    ~ "implementation" ~ "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines"
+    ) ^^ {
+      case ("function" ~ a
+           ~ "over" ~ "like" ~ b
+           ~ "returns" ~ "like" ~ c
+           ~ "implementation" ~ "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") =>
+             FunctionElement(a, b, c, d, e)
+    }
 
-  def extractionRule : Parser[ExtractionRule] = query  ^^ {
-    case (q) => ExtractionRule(q)
-    // case (q ~ "udf" ~ "=" ~ None)       => ExtractionRule(q,None)
-  }
+  def extractionRule : Parser[ExtractionRule] =
+    query ^^ {
+      ExtractionRule(_)
+    }
 
-  def functionRule : Parser[FunctionRule] = stringliteral ~ ":-" ~ "!" ~ stringliteral ~ "(" ~ stringliteral ~ ")" ^^ {
-    case (a ~ ":-" ~ "!" ~ b ~ "(" ~ c ~ ")") => FunctionRule(c, a, b)
-  }
+  def functionRule : Parser[FunctionRule] =
+    ( stringliteral ~ ":-" ~ "!"
+    ~ stringliteral ~ "(" ~ stringliteral ~ ")"
+    ) ^^ {
+      case (out ~ ":-" ~ "!" ~ fn ~ "(" ~ in ~ ")") =>
+        FunctionRule(in, out, fn)
+    }
 
-  def constantWeight = "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ { x => KnownFactorWeight(x.toDouble) }
-  def unknwonWeight = "weight" ~> "=" ~> opt(rep1sep(col, ",")) ^^ {
-    case Some(varList) => UnknownFactorWeight(varList.toList)
-    case _ => UnknownFactorWeight(List())
-  }
+  def constantWeight =
+    "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ {
+      x => KnownFactorWeight(x.toDouble)
+    }
+  def unknwonWeight =
+    "weight" ~> "=" ~> opt(rep1sep(col, ",")) ^^ {
+      case Some(varList) => UnknownFactorWeight(varList.toList)
+      case _ => UnknownFactorWeight(List())
+    }
   def factorWeight = constantWeight | unknwonWeight
 
   def supervision = "label" ~> "=" ~> col
 
-  def inferenceRule : Parser[InferenceRule] = query ~ factorWeight ~ supervision ^^ {
-    case (q ~ weight ~ supervision) => InferenceRule(q, weight, supervision)
-  }
+  def inferenceRule : Parser[InferenceRule] =
+    ( query ~ factorWeight ~ supervision
+    ) ^^ {
+      case (q ~ weight ~ supervision) => InferenceRule(q, weight, supervision)
+    }
 
   // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = (functionElement | inferenceRule | extractionRule | functionRule | schemaElement) ^^ {case(x) => x}
-
-  def program : Parser[List[Statement]] = rep1sep(statement, ".") ^^ { case(x) => x }
+  def statement : Parser[Statement] = ( functionElement
+                                      | inferenceRule
+                                      | extractionRule
+                                      | functionRule
+                                      | schemaElement
+                                      )
+  def program : Parser[List[Statement]] = rep1sep(statement, ".")
 
   def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
     parse(program, inputProgram) match {

From 4e367815f6267a61bf75fc33631a12b172e8ff94 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 05:02:46 -0700
Subject: [PATCH 041/347] Renames some misleading grammar variables

e.g., stringliteral, attr, col
---
 DeepDiveLogParser.scala | 52 ++++++++++++++++++++++-------------------
 1 file changed, 28 insertions(+), 24 deletions(-)

diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 00478f4ce..3ba2300a4 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -1,4 +1,5 @@
 // DeepDiveLog syntax
+// See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
 import scala.util.parsing.combinator._
 
@@ -27,25 +28,28 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
   // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
   // def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
-  def stringliteral: Parser[String] = """[a-zA-Z0-9_\[\]]+""".r
+  def name: Parser[String] = """[a-zA-Z0-9_\[\]]+""".r
   def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
 
   // relation names and columns are just strings.
-  def relation_name: Parser[String] = stringliteral
-  def col : Parser[String] = stringliteral
-  def attr : Parser[Column] =
-    stringliteral ~ stringliteral ^^ {
-      case(x ~ y) => Column(x, y)
+  def relationName = name
+  def columnName = name
+  def columnType = name
+  def variableName = name
+  def functionName = name
+  def columnDeclaration : Parser[Column] =
+    columnName ~ columnType ^^ {
+      case(name ~ ty) => Column(name, ty)
     }
 
   def atom: Parser[Atom] =
-    relation_name ~ "(" ~ rep1sep(col, ",") ~ ")" ^^ {
+    relationName ~ "(" ~ rep1sep(variableName, ",") ~ ")" ^^ {
       case (r ~ "(" ~ cols ~ ")") =>
         Atom(r, cols.zipWithIndex map { case(name,i) => Variable(name, r, i) })
     }
 
-  def attribute: Parser[Attribute] =
-    relation_name ~ "(" ~ rep1sep(attr, ",") ~ ")" ^^ {
+  def relationDeclaration: Parser[Attribute] =
+    relationName ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ^^ {
       case (r ~ "(" ~ attrs ~ ")") => {
         val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
         var types = attrs map { case(x) => x.t }
@@ -59,18 +63,18 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
         ConjunctiveQuery(headatom, bodyatoms.toList)
     }
 
-  def schemaElement : Parser[SchemaElement] =
-    attribute ~ opt("?") ^^ {
+  def schemaDeclaration : Parser[SchemaElement] =
+    relationDeclaration ~ opt("?") ^^ {
       case (a ~ None   ) => SchemaElement(a,true)
       case (a ~ Some(_)) => SchemaElement(a,false)
     }
 
 
-  def functionElement : Parser[FunctionElement] =
-    ( "function" ~ stringliteral
-    ~ "over" ~ "like" ~ stringliteral
-    ~ "returns" ~ "like" ~ stringliteral
-    ~ "implementation" ~ "\"" ~ path ~ "\"" ~ "handles" ~ stringliteral ~ "lines"
+  def functionDeclaration : Parser[FunctionElement] =
+    ( "function" ~ functionName
+    ~ "over" ~ "like" ~ relationName
+    ~ "returns" ~ "like" ~ relationName
+    ~ "implementation" ~ "\"" ~ path ~ "\"" ~ "handles" ~ ("tsv" | "json") ~ "lines"
     ) ^^ {
       case ("function" ~ a
            ~ "over" ~ "like" ~ b
@@ -84,9 +88,9 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
       ExtractionRule(_)
     }
 
-  def functionRule : Parser[FunctionRule] =
-    ( stringliteral ~ ":-" ~ "!"
-    ~ stringliteral ~ "(" ~ stringliteral ~ ")"
+  def functionCallRule : Parser[FunctionRule] =
+    ( relationName ~ ":-" ~ "!"
+    ~ functionName ~ "(" ~ relationName ~ ")"
     ) ^^ {
       case (out ~ ":-" ~ "!" ~ fn ~ "(" ~ in ~ ")") =>
         FunctionRule(in, out, fn)
@@ -97,13 +101,13 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
       x => KnownFactorWeight(x.toDouble)
     }
   def unknwonWeight =
-    "weight" ~> "=" ~> opt(rep1sep(col, ",")) ^^ {
+    "weight" ~> "=" ~> opt(rep1sep(variableName, ",")) ^^ {
       case Some(varList) => UnknownFactorWeight(varList.toList)
       case _ => UnknownFactorWeight(List())
     }
   def factorWeight = constantWeight | unknwonWeight
 
-  def supervision = "label" ~> "=" ~> col
+  def supervision = "label" ~> "=" ~> variableName
 
   def inferenceRule : Parser[InferenceRule] =
     ( query ~ factorWeight ~ supervision
@@ -112,11 +116,11 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     }
 
   // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = ( functionElement
+  def statement : Parser[Statement] = ( functionDeclaration
                                       | inferenceRule
                                       | extractionRule
-                                      | functionRule
-                                      | schemaElement
+                                      | functionCallRule
+                                      | schemaDeclaration
                                       )
   def program : Parser[List[Statement]] = rep1sep(statement, ".")
 

From 2fa5613bdefe6d55725adbeb180244cabb1be0c8 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 13:06:54 -0700
Subject: [PATCH 042/347] Replaces our clunky parsers for names, numbers,
 strings with JavaTokenParsers'

---
 DeepDiveLogCompiler.scala |  3 ++-
 DeepDiveLogParser.scala   | 57 +++++++++++++++++++--------------------
 build.sbt                 |  1 +
 project/assembly.sbt      |  1 +
 4 files changed, 32 insertions(+), 30 deletions(-)
 create mode 100644 build.sbt
 create mode 100644 project/assembly.sbt

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index a8e0a8639..6a676d0f2 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -57,6 +57,7 @@ Consider
 */
 
 import scala.collection.immutable.HashMap
+import org.apache.commons.lang3.StringEscapeUtils
 
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
@@ -285,7 +286,7 @@ case class FunctionRule(input : String, output : String, function : String) exte
         input: \"\"\" SELECT * FROM ${input}
         \"\"\"
         output_relation: \"${output}\"
-        udf: \"${function.implementation}\"
+        udf: \"${StringEscapeUtils.escapeJava(function.implementation)}\"
         style: \"${function.mode}_extractor\"
         ${ss.generateDependenciesOfCompiledBlockFor(this)}
       }
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 3ba2300a4..c507f8f3e 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -2,6 +2,7 @@
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
 import scala.util.parsing.combinator._
+import org.apache.commons.lang3.StringEscapeUtils
 
 // ***************************************
 // * The union types for for the parser. *
@@ -24,19 +25,23 @@ case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
 
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {
-  // Odd definitions, but we'll keep them.
-  // def stringliteral1: Parser[String] = ("'"+"""([^'\p{Cntrl}\\]|\\[\\"'bfnrt]|\\u[a-fA-F0-9]{4})*"""+"'").r ^^ {case (x) => x}
-  // def stringliteral2: Parser[String] = """[a-zA-Z_0-9\./]*""".r ^^ {case (x) => x}
-  // def stringliteral: Parser[String] = (stringliteral1 | stringliteral2) ^^ {case (x) => x}
-  def name: Parser[String] = """[a-zA-Z0-9_\[\]]+""".r
-  def path: Parser[String] = """[a-zA-Z0-9\./_]+""".r
-
-  // relation names and columns are just strings.
-  def relationName = name
-  def columnName = name
-  def columnType = name
-  def variableName = name
-  def functionName = name
+
+  // JavaTokenParsers provides several useful number parsers:
+  //   wholeNumber, decimalNumber, floatingPointNumber 
+  def floatingPointNumberAsDouble = floatingPointNumber ^^ { _.toDouble }
+  def stringLiteralAsString = stringLiteral ^^ {
+    s => StringEscapeUtils.unescapeJava(
+      s.stripPrefix("\"").stripSuffix("\""))
+  }
+
+  // We just use Java identifiers to parse various names
+  def relationName = ident
+  def columnName   = ident
+  def columnType   = ident ~ ("[]"?) ^^ {
+      case ty ~ isArrayType => ty + isArrayType.getOrElse("")
+    }
+  def variableName = ident
+  def functionName = ident
   def columnDeclaration : Parser[Column] =
     columnName ~ columnType ^^ {
       case(name ~ ty) => Column(name, ty)
@@ -74,12 +79,12 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     ( "function" ~ functionName
     ~ "over" ~ "like" ~ relationName
     ~ "returns" ~ "like" ~ relationName
-    ~ "implementation" ~ "\"" ~ path ~ "\"" ~ "handles" ~ ("tsv" | "json") ~ "lines"
+    ~ "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines"
     ) ^^ {
       case ("function" ~ a
            ~ "over" ~ "like" ~ b
            ~ "returns" ~ "like" ~ c
-           ~ "implementation" ~ "\"" ~ d ~ "\"" ~ "handles" ~ e ~ "lines") =>
+           ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") =>
              FunctionElement(a, b, c, d, e)
     }
 
@@ -96,33 +101,27 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
         FunctionRule(in, out, fn)
     }
 
-  def constantWeight =
-    "weight" ~> "=" ~> """-?[\d\.]+""".r ^^ {
-      x => KnownFactorWeight(x.toDouble)
-    }
-  def unknwonWeight =
-    "weight" ~> "=" ~> opt(rep1sep(variableName, ",")) ^^ {
-      case Some(varList) => UnknownFactorWeight(varList.toList)
-      case _ => UnknownFactorWeight(List())
-    }
-  def factorWeight = constantWeight | unknwonWeight
+  def constantWeight = floatingPointNumberAsDouble ^^ {   KnownFactorWeight(_) }
+  def unknownWeight  = repsep(variableName, ",")   ^^ { UnknownFactorWeight(_) }
+  def factorWeight = "weight" ~> "=" ~> (constantWeight | unknownWeight)
 
   def supervision = "label" ~> "=" ~> variableName
 
   def inferenceRule : Parser[InferenceRule] =
     ( query ~ factorWeight ~ supervision
     ) ^^ {
-      case (q ~ weight ~ supervision) => InferenceRule(q, weight, supervision)
+      case (q ~ weight ~ supervision) =>
+        InferenceRule(q, weight, supervision)
     }
 
   // rules or schema elements in aribitrary order
-  def statement : Parser[Statement] = ( functionDeclaration
+  def statement : Parser[Statement] = ( schemaDeclaration
                                       | inferenceRule
                                       | extractionRule
+                                      | functionDeclaration
                                       | functionCallRule
-                                      | schemaDeclaration
                                       )
-  def program : Parser[List[Statement]] = rep1sep(statement, ".")
+  def program : Parser[List[Statement]] = phrase(rep1(statement <~ "."))
 
   def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
     parse(program, inputProgram) match {
diff --git a/build.sbt b/build.sbt
new file mode 100644
index 000000000..1d2b3a28a
--- /dev/null
+++ b/build.sbt
@@ -0,0 +1 @@
+libraryDependencies += "org.apache.commons" % "commons-lang3" % "3.4"
diff --git a/project/assembly.sbt b/project/assembly.sbt
new file mode 100644
index 000000000..74adde3fc
--- /dev/null
+++ b/project/assembly.sbt
@@ -0,0 +1 @@
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.13.0")

From c156884994edc7cec2f75ebb39b99be6161ca491 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 14:05:58 -0700
Subject: [PATCH 043/347] Cleans up conjunctiveQuery grammar

making it more extensible in the future.
---
 DeepDiveLogCompiler.scala |  2 +-
 DeepDiveLogParser.scala   | 57 ++++++++++++++++++++++++---------------
 examples/test6.ddl        |  2 +-
 3 files changed, 37 insertions(+), 24 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 6a676d0f2..dfc90fada 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -83,7 +83,7 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
         terms.foreach {
           case Variable(n,r,i) =>
             schema           += { (r,i) -> n }
-            ground_relations += { r -> query } // record whether a query or a ground term.
+            ground_relations += { r -> !query } // record whether a query or a ground term.
         }
       case ExtractionRule(_) => ()
       case InferenceRule(_,_,_) => ()
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index c507f8f3e..b3181a024 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -8,6 +8,7 @@ import org.apache.commons.lang3.StringEscapeUtils
 // * The union types for for the parser. *
 // ***************************************
 case class Variable(varName : String, relName : String, index : Int )
+// TODO make Atom a trait, and have multiple case classes, e.g., RelationAtom and CondExprAtom
 case class Atom(name : String, terms : List[Variable])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
 case class ConjunctiveQuery(head: Atom, body: List[Atom])
@@ -42,36 +43,48 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     }
   def variableName = ident
   def functionName = ident
-  def columnDeclaration : Parser[Column] =
+
+  def columnDeclaration: Parser[Column] =
     columnName ~ columnType ^^ {
       case(name ~ ty) => Column(name, ty)
     }
-
-  def atom: Parser[Atom] =
-    relationName ~ "(" ~ rep1sep(variableName, ",") ~ ")" ^^ {
-      case (r ~ "(" ~ cols ~ ")") =>
-        Atom(r, cols.zipWithIndex map { case(name,i) => Variable(name, r, i) })
-    }
-
-  def relationDeclaration: Parser[Attribute] =
-    relationName ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ^^ {
-      case (r ~ "(" ~ attrs ~ ")") => {
+  def schemaDeclaration: Parser[SchemaElement] =
+    relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ^^ {
+      case (r ~ isQuery ~ "(" ~ attrs ~ ")") => {
         val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
         var types = attrs map { case(x) => x.t }
-        Attribute(r, vars, types)
+        SchemaElement(Attribute(r, vars, types), (isQuery != None))
       }
     }
 
-  def query : Parser[ConjunctiveQuery] =
-    atom ~ ":-" ~ rep1sep(atom, ",") ^^ {
-      case (headatom ~ ":-" ~ bodyatoms) =>
-        ConjunctiveQuery(headatom, bodyatoms.toList)
+
+  // TODO support aggregate function syntax somehow
+  def cqHead = relationName ~ "(" ~ repsep(variableName, ",") ~ ")" ^^ {
+      case (r ~ "(" ~ variableUses ~ ")") =>
+        Atom(r, variableUses.zipWithIndex map {
+          case(name,i) => Variable(name, r, i)
+        })
     }
 
-  def schemaDeclaration : Parser[SchemaElement] =
-    relationDeclaration ~ opt("?") ^^ {
-      case (a ~ None   ) => SchemaElement(a,true)
-      case (a ~ Some(_)) => SchemaElement(a,false)
+  // TODO add conditional expressions for where clause
+  def cqConditionalExpr = failure("No conditional expression supported yet")
+  def cqBodyAtom: Parser[Atom] =
+    ( relationName ~ "(" ~ repsep(variableName, ",") ~ ")" ^^ {
+        case (r ~ "(" ~ variableBindings ~ ")") =>
+          Atom(r, variableBindings.zipWithIndex map {
+            case(name,i) => Variable(name, r, i)
+          })
+      }
+    | cqConditionalExpr
+    )
+  def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
+  def conjunctiveQuery : Parser[ConjunctiveQuery] =
+    cqHead ~ ":-" ~ rep1sep(cqBody, ";") ^^ {
+      case (headatom ~ ":-" ~ disjunctiveBodies) =>
+        // TODO handle all disjunctiveBodies
+        // XXX only compiling the first body
+        val bodyatoms = disjunctiveBodies(0)
+        ConjunctiveQuery(headatom, bodyatoms.toList)
     }
 
 
@@ -89,7 +102,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     }
 
   def extractionRule : Parser[ExtractionRule] =
-    query ^^ {
+    conjunctiveQuery ^^ {
       ExtractionRule(_)
     }
 
@@ -108,7 +121,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
   def supervision = "label" ~> "=" ~> variableName
 
   def inferenceRule : Parser[InferenceRule] =
-    ( query ~ factorWeight ~ supervision
+    ( conjunctiveQuery ~ factorWeight ~ supervision
     ) ^^ {
       case (q ~ weight ~ supervision) =>
         InferenceRule(q, weight, supervision)
diff --git a/examples/test6.ddl b/examples/test6.ddl
index 753bea2e5..f7b87deed 100644
--- a/examples/test6.ddl
+++ b/examples/test6.ddl
@@ -28,7 +28,7 @@ has_spouse_features(
   relation_id text,
   feature     text).
 
-has_spouse(relation_id text)?.
+has_spouse?(relation_id text).
 
 people_mentions :-
   !ext_people(ext_people_input).

From 2d8fa1093ee0f71fb8e156bf2344b45ebd5f19c6 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 23 Apr 2015 14:16:06 -0700
Subject: [PATCH 044/347] Renames Statement classes

---
 DeepDiveLogCompiler.scala | 39 +++++++++++++++++----------------------
 DeepDiveLogParser.scala   | 12 ++++++------
 2 files changed, 23 insertions(+), 28 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index dfc90fada..33d0a38d0 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -71,7 +71,7 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
 
   var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
 
-  var function_schema : Map[String, FunctionElement] = new HashMap[ String, FunctionElement]()
+  var function_schema : Map[String, FunctionDeclaration] = new HashMap[ String, FunctionDeclaration]()
 
   // The dependency graph between statements.
   var dependencies : Map[Statement, Set[Statement]] = new HashMap()
@@ -79,16 +79,16 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
   def init() = {
     // generate the statements.
     statements.foreach {
-      case SchemaElement(Attribute(r, terms, types),query) =>
+      case SchemaDeclaration(Attribute(r, terms, types), isQuery) =>
         terms.foreach {
           case Variable(n,r,i) =>
             schema           += { (r,i) -> n }
-            ground_relations += { r -> !query } // record whether a query or a ground term.
+            ground_relations += { r -> !isQuery } // record whether a query or a ground term.
         }
       case ExtractionRule(_) => ()
       case InferenceRule(_,_,_) => ()
-      case FunctionElement(a, b, c, d, e) => function_schema += {a -> FunctionElement(a, b, c, d, e)}
-      case FunctionRule(_,_,_) => ()
+      case FunctionDeclaration(a, b, c, d, e) => function_schema += {a -> FunctionDeclaration(a, b, c, d, e)}
+      case FunctionCallRule(_,_,_) => ()
     }
 
     analyzeDependency(statements)
@@ -98,9 +98,9 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
 
   // Given a statement, resolve its name for the compiled extractor block.
   def resolveExtractorBlockName(s: Statement): String = s match {
-    case s: ExtractionRule => s"extraction_rule_${statements indexOf s}"
-    case s: FunctionRule   => s"extraction_rule_${statements indexOf s}"
-    case s: InferenceRule  => s"extraction_rule_${s.q.head.name}"
+    case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
+    case s: ExtractionRule   => s"extraction_rule_${statements indexOf s}"
+    case s: InferenceRule    => s"extraction_rule_${s.q.head.name}"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
@@ -116,13 +116,8 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
     }
   }
 
-  def resolveFunctionName( v : String ) : FunctionElement = {
-    if (function_schema contains v) {
-      function_schema(v)
-    } else {
-      return FunctionElement("0","0","0","0","0")
-    }
-
+  def resolveFunctionName( v : String ) : FunctionDeclaration = {
+    function_schema(v)
   }
 
   // The default is query term.
@@ -178,15 +173,15 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
     var stmtByHeadName = new HashMap[String, Statement]()
     statements foreach {
       case e : ExtractionRule => stmtByHeadName += { e.q.head.name -> e }
-      case f : FunctionRule   => stmtByHeadName += { f.output      -> f }
+      case f : FunctionCallRule   => stmtByHeadName += { f.output      -> f }
       case w : InferenceRule  => stmtByHeadName += { w.q.head.name -> w }
       case _ =>
     }
     // then, look at the body of each statement to construct a dependency graph
     statements foreach {
-      case f : FunctionRule   => dependencies += { f -> (        Some(f.input) flatMap (stmtByHeadName get _)).toSet }
-      case e : ExtractionRule => dependencies += { e -> (e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
-      case w : InferenceRule  => dependencies += { w -> (w.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
+      case f : FunctionCallRule => dependencies += { f -> (        Some(f.input) flatMap (stmtByHeadName get _)).toSet }
+      case e : ExtractionRule   => dependencies += { e -> (e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
+      case w : InferenceRule    => dependencies += { w -> (w.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
       case _ =>
     }
   }
@@ -237,8 +232,8 @@ trait Statement {
   type CompiledBlocks = DeepDiveLogCompiler.CompiledBlocks
   def compile(state: CompilationState): CompiledBlocks = List()
 }
-case class SchemaElement( a : Attribute , query : Boolean ) extends Statement // atom and whether this is a query relation.
-case class FunctionElement( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
+case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
+case class FunctionDeclaration( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 {
   // Generate extraction rule part for deepdive
@@ -271,7 +266,7 @@ case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction
     List(extractor)
   }
 }
-case class FunctionRule(input : String, output : String, function : String) extends Statement // Extraction rule
+case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
 {
   override def compile(ss: CompilationState): CompiledBlocks = {
     val inputQuery = s"""
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index b3181a024..dc07e2d4a 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -48,12 +48,12 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     columnName ~ columnType ^^ {
       case(name ~ ty) => Column(name, ty)
     }
-  def schemaDeclaration: Parser[SchemaElement] =
+  def schemaDeclaration: Parser[SchemaDeclaration] =
     relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ^^ {
       case (r ~ isQuery ~ "(" ~ attrs ~ ")") => {
         val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
         var types = attrs map { case(x) => x.t }
-        SchemaElement(Attribute(r, vars, types), (isQuery != None))
+        SchemaDeclaration(Attribute(r, vars, types), (isQuery != None))
       }
     }
 
@@ -88,7 +88,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     }
 
 
-  def functionDeclaration : Parser[FunctionElement] =
+  def functionDeclaration : Parser[FunctionDeclaration] =
     ( "function" ~ functionName
     ~ "over" ~ "like" ~ relationName
     ~ "returns" ~ "like" ~ relationName
@@ -98,7 +98,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
            ~ "over" ~ "like" ~ b
            ~ "returns" ~ "like" ~ c
            ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") =>
-             FunctionElement(a, b, c, d, e)
+             FunctionDeclaration(a, b, c, d, e)
     }
 
   def extractionRule : Parser[ExtractionRule] =
@@ -106,12 +106,12 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
       ExtractionRule(_)
     }
 
-  def functionCallRule : Parser[FunctionRule] =
+  def functionCallRule : Parser[FunctionCallRule] =
     ( relationName ~ ":-" ~ "!"
     ~ functionName ~ "(" ~ relationName ~ ")"
     ) ^^ {
       case (out ~ ":-" ~ "!" ~ fn ~ "(" ~ in ~ ")") =>
-        FunctionRule(in, out, fn)
+        FunctionCallRule(in, out, fn)
     }
 
   def constantWeight = floatingPointNumberAsDouble ^^ {   KnownFactorWeight(_) }

From 381d08419ffd2551ed3e8784be4769b80d8d9864 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 24 Apr 2015 02:06:54 -0700
Subject: [PATCH 045/347] Separates RelationType parsing

---
 DeepDiveLogCompiler.scala |  4 ++--
 DeepDiveLogParser.scala   | 21 +++++++++++++++------
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 33d0a38d0..ed286e791 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -87,7 +87,7 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
         }
       case ExtractionRule(_) => ()
       case InferenceRule(_,_,_) => ()
-      case FunctionDeclaration(a, b, c, d, e) => function_schema += {a -> FunctionDeclaration(a, b, c, d, e)}
+      case f @ FunctionDeclaration(a, b, c, d, e) => function_schema += {a -> f}
       case FunctionCallRule(_,_,_) => ()
     }
 
@@ -233,7 +233,7 @@ trait Statement {
   def compile(state: CompilationState): CompiledBlocks = List()
 }
 case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
-case class FunctionDeclaration( functionName: String, input: String, output: String, implementation: String, mode: String) extends Statement
+case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementation: String, mode: String) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 {
   // Generate extraction rule part for deepdive
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index dc07e2d4a..84028f532 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -21,9 +21,12 @@ sealed trait FactorWeight {
 case class KnownFactorWeight(value: Double) extends FactorWeight {
   def variables = Nil
 }
-
 case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
 
+trait RelationType
+case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
+case class RelationTypeAlias(likeRelationName: String) extends RelationType
+
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {
 
@@ -87,18 +90,24 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
         ConjunctiveQuery(headatom, bodyatoms.toList)
     }
 
+  def relationType: Parser[RelationType] =
+    ( rep1sep(columnDeclaration, ",") ^^ {
+        attrs => RelationTypeDeclaration(attrs map { _.name }, attrs map { _.t })
+      }
+    | "like" ~> relationName ^^ { RelationTypeAlias(_) }
+    )
 
   def functionDeclaration : Parser[FunctionDeclaration] =
     ( "function" ~ functionName
-    ~ "over" ~ "like" ~ relationName
-    ~ "returns" ~ "like" ~ relationName
+    ~ "over" ~ relationType
+    ~ "returns" ~ relationType
     ~ "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines"
     ) ^^ {
       case ("function" ~ a
-           ~ "over" ~ "like" ~ b
-           ~ "returns" ~ "like" ~ c
+           ~ "over" ~ inTy
+           ~ "returns" ~ outTy
            ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") =>
-             FunctionDeclaration(a, b, c, d, e)
+             FunctionDeclaration(a, inTy, outTy, d, e)
     }
 
   def extractionRule : Parser[ExtractionRule] =

From 61dda30aa90620c7e7f4d5afcc869b1031b44069 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 24 Apr 2015 02:42:47 -0700
Subject: [PATCH 046/347] Refactors grammar to keep implementation declarations
 separate

---
 DeepDiveLogCompiler.scala | 39 ++++++++++++++++++++++++---------------
 DeepDiveLogParser.scala   | 25 ++++++++++++++++---------
 2 files changed, 40 insertions(+), 24 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index ed286e791..fe05f1fa4 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -87,7 +87,7 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
         }
       case ExtractionRule(_) => ()
       case InferenceRule(_,_,_) => ()
-      case f @ FunctionDeclaration(a, b, c, d, e) => function_schema += {a -> f}
+      case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case FunctionCallRule(_,_,_) => ()
     }
 
@@ -96,6 +96,10 @@ class CompilationState( statements : DeepDiveLogCompiler.Program )  {
 
   init()
 
+  def error(message: String) {
+    throw new RuntimeException(message)
+  }
+
   // Given a statement, resolve its name for the compiled extractor block.
   def resolveExtractorBlockName(s: Statement): String = s match {
     case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
@@ -233,7 +237,7 @@ trait Statement {
   def compile(state: CompilationState): CompiledBlocks = List()
 }
 case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
-case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementation: String, mode: String) extends Statement
+case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 {
   // Generate extraction rule part for deepdive
@@ -274,6 +278,15 @@ case class FunctionCallRule(input : String, output : String, function : String)
     """
 
     val function = ss.resolveFunctionName(this.function)
+    val udfDetails = (function.implementations collectFirst {
+      case impl: RowWiseLineHandler =>
+        s"""udf: \"${StringEscapeUtils.escapeJava(impl.command)}\"
+        style: \"${impl.format}_extractor\""""
+    })
+
+    if (udfDetails.isEmpty)
+      ss.error(s"Cannot find compilable implementation for function ${this.function} among:\n  "
+        + (function.implementations mkString "\n  "))
 
     val blockName = ss.resolveExtractorBlockName(this)
     val extractor = s"""
@@ -281,8 +294,7 @@ case class FunctionCallRule(input : String, output : String, function : String)
         input: \"\"\" SELECT * FROM ${input}
         \"\"\"
         output_relation: \"${output}\"
-        udf: \"${StringEscapeUtils.escapeJava(function.implementation)}\"
-        style: \"${function.mode}_extractor\"
+        ${udfDetails.get}
         ${ss.generateDependenciesOfCompiledBlockFor(this)}
       }
     """
@@ -378,15 +390,8 @@ object DeepDiveLogCompiler {
   type CompiledBlocks = List[CompiledBlock]
 
   val parser = new ConjunctiveQueryParser
-  def parseFilesOrExit(fileNames: Array[String]): Program = {
-    try {
-      fileNames.toList flatMap { parser.parseProgramFile(_) }
-    } catch {
-      case e: RuntimeException =>
-        System.err.println("[error] " + e.getMessage)
-        System.exit(1)
-        null
-    }
+  def parseFiles(fileNames: Array[String]): Program = {
+    fileNames.toList flatMap { parser.parseProgramFile(_) }
   }
 
   def compileUserSettings(): CompiledBlocks = {
@@ -423,9 +428,9 @@ object DeepDiveLogCompiler {
   }
 
   // entry point for command-line interface
-  def main(args: Array[String]) {
+  def main(args: Array[String]) = try {
     // parse each file into a single program
-    val parsedProgram = parseFilesOrExit(args)
+    val parsedProgram = parseFiles(args)
 
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( parsedProgram )
@@ -441,5 +446,9 @@ object DeepDiveLogCompiler {
 
     // emit the generated code
     blocks foreach println
+  } catch {
+    case e: RuntimeException =>
+      System.err.println("[error] " + e.getMessage)
+      System.exit(1)
   }
 }
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 84028f532..46c518bb6 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -27,6 +27,10 @@ trait RelationType
 case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
 case class RelationTypeAlias(likeRelationName: String) extends RelationType
 
+trait FunctionImplementationDeclaration
+case class RowWiseLineHandler(format: String, command: String) extends FunctionImplementationDeclaration
+
+
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {
 
@@ -97,17 +101,20 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
     | "like" ~> relationName ^^ { RelationTypeAlias(_) }
     )
 
+  def functionImplementation : Parser[FunctionImplementationDeclaration] =
+    "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
+      case (_ ~ command ~ _ ~ format ~ _) => RowWiseLineHandler(command=command, format=format)
+    }
+
   def functionDeclaration : Parser[FunctionDeclaration] =
-    ( "function" ~ functionName
-    ~ "over" ~ relationType
-    ~ "returns" ~ relationType
-    ~ "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines"
+    ( "function" ~ functionName ~ "over" ~ relationType
+                             ~ "returns" ~ relationType
+                 ~ (functionImplementation+)
     ) ^^ {
-      case ("function" ~ a
-           ~ "over" ~ inTy
-           ~ "returns" ~ outTy
-           ~ "implementation" ~ d ~ "handles" ~ e ~ "lines") =>
-             FunctionDeclaration(a, inTy, outTy, d, e)
+      case ("function" ~ a ~ "over" ~ inTy
+                           ~ "returns" ~ outTy
+                       ~ implementationDecls) =>
+             FunctionDeclaration(a, inTy, outTy, implementationDecls)
     }
 
   def extractionRule : Parser[ExtractionRule] =

From 8e2c5657086e1662e3495b7688cc8d24971b456a Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 24 Apr 2015 03:05:40 -0700
Subject: [PATCH 047/347] Updates README, renames spouse_example

---
 Makefile                                            |  2 +-
 README.md                                           | 13 +++++++++++--
 examples/{test6.ddl => spouse_example.ddl}          |  0
 .../{test6.expected => spouse_example.expected}     |  0
 4 files changed, 12 insertions(+), 3 deletions(-)
 rename examples/{test6.ddl => spouse_example.ddl} (100%)
 rename examples/{test6.expected => spouse_example.expected} (100%)

diff --git a/Makefile b/Makefile
index 5a36a213a..02dc2d557 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 # Makefile for DeepDiveLogCompiler
 
 TESTJAR = ddlc-test.jar
-TEST = examples/test6.ddl
+TEST = examples/spouse_example.ddl
 
 test: $(TESTJAR)
 	CLASSPATH=$(shell sbt "export compile:dependency-classpath" | tail -1) \
diff --git a/README.md b/README.md
index 87f79a46d..5f4807a65 100644
--- a/README.md
+++ b/README.md
@@ -3,14 +3,23 @@ DeepDiveLogCompiler
 
 A compiler that enables writing DeepDive apps in a Datalog-like syntax.
 
-## Building
+## Testing
 
 ```bash
 make
 ```
 
+## Building
+The following command produces a standalone jar.
+
+```bash
+make ddlc.jar
+```
+
 ## Running
 The following will generate an application.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
 ```bash
-scala ddlc.jar examples/spouse_example.ddl >application.conf
+mkdir -p examples/spouse_example
+java -jar ddlc.jar examples/spouse_example.ddl >examples/spouse_example/application.conf
 ```
+
diff --git a/examples/test6.ddl b/examples/spouse_example.ddl
similarity index 100%
rename from examples/test6.ddl
rename to examples/spouse_example.ddl
diff --git a/examples/test6.expected b/examples/spouse_example.expected
similarity index 100%
rename from examples/test6.expected
rename to examples/spouse_example.expected

From 2bd3219f200c4d51afe2d2844f3b9bba51791c4d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 20:27:09 -0700
Subject: [PATCH 048/347] Adds scopt to support more than one mode

Namely, compiling and pretty printing for now.
---
 DeepDiveLogCompiler.scala | 87 ++++++++++++++++++++++++++++++---------
 Makefile                  |  4 +-
 build.sbt                 |  4 ++
 3 files changed, 74 insertions(+), 21 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index fe05f1fa4..04cff9d17 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -62,7 +62,7 @@ import org.apache.commons.lang3.StringEscapeUtils
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
-class CompilationState( statements : DeepDiveLogCompiler.Program )  {
+class CompilationState( statements : DeepDiveLog.Program )  {
     // TODO: refactor the schema into a class that constructs and
     // manages these maps. Also it should have appropriate
     // abstractions and error handling for missing values.
@@ -382,18 +382,37 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
   }
 }
 
+// An abstraction of DeepDiveLog handlers
+trait DeepDiveLogHandler {
+  def run(program: DeepDiveLog.Program, config: DeepDiveLog.Config): Unit
 
-// Compiler object that wires up everything together
-object DeepDiveLogCompiler {
-  type Program = List[Statement]
-  type CompiledBlock = String
-  type CompiledBlocks = List[CompiledBlock]
+  def run(config: DeepDiveLog.Config): Unit = try {
+    // parse each file into a single program
+    val parsedProgram = parseFiles(config.inputFiles)
+
+    // run handler with the parsed program
+    run(parsedProgram, config)
+  } catch {
+    case e: RuntimeException => die(e.getMessage)
+  }
 
-  val parser = new ConjunctiveQueryParser
-  def parseFiles(fileNames: Array[String]): Program = {
-    fileNames.toList flatMap { parser.parseProgramFile(_) }
+  def parseFiles(fileNames: List[String]): DeepDiveLog.Program = {
+    val ddlParser = new ConjunctiveQueryParser
+    fileNames flatMap { ddlParser.parseProgramFile(_) }
   }
 
+  def die(message: String = null) = {
+    if (message != null)
+      System.err.println("[error] " + message)
+    System.exit(1)
+  }
+}
+
+// Compiler that wires up everything together
+object DeepDiveLogCompiler extends DeepDiveLogHandler {
+  type CompiledBlock = String
+  type CompiledBlocks = List[CompiledBlock]
+
   def compileUserSettings(): CompiledBlocks = {
     // TODO read user's proto-application.conf and augment it
     List("""
@@ -410,7 +429,7 @@ object DeepDiveLogCompiler {
   }
 
   // generate variable schema statements
-  def compileVariableSchema(statements: Program, ss: CompilationState): CompiledBlocks = {
+  def compileVariableSchema(statements: DeepDiveLog.Program, ss: CompilationState): CompiledBlocks = {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
@@ -427,11 +446,8 @@ object DeepDiveLogCompiler {
     List(ddSchema)
   }
 
-  // entry point for command-line interface
-  def main(args: Array[String]) = try {
-    // parse each file into a single program
-    val parsedProgram = parseFiles(args)
-
+  // entry point for compilation
+  override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( parsedProgram )
 
@@ -446,9 +462,42 @@ object DeepDiveLogCompiler {
 
     // emit the generated code
     blocks foreach println
-  } catch {
-    case e: RuntimeException =>
-      System.err.println("[error] " + e.getMessage)
-      System.exit(1)
+  }
+}
+
+// Pretty printer that simply prints the parsed input
+object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
+  override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    // TODO pretty print in original syntax
+    println(parsedProgram)
+  }
+}
+
+// A command-line interface
+object DeepDiveLog {
+  type Program = List[Statement]
+
+  case class Config
+  ( handler: DeepDiveLogHandler = null
+  , inputFiles: List[String] = List()
+  )
+  val parser = new scopt.OptionParser[Config]("ddlogc") {
+    head("ddlogc", "0.0.1")
+    cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
+    cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
+    arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
+    checkConfig { c =>
+      if (c.handler == null) failure("No command specified")
+      else success
+    }
+  }
+
+  def main(args: Array[String]) = {
+    parser.parse(args, Config()) match {
+      case Some(config) =>
+        config.handler.run(config)
+      case None =>
+        System.err.println("[error] ")
+    }
   }
 }
diff --git a/Makefile b/Makefile
index 02dc2d557..5d046e928 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ TEST = examples/spouse_example.ddl
 
 test: $(TESTJAR)
 	CLASSPATH=$(shell sbt "export compile:dependency-classpath" | tail -1) \
-	scala $< $(TEST) | diff -u $(TEST:.ddl=.expected) -
+	scala $< compile $(TEST) | diff -u $(TEST:.ddl=.expected) -
 $(TESTJAR): $(wildcard *.scala)
 	sbt package
 	ln -sfn $(shell ls -t target/scala-*/*_*.jar | head -1) $@
@@ -14,7 +14,7 @@ $(TESTJAR): $(wildcard *.scala)
 # standalone jar
 JAR = ddlc.jar
 test-package: $(JAR)
-	scala $< $(TEST) | diff -u $(TEST:.ddl=.expected) -
+	scala $< compile $(TEST) | diff -u $(TEST:.ddl=.expected) -
 $(JAR): $(wildcard *.scala)
 	sbt assembly
 	ln -sfn $(shell ls -t target/scala-*/*-assembly-*.jar | head -1) $@
diff --git a/build.sbt b/build.sbt
index 1d2b3a28a..198955f7d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1 +1,5 @@
 libraryDependencies += "org.apache.commons" % "commons-lang3" % "3.4"
+
+libraryDependencies += "com.github.scopt" %% "scopt" % "3.3.0"
+
+resolvers += Resolver.sonatypeRepo("public")

From 9d424368381fa7ac2ed562415af3e17268599826 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 20:44:57 -0700
Subject: [PATCH 049/347] Adds skeleton code for deriving the delta program

---
 DeepDiveLogCompiler.scala     | 25 +++++++++++++++++++++----
 DeepDiveLogDeltaDeriver.scala |  6 ++++++
 2 files changed, 27 insertions(+), 4 deletions(-)
 create mode 100644 DeepDiveLogDeltaDeriver.scala

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 04cff9d17..ad960b49e 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -448,28 +448,43 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    // determine the program to compile
+    val programToCompile =
+      // derive and compile the program with delta rules instead for incremental version
+      if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
+      else parsedProgram
+
     // take an initial pass to analyze the parsed program
-    val state = new CompilationState( parsedProgram )
+    val state = new CompilationState( programToCompile )
 
     // compile the program into blocks of application.conf
     val blocks = (
       compileUserSettings
       :::
-      compileVariableSchema(parsedProgram, state)
+      compileVariableSchema(programToCompile, state)
       :::
-      (parsedProgram flatMap (_.compile(state)))
+      (programToCompile flatMap (_.compile(state)))
     )
 
     // emit the generated code
     blocks foreach println
+
+    if (config.isIncremental) {
+      // TODO emit extra extractor for moving rows of dd_delta_* to *
+    }
   }
 }
 
 // Pretty printer that simply prints the parsed input
 object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    val programToPrint =
+      // derive the delta rules for incremental version
+      if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
+      else parsedProgram
+
     // TODO pretty print in original syntax
-    println(parsedProgram)
+    println(programToPrint)
   }
 }
 
@@ -480,11 +495,13 @@ object DeepDiveLog {
   case class Config
   ( handler: DeepDiveLogHandler = null
   , inputFiles: List[String] = List()
+  , isIncremental: Boolean = false
   )
   val parser = new scopt.OptionParser[Config]("ddlogc") {
     head("ddlogc", "0.0.1")
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
+    opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(isIncremental = true)                 } text("Whether to derive delta rules")
     arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
     checkConfig { c =>
       if (c.handler == null) failure("No command specified")
diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
new file mode 100644
index 000000000..cb3616e50
--- /dev/null
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -0,0 +1,6 @@
+object DeepDiveLogDeltaDeriver {
+  def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
+    // TODO derive delta relations and delta rules
+    program
+  }
+}

From 0682d2642ee43a01207990642598f24b98d719a6 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 20:54:02 -0700
Subject: [PATCH 050/347] Splits DeepDiveLogCompiler.scala into several pieces

---
 DeepDiveLog.scala              | 56 +++++++++++++++++++++++++++
 DeepDiveLogCompiler.scala      | 70 ----------------------------------
 DeepDiveLogPrettyPrinter.scala | 12 ++++++
 3 files changed, 68 insertions(+), 70 deletions(-)
 create mode 100644 DeepDiveLog.scala
 create mode 100644 DeepDiveLogPrettyPrinter.scala

diff --git a/DeepDiveLog.scala b/DeepDiveLog.scala
new file mode 100644
index 000000000..b524a4846
--- /dev/null
+++ b/DeepDiveLog.scala
@@ -0,0 +1,56 @@
+// A command-line interface
+object DeepDiveLog {
+  type Program = List[Statement]
+
+  case class Config
+  ( handler: DeepDiveLogHandler = null
+  , inputFiles: List[String] = List()
+  , isIncremental: Boolean = false
+  )
+  val parser = new scopt.OptionParser[Config]("ddlogc") {
+    head("ddlogc", "0.0.1")
+    cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
+    cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
+    opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(isIncremental = true)                 } text("Whether to derive delta rules")
+    arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
+    checkConfig { c =>
+      if (c.handler == null) failure("No command specified")
+      else success
+    }
+  }
+
+  def main(args: Array[String]) = {
+    parser.parse(args, Config()) match {
+      case Some(config) =>
+        config.handler.run(config)
+      case None =>
+        System.err.println("[error] ")
+    }
+  }
+}
+
+// An abstraction of DeepDiveLog handlers
+trait DeepDiveLogHandler {
+  def run(program: DeepDiveLog.Program, config: DeepDiveLog.Config): Unit
+
+  def run(config: DeepDiveLog.Config): Unit = try {
+    // parse each file into a single program
+    val parsedProgram = parseFiles(config.inputFiles)
+
+    // run handler with the parsed program
+    run(parsedProgram, config)
+  } catch {
+    case e: RuntimeException => die(e.getMessage)
+  }
+
+  def parseFiles(fileNames: List[String]): DeepDiveLog.Program = {
+    val ddlParser = new ConjunctiveQueryParser
+    fileNames flatMap { ddlParser.parseProgramFile(_) }
+  }
+
+  def die(message: String = null) = {
+    if (message != null)
+      System.err.println("[error] " + message)
+    System.exit(1)
+  }
+}
diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index ad960b49e..256825910 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -382,32 +382,6 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
   }
 }
 
-// An abstraction of DeepDiveLog handlers
-trait DeepDiveLogHandler {
-  def run(program: DeepDiveLog.Program, config: DeepDiveLog.Config): Unit
-
-  def run(config: DeepDiveLog.Config): Unit = try {
-    // parse each file into a single program
-    val parsedProgram = parseFiles(config.inputFiles)
-
-    // run handler with the parsed program
-    run(parsedProgram, config)
-  } catch {
-    case e: RuntimeException => die(e.getMessage)
-  }
-
-  def parseFiles(fileNames: List[String]): DeepDiveLog.Program = {
-    val ddlParser = new ConjunctiveQueryParser
-    fileNames flatMap { ddlParser.parseProgramFile(_) }
-  }
-
-  def die(message: String = null) = {
-    if (message != null)
-      System.err.println("[error] " + message)
-    System.exit(1)
-  }
-}
-
 // Compiler that wires up everything together
 object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlock = String
@@ -474,47 +448,3 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     }
   }
 }
-
-// Pretty printer that simply prints the parsed input
-object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
-  override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    val programToPrint =
-      // derive the delta rules for incremental version
-      if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
-      else parsedProgram
-
-    // TODO pretty print in original syntax
-    println(programToPrint)
-  }
-}
-
-// A command-line interface
-object DeepDiveLog {
-  type Program = List[Statement]
-
-  case class Config
-  ( handler: DeepDiveLogHandler = null
-  , inputFiles: List[String] = List()
-  , isIncremental: Boolean = false
-  )
-  val parser = new scopt.OptionParser[Config]("ddlogc") {
-    head("ddlogc", "0.0.1")
-    cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
-    cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
-    opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(isIncremental = true)                 } text("Whether to derive delta rules")
-    arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
-    checkConfig { c =>
-      if (c.handler == null) failure("No command specified")
-      else success
-    }
-  }
-
-  def main(args: Array[String]) = {
-    parser.parse(args, Config()) match {
-      case Some(config) =>
-        config.handler.run(config)
-      case None =>
-        System.err.println("[error] ")
-    }
-  }
-}
diff --git a/DeepDiveLogPrettyPrinter.scala b/DeepDiveLogPrettyPrinter.scala
new file mode 100644
index 000000000..d6429a060
--- /dev/null
+++ b/DeepDiveLogPrettyPrinter.scala
@@ -0,0 +1,12 @@
+// Pretty printer that simply prints the parsed input
+object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
+  override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    val programToPrint =
+      // derive the delta rules for incremental version
+      if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
+      else parsedProgram
+
+    // TODO pretty print in original syntax
+    println(programToPrint)
+  }
+}

From fdb579f92b742b12383186ac33aca7b56cdf79dd Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 22:47:14 -0700
Subject: [PATCH 051/347] Reverts visitor pattern refactor

and moves the Statement classes back to DeepDiveLogParser, but retaining
the compile() functions under DeepDiveLogCompiler.
---
 DeepDiveLogCompiler.scala | 100 ++++++++++++++++++--------------------
 DeepDiveLogParser.scala   |   7 +++
 2 files changed, 54 insertions(+), 53 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 256825910..d03bfe431 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -229,24 +229,26 @@ class QuerySchema(q : ConjunctiveQuery) {
 }
 
 
-// Statements that will be parsed and compiled
-// Statement-local compilation logic is kept in each case class' compile() method.
-// Any global compilation logic should be kept in DeepDiveLogCompiler object.
-trait Statement {
-  type CompiledBlocks = DeepDiveLogCompiler.CompiledBlocks
-  def compile(state: CompilationState): CompiledBlocks = List()
-}
-case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
-case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
-case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
-{
+// Compiler that takes parsed program as input and prints blocks of application.conf
+object DeepDiveLogCompiler extends DeepDiveLogHandler {
+  type CompiledBlock = String
+  type CompiledBlocks = List[CompiledBlock]
+
+  // Dispatch to the corresponding compile function
+  def compile(stmt: Statement, ss: CompilationState): CompiledBlocks = stmt match {
+    case s:  ExtractionRule   => compile(s, ss)
+    case s:  FunctionCallRule => compile(s, ss)
+    case s:  InferenceRule    => compile(s, ss)
+    case _                    => List()  // defaults to compiling into empty block
+  }
+
   // Generate extraction rule part for deepdive
-  override def compile(ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: ExtractionRule, ss: CompilationState): CompiledBlocks = {
     // Generate the body of the query.
-    val qs              = new QuerySchema( q )
+    val qs              = new QuerySchema( stmt.q )
     // variable columns
-    val variableCols = q.head.terms flatMap {
-      case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, q, true)
+    val variableCols = stmt.q.head.terms flatMap {
+      case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, stmt.q, true)
     }
 
     val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
@@ -255,29 +257,27 @@ case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction
 
     val inputQuery = s"""
       SELECT ${selectStr}
-      ${ ss.generateSQLBody(q) }"""
+      ${ ss.generateSQLBody(stmt.q) }"""
 
-    val blockName = ss.resolveExtractorBlockName(this)
+    val blockName = ss.resolveExtractorBlockName(stmt)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" DROP VIEW IF EXISTS ${q.head.name};
-        CREATE VIEW ${q.head.name} AS ${inputQuery}
+        sql: \"\"\" DROP VIEW IF EXISTS ${stmt.q.head.name};
+        CREATE VIEW ${stmt.q.head.name} AS ${inputQuery}
         \"\"\"
         style: "sql_extractor"
-        ${ss.generateDependenciesOfCompiledBlockFor(this)}
+        ${ss.generateDependenciesOfCompiledBlockFor(stmt)}
       }
     """
     List(extractor)
   }
-}
-case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-{
-  override def compile(ss: CompilationState): CompiledBlocks = {
+
+  def compile(stmt: FunctionCallRule, ss: CompilationState): CompiledBlocks = {
     val inputQuery = s"""
-    SELECT * FROM ${input}
+    SELECT * FROM ${stmt.input}
     """
 
-    val function = ss.resolveFunctionName(this.function)
+    val function = ss.resolveFunctionName(stmt.function)
     val udfDetails = (function.implementations collectFirst {
       case impl: RowWiseLineHandler =>
         s"""udf: \"${StringEscapeUtils.escapeJava(impl.command)}\"
@@ -285,28 +285,26 @@ case class FunctionCallRule(input : String, output : String, function : String)
     })
 
     if (udfDetails.isEmpty)
-      ss.error(s"Cannot find compilable implementation for function ${this.function} among:\n  "
+      ss.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
         + (function.implementations mkString "\n  "))
 
-    val blockName = ss.resolveExtractorBlockName(this)
+    val blockName = ss.resolveExtractorBlockName(stmt)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        input: \"\"\" SELECT * FROM ${input}
+        input: \"\"\" SELECT * FROM ${stmt.input}
         \"\"\"
-        output_relation: \"${output}\"
+        output_relation: \"${stmt.output}\"
         ${udfDetails.get}
-        ${ss.generateDependenciesOfCompiledBlockFor(this)}
+        ${ss.generateDependenciesOfCompiledBlockFor(stmt)}
       }
     """
     List(extractor)
   }
-}
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
-{
+
   // generate inference rule part for deepdive
-  override def compile(ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: InferenceRule, ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
-    val qs = new QuerySchema( q )
+    val qs = new QuerySchema( stmt.q )
 
     // node query
     // generate the node portion (V) of the factor graph
@@ -334,20 +332,20 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
     """
       List(ext)
     }
-    if (ss.isQueryTerm(q.head.name))
-      blocks :::= compileNodeRule(this, qs, ss)
+    if (ss.isQueryTerm(stmt.q.head.name))
+      blocks :::= compileNodeRule(stmt, qs, ss)
 
     // edge query
-    val fakeBody        = q.head +: q.body
-    val fakeCQ          = ConjunctiveQuery(q.head, fakeBody) // we will just use the fakeBody below.
+    val fakeBody        = stmt.q.head +: stmt.q.body
+    val fakeCQ          = ConjunctiveQuery(stmt.q.head, fakeBody) // we will just use the fakeBody below.
 
-    val index = q.body.length + 1
+    val index = stmt.q.body.length + 1
     val qs2 = new QuerySchema( fakeCQ )
-    val variableIdsStr = Some(s"""R0.id AS "${q.head.name}.R0.id" """)
-    val variableColsStr = Some(s"""R0.label AS "${q.head.name}.R0.label" """)
+    val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
+    val variableColsStr = Some(s"""R0.label AS "${stmt.q.head.name}.R0.label" """)
 
     // weight string
-    val uwStr = weights match {
+    val uwStr = stmt.weights match {
       case KnownFactorWeight(x) => None
       case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
     }
@@ -360,10 +358,10 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
       ${ ss.generateSQLBody(fakeCQ) }"""
 
     // factor function
-    val func = s"""Imply(${q.head.name}.R0.label)"""
+    val func = s"""Imply(${stmt.q.head.name}.R0.label)"""
 
     // weight
-    val weight = weights match {
+    val weight = stmt.weights match {
       case KnownFactorWeight(x) => s"${x}"
       case UnknownFactorWeight(w) => {
         s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, false)).mkString(", ")})"""
@@ -371,7 +369,7 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
     }
 
     blocks ::= s"""
-      deepdive.inference.factors.factor_${q.head.name} {
+      deepdive.inference.factors.factor_${stmt.q.head.name} {
         input_query: \"\"\"${inputQuery}\"\"\"
         function: "${func}"
         weight: "${weight}"
@@ -380,12 +378,7 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervisi
 
     blocks.reverse
   }
-}
 
-// Compiler that wires up everything together
-object DeepDiveLogCompiler extends DeepDiveLogHandler {
-  type CompiledBlock = String
-  type CompiledBlocks = List[CompiledBlock]
 
   def compileUserSettings(): CompiledBlocks = {
     // TODO read user's proto-application.conf and augment it
@@ -420,6 +413,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     List(ddSchema)
   }
 
+
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     // determine the program to compile
@@ -437,7 +431,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       :::
       compileVariableSchema(programToCompile, state)
       :::
-      (programToCompile flatMap (_.compile(state)))
+      (programToCompile flatMap {compile(_, state)})
     )
 
     // emit the generated code
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 46c518bb6..7c3fb8a12 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -30,6 +30,13 @@ case class RelationTypeAlias(likeRelationName: String) extends RelationType
 trait FunctionImplementationDeclaration
 case class RowWiseLineHandler(format: String, command: String) extends FunctionImplementationDeclaration
 
+// Statements that will be parsed and compiled
+trait Statement
+case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
+case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
+case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
+case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
 
 // Parser
 class ConjunctiveQueryParser extends JavaTokenParsers {

From 284185dd8b1a6e30e3f486590bf5692dfacfd5c8 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 22:49:32 -0700
Subject: [PATCH 052/347] Renames to DeepDiveLogParser

---
 DeepDiveLog.scala       | 2 +-
 DeepDiveLogParser.scala | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/DeepDiveLog.scala b/DeepDiveLog.scala
index b524a4846..859128685 100644
--- a/DeepDiveLog.scala
+++ b/DeepDiveLog.scala
@@ -44,7 +44,7 @@ trait DeepDiveLogHandler {
   }
 
   def parseFiles(fileNames: List[String]): DeepDiveLog.Program = {
-    val ddlParser = new ConjunctiveQueryParser
+    val ddlParser = new DeepDiveLogParser
     fileNames flatMap { ddlParser.parseProgramFile(_) }
   }
 
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 7c3fb8a12..963e585ec 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -38,8 +38,9 @@ case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
 case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
 
+
 // Parser
-class ConjunctiveQueryParser extends JavaTokenParsers {
+class DeepDiveLogParser extends JavaTokenParsers {
 
   // JavaTokenParsers provides several useful number parsers:
   //   wholeNumber, decimalNumber, floatingPointNumber 
@@ -157,7 +158,7 @@ class ConjunctiveQueryParser extends JavaTokenParsers {
                                       | functionDeclaration
                                       | functionCallRule
                                       )
-  def program : Parser[List[Statement]] = phrase(rep1(statement <~ "."))
+  def program : Parser[DeepDiveLog.Program] = phrase(rep1(statement <~ "."))
 
   def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
     parse(program, inputProgram) match {

From f7ee393f1452fb1f9f1c50c0bd3d9b3e7b2dd303 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 23:50:48 -0700
Subject: [PATCH 053/347] Migrates tests to Bats for easy addition

which stands for Bash Automated Testing System.
---
 .gitignore                                    |  6 ++--
 Makefile                                      | 31 +++++++++++++------
 README.md                                     |  4 +--
 ...pected => spouse_example.compile.expected} |  0
 test/compile-example.bats                     | 19 ++++++++++++
 test/test.sh                                  | 26 ++++++++++++++++
 6 files changed, 72 insertions(+), 14 deletions(-)
 rename examples/{spouse_example.expected => spouse_example.compile.expected} (100%)
 create mode 100755 test/compile-example.bats
 create mode 100755 test/test.sh

diff --git a/.gitignore b/.gitignore
index a57fd1549..8ec9fb651 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
-/ddlc.jar
-/ddlc-test.jar
+/ddlog.jar
+/ddlog-test.jar
+/ddlog-test.jar.classpath
 target
+/test/bats
diff --git a/Makefile b/Makefile
index 5d046e928..307062664 100644
--- a/Makefile
+++ b/Makefile
@@ -1,24 +1,35 @@
 # Makefile for DeepDiveLogCompiler
 
-TESTJAR = ddlc-test.jar
-TEST = examples/spouse_example.ddl
+JAR = ddlog.jar
+TEST_JAR = ddlog-test.jar
+TEST_CLASSPATH_CACHE = ddlog-test.jar.classpath
 
-test: $(TESTJAR)
-	CLASSPATH=$(shell sbt "export compile:dependency-classpath" | tail -1) \
-	scala $< compile $(TEST) | diff -u $(TEST:.ddl=.expected) -
-$(TESTJAR): $(wildcard *.scala)
+# test
+.PHONY: test
+test: $(TEST_JAR) $(TEST_CLASSPATH_CACHE)
+	DDLOG_JAR=$(realpath $<) \
+CLASSPATH=$(shell cat $(TEST_CLASSPATH_CACHE)) \
+test/test.sh
+$(TEST_CLASSPATH_CACHE): build.sbt $(wildcard project/*.sbt)
+	sbt "export compile:dependency-classpath" | tail -1 >$@
+
+# test standalone package
+.PHONY: test-package
+test-package: $(JAR)
+	$(MAKE) test TEST_JAR=$<
+
+# build test jar
+$(TEST_JAR): $(wildcard *.scala)
 	sbt package
 	ln -sfn $(shell ls -t target/scala-*/*_*.jar | head -1) $@
 	touch $@
 
-# standalone jar
-JAR = ddlc.jar
-test-package: $(JAR)
-	scala $< compile $(TEST) | diff -u $(TEST:.ddl=.expected) -
+# build standalone jar
 $(JAR): $(wildcard *.scala)
 	sbt assembly
 	ln -sfn $(shell ls -t target/scala-*/*-assembly-*.jar | head -1) $@
 	touch $@
 
+.PHONY: clean
 clean:
 	sbt clean
diff --git a/README.md b/README.md
index 5f4807a65..25a0459f7 100644
--- a/README.md
+++ b/README.md
@@ -13,13 +13,13 @@ make
 The following command produces a standalone jar.
 
 ```bash
-make ddlc.jar
+make ddlog.jar
 ```
 
 ## Running
 The following will generate an application.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
 ```bash
 mkdir -p examples/spouse_example
-java -jar ddlc.jar examples/spouse_example.ddl >examples/spouse_example/application.conf
+java -jar ddlog.jar examples/spouse_example.ddl >examples/spouse_example/application.conf
 ```
 
diff --git a/examples/spouse_example.expected b/examples/spouse_example.compile.expected
similarity index 100%
rename from examples/spouse_example.expected
rename to examples/spouse_example.compile.expected
diff --git a/test/compile-example.bats b/test/compile-example.bats
new file mode 100755
index 000000000..ed88f6bca
--- /dev/null
+++ b/test/compile-example.bats
@@ -0,0 +1,19 @@
+#!/usr/bin/env bats
+
+# required variables
+: ${DDLOG_JAR:?path to ddlog jar}
+: ${EXAMPLE:?path to input ddlog program}
+EXAMPLE_NAME=${EXAMPLE%.ddl}
+EXAMPLE_NAME=${EXAMPLE_NAME##*/}
+
+setup() {
+    [ -e "$DDLOG_JAR" ]
+    [ -e "$EXAMPLE" ]
+}
+
+@test "compile $EXAMPLE_NAME" {
+    expectedOutput=${EXAMPLE%.ddl}.compile.expected
+    [ -e "$expectedOutput" ] || skip
+    scala "$DDLOG_JAR" compile "$EXAMPLE" |
+    diff -u "$expectedOutput" -
+}
diff --git a/test/test.sh b/test/test.sh
new file mode 100755
index 000000000..722bed8da
--- /dev/null
+++ b/test/test.sh
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+set -eu
+cd "$(dirname "$0")"
+
+# make sure bats is available
+PATH="$PWD/bats/bin:$PATH"
+type bats &>/dev/null ||
+    git clone https://github.com/sstephenson/bats.git
+
+# run all .bats tests
+c=0
+for t in *.bats; do
+    case $t in
+        *-example.bats)
+            # run bats test for every example
+            for ddl in ../examples/*.ddl; do
+                EXAMPLE=$ddl bats $t || c=$?
+            done
+            ;;
+
+        *)
+            # otherwise, simply run the bats
+            bats $t
+    esac
+done
+exit $c

From 1d784fbe69523417471e6202eec01be65138fd1a Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 23:52:54 -0700
Subject: [PATCH 054/347] Fixes glitches in symlinking

---
 Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 307062664..9f6d4a8f7 100644
--- a/Makefile
+++ b/Makefile
@@ -21,13 +21,13 @@ test-package: $(JAR)
 # build test jar
 $(TEST_JAR): $(wildcard *.scala)
 	sbt package
-	ln -sfn $(shell ls -t target/scala-*/*_*.jar | head -1) $@
+	ln -sfn $$(ls -t target/scala-*/*_*.jar | head -1) $@
 	touch $@
 
 # build standalone jar
 $(JAR): $(wildcard *.scala)
 	sbt assembly
-	ln -sfn $(shell ls -t target/scala-*/*-assembly-*.jar | head -1) $@
+	ln -sfn $$(ls -t target/scala-*/*-assembly-*.jar | head -1) $@
 	touch $@
 
 .PHONY: clean

From af7ad6f2b2983a54c21d9089f296d96c97803492 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 28 Apr 2015 23:56:26 -0700
Subject: [PATCH 055/347] Updates README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 25a0459f7..9c4866568 100644
--- a/README.md
+++ b/README.md
@@ -20,6 +20,6 @@ make ddlog.jar
 The following will generate an application.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
 ```bash
 mkdir -p examples/spouse_example
-java -jar ddlog.jar examples/spouse_example.ddl >examples/spouse_example/application.conf
+java -jar ddlog.jar compile examples/spouse_example.ddl >examples/spouse_example/application.conf
 ```
 

From 21fe888e821d6d0d749563af7b02067a93a48deb Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 29 Apr 2015 00:00:30 -0700
Subject: [PATCH 056/347] Adds a short description about the tests

---
 test/README.md | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 test/README.md

diff --git a/test/README.md b/test/README.md
new file mode 100644
index 000000000..a11b0e734
--- /dev/null
+++ b/test/README.md
@@ -0,0 +1,8 @@
+DDLog tests
+===========
+
+`test.sh` runs all tests.
+
+[Bats](https://github.com/sstephenson/bats.git) is used for most end-to-end tests.
+Every `*-example.bats` will be run for each .ddl example under `../examples/`, with the path to the .ddl file set in the `EXAMPLE` environment variable.
+Other .bats tests will run once.

From f00933025ccd557748789bded68259d88811db57 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 29 Apr 2015 00:03:30 -0700
Subject: [PATCH 057/347] Clarifies test/README

---
 test/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/README.md b/test/README.md
index a11b0e734..84d2e324d 100644
--- a/test/README.md
+++ b/test/README.md
@@ -4,5 +4,5 @@ DDLog tests
 `test.sh` runs all tests.
 
 [Bats](https://github.com/sstephenson/bats.git) is used for most end-to-end tests.
-Every `*-example.bats` will be run for each .ddl example under `../examples/`, with the path to the .ddl file set in the `EXAMPLE` environment variable.
-Other .bats tests will run once.
+Every `*-example.bats` will be run for each `.ddl` example under `../examples/`, with the `EXAMPLE` environment variable set to the path to the example.
+Rest of the `.bats` tests will run once.

From 386534b794896eead93eaef824929193ece27826 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 29 Apr 2015 00:07:18 -0700
Subject: [PATCH 058/347] Adds comments to the .bats file

---
 test/compile-example.bats | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/test/compile-example.bats b/test/compile-example.bats
index ed88f6bca..13944c2b0 100755
--- a/test/compile-example.bats
+++ b/test/compile-example.bats
@@ -1,4 +1,8 @@
 #!/usr/bin/env bats
+# Per example compilation test
+#
+# This test compares the `ddlog compile` output of a .ddl file with its expected output in .compile.expected file.
+# Test is skipped if no expected output is there.
 
 # required variables
 : ${DDLOG_JAR:?path to ddlog jar}
@@ -6,11 +10,13 @@
 EXAMPLE_NAME=${EXAMPLE%.ddl}
 EXAMPLE_NAME=${EXAMPLE_NAME##*/}
 
+# some preconditions
 setup() {
     [ -e "$DDLOG_JAR" ]
     [ -e "$EXAMPLE" ]
 }
 
+# actual test that compares the compiled output
 @test "compile $EXAMPLE_NAME" {
     expectedOutput=${EXAMPLE%.ddl}.compile.expected
     [ -e "$expectedOutput" ] || skip

From 5cd4608640970ca3e639b47c14219251a0122132 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 29 Apr 2015 01:44:16 -0700
Subject: [PATCH 059/347] Adds pretty printer implementation

- Renames the test to per-example.bats for testing both compilation and
  pretty printing.
- Also fixes a bug in the grammar parsing "like".
---
 DeepDiveLogParser.scala                |  4 +-
 DeepDiveLogPrettyPrinter.scala         | 81 ++++++++++++++++++++++-
 examples/spouse_example.print.expected | 89 ++++++++++++++++++++++++++
 test/compile-example.bats              | 25 --------
 test/per-example.bats                  | 46 +++++++++++++
 5 files changed, 216 insertions(+), 29 deletions(-)
 create mode 100644 examples/spouse_example.print.expected
 delete mode 100755 test/compile-example.bats
 create mode 100755 test/per-example.bats

diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 963e585ec..d48732625 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -103,10 +103,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def relationType: Parser[RelationType] =
-    ( rep1sep(columnDeclaration, ",") ^^ {
+    ( "like" ~> relationName ^^ { RelationTypeAlias(_) }
+    | rep1sep(columnDeclaration, ",") ^^ {
         attrs => RelationTypeDeclaration(attrs map { _.name }, attrs map { _.t })
       }
-    | "like" ~> relationName ^^ { RelationTypeAlias(_) }
     )
 
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
diff --git a/DeepDiveLogPrettyPrinter.scala b/DeepDiveLogPrettyPrinter.scala
index d6429a060..1bfe0fe8e 100644
--- a/DeepDiveLogPrettyPrinter.scala
+++ b/DeepDiveLogPrettyPrinter.scala
@@ -1,12 +1,89 @@
+import org.apache.commons.lang3.StringEscapeUtils
+
 // Pretty printer that simply prints the parsed input
 object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
+
+  // Dispatch to the corresponding function
+  def print(stmt: Statement): String = stmt match {
+    case s: SchemaDeclaration   => print(s)
+    case s: FunctionDeclaration => print(s)
+    case s: ExtractionRule      => print(s)
+    case s: FunctionCallRule    => print(s)
+    case s: InferenceRule       => print(s)
+  }
+
+  def print(stmt: SchemaDeclaration): String = {
+    val columnDecls = stmt.a.terms map {
+      case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
+    }
+    val prefix = s"${stmt.a.name}${if (stmt.isQuery) "?" else ""}("
+    val indentation = " " * prefix.length
+    s"""${prefix}${columnDecls.mkString(",\n" + indentation)}).
+       |""".stripMargin
+  }
+
+  def print(relationType: RelationType): String = relationType match {
+    case ty: RelationTypeAlias => s"like ${ty.likeRelationName}"
+    case ty: RelationTypeDeclaration =>
+      val namesWithTypes = (ty.names, ty.types).zipped map {
+        (colName,colType) => s"${colName} ${colType}"}
+      s"(${namesWithTypes.mkString(", ")})"
+  }
+  def print(stmt: FunctionDeclaration): String = {
+    val inputType = print(stmt.inputType)
+    val outputType = print(stmt.outputType)
+    val impls = stmt.implementations map {
+      case impl: RowWiseLineHandler =>
+        "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" +
+        s"\n        handles ${impl.format} lines"
+    }
+    s"""function ${stmt.functionName}
+       |    over ${inputType}
+       | returns ${outputType}
+       | ${(impls map {"implementation " + _}).mkString("\n ")}.
+       |""".stripMargin
+  }
+
+  def print(cq: ConjunctiveQuery): String = {
+    val printAtom = {a:Atom =>
+      val vars = a.terms map { _.varName }
+      s"${a.name}(${vars.mkString(", ")})"
+    }
+    s"""${printAtom(cq.head)} :-
+       |    ${(cq.body map printAtom).mkString(",\n    ")}""".stripMargin
+  }
+
+  def print(stmt: ExtractionRule): String = {
+    s"""${print(stmt.q)}.
+       |""".stripMargin
+  }
+
+  def print(stmt: FunctionCallRule): String = {
+    s"""${stmt.output} :- !${stmt.function}(${stmt.input}).
+       |""".stripMargin
+  }
+
+  def print(stmt: InferenceRule): String = {
+    print(stmt.q) +
+    ( if (stmt.weights == null) ""
+      else "\n  weight = " + (stmt.weights match {
+        case KnownFactorWeight(w) => w.toString
+        case UnknownFactorWeight(vs) => vs.mkString(", ")
+      })
+    ) +
+    ( if (stmt.supervision == null) ""
+      else "\n  label = " + stmt.supervision
+    ) +
+    "."
+  }
+
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     val programToPrint =
       // derive the delta rules for incremental version
       if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
       else parsedProgram
 
-    // TODO pretty print in original syntax
-    println(programToPrint)
+    // pretty print in original syntax
+    programToPrint foreach {stmt => println(print(stmt))}
   }
 }
diff --git a/examples/spouse_example.print.expected b/examples/spouse_example.print.expected
new file mode 100644
index 000000000..6787de76d
--- /dev/null
+++ b/examples/spouse_example.print.expected
@@ -0,0 +1,89 @@
+articles(article_id text,
+         text text).
+
+sentences(document_id text,
+          sentence text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
+          sentence_offset int,
+          sentence_id text).
+
+people_mentions(sentence_id text,
+                start_position int,
+                length int,
+                text text,
+                mention_id text).
+
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text).
+
+has_spouse_features(relation_id text,
+                    feature text).
+
+has_spouse?(relation_id text).
+
+people_mentions :- !ext_people(ext_people_input).
+
+ext_people_input(sentence_id text,
+                 words text[],
+                 ner_tags text[]).
+
+ext_people_input(s, words, ner_tags) :-
+    sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people
+    over like ext_people_input
+ returns like people_mentions
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+        handles tsv lines.
+
+has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
+
+ext_has_spouse_input(sentence_id text,
+                     p1_id text,
+                     p1_text text,
+                     p2_id text,
+                     p2_text text).
+
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    people_mentions(s, a, b, p1_text, p1_id),
+    people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse
+    over like ext_has_spouse_input
+ returns like has_spouse_candidates
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+        handles tsv lines.
+
+has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(words text[],
+                              relation_id text,
+                              p1_start_position int,
+                              p1_length int,
+                              p2_start_position int,
+                              p2_length int).
+
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+function ext_has_spouse_features
+    over like ext_has_spouse_features_input
+ returns like has_spouse_features
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+        handles tsv lines.
+
+has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_features(rid, f)
+  weight = f
+  label = l.
diff --git a/test/compile-example.bats b/test/compile-example.bats
deleted file mode 100755
index 13944c2b0..000000000
--- a/test/compile-example.bats
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env bats
-# Per example compilation test
-#
-# This test compares the `ddlog compile` output of a .ddl file with its expected output in .compile.expected file.
-# Test is skipped if no expected output is there.
-
-# required variables
-: ${DDLOG_JAR:?path to ddlog jar}
-: ${EXAMPLE:?path to input ddlog program}
-EXAMPLE_NAME=${EXAMPLE%.ddl}
-EXAMPLE_NAME=${EXAMPLE_NAME##*/}
-
-# some preconditions
-setup() {
-    [ -e "$DDLOG_JAR" ]
-    [ -e "$EXAMPLE" ]
-}
-
-# actual test that compares the compiled output
-@test "compile $EXAMPLE_NAME" {
-    expectedOutput=${EXAMPLE%.ddl}.compile.expected
-    [ -e "$expectedOutput" ] || skip
-    scala "$DDLOG_JAR" compile "$EXAMPLE" |
-    diff -u "$expectedOutput" -
-}
diff --git a/test/per-example.bats b/test/per-example.bats
new file mode 100755
index 000000000..b8400dd0b
--- /dev/null
+++ b/test/per-example.bats
@@ -0,0 +1,46 @@
+#!/usr/bin/env bats
+# Per example tests
+#
+# This test compares outputs of various modes of ddlog against a .ddl example file with its expected output.
+# Test is skipped if no expected output is found.
+
+# required variables
+: ${DDLOG_JAR:?path to ddlog jar}
+: ${EXAMPLE:?path to input ddlog program}
+EXAMPLE_BASEPATH=${EXAMPLE%.ddl}
+EXAMPLE_NAME=${EXAMPLE_BASEPATH##*/}
+
+# some preconditions
+setup() {
+    [ -e "$DDLOG_JAR" ]
+    [ -e "$EXAMPLE" ]
+}
+
+# compare the compiled output with what's expected
+@test "compile $EXAMPLE_NAME" {
+    expectedOutput=$EXAMPLE_BASEPATH.compile.expected
+    [ -e "$expectedOutput" ] || skip
+    scala "$DDLOG_JAR" compile "$EXAMPLE" |
+    diff -u "$expectedOutput" -
+}
+
+# compare the pretty-printed output with the input
+@test "print $EXAMPLE_NAME as expected" {
+    expectedOutput=$EXAMPLE_BASEPATH.print.expected
+    [ -e "$expectedOutput" ] || skip
+    scala "$DDLOG_JAR" print "$EXAMPLE" |
+    diff -u "$expectedOutput" -
+}
+
+# check if print is idempotent
+@test "print $EXAMPLE_NAME is idempotent" {
+    printed=$BATS_TMPDIR/ddlog-$EXAMPLE_NAME-printed.ddl
+    scala "$DDLOG_JAR" print "$EXAMPLE" >"$printed" || skip
+    scala "$DDLOG_JAR" print "$printed" |
+    diff -u "$printed" -
+}
+
+
+# TODO incremental print
+
+# TODO incremental compile

From 1734d4b6fb33c88c701d659d61d5f6cce5cc4104 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 30 Apr 2015 22:22:36 -0700
Subject: [PATCH 060/347] add function: derive delta relations and delta rules

---
 DeepDiveLogDeltaDeriver.scala | 131 +++++++++++++++++++++++++++++++++-
 1 file changed, 128 insertions(+), 3 deletions(-)

diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
index cb3616e50..7be0eb238 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -1,6 +1,131 @@
-object DeepDiveLogDeltaDeriver {
+import scala.collection.mutable.ListBuffer
+
+object DeepDiveLogDeltaDeriver{
+
+  val deltaPrefix = "dd_delta_"
+
+  def transfer(stmt: Statement): List[Statement] = stmt match {
+    case s: SchemaDeclaration   => transfer(s)
+    case s: FunctionDeclaration => transfer(s)
+    case s: ExtractionRule      => transfer(s)
+    case s: FunctionCallRule    => transfer(s)
+    case s: InferenceRule       => transfer(s)
+  }
+
+  def transfer(stmt: SchemaDeclaration): List[Statement] = {
+    var incrementalStatement = new ListBuffer[Statement]()
+    incrementalStatement += stmt
+    var newTerms = new ListBuffer[Variable]()
+    for (term <- stmt.a.terms) {
+      newTerms += Variable(term.varName, deltaPrefix + term.relName, term.index)
+    }
+    incrementalStatement += SchemaDeclaration(Attribute(deltaPrefix + stmt.a.name, newTerms.toList, stmt.a.types), stmt.isQuery)
+    incrementalStatement.toList
+  }
+
+  def transfer(stmt: FunctionDeclaration): List[Statement] = {
+    var incrementalStatement = new ListBuffer[Statement]()
+    // incrementalStatement += stmt
+    var newTerms = new ListBuffer[Variable]()
+    var newInputType: RelationType = stmt.inputType match {
+      case inTy: RelationTypeDeclaration => {
+        var newNames = new ListBuffer[String]()
+        for (name <- inTy.names)
+          newNames += deltaPrefix + name
+        RelationTypeDeclaration(newNames.toList, inTy.types)
+      }
+      case inTy: RelationTypeAlias => RelationTypeAlias(deltaPrefix + inTy.likeRelationName)
+    }
+    var newOutputType: RelationType = stmt.outputType match {
+      case outTy: RelationTypeDeclaration => {
+        var newNames = new ListBuffer[String]()
+        for (name <- outTy.names)
+          newNames += deltaPrefix + name
+        RelationTypeDeclaration(newNames.toList, outTy.types)
+      }
+      case outTy: RelationTypeAlias => RelationTypeAlias(deltaPrefix + outTy.likeRelationName)
+    }
+    incrementalStatement += FunctionDeclaration(stmt.functionName, newInputType, newOutputType, stmt.implementations)
+    incrementalStatement.toList
+  }
+
+  def transfer(stmt: ExtractionRule): List[Statement] = {
+    var incrementalStatement = new ListBuffer[Statement]()
+    
+    var newStmtCqHeadTerms = new ListBuffer[Variable]()
+    for (headTerm <- stmt.q.head.terms) {
+      newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
+    }
+    var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
+
+    var deltaStmtCqBody = new ListBuffer[Atom]()
+    for (stmtCqBody <- stmt.q.body) { // List[Atom]
+      var stmtCqBodyTerms = new ListBuffer[Variable]()
+      for (bodyTerm <- stmtCqBody.terms) {
+        stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
+      }
+      deltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
+    }
+
+    var i = 0
+    var j = 0
+    for (i <- 1 to ((1 << stmt.q.body.length) - 1)) {
+      var newStmtCqBody = new ListBuffer[Atom]()
+      for (j <- 0 to (stmt.q.body.length - 1)) {
+        if ((i & (1 << j)) == 0)
+          newStmtCqBody += stmt.q.body(j)
+        else
+          newStmtCqBody += deltaStmtCqBody(j)
+      }
+      incrementalStatement += ExtractionRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList))
+    }
+    incrementalStatement.toList
+  }
+
+  def transfer(stmt: FunctionCallRule): List[Statement] = {
+    var incrementalStatement = new ListBuffer[Statement]()
+    incrementalStatement += FunctionCallRule(deltaPrefix + stmt.input, deltaPrefix + stmt.output, stmt.function)
+    incrementalStatement.toList
+  }
+
+  def transfer(stmt: InferenceRule): List[Statement] = {
+    var incrementalStatement = new ListBuffer[Statement]()
+    
+    var newStmtCqHeadTerms = new ListBuffer[Variable]()
+    for (headTerm <- stmt.q.head.terms) {
+      newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
+    }
+    var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
+
+    var deltaStmtCqBody = new ListBuffer[Atom]()
+    for (stmtCqBody <- stmt.q.body) { // List[Atom]
+      var stmtCqBodyTerms = new ListBuffer[Variable]()
+      for (bodyTerm <- stmtCqBody.terms) {
+        stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
+      }
+      deltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
+    }
+
+    var i = 0
+    var j = 0
+    for (i <- 1 to ((1 << stmt.q.body.length) - 1)) {
+      var newStmtCqBody = new ListBuffer[Atom]()
+      for (j <- 0 to (stmt.q.body.length - 1)) {
+        if ((i & (1 << j)) == 0)
+          newStmtCqBody += stmt.q.body(j)
+        else
+          newStmtCqBody += deltaStmtCqBody(j)
+      }
+      incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList), stmt.weights, stmt.supervision)
+    }
+    incrementalStatement.toList
+  }
+
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
-    // TODO derive delta relations and delta rules
-    program
+    var incrementalProgram = new ListBuffer[Statement]()
+    for (x <- program) {
+      incrementalProgram = incrementalProgram ++ transfer(x)
+    }
+    incrementalProgram.toList
   }
 }

From fa91f7f0810c2cba777e062c154cd020507ad95e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 1 May 2015 14:54:04 -0700
Subject: [PATCH 061/347] Adds a simple test for DeepDiveLogDeltaDeriver

---
 examples/rstu.ddl            | 15 ++++++++++
 examples/rstu.delta.expected | 57 ++++++++++++++++++++++++++++++++++++
 test/per-example.bats        | 10 +++++--
 3 files changed, 80 insertions(+), 2 deletions(-)
 create mode 100644 examples/rstu.ddl
 create mode 100644 examples/rstu.delta.expected

diff --git a/examples/rstu.ddl b/examples/rstu.ddl
new file mode 100644
index 000000000..9f4abbd2c
--- /dev/null
+++ b/examples/rstu.ddl
@@ -0,0 +1,15 @@
+R?(x text).
+
+S(x text).
+
+T(x text,
+  f text).
+
+U(x text,
+  l text).
+
+R(x) :-
+    S(x),
+    T(x, f),
+    U(x, l).
+
diff --git a/examples/rstu.delta.expected b/examples/rstu.delta.expected
new file mode 100644
index 000000000..7c5ac4359
--- /dev/null
+++ b/examples/rstu.delta.expected
@@ -0,0 +1,57 @@
+R?(x text).
+
+dd_delta_R?(x text).
+
+S(x text).
+
+dd_delta_S(x text).
+
+dd_new_S(x text).
+
+dd_new_S(x) :-
+    S(x).
+
+dd_new_S(x) :-
+    dd_delta_S(x).
+
+T(x text,
+  f text).
+
+dd_delta_T(x text,
+           f text).
+
+dd_new_T(x text,
+         f text).
+
+dd_new_T(x, f) :-
+    T(x, f).
+
+dd_new_T(x, f) :-
+    dd_delta_T(x, f).
+
+U(x text,
+  l text).
+
+dd_delta_U(x text,
+           l text).
+
+R(x) :-
+    S(x),
+    T(x, f),
+    U(x, l).
+
+dd_delta_R(x) :-
+    dd_delta_S(x),
+    T(x, f),
+    U(x, l).
+
+dd_delta_R(x) :-
+    dd_new_S(x),
+    dd_delta_T(x, f),
+    U(x, l).
+
+dd_delta_R(x) :-
+    dd_new_S(x),
+    dd_new_T(x, f),
+    dd_delta_U(x, l).
+
diff --git a/test/per-example.bats b/test/per-example.bats
index b8400dd0b..888fd32dd 100755
--- a/test/per-example.bats
+++ b/test/per-example.bats
@@ -24,7 +24,7 @@ setup() {
     diff -u "$expectedOutput" -
 }
 
-# compare the pretty-printed output with the input
+# compare the pretty-printed output with what's expected
 @test "print $EXAMPLE_NAME as expected" {
     expectedOutput=$EXAMPLE_BASEPATH.print.expected
     [ -e "$expectedOutput" ] || skip
@@ -41,6 +41,12 @@ setup() {
 }
 
 
-# TODO incremental print
+# compare the pretty-printed incremental output with what's expected
+@test "print $EXAMPLE_NAME as expected" {
+    expectedOutput=$EXAMPLE_BASEPATH.delta.expected
+    [ -e "$expectedOutput" ] || skip
+    scala "$DDLOG_JAR" print --incremental "$EXAMPLE" |
+    diff -u "$expectedOutput" -
+}
 
 # TODO incremental compile

From e1b5b59e87e39f95bbad009d95c1579efcfb34a3 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 5 May 2015 13:15:58 -0700
Subject: [PATCH 062/347] add more comments in DeepDiveLogDeltaDeriver function

---
 DeepDiveLogDeltaDeriver.scala | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
index 7be0eb238..51f4242f1 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -2,6 +2,7 @@ import scala.collection.mutable.ListBuffer
 
 object DeepDiveLogDeltaDeriver{
 
+  // Default prefix for incremental tables
   val deltaPrefix = "dd_delta_"
 
   def transfer(stmt: Statement): List[Statement] = stmt match {
@@ -12,6 +13,8 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transfer(s)
   }
 
+  // Incremental scheme declaration,
+  // keep the original scheme and create one delta scheme
   def transfer(stmt: SchemaDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     incrementalStatement += stmt
@@ -23,9 +26,10 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement.toList
   }
 
+  // Incremental function declaration,
+  // create one delta function scheme based on original function scheme
   def transfer(stmt: FunctionDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
-    // incrementalStatement += stmt
     var newTerms = new ListBuffer[Variable]()
     var newInputType: RelationType = stmt.inputType match {
       case inTy: RelationTypeDeclaration => {
@@ -49,9 +53,12 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement.toList
   }
 
+  // Incremental extraction rule,
+  // create delta rules based on original extraction rule
   def transfer(stmt: ExtractionRule): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     
+    // New head
     var newStmtCqHeadTerms = new ListBuffer[Variable]()
     for (headTerm <- stmt.q.head.terms) {
       newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
@@ -67,6 +74,7 @@ object DeepDiveLogDeltaDeriver{
       deltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
     }
 
+    // New body
     var i = 0
     var j = 0
     for (i <- 1 to ((1 << stmt.q.body.length) - 1)) {
@@ -82,15 +90,20 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement.toList
   }
 
+  // Incremental function call rule,
+  // modify function input and output
   def transfer(stmt: FunctionCallRule): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     incrementalStatement += FunctionCallRule(deltaPrefix + stmt.input, deltaPrefix + stmt.output, stmt.function)
     incrementalStatement.toList
   }
 
+  // Incremental inference rule,
+  // create delta rules based on original extraction rule
   def transfer(stmt: InferenceRule): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     
+    // New head
     var newStmtCqHeadTerms = new ListBuffer[Variable]()
     for (headTerm <- stmt.q.head.terms) {
       newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
@@ -106,6 +119,7 @@ object DeepDiveLogDeltaDeriver{
       deltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
     }
 
+    // New body
     var i = 0
     var j = 0
     for (i <- 1 to ((1 << stmt.q.body.length) - 1)) {

From 0a5e43742accf414602be23a209930f5bfe543bf Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 5 May 2015 15:40:04 -0700
Subject: [PATCH 063/347] add dd_count calculation when isIncremental is true

---
 DeepDiveLogCompiler.scala | 31 ++++++++++++++++++++-----------
 1 file changed, 20 insertions(+), 11 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index d03bfe431..3ebac870f 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -235,15 +235,15 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlocks = List[CompiledBlock]
 
   // Dispatch to the corresponding compile function
-  def compile(stmt: Statement, ss: CompilationState): CompiledBlocks = stmt match {
-    case s:  ExtractionRule   => compile(s, ss)
-    case s:  FunctionCallRule => compile(s, ss)
-    case s:  InferenceRule    => compile(s, ss)
+  def compile(stmt: Statement, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = stmt match {
+    case s:  ExtractionRule   => compile(s, ss, isIncremental)
+    case s:  FunctionCallRule => compile(s, ss, isIncremental)
+    case s:  InferenceRule    => compile(s, ss, isIncremental)
     case _                    => List()  // defaults to compiling into empty block
   }
 
   // Generate extraction rule part for deepdive
-  def compile(stmt: ExtractionRule, ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: ExtractionRule, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
     // Generate the body of the query.
     val qs              = new QuerySchema( stmt.q )
     // variable columns
@@ -255,8 +255,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
     val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
 
+    val ddCount = if (isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+    val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\"""" else ""
+
     val inputQuery = s"""
-      SELECT ${selectStr}
+      SELECT ${selectStr}${ddCountStr}
       ${ ss.generateSQLBody(stmt.q) }"""
 
     val blockName = ss.resolveExtractorBlockName(stmt)
@@ -272,7 +275,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     List(extractor)
   }
 
-  def compile(stmt: FunctionCallRule, ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: FunctionCallRule, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
     val inputQuery = s"""
     SELECT * FROM ${stmt.input}
     """
@@ -302,7 +305,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   }
 
   // generate inference rule part for deepdive
-  def compile(stmt: InferenceRule, ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: InferenceRule, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
     var blocks = List[String]()
     val qs = new QuerySchema( stmt.q )
 
@@ -316,7 +319,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val name  = ss.resolveName(qs.getVar(z.supervision))
       val labelCol = s"R${index}.${name}"
       val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-      val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
+      val ddCount = if (isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+      val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
+
+      val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
     ${ ss.generateSQLBody(z.q) }"""
 
       val blockName = ss.resolveExtractorBlockName(z)
@@ -352,9 +358,12 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
     val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
 
+    val ddCount = if (isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+    val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\"""" else ""
+
     // factor input query
     val inputQuery = s"""
-      SELECT ${selectStr}
+      SELECT ${selectStr} ${ddCountStr}
       ${ ss.generateSQLBody(fakeCQ) }"""
 
     // factor function
@@ -431,7 +440,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       :::
       compileVariableSchema(programToCompile, state)
       :::
-      (programToCompile flatMap {compile(_, state)})
+      (programToCompile flatMap {compile(_, state, config.isIncremental)})
     )
 
     // emit the generated code

From 2dbb3d1cb3b551daf1ed140a2f28f47b7d707500 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Wed, 6 May 2015 23:16:53 -0700
Subject: [PATCH 064/347] reslove dependency issue: first, based on statement
 type, union statements with same head to blocks; then reslove dependency
 among different blocks

---
 DeepDiveLogCompiler.scala | 334 +++++++++++++++++++++++---------------
 1 file changed, 206 insertions(+), 128 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 3ebac870f..aed9bb916 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -58,6 +58,7 @@ Consider
 
 import scala.collection.immutable.HashMap
 import org.apache.commons.lang3.StringEscapeUtils
+import scala.collection.mutable.ListBuffer
 
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
@@ -76,6 +77,8 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   // The dependency graph between statements.
   var dependencies : Map[Statement, Set[Statement]] = new HashMap()
 
+  var visable : Set[Statement] = Set()
+
   def init() = {
     // generate the statements.
     statements.foreach {
@@ -91,6 +94,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
       case FunctionCallRule(_,_,_) => ()
     }
 
+    analyzeVisable(statements)
     analyzeDependency(statements)
   }
 
@@ -101,10 +105,14 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   }
 
   // Given a statement, resolve its name for the compiled extractor block.
-  def resolveExtractorBlockName(s: Statement): String = s match {
-    case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
-    case s: ExtractionRule   => s"extraction_rule_${statements indexOf s}"
-    case s: InferenceRule    => s"extraction_rule_${s.q.head.name}"
+  def resolveExtractorBlockName(s: Statement): String = {
+    if (visable contains s) {
+      s match {
+        case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
+        case s: ExtractionRule   => s"extraction_rule_${statements indexOf s}"
+        case s: InferenceRule    => s"extraction_rule_${s.q.head.name}"
+      }
+    } else ""
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
@@ -170,29 +178,68 @@ class CompilationState( statements : DeepDiveLog.Program )  {
         ${ whereClauseStr }"""
   }
 
+  // Analyze the block visibility among statements 
+  def analyzeVisable(statements: List[Statement]) = {
+    val extractionRules   = new ListBuffer[ExtractionRule]()
+    val functionCallRules = new ListBuffer[FunctionCallRule]()
+    val inferenceRules    = new ListBuffer[InferenceRule]()
+    
+    statements foreach (_ match {
+      case s: ExtractionRule   => extractionRules += s
+      case s: FunctionCallRule => functionCallRules += s
+      case s: InferenceRule    => inferenceRules += s
+      case _                   => 
+    })
+
+    val extractionRulesGroup   = extractionRules.groupBy(_.q.head.name)
+    val functionCallRulesGroup = functionCallRules.groupBy(_.input)
+    val inferenceRulesGroup    = inferenceRules.groupBy(_.q.head.name)
+
+    extractionRulesGroup   foreach {keyVal => visable += keyVal._2(0)}
+    functionCallRulesGroup foreach {keyVal => visable += keyVal._2(0)}
+    inferenceRulesGroup    foreach {keyVal => visable += keyVal._2(0)}
+  }
 
   // Analyze the dependency between statements and construct a graph.
   def analyzeDependency(statements: List[Statement]) = {
     // first map head names to the actual statement
-    var stmtByHeadName = new HashMap[String, Statement]()
+    val extractionRuleByHeadName   = new ListBuffer[ExtractionRule]()
+    val inferenceRuleByHeadName    = new ListBuffer[InferenceRule]()
+    val functionCallRuleByHeadName = new ListBuffer[FunctionCallRule]()
+    
     statements foreach {
-      case e : ExtractionRule => stmtByHeadName += { e.q.head.name -> e }
-      case f : FunctionCallRule   => stmtByHeadName += { f.output      -> f }
-      case w : InferenceRule  => stmtByHeadName += { w.q.head.name -> w }
-      case _ =>
+      case s: ExtractionRule   => extractionRuleByHeadName += s
+      case s: FunctionCallRule => functionCallRuleByHeadName += s
+      case s: InferenceRule    => inferenceRuleByHeadName += s
+      case _                   => 
     }
+
+    val eByHeadNameGroup = extractionRuleByHeadName.toList.groupBy(_.q.head.name)
+    val iByHeadNameGroup = inferenceRuleByHeadName.toList.groupBy(_.q.head.name)
+    val fByHeadNameGroup = functionCallRuleByHeadName.toList.groupBy(_.output)
+
+    var stmtByHeadName = (eByHeadNameGroup.toSeq ++ iByHeadNameGroup.toSeq ++ fByHeadNameGroup.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
+    // var stmtByHeadName = new HashMap[String, Statement]()
+    // statements foreach {
+    //   case e : ExtractionRule => stmtByHeadName += { e.q.head.name -> e }
+    //   case f : FunctionCallRule   => stmtByHeadName += { f.output      -> f }
+    //   case w : InferenceRule  => stmtByHeadName += { w.q.head.name -> w }
+    //   case _ =>
+    // }
     // then, look at the body of each statement to construct a dependency graph
     statements foreach {
-      case f : FunctionCallRule => dependencies += { f -> (        Some(f.input) flatMap (stmtByHeadName get _)).toSet }
-      case e : ExtractionRule   => dependencies += { e -> (e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
-      case w : InferenceRule    => dependencies += { w -> (w.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet }
+      case f : FunctionCallRule => dependencies += { f -> ((        Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case e : ExtractionRule   => dependencies += { e -> ((e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case w : InferenceRule    => dependencies += { w -> ((w.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case _ =>
     }
   }
   // Generates a "dependencies" value for a compiled block of given statement.
-  def generateDependenciesOfCompiledBlockFor(statement: Statement): String = {
-    val dependentExtractorBlockNames =
-      dependencies getOrElse (statement, Set()) map resolveExtractorBlockName
+  def generateDependenciesOfCompiledBlockFor(statements: List[Statement]): String = {
+    var dependentExtractorBlockNames = Set[String]()
+    for (statement <- statements) {
+      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & visable) map resolveExtractorBlockName
+    }
     if (dependentExtractorBlockNames.size == 0) "" else {
       val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")
       s"dependencies: [${depStr}]"
@@ -235,156 +282,168 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlocks = List[CompiledBlock]
 
   // Dispatch to the corresponding compile function
-  def compile(stmt: Statement, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = stmt match {
-    case s:  ExtractionRule   => compile(s, ss, isIncremental)
-    case s:  FunctionCallRule => compile(s, ss, isIncremental)
-    case s:  InferenceRule    => compile(s, ss, isIncremental)
-    case _                    => List()  // defaults to compiling into empty block
-  }
+  // def compile(stmts: List[Statement], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = stmts(0) match {
+  //   case s: ExtractionRule   => compileE(stmts, ss, isIncremental)
+  //   case s: FunctionCallRule => compileF(stmts, ss, isIncremental)
+  //   case s: InferenceRule    => compileI(stmts, ss, isIncremental)
+  //   case _                   => List()  // defaults to compiling into empty block
+  // }
 
   // Generate extraction rule part for deepdive
-  def compile(stmt: ExtractionRule, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
-    // Generate the body of the query.
-    val qs              = new QuerySchema( stmt.q )
-    // variable columns
-    val variableCols = stmt.q.head.terms flatMap {
-      case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, stmt.q, true)
-    }
+  def compileE(stmts: List[ExtractionRule], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
+    var inputQueries = new ListBuffer[String]()
+    for (stmt <- stmts) {
+      // Generate the body of the query.
+      val qs              = new QuerySchema( stmt.q )
+      // variable columns
+      val variableCols = stmt.q.head.terms flatMap {
+        case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, stmt.q, true)
+      }
 
-    val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
+      val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
 
-    val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
+      val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
 
-    val ddCount = if (isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-    val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\"""" else ""
+      val ddCount = if (isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+      val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
 
-    val inputQuery = s"""
-      SELECT ${selectStr}${ddCountStr}
-      ${ ss.generateSQLBody(stmt.q) }"""
+      inputQueries += s"""
+        SELECT ${selectStr}${ddCountStr}
+        ${ ss.generateSQLBody(stmt.q) }"""
 
-    val blockName = ss.resolveExtractorBlockName(stmt)
+    }
+    val blockName = ss.resolveExtractorBlockName(stmts(0))
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" DROP VIEW IF EXISTS ${stmt.q.head.name};
-        CREATE VIEW ${stmt.q.head.name} AS ${inputQuery}
+        sql: \"\"\" DROP VIEW IF EXISTS ${stmts(0).q.head.name};
+        CREATE VIEW ${stmts(0).q.head.name} AS ${inputQueries.mkString(" UNION ")}
         \"\"\"
         style: "sql_extractor"
-        ${ss.generateDependenciesOfCompiledBlockFor(stmt)}
+          ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
       }
     """
     List(extractor)
   }
 
-  def compile(stmt: FunctionCallRule, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
-    val inputQuery = s"""
-    SELECT * FROM ${stmt.input}
-    """
-
-    val function = ss.resolveFunctionName(stmt.function)
-    val udfDetails = (function.implementations collectFirst {
-      case impl: RowWiseLineHandler =>
-        s"""udf: \"${StringEscapeUtils.escapeJava(impl.command)}\"
-        style: \"${impl.format}_extractor\""""
-    })
-
-    if (udfDetails.isEmpty)
-      ss.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
-        + (function.implementations mkString "\n  "))
-
-    val blockName = ss.resolveExtractorBlockName(stmt)
-    val extractor = s"""
-      deepdive.extraction.extractors.${blockName} {
-        input: \"\"\" SELECT * FROM ${stmt.input}
-        \"\"\"
-        output_relation: \"${stmt.output}\"
-        ${udfDetails.get}
-        ${ss.generateDependenciesOfCompiledBlockFor(stmt)}
-      }
-    """
-    List(extractor)
+  def compileF(stmts: List[FunctionCallRule], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
+    var extractors = new ListBuffer[String]()
+    for (stmt <- stmts) {
+      val inputQuery = s"""
+      SELECT * FROM ${stmt.input}
+      """
+
+      val function = ss.resolveFunctionName(stmt.function)
+      val udfDetails = (function.implementations collectFirst {
+        case impl: RowWiseLineHandler =>
+          s"""udf: \"${StringEscapeUtils.escapeJava(impl.command)}\"
+          style: \"${impl.format}_extractor\" """
+      })
+
+      if (udfDetails.isEmpty)
+        ss.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
+          + (function.implementations mkString "\n  "))
+
+      val blockName = ss.resolveExtractorBlockName(stmt)
+      val extractor = s"""
+        deepdive.extraction.extractors.${blockName} {
+          input: \"\"\" SELECT * FROM ${stmt.input}
+          \"\"\"
+          output_relation: \"${stmt.output}\"
+          ${udfDetails.get}
+          ${ss.generateDependenciesOfCompiledBlockFor(List(stmt))}
+        }
+      """
+      extractors += extractor
+    }
+    extractors.toList
   }
 
   // generate inference rule part for deepdive
-  def compile(stmt: InferenceRule, ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
+  def compileI(stmts: List[InferenceRule], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
     var blocks = List[String]()
-    val qs = new QuerySchema( stmt.q )
-
+    val qs = new QuerySchema( stmts(0).q )
     // node query
     // generate the node portion (V) of the factor graph
-    def compileNodeRule(z: InferenceRule, qs: QuerySchema, ss: CompilationState) : CompiledBlocks = {
-      val headTerms = z.q.head.terms map {
-        case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+    def compileNodeRule(zs: List[InferenceRule], qs: QuerySchema, ss: CompilationState) : CompiledBlocks = {
+      var inputQueries = new ListBuffer[String]()
+      for (z <- zs) {
+        val headTerms = z.q.head.terms map {
+          case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+        }
+        val index = qs.getBodyIndex(z.supervision)
+        val name  = ss.resolveName(qs.getVar(z.supervision))
+        val labelCol = s"R${index}.${name}"
+        val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
+        val ddCount = if (isIncremental) ( z.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
+
+        inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
+        ${ ss.generateSQLBody(z.q) }
+        """
       }
-      val index = qs.getBodyIndex(z.supervision)
-      val name  = ss.resolveName(qs.getVar(z.supervision))
-      val labelCol = s"R${index}.${name}"
-      val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-      val ddCount = if (isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-      val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
-
-      val query = s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
-    ${ ss.generateSQLBody(z.q) }"""
-
-      val blockName = ss.resolveExtractorBlockName(z)
+      val blockName = ss.resolveExtractorBlockName(zs(0))
       val ext = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" DROP TABLE IF EXISTS ${z.q.head.name};
-        CREATE TABLE ${z.q.head.name} AS
-        ${query}
+        sql: \"\"\" DROP TABLE IF EXISTS ${zs(0).q.head.name};
+        CREATE TABLE ${zs(0).q.head.name} AS
+        ${inputQueries.mkString(" UNION ")}
         \"\"\"
         style: "sql_extractor"
-        ${ss.generateDependenciesOfCompiledBlockFor(z)}
+        ${ss.generateDependenciesOfCompiledBlockFor(zs)}
       }
     """
       List(ext)
     }
-    if (ss.isQueryTerm(stmt.q.head.name))
-      blocks :::= compileNodeRule(stmt, qs, ss)
-
-    // edge query
-    val fakeBody        = stmt.q.head +: stmt.q.body
-    val fakeCQ          = ConjunctiveQuery(stmt.q.head, fakeBody) // we will just use the fakeBody below.
-
-    val index = stmt.q.body.length + 1
-    val qs2 = new QuerySchema( fakeCQ )
-    val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
-    val variableColsStr = Some(s"""R0.label AS "${stmt.q.head.name}.R0.label" """)
-
-    // weight string
-    val uwStr = stmt.weights match {
-      case KnownFactorWeight(x) => None
-      case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
-    }
+    if (ss.isQueryTerm(stmts(0).q.head.name))
+      blocks :::= compileNodeRule(stmts, qs, ss)
 
-    val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
+    val inferenceRuleToCompileGroup    = stmts.groupBy(_.q.head.name)
 
-    val ddCount = if (isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-    val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\"""" else ""
+    for (stmt <- stmts) {
+      // edge query
+      val fakeBody        = stmt.q.head +: stmt.q.body
+      val fakeCQ          = ConjunctiveQuery(stmt.q.head, fakeBody) // we will just use the fakeBody below.
 
-    // factor input query
-    val inputQuery = s"""
-      SELECT ${selectStr} ${ddCountStr}
-      ${ ss.generateSQLBody(fakeCQ) }"""
+      val index = stmt.q.body.length + 1
+      val qs2 = new QuerySchema( fakeCQ )
+      val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
+      val variableColsStr = Some(s"""R0.label AS "${stmt.q.head.name}.R0.label" """)
 
-    // factor function
-    val func = s"""Imply(${stmt.q.head.name}.R0.label)"""
-
-    // weight
-    val weight = stmt.weights match {
-      case KnownFactorWeight(x) => s"${x}"
-      case UnknownFactorWeight(w) => {
-        s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, false)).mkString(", ")})"""
+      // weight string
+      val uwStr = stmt.weights match {
+        case KnownFactorWeight(x) => None
+        case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
       }
-    }
 
-    blocks ::= s"""
-      deepdive.inference.factors.factor_${stmt.q.head.name} {
-        input_query: \"\"\"${inputQuery}\"\"\"
-        function: "${func}"
-        weight: "${weight}"
+      val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
+
+      val ddCount = if (isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+      val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
+
+      // factor input query
+      val inputQuery = s"""
+        SELECT ${selectStr} ${ddCountStr}
+        ${ ss.generateSQLBody(fakeCQ) }"""
+
+      // factor function
+      val func = s"""Imply(${stmt.q.head.name}.R0.label)"""
+
+      // weight
+      val weight = stmt.weights match {
+        case KnownFactorWeight(x) => s"${x}"
+        case UnknownFactorWeight(w) => {
+          s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, false)).mkString(", ")})"""
+        }
       }
-    """
 
+      blocks ::= s"""
+        deepdive.inference.factors.factor_${stmt.q.head.name} {
+          input_query: \"\"\"${inputQuery}\"\"\"
+          function: "${func}"
+          weight: "${weight}"
+        }
+      """
+    }
     blocks.reverse
   }
 
@@ -422,7 +481,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     List(ddSchema)
   }
 
-
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     // determine the program to compile
@@ -434,13 +492,33 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile )
 
+
+    val extractionRuleToCompile = new ListBuffer[ExtractionRule]()
+    val inferenceRuleToCompile = new ListBuffer[InferenceRule]()
+    val functionCallRuleToCompile = new ListBuffer[FunctionCallRule]()
+    programToCompile foreach (_ match {
+      case s: ExtractionRule   => extractionRuleToCompile += s
+      case s: FunctionCallRule => functionCallRuleToCompile += s
+      case s: InferenceRule    => inferenceRuleToCompile += s
+      case _                   => 
+    })
+
+    val extractionRuleToCompileGroup   = extractionRuleToCompile.groupBy(_.q.head.name)
+    val inferenceRuleToCompileGroup    = inferenceRuleToCompile.groupBy(_.q.head.name)
+    val functionCallRuleToCompileGroup = functionCallRuleToCompile.groupBy(_.input)
+
+    val body = new ListBuffer[String]()
+    extractionRuleToCompileGroup   foreach {keyVal => body ++= compileE(keyVal._2.toList, state, config.isIncremental)}
+    functionCallRuleToCompileGroup foreach {keyVal => body ++= compileF(keyVal._2.toList, state, config.isIncremental)}
+    inferenceRuleToCompileGroup    foreach {keyVal => body ++= compileI(keyVal._2.toList, state, config.isIncremental)}
+    
     // compile the program into blocks of application.conf
     val blocks = (
       compileUserSettings
       :::
       compileVariableSchema(programToCompile, state)
       :::
-      (programToCompile flatMap {compile(_, state, config.isIncremental)})
+      body.toList 
     )
 
     // emit the generated code

From 1bd05f426a2cc0dda384ea90292d2866f819f09c Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Wed, 6 May 2015 23:22:18 -0700
Subject: [PATCH 065/347] add spouse incremental example

---
 ...pouse_incremental_example.compile.expected | 179 +++++++++++++
 examples/spouse_incremental_example.ddl       | 101 ++++++++
 .../spouse_incremental_example.print.expected | 238 ++++++++++++++++++
 3 files changed, 518 insertions(+)
 create mode 100644 examples/spouse_incremental_example.compile.expected
 create mode 100644 examples/spouse_incremental_example.ddl
 create mode 100644 examples/spouse_incremental_example.print.expected

diff --git a/examples/spouse_incremental_example.compile.expected b/examples/spouse_incremental_example.compile.expected
new file mode 100644
index 000000000..d02f580f9
--- /dev/null
+++ b/examples/spouse_incremental_example.compile.expected
@@ -0,0 +1,179 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  
+
+      deepdive.schema.variables {
+        dd_delta_has_spouse.label: Boolean
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
+        CREATE VIEW dd_delta_ext_people_input AS 
+        SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_27 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
+        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_17" ,  "extraction_rule_12" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_20 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
+        CREATE VIEW dd_delta_ext_has_spouse_input AS 
+        SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+        FROM dd_delta_people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id  UNION 
+        SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+        FROM people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id  UNION 
+        SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+        FROM dd_delta_people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_12" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_12 {
+          input: """ SELECT * FROM dd_delta_ext_people_input
+          """
+          output_relation: "dd_delta_people_mentions"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_15" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_24 {
+          input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
+          """
+          output_relation: "dd_delta_has_spouse_features"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_27" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_17 {
+          input: """ SELECT * FROM dd_delta_ext_has_spouse_input
+          """
+          output_relation: "dd_delta_has_spouse_candidates"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_20" ]
+        }
+      
+
+      deepdive.extraction.extractors.extraction_rule_dd_delta_has_spouse {
+        sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse;
+        CREATE TABLE dd_delta_has_spouse AS
+        SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label , R0.dd_count * R1.dd_count AS dd_count
+        FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
+        WHERE R1.relation_id = R0.relation_id 
+         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label , R0.dd_count * R1.dd_count AS dd_count
+        FROM has_spouse_candidates R0, dd_delta_has_spouse_features R1
+        WHERE R1.relation_id = R0.relation_id 
+         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label , R0.dd_count * R1.dd_count AS dd_count
+        FROM dd_delta_has_spouse_candidates R0, dd_delta_has_spouse_features R1
+        WHERE R1.relation_id = R0.relation_id 
+        
+        """
+        style: "sql_extractor"
+        dependencies: [ "extraction_rule_17" ,  "extraction_rule_24" ]
+      }
+    
+
+        deepdive.inference.factors.factor_dd_delta_has_spouse {
+          input_query: """
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Imply(dd_delta_has_spouse.R0.label)"
+          weight: "?(has_spouse_features.R2.feature)"
+        }
+      
+
+        deepdive.inference.factors.factor_dd_delta_has_spouse {
+          input_query: """
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Imply(dd_delta_has_spouse.R0.label)"
+          weight: "?(dd_delta_has_spouse_features.R2.feature)"
+        }
+      
+
+        deepdive.inference.factors.factor_dd_delta_has_spouse {
+          input_query: """
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Imply(dd_delta_has_spouse.R0.label)"
+          weight: "?(dd_delta_has_spouse_features.R2.feature)"
+        }
+      
diff --git a/examples/spouse_incremental_example.ddl b/examples/spouse_incremental_example.ddl
new file mode 100644
index 000000000..6ff0ae117
--- /dev/null
+++ b/examples/spouse_incremental_example.ddl
@@ -0,0 +1,101 @@
+articles(
+  article_id text,
+  text       text,
+  dd_count   int).
+sentences(
+  document_id     text,
+  sentence        text,
+  words           text[],
+  lemma           text[],
+  pos_tags        text[],
+  dependencies    text[],
+  ner_tags        text[],
+  sentence_offset int,
+  sentence_id     text,
+  dd_count        int).
+people_mentions(
+  sentence_id    text,
+  start_position int,
+  length         int,
+  text           text,
+  mention_id     text,
+  dd_count       int).
+
+has_spouse_candidates(
+  person1_id  text,
+  person2_id  text,
+  sentence_id text,
+  description text,
+  relation_id text,
+  dd_count    int).
+has_spouse_features(
+  relation_id text,
+  feature     text,
+  dd_count    int).
+
+has_spouse?(
+  relation_id text,
+  dd_count    int).
+
+people_mentions :-
+  !ext_people(ext_people_input).
+
+ext_people_input(
+  sentence_id text,
+  words       text[],
+  ner_tags    text[],
+  dd_count    int).
+
+ext_people_input(s, words, ner_tags) :-
+  sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people over like ext_people_input
+                 returns like people_mentions
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
+
+has_spouse_candidates :-
+  !ext_has_spouse(ext_has_spouse_input).
+
+ext_has_spouse_input(
+  sentence_id text,
+  p1_id       text,
+  p1_text     text,
+  p2_id       text,
+  p2_text     text,
+  dd_count    int).
+
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, a, b, p1_text, p1_id),
+  people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse over like ext_has_spouse_input
+                     returns like has_spouse_candidates
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
+
+has_spouse_features :-
+  !ext_has_spouse_features(ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(
+  words             text[],
+  relation_id       text,
+  p1_start_position int,
+  p1_length         int,
+  p2_start_position int,
+  p2_length         int,
+  dd_count          int).
+
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(a, b, words, c, d, e, f, g, s),
+  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+  people_mentions(s, p1idx, p1len, k, person1_id),
+  people_mentions(s, p2idx, p2len, l, person2_id).
+  
+function ext_has_spouse_features over like ext_has_spouse_features_input
+                              returns like has_spouse_features
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
+
+has_spouse(rid) :-
+  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_features(rid, f)
+weight = f
+label = l.
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_incremental_example.print.expected
new file mode 100644
index 000000000..a9e5ad633
--- /dev/null
+++ b/examples/spouse_incremental_example.print.expected
@@ -0,0 +1,238 @@
+articles(article_id text,
+         text text).
+
+dd_delta_articles(article_id text,
+                  text text).
+
+sentences(document_id text,
+          sentence text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
+          sentence_offset int,
+          sentence_id text).
+
+dd_delta_sentences(document_id text,
+                   sentence text,
+                   words text[],
+                   lemma text[],
+                   pos_tags text[],
+                   dependencies text[],
+                   ner_tags text[],
+                   sentence_offset int,
+                   sentence_id text).
+
+people_mentions(sentence_id text,
+                start_position int,
+                length int,
+                text text,
+                mention_id text).
+
+dd_delta_people_mentions(sentence_id text,
+                         start_position int,
+                         length int,
+                         text text,
+                         mention_id text).
+
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text).
+
+dd_delta_has_spouse_candidates(person1_id text,
+                               person2_id text,
+                               sentence_id text,
+                               description text,
+                               relation_id text).
+
+has_spouse_features(relation_id text,
+                    feature text).
+
+dd_delta_has_spouse_features(relation_id text,
+                             feature text).
+
+has_spouse?(relation_id text).
+
+dd_delta_has_spouse?(relation_id text).
+
+dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
+
+ext_people_input(sentence_id text,
+                 words text[],
+                 ner_tags text[]).
+
+dd_delta_ext_people_input(sentence_id text,
+                          words text[],
+                          ner_tags text[]).
+
+dd_delta_ext_people_input(s, words, ner_tags) :-
+    dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people
+    over like dd_delta_ext_people_input
+ returns like dd_delta_people_mentions
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+        handles tsv lines.
+
+dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
+
+ext_has_spouse_input(sentence_id text,
+                     p1_id text,
+                     p1_text text,
+                     p2_id text,
+                     p2_text text).
+
+dd_delta_ext_has_spouse_input(sentence_id text,
+                              p1_id text,
+                              p1_text text,
+                              p2_id text,
+                              p2_text text).
+
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
+    people_mentions(s, c, d, p2_text, p2_id).
+
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    people_mentions(s, a, b, p1_text, p1_id),
+    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
+    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse
+    over like dd_delta_ext_has_spouse_input
+ returns like dd_delta_has_spouse_candidates
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+        handles tsv lines.
+
+dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(words text[],
+                              relation_id text,
+                              p1_start_position int,
+                              p1_length int,
+                              p2_start_position int,
+                              p2_length int).
+
+dd_delta_ext_has_spouse_features_input(words text[],
+                                       relation_id text,
+                                       p1_start_position int,
+                                       p1_length int,
+                                       p2_start_position int,
+                                       p2_length int).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+function ext_has_spouse_features
+    over like dd_delta_ext_has_spouse_features_input
+ returns like dd_delta_has_spouse_features
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+        handles tsv lines.
+
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_features(rid, f)
+  weight = f
+  label = l.
+dd_delta_has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_features(rid, f)
+  weight = f
+  label = l.
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_features(rid, f)
+  weight = f
+  label = l.

From 9c3aec08344fb4dde6f6dbc15bb73a1aadbff3d3 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Mon, 11 May 2015 22:20:27 -0700
Subject: [PATCH 066/347] fix error in spouse example

---
 examples/spouse_example.compile.expected      | 113 +++++++++---------
 examples/spouse_example.ddl                   |  20 ++--
 examples/spouse_example.print.expected        |  23 ++--
 ...pouse_incremental_example.compile.expected | 106 ++++++++--------
 examples/spouse_incremental_example.ddl       |  20 ++--
 .../spouse_incremental_example.print.expected |  74 ++++++------
 6 files changed, 183 insertions(+), 173 deletions(-)

diff --git a/examples/spouse_example.compile.expected b/examples/spouse_example.compile.expected
index cb5252ee9..d463a2f83 100644
--- a/examples/spouse_example.compile.expected
+++ b/examples/spouse_example.compile.expected
@@ -11,94 +11,95 @@
   
 
       deepdive.schema.variables {
-        has_spouse.label: Boolean
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_6 {
-        input: """ SELECT * FROM ext_people_input
-        """
-        output_relation: "people_mentions"
-        udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
-        style: "tsv_extractor"
-        dependencies: [ "extraction_rule_8" ]
+        f_has_spouse.label: Boolean
       }
     
 
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-      SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-      FROM sentences R0
+        SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+        FROM sentences R0
         
         """
         style: "sql_extractor"
-        
+          
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_10 {
-        input: """ SELECT * FROM ext_has_spouse_input
+      deepdive.extraction.extractors.extraction_rule_16 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
+        CREATE VIEW ext_has_spouse_features_input AS 
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        FROM sentences R0, has_spouse R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
-        output_relation: "has_spouse_candidates"
-        udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
-        style: "tsv_extractor"
-        dependencies: [ "extraction_rule_12" ]
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_10" ,  "extraction_rule_6" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-      SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-      FROM people_mentions R0, people_mentions R1
+        SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
-        dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_6" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_14 {
-        input: """ SELECT * FROM ext_has_spouse_features_input
-        """
-        output_relation: "has_spouse_features"
-        udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
-        style: "tsv_extractor"
-        dependencies: [ "extraction_rule_16" ]
-      }
-    
+        deepdive.extraction.extractors.extraction_rule_6 {
+          input: """ SELECT * FROM ext_people_input
+          """
+          output_relation: "people_mentions"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_8" ]
+        }
+      
 
-      deepdive.extraction.extractors.extraction_rule_16 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
-        CREATE VIEW ext_has_spouse_features_input AS 
-      SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-      FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-        dependencies: [ "extraction_rule_10" ,  "extraction_rule_6" ]
-      }
-    
+        deepdive.extraction.extractors.extraction_rule_14 {
+          input: """ SELECT * FROM ext_has_spouse_features_input
+          """
+          output_relation: "has_spouse_features"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_16" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_10 {
+          input: """ SELECT * FROM ext_has_spouse_input
+          """
+          output_relation: "has_spouse"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_12" ]
+        }
+      
 
-      deepdive.extraction.extractors.extraction_rule_has_spouse {
-        sql: """ DROP TABLE IF EXISTS has_spouse;
-        CREATE TABLE has_spouse AS
-        SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label
-    FROM has_spouse_candidates R0, has_spouse_features R1
+      deepdive.extraction.extractors.extraction_rule_f_has_spouse {
+        sql: """ DROP TABLE IF EXISTS f_has_spouse;
+        CREATE TABLE f_has_spouse AS
+        SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
+        FROM has_spouse R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
+        
         """
         style: "sql_extractor"
         dependencies: [ "extraction_rule_10" ,  "extraction_rule_14" ]
       }
     
 
-      deepdive.inference.factors.factor_has_spouse {
-        input_query: """
-      SELECT R0.id AS "has_spouse.R0.id" , R0.label AS "has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature" 
-      FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+        deepdive.inference.factors.factor_f_has_spouse {
+          input_query: """
+        SELECT R0.id AS "f_has_spouse.R0.id" , R0.label AS "f_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  
+        FROM f_has_spouse R0, has_spouse R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-        function: "Imply(has_spouse.R0.label)"
-        weight: "?(has_spouse_features.R2.feature)"
-      }
-    
+          function: "Imply(f_has_spouse.R0.label)"
+          weight: "?(has_spouse_features.R2.feature)"
+        }
+      
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index f7b87deed..8a647f61b 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -1,6 +1,7 @@
 articles(
   article_id text,
   text       text).
+
 sentences(
   document_id     text,
   sentence        text,
@@ -11,6 +12,7 @@ sentences(
   ner_tags        text[],
   sentence_offset int,
   sentence_id     text).
+
 people_mentions(
   sentence_id    text,
   start_position int,
@@ -18,17 +20,19 @@ people_mentions(
   text           text,
   mention_id     text).
 
-has_spouse_candidates(
+has_spouse(
   person1_id  text,
   person2_id  text,
   sentence_id text,
   description text,
-  relation_id text).
+  relation_id text,
+  is_true boolean).
+
 has_spouse_features(
   relation_id text,
   feature     text).
 
-has_spouse?(relation_id text).
+f_has_spouse?(relation_id text).
 
 people_mentions :-
   !ext_people(ext_people_input).
@@ -45,7 +49,7 @@ function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates :-
+has_spouse :-
   !ext_has_spouse(ext_has_spouse_input).
 
 ext_has_spouse_input(
@@ -60,7 +64,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse over like ext_has_spouse_input
-                     returns like has_spouse_candidates
+                     returns like has_spouse
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
@@ -76,7 +80,7 @@ ext_has_spouse_features_input(
 
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+  has_spouse(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
   
@@ -84,8 +88,8 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
 
-has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
+f_has_spouse(rid) :-
+  has_spouse(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
 label = l.
diff --git a/examples/spouse_example.print.expected b/examples/spouse_example.print.expected
index 6787de76d..fe9cf190c 100644
--- a/examples/spouse_example.print.expected
+++ b/examples/spouse_example.print.expected
@@ -17,16 +17,17 @@ people_mentions(sentence_id text,
                 text text,
                 mention_id text).
 
-has_spouse_candidates(person1_id text,
-                      person2_id text,
-                      sentence_id text,
-                      description text,
-                      relation_id text).
+has_spouse(person1_id text,
+           person2_id text,
+           sentence_id text,
+           description text,
+           relation_id text,
+           is_true boolean).
 
 has_spouse_features(relation_id text,
                     feature text).
 
-has_spouse?(relation_id text).
+f_has_spouse?(relation_id text).
 
 people_mentions :- !ext_people(ext_people_input).
 
@@ -43,7 +44,7 @@ function ext_people
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
+has_spouse :- !ext_has_spouse(ext_has_spouse_input).
 
 ext_has_spouse_input(sentence_id text,
                      p1_id text,
@@ -57,7 +58,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse
     over like ext_has_spouse_input
- returns like has_spouse_candidates
+ returns like has_spouse
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -72,7 +73,7 @@ ext_has_spouse_features_input(words text[],
 
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
@@ -82,8 +83,8 @@ function ext_has_spouse_features
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l),
+f_has_spouse(rid) :-
+    has_spouse(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
   label = l.
diff --git a/examples/spouse_incremental_example.compile.expected b/examples/spouse_incremental_example.compile.expected
index d02f580f9..2e39ffc25 100644
--- a/examples/spouse_incremental_example.compile.expected
+++ b/examples/spouse_incremental_example.compile.expected
@@ -11,7 +11,7 @@
   
 
       deepdive.schema.variables {
-        dd_delta_has_spouse.label: Boolean
+        dd_delta_f_has_spouse.label: Boolean
       }
     
 
@@ -30,50 +30,50 @@
       deepdive.extraction.extractors.extraction_rule_27 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
@@ -122,24 +122,24 @@
         deepdive.extraction.extractors.extraction_rule_17 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
-          output_relation: "dd_delta_has_spouse_candidates"
+          output_relation: "dd_delta_has_spouse"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_20" ]
         }
       
 
-      deepdive.extraction.extractors.extraction_rule_dd_delta_has_spouse {
-        sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse;
-        CREATE TABLE dd_delta_has_spouse AS
-        SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
+      deepdive.extraction.extractors.extraction_rule_dd_delta_f_has_spouse {
+        sql: """ DROP TABLE IF EXISTS dd_delta_f_has_spouse;
+        CREATE TABLE dd_delta_f_has_spouse AS
+        SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
+        FROM dd_delta_has_spouse R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
-         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM has_spouse_candidates R0, dd_delta_has_spouse_features R1
+         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
+        FROM has_spouse R0, dd_delta_has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
-         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.l AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_delta_has_spouse_candidates R0, dd_delta_has_spouse_features R1
+         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
+        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
         
         """
@@ -148,32 +148,32 @@
       }
     
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_f_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+        SELECT R0.id AS "dd_delta_f_has_spouse.R0.id" , R0.label AS "dd_delta_f_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_f_has_spouse R0, dd_delta_has_spouse R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
+          function: "Imply(dd_delta_f_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_f_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        SELECT R0.id AS "dd_delta_f_has_spouse.R0.id" , R0.label AS "dd_delta_f_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_f_has_spouse R0, has_spouse R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
+          function: "Imply(dd_delta_f_has_spouse.R0.label)"
           weight: "?(dd_delta_has_spouse_features.R2.feature)"
         }
       
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_f_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        SELECT R0.id AS "dd_delta_f_has_spouse.R0.id" , R0.label AS "dd_delta_f_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_f_has_spouse R0, dd_delta_has_spouse R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
+          function: "Imply(dd_delta_f_has_spouse.R0.label)"
           weight: "?(dd_delta_has_spouse_features.R2.feature)"
         }
       
diff --git a/examples/spouse_incremental_example.ddl b/examples/spouse_incremental_example.ddl
index 6ff0ae117..04501621e 100644
--- a/examples/spouse_incremental_example.ddl
+++ b/examples/spouse_incremental_example.ddl
@@ -2,6 +2,7 @@ articles(
   article_id text,
   text       text,
   dd_count   int).
+
 sentences(
   document_id     text,
   sentence        text,
@@ -13,6 +14,7 @@ sentences(
   sentence_offset int,
   sentence_id     text,
   dd_count        int).
+
 people_mentions(
   sentence_id    text,
   start_position int,
@@ -21,21 +23,21 @@ people_mentions(
   mention_id     text,
   dd_count       int).
 
-has_spouse_candidates(
+has_spouse(
   person1_id  text,
   person2_id  text,
   sentence_id text,
   description text,
   relation_id text,
+  is_true     boolean,
   dd_count    int).
+
 has_spouse_features(
   relation_id text,
   feature     text,
   dd_count    int).
 
-has_spouse?(
-  relation_id text,
-  dd_count    int).
+f_has_spouse?(relation_id text).
 
 people_mentions :-
   !ext_people(ext_people_input).
@@ -53,7 +55,7 @@ function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates :-
+has_spouse :-
   !ext_has_spouse(ext_has_spouse_input).
 
 ext_has_spouse_input(
@@ -69,7 +71,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse over like ext_has_spouse_input
-                     returns like has_spouse_candidates
+                     returns like has_spouse
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
@@ -86,7 +88,7 @@ ext_has_spouse_features_input(
 
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+  has_spouse(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
   
@@ -94,8 +96,8 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
 
-has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
+f_has_spouse(rid) :-
+  has_spouse(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
 label = l.
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_incremental_example.print.expected
index a9e5ad633..fb6e1e3d8 100644
--- a/examples/spouse_incremental_example.print.expected
+++ b/examples/spouse_incremental_example.print.expected
@@ -36,17 +36,19 @@ dd_delta_people_mentions(sentence_id text,
                          text text,
                          mention_id text).
 
-has_spouse_candidates(person1_id text,
-                      person2_id text,
-                      sentence_id text,
-                      description text,
-                      relation_id text).
-
-dd_delta_has_spouse_candidates(person1_id text,
-                               person2_id text,
-                               sentence_id text,
-                               description text,
-                               relation_id text).
+has_spouse(person1_id text,
+           person2_id text,
+           sentence_id text,
+           description text,
+           relation_id text,
+           is_true boolean).
+
+dd_delta_has_spouse(person1_id text,
+                    person2_id text,
+                    sentence_id text,
+                    description text,
+                    relation_id text,
+                    is_true boolean).
 
 has_spouse_features(relation_id text,
                     feature text).
@@ -54,9 +56,9 @@ has_spouse_features(relation_id text,
 dd_delta_has_spouse_features(relation_id text,
                              feature text).
 
-has_spouse?(relation_id text).
+f_has_spouse?(relation_id text).
 
-dd_delta_has_spouse?(relation_id text).
+dd_delta_f_has_spouse?(relation_id text).
 
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
@@ -77,7 +79,7 @@ function ext_people
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
+dd_delta_has_spouse :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
 ext_has_spouse_input(sentence_id text,
                      p1_id text,
@@ -105,7 +107,7 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
- returns like dd_delta_has_spouse_candidates
+ returns like dd_delta_has_spouse
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -127,91 +129,91 @@ dd_delta_ext_has_spouse_features_input(words text[],
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
@@ -221,18 +223,18 @@ function ext_has_spouse_features
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-dd_delta_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+dd_delta_f_has_spouse(rid) :-
+    dd_delta_has_spouse(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
   label = l.
-dd_delta_has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l),
+dd_delta_f_has_spouse(rid) :-
+    has_spouse(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l.
-dd_delta_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+dd_delta_f_has_spouse(rid) :-
+    dd_delta_has_spouse(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l.

From 6a1805f73d4d77b045e719a5a96c54a29573f72d Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Mon, 11 May 2015 22:31:35 -0700
Subject: [PATCH 067/347] code clean & add more comments

---
 DeepDiveLogCompiler.scala | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index aed9bb916..fd41dad06 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -77,6 +77,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   // The dependency graph between statements.
   var dependencies : Map[Statement, Set[Statement]] = new HashMap()
 
+  // The statement whether will compile or union to other statements
   var visable : Set[Statement] = Set()
 
   def init() = {
@@ -106,13 +107,11 @@ class CompilationState( statements : DeepDiveLog.Program )  {
 
   // Given a statement, resolve its name for the compiled extractor block.
   def resolveExtractorBlockName(s: Statement): String = {
-    if (visable contains s) {
-      s match {
-        case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
-        case s: ExtractionRule   => s"extraction_rule_${statements indexOf s}"
-        case s: InferenceRule    => s"extraction_rule_${s.q.head.name}"
-      }
-    } else ""
+    s match {
+      case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
+      case s: ExtractionRule   => s"extraction_rule_${statements indexOf s}"
+      case s: InferenceRule    => s"extraction_rule_${s.q.head.name}"
+    }
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
@@ -492,7 +491,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile )
 
-
+    // compile compilation states by head name based on type
     val extractionRuleToCompile = new ListBuffer[ExtractionRule]()
     val inferenceRuleToCompile = new ListBuffer[InferenceRule]()
     val functionCallRuleToCompile = new ListBuffer[FunctionCallRule]()

From f16166e4d730b08cbad3d59440954a035f8e9014 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 12 May 2015 03:19:41 -0700
Subject: [PATCH 068/347] fix inference rule name in spouse example

---
 examples/spouse_example.compile.expected      |  24 ++--
 examples/spouse_example.ddl                   |  14 +-
 examples/spouse_example.print.expected        |  24 ++--
 ...pouse_incremental_example.compile.expected | 100 +++++++-------
 examples/spouse_incremental_example.ddl       |  14 +-
 .../spouse_incremental_example.print.expected | 122 ++++++++++--------
 6 files changed, 157 insertions(+), 141 deletions(-)

diff --git a/examples/spouse_example.compile.expected b/examples/spouse_example.compile.expected
index d463a2f83..10a58e063 100644
--- a/examples/spouse_example.compile.expected
+++ b/examples/spouse_example.compile.expected
@@ -11,7 +11,7 @@
   
 
       deepdive.schema.variables {
-        f_has_spouse.label: Boolean
+        has_spouse.label: Boolean
       }
     
 
@@ -30,8 +30,8 @@
       deepdive.extraction.extractors.extraction_rule_16 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-        FROM sentences R0, has_spouse R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
@@ -74,18 +74,18 @@
         deepdive.extraction.extractors.extraction_rule_10 {
           input: """ SELECT * FROM ext_has_spouse_input
           """
-          output_relation: "has_spouse"
+          output_relation: "has_spouse_candidates"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_12" ]
         }
       
 
-      deepdive.extraction.extractors.extraction_rule_f_has_spouse {
-        sql: """ DROP TABLE IF EXISTS f_has_spouse;
-        CREATE TABLE f_has_spouse AS
+      deepdive.extraction.extractors.extraction_rule_has_spouse {
+        sql: """ DROP TABLE IF EXISTS has_spouse;
+        CREATE TABLE has_spouse AS
         SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
-        FROM has_spouse R0, has_spouse_features R1
+        FROM has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
         
         """
@@ -94,12 +94,12 @@
       }
     
 
-        deepdive.inference.factors.factor_f_has_spouse {
+        deepdive.inference.factors.factor_has_spouse {
           input_query: """
-        SELECT R0.id AS "f_has_spouse.R0.id" , R0.label AS "f_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  
-        FROM f_has_spouse R0, has_spouse R1, has_spouse_features R2
+        SELECT R0.id AS "has_spouse.R0.id" , R0.label AS "has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  
+        FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(f_has_spouse.R0.label)"
+          function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 8a647f61b..ac5546486 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -20,7 +20,7 @@ people_mentions(
   text           text,
   mention_id     text).
 
-has_spouse(
+has_spouse_candidates(
   person1_id  text,
   person2_id  text,
   sentence_id text,
@@ -32,7 +32,7 @@ has_spouse_features(
   relation_id text,
   feature     text).
 
-f_has_spouse?(relation_id text).
+has_spouse?(relation_id text).
 
 people_mentions :-
   !ext_people(ext_people_input).
@@ -49,7 +49,7 @@ function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
 
-has_spouse :-
+has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
 
 ext_has_spouse_input(
@@ -64,7 +64,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse over like ext_has_spouse_input
-                     returns like has_spouse
+                     returns like has_spouse_candidates
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
@@ -80,7 +80,7 @@ ext_has_spouse_features_input(
 
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse(person1_id, person2_id, s, h, rid, x),
+  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
   
@@ -88,8 +88,8 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
 
-f_has_spouse(rid) :-
-  has_spouse(a, b, c, d, rid, l),
+has_spouse(rid) :-
+  has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
 label = l.
diff --git a/examples/spouse_example.print.expected b/examples/spouse_example.print.expected
index fe9cf190c..4aedd134f 100644
--- a/examples/spouse_example.print.expected
+++ b/examples/spouse_example.print.expected
@@ -17,17 +17,17 @@ people_mentions(sentence_id text,
                 text text,
                 mention_id text).
 
-has_spouse(person1_id text,
-           person2_id text,
-           sentence_id text,
-           description text,
-           relation_id text,
-           is_true boolean).
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text,
+                      is_true boolean).
 
 has_spouse_features(relation_id text,
                     feature text).
 
-f_has_spouse?(relation_id text).
+has_spouse?(relation_id text).
 
 people_mentions :- !ext_people(ext_people_input).
 
@@ -44,7 +44,7 @@ function ext_people
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
         handles tsv lines.
 
-has_spouse :- !ext_has_spouse(ext_has_spouse_input).
+has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
 
 ext_has_spouse_input(sentence_id text,
                      p1_id text,
@@ -58,7 +58,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse
     over like ext_has_spouse_input
- returns like has_spouse
+ returns like has_spouse_candidates
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -73,7 +73,7 @@ ext_has_spouse_features_input(words text[],
 
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
@@ -83,8 +83,8 @@ function ext_has_spouse_features
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-f_has_spouse(rid) :-
-    has_spouse(a, b, c, d, rid, l),
+has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
   label = l.
diff --git a/examples/spouse_incremental_example.compile.expected b/examples/spouse_incremental_example.compile.expected
index 2e39ffc25..4e009898a 100644
--- a/examples/spouse_incremental_example.compile.expected
+++ b/examples/spouse_incremental_example.compile.expected
@@ -11,7 +11,7 @@
   
 
       deepdive.schema.variables {
-        dd_delta_f_has_spouse.label: Boolean
+        dd_delta_has_spouse.label: Boolean
       }
     
 
@@ -30,50 +30,50 @@
       deepdive.extraction.extractors.extraction_rule_27 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
@@ -122,24 +122,24 @@
         deepdive.extraction.extractors.extraction_rule_17 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
-          output_relation: "dd_delta_has_spouse"
+          output_relation: "dd_delta_has_spouse_candidates"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_20" ]
         }
       
 
-      deepdive.extraction.extractors.extraction_rule_dd_delta_f_has_spouse {
-        sql: """ DROP TABLE IF EXISTS dd_delta_f_has_spouse;
-        CREATE TABLE dd_delta_f_has_spouse AS
+      deepdive.extraction.extractors.extraction_rule_dd_delta_has_spouse {
+        sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse;
+        CREATE TABLE dd_delta_has_spouse AS
         SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_delta_has_spouse R0, has_spouse_features R1
+        FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
          UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM has_spouse R0, dd_delta_has_spouse_features R1
+        FROM has_spouse_candidates R0, dd_delta_has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
          UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_features R1
+        FROM dd_delta_has_spouse_candidates R0, dd_delta_has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
         
         """
@@ -148,32 +148,32 @@
       }
     
 
-        deepdive.inference.factors.factor_dd_delta_f_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_f_has_spouse.R0.id" , R0.label AS "dd_delta_f_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_f_has_spouse R0, dd_delta_has_spouse R1, has_spouse_features R2
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_f_has_spouse.R0.label)"
+          function: "Imply(dd_delta_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
 
-        deepdive.inference.factors.factor_dd_delta_f_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_f_has_spouse.R0.id" , R0.label AS "dd_delta_f_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_f_has_spouse R0, has_spouse R1, dd_delta_has_spouse_features R2
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_f_has_spouse.R0.label)"
+          function: "Imply(dd_delta_has_spouse.R0.label)"
           weight: "?(dd_delta_has_spouse_features.R2.feature)"
         }
       
 
-        deepdive.inference.factors.factor_dd_delta_f_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_f_has_spouse.R0.id" , R0.label AS "dd_delta_f_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_f_has_spouse R0, dd_delta_has_spouse R1, dd_delta_has_spouse_features R2
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_f_has_spouse.R0.label)"
+          function: "Imply(dd_delta_has_spouse.R0.label)"
           weight: "?(dd_delta_has_spouse_features.R2.feature)"
         }
       
diff --git a/examples/spouse_incremental_example.ddl b/examples/spouse_incremental_example.ddl
index 04501621e..cf467ac8c 100644
--- a/examples/spouse_incremental_example.ddl
+++ b/examples/spouse_incremental_example.ddl
@@ -23,7 +23,7 @@ people_mentions(
   mention_id     text,
   dd_count       int).
 
-has_spouse(
+has_spouse_candidates(
   person1_id  text,
   person2_id  text,
   sentence_id text,
@@ -37,7 +37,7 @@ has_spouse_features(
   feature     text,
   dd_count    int).
 
-f_has_spouse?(relation_id text).
+has_spouse?(relation_id text).
 
 people_mentions :-
   !ext_people(ext_people_input).
@@ -55,7 +55,7 @@ function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
 
-has_spouse :-
+has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
 
 ext_has_spouse_input(
@@ -71,7 +71,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse over like ext_has_spouse_input
-                     returns like has_spouse
+                     returns like has_spouse_candidates
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
@@ -88,7 +88,7 @@ ext_has_spouse_features_input(
 
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse(person1_id, person2_id, s, h, rid, x),
+  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
   
@@ -96,8 +96,8 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
 
-f_has_spouse(rid) :-
-  has_spouse(a, b, c, d, rid, l),
+has_spouse(rid) :-
+  has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
 label = l.
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_incremental_example.print.expected
index fb6e1e3d8..406f28b4a 100644
--- a/examples/spouse_incremental_example.print.expected
+++ b/examples/spouse_incremental_example.print.expected
@@ -1,8 +1,10 @@
 articles(article_id text,
-         text text).
+         text text,
+         dd_count int).
 
 dd_delta_articles(article_id text,
-                  text text).
+                  text text,
+                  dd_count int).
 
 sentences(document_id text,
           sentence text,
@@ -12,7 +14,8 @@ sentences(document_id text,
           dependencies text[],
           ner_tags text[],
           sentence_offset int,
-          sentence_id text).
+          sentence_id text,
+          dd_count int).
 
 dd_delta_sentences(document_id text,
                    sentence text,
@@ -22,53 +25,62 @@ dd_delta_sentences(document_id text,
                    dependencies text[],
                    ner_tags text[],
                    sentence_offset int,
-                   sentence_id text).
+                   sentence_id text,
+                   dd_count int).
 
 people_mentions(sentence_id text,
                 start_position int,
                 length int,
                 text text,
-                mention_id text).
+                mention_id text,
+                dd_count int).
 
 dd_delta_people_mentions(sentence_id text,
                          start_position int,
                          length int,
                          text text,
-                         mention_id text).
-
-has_spouse(person1_id text,
-           person2_id text,
-           sentence_id text,
-           description text,
-           relation_id text,
-           is_true boolean).
-
-dd_delta_has_spouse(person1_id text,
-                    person2_id text,
-                    sentence_id text,
-                    description text,
-                    relation_id text,
-                    is_true boolean).
+                         mention_id text,
+                         dd_count int).
+
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text,
+                      is_true boolean,
+                      dd_count int).
+
+dd_delta_has_spouse_candidates(person1_id text,
+                               person2_id text,
+                               sentence_id text,
+                               description text,
+                               relation_id text,
+                               is_true boolean,
+                               dd_count int).
 
 has_spouse_features(relation_id text,
-                    feature text).
+                    feature text,
+                    dd_count int).
 
 dd_delta_has_spouse_features(relation_id text,
-                             feature text).
+                             feature text,
+                             dd_count int).
 
-f_has_spouse?(relation_id text).
+has_spouse?(relation_id text).
 
-dd_delta_f_has_spouse?(relation_id text).
+dd_delta_has_spouse?(relation_id text).
 
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
 ext_people_input(sentence_id text,
                  words text[],
-                 ner_tags text[]).
+                 ner_tags text[],
+                 dd_count int).
 
 dd_delta_ext_people_input(sentence_id text,
                           words text[],
-                          ner_tags text[]).
+                          ner_tags text[],
+                          dd_count int).
 
 dd_delta_ext_people_input(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
@@ -79,19 +91,21 @@ function ext_people
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
+dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
 ext_has_spouse_input(sentence_id text,
                      p1_id text,
                      p1_text text,
                      p2_id text,
-                     p2_text text).
+                     p2_text text,
+                     dd_count int).
 
 dd_delta_ext_has_spouse_input(sentence_id text,
                               p1_id text,
                               p1_text text,
                               p2_id text,
-                              p2_text text).
+                              p2_text text,
+                              dd_count int).
 
 dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
@@ -107,7 +121,7 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
- returns like dd_delta_has_spouse
+ returns like dd_delta_has_spouse_candidates
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -118,102 +132,104 @@ ext_has_spouse_features_input(words text[],
                               p1_start_position int,
                               p1_length int,
                               p2_start_position int,
-                              p2_length int).
+                              p2_length int,
+                              dd_count int).
 
 dd_delta_ext_has_spouse_features_input(words text[],
                                        relation_id text,
                                        p1_start_position int,
                                        p1_length int,
                                        p2_start_position int,
-                                       p2_length int).
+                                       p2_length int,
+                                       dd_count int).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse(person1_id, person2_id, s, h, rid, x),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse(person1_id, person2_id, s, h, rid, x),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
@@ -223,18 +239,18 @@ function ext_has_spouse_features
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-dd_delta_f_has_spouse(rid) :-
-    dd_delta_has_spouse(a, b, c, d, rid, l),
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
   label = l.
-dd_delta_f_has_spouse(rid) :-
-    has_spouse(a, b, c, d, rid, l),
+dd_delta_has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l.
-dd_delta_f_has_spouse(rid) :-
-    dd_delta_has_spouse(a, b, c, d, rid, l),
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l.

From 1e65dbd11b8f70cd4ae6c34279958e08de0f1bf3 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 12 May 2015 03:23:45 -0700
Subject: [PATCH 069/347] fix typos

---
 DeepDiveLogCompiler.scala | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index fd41dad06..8c592d31a 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -78,7 +78,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   var dependencies : Map[Statement, Set[Statement]] = new HashMap()
 
   // The statement whether will compile or union to other statements
-  var visable : Set[Statement] = Set()
+  var visible : Set[Statement] = Set()
 
   def init() = {
     // generate the statements.
@@ -95,7 +95,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
       case FunctionCallRule(_,_,_) => ()
     }
 
-    analyzeVisable(statements)
+    analyzeVisible(statements)
     analyzeDependency(statements)
   }
 
@@ -178,7 +178,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   }
 
   // Analyze the block visibility among statements 
-  def analyzeVisable(statements: List[Statement]) = {
+  def analyzeVisible(statements: List[Statement]) = {
     val extractionRules   = new ListBuffer[ExtractionRule]()
     val functionCallRules = new ListBuffer[FunctionCallRule]()
     val inferenceRules    = new ListBuffer[InferenceRule]()
@@ -194,9 +194,9 @@ class CompilationState( statements : DeepDiveLog.Program )  {
     val functionCallRulesGroup = functionCallRules.groupBy(_.input)
     val inferenceRulesGroup    = inferenceRules.groupBy(_.q.head.name)
 
-    extractionRulesGroup   foreach {keyVal => visable += keyVal._2(0)}
-    functionCallRulesGroup foreach {keyVal => visable += keyVal._2(0)}
-    inferenceRulesGroup    foreach {keyVal => visable += keyVal._2(0)}
+    extractionRulesGroup   foreach {keyVal => visible += keyVal._2(0)}
+    functionCallRulesGroup foreach {keyVal => visible += keyVal._2(0)}
+    inferenceRulesGroup    foreach {keyVal => visible += keyVal._2(0)}
   }
 
   // Analyze the dependency between statements and construct a graph.
@@ -237,7 +237,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   def generateDependenciesOfCompiledBlockFor(statements: List[Statement]): String = {
     var dependentExtractorBlockNames = Set[String]()
     for (statement <- statements) {
-      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & visable) map resolveExtractorBlockName
+      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & visible) map resolveExtractorBlockName
     }
     if (dependentExtractorBlockNames.size == 0) "" else {
       val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")

From da69fac695bf910a4b60781f9d687ac439fc5468 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 12 May 2015 04:19:11 -0700
Subject: [PATCH 070/347] address all Jaeho\ comments

---
 DeepDiveLogCompiler.scala | 127 ++++++++++++++------------------------
 1 file changed, 46 insertions(+), 81 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 8c592d31a..eddc6b10d 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -63,7 +63,7 @@ import scala.collection.mutable.ListBuffer
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
-class CompilationState( statements : DeepDiveLog.Program )  {
+class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.Config )  {
     // TODO: refactor the schema into a class that constructs and
     // manages these maps. Also it should have appropriate
     // abstractions and error handling for missing values.
@@ -80,8 +80,17 @@ class CompilationState( statements : DeepDiveLog.Program )  {
   // The statement whether will compile or union to other statements
   var visible : Set[Statement] = Set()
 
+  var isIncremental : Boolean = false
+
+  // Mapping head names to the actual statements
+  var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
+  var inferenceRuleGroupByHead      : Map[String, List[InferenceRule]] = new HashMap[String, List[InferenceRule]]()
+  var functionCallRuleGroupByInput  : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
+  var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
+
   def init() = {
     // generate the statements.
+    isIncremental = config.isIncremental
     statements.foreach {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery) =>
         terms.foreach {
@@ -94,7 +103,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case FunctionCallRule(_,_,_) => ()
     }
-
+    groupByHead(statements)
     analyzeVisible(statements)
     analyzeDependency(statements)
   }
@@ -136,7 +145,7 @@ class CompilationState( statements : DeepDiveLog.Program )  {
     if( ground_relations contains relName ) !ground_relations(relName) else true
   }
 
-  // resolve a column name with alias
+  // Resolve a column name with alias
   def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: Boolean) : Option[String] = {
     val index = qs.getBodyIndex(s)
     val name  = resolveName(qs.getVar(s))
@@ -177,55 +186,37 @@ class CompilationState( statements : DeepDiveLog.Program )  {
         ${ whereClauseStr }"""
   }
 
-  // Analyze the block visibility among statements 
-  def analyzeVisible(statements: List[Statement]) = {
-    val extractionRules   = new ListBuffer[ExtractionRule]()
-    val functionCallRules = new ListBuffer[FunctionCallRule]()
-    val inferenceRules    = new ListBuffer[InferenceRule]()
-    
+  // Group statements by head
+  def groupByHead(statements: List[Statement]) = {
+    // Compile compilation states by head name based on type
+    val extractionRuleToCompile = new ListBuffer[ExtractionRule]()
+    val inferenceRuleToCompile = new ListBuffer[InferenceRule]()
+    val functionCallRuleToCompile = new ListBuffer[FunctionCallRule]()
     statements foreach (_ match {
-      case s: ExtractionRule   => extractionRules += s
-      case s: FunctionCallRule => functionCallRules += s
-      case s: InferenceRule    => inferenceRules += s
+      case s: ExtractionRule   => extractionRuleToCompile += s
+      case s: FunctionCallRule => functionCallRuleToCompile += s
+      case s: InferenceRule    => inferenceRuleToCompile += s
       case _                   => 
     })
 
-    val extractionRulesGroup   = extractionRules.groupBy(_.q.head.name)
-    val functionCallRulesGroup = functionCallRules.groupBy(_.input)
-    val inferenceRulesGroup    = inferenceRules.groupBy(_.q.head.name)
+    extractionRuleGroupByHead     = extractionRuleToCompile.toList.groupBy(_.q.head.name)
+    inferenceRuleGroupByHead      = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
+    functionCallRuleGroupByInput  = functionCallRuleToCompile.toList.groupBy(_.input)
+    functionCallRuleGroupByOutput = functionCallRuleToCompile.toList.groupBy(_.output)
+  }
 
-    extractionRulesGroup   foreach {keyVal => visible += keyVal._2(0)}
-    functionCallRulesGroup foreach {keyVal => visible += keyVal._2(0)}
-    inferenceRulesGroup    foreach {keyVal => visible += keyVal._2(0)}
+  // Analyze the block visibility among statements 
+  def analyzeVisible(statements: List[Statement]) = {
+    extractionRuleGroupByHead   foreach {keyVal => visible += keyVal._2(0)}
+    functionCallRuleGroupByInput foreach {keyVal => visible += keyVal._2(0)}
+    inferenceRuleGroupByHead    foreach {keyVal => visible += keyVal._2(0)}
   }
 
   // Analyze the dependency between statements and construct a graph.
   def analyzeDependency(statements: List[Statement]) = {
-    // first map head names to the actual statement
-    val extractionRuleByHeadName   = new ListBuffer[ExtractionRule]()
-    val inferenceRuleByHeadName    = new ListBuffer[InferenceRule]()
-    val functionCallRuleByHeadName = new ListBuffer[FunctionCallRule]()
-    
-    statements foreach {
-      case s: ExtractionRule   => extractionRuleByHeadName += s
-      case s: FunctionCallRule => functionCallRuleByHeadName += s
-      case s: InferenceRule    => inferenceRuleByHeadName += s
-      case _                   => 
-    }
+    var stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++ functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
-    val eByHeadNameGroup = extractionRuleByHeadName.toList.groupBy(_.q.head.name)
-    val iByHeadNameGroup = inferenceRuleByHeadName.toList.groupBy(_.q.head.name)
-    val fByHeadNameGroup = functionCallRuleByHeadName.toList.groupBy(_.output)
-
-    var stmtByHeadName = (eByHeadNameGroup.toSeq ++ iByHeadNameGroup.toSeq ++ fByHeadNameGroup.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
-    // var stmtByHeadName = new HashMap[String, Statement]()
-    // statements foreach {
-    //   case e : ExtractionRule => stmtByHeadName += { e.q.head.name -> e }
-    //   case f : FunctionCallRule   => stmtByHeadName += { f.output      -> f }
-    //   case w : InferenceRule  => stmtByHeadName += { w.q.head.name -> w }
-    //   case _ =>
-    // }
-    // then, look at the body of each statement to construct a dependency graph
+    // Look at the body of each statement to construct a dependency graph
     statements foreach {
       case f : FunctionCallRule => dependencies += { f -> ((        Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case e : ExtractionRule   => dependencies += { e -> ((e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
@@ -280,16 +271,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
 
-  // Dispatch to the corresponding compile function
-  // def compile(stmts: List[Statement], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = stmts(0) match {
-  //   case s: ExtractionRule   => compileE(stmts, ss, isIncremental)
-  //   case s: FunctionCallRule => compileF(stmts, ss, isIncremental)
-  //   case s: InferenceRule    => compileI(stmts, ss, isIncremental)
-  //   case _                   => List()  // defaults to compiling into empty block
-  // }
-
   // Generate extraction rule part for deepdive
-  def compileE(stmts: List[ExtractionRule], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
+  def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
       // Generate the body of the query.
@@ -299,11 +282,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, stmt.q, true)
       }
 
-      val variableColsStr = if (variableCols.length > 0) Some(variableCols.mkString(", ")) else None
-
-      val selectStr = (List(variableColsStr) flatMap (u => u)).mkString(", ")
-
-      val ddCount = if (isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+      val selectStr = variableCols.mkString(", ")
+      val ddCount = if (ss.isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
       val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
 
       inputQueries += s"""
@@ -324,7 +304,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     List(extractor)
   }
 
-  def compileF(stmts: List[FunctionCallRule], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
+  def compileFunctionCallRules(stmts: List[FunctionCallRule], ss: CompilationState): CompiledBlocks = {
     var extractors = new ListBuffer[String]()
     for (stmt <- stmts) {
       val inputQuery = s"""
@@ -358,7 +338,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   }
 
   // generate inference rule part for deepdive
-  def compileI(stmts: List[InferenceRule], ss: CompilationState, isIncremental: Boolean): CompiledBlocks = {
+  def compileInferenceRules(stmts: List[InferenceRule], ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
     val qs = new QuerySchema( stmts(0).q )
     // node query
@@ -373,7 +353,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val name  = ss.resolveName(qs.getVar(z.supervision))
         val labelCol = s"R${index}.${name}"
         val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-        val ddCount = if (isIncremental) ( z.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        val ddCount = if (ss.isIncremental) ( z.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
         val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
 
         inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
@@ -396,7 +376,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     if (ss.isQueryTerm(stmts(0).q.head.name))
       blocks :::= compileNodeRule(stmts, qs, ss)
 
-    val inferenceRuleToCompileGroup    = stmts.groupBy(_.q.head.name)
+    val inferenceRuleGroupByHead    = stmts.groupBy(_.q.head.name)
 
     for (stmt <- stmts) {
       // edge query
@@ -414,9 +394,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
       }
 
-      val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatMap (u => u)).mkString(", ")
+      val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatten).mkString(", ")
 
-      val ddCount = if (isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+      val ddCount = if (ss.isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
       val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
 
       // factor input query
@@ -489,27 +469,12 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       else parsedProgram
 
     // take an initial pass to analyze the parsed program
-    val state = new CompilationState( programToCompile )
-
-    // compile compilation states by head name based on type
-    val extractionRuleToCompile = new ListBuffer[ExtractionRule]()
-    val inferenceRuleToCompile = new ListBuffer[InferenceRule]()
-    val functionCallRuleToCompile = new ListBuffer[FunctionCallRule]()
-    programToCompile foreach (_ match {
-      case s: ExtractionRule   => extractionRuleToCompile += s
-      case s: FunctionCallRule => functionCallRuleToCompile += s
-      case s: InferenceRule    => inferenceRuleToCompile += s
-      case _                   => 
-    })
-
-    val extractionRuleToCompileGroup   = extractionRuleToCompile.groupBy(_.q.head.name)
-    val inferenceRuleToCompileGroup    = inferenceRuleToCompile.groupBy(_.q.head.name)
-    val functionCallRuleToCompileGroup = functionCallRuleToCompile.groupBy(_.input)
+    val state = new CompilationState( programToCompile, config )
 
     val body = new ListBuffer[String]()
-    extractionRuleToCompileGroup   foreach {keyVal => body ++= compileE(keyVal._2.toList, state, config.isIncremental)}
-    functionCallRuleToCompileGroup foreach {keyVal => body ++= compileF(keyVal._2.toList, state, config.isIncremental)}
-    inferenceRuleToCompileGroup    foreach {keyVal => body ++= compileI(keyVal._2.toList, state, config.isIncremental)}
+    state.extractionRuleGroupByHead    foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
+    state.functionCallRuleGroupByInput foreach {keyVal => body ++= compileFunctionCallRules(keyVal._2, state)}
+    state.inferenceRuleGroupByHead     foreach {keyVal => body ++= compileInferenceRules(keyVal._2, state)}
     
     // compile the program into blocks of application.conf
     val blocks = (

From f7e7f712de07d7eb280dd2da54ad9debca5136f0 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 15 May 2015 01:50:00 -0700
Subject: [PATCH 071/347] remove variable column string to make the head body
 only contains unique keys

---
 DeepDiveLogCompiler.scala | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index eddc6b10d..13f08c214 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -386,7 +386,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val index = stmt.q.body.length + 1
       val qs2 = new QuerySchema( fakeCQ )
       val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
-      val variableColsStr = Some(s"""R0.label AS "${stmt.q.head.name}.R0.label" """)
 
       // weight string
       val uwStr = stmt.weights match {
@@ -394,7 +393,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
       }
 
-      val selectStr = (List(variableIdsStr, variableColsStr, uwStr) flatten).mkString(", ")
+      val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
 
       val ddCount = if (ss.isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
       val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""

From 8bdafbadf14490155bc492b1ab6bbdc7e90a49b5 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Sat, 16 May 2015 00:10:36 -0700
Subject: [PATCH 072/347] add dd_new table in delta deriver

---
 DeepDiveLogDeltaDeriver.scala | 75 ++++++++++++++++++++++++++---------
 1 file changed, 56 insertions(+), 19 deletions(-)

diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
index 51f4242f1..336a6429d 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -4,6 +4,7 @@ object DeepDiveLogDeltaDeriver{
 
   // Default prefix for incremental tables
   val deltaPrefix = "dd_delta_"
+  val newPrefix = "dd_new_"
 
   def transfer(stmt: Statement): List[Statement] = stmt match {
     case s: SchemaDeclaration   => transfer(s)
@@ -17,12 +18,26 @@ object DeepDiveLogDeltaDeriver{
   // keep the original scheme and create one delta scheme
   def transfer(stmt: SchemaDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
+    // Origin table
     incrementalStatement += stmt
-    var newTerms = new ListBuffer[Variable]()
+    // Delta table
+    var deltaTerms = new ListBuffer[Variable]()
+    for (term <- stmt.a.terms) {
+      deltaTerms += Variable(term.varName, deltaPrefix + term.relName, term.index)
+    }
+    var deltaStmt = SchemaDeclaration(Attribute(deltaPrefix + stmt.a.name, deltaTerms.toList, stmt.a.types), stmt.isQuery)
+    incrementalStatement += deltaStmt
+    // New table
+    val newTerms = new ListBuffer[Variable]()
     for (term <- stmt.a.terms) {
-      newTerms += Variable(term.varName, deltaPrefix + term.relName, term.index)
+      newTerms += Variable(term.varName, newPrefix + term.relName, term.index)
+    }
+    var newStmt = SchemaDeclaration(Attribute(newPrefix + stmt.a.name, newTerms.toList, stmt.a.types), stmt.isQuery)
+    incrementalStatement += newStmt
+    if (!stmt.isQuery) {
+      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), List(Atom(stmt.a.name, stmt.a.terms.toList))))
+      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), List(Atom(deltaStmt.a.name, deltaStmt.a.terms.toList))))
     }
-    incrementalStatement += SchemaDeclaration(Attribute(deltaPrefix + stmt.a.name, newTerms.toList, stmt.a.types), stmt.isQuery)
     incrementalStatement.toList
   }
 
@@ -64,26 +79,37 @@ object DeepDiveLogDeltaDeriver{
       newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
     }
     var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
-
-    var deltaStmtCqBody = new ListBuffer[Atom]()
+    // dd delta table from dd_delta_ table
+    var ddDeltaStmtCqBody = new ListBuffer[Atom]()
     for (stmtCqBody <- stmt.q.body) { // List[Atom]
       var stmtCqBodyTerms = new ListBuffer[Variable]()
       for (bodyTerm <- stmtCqBody.terms) {
         stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
       }
-      deltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
+      ddDeltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
+    }
+    // dd new body from dd_new_ table
+    var ddNewStmtCqBody = new ListBuffer[Atom]()
+    for (stmtCqBody <- stmt.q.body) { // List[Atom]
+      var stmtCqBodyTerms = new ListBuffer[Variable]()
+      for (bodyTerm <- stmtCqBody.terms) {
+        stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
+      }
+      ddNewStmtCqBody += Atom(newPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
     }
 
-    // New body
+    // New statement
     var i = 0
     var j = 0
-    for (i <- 1 to ((1 << stmt.q.body.length) - 1)) {
+    for (i <- 0 to (stmt.q.body.length - 1)) {
       var newStmtCqBody = new ListBuffer[Atom]()
       for (j <- 0 to (stmt.q.body.length - 1)) {
-        if ((i & (1 << j)) == 0)
+        if (j > i)
           newStmtCqBody += stmt.q.body(j)
-        else
-          newStmtCqBody += deltaStmtCqBody(j)
+        else if (j < i)
+          newStmtCqBody += ddNewStmtCqBody(j)
+          else if (j == i)
+            newStmtCqBody += ddDeltaStmtCqBody(j)
       }
       incrementalStatement += ExtractionRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList))
     }
@@ -109,26 +135,37 @@ object DeepDiveLogDeltaDeriver{
       newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
     }
     var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
-
-    var deltaStmtCqBody = new ListBuffer[Atom]()
+    // dd delta table from dd_delta_ table
+    var ddDeltaStmtCqBody = new ListBuffer[Atom]()
     for (stmtCqBody <- stmt.q.body) { // List[Atom]
       var stmtCqBodyTerms = new ListBuffer[Variable]()
       for (bodyTerm <- stmtCqBody.terms) {
         stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
       }
-      deltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
+      ddDeltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
+    }
+    // dd new body from dd_new_ table
+    var ddNewStmtCqBody = new ListBuffer[Atom]()
+    for (stmtCqBody <- stmt.q.body) { // List[Atom]
+      var stmtCqBodyTerms = new ListBuffer[Variable]()
+      for (bodyTerm <- stmtCqBody.terms) {
+        stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
+      }
+      ddNewStmtCqBody += Atom(newPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
     }
 
-    // New body
+    // New statement
     var i = 0
     var j = 0
-    for (i <- 1 to ((1 << stmt.q.body.length) - 1)) {
+    for (i <- 0 to (stmt.q.body.length - 1)) {
       var newStmtCqBody = new ListBuffer[Atom]()
       for (j <- 0 to (stmt.q.body.length - 1)) {
-        if ((i & (1 << j)) == 0)
+        if (j > i)
           newStmtCqBody += stmt.q.body(j)
-        else
-          newStmtCqBody += deltaStmtCqBody(j)
+        else if (j < i)
+          newStmtCqBody += ddNewStmtCqBody(j)
+          else if (j == i)
+            newStmtCqBody += ddDeltaStmtCqBody(j)
       }
       incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList), stmt.weights, stmt.supervision)
     }

From 2dafd684b1a399133ed41e449648a85a8becaf96 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Sat, 16 May 2015 06:15:06 -0700
Subject: [PATCH 073/347] rename funciton to transform

---
 DeepDiveLogDeltaDeriver.scala | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
index 336a6429d..bc79f1c11 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -6,17 +6,17 @@ object DeepDiveLogDeltaDeriver{
   val deltaPrefix = "dd_delta_"
   val newPrefix = "dd_new_"
 
-  def transfer(stmt: Statement): List[Statement] = stmt match {
-    case s: SchemaDeclaration   => transfer(s)
-    case s: FunctionDeclaration => transfer(s)
-    case s: ExtractionRule      => transfer(s)
-    case s: FunctionCallRule    => transfer(s)
-    case s: InferenceRule       => transfer(s)
+  def transform(stmt: Statement): List[Statement] = stmt match {
+    case s: SchemaDeclaration   => transform(s)
+    case s: FunctionDeclaration => transform(s)
+    case s: ExtractionRule      => transform(s)
+    case s: FunctionCallRule    => transform(s)
+    case s: InferenceRule       => transform(s)
   }
 
   // Incremental scheme declaration,
   // keep the original scheme and create one delta scheme
-  def transfer(stmt: SchemaDeclaration): List[Statement] = {
+  def transform(stmt: SchemaDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     // Origin table
     incrementalStatement += stmt
@@ -26,6 +26,7 @@ object DeepDiveLogDeltaDeriver{
       deltaTerms += Variable(term.varName, deltaPrefix + term.relName, term.index)
     }
     var deltaStmt = SchemaDeclaration(Attribute(deltaPrefix + stmt.a.name, deltaTerms.toList, stmt.a.types), stmt.isQuery)
+    
     incrementalStatement += deltaStmt
     // New table
     val newTerms = new ListBuffer[Variable]()
@@ -43,7 +44,7 @@ object DeepDiveLogDeltaDeriver{
 
   // Incremental function declaration,
   // create one delta function scheme based on original function scheme
-  def transfer(stmt: FunctionDeclaration): List[Statement] = {
+  def transform(stmt: FunctionDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     var newTerms = new ListBuffer[Variable]()
     var newInputType: RelationType = stmt.inputType match {
@@ -70,7 +71,7 @@ object DeepDiveLogDeltaDeriver{
 
   // Incremental extraction rule,
   // create delta rules based on original extraction rule
-  def transfer(stmt: ExtractionRule): List[Statement] = {
+  def transform(stmt: ExtractionRule): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     
     // New head
@@ -118,7 +119,7 @@ object DeepDiveLogDeltaDeriver{
 
   // Incremental function call rule,
   // modify function input and output
-  def transfer(stmt: FunctionCallRule): List[Statement] = {
+  def transform(stmt: FunctionCallRule): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     incrementalStatement += FunctionCallRule(deltaPrefix + stmt.input, deltaPrefix + stmt.output, stmt.function)
     incrementalStatement.toList
@@ -126,7 +127,7 @@ object DeepDiveLogDeltaDeriver{
 
   // Incremental inference rule,
   // create delta rules based on original extraction rule
-  def transfer(stmt: InferenceRule): List[Statement] = {
+  def transform(stmt: InferenceRule): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     
     // New head
@@ -175,7 +176,7 @@ object DeepDiveLogDeltaDeriver{
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
     var incrementalProgram = new ListBuffer[Statement]()
     for (x <- program) {
-      incrementalProgram = incrementalProgram ++ transfer(x)
+      incrementalProgram = incrementalProgram ++ transform(x)
     }
     incrementalProgram.toList
   }

From 51075ea272a8478eb74bfb501d148426047b0ca9 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Sat, 16 May 2015 06:15:42 -0700
Subject: [PATCH 074/347] update new example output

---
 ...pouse_incremental_example.compile.expected | 233 ++++++++++++------
 .../spouse_incremental_example.print.expected | 193 +++++++++------
 2 files changed, 263 insertions(+), 163 deletions(-)

diff --git a/examples/spouse_incremental_example.compile.expected b/examples/spouse_incremental_example.compile.expected
index 4e009898a..d376e5097 100644
--- a/examples/spouse_incremental_example.compile.expected
+++ b/examples/spouse_incremental_example.compile.expected
@@ -15,7 +15,73 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.extraction_rule_51 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
+        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
+        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+        FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_28" ,  "extraction_rule_8" ,  "extraction_rule_36" ,  "extraction_rule_13" ,  "extraction_rule_18" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_13 {
+        sql: """ DROP VIEW IF EXISTS dd_new_people_mentions;
+        CREATE VIEW dd_new_people_mentions AS 
+        SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.start_position AS "people_mentions.R0.start_position" , R0.length AS "people_mentions.R0.length" , R0.text AS "people_mentions.R0.text" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.dd_count AS "people_mentions.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM people_mentions R0
+         UNION 
+        SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.start_position AS "dd_delta_people_mentions.R0.start_position" , R0.length AS "dd_delta_people_mentions.R0.length" , R0.text AS "dd_delta_people_mentions.R0.text" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.dd_count AS "dd_delta_people_mentions.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_people_mentions R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_28" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_32 {
+        sql: """ DROP VIEW IF EXISTS dd_new_ext_people_input;
+        CREATE VIEW dd_new_ext_people_input AS 
+        SELECT R0.sentence_id AS "ext_people_input.R0.sentence_id" , R0.words AS "ext_people_input.R0.words" , R0.ner_tags AS "ext_people_input.R0.ner_tags" , R0.dd_count AS "ext_people_input.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM ext_people_input R0
+         UNION 
+        SELECT R0.sentence_id AS "dd_delta_ext_people_input.R0.sentence_id" , R0.words AS "dd_delta_ext_people_input.R0.words" , R0.ner_tags AS "dd_delta_ext_people_input.R0.ner_tags" , R0.dd_count AS "dd_delta_ext_people_input.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_ext_people_input R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_34" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ DROP VIEW IF EXISTS dd_new_articles;
+        CREATE VIEW dd_new_articles AS 
+        SELECT R0.article_id AS "articles.R0.article_id" , R0.text AS "articles.R0.text" , R0.dd_count AS "articles.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM articles R0
+         UNION 
+        SELECT R0.article_id AS "dd_delta_articles.R0.article_id" , R0.text AS "dd_delta_articles.R0.text" , R0.dd_count AS "dd_delta_articles.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_articles R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_34 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
         SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
@@ -27,105 +93,123 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_27 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
-        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, dd_delta_has_spouse_candidates R1, dd_delta_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+      deepdive.extraction.extractors.extraction_rule_18 {
+        sql: """ DROP VIEW IF EXISTS dd_new_has_spouse_candidates;
+        CREATE VIEW dd_new_has_spouse_candidates AS 
+        SELECT R0.person1_id AS "has_spouse_candidates.R0.person1_id" , R0.person2_id AS "has_spouse_candidates.R0.person2_id" , R0.sentence_id AS "has_spouse_candidates.R0.sentence_id" , R0.description AS "has_spouse_candidates.R0.description" , R0.relation_id AS "has_spouse_candidates.R0.relation_id" , R0.is_true AS "has_spouse_candidates.R0.is_true" , R0.dd_count AS "has_spouse_candidates.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM has_spouse_candidates R0
+         UNION 
+        SELECT R0.person1_id AS "dd_delta_has_spouse_candidates.R0.person1_id" , R0.person2_id AS "dd_delta_has_spouse_candidates.R0.person2_id" , R0.sentence_id AS "dd_delta_has_spouse_candidates.R0.sentence_id" , R0.description AS "dd_delta_has_spouse_candidates.R0.description" , R0.relation_id AS "dd_delta_has_spouse_candidates.R0.relation_id" , R0.is_true AS "dd_delta_has_spouse_candidates.R0.is_true" , R0.dd_count AS "dd_delta_has_spouse_candidates.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse_candidates R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_36" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_49 {
+        sql: """ DROP VIEW IF EXISTS dd_new_ext_has_spouse_features_input;
+        CREATE VIEW dd_new_ext_has_spouse_features_input AS 
+        SELECT R0.words AS "ext_has_spouse_features_input.R0.words" , R0.relation_id AS "ext_has_spouse_features_input.R0.relation_id" , R0.p1_start_position AS "ext_has_spouse_features_input.R0.p1_start_position" , R0.p1_length AS "ext_has_spouse_features_input.R0.p1_length" , R0.p2_start_position AS "ext_has_spouse_features_input.R0.p2_start_position" , R0.p2_length AS "ext_has_spouse_features_input.R0.p2_length" , R0.dd_count AS "ext_has_spouse_features_input.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM ext_has_spouse_features_input R0
+         UNION 
+        SELECT R0.words AS "dd_delta_ext_has_spouse_features_input.R0.words" , R0.relation_id AS "dd_delta_ext_has_spouse_features_input.R0.relation_id" , R0.p1_start_position AS "dd_delta_ext_has_spouse_features_input.R0.p1_start_position" , R0.p1_length AS "dd_delta_ext_has_spouse_features_input.R0.p1_length" , R0.p2_start_position AS "dd_delta_ext_has_spouse_features_input.R0.p2_start_position" , R0.p2_length AS "dd_delta_ext_has_spouse_features_input.R0.p2_length" , R0.dd_count AS "dd_delta_ext_has_spouse_features_input.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_ext_has_spouse_features_input R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_51" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_40 {
+        sql: """ DROP VIEW IF EXISTS dd_new_ext_has_spouse_input;
+        CREATE VIEW dd_new_ext_has_spouse_input AS 
+        SELECT R0.sentence_id AS "ext_has_spouse_input.R0.sentence_id" , R0.p1_id AS "ext_has_spouse_input.R0.p1_id" , R0.p1_text AS "ext_has_spouse_input.R0.p1_text" , R0.p2_id AS "ext_has_spouse_input.R0.p2_id" , R0.p2_text AS "ext_has_spouse_input.R0.p2_text" , R0.dd_count AS "ext_has_spouse_input.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM ext_has_spouse_input R0
+         UNION 
+        SELECT R0.sentence_id AS "dd_delta_ext_has_spouse_input.R0.sentence_id" , R0.p1_id AS "dd_delta_ext_has_spouse_input.R0.p1_id" , R0.p1_text AS "dd_delta_ext_has_spouse_input.R0.p1_text" , R0.p2_id AS "dd_delta_ext_has_spouse_input.R0.p2_id" , R0.p2_text AS "dd_delta_ext_has_spouse_input.R0.p2_text" , R0.dd_count AS "dd_delta_ext_has_spouse_input.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_ext_has_spouse_input R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_42" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ DROP VIEW IF EXISTS dd_new_has_spouse_features;
+        CREATE VIEW dd_new_has_spouse_features AS 
+        SELECT R0.relation_id AS "has_spouse_features.R0.relation_id" , R0.feature AS "has_spouse_features.R0.feature" , R0.dd_count AS "has_spouse_features.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM has_spouse_features R0
+         UNION 
+        SELECT R0.relation_id AS "dd_delta_has_spouse_features.R0.relation_id" , R0.feature AS "dd_delta_has_spouse_features.R0.feature" , R0.dd_count AS "dd_delta_has_spouse_features.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse_features R0
+        
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_17" ,  "extraction_rule_12" ]
+          dependencies: [ "extraction_rule_45" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_8 {
+        sql: """ DROP VIEW IF EXISTS dd_new_sentences;
+        CREATE VIEW dd_new_sentences AS 
+        SELECT R0.document_id AS "sentences.R0.document_id" , R0.sentence AS "sentences.R0.sentence" , R0.words AS "sentences.R0.words" , R0.lemma AS "sentences.R0.lemma" , R0.pos_tags AS "sentences.R0.pos_tags" , R0.dependencies AS "sentences.R0.dependencies" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.sentence_offset AS "sentences.R0.sentence_offset" , R0.sentence_id AS "sentences.R0.sentence_id" , R0.dd_count AS "sentences.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM sentences R0
+         UNION 
+        SELECT R0.document_id AS "dd_delta_sentences.R0.document_id" , R0.sentence AS "dd_delta_sentences.R0.sentence" , R0.words AS "dd_delta_sentences.R0.words" , R0.lemma AS "dd_delta_sentences.R0.lemma" , R0.pos_tags AS "dd_delta_sentences.R0.pos_tags" , R0.dependencies AS "dd_delta_sentences.R0.dependencies" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.sentence_offset AS "dd_delta_sentences.R0.sentence_offset" , R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.dd_count AS "dd_delta_sentences.R0.dd_count" , R0.dd_count AS "dd_count" 
+        FROM dd_delta_sentences R0
+        
+        """
+        style: "sql_extractor"
+          
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_20 {
+      deepdive.extraction.extractors.extraction_rule_42 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
         SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
         FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id  UNION 
-        SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
-        FROM people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION 
-        SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
-        FROM dd_delta_people_mentions R0, dd_delta_people_mentions R1
+        SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+        FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_12" ]
+          dependencies: [ "extraction_rule_28" ,  "extraction_rule_13" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_12 {
+        deepdive.extraction.extractors.extraction_rule_28 {
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ]
+          dependencies: [ "extraction_rule_34" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_24 {
+        deepdive.extraction.extractors.extraction_rule_45 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_51" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_17 {
+        deepdive.extraction.extractors.extraction_rule_36 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_20" ]
+          dependencies: [ "extraction_rule_42" ]
         }
       
 
@@ -136,21 +220,18 @@
         FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
          UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM has_spouse_candidates R0, dd_delta_has_spouse_features R1
-        WHERE R1.relation_id = R0.relation_id 
-         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_delta_has_spouse_candidates R0, dd_delta_has_spouse_features R1
+        FROM dd_new_has_spouse_candidates R0, dd_delta_has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
         
         """
         style: "sql_extractor"
-        dependencies: [ "extraction_rule_17" ,  "extraction_rule_24" ]
+        dependencies: [ "extraction_rule_36" ,  "extraction_rule_18" ,  "extraction_rule_45" ]
       }
     
 
         deepdive.inference.factors.factor_dd_delta_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
         FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_delta_has_spouse.R0.label)"
@@ -160,18 +241,8 @@
 
         deepdive.inference.factors.factor_dd_delta_has_spouse {
           input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
-          weight: "?(dd_delta_has_spouse_features.R2.feature)"
-        }
-      
-
-        deepdive.inference.factors.factor_dd_delta_has_spouse {
-          input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R0.label AS "dd_delta_has_spouse.R0.label" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+        FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_delta_has_spouse.R0.label)"
           weight: "?(dd_delta_has_spouse_features.R2.feature)"
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_incremental_example.print.expected
index 406f28b4a..93fe809c5 100644
--- a/examples/spouse_incremental_example.print.expected
+++ b/examples/spouse_incremental_example.print.expected
@@ -6,6 +6,16 @@ dd_delta_articles(article_id text,
                   text text,
                   dd_count int).
 
+dd_new_articles(article_id text,
+                text text,
+                dd_count int).
+
+dd_new_articles(article_id, text, dd_count) :-
+    articles(article_id, text, dd_count).
+
+dd_new_articles(article_id, text, dd_count) :-
+    dd_delta_articles(article_id, text, dd_count).
+
 sentences(document_id text,
           sentence text,
           words text[],
@@ -28,6 +38,23 @@ dd_delta_sentences(document_id text,
                    sentence_id text,
                    dd_count int).
 
+dd_new_sentences(document_id text,
+                 sentence text,
+                 words text[],
+                 lemma text[],
+                 pos_tags text[],
+                 dependencies text[],
+                 ner_tags text[],
+                 sentence_offset int,
+                 sentence_id text,
+                 dd_count int).
+
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count) :-
+    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count).
+
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count) :-
+    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count).
+
 people_mentions(sentence_id text,
                 start_position int,
                 length int,
@@ -42,6 +69,19 @@ dd_delta_people_mentions(sentence_id text,
                          mention_id text,
                          dd_count int).
 
+dd_new_people_mentions(sentence_id text,
+                       start_position int,
+                       length int,
+                       text text,
+                       mention_id text,
+                       dd_count int).
+
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count) :-
+    people_mentions(sentence_id, start_position, length, text, mention_id, dd_count).
+
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count) :-
+    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count).
+
 has_spouse_candidates(person1_id text,
                       person2_id text,
                       sentence_id text,
@@ -58,6 +98,20 @@ dd_delta_has_spouse_candidates(person1_id text,
                                is_true boolean,
                                dd_count int).
 
+dd_new_has_spouse_candidates(person1_id text,
+                             person2_id text,
+                             sentence_id text,
+                             description text,
+                             relation_id text,
+                             is_true boolean,
+                             dd_count int).
+
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count) :-
+    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count).
+
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count) :-
+    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count).
+
 has_spouse_features(relation_id text,
                     feature text,
                     dd_count int).
@@ -66,10 +120,22 @@ dd_delta_has_spouse_features(relation_id text,
                              feature text,
                              dd_count int).
 
+dd_new_has_spouse_features(relation_id text,
+                           feature text,
+                           dd_count int).
+
+dd_new_has_spouse_features(relation_id, feature, dd_count) :-
+    has_spouse_features(relation_id, feature, dd_count).
+
+dd_new_has_spouse_features(relation_id, feature, dd_count) :-
+    dd_delta_has_spouse_features(relation_id, feature, dd_count).
+
 has_spouse?(relation_id text).
 
 dd_delta_has_spouse?(relation_id text).
 
+dd_new_has_spouse?(relation_id text).
+
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
 ext_people_input(sentence_id text,
@@ -82,6 +148,17 @@ dd_delta_ext_people_input(sentence_id text,
                           ner_tags text[],
                           dd_count int).
 
+dd_new_ext_people_input(sentence_id text,
+                        words text[],
+                        ner_tags text[],
+                        dd_count int).
+
+dd_new_ext_people_input(sentence_id, words, ner_tags, dd_count) :-
+    ext_people_input(sentence_id, words, ner_tags, dd_count).
+
+dd_new_ext_people_input(sentence_id, words, ner_tags, dd_count) :-
+    dd_delta_ext_people_input(sentence_id, words, ner_tags, dd_count).
+
 dd_delta_ext_people_input(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
@@ -107,16 +184,25 @@ dd_delta_ext_has_spouse_input(sentence_id text,
                               p2_text text,
                               dd_count int).
 
+dd_new_ext_has_spouse_input(sentence_id text,
+                            p1_id text,
+                            p1_text text,
+                            p2_id text,
+                            p2_text text,
+                            dd_count int).
+
+dd_new_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count) :-
+    ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count).
+
+dd_new_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count) :-
+    dd_delta_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count).
+
 dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
 dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
-    people_mentions(s, a, b, p1_text, p1_id),
-    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
-
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
+    dd_new_people_mentions(s, a, b, p1_text, p1_id),
     dd_delta_people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse
@@ -143,94 +229,42 @@ dd_delta_ext_has_spouse_features_input(words text[],
                                        p2_length int,
                                        dd_count int).
 
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
+dd_new_ext_has_spouse_features_input(words text[],
+                                     relation_id text,
+                                     p1_start_position int,
+                                     p1_length int,
+                                     p2_start_position int,
+                                     p2_length int,
+                                     dd_count int).
 
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
+dd_new_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count) :-
+    ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count).
 
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
+dd_new_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count) :-
+    dd_delta_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
     dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
     people_mentions(s, p2idx, p2len, l, person2_id).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
 
 function ext_has_spouse_features
@@ -245,12 +279,7 @@ dd_delta_has_spouse(rid) :-
   weight = f
   label = l.
 dd_delta_has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l),
-    dd_delta_has_spouse_features(rid, f)
-  weight = f
-  label = l.
-dd_delta_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l.

From 6e42fe4c9383c0acbf4fee26f021c80e17dc70fd Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Mon, 18 May 2015 23:41:27 -0700
Subject: [PATCH 075/347] modify spouse example

---
 examples/spouse_example.compile.expected           | 2 +-
 examples/spouse_example.ddl                        | 3 ++-
 examples/spouse_example.print.expected             | 3 ++-
 examples/spouse_incremental_example.ddl            | 3 ++-
 examples/spouse_incremental_example.print.expected | 6 ++++--
 5 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/examples/spouse_example.compile.expected b/examples/spouse_example.compile.expected
index 10a58e063..2d2b39a35 100644
--- a/examples/spouse_example.compile.expected
+++ b/examples/spouse_example.compile.expected
@@ -96,7 +96,7 @@
 
         deepdive.inference.factors.factor_has_spouse {
           input_query: """
-        SELECT R0.id AS "has_spouse.R0.id" , R0.label AS "has_spouse.R0.label" , R2.feature AS "has_spouse_features.R2.feature"  
+        SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
         FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index ac5546486..94a0266e6 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -92,4 +92,5 @@ has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
-label = l.
+label = l
+rule = imply.
diff --git a/examples/spouse_example.print.expected b/examples/spouse_example.print.expected
index 4aedd134f..ba4d0d933 100644
--- a/examples/spouse_example.print.expected
+++ b/examples/spouse_example.print.expected
@@ -87,4 +87,5 @@ has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
-  label = l.
+  label = l
+  rule = imply.
diff --git a/examples/spouse_incremental_example.ddl b/examples/spouse_incremental_example.ddl
index cf467ac8c..11503d7d9 100644
--- a/examples/spouse_incremental_example.ddl
+++ b/examples/spouse_incremental_example.ddl
@@ -100,4 +100,5 @@ has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
-label = l.
+label = l
+rule = imply.
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_incremental_example.print.expected
index 93fe809c5..b47c1eb17 100644
--- a/examples/spouse_incremental_example.print.expected
+++ b/examples/spouse_incremental_example.print.expected
@@ -277,9 +277,11 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
-  label = l.
+  label = l
+  rule = imply.
 dd_delta_has_spouse(rid) :-
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
-  label = l.
+  label = l
+  rule = imply.

From 6ba3030c8c5f1989a4bfa2bfcd82cc23a27265b1 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Mon, 18 May 2015 23:42:06 -0700
Subject: [PATCH 076/347] add rule in inference rule to support different rules

---
 DeepDiveLogCompiler.scala      |  4 ++--
 DeepDiveLogDeltaDeriver.scala  |  2 +-
 DeepDiveLogParser.scala        | 13 ++++++++-----
 DeepDiveLogPrettyPrinter.scala |  4 +++-
 4 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 13f08c214..31fcc264b 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -99,7 +99,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
         }
       case ExtractionRule(_) => ()
-      case InferenceRule(_,_,_) => ()
+      case InferenceRule(_,_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case FunctionCallRule(_,_,_) => ()
     }
@@ -446,7 +446,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
-      case InferenceRule(q, weights, supervision) =>
+      case InferenceRule(q, weights, supervision, rule) =>
         val qs = new QuerySchema(q)
         schema += s"${q.head.name}.label: Boolean"
       case _ => ()
diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
index bc79f1c11..a80045d47 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -168,7 +168,7 @@ object DeepDiveLogDeltaDeriver{
           else if (j == i)
             newStmtCqBody += ddDeltaStmtCqBody(j)
       }
-      incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList), stmt.weights, stmt.supervision)
+      incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList), stmt.weights, stmt.supervision, stmt.rule)
     }
     incrementalStatement.toList
   }
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index d48732625..7329f56a2 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -36,7 +36,7 @@ case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statem
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String) extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, rule : String) extends Statement // Weighted rule
 
 
 // Parser
@@ -58,6 +58,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   def variableName = ident
   def functionName = ident
+  def ruleType = ident
 
   def columnDeclaration: Parser[Column] =
     columnName ~ columnType ^^ {
@@ -144,14 +145,16 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def supervision = "label" ~> "=" ~> variableName
 
+  def rule = "rule" ~> "=" ~> ruleType
+
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ supervision
+    ( conjunctiveQuery ~ factorWeight ~ supervision ~ rule
     ) ^^ {
-      case (q ~ weight ~ supervision) =>
-        InferenceRule(q, weight, supervision)
+      case (q ~ weight ~ supervision ~ rule) =>
+        InferenceRule(q, weight, supervision, rule)
     }
 
-  // rules or schema elements in aribitrary order
+  // rules or schema elements in arbitrary order
   def statement : Parser[Statement] = ( schemaDeclaration
                                       | inferenceRule
                                       | extractionRule
diff --git a/DeepDiveLogPrettyPrinter.scala b/DeepDiveLogPrettyPrinter.scala
index 1bfe0fe8e..d387d9fc8 100644
--- a/DeepDiveLogPrettyPrinter.scala
+++ b/DeepDiveLogPrettyPrinter.scala
@@ -74,7 +74,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     ( if (stmt.supervision == null) ""
       else "\n  label = " + stmt.supervision
     ) +
-    "."
+    ( if (stmt.rule == null) ""
+      else "\n  rule = " + stmt.rule
+    ) + "."
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {

From cf493e2993e1574e8223e201c575e37474826cce Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 19 May 2015 17:40:47 -0700
Subject: [PATCH 077/347] Rebases incremental test cases to the original
 example

---
 ...ouse_example.compile-incremental.expected} |   0
 ...spouse_example.print-incremental.expected} |   0
 examples/spouse_incremental_example.ddl       | 103 ------------------
 test/per-example.bats                         |  23 +++-
 4 files changed, 20 insertions(+), 106 deletions(-)
 rename examples/{spouse_incremental_example.compile.expected => spouse_example.compile-incremental.expected} (100%)
 rename examples/{spouse_incremental_example.print.expected => spouse_example.print-incremental.expected} (100%)
 delete mode 100644 examples/spouse_incremental_example.ddl

diff --git a/examples/spouse_incremental_example.compile.expected b/examples/spouse_example.compile-incremental.expected
similarity index 100%
rename from examples/spouse_incremental_example.compile.expected
rename to examples/spouse_example.compile-incremental.expected
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_example.print-incremental.expected
similarity index 100%
rename from examples/spouse_incremental_example.print.expected
rename to examples/spouse_example.print-incremental.expected
diff --git a/examples/spouse_incremental_example.ddl b/examples/spouse_incremental_example.ddl
deleted file mode 100644
index cf467ac8c..000000000
--- a/examples/spouse_incremental_example.ddl
+++ /dev/null
@@ -1,103 +0,0 @@
-articles(
-  article_id text,
-  text       text,
-  dd_count   int).
-
-sentences(
-  document_id     text,
-  sentence        text,
-  words           text[],
-  lemma           text[],
-  pos_tags        text[],
-  dependencies    text[],
-  ner_tags        text[],
-  sentence_offset int,
-  sentence_id     text,
-  dd_count        int).
-
-people_mentions(
-  sentence_id    text,
-  start_position int,
-  length         int,
-  text           text,
-  mention_id     text,
-  dd_count       int).
-
-has_spouse_candidates(
-  person1_id  text,
-  person2_id  text,
-  sentence_id text,
-  description text,
-  relation_id text,
-  is_true     boolean,
-  dd_count    int).
-
-has_spouse_features(
-  relation_id text,
-  feature     text,
-  dd_count    int).
-
-has_spouse?(relation_id text).
-
-people_mentions :-
-  !ext_people(ext_people_input).
-
-ext_people_input(
-  sentence_id text,
-  words       text[],
-  ner_tags    text[],
-  dd_count    int).
-
-ext_people_input(s, words, ner_tags) :-
-  sentences(a, b, words, c, d, e, ner_tags, f, s).
-
-function ext_people over like ext_people_input
-                 returns like people_mentions
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
-
-has_spouse_candidates :-
-  !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(
-  sentence_id text,
-  p1_id       text,
-  p1_text     text,
-  p2_id       text,
-  p2_text     text,
-  dd_count    int).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, a, b, p1_text, p1_id),
-  people_mentions(s, c, d, p2_text, p2_id).
-
-function ext_has_spouse over like ext_has_spouse_input
-                     returns like has_spouse_candidates
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
-
-has_spouse_features :-
-  !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(
-  words             text[],
-  relation_id       text,
-  p1_start_position int,
-  p1_length         int,
-  p2_start_position int,
-  p2_length         int,
-  dd_count          int).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-  people_mentions(s, p1idx, p1len, k, person1_id),
-  people_mentions(s, p2idx, p2len, l, person2_id).
-  
-function ext_has_spouse_features over like ext_has_spouse_features_input
-                              returns like has_spouse_features
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
-
-has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
-  has_spouse_features(rid, f)
-weight = f
-label = l.
diff --git a/test/per-example.bats b/test/per-example.bats
index b8400dd0b..42d459e05 100755
--- a/test/per-example.bats
+++ b/test/per-example.bats
@@ -16,6 +16,8 @@ setup() {
     [ -e "$EXAMPLE" ]
 }
 
+## tests for basic compilation and pretty-printing
+
 # compare the compiled output with what's expected
 @test "compile $EXAMPLE_NAME" {
     expectedOutput=$EXAMPLE_BASEPATH.compile.expected
@@ -24,7 +26,7 @@ setup() {
     diff -u "$expectedOutput" -
 }
 
-# compare the pretty-printed output with the input
+# compare the pretty-printed output with what's expected
 @test "print $EXAMPLE_NAME as expected" {
     expectedOutput=$EXAMPLE_BASEPATH.print.expected
     [ -e "$expectedOutput" ] || skip
@@ -41,6 +43,21 @@ setup() {
 }
 
 
-# TODO incremental print
+## tests for --incremental support
+
+# compare the compiled output of the incremental version with what's expected
+@test "print $EXAMPLE_NAME as expected" {
+    expectedOutput=$EXAMPLE_BASEPATH.compile-incremental.expected
+    [ -e "$expectedOutput" ] || skip
+    scala "$DDLOG_JAR" compile --incremental "$EXAMPLE" |
+    diff -u "$expectedOutput" -
+}
+
+# compare the pretty-printed output of the incremental version with what's expected
+@test "print $EXAMPLE_NAME as expected" {
+    expectedOutput=$EXAMPLE_BASEPATH.print-incremental.expected
+    [ -e "$expectedOutput" ] || skip
+    scala "$DDLOG_JAR" print --incremental "$EXAMPLE" |
+    diff -u "$expectedOutput" -
+}
 
-# TODO incremental compile

From bf27fc63b10bf18078423410122ee77e68b1c735 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 19 May 2015 17:45:22 -0700
Subject: [PATCH 078/347] Reorgs into a standard scala project structure

with package name org.deepdive.ddlog
---
 Makefile                                                        | 2 +-
 .../main/scala/org/deepdive/ddlog/DeepDiveLog.scala             | 2 ++
 .../main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala     | 2 ++
 .../main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala | 2 ++
 .../main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala       | 2 ++
 .../scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala     | 2 ++
 6 files changed, 11 insertions(+), 1 deletion(-)
 rename DeepDiveLog.scala => src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala (98%)
 rename DeepDiveLogCompiler.scala => src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala (99%)
 rename DeepDiveLogDeltaDeriver.scala => src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala (99%)
 rename DeepDiveLogParser.scala => src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala (99%)
 rename DeepDiveLogPrettyPrinter.scala => src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala (99%)

diff --git a/Makefile b/Makefile
index 9f6d4a8f7..32c9c3e24 100644
--- a/Makefile
+++ b/Makefile
@@ -19,7 +19,7 @@ test-package: $(JAR)
 	$(MAKE) test TEST_JAR=$<
 
 # build test jar
-$(TEST_JAR): $(wildcard *.scala)
+$(TEST_JAR): $(wildcard src/main/scala/org/deepdive/ddlog/*.scala)
 	sbt package
 	ln -sfn $$(ls -t target/scala-*/*_*.jar | head -1) $@
 	touch $@
diff --git a/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
similarity index 98%
rename from DeepDiveLog.scala
rename to src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 859128685..df647b932 100644
--- a/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -1,3 +1,5 @@
+package org.deepdive.ddlog
+
 // A command-line interface
 object DeepDiveLog {
   type Program = List[Statement]
diff --git a/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
similarity index 99%
rename from DeepDiveLogCompiler.scala
rename to src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 13f08c214..1f4e1e73a 100644
--- a/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -1,3 +1,5 @@
+package org.deepdive.ddlog
+
 // DeepDiveLog compiler
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
diff --git a/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
similarity index 99%
rename from DeepDiveLogDeltaDeriver.scala
rename to src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index bc79f1c11..8368f0428 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -1,3 +1,5 @@
+package org.deepdive.ddlog
+
 import scala.collection.mutable.ListBuffer
 
 object DeepDiveLogDeltaDeriver{
diff --git a/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
similarity index 99%
rename from DeepDiveLogParser.scala
rename to src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index d48732625..66a885812 100644
--- a/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -1,3 +1,5 @@
+package org.deepdive.ddlog
+
 // DeepDiveLog syntax
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
diff --git a/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
similarity index 99%
rename from DeepDiveLogPrettyPrinter.scala
rename to src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 1bfe0fe8e..f9e6ea214 100644
--- a/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -1,3 +1,5 @@
+package org.deepdive.ddlog
+
 import org.apache.commons.lang3.StringEscapeUtils
 
 // Pretty printer that simply prints the parsed input

From 607153e661bf487cd66e72aa38e9b5b4dd6c5252 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 19 May 2015 17:57:10 -0700
Subject: [PATCH 079/347] Rewrites test.sh to generate all .bats first and run
 them at once

---
 .gitignore                                    |  1 +
 ... => expected-output-test.bats.per-example} |  0
 test/test.sh                                  | 32 +++++++++----------
 3 files changed, 17 insertions(+), 16 deletions(-)
 rename test/{per-example.bats => expected-output-test.bats.per-example} (100%)
 mode change 100755 => 100644

diff --git a/.gitignore b/.gitignore
index 8ec9fb651..67ba8778f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
 /ddlog-test.jar.classpath
 target
 /test/bats
+/test/*.for-example-*.bats
diff --git a/test/per-example.bats b/test/expected-output-test.bats.per-example
old mode 100755
new mode 100644
similarity index 100%
rename from test/per-example.bats
rename to test/expected-output-test.bats.per-example
diff --git a/test/test.sh b/test/test.sh
index 722bed8da..6fe8347cc 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -7,20 +7,20 @@ PATH="$PWD/bats/bin:$PATH"
 type bats &>/dev/null ||
     git clone https://github.com/sstephenson/bats.git
 
-# run all .bats tests
-c=0
-for t in *.bats; do
-    case $t in
-        *-example.bats)
-            # run bats test for every example
-            for ddl in ../examples/*.ddl; do
-                EXAMPLE=$ddl bats $t || c=$?
-            done
-            ;;
-
-        *)
-            # otherwise, simply run the bats
-            bats $t
-    esac
+# generate bats tests for every per-example templates
+for t in *.bats.per-example; do
+    testName=${t%.bats.per-example}
+    # generate one for each example
+    for ddl in ../examples/*.ddl; do
+        exampleName=${ddl%.ddl}
+        exampleName=${exampleName#../examples/}
+        batsFile="$testName".for-example-"$exampleName".bats
+        {
+            printf "EXAMPLE=%q\n" "$ddl"
+            cat $t
+        } >$batsFile
+    done
 done
-exit $c
+
+# run all .bats tests
+bats *.bats

From 4770a263859da0d6782d3ab40492a5d3f8bfe0c3 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 19 May 2015 21:34:25 -0700
Subject: [PATCH 080/347] modify spouse example

---
 examples/spouse_example.compile.expected      |  22 +--
 ...pouse_incremental_example.compile.expected | 169 +++++++++---------
 .../spouse_incremental_example.print.expected |  54 ++----
 examples/test.ddl                             |   8 +
 examples/test6.ddl                            |   5 +
 examples/test7.ddl                            |   6 +
 examples/test8.ddl                            |   6 +
 examples/test9.ddl                            |   9 +
 8 files changed, 139 insertions(+), 140 deletions(-)
 create mode 100644 examples/test.ddl
 create mode 100644 examples/test6.ddl
 create mode 100644 examples/test7.ddl
 create mode 100644 examples/test8.ddl
 create mode 100644 examples/test9.ddl

diff --git a/examples/spouse_example.compile.expected b/examples/spouse_example.compile.expected
index 2d2b39a35..2dfb73e7c 100644
--- a/examples/spouse_example.compile.expected
+++ b/examples/spouse_example.compile.expected
@@ -18,8 +18,8 @@
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-        SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-        FROM sentences R0
+          SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+          FROM sentences R0
         
         """
         style: "sql_extractor"
@@ -30,8 +30,8 @@
       deepdive.extraction.extractors.extraction_rule_16 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-        SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-        FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+          SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+          FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
@@ -42,8 +42,8 @@
       deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-        SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-        FROM people_mentions R0, people_mentions R1
+          SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+          FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
@@ -85,19 +85,19 @@
         sql: """ DROP TABLE IF EXISTS has_spouse;
         CREATE TABLE has_spouse AS
         SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
-        FROM has_spouse_candidates R0, has_spouse_features R1
+          FROM has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
-        
+          
         """
         style: "sql_extractor"
         dependencies: [ "extraction_rule_10" ,  "extraction_rule_14" ]
       }
     
 
-        deepdive.inference.factors.factor_has_spouse {
+        deepdive.inference.factors.factor_has_spouse_0 {
           input_query: """
-        SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
-        FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
+          FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
diff --git a/examples/spouse_incremental_example.compile.expected b/examples/spouse_incremental_example.compile.expected
index d376e5097..415587dc8 100644
--- a/examples/spouse_incremental_example.compile.expected
+++ b/examples/spouse_incremental_example.compile.expected
@@ -15,65 +15,65 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_51 {
+      deepdive.extraction.extractors.extraction_rule_42 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-        SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+          SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+          FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+          SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+          FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+          SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+          FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-        SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-        FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+          SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+          FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ,  "extraction_rule_8" ,  "extraction_rule_36" ,  "extraction_rule_13" ,  "extraction_rule_18" ]
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_30" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_13 {
+      deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ DROP VIEW IF EXISTS dd_new_people_mentions;
         CREATE VIEW dd_new_people_mentions AS 
-        SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.start_position AS "people_mentions.R0.start_position" , R0.length AS "people_mentions.R0.length" , R0.text AS "people_mentions.R0.text" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.dd_count AS "people_mentions.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM people_mentions R0
+          SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+          FROM people_mentions R0
          UNION 
-        SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.start_position AS "dd_delta_people_mentions.R0.start_position" , R0.length AS "dd_delta_people_mentions.R0.length" , R0.text AS "dd_delta_people_mentions.R0.text" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.dd_count AS "dd_delta_people_mentions.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_people_mentions R0
+          SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+          FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_23" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_32 {
+      deepdive.extraction.extractors.extraction_rule_27 {
         sql: """ DROP VIEW IF EXISTS dd_new_ext_people_input;
         CREATE VIEW dd_new_ext_people_input AS 
-        SELECT R0.sentence_id AS "ext_people_input.R0.sentence_id" , R0.words AS "ext_people_input.R0.words" , R0.ner_tags AS "ext_people_input.R0.ner_tags" , R0.dd_count AS "ext_people_input.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM ext_people_input R0
+          SELECT R0.sentence_id, R0.words, R0.ner_tags, R0.dd_count
+          FROM ext_people_input R0
          UNION 
-        SELECT R0.sentence_id AS "dd_delta_ext_people_input.R0.sentence_id" , R0.words AS "dd_delta_ext_people_input.R0.words" , R0.ner_tags AS "dd_delta_ext_people_input.R0.ner_tags" , R0.dd_count AS "dd_delta_ext_people_input.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_ext_people_input R0
+          SELECT R0.sentence_id, R0.words, R0.ner_tags, R0.dd_count
+          FROM dd_delta_ext_people_input R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_34" ]
+          dependencies: [ "extraction_rule_28" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS dd_new_articles;
         CREATE VIEW dd_new_articles AS 
-        SELECT R0.article_id AS "articles.R0.article_id" , R0.text AS "articles.R0.text" , R0.dd_count AS "articles.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM articles R0
+          SELECT R0.article_id, R0.text, R0.dd_count
+          FROM articles R0
          UNION 
-        SELECT R0.article_id AS "dd_delta_articles.R0.article_id" , R0.text AS "dd_delta_articles.R0.text" , R0.dd_count AS "dd_delta_articles.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_articles R0
+          SELECT R0.article_id, R0.text, R0.dd_count
+          FROM dd_delta_articles R0
         
         """
         style: "sql_extractor"
@@ -81,11 +81,11 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_34 {
+      deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-        SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0
+          SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+          FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -93,74 +93,74 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_18 {
+      deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ DROP VIEW IF EXISTS dd_new_has_spouse_candidates;
         CREATE VIEW dd_new_has_spouse_candidates AS 
-        SELECT R0.person1_id AS "has_spouse_candidates.R0.person1_id" , R0.person2_id AS "has_spouse_candidates.R0.person2_id" , R0.sentence_id AS "has_spouse_candidates.R0.sentence_id" , R0.description AS "has_spouse_candidates.R0.description" , R0.relation_id AS "has_spouse_candidates.R0.relation_id" , R0.is_true AS "has_spouse_candidates.R0.is_true" , R0.dd_count AS "has_spouse_candidates.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM has_spouse_candidates R0
+          SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+          FROM has_spouse_candidates R0
          UNION 
-        SELECT R0.person1_id AS "dd_delta_has_spouse_candidates.R0.person1_id" , R0.person2_id AS "dd_delta_has_spouse_candidates.R0.person2_id" , R0.sentence_id AS "dd_delta_has_spouse_candidates.R0.sentence_id" , R0.description AS "dd_delta_has_spouse_candidates.R0.description" , R0.relation_id AS "dd_delta_has_spouse_candidates.R0.relation_id" , R0.is_true AS "dd_delta_has_spouse_candidates.R0.is_true" , R0.dd_count AS "dd_delta_has_spouse_candidates.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse_candidates R0
+          SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+          FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_36" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_49 {
+      deepdive.extraction.extractors.extraction_rule_41 {
         sql: """ DROP VIEW IF EXISTS dd_new_ext_has_spouse_features_input;
         CREATE VIEW dd_new_ext_has_spouse_features_input AS 
-        SELECT R0.words AS "ext_has_spouse_features_input.R0.words" , R0.relation_id AS "ext_has_spouse_features_input.R0.relation_id" , R0.p1_start_position AS "ext_has_spouse_features_input.R0.p1_start_position" , R0.p1_length AS "ext_has_spouse_features_input.R0.p1_length" , R0.p2_start_position AS "ext_has_spouse_features_input.R0.p2_start_position" , R0.p2_length AS "ext_has_spouse_features_input.R0.p2_length" , R0.dd_count AS "ext_has_spouse_features_input.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM ext_has_spouse_features_input R0
+          SELECT R0.words, R0.relation_id, R0.p1_start_position, R0.p1_length, R0.p2_start_position, R0.p2_length, R0.dd_count
+          FROM ext_has_spouse_features_input R0
          UNION 
-        SELECT R0.words AS "dd_delta_ext_has_spouse_features_input.R0.words" , R0.relation_id AS "dd_delta_ext_has_spouse_features_input.R0.relation_id" , R0.p1_start_position AS "dd_delta_ext_has_spouse_features_input.R0.p1_start_position" , R0.p1_length AS "dd_delta_ext_has_spouse_features_input.R0.p1_length" , R0.p2_start_position AS "dd_delta_ext_has_spouse_features_input.R0.p2_start_position" , R0.p2_length AS "dd_delta_ext_has_spouse_features_input.R0.p2_length" , R0.dd_count AS "dd_delta_ext_has_spouse_features_input.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_ext_has_spouse_features_input R0
+          SELECT R0.words, R0.relation_id, R0.p1_start_position, R0.p1_length, R0.p2_start_position, R0.p2_length, R0.dd_count
+          FROM dd_delta_ext_has_spouse_features_input R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_51" ]
+          dependencies: [ "extraction_rule_42" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_40 {
+      deepdive.extraction.extractors.extraction_rule_34 {
         sql: """ DROP VIEW IF EXISTS dd_new_ext_has_spouse_input;
         CREATE VIEW dd_new_ext_has_spouse_input AS 
-        SELECT R0.sentence_id AS "ext_has_spouse_input.R0.sentence_id" , R0.p1_id AS "ext_has_spouse_input.R0.p1_id" , R0.p1_text AS "ext_has_spouse_input.R0.p1_text" , R0.p2_id AS "ext_has_spouse_input.R0.p2_id" , R0.p2_text AS "ext_has_spouse_input.R0.p2_text" , R0.dd_count AS "ext_has_spouse_input.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM ext_has_spouse_input R0
+          SELECT R0.sentence_id, R0.p1_id, R0.p1_text, R0.p2_id, R0.p2_text, R0.dd_count
+          FROM ext_has_spouse_input R0
          UNION 
-        SELECT R0.sentence_id AS "dd_delta_ext_has_spouse_input.R0.sentence_id" , R0.p1_id AS "dd_delta_ext_has_spouse_input.R0.p1_id" , R0.p1_text AS "dd_delta_ext_has_spouse_input.R0.p1_text" , R0.p2_id AS "dd_delta_ext_has_spouse_input.R0.p2_id" , R0.p2_text AS "dd_delta_ext_has_spouse_input.R0.p2_text" , R0.dd_count AS "dd_delta_ext_has_spouse_input.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_ext_has_spouse_input R0
+          SELECT R0.sentence_id, R0.p1_id, R0.p1_text, R0.p2_id, R0.p2_text, R0.dd_count
+          FROM dd_delta_ext_has_spouse_input R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_42" ]
+          dependencies: [ "extraction_rule_35" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ DROP VIEW IF EXISTS dd_new_has_spouse_features;
         CREATE VIEW dd_new_has_spouse_features AS 
-        SELECT R0.relation_id AS "has_spouse_features.R0.relation_id" , R0.feature AS "has_spouse_features.R0.feature" , R0.dd_count AS "has_spouse_features.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM has_spouse_features R0
+          SELECT R0.relation_id, R0.feature, R0.dd_count
+          FROM has_spouse_features R0
          UNION 
-        SELECT R0.relation_id AS "dd_delta_has_spouse_features.R0.relation_id" , R0.feature AS "dd_delta_has_spouse_features.R0.feature" , R0.dd_count AS "dd_delta_has_spouse_features.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse_features R0
+          SELECT R0.relation_id, R0.feature, R0.dd_count
+          FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_45" ]
+          dependencies: [ "extraction_rule_37" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_8 {
+      deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS dd_new_sentences;
         CREATE VIEW dd_new_sentences AS 
-        SELECT R0.document_id AS "sentences.R0.document_id" , R0.sentence AS "sentences.R0.sentence" , R0.words AS "sentences.R0.words" , R0.lemma AS "sentences.R0.lemma" , R0.pos_tags AS "sentences.R0.pos_tags" , R0.dependencies AS "sentences.R0.dependencies" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.sentence_offset AS "sentences.R0.sentence_offset" , R0.sentence_id AS "sentences.R0.sentence_id" , R0.dd_count AS "sentences.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM sentences R0
+          SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+          FROM sentences R0
          UNION 
-        SELECT R0.document_id AS "dd_delta_sentences.R0.document_id" , R0.sentence AS "dd_delta_sentences.R0.sentence" , R0.words AS "dd_delta_sentences.R0.words" , R0.lemma AS "dd_delta_sentences.R0.lemma" , R0.pos_tags AS "dd_delta_sentences.R0.pos_tags" , R0.dependencies AS "dd_delta_sentences.R0.dependencies" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.sentence_offset AS "dd_delta_sentences.R0.sentence_offset" , R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.dd_count AS "dd_delta_sentences.R0.dd_count" , R0.dd_count AS "dd_count" 
-        FROM dd_delta_sentences R0
+          SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+          FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -168,48 +168,48 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_42 {
+      deepdive.extraction.extractors.extraction_rule_35 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-        SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
-        FROM dd_delta_people_mentions R0, people_mentions R1
+          SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+          FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id  UNION 
-        SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
-        FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+          SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+          FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ,  "extraction_rule_13" ]
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_11" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_28 {
+        deepdive.extraction.extractors.extraction_rule_23 {
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_34" ]
+          dependencies: [ "extraction_rule_28" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_45 {
+        deepdive.extraction.extractors.extraction_rule_37 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_51" ]
+          dependencies: [ "extraction_rule_42" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_36 {
+        deepdive.extraction.extractors.extraction_rule_30 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_42" ]
+          dependencies: [ "extraction_rule_35" ]
         }
       
 
@@ -217,34 +217,27 @@
         sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse;
         CREATE TABLE dd_delta_has_spouse AS
         SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
+          FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
-         UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-        FROM dd_new_has_spouse_candidates R0, dd_delta_has_spouse_features R1
+           UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
+          FROM dd_new_has_spouse_candidates R0, dd_delta_has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
-        
+          
         """
         style: "sql_extractor"
-        dependencies: [ "extraction_rule_36" ,  "extraction_rule_18" ,  "extraction_rule_45" ]
+        dependencies: [ "extraction_rule_30" ,  "extraction_rule_15" ,  "extraction_rule_37" ]
       }
     
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse {
+        deepdive.inference.factors.factor_dd_delta_has_spouse_0 {
           input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_delta_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
-
-        deepdive.inference.factors.factor_dd_delta_has_spouse {
-          input_query: """
-        SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-        FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
-          weight: "?(dd_delta_has_spouse_features.R2.feature)"
-        }
-      
diff --git a/examples/spouse_incremental_example.print.expected b/examples/spouse_incremental_example.print.expected
index b47c1eb17..0b2a5e9e2 100644
--- a/examples/spouse_incremental_example.print.expected
+++ b/examples/spouse_incremental_example.print.expected
@@ -11,9 +11,7 @@ dd_new_articles(article_id text,
                 dd_count int).
 
 dd_new_articles(article_id, text, dd_count) :-
-    articles(article_id, text, dd_count).
-
-dd_new_articles(article_id, text, dd_count) :-
+    articles(article_id, text, dd_count);
     dd_delta_articles(article_id, text, dd_count).
 
 sentences(document_id text,
@@ -50,9 +48,7 @@ dd_new_sentences(document_id text,
                  dd_count int).
 
 dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count) :-
-    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count).
-
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count) :-
+    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count).
 
 people_mentions(sentence_id text,
@@ -77,9 +73,7 @@ dd_new_people_mentions(sentence_id text,
                        dd_count int).
 
 dd_new_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count) :-
-    people_mentions(sentence_id, start_position, length, text, mention_id, dd_count).
-
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count) :-
+    people_mentions(sentence_id, start_position, length, text, mention_id, dd_count);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count).
 
 has_spouse_candidates(person1_id text,
@@ -107,9 +101,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              dd_count int).
 
 dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count) :-
-    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count).
-
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count) :-
+    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count).
 
 has_spouse_features(relation_id text,
@@ -125,9 +117,7 @@ dd_new_has_spouse_features(relation_id text,
                            dd_count int).
 
 dd_new_has_spouse_features(relation_id, feature, dd_count) :-
-    has_spouse_features(relation_id, feature, dd_count).
-
-dd_new_has_spouse_features(relation_id, feature, dd_count) :-
+    has_spouse_features(relation_id, feature, dd_count);
     dd_delta_has_spouse_features(relation_id, feature, dd_count).
 
 has_spouse?(relation_id text).
@@ -154,9 +144,7 @@ dd_new_ext_people_input(sentence_id text,
                         dd_count int).
 
 dd_new_ext_people_input(sentence_id, words, ner_tags, dd_count) :-
-    ext_people_input(sentence_id, words, ner_tags, dd_count).
-
-dd_new_ext_people_input(sentence_id, words, ner_tags, dd_count) :-
+    ext_people_input(sentence_id, words, ner_tags, dd_count);
     dd_delta_ext_people_input(sentence_id, words, ner_tags, dd_count).
 
 dd_delta_ext_people_input(s, words, ner_tags) :-
@@ -192,16 +180,12 @@ dd_new_ext_has_spouse_input(sentence_id text,
                             dd_count int).
 
 dd_new_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count) :-
-    ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count).
-
-dd_new_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count) :-
+    ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count);
     dd_delta_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count).
 
 dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
-    people_mentions(s, c, d, p2_text, p2_id).
-
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
     dd_delta_people_mentions(s, c, d, p2_text, p2_id).
 
@@ -238,30 +222,22 @@ dd_new_ext_has_spouse_features_input(words text[],
                                      dd_count int).
 
 dd_new_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count) :-
-    ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count).
-
-dd_new_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count) :-
+    ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count);
     dd_delta_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count).
 
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    people_mentions(s, p2idx, p2len, l, person2_id);
     dd_new_sentences(a, b, words, c, d, e, f, g, s),
     dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    people_mentions(s, p2idx, p2len, l, person2_id);
     dd_new_sentences(a, b, words, c, d, e, f, g, s),
     dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    people_mentions(s, p2idx, p2len, l, person2_id);
     dd_new_sentences(a, b, words, c, d, e, f, g, s),
     dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
@@ -275,11 +251,7 @@ function ext_has_spouse_features
 
 dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
-    has_spouse_features(rid, f)
-  weight = f
-  label = l
-  rule = imply.
-dd_delta_has_spouse(rid) :-
+    has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
diff --git a/examples/test.ddl b/examples/test.ddl
new file mode 100644
index 000000000..bf6b427cf
--- /dev/null
+++ b/examples/test.ddl
@@ -0,0 +1,8 @@
+A(a1 int,
+  a2 int).
+B(a1 int,
+  a2 int).
+C(a1 int,
+  a2 int,
+  a3 int).
+Q(a1) :- A(a1, x); B(y, a1); C(a, b, a1).
diff --git a/examples/test6.ddl b/examples/test6.ddl
new file mode 100644
index 000000000..35820ed03
--- /dev/null
+++ b/examples/test6.ddl
@@ -0,0 +1,5 @@
+R(a int, b int).
+S(a int, b int).
+Q(x int).
+
+Q(y) :- R(x, y); R(x, y), S(y, z).
\ No newline at end of file
diff --git a/examples/test7.ddl b/examples/test7.ddl
new file mode 100644
index 000000000..6c1c7f0fe
--- /dev/null
+++ b/examples/test7.ddl
@@ -0,0 +1,6 @@
+R(a int, b int).
+S(a int, b int).
+T(a int, b int).
+Q(x int).
+
+Q(y) :- R(x, y); R(x, y), S(y, z); S(y, x), T(x, z).
\ No newline at end of file
diff --git a/examples/test8.ddl b/examples/test8.ddl
new file mode 100644
index 000000000..ecf3c4b7e
--- /dev/null
+++ b/examples/test8.ddl
@@ -0,0 +1,6 @@
+R(a int, b int).
+S(a int, b int, c int).
+T(a int, b int, c int).
+Q(x int, z int).
+
+Q(x, y) :- R(x, y); R(x, y), S(y, z, w); S(y, x, w), T(x, z, w).
\ No newline at end of file
diff --git a/examples/test9.ddl b/examples/test9.ddl
new file mode 100644
index 000000000..e93f7ad0f
--- /dev/null
+++ b/examples/test9.ddl
@@ -0,0 +1,9 @@
+R(a int, b int, c int).
+S(a int, b int, c int).
+T(a int, b int, c int).
+Q?(x int).
+
+Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w)
+weight = y
+label   = z
+rule = imply.
\ No newline at end of file

From cc7e3cdea66fe3aff178cf9fd36527b4ebdeb273 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 19 May 2015 21:38:55 -0700
Subject: [PATCH 081/347] support disjunction

---
 DeepDiveLogCompiler.scala      | 170 ++++++++++++++++++---------------
 DeepDiveLogDeltaDeriver.scala  | 132 +++++++++++++------------
 DeepDiveLogParser.scala        |   9 +-
 DeepDiveLogPrettyPrinter.scala |   5 +-
 4 files changed, 176 insertions(+), 140 deletions(-)

diff --git a/DeepDiveLogCompiler.scala b/DeepDiveLogCompiler.scala
index 31fcc264b..6e1351322 100644
--- a/DeepDiveLogCompiler.scala
+++ b/DeepDiveLogCompiler.scala
@@ -146,25 +146,30 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // Resolve a column name with alias
-  def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: Boolean) : Option[String] = {
+  def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: Int) : Option[String] = {
     val index = qs.getBodyIndex(s)
     val name  = resolveName(qs.getVar(s))
-    val relation = q.body(index).name
-    if (alias)
-      Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
-    else
-      Some(s"${relation}.R${index}.${name}")
+    val relation = q.bodies(0)(index).name
+    // Three kinds of column expressions:
+    // 0 => use alias for unknown weight in inference
+    // 1 => use column name and alias for normal extraction rule
+    // 2 => use column name for dd_new_ tables
+    alias match {
+      case 0 => Some(s"${relation}.R${index}.${name}")
+      case 1 => Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
+      case 2 => Some(s"R${index}.${name}")
+    }
   }
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
   def generateSQLBody(z : ConjunctiveQuery) : String = {
-    val bodyNames = ( z.body.zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
+    val bodyNames = ( z.bodies(0).zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
     // Simple logic for the where clause, first find every first occurence of a
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    val whereClause = z.body.zipWithIndex flatMap {
+    val whereClause = z.bodies(0).zipWithIndex flatMap {
       case (Atom(relName, terms),body_index) =>
         terms flatMap {
           case Variable(varName, relName, index) =>
@@ -219,8 +224,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // Look at the body of each statement to construct a dependency graph
     statements foreach {
       case f : FunctionCallRule => dependencies += { f -> ((        Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case e : ExtractionRule   => dependencies += { e -> ((e.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case w : InferenceRule    => dependencies += { w -> ((w.q.body map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case e : ExtractionRule   => dependencies += { e -> ((e.q.bodies.flatten map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case w : InferenceRule    => dependencies += { w -> ((w.q.bodies.flatten map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case _ =>
     }
   }
@@ -248,7 +253,7 @@ class QuerySchema(q : ConjunctiveQuery) {
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
   def generateCanonicalVar()  = {
-    q.body.zipWithIndex.foreach {
+    q.bodies(0).zipWithIndex.foreach {
       case (Atom(relName,terms),index) =>  {
         terms.foreach {
           case Variable(v, r, i) =>
@@ -275,21 +280,27 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
-      // Generate the body of the query.
-      val qs              = new QuerySchema( stmt.q )
-      // variable columns
-      val variableCols = stmt.q.head.terms flatMap {
-        case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, stmt.q, true)
-      }
-
-      val selectStr = variableCols.mkString(", ")
-      val ddCount = if (ss.isIncremental) ( stmt.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-      val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
+      for (cqBody <- stmt.q.bodies) {
+        var tmpStmt = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        // Generate the body of the query.
+        val qs              = new QuerySchema( tmpStmt )
+        // variable columns
+        var resolveColumnFlag = tmpStmt.head.name.startsWith("dd_new_") match {
+          case true => 2
+          case false => 1
+        }
+        val variableCols = tmpStmt.head.terms flatMap {
+          case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpStmt, resolveColumnFlag)
+        }
 
-      inputQueries += s"""
-        SELECT ${selectStr}${ddCountStr}
-        ${ ss.generateSQLBody(stmt.q) }"""
+        val selectStr = variableCols.mkString(", ")
+        val ddCount = if (ss.isIncremental && (resolveColumnFlag == 1)) ( tmpStmt.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
 
+        inputQueries += s"""
+          SELECT ${selectStr}${ddCountStr}
+          ${ ss.generateSQLBody(tmpStmt) }"""
+      }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
     val extractor = s"""
@@ -340,25 +351,28 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   // generate inference rule part for deepdive
   def compileInferenceRules(stmts: List[InferenceRule], ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
-    val qs = new QuerySchema( stmts(0).q )
     // node query
     // generate the node portion (V) of the factor graph
-    def compileNodeRule(zs: List[InferenceRule], qs: QuerySchema, ss: CompilationState) : CompiledBlocks = {
+    def compileNodeRule(zs: List[InferenceRule], ss: CompilationState) : CompiledBlocks = {
       var inputQueries = new ListBuffer[String]()
       for (z <- zs) {
-        val headTerms = z.q.head.terms map {
-          case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+        for (cqBody <- z.q.bodies) {
+          var tmpStmt = ConjunctiveQuery(z.q.head, List(cqBody))
+          val qs = new QuerySchema(tmpStmt)
+          val headTerms = tmpStmt.head.terms map {
+            case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+          }
+          val index = qs.getBodyIndex(z.supervision)
+          val name  = ss.resolveName(qs.getVar(z.supervision))
+          val labelCol = s"R${index}.${name}"
+          val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
+          val ddCount = if (ss.isIncremental) ( tmpStmt.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
+
+          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
+          ${ ss.generateSQLBody(tmpStmt) }
+          """
         }
-        val index = qs.getBodyIndex(z.supervision)
-        val name  = ss.resolveName(qs.getVar(z.supervision))
-        val labelCol = s"R${index}.${name}"
-        val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-        val ddCount = if (ss.isIncremental) ( z.q.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-        val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
-
-        inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
-        ${ ss.generateSQLBody(z.q) }
-        """
       }
       val blockName = ss.resolveExtractorBlockName(zs(0))
       val ext = s"""
@@ -374,53 +388,59 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       List(ext)
     }
     if (ss.isQueryTerm(stmts(0).q.head.name))
-      blocks :::= compileNodeRule(stmts, qs, ss)
+      blocks :::= compileNodeRule(stmts, ss)
 
     val inferenceRuleGroupByHead    = stmts.groupBy(_.q.head.name)
-
+    var stmtIndex = 0
     for (stmt <- stmts) {
-      // edge query
-      val fakeBody        = stmt.q.head +: stmt.q.body
-      val fakeCQ          = ConjunctiveQuery(stmt.q.head, fakeBody) // we will just use the fakeBody below.
-
-      val index = stmt.q.body.length + 1
-      val qs2 = new QuerySchema( fakeCQ )
-      val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
-
-      // weight string
-      val uwStr = stmt.weights match {
-        case KnownFactorWeight(x) => None
-        case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, true)).mkString(", "))
-      }
-
-      val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
-
-      val ddCount = if (ss.isIncremental) ( fakeCQ.body.zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-      val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
-
-      // factor input query
-      val inputQuery = s"""
-        SELECT ${selectStr} ${ddCountStr}
-        ${ ss.generateSQLBody(fakeCQ) }"""
-
-      // factor function
-      val func = s"""Imply(${stmt.q.head.name}.R0.label)"""
-
-      // weight
-      val weight = stmt.weights match {
-        case KnownFactorWeight(x) => s"${x}"
-        case UnknownFactorWeight(w) => {
-          s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, false)).mkString(", ")})"""
+      var inputQueries = new ListBuffer[String]()
+      var func = ""
+      var weight = ""
+      for (cqBody <- stmt.q.bodies) {
+        var tmpStmt = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        // edge query
+        val fakeBody        = tmpStmt.head +: tmpStmt.bodies(0)
+        // val fakeBody        = stmt.q.bodies +: List(stmt.q.head)
+        val fakeCQ          = ConjunctiveQuery(tmpStmt.head, List(fakeBody)) // we will just use the fakeBody below.
+
+        val index = tmpStmt.bodies(0).length + 1
+        val qs2 = new QuerySchema( fakeCQ )
+        val variableIdsStr = Some(s"""R0.id AS "${tmpStmt.head.name}.R0.id" """)
+
+        // weight string
+        val uwStr = stmt.weights match {
+          case KnownFactorWeight(x) => None
+          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, 1)).mkString(", "))
         }
-      }
 
+        val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
+
+        val ddCount = if (ss.isIncremental) ( fakeCQ.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
+
+        // factor input query
+        inputQueries += s"""
+          SELECT ${selectStr} ${ddCountStr}
+          ${ ss.generateSQLBody(fakeCQ) }"""
+        // factor function
+        func = s"""Imply(${stmt.q.head.name}.R0.label)"""
+        // weight
+        if (weight.length == 0)
+          weight = stmt.weights match {
+            case KnownFactorWeight(x) => s"${x}"
+            case UnknownFactorWeight(w) => {
+              s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, 0)).mkString(", ")})"""
+            }
+          }
+      }
       blocks ::= s"""
-        deepdive.inference.factors.factor_${stmt.q.head.name} {
-          input_query: \"\"\"${inputQuery}\"\"\"
+        deepdive.inference.factors.factor_${stmt.q.head.name}_${stmtIndex} {
+          input_query: \"\"\"${inputQueries.mkString(" UNION ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
         }
       """
+      stmtIndex += 1
     }
     blocks.reverse
   }
diff --git a/DeepDiveLogDeltaDeriver.scala b/DeepDiveLogDeltaDeriver.scala
index a80045d47..7bece44f3 100644
--- a/DeepDiveLogDeltaDeriver.scala
+++ b/DeepDiveLogDeltaDeriver.scala
@@ -36,8 +36,12 @@ object DeepDiveLogDeltaDeriver{
     var newStmt = SchemaDeclaration(Attribute(newPrefix + stmt.a.name, newTerms.toList, stmt.a.types), stmt.isQuery)
     incrementalStatement += newStmt
     if (!stmt.isQuery) {
-      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), List(Atom(stmt.a.name, stmt.a.terms.toList))))
-      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), List(Atom(deltaStmt.a.name, deltaStmt.a.terms.toList))))
+      var newStmtCqBodies = new ListBuffer[List[Atom]]()
+      newStmtCqBodies += List(Atom(stmt.a.name, stmt.a.terms.toList))
+      newStmtCqBodies += List(Atom(deltaStmt.a.name, deltaStmt.a.terms.toList))
+      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), newStmtCqBodies.toList))
+      
+      // incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), List(Atom(deltaStmt.a.name, deltaStmt.a.terms.toList))))
     }
     incrementalStatement.toList
   }
@@ -80,40 +84,44 @@ object DeepDiveLogDeltaDeriver{
       newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
     }
     var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
-    // dd delta table from dd_delta_ table
-    var ddDeltaStmtCqBody = new ListBuffer[Atom]()
-    for (stmtCqBody <- stmt.q.body) { // List[Atom]
-      var stmtCqBodyTerms = new ListBuffer[Variable]()
-      for (bodyTerm <- stmtCqBody.terms) {
-        stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
+    var newStmtCqBodies = new ListBuffer[List[Atom]]()
+    for (stmtCqBody <- stmt.q.bodies) {
+      // dd delta table from dd_delta_ table
+      var ddDeltaStmtCqBody = new ListBuffer[Atom]()
+      for (cqBody <- stmtCqBody) { // List[Atom]
+        var stmtCqBodyTerms = new ListBuffer[Variable]()
+        for (bodyTerm <- cqBody.terms) {
+          stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
+        }
+        ddDeltaStmtCqBody += Atom(deltaPrefix + cqBody.name, stmtCqBodyTerms.toList)
       }
-      ddDeltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
-    }
-    // dd new body from dd_new_ table
-    var ddNewStmtCqBody = new ListBuffer[Atom]()
-    for (stmtCqBody <- stmt.q.body) { // List[Atom]
-      var stmtCqBodyTerms = new ListBuffer[Variable]()
-      for (bodyTerm <- stmtCqBody.terms) {
-        stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
+      // dd new body from dd_new_ table
+      var ddNewStmtCqBody = new ListBuffer[Atom]()
+      for (cqBody <- stmtCqBody) { // List[Atom]
+        var stmtCqBodyTerms = new ListBuffer[Variable]()
+        for (bodyTerm <- cqBody.terms) {
+          stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
+        }
+        ddNewStmtCqBody += Atom(newPrefix + cqBody.name, stmtCqBodyTerms.toList)
       }
-      ddNewStmtCqBody += Atom(newPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
-    }
 
-    // New statement
-    var i = 0
-    var j = 0
-    for (i <- 0 to (stmt.q.body.length - 1)) {
-      var newStmtCqBody = new ListBuffer[Atom]()
-      for (j <- 0 to (stmt.q.body.length - 1)) {
-        if (j > i)
-          newStmtCqBody += stmt.q.body(j)
-        else if (j < i)
-          newStmtCqBody += ddNewStmtCqBody(j)
-          else if (j == i)
-            newStmtCqBody += ddDeltaStmtCqBody(j)
+      // New statement
+      var i = 0
+      var j = 0
+      for (i <- 0 to (stmtCqBody.length - 1)) {
+        var newStmtCqBody = new ListBuffer[Atom]()
+        for (j <- 0 to (stmtCqBody.length - 1)) {
+          if (j > i)
+            newStmtCqBody += stmtCqBody(j)
+          else if (j < i)
+            newStmtCqBody += ddNewStmtCqBody(j)
+            else if (j == i)
+              newStmtCqBody += ddDeltaStmtCqBody(j)
+        }
+        newStmtCqBodies += newStmtCqBody.toList
       }
-      incrementalStatement += ExtractionRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList))
     }
+    incrementalStatement += ExtractionRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBodies.toList))
     incrementalStatement.toList
   }
 
@@ -136,40 +144,44 @@ object DeepDiveLogDeltaDeriver{
       newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
     }
     var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
-    // dd delta table from dd_delta_ table
-    var ddDeltaStmtCqBody = new ListBuffer[Atom]()
-    for (stmtCqBody <- stmt.q.body) { // List[Atom]
-      var stmtCqBodyTerms = new ListBuffer[Variable]()
-      for (bodyTerm <- stmtCqBody.terms) {
-        stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
+    var newStmtCqBodies = new ListBuffer[List[Atom]]()
+    for (stmtCqBody <- stmt.q.bodies) {
+      // dd delta table from dd_delta_ table
+      var ddDeltaStmtCqBody = new ListBuffer[Atom]()
+      for (cqBody <- stmtCqBody) { // List[Atom]
+        var stmtCqBodyTerms = new ListBuffer[Variable]()
+        for (bodyTerm <- cqBody.terms) {
+          stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
+        }
+        ddDeltaStmtCqBody += Atom(deltaPrefix + cqBody.name, stmtCqBodyTerms.toList)
       }
-      ddDeltaStmtCqBody += Atom(deltaPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
-    }
-    // dd new body from dd_new_ table
-    var ddNewStmtCqBody = new ListBuffer[Atom]()
-    for (stmtCqBody <- stmt.q.body) { // List[Atom]
-      var stmtCqBodyTerms = new ListBuffer[Variable]()
-      for (bodyTerm <- stmtCqBody.terms) {
-        stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
+      // dd new body from dd_new_ table
+      var ddNewStmtCqBody = new ListBuffer[Atom]()
+      for (cqBody <- stmtCqBody) { // List[Atom]
+        var stmtCqBodyTerms = new ListBuffer[Variable]()
+        for (bodyTerm <- cqBody.terms) {
+          stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
+        }
+        ddNewStmtCqBody += Atom(newPrefix + cqBody.name, stmtCqBodyTerms.toList)
       }
-      ddNewStmtCqBody += Atom(newPrefix + stmtCqBody.name, stmtCqBodyTerms.toList)
-    }
 
-    // New statement
-    var i = 0
-    var j = 0
-    for (i <- 0 to (stmt.q.body.length - 1)) {
-      var newStmtCqBody = new ListBuffer[Atom]()
-      for (j <- 0 to (stmt.q.body.length - 1)) {
-        if (j > i)
-          newStmtCqBody += stmt.q.body(j)
-        else if (j < i)
-          newStmtCqBody += ddNewStmtCqBody(j)
-          else if (j == i)
-            newStmtCqBody += ddDeltaStmtCqBody(j)
+      // New statement
+      var i = 0
+      var j = 0
+      for (i <- 0 to (stmtCqBody.length - 1)) {
+        var newStmtCqBody = new ListBuffer[Atom]()
+        for (j <- 0 to (stmtCqBody.length - 1)) {
+          if (j > i)
+            newStmtCqBody += stmtCqBody(j)
+          else if (j < i)
+            newStmtCqBody += ddNewStmtCqBody(j)
+            else if (j == i)
+              newStmtCqBody += ddDeltaStmtCqBody(j)
+        }
+        newStmtCqBodies += newStmtCqBody.toList
       }
-      incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBody.toList), stmt.weights, stmt.supervision, stmt.rule)
     }
+    incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBodies.toList), stmt.weights, stmt.supervision, stmt.rule)
     incrementalStatement.toList
   }
 
diff --git a/DeepDiveLogParser.scala b/DeepDiveLogParser.scala
index 7329f56a2..0072c6c6d 100644
--- a/DeepDiveLogParser.scala
+++ b/DeepDiveLogParser.scala
@@ -11,7 +11,7 @@ case class Variable(varName : String, relName : String, index : Int )
 // TODO make Atom a trait, and have multiple case classes, e.g., RelationAtom and CondExprAtom
 case class Atom(name : String, terms : List[Variable])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, body: List[Atom])
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]])
 case class Column(name : String, t : String)
 
 sealed trait FactorWeight {
@@ -36,7 +36,7 @@ case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statem
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, rule : String) extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, rule : String = "imply") extends Statement // Weighted rule
 
 
 // Parser
@@ -99,8 +99,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case (headatom ~ ":-" ~ disjunctiveBodies) =>
         // TODO handle all disjunctiveBodies
         // XXX only compiling the first body
-        val bodyatoms = disjunctiveBodies(0)
-        ConjunctiveQuery(headatom, bodyatoms.toList)
+        // val bodyatoms = disjunctiveBodies(0)
+        // ConjunctiveQuery(headatom, bodyatoms.toList)
+        ConjunctiveQuery(headatom, disjunctiveBodies)
     }
 
   def relationType: Parser[RelationType] =
diff --git a/DeepDiveLogPrettyPrinter.scala b/DeepDiveLogPrettyPrinter.scala
index d387d9fc8..5b3171b9a 100644
--- a/DeepDiveLogPrettyPrinter.scala
+++ b/DeepDiveLogPrettyPrinter.scala
@@ -49,8 +49,11 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       val vars = a.terms map { _.varName }
       s"${a.name}(${vars.mkString(", ")})"
     }
+    val printListAtom = {a:List[Atom] =>
+      s"${(a map printAtom).mkString(",\n    ")}"
+    }
     s"""${printAtom(cq.head)} :-
-       |    ${(cq.body map printAtom).mkString(",\n    ")}""".stripMargin
+       |    ${(cq.bodies map printListAtom).mkString(";\n    ")}""".stripMargin
   }
 
   def print(stmt: ExtractionRule): String = {

From 7dcd16d01bd4766a84b1dbda1eae4b1e33893b24 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 21 May 2015 15:34:00 -0700
Subject: [PATCH 082/347] change rule to semantics in example

---
 examples/spouse_example.ddl                        | 2 +-
 examples/spouse_example.print-incremental.expected | 2 +-
 examples/spouse_example.print.expected             | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 94a0266e6..1e910528d 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -93,4 +93,4 @@ has_spouse(rid) :-
   has_spouse_features(rid, f)
 weight = f
 label = l
-rule = imply.
+semantics = imply.
diff --git a/examples/spouse_example.print-incremental.expected b/examples/spouse_example.print-incremental.expected
index 0b2a5e9e2..0dececb3e 100644
--- a/examples/spouse_example.print-incremental.expected
+++ b/examples/spouse_example.print-incremental.expected
@@ -256,4 +256,4 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l
-  rule = imply.
+  semantics = imply.
diff --git a/examples/spouse_example.print.expected b/examples/spouse_example.print.expected
index ba4d0d933..eefd87be5 100644
--- a/examples/spouse_example.print.expected
+++ b/examples/spouse_example.print.expected
@@ -88,4 +88,4 @@ has_spouse(rid) :-
     has_spouse_features(rid, f)
   weight = f
   label = l
-  rule = imply.
+  semantics = imply.

From 3d18125b67c72faa27d6adf86d5ce5da1ff43578 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 21 May 2015 15:35:33 -0700
Subject: [PATCH 083/347] change rule to semantics in deriver and printer

---
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 12 ++++++------
 .../deepdive/ddlog/DeepDiveLogPrettyPrinter.scala    |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 2eec10f71..4b84267d4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -38,7 +38,7 @@ case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statem
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, rule : String = "imply") extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, semantics : String = "imply") extends Statement // Weighted rule
 
 
 // Parser
@@ -60,7 +60,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   def variableName = ident
   def functionName = ident
-  def ruleType = ident
+  def semanticType = ident
 
   def columnDeclaration: Parser[Column] =
     columnName ~ columnType ^^ {
@@ -148,13 +148,13 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def supervision = "label" ~> "=" ~> variableName
 
-  def rule = "rule" ~> "=" ~> ruleType
+  def semantics = "semantics" ~> "=" ~> semanticType
 
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ supervision ~ rule
+    ( conjunctiveQuery ~ factorWeight ~ supervision ~ semantics
     ) ^^ {
-      case (q ~ weight ~ supervision ~ rule) =>
-        InferenceRule(q, weight, supervision, rule)
+      case (q ~ weight ~ supervision ~ semantics) =>
+        InferenceRule(q, weight, supervision, semantics)
     }
 
   // rules or schema elements in arbitrary order
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index e7b52565c..f0b2a944b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -79,8 +79,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     ( if (stmt.supervision == null) ""
       else "\n  label = " + stmt.supervision
     ) +
-    ( if (stmt.rule == null) ""
-      else "\n  rule = " + stmt.rule
+    ( if (stmt.semantics == null) ""
+      else "\n  semantics = " + stmt.semantics
     ) + "."
   }
 

From cc852dfd3dbc6f3a6e2341eff5f4be31f5d7bc4a Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 21 May 2015 15:36:31 -0700
Subject: [PATCH 084/347] refactor derivation function

---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 244 ++++++++----------
 1 file changed, 105 insertions(+), 139 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index a1fa2dbc8..3508b784c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -16,34 +16,102 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
+  def transform(cq: ConjunctiveQuery): ConjunctiveQuery = {
+    // New head
+    val incCqHead = cq.head.copy(
+      name = deltaPrefix + cq.head.name,
+      terms = cq.head.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
+    )
+    var incCqBodies = new ListBuffer[List[Atom]]()
+    // New incremental bodies
+    for (body <- cq.bodies) {
+      // Delta body
+      val incDeltaBody = body map {
+        a => a.copy(
+          name = deltaPrefix + a.name,
+          terms = a.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
+        )
+      }
+      // New body
+      val incNewBody = body map {
+        a => a.copy(
+          name = newPrefix + a.name,
+          terms = a.terms map {term => term.copy(relName = newPrefix + term.relName)}
+        )
+      }
+      var i = 0
+      var j = 0
+      for (i <- 0 to (body.length - 1)) {
+        var newBody = new ListBuffer[Atom]()
+        for (j <- 0 to (body.length - 1)) {
+          if (j > i)
+            newBody += body(j)
+          else if (j < i)
+            newBody += incNewBody(j)
+          else if (j == i)
+            newBody += incDeltaBody(j)
+        }
+        incCqBodies += newBody.toList
+      }
+    }
+    ConjunctiveQuery(incCqHead, incCqBodies.toList)
+  }
+
   // Incremental scheme declaration,
   // keep the original scheme and create one delta scheme
   def transform(stmt: SchemaDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
-    // Origin table
-    incrementalStatement += stmt
+    // Incremental table
+    val incStmt = stmt.copy(
+      a = stmt.a.copy(
+          terms = stmt.isQuery match {
+            case true  => stmt.a.terms
+            case false => stmt.a.terms :+ Variable("dd_count", stmt.a.name, stmt.a.terms.length)
+          },
+          types = stmt.isQuery match { 
+            case true  => stmt.a.types
+            case false => stmt.a.types :+ "int"
+          })
+    )
+    incrementalStatement += incStmt
+
     // Delta table
-    var deltaTerms = new ListBuffer[Variable]()
-    for (term <- stmt.a.terms) {
-      deltaTerms += Variable(term.varName, deltaPrefix + term.relName, term.index)
-    }
-    var deltaStmt = SchemaDeclaration(Attribute(deltaPrefix + stmt.a.name, deltaTerms.toList, stmt.a.types), stmt.isQuery)
-    
-    incrementalStatement += deltaStmt
+    val incDeltaStmt = stmt.copy(
+      a = stmt.a.copy(
+        name = deltaPrefix + stmt.a.name,
+        terms = stmt.isQuery match {
+          case true  => stmt.a.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
+          case false => (stmt.a.terms map {term => term.copy(relName = deltaPrefix + term.relName)}) :+ 
+            Variable("dd_count", deltaPrefix + stmt.a.name, stmt.a.terms.length)
+        },
+        types = stmt.isQuery match { 
+          case true  => stmt.a.types
+          case false => stmt.a.types :+ "int"
+        }
+      )
+    )    
+    incrementalStatement += incDeltaStmt
+
     // New table
-    val newTerms = new ListBuffer[Variable]()
-    for (term <- stmt.a.terms) {
-      newTerms += Variable(term.varName, newPrefix + term.relName, term.index)
-    }
-    var newStmt = SchemaDeclaration(Attribute(newPrefix + stmt.a.name, newTerms.toList, stmt.a.types), stmt.isQuery)
-    incrementalStatement += newStmt
+    val incNewStmt = stmt.copy(
+      a = stmt.a.copy(
+        name = newPrefix + stmt.a.name,
+        terms = stmt.isQuery match {
+          case true  => stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)}
+          case false => (stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)}) :+ 
+            Variable("dd_count", newPrefix + stmt.a.name, stmt.a.terms.length)
+        },
+        types = stmt.isQuery match { 
+          case true  => stmt.a.types
+          case false => stmt.a.types :+ "int"
+        }
+      )
+    )
+    incrementalStatement += incNewStmt
+
     if (!stmt.isQuery) {
-      var newStmtCqBodies = new ListBuffer[List[Atom]]()
-      newStmtCqBodies += List(Atom(stmt.a.name, stmt.a.terms.toList))
-      newStmtCqBodies += List(Atom(deltaStmt.a.name, deltaStmt.a.terms.toList))
-      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), newStmtCqBodies.toList))
-      
-      // incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(newStmt.a.name, newStmt.a.terms.toList), List(Atom(deltaStmt.a.name, deltaStmt.a.terms.toList))))
+      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(incNewStmt.a.name, incNewStmt.a.terms),
+        List(List(Atom(incStmt.a.name, incStmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms)))))
     }
     incrementalStatement.toList
   }
@@ -51,140 +119,38 @@ object DeepDiveLogDeltaDeriver{
   // Incremental function declaration,
   // create one delta function scheme based on original function scheme
   def transform(stmt: FunctionDeclaration): List[Statement] = {
-    var incrementalStatement = new ListBuffer[Statement]()
-    var newTerms = new ListBuffer[Variable]()
-    var newInputType: RelationType = stmt.inputType match {
-      case inTy: RelationTypeDeclaration => {
-        var newNames = new ListBuffer[String]()
-        for (name <- inTy.names)
-          newNames += deltaPrefix + name
-        RelationTypeDeclaration(newNames.toList, inTy.types)
-      }
-      case inTy: RelationTypeAlias => RelationTypeAlias(deltaPrefix + inTy.likeRelationName)
-    }
-    var newOutputType: RelationType = stmt.outputType match {
-      case outTy: RelationTypeDeclaration => {
-        var newNames = new ListBuffer[String]()
-        for (name <- outTy.names)
-          newNames += deltaPrefix + name
-        RelationTypeDeclaration(newNames.toList, outTy.types)
+    List(stmt.copy(
+      inputType = stmt.inputType match {
+        case inTy: RelationTypeDeclaration => 
+          inTy.copy(names = inTy.names map {name => deltaPrefix + name})
+        case inTy: RelationTypeAlias => 
+          inTy.copy(likeRelationName = deltaPrefix + inTy.likeRelationName)
+      },
+      outputType = stmt.outputType match {
+        case outTy: RelationTypeDeclaration =>
+          outTy.copy(names = outTy.names map {name => deltaPrefix + name})
+        case outTy: RelationTypeAlias =>
+          outTy.copy(likeRelationName = deltaPrefix + outTy.likeRelationName)
       }
-      case outTy: RelationTypeAlias => RelationTypeAlias(deltaPrefix + outTy.likeRelationName)
-    }
-    incrementalStatement += FunctionDeclaration(stmt.functionName, newInputType, newOutputType, stmt.implementations)
-    incrementalStatement.toList
+    ))
   }
 
   // Incremental extraction rule,
   // create delta rules based on original extraction rule
   def transform(stmt: ExtractionRule): List[Statement] = {
-    var incrementalStatement = new ListBuffer[Statement]()
-    
-    // New head
-    var newStmtCqHeadTerms = new ListBuffer[Variable]()
-    for (headTerm <- stmt.q.head.terms) {
-      newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
-    }
-    var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
-    var newStmtCqBodies = new ListBuffer[List[Atom]]()
-    for (stmtCqBody <- stmt.q.bodies) {
-      // dd delta table from dd_delta_ table
-      var ddDeltaStmtCqBody = new ListBuffer[Atom]()
-      for (cqBody <- stmtCqBody) { // List[Atom]
-        var stmtCqBodyTerms = new ListBuffer[Variable]()
-        for (bodyTerm <- cqBody.terms) {
-          stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
-        }
-        ddDeltaStmtCqBody += Atom(deltaPrefix + cqBody.name, stmtCqBodyTerms.toList)
-      }
-      // dd new body from dd_new_ table
-      var ddNewStmtCqBody = new ListBuffer[Atom]()
-      for (cqBody <- stmtCqBody) { // List[Atom]
-        var stmtCqBodyTerms = new ListBuffer[Variable]()
-        for (bodyTerm <- cqBody.terms) {
-          stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
-        }
-        ddNewStmtCqBody += Atom(newPrefix + cqBody.name, stmtCqBodyTerms.toList)
-      }
-
-      // New statement
-      var i = 0
-      var j = 0
-      for (i <- 0 to (stmtCqBody.length - 1)) {
-        var newStmtCqBody = new ListBuffer[Atom]()
-        for (j <- 0 to (stmtCqBody.length - 1)) {
-          if (j > i)
-            newStmtCqBody += stmtCqBody(j)
-          else if (j < i)
-            newStmtCqBody += ddNewStmtCqBody(j)
-            else if (j == i)
-              newStmtCqBody += ddDeltaStmtCqBody(j)
-        }
-        newStmtCqBodies += newStmtCqBody.toList
-      }
-    }
-    incrementalStatement += ExtractionRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBodies.toList))
-    incrementalStatement.toList
+    List(ExtractionRule(transform(stmt.q)))
   }
 
   // Incremental function call rule,
   // modify function input and output
   def transform(stmt: FunctionCallRule): List[Statement] = {
-    var incrementalStatement = new ListBuffer[Statement]()
-    incrementalStatement += FunctionCallRule(deltaPrefix + stmt.input, deltaPrefix + stmt.output, stmt.function)
-    incrementalStatement.toList
+    List(FunctionCallRule(deltaPrefix + stmt.input, deltaPrefix + stmt.output, stmt.function))
   }
 
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    var incrementalStatement = new ListBuffer[Statement]()
-    
-    // New head
-    var newStmtCqHeadTerms = new ListBuffer[Variable]()
-    for (headTerm <- stmt.q.head.terms) {
-      newStmtCqHeadTerms += Variable(headTerm.varName, deltaPrefix + headTerm.relName, headTerm.index)
-    }
-    var newStmtCqHead = Atom(deltaPrefix + stmt.q.head.name, newStmtCqHeadTerms.toList)
-    var newStmtCqBodies = new ListBuffer[List[Atom]]()
-    for (stmtCqBody <- stmt.q.bodies) {
-      // dd delta table from dd_delta_ table
-      var ddDeltaStmtCqBody = new ListBuffer[Atom]()
-      for (cqBody <- stmtCqBody) { // List[Atom]
-        var stmtCqBodyTerms = new ListBuffer[Variable]()
-        for (bodyTerm <- cqBody.terms) {
-          stmtCqBodyTerms += Variable(bodyTerm.varName, deltaPrefix + bodyTerm.relName, bodyTerm.index)
-        }
-        ddDeltaStmtCqBody += Atom(deltaPrefix + cqBody.name, stmtCqBodyTerms.toList)
-      }
-      // dd new body from dd_new_ table
-      var ddNewStmtCqBody = new ListBuffer[Atom]()
-      for (cqBody <- stmtCqBody) { // List[Atom]
-        var stmtCqBodyTerms = new ListBuffer[Variable]()
-        for (bodyTerm <- cqBody.terms) {
-          stmtCqBodyTerms += Variable(bodyTerm.varName, newPrefix + bodyTerm.relName, bodyTerm.index)
-        }
-        ddNewStmtCqBody += Atom(newPrefix + cqBody.name, stmtCqBodyTerms.toList)
-      }
-
-      // New statement
-      var i = 0
-      var j = 0
-      for (i <- 0 to (stmtCqBody.length - 1)) {
-        var newStmtCqBody = new ListBuffer[Atom]()
-        for (j <- 0 to (stmtCqBody.length - 1)) {
-          if (j > i)
-            newStmtCqBody += stmtCqBody(j)
-          else if (j < i)
-            newStmtCqBody += ddNewStmtCqBody(j)
-            else if (j == i)
-              newStmtCqBody += ddDeltaStmtCqBody(j)
-        }
-        newStmtCqBodies += newStmtCqBody.toList
-      }
-    }
-    incrementalStatement += InferenceRule(ConjunctiveQuery(newStmtCqHead, newStmtCqBodies.toList), stmt.weights, stmt.supervision, stmt.rule)
-    incrementalStatement.toList
+    List(InferenceRule(transform(stmt.q), stmt.weights, stmt.supervision, stmt.semantics))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {

From 57ae857529d2b12e5689c035ff362a4e047f2299 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 21 May 2015 16:01:53 -0700
Subject: [PATCH 085/347] refactor compile function

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 62 +++++++++++--------
 1 file changed, 36 insertions(+), 26 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 6ee7c18ef..e177de92a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -62,6 +62,12 @@ import scala.collection.immutable.HashMap
 import org.apache.commons.lang3.StringEscapeUtils
 import scala.collection.mutable.ListBuffer
 
+object AliasStyle extends Enumeration {
+  type AliasStyle = Value
+  val OriginalOnly, AliasOnly, OriginalAndAlias = Value
+}
+import AliasStyle._
+
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
@@ -89,7 +95,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   var inferenceRuleGroupByHead      : Map[String, List[InferenceRule]] = new HashMap[String, List[InferenceRule]]()
   var functionCallRuleGroupByInput  : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
   var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
-
+  
   def init() = {
     // generate the statements.
     isIncremental = config.isIncremental
@@ -148,7 +154,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // Resolve a column name with alias
-  def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: Int) : Option[String] = {
+  def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: AliasStyle) : Option[String] = {
     val index = qs.getBodyIndex(s)
     val name  = resolveName(qs.getVar(s))
     val relation = q.bodies(0)(index).name
@@ -157,9 +163,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // 1 => use column name and alias for normal extraction rule
     // 2 => use column name for dd_new_ tables
     alias match {
-      case 0 => Some(s"${relation}.R${index}.${name}")
-      case 1 => Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
-      case 2 => Some(s"R${index}.${name}")
+      case AliasStyle.OriginalOnly => Some(s"R${index}.${name}")
+      case AliasStyle.AliasOnly => Some(s"${relation}.R${index}.${name}")
+      case AliasStyle.OriginalAndAlias => Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
     }
   }
 
@@ -283,25 +289,29 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
       for (cqBody <- stmt.q.bodies) {
-        var tmpStmt = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        var tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // Generate the body of the query.
-        val qs              = new QuerySchema( tmpStmt )
+        val qs              = new QuerySchema( tmpCq )
         // variable columns
-        var resolveColumnFlag = tmpStmt.head.name.startsWith("dd_new_") match {
-          case true => 2
-          case false => 1
+        // dd_new_ tale only need original column name to make sure the schema is the same with original table
+        val tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
+        var resolveColumnFlag = tmpCqIsForNewTable match {
+          case true => AliasStyle.OriginalOnly
+          case false => AliasStyle.OriginalAndAlias
         }
-        val variableCols = tmpStmt.head.terms flatMap {
-          case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpStmt, resolveColumnFlag)
+        val variableCols = tmpCq.head.terms flatMap {
+          case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpCq, resolveColumnFlag)
         }
 
         val selectStr = variableCols.mkString(", ")
-        val ddCount = if (ss.isIncremental && (resolveColumnFlag == 1)) ( tmpStmt.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        // additional dd_count column will be added in incremental version not dd_new_ table
+        // dd_new_ table does not need additional dd_count column
+        val ddCount = if (ss.isIncremental && !tmpCqIsForNewTable) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
         val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
 
         inputQueries += s"""
           SELECT ${selectStr}${ddCountStr}
-          ${ ss.generateSQLBody(tmpStmt) }"""
+          ${ ss.generateSQLBody(tmpCq) }"""
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
@@ -359,20 +369,20 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var inputQueries = new ListBuffer[String]()
       for (z <- zs) {
         for (cqBody <- z.q.bodies) {
-          var tmpStmt = ConjunctiveQuery(z.q.head, List(cqBody))
-          val qs = new QuerySchema(tmpStmt)
-          val headTerms = tmpStmt.head.terms map {
+          var tmpCq = ConjunctiveQuery(z.q.head, List(cqBody))
+          val qs = new QuerySchema(tmpCq)
+          val headTerms = tmpCq.head.terms map {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
           }
           val index = qs.getBodyIndex(z.supervision)
           val name  = ss.resolveName(qs.getVar(z.supervision))
           val labelCol = s"R${index}.${name}"
           val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-          val ddCount = if (ss.isIncremental) ( tmpStmt.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
           val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
 
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
-          ${ ss.generateSQLBody(tmpStmt) }
+          ${ ss.generateSQLBody(tmpCq) }
           """
         }
       }
@@ -399,20 +409,20 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var func = ""
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
-        var tmpStmt = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        var tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // edge query
-        val fakeBody        = tmpStmt.head +: tmpStmt.bodies(0)
+        val fakeBody        = tmpCq.head +: tmpCq.bodies(0)
         // val fakeBody        = stmt.q.bodies +: List(stmt.q.head)
-        val fakeCQ          = ConjunctiveQuery(tmpStmt.head, List(fakeBody)) // we will just use the fakeBody below.
+        val fakeCQ          = ConjunctiveQuery(tmpCq.head, List(fakeBody)) // we will just use the fakeBody below.
 
-        val index = tmpStmt.bodies(0).length + 1
+        val index = tmpCq.bodies(0).length + 1
         val qs2 = new QuerySchema( fakeCQ )
-        val variableIdsStr = Some(s"""R0.id AS "${tmpStmt.head.name}.R0.id" """)
+        val variableIdsStr = Some(s"""R0.id AS "${tmpCq.head.name}.R0.id" """)
 
         // weight string
         val uwStr = stmt.weights match {
           case KnownFactorWeight(x) => None
-          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, 1)).mkString(", "))
+          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasStyle.OriginalAndAlias)).mkString(", "))
         }
 
         val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
@@ -431,7 +441,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, 0)).mkString(", ")})"""
+              s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasStyle.AliasOnly)).mkString(", ")})"""
             }
           }
       }

From b83824e92a31a2d8bca1277eab725607f1e5d804 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 21 May 2015 16:07:07 -0700
Subject: [PATCH 086/347] minor changes

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index e177de92a..2dcf267e8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -227,7 +227,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Analyze the dependency between statements and construct a graph.
   def analyzeDependency(statements: List[Statement]) = {
-    var stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++ functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
+    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++ functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
     // Look at the body of each statement to construct a dependency graph
     statements foreach {
@@ -289,13 +289,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
       for (cqBody <- stmt.q.bodies) {
-        var tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
         // variable columns
         // dd_new_ tale only need original column name to make sure the schema is the same with original table
         val tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
-        var resolveColumnFlag = tmpCqIsForNewTable match {
+        val resolveColumnFlag = tmpCqIsForNewTable match {
           case true => AliasStyle.OriginalOnly
           case false => AliasStyle.OriginalAndAlias
         }
@@ -369,7 +369,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var inputQueries = new ListBuffer[String]()
       for (z <- zs) {
         for (cqBody <- z.q.bodies) {
-          var tmpCq = ConjunctiveQuery(z.q.head, List(cqBody))
+          val tmpCq = ConjunctiveQuery(z.q.head, List(cqBody))
           val qs = new QuerySchema(tmpCq)
           val headTerms = tmpCq.head.terms map {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
@@ -409,7 +409,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var func = ""
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
-        var tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // edge query
         val fakeBody        = tmpCq.head +: tmpCq.bodies(0)
         // val fakeBody        = stmt.q.bodies +: List(stmt.q.head)

From e23d99ed8f84edd87661cba7b80aaf9dd9e2012a Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 21 May 2015 16:58:26 -0700
Subject: [PATCH 087/347] refactor

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 32 ++++++------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 51 ++++++++-----------
 2 files changed, 38 insertions(+), 45 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 2dcf267e8..f8cab1cbd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -64,7 +64,12 @@ import scala.collection.mutable.ListBuffer
 
 object AliasStyle extends Enumeration {
   type AliasStyle = Value
+  // Three kinds of column expressions:
+  // OriginalOnly => use column name for dd_new_ tables
+  // AliasOnly => use alias for unknown weight in inference
+  // OriginalAndAlias => use column name and alias for normal extraction rule
   val OriginalOnly, AliasOnly, OriginalAndAlias = Value
+
 }
 import AliasStyle._
 
@@ -158,14 +163,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     val index = qs.getBodyIndex(s)
     val name  = resolveName(qs.getVar(s))
     val relation = q.bodies(0)(index).name
-    // Three kinds of column expressions:
-    // 0 => use alias for unknown weight in inference
-    // 1 => use column name and alias for normal extraction rule
-    // 2 => use column name for dd_new_ tables
     alias match {
-      case AliasStyle.OriginalOnly => Some(s"R${index}.${name}")
-      case AliasStyle.AliasOnly => Some(s"${relation}.R${index}.${name}")
-      case AliasStyle.OriginalAndAlias => Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
+      case OriginalOnly => Some(s"R${index}.${name}")
+      case AliasOnly => Some(s"${relation}.R${index}.${name}")
+      case OriginalAndAlias => Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
     }
   }
 
@@ -296,8 +297,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // dd_new_ tale only need original column name to make sure the schema is the same with original table
         val tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
         val resolveColumnFlag = tmpCqIsForNewTable match {
-          case true => AliasStyle.OriginalOnly
-          case false => AliasStyle.OriginalAndAlias
+          case true => OriginalOnly
+          case false => OriginalAndAlias
         }
         val variableCols = tmpCq.head.terms flatMap {
           case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpCq, resolveColumnFlag)
@@ -409,20 +410,19 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var func = ""
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
-        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // edge query
-        val fakeBody        = tmpCq.head +: tmpCq.bodies(0)
+        val fakeBody        = stmt.q.head +: cqBody
         // val fakeBody        = stmt.q.bodies +: List(stmt.q.head)
-        val fakeCQ          = ConjunctiveQuery(tmpCq.head, List(fakeBody)) // we will just use the fakeBody below.
+        val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody)) // we will just use the fakeBody below.
 
-        val index = tmpCq.bodies(0).length + 1
+        val index = cqBody.length + 1
         val qs2 = new QuerySchema( fakeCQ )
-        val variableIdsStr = Some(s"""R0.id AS "${tmpCq.head.name}.R0.id" """)
+        val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
 
         // weight string
         val uwStr = stmt.weights match {
           case KnownFactorWeight(x) => None
-          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasStyle.OriginalAndAlias)).mkString(", "))
+          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, OriginalAndAlias)).mkString(", "))
         }
 
         val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
@@ -441,7 +441,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasStyle.AliasOnly)).mkString(", ")})"""
+              s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasOnly)).mkString(", ")})"""
             }
           }
       }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 3508b784c..fda08cc32 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -62,49 +62,42 @@ object DeepDiveLogDeltaDeriver{
   def transform(stmt: SchemaDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     // Incremental table
-    val incStmt = stmt.copy(
+    val incStmt = if (stmt.isQuery) stmt else stmt.copy(
       a = stmt.a.copy(
-          terms = stmt.isQuery match {
-            case true  => stmt.a.terms
-            case false => stmt.a.terms :+ Variable("dd_count", stmt.a.name, stmt.a.terms.length)
-          },
-          types = stmt.isQuery match { 
-            case true  => stmt.a.types
-            case false => stmt.a.types :+ "int"
-          })
+          terms = stmt.a.terms :+ Variable("dd_count", stmt.a.name, stmt.a.terms.length),
+          types = stmt.a.types :+ "int"
+          )
     )
     incrementalStatement += incStmt
 
     // Delta table
-    val incDeltaStmt = stmt.copy(
+    var incDeltaStmt = stmt.copy(
       a = stmt.a.copy(
         name = deltaPrefix + stmt.a.name,
-        terms = stmt.isQuery match {
-          case true  => stmt.a.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
-          case false => (stmt.a.terms map {term => term.copy(relName = deltaPrefix + term.relName)}) :+ 
-            Variable("dd_count", deltaPrefix + stmt.a.name, stmt.a.terms.length)
-        },
-        types = stmt.isQuery match { 
-          case true  => stmt.a.types
-          case false => stmt.a.types :+ "int"
-        }
+        terms = stmt.a.terms map {term => term.copy(relName = deltaPrefix + term.relName)},
+        types = stmt.a.types
+      )
+    )
+    if (!stmt.isQuery) incDeltaStmt = incDeltaStmt.copy(
+      a = incDeltaStmt.a.copy(
+        terms = incDeltaStmt.a.terms :+ Variable("dd_count", deltaPrefix + stmt.a.name, stmt.a.terms.length),
+        types = incDeltaStmt.a.types :+ "int"
       )
     )    
     incrementalStatement += incDeltaStmt
 
     // New table
-    val incNewStmt = stmt.copy(
+    var incNewStmt = stmt.copy(
       a = stmt.a.copy(
         name = newPrefix + stmt.a.name,
-        terms = stmt.isQuery match {
-          case true  => stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)}
-          case false => (stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)}) :+ 
-            Variable("dd_count", newPrefix + stmt.a.name, stmt.a.terms.length)
-        },
-        types = stmt.isQuery match { 
-          case true  => stmt.a.types
-          case false => stmt.a.types :+ "int"
-        }
+        terms = stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)},
+        types = stmt.a.types
+      )
+    )
+    if (!stmt.isQuery) incNewStmt = incNewStmt.copy(
+      a = incNewStmt.a.copy(
+        terms = stmt.a.terms :+ Variable("dd_count", newPrefix + stmt.a.name, stmt.a.terms.length),
+        types = stmt.a.types :+ "int"
       )
     )
     incrementalStatement += incNewStmt

From 69c64e7fe7cb810cf461324ced34cd2d7aa884f1 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 00:35:41 -0700
Subject: [PATCH 088/347] Corrects confusing bats test names for --incremental

---
 test/expected-output-test.bats.per-example | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/expected-output-test.bats.per-example b/test/expected-output-test.bats.per-example
index a6dfe2361..5df8042a3 100644
--- a/test/expected-output-test.bats.per-example
+++ b/test/expected-output-test.bats.per-example
@@ -46,7 +46,7 @@ setup() {
 ## tests for --incremental support
 
 # compare the compiled output of the incremental version with what's expected
-@test "print $EXAMPLE_NAME as expected" {
+@test "compile --incremental $EXAMPLE_NAME as expected" {
     expectedOutput=$EXAMPLE_BASEPATH.compile-incremental.expected
     [ -e "$expectedOutput" ] || skip
     scala "$DDLOG_JAR" compile --incremental "$EXAMPLE" |
@@ -54,9 +54,9 @@ setup() {
 }
 
 # compare the pretty-printed output of the incremental version with what's expected
-@test "print $EXAMPLE_NAME as expected" {
+@test "print --incremental $EXAMPLE_NAME as expected" {
     expectedOutput=$EXAMPLE_BASEPATH.print-incremental.expected
     [ -e "$expectedOutput" ] || skip
     scala "$DDLOG_JAR" print --incremental "$EXAMPLE" |
     diff -u "$expectedOutput" -
-}
\ No newline at end of file
+}

From eb9708110ac25ad8d7e02d0486001756bfe0c79a Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 00:41:48 -0700
Subject: [PATCH 089/347] Cleans up tests

- Removes stale test examples
- Corrects some expected outputs
- Renames to more meaningful names
- test.sh will clean up generated ones that don't exist any longer
---
 ...pected => rstu.print-incremental.expected} |   0
 examples/spouse_incremental_example.ddl       | 104 ------------------
 examples/{test9.ddl => test-semantics.ddl}    |   2 +-
 examples/test1.ddl                            |   4 -
 examples/test2.ddl                            |   7 --
 examples/test3.ddl                            |  19 ----
 examples/test4.ddl                            |  18 ---
 examples/test5.ddl                            |  16 ---
 test/test.sh                                  |   1 +
 9 files changed, 2 insertions(+), 169 deletions(-)
 rename examples/{rstu.delta.expected => rstu.print-incremental.expected} (100%)
 delete mode 100644 examples/spouse_incremental_example.ddl
 rename examples/{test9.ddl => test-semantics.ddl} (90%)
 delete mode 100644 examples/test1.ddl
 delete mode 100644 examples/test2.ddl
 delete mode 100644 examples/test3.ddl
 delete mode 100644 examples/test4.ddl
 delete mode 100644 examples/test5.ddl

diff --git a/examples/rstu.delta.expected b/examples/rstu.print-incremental.expected
similarity index 100%
rename from examples/rstu.delta.expected
rename to examples/rstu.print-incremental.expected
diff --git a/examples/spouse_incremental_example.ddl b/examples/spouse_incremental_example.ddl
deleted file mode 100644
index 11503d7d9..000000000
--- a/examples/spouse_incremental_example.ddl
+++ /dev/null
@@ -1,104 +0,0 @@
-articles(
-  article_id text,
-  text       text,
-  dd_count   int).
-
-sentences(
-  document_id     text,
-  sentence        text,
-  words           text[],
-  lemma           text[],
-  pos_tags        text[],
-  dependencies    text[],
-  ner_tags        text[],
-  sentence_offset int,
-  sentence_id     text,
-  dd_count        int).
-
-people_mentions(
-  sentence_id    text,
-  start_position int,
-  length         int,
-  text           text,
-  mention_id     text,
-  dd_count       int).
-
-has_spouse_candidates(
-  person1_id  text,
-  person2_id  text,
-  sentence_id text,
-  description text,
-  relation_id text,
-  is_true     boolean,
-  dd_count    int).
-
-has_spouse_features(
-  relation_id text,
-  feature     text,
-  dd_count    int).
-
-has_spouse?(relation_id text).
-
-people_mentions :-
-  !ext_people(ext_people_input).
-
-ext_people_input(
-  sentence_id text,
-  words       text[],
-  ner_tags    text[],
-  dd_count    int).
-
-ext_people_input(s, words, ner_tags) :-
-  sentences(a, b, words, c, d, e, ner_tags, f, s).
-
-function ext_people over like ext_people_input
-                 returns like people_mentions
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
-
-has_spouse_candidates :-
-  !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(
-  sentence_id text,
-  p1_id       text,
-  p1_text     text,
-  p2_id       text,
-  p2_text     text,
-  dd_count    int).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, a, b, p1_text, p1_id),
-  people_mentions(s, c, d, p2_text, p2_id).
-
-function ext_has_spouse over like ext_has_spouse_input
-                     returns like has_spouse_candidates
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
-
-has_spouse_features :-
-  !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(
-  words             text[],
-  relation_id       text,
-  p1_start_position int,
-  p1_length         int,
-  p2_start_position int,
-  p2_length         int,
-  dd_count          int).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-  people_mentions(s, p1idx, p1len, k, person1_id),
-  people_mentions(s, p2idx, p2len, l, person2_id).
-  
-function ext_has_spouse_features over like ext_has_spouse_features_input
-                              returns like has_spouse_features
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
-
-has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
-  has_spouse_features(rid, f)
-weight = f
-label = l
-rule = imply.
diff --git a/examples/test9.ddl b/examples/test-semantics.ddl
similarity index 90%
rename from examples/test9.ddl
rename to examples/test-semantics.ddl
index e93f7ad0f..3de8d36d1 100644
--- a/examples/test9.ddl
+++ b/examples/test-semantics.ddl
@@ -6,4 +6,4 @@ Q?(x int).
 Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w)
 weight = y
 label   = z
-rule = imply.
\ No newline at end of file
+semantics = imply.
diff --git a/examples/test1.ddl b/examples/test1.ddl
deleted file mode 100644
index 2e0e20fdc..000000000
--- a/examples/test1.ddl
+++ /dev/null
@@ -1,4 +0,0 @@
-      S(a1,a2); 
-      R(pk,f)!; 
-      Q(x) :- R(x,f) weight=f;
-      Q2(x) :- R(x, f), S(x, y) weight = f
diff --git a/examples/test2.ddl b/examples/test2.ddl
deleted file mode 100644
index 6add95d11..000000000
--- a/examples/test2.ddl
+++ /dev/null
@@ -1,7 +0,0 @@
-      S(a1,a2); 
-      R(pk,f); 
-      Q(x) :- R(x,f) weight=f; 
-      Q(x) :- S(x,y),T(y); 
-      T(base_attr)!; 
-      R(y,x) :- U(x,y); 
-      S(x,y) :- R(x,y);
diff --git a/examples/test3.ddl b/examples/test3.ddl
deleted file mode 100644
index a5fdbc227..000000000
--- a/examples/test3.ddl
+++ /dev/null
@@ -1,19 +0,0 @@
-      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id);
-      has_spouse_features(relation_id, feature);
-      q(rid)!;
-
-      q(y) :-
-        has_spouse(a, b, c, d, x, y),
-        has_spouse_features(y, f)
-        weight = f
-        label = x;
-      q(y) :-
-        has_spouse(a, b, c, d, x, y),
-        has_spouse_features(y, f)
-        weight = f
-        label = x;
-
-    //   f_has_spouse_symmetry(x, y) :-
-    //     has_spouse(a1, a2, a3, a4, x, a6),
-    //     has_spouse(a2, a1, b3, b4, y, b6)
-    //     weight = 1;
diff --git a/examples/test4.ddl b/examples/test4.ddl
deleted file mode 100644
index 47989f676..000000000
--- a/examples/test4.ddl
+++ /dev/null
@@ -1,18 +0,0 @@
-      articles(article_id, text);
-      sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
-      people_mentions(sentence_id, start_position, length, text, mention_id);
-      has_spouse(person1_id, person2_id, sentence_id, description, is_true, relation_id, id);
-      has_spouse_features(relation_id, feature);
-      people_mentions(sentence_id, words, ner_tags):- 
-        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)
-      udf=ext_people;
-      has_spouse(sentence_id, p1.mention_id, p1.text, p2.mention_id, p2.text):-
-        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, p1.mention_id),
-        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, p2.mention_id)
-      udf=ext_has_spouse;
-      has_spouse_features(words, relation_id, p1.start_position, p1.length, p2.start_position, p2.length):-
-        sentences(s.document_id, s.sentence, words, s.lemma, s.pos_tags, s.dependencies, s.ner_tags, s.sentence_offset, sentence_id),
-        has_spouse(person1_id, person2_id, sentence_id, h.description, h.is_true, relation_id, h.id),
-        people_mentions(sentence_id, p1.start_position, p1.length, p1.text, person1_id),
-        people_mentions(sentence_id, p2.start_position, p2.length, p2.text, person2_id)
-      udf=ext_has_spouse_features;
diff --git a/examples/test5.ddl b/examples/test5.ddl
deleted file mode 100644
index 55144dda4..000000000
--- a/examples/test5.ddl
+++ /dev/null
@@ -1,16 +0,0 @@
-      ext_people_input(
-        sentence_id,
-        words,
-        ner_tags).
-      function ext_has_spouse_features over like ext_has_spouse_features_input
-                                  returns like has_spouse_features
-      implementation udf/ext_has_spouse_features.py handles tsv lines.
-      function ext_people over like ext_people_input
-                     returns like people_mentions
-      implementation udf/ext_people.py handles tsv lines.
-      ext_people_input(sentence_id, words, ner_tags):- 
-        sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
-      people_mentions :-
-      !ext_people(ext_people_input).
-      people_mentions_1 :-
-      !ext_people(people_mentions).
diff --git a/test/test.sh b/test/test.sh
index 6fe8347cc..643142895 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -8,6 +8,7 @@ type bats &>/dev/null ||
     git clone https://github.com/sstephenson/bats.git
 
 # generate bats tests for every per-example templates
+rm -f *.for-example-*.bats
 for t in *.bats.per-example; do
     testName=${t%.bats.per-example}
     # generate one for each example

From fb9650fa52402ab3e5928ce1b0763cd60ca5603f Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 00:40:12 -0700
Subject: [PATCH 090/347] Improves parser to support comments

C/Java/Scala style comments: // single line or /* multi line */
as well as shell script style comments: # single line
---
 examples/test-comments.ddl                       | 16 ++++++++++++++++
 examples/test-comments.print.expected            |  9 +++++++++
 .../org/deepdive/ddlog/DeepDiveLogParser.scala   |  4 ++++
 3 files changed, 29 insertions(+)
 create mode 100644 examples/test-comments.ddl
 create mode 100644 examples/test-comments.print.expected

diff --git a/examples/test-comments.ddl b/examples/test-comments.ddl
new file mode 100644
index 000000000..147644b75
--- /dev/null
+++ b/examples/test-comments.ddl
@@ -0,0 +1,16 @@
+# This is a comment
+// This is also a comment
+
+R(a int).
+S( a int   # this is an integer field
+ , b text  // seond one is a text field
+ , c /* third one is a float field */ float
+).
+
+R(x) :- S(x, y, z).
+
+/*
+Multi
+-line
+comments
+    /* unfortunately cannot be nested */
diff --git a/examples/test-comments.print.expected b/examples/test-comments.print.expected
new file mode 100644
index 000000000..8b8213f4c
--- /dev/null
+++ b/examples/test-comments.print.expected
@@ -0,0 +1,9 @@
+R(a int).
+
+S(a int,
+  b text,
+  c float).
+
+R(x) :-
+    S(x, y, z).
+
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 4b84267d4..221b1cfd5 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -52,6 +52,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
       s.stripPrefix("\"").stripSuffix("\""))
   }
 
+  // C/Java/Scala-style as well as shell script-style comments are supported
+  // by treating them as whiteSpace
+  protected override val whiteSpace = """(?:(?:^|\s+)#.*|//.*|(?m)/\*(\*(?!/)|[^*])*\*/|\s)+""".r
+
   // We just use Java identifiers to parse various names
   def relationName = ident
   def columnName   = ident

From 74f8959f19f694136c98cff14bb8b2da4de2053e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 03:48:03 -0700
Subject: [PATCH 091/347] Makes expected output test leave actual output

---
 .gitignore                                 | 1 +
 test/expected-output-test.bats.per-example | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/.gitignore b/.gitignore
index 67ba8778f..91b68d153 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@
 target
 /test/bats
 /test/*.for-example-*.bats
+/examples/*.actual
diff --git a/test/expected-output-test.bats.per-example b/test/expected-output-test.bats.per-example
index 5df8042a3..fe5e0d12f 100644
--- a/test/expected-output-test.bats.per-example
+++ b/test/expected-output-test.bats.per-example
@@ -23,6 +23,7 @@ setup() {
     expectedOutput=$EXAMPLE_BASEPATH.compile.expected
     [ -e "$expectedOutput" ] || skip
     scala "$DDLOG_JAR" compile "$EXAMPLE" |
+    tee "${expectedOutput%.expected}.actual" |
     diff -u "$expectedOutput" -
 }
 
@@ -31,6 +32,7 @@ setup() {
     expectedOutput=$EXAMPLE_BASEPATH.print.expected
     [ -e "$expectedOutput" ] || skip
     scala "$DDLOG_JAR" print "$EXAMPLE" |
+    tee "${expectedOutput%.expected}.actual" |
     diff -u "$expectedOutput" -
 }
 
@@ -50,6 +52,7 @@ setup() {
     expectedOutput=$EXAMPLE_BASEPATH.compile-incremental.expected
     [ -e "$expectedOutput" ] || skip
     scala "$DDLOG_JAR" compile --incremental "$EXAMPLE" |
+    tee "${expectedOutput%.expected}.actual" |
     diff -u "$expectedOutput" -
 }
 
@@ -58,5 +61,6 @@ setup() {
     expectedOutput=$EXAMPLE_BASEPATH.print-incremental.expected
     [ -e "$expectedOutput" ] || skip
     scala "$DDLOG_JAR" print --incremental "$EXAMPLE" |
+    tee "${expectedOutput%.expected}.actual" |
     diff -u "$expectedOutput" -
 }

From 198afe0faa55f6329ca47a8223b5029743db4eb6 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 03:48:32 -0700
Subject: [PATCH 092/347] Fixes a test case to use multiple bodies for delta
 rules

---
 examples/rstu.print-incremental.expected | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/examples/rstu.print-incremental.expected b/examples/rstu.print-incremental.expected
index 7c5ac4359..c0e725b31 100644
--- a/examples/rstu.print-incremental.expected
+++ b/examples/rstu.print-incremental.expected
@@ -23,11 +23,9 @@ dd_delta_T(x text,
 dd_new_T(x text,
          f text).
 
-dd_new_T(x, f) :-
-    T(x, f).
-
-dd_new_T(x, f) :-
-    dd_delta_T(x, f).
+dd_new_T(x, f, dd_count) :-
+    T(x, f, dd_count);
+    dd_delta_T(x, f, dd_count).
 
 U(x text,
   l text).
@@ -43,14 +41,10 @@ R(x) :-
 dd_delta_R(x) :-
     dd_delta_S(x),
     T(x, f),
-    U(x, l).
-
-dd_delta_R(x) :-
+    U(x, l);
     dd_new_S(x),
     dd_delta_T(x, f),
-    U(x, l).
-
-dd_delta_R(x) :-
+    U(x, l);
     dd_new_S(x),
     dd_new_T(x, f),
     dd_delta_U(x, l).

From f40d64a84ab30ee4ac256d8d8a7660113d887a47 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 03:59:00 -0700
Subject: [PATCH 093/347] Removes redundant test examples

---
 examples/{test8.ddl => test-multibody.ddl} | 0
 examples/test.ddl                          | 8 --------
 examples/test6.ddl                         | 5 -----
 examples/test7.ddl                         | 6 ------
 4 files changed, 19 deletions(-)
 rename examples/{test8.ddl => test-multibody.ddl} (100%)
 delete mode 100644 examples/test.ddl
 delete mode 100644 examples/test6.ddl
 delete mode 100644 examples/test7.ddl

diff --git a/examples/test8.ddl b/examples/test-multibody.ddl
similarity index 100%
rename from examples/test8.ddl
rename to examples/test-multibody.ddl
diff --git a/examples/test.ddl b/examples/test.ddl
deleted file mode 100644
index bf6b427cf..000000000
--- a/examples/test.ddl
+++ /dev/null
@@ -1,8 +0,0 @@
-A(a1 int,
-  a2 int).
-B(a1 int,
-  a2 int).
-C(a1 int,
-  a2 int,
-  a3 int).
-Q(a1) :- A(a1, x); B(y, a1); C(a, b, a1).
diff --git a/examples/test6.ddl b/examples/test6.ddl
deleted file mode 100644
index 35820ed03..000000000
--- a/examples/test6.ddl
+++ /dev/null
@@ -1,5 +0,0 @@
-R(a int, b int).
-S(a int, b int).
-Q(x int).
-
-Q(y) :- R(x, y); R(x, y), S(y, z).
\ No newline at end of file
diff --git a/examples/test7.ddl b/examples/test7.ddl
deleted file mode 100644
index 6c1c7f0fe..000000000
--- a/examples/test7.ddl
+++ /dev/null
@@ -1,6 +0,0 @@
-R(a int, b int).
-S(a int, b int).
-T(a int, b int).
-Q(x int).
-
-Q(y) :- R(x, y); R(x, y), S(y, z); S(y, x), T(x, z).
\ No newline at end of file

From 24c80282c1febef01544f7ab38bc9b43e7c8a9ba Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 04:01:00 -0700
Subject: [PATCH 094/347] Renames a test case to many_joins

---
 examples/{rstu.ddl => test-many_joins.ddl}                        | 0
 ...mental.expected => test-many_joins.print-incremental.expected} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename examples/{rstu.ddl => test-many_joins.ddl} (100%)
 rename examples/{rstu.print-incremental.expected => test-many_joins.print-incremental.expected} (100%)

diff --git a/examples/rstu.ddl b/examples/test-many_joins.ddl
similarity index 100%
rename from examples/rstu.ddl
rename to examples/test-many_joins.ddl
diff --git a/examples/rstu.print-incremental.expected b/examples/test-many_joins.print-incremental.expected
similarity index 100%
rename from examples/rstu.print-incremental.expected
rename to examples/test-many_joins.print-incremental.expected

From 567ca5c6d7d21a76064844834c374eaedf48bc6e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 04:03:12 -0700
Subject: [PATCH 095/347] Adds a test for parsing every example

---
 test/expected-output-test.bats.per-example | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/test/expected-output-test.bats.per-example b/test/expected-output-test.bats.per-example
index fe5e0d12f..61b49201d 100644
--- a/test/expected-output-test.bats.per-example
+++ b/test/expected-output-test.bats.per-example
@@ -18,6 +18,20 @@ setup() {
 
 ## tests for basic compilation and pretty-printing
 
+# check if example can be parsed
+@test "parse $EXAMPLE_NAME" {
+    scala "$DDLOG_JAR" print "$EXAMPLE" >/dev/null
+}
+
+# check if print is idempotent
+@test "print $EXAMPLE_NAME is idempotent" {
+    printed=$BATS_TMPDIR/ddlog-$EXAMPLE_NAME-printed.ddl
+    scala "$DDLOG_JAR" print "$EXAMPLE" >"$printed" || skip
+    scala "$DDLOG_JAR" print "$printed" |
+    diff -u "$printed" -
+}
+
+
 # compare the compiled output with what's expected
 @test "compile $EXAMPLE_NAME" {
     expectedOutput=$EXAMPLE_BASEPATH.compile.expected
@@ -36,14 +50,6 @@ setup() {
     diff -u "$expectedOutput" -
 }
 
-# check if print is idempotent
-@test "print $EXAMPLE_NAME is idempotent" {
-    printed=$BATS_TMPDIR/ddlog-$EXAMPLE_NAME-printed.ddl
-    scala "$DDLOG_JAR" print "$EXAMPLE" >"$printed" || skip
-    scala "$DDLOG_JAR" print "$printed" |
-    diff -u "$printed" -
-}
-
 
 ## tests for --incremental support
 

From e1aaff493cd7bcfb28814b1786f8c7e0c0dd0546 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 04:51:18 -0700
Subject: [PATCH 096/347] Moves expected output tests under test/

- Each set of input with expected outputs is now put under a standard
  directory, which makes it super easy to add more tests by cloning
  existing ones.
---
 .gitignore                                    |  5 +-
 test/expected-output-test.bats.per-example    | 72 ----------------
 test/expected-output-test.bats.template       | 85 +++++++++++++++++++
 test/expected-output-test/README.md           | 13 +++
 .../expected-output-test/many_joins/input.ddl |  0
 .../many_joins/print-incremental.expected     |  0
 .../expected-output-test/multibody/input.ddl  |  0
 .../expected-output-test/semantics/input.ddl  |  0
 .../compile-incremental.expected              |  0
 .../spouse_example/compile.expected           |  0
 .../spouse_example/input.ddl                  |  1 +
 .../spouse_example/print-incremental.expected |  0
 .../spouse_example/print.expected             |  0
 test/test.sh                                  | 27 +++---
 14 files changed, 115 insertions(+), 88 deletions(-)
 delete mode 100644 test/expected-output-test.bats.per-example
 create mode 100644 test/expected-output-test.bats.template
 create mode 100644 test/expected-output-test/README.md
 rename examples/test-many_joins.ddl => test/expected-output-test/many_joins/input.ddl (100%)
 rename examples/test-many_joins.print-incremental.expected => test/expected-output-test/many_joins/print-incremental.expected (100%)
 rename examples/test-multibody.ddl => test/expected-output-test/multibody/input.ddl (100%)
 rename examples/test-semantics.ddl => test/expected-output-test/semantics/input.ddl (100%)
 rename examples/spouse_example.compile-incremental.expected => test/expected-output-test/spouse_example/compile-incremental.expected (100%)
 rename examples/spouse_example.compile.expected => test/expected-output-test/spouse_example/compile.expected (100%)
 create mode 120000 test/expected-output-test/spouse_example/input.ddl
 rename examples/spouse_example.print-incremental.expected => test/expected-output-test/spouse_example/print-incremental.expected (100%)
 rename examples/spouse_example.print.expected => test/expected-output-test/spouse_example/print.expected (100%)

diff --git a/.gitignore b/.gitignore
index 91b68d153..9ccfab0ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@
 /ddlog-test.jar
 /ddlog-test.jar.classpath
 target
+
 /test/bats
-/test/*.for-example-*.bats
-/examples/*.actual
+/test/expected-output-test/**/*.bats
+/test/expected-output-test/**/*.actual
diff --git a/test/expected-output-test.bats.per-example b/test/expected-output-test.bats.per-example
deleted file mode 100644
index 61b49201d..000000000
--- a/test/expected-output-test.bats.per-example
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env bats
-# Per example tests
-#
-# This test compares outputs of various modes of ddlog against a .ddl example file with its expected output.
-# Test is skipped if no expected output is found.
-
-# required variables
-: ${DDLOG_JAR:?path to ddlog jar}
-: ${EXAMPLE:?path to input ddlog program}
-EXAMPLE_BASEPATH=${EXAMPLE%.ddl}
-EXAMPLE_NAME=${EXAMPLE_BASEPATH##*/}
-
-# some preconditions
-setup() {
-    [ -e "$DDLOG_JAR" ]
-    [ -e "$EXAMPLE" ]
-}
-
-## tests for basic compilation and pretty-printing
-
-# check if example can be parsed
-@test "parse $EXAMPLE_NAME" {
-    scala "$DDLOG_JAR" print "$EXAMPLE" >/dev/null
-}
-
-# check if print is idempotent
-@test "print $EXAMPLE_NAME is idempotent" {
-    printed=$BATS_TMPDIR/ddlog-$EXAMPLE_NAME-printed.ddl
-    scala "$DDLOG_JAR" print "$EXAMPLE" >"$printed" || skip
-    scala "$DDLOG_JAR" print "$printed" |
-    diff -u "$printed" -
-}
-
-
-# compare the compiled output with what's expected
-@test "compile $EXAMPLE_NAME" {
-    expectedOutput=$EXAMPLE_BASEPATH.compile.expected
-    [ -e "$expectedOutput" ] || skip
-    scala "$DDLOG_JAR" compile "$EXAMPLE" |
-    tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
-}
-
-# compare the pretty-printed output with what's expected
-@test "print $EXAMPLE_NAME as expected" {
-    expectedOutput=$EXAMPLE_BASEPATH.print.expected
-    [ -e "$expectedOutput" ] || skip
-    scala "$DDLOG_JAR" print "$EXAMPLE" |
-    tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
-}
-
-
-## tests for --incremental support
-
-# compare the compiled output of the incremental version with what's expected
-@test "compile --incremental $EXAMPLE_NAME as expected" {
-    expectedOutput=$EXAMPLE_BASEPATH.compile-incremental.expected
-    [ -e "$expectedOutput" ] || skip
-    scala "$DDLOG_JAR" compile --incremental "$EXAMPLE" |
-    tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
-}
-
-# compare the pretty-printed output of the incremental version with what's expected
-@test "print --incremental $EXAMPLE_NAME as expected" {
-    expectedOutput=$EXAMPLE_BASEPATH.print-incremental.expected
-    [ -e "$expectedOutput" ] || skip
-    scala "$DDLOG_JAR" print --incremental "$EXAMPLE" |
-    tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
-}
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
new file mode 100644
index 000000000..fc3ae84f5
--- /dev/null
+++ b/test/expected-output-test.bats.template
@@ -0,0 +1,85 @@
+#!/usr/bin/env bats
+# Expected output test with Bats
+#
+# These test cases compares outputs of various modes of ddlog against a .ddl example file with its expected output.
+# Tests are skipped if no expected output is found.
+#
+# This .bats.template file should be run by creating a .bats symlink to it
+# next to a directory with the same name (without .bats) that contains
+# input.ddl.
+
+# required variables
+: ${DDLOG_JAR:?path to ddlog jar}
+
+# some shorthands
+cd "$BATS_TEST_DIRNAME"
+TESTDIR=${BATS_TEST_FILENAME%.bats}
+TESTDIR=${TESTDIR#$PWD/}
+TEST=${BATS_TEST_FILENAME#$PWD/}
+it="${TEST%.bats}:"
+
+# how to invoke ddlog compiler
+ddlog() {
+    scala "$DDLOG_JAR" "$@"
+}
+
+# some preconditions
+setup() {
+    [ -e "$DDLOG_JAR" ]
+    [ -e "$TESTDIR" ]
+}
+
+## tests for basic compilation and pretty-printing
+
+# check if example can be parsed
+@test "$it parses input" {
+    ddlog print "$TESTDIR"/input.ddl >/dev/null
+}
+
+# check if print is idempotent
+@test "$it parses and prints what it prints (idempotent)" {
+    printed=$TESTDIR/print-idempotent.actual
+    ddlog print "$TESTDIR"/input.ddl >"$printed" || skip
+    ddlog print "$printed" |
+    diff -u "$printed" -
+}
+
+
+# compare the compiled output with what's expected
+@test "$it compiles input as expected" {
+    expectedOutput=$TESTDIR/compile.expected
+    [ -e "$expectedOutput" ] || skip
+    ddlog compile "$TESTDIR"/input.ddl |
+    tee "${expectedOutput%.expected}.actual" |
+    diff -u "$expectedOutput" -
+}
+
+# compare the pretty-printed output with what's expected
+@test "$it prints input as expected" {
+    expectedOutput=$TESTDIR/print.expected
+    [ -e "$expectedOutput" ] || skip
+    ddlog print "$TESTDIR"/input.ddl |
+    tee "${expectedOutput%.expected}.actual" |
+    diff -u "$expectedOutput" -
+}
+
+
+## tests for --incremental support
+
+# compare the compiled output of the incremental version with what's expected
+@test "$it compiles --incremental input as expected" {
+    expectedOutput=$TESTDIR/compile-incremental.expected
+    [ -e "$expectedOutput" ] || skip
+    ddlog compile --incremental "$TESTDIR"/input.ddl |
+    tee "${expectedOutput%.expected}.actual" |
+    diff -u "$expectedOutput" -
+}
+
+# compare the pretty-printed output of the incremental version with what's expected
+@test "$it prints --incremental input as expected" {
+    expectedOutput=$TESTDIR/print-incremental.expected
+    [ -e "$expectedOutput" ] || skip
+    ddlog print --incremental "$TESTDIR"/input.ddl |
+    tee "${expectedOutput%.expected}.actual" |
+    diff -u "$expectedOutput" -
+}
diff --git a/test/expected-output-test/README.md b/test/expected-output-test/README.md
new file mode 100644
index 000000000..2e9915962
--- /dev/null
+++ b/test/expected-output-test/README.md
@@ -0,0 +1,13 @@
+Here are test cases for running the "expected-output-test".
+
+Each test case is a directory that contains the following files:
+
+* `input.ddl` is the input DDLog program.
+    * Parser is tested against every input program.
+    * If the input is supposed to cause a parse error, `parse.error.expected` containing an expected error message should be there.
+* `print.expected` is the expected output of running the `print` command.  Test is skipped if not available.
+* `compile.expected` is the expected output of running the `compile` command.  Test is skipped if not available.
+* `print-incremental.expected` is the expected output of running the `print --incremental` command.  Test is skipped if not available.
+* `compile-incremental.expected` is the expected output of running the `compile --incremental` command.  Test is skipped if not available.
+
+The tests will create `.actual` files corresponding to each `.expected` file.
diff --git a/examples/test-many_joins.ddl b/test/expected-output-test/many_joins/input.ddl
similarity index 100%
rename from examples/test-many_joins.ddl
rename to test/expected-output-test/many_joins/input.ddl
diff --git a/examples/test-many_joins.print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
similarity index 100%
rename from examples/test-many_joins.print-incremental.expected
rename to test/expected-output-test/many_joins/print-incremental.expected
diff --git a/examples/test-multibody.ddl b/test/expected-output-test/multibody/input.ddl
similarity index 100%
rename from examples/test-multibody.ddl
rename to test/expected-output-test/multibody/input.ddl
diff --git a/examples/test-semantics.ddl b/test/expected-output-test/semantics/input.ddl
similarity index 100%
rename from examples/test-semantics.ddl
rename to test/expected-output-test/semantics/input.ddl
diff --git a/examples/spouse_example.compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
similarity index 100%
rename from examples/spouse_example.compile-incremental.expected
rename to test/expected-output-test/spouse_example/compile-incremental.expected
diff --git a/examples/spouse_example.compile.expected b/test/expected-output-test/spouse_example/compile.expected
similarity index 100%
rename from examples/spouse_example.compile.expected
rename to test/expected-output-test/spouse_example/compile.expected
diff --git a/test/expected-output-test/spouse_example/input.ddl b/test/expected-output-test/spouse_example/input.ddl
new file mode 120000
index 000000000..63c01729c
--- /dev/null
+++ b/test/expected-output-test/spouse_example/input.ddl
@@ -0,0 +1 @@
+../../../examples/spouse_example.ddl
\ No newline at end of file
diff --git a/examples/spouse_example.print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
similarity index 100%
rename from examples/spouse_example.print-incremental.expected
rename to test/expected-output-test/spouse_example/print-incremental.expected
diff --git a/examples/spouse_example.print.expected b/test/expected-output-test/spouse_example/print.expected
similarity index 100%
rename from examples/spouse_example.print.expected
rename to test/expected-output-test/spouse_example/print.expected
diff --git a/test/test.sh b/test/test.sh
index 643142895..2567f1771 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
 set -eu
+shopt -s nullglob
 cd "$(dirname "$0")"
 
 # make sure bats is available
@@ -7,21 +8,19 @@ PATH="$PWD/bats/bin:$PATH"
 type bats &>/dev/null ||
     git clone https://github.com/sstephenson/bats.git
 
-# generate bats tests for every per-example templates
-rm -f *.for-example-*.bats
-for t in *.bats.per-example; do
-    testName=${t%.bats.per-example}
-    # generate one for each example
-    for ddl in ../examples/*.ddl; do
-        exampleName=${ddl%.ddl}
-        exampleName=${exampleName#../examples/}
-        batsFile="$testName".for-example-"$exampleName".bats
-        {
-            printf "EXAMPLE=%q\n" "$ddl"
-            cat $t
-        } >$batsFile
+# instantiate bats tests templates under its directory
+for t in *.bats.template; do
+    [[ -e "$t" ]] || continue
+    testSpecDir=${t%.bats.template}
+    rm -f "$testSpecDir"/*.bats
+    # create a .bats symlink for each test specification
+    for testSpec in "$testSpecDir"/*/input.ddl; do
+        [[ -e "$testSpec" ]] || continue
+        testSpec=${testSpec%/input.ddl}
+        batsFile="$testSpec".bats
+        ln -sfn ../"$t" "$batsFile"
     done
 done
 
 # run all .bats tests
-bats *.bats
+bats *.bats */*.bats

From 8fd0cd195578d60a56ac501e9bb17bb261397a50 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 05:05:46 -0700
Subject: [PATCH 097/347] Uses wdiff (word diff) when it can in expected output
 tests

---
 test/expected-output-test.bats.template | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index fc3ae84f5..1d39f1c80 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -22,6 +22,16 @@ it="${TEST%.bats}:"
 ddlog() {
     scala "$DDLOG_JAR" "$@"
 }
+# how to diff (prefer wdiff)
+if type wdiff &>/dev/null; then
+    diff() {
+        wdiff --terminal --statistics -- "$@"
+    }
+else
+    diff() {
+        command diff --unified --ignore-all-space -- "$@"
+    }
+fi
 
 # some preconditions
 setup() {
@@ -41,7 +51,7 @@ setup() {
     printed=$TESTDIR/print-idempotent.actual
     ddlog print "$TESTDIR"/input.ddl >"$printed" || skip
     ddlog print "$printed" |
-    diff -u "$printed" -
+    diff "$printed" -
 }
 
 
@@ -51,7 +61,7 @@ setup() {
     [ -e "$expectedOutput" ] || skip
     ddlog compile "$TESTDIR"/input.ddl |
     tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
+    diff "$expectedOutput" -
 }
 
 # compare the pretty-printed output with what's expected
@@ -60,7 +70,7 @@ setup() {
     [ -e "$expectedOutput" ] || skip
     ddlog print "$TESTDIR"/input.ddl |
     tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
+    diff "$expectedOutput" -
 }
 
 
@@ -72,7 +82,7 @@ setup() {
     [ -e "$expectedOutput" ] || skip
     ddlog compile --incremental "$TESTDIR"/input.ddl |
     tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
+    diff "$expectedOutput" -
 }
 
 # compare the pretty-printed output of the incremental version with what's expected
@@ -81,5 +91,5 @@ setup() {
     [ -e "$expectedOutput" ] || skip
     ddlog print --incremental "$TESTDIR"/input.ddl |
     tee "${expectedOutput%.expected}.actual" |
-    diff -u "$expectedOutput" -
+    diff "$expectedOutput" -
 }

From 14f90a685ffd8878aaec2f01ea98923525cc142b Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 05:20:34 -0700
Subject: [PATCH 098/347] Updates test/README

---
 test/README.md | 5 +++--
 test/test.sh   | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/README.md b/test/README.md
index 84d2e324d..24a3b94a3 100644
--- a/test/README.md
+++ b/test/README.md
@@ -4,5 +4,6 @@ DDLog tests
 `test.sh` runs all tests.
 
 [Bats](https://github.com/sstephenson/bats.git) is used for most end-to-end tests.
-Every `*-example.bats` will be run for each `.ddl` example under `../examples/`, with the `EXAMPLE` environment variable set to the path to the example.
-Rest of the `.bats` tests will run once.
+Before running Bats, `.bats` files will be prepared for each `*.bats.template` if they have a directory with the same name (without `.bats.template`) contaning test spec subdirectories.
+For each test spec, a `.bats` symlink pointing to the `.bats.template` is created, which is in turn run with Bats.
+This way, creating new tests for different inputs is it's very easy as we can simply clone existing test specs.
diff --git a/test/test.sh b/test/test.sh
index 2567f1771..408322d64 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -14,8 +14,8 @@ for t in *.bats.template; do
     testSpecDir=${t%.bats.template}
     rm -f "$testSpecDir"/*.bats
     # create a .bats symlink for each test specification
-    for testSpec in "$testSpecDir"/*/input.ddl; do
-        [[ -e "$testSpec" ]] || continue
+    for testSpec in "$testSpecDir"/*; do
+        [[ -d "$testSpec" ]] || continue
         testSpec=${testSpec%/input.ddl}
         batsFile="$testSpec".bats
         ln -sfn ../"$t" "$batsFile"

From 6eba6eb8d3a2693635988658e874e14a3659d86d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 05:34:30 -0700
Subject: [PATCH 099/347] Adds a TravisCI config

---
 .travis.yml | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 000000000..1d605eaaa
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,5 @@
+scala:
+    - "2.11.1"
+before_install:
+    - sudo apt-get install -qq make bats wdiff
+script: make

From 3e680fa5dfd4320ecd55b722868db840b925a779 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 05:36:09 -0700
Subject: [PATCH 100/347] Adds a TravisCI badge to README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9c4866568..d2b647407 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-DeepDiveLogCompiler
+DeepDiveLogCompiler [![Build Status](https://travis-ci.org/HazyResearch/ddlog.svg)](https://travis-ci.org/HazyResearch/ddlog)
 ===================
 
 A compiler that enables writing DeepDive apps in a Datalog-like syntax.

From b5b2431a19db2c9a87a16e91ba8e04162c582e45 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 06:16:26 -0700
Subject: [PATCH 101/347] Makes test directly use .class files not packaged jar

and improves make clean to do a better job
---
 .gitignore                              |  2 --
 Makefile                                | 30 +++++++++++++------------
 test/expected-output-test.bats.template |  5 ++---
 3 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/.gitignore b/.gitignore
index 9ccfab0ac..2fb25d6c0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,4 @@
 /ddlog.jar
-/ddlog-test.jar
-/ddlog-test.jar.classpath
 target
 
 /test/bats
diff --git a/Makefile b/Makefile
index 32c9c3e24..595218e61 100644
--- a/Makefile
+++ b/Makefile
@@ -1,35 +1,37 @@
 # Makefile for DeepDiveLogCompiler
 
+SOURCE_DIR = src/main/scala/org/deepdive/ddlog
+TARGET_DIR = target/scala-2.10/classes
+TEST_CLASSPATH_CACHE = $(TARGET_DIR)/dependency-classpath
 JAR = ddlog.jar
-TEST_JAR = ddlog-test.jar
-TEST_CLASSPATH_CACHE = ddlog-test.jar.classpath
 
 # test
 .PHONY: test
-test: $(TEST_JAR) $(TEST_CLASSPATH_CACHE)
-	DDLOG_JAR=$(realpath $<) \
-CLASSPATH=$(shell cat $(TEST_CLASSPATH_CACHE)) \
+test: $(TARGET_DIR) $(TEST_CLASSPATH_CACHE)
+	CLASSPATH=$(realpath $<):$(shell cat $(TEST_CLASSPATH_CACHE)) \
+TEST_CLASS_OR_JAR=org.deepdive.ddlog.DeepDiveLog \
 test/test.sh
 $(TEST_CLASSPATH_CACHE): build.sbt $(wildcard project/*.sbt)
 	sbt "export compile:dependency-classpath" | tail -1 >$@
+$(TARGET_DIR): $(wildcard $(SOURCE_DIR)/*.scala)
+	sbt compile
 
 # test standalone package
 .PHONY: test-package
 test-package: $(JAR)
-	$(MAKE) test TEST_JAR=$<
-
-# build test jar
-$(TEST_JAR): $(wildcard src/main/scala/org/deepdive/ddlog/*.scala)
-	sbt package
-	ln -sfn $$(ls -t target/scala-*/*_*.jar | head -1) $@
-	touch $@
+	CLASSPATH= \
+TEST_CLASS_OR_JAR=$(realpath $(JAR)) \
+test/test.sh
 
 # build standalone jar
-$(JAR): $(wildcard *.scala)
-	sbt assembly
+$(JAR): $(wildcard $(SOURCE_DIR)/*.scala)
+	sbt clean assembly
 	ln -sfn $$(ls -t target/scala-*/*-assembly-*.jar | head -1) $@
 	touch $@
 
 .PHONY: clean
 clean:
 	sbt clean
+	# clean test artifacts
+	rm -f $(JAR) $(TEST_CLASSPATH_CACHE) $(wildcard test/*/*/*.actual)
+	find test/ -name '*.bats' -type l -exec rm -f {} +
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index 1d39f1c80..acc0320df 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -9,7 +9,7 @@
 # input.ddl.
 
 # required variables
-: ${DDLOG_JAR:?path to ddlog jar}
+: ${TEST_CLASS_OR_JAR:?class name or path to the ddlog.jar to test}
 
 # some shorthands
 cd "$BATS_TEST_DIRNAME"
@@ -20,7 +20,7 @@ it="${TEST%.bats}:"
 
 # how to invoke ddlog compiler
 ddlog() {
-    scala "$DDLOG_JAR" "$@"
+    scala "$TEST_CLASS_OR_JAR" "$@"
 }
 # how to diff (prefer wdiff)
 if type wdiff &>/dev/null; then
@@ -35,7 +35,6 @@ fi
 
 # some preconditions
 setup() {
-    [ -e "$DDLOG_JAR" ]
     [ -e "$TESTDIR" ]
 }
 

From af13f75b63637480f1456a3ff0705373884d6d13 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 07:05:19 -0700
Subject: [PATCH 102/347] Fixes TravisCI config, adds Coveralls

---
 .travis.yml              |  7 +++++--
 Makefile                 | 18 ++++++++++++++++++
 README.md                | 27 ++++++++++++++++++---------
 project/build.properties |  1 +
 project/build.sbt        |  5 +++++
 5 files changed, 47 insertions(+), 11 deletions(-)
 create mode 100644 project/build.properties
 create mode 100644 project/build.sbt

diff --git a/.travis.yml b/.travis.yml
index 1d605eaaa..881c92d55 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,8 @@
 scala:
     - "2.11.1"
 before_install:
-    - sudo apt-get install -qq make bats wdiff
-script: make
+    - sudo apt-get install -qq make wdiff
+script:
+    - make
+after_success:
+    - sbt coverageReport coveralls
diff --git a/Makefile b/Makefile
index 595218e61..dd6d958d4 100644
--- a/Makefile
+++ b/Makefile
@@ -14,7 +14,23 @@ test/test.sh
 $(TEST_CLASSPATH_CACHE): build.sbt $(wildcard project/*.sbt)
 	sbt "export compile:dependency-classpath" | tail -1 >$@
 $(TARGET_DIR): $(wildcard $(SOURCE_DIR)/*.scala)
+ifndef MEASURE_COVERAGE
 	sbt compile
+else
+	# enabling coverage measurement
+	sbt coverage compile
+endif
+
+# test coverage report from a clean build
+.PHONY: coverage-report test-coverage
+coverage-report: test-coverage
+	sbt coverageReport
+test-coverage: clean
+	-$(MAKE) test MEASURE_COVERAGE=1
+coveralls: coverage-report
+	# submit coverage data to https://coveralls.io/r/HazyResearch/ddlog
+	# (Make sure you have set COVERALLS_REPO_TOKEN=...)
+	sbt coveralls
 
 # test standalone package
 .PHONY: test-package
@@ -24,6 +40,8 @@ TEST_CLASS_OR_JAR=$(realpath $(JAR)) \
 test/test.sh
 
 # build standalone jar
+.PHONY: package
+package: $(JAR)
 $(JAR): $(wildcard $(SOURCE_DIR)/*.scala)
 	sbt clean assembly
 	ln -sfn $$(ls -t target/scala-*/*-assembly-*.jar | head -1) $@
diff --git a/README.md b/README.md
index d2b647407..af122c6bd 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,10 @@
-DeepDiveLogCompiler [![Build Status](https://travis-ci.org/HazyResearch/ddlog.svg)](https://travis-ci.org/HazyResearch/ddlog)
+DeepDiveLog [![Build Status](https://travis-ci.org/HazyResearch/ddlog.svg)](https://travis-ci.org/HazyResearch/ddlog) [![Coverage Status](https://coveralls.io/repos/HazyResearch/ddlog/badge.svg)](https://coveralls.io/r/HazyResearch/ddlog)
 ===================
 
-A compiler that enables writing DeepDive apps in a Datalog-like syntax.
-
-## Testing
-
-```bash
-make
-```
+A Datalog-like language for writing DeepDive apps.
 
 ## Building
-The following command produces a standalone jar.
+The following command produces a standalone jar that contains the compiler.
 
 ```bash
 make ddlog.jar
@@ -18,8 +12,23 @@ make ddlog.jar
 
 ## Running
 The following will generate an application.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
+
 ```bash
 mkdir -p examples/spouse_example
 java -jar ddlog.jar compile examples/spouse_example.ddl >examples/spouse_example/application.conf
 ```
 
+
+## Testing
+The following command runs all tests under test/.
+
+```bash
+make  # or make test
+```
+
+## Coverage
+The following command produces a test coverage report.
+
+```bash
+make coverage-report
+```
diff --git a/project/build.properties b/project/build.properties
new file mode 100644
index 000000000..748703f77
--- /dev/null
+++ b/project/build.properties
@@ -0,0 +1 @@
+sbt.version=0.13.7
diff --git a/project/build.sbt b/project/build.sbt
new file mode 100644
index 000000000..20c696dc3
--- /dev/null
+++ b/project/build.sbt
@@ -0,0 +1,5 @@
+resolvers += Classpaths.sbtPluginReleases
+
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.0.4") //  for sbt-0.13.5 or higher
+
+addSbtPlugin("org.scoverage" % "sbt-coveralls" % "1.0.0") //  for sbt-0.13.5 or higher

From 7631917d45c1e62bfcf461b06d8dea5d2253301a Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 07:15:13 -0700
Subject: [PATCH 103/347] Fixes TravisCI to declare language

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 881c92d55..9782dd099 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,3 +1,4 @@
+language: scala
 scala:
     - "2.11.1"
 before_install:

From e45ca3adc598ee83322ed823a9818df7b4fa4e6f Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 07:22:32 -0700
Subject: [PATCH 104/347] Fixes Travis builds to measure coverage

---
 .travis.yml | 6 +++---
 Makefile    | 7 +++----
 README.md   | 2 +-
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 9782dd099..db7cc0cee 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,8 +2,8 @@ language: scala
 scala:
     - "2.11.1"
 before_install:
-    - sudo apt-get install -qq make wdiff
+    - sudo apt-get install -qq scala make wdiff
 script:
-    - make
+    - make test MEASURE_COVERAGE=true
 after_success:
-    - sbt coverageReport coveralls
+    - sbt coveralls
diff --git a/Makefile b/Makefile
index dd6d958d4..44e19fd75 100644
--- a/Makefile
+++ b/Makefile
@@ -22,12 +22,11 @@ else
 endif
 
 # test coverage report from a clean build
-.PHONY: coverage-report test-coverage
-coverage-report: test-coverage
-	sbt coverageReport
+.PHONY: test-coverage coveralls
 test-coverage: clean
 	-$(MAKE) test MEASURE_COVERAGE=1
-coveralls: coverage-report
+	sbt coverageReport
+coveralls: test-coverage
 	# submit coverage data to https://coveralls.io/r/HazyResearch/ddlog
 	# (Make sure you have set COVERALLS_REPO_TOKEN=...)
 	sbt coveralls
diff --git a/README.md b/README.md
index af122c6bd..78933f57c 100644
--- a/README.md
+++ b/README.md
@@ -30,5 +30,5 @@ make  # or make test
 The following command produces a test coverage report.
 
 ```bash
-make coverage-report
+make test-coverage
 ```

From d162ee44e60493ddc80bee65d2f5d7421157f986 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 07:43:59 -0700
Subject: [PATCH 105/347] Fixes Makefile to play nice with Travis

by not using scala command
---
 .travis.yml                             | 2 +-
 Makefile                                | 4 ++--
 test/expected-output-test.bats.template | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index db7cc0cee..eacfee640 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,7 +2,7 @@ language: scala
 scala:
     - "2.11.1"
 before_install:
-    - sudo apt-get install -qq scala make wdiff
+    - sudo apt-get install -qq make wdiff
 script:
     - make test MEASURE_COVERAGE=true
 after_success:
diff --git a/Makefile b/Makefile
index 44e19fd75..355386c94 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@
 
 SOURCE_DIR = src/main/scala/org/deepdive/ddlog
 TARGET_DIR = target/scala-2.10/classes
-TEST_CLASSPATH_CACHE = $(TARGET_DIR)/dependency-classpath
+TEST_CLASSPATH_CACHE = $(TARGET_DIR)/../dependency-classpath
 JAR = ddlog.jar
 
 # test
@@ -35,7 +35,7 @@ coveralls: test-coverage
 .PHONY: test-package
 test-package: $(JAR)
 	CLASSPATH= \
-TEST_CLASS_OR_JAR=$(realpath $(JAR)) \
+TEST_CLASS_OR_JAR="-jar $(realpath $(JAR))" \
 test/test.sh
 
 # build standalone jar
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index acc0320df..174f3a907 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -20,7 +20,7 @@ it="${TEST%.bats}:"
 
 # how to invoke ddlog compiler
 ddlog() {
-    scala "$TEST_CLASS_OR_JAR" "$@"
+    java $TEST_CLASS_OR_JAR "$@"
 }
 # how to diff (prefer wdiff)
 if type wdiff &>/dev/null; then

From cea1156554066f593eb43102f71789faed3f955e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 07:52:56 -0700
Subject: [PATCH 106/347] Forces bats --pretty on Travis

---
 test/test.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/test.sh b/test/test.sh
index 408322d64..36641c621 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -22,5 +22,8 @@ for t in *.bats.template; do
     done
 done
 
+# TravisCI supports colorful output
+! ${TRAVIS:-false} || set -- --pretty "$@"
+
 # run all .bats tests
-bats *.bats */*.bats
+bats "$@" *.bats */*.bats

From a01370e2c7bd88c659dff572914aee5c8c3fa1ee Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 07:55:12 -0700
Subject: [PATCH 107/347] Polishes wdiff output for Travis as well

---
 test/expected-output-test.bats.template | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index 174f3a907..cad5ac21b 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -9,7 +9,7 @@
 # input.ddl.
 
 # required variables
-: ${TEST_CLASS_OR_JAR:?class name or path to the ddlog.jar to test}
+: ${TEST_CLASS_OR_JAR:?class name or -jar with the path to the ddlog.jar to test}
 
 # some shorthands
 cd "$BATS_TEST_DIRNAME"
@@ -24,13 +24,13 @@ ddlog() {
 }
 # how to diff (prefer wdiff)
 if type wdiff &>/dev/null; then
-    diff() {
-        wdiff --terminal --statistics -- "$@"
-    }
+    if ${TRAVIS:-false}; then
+        diff() { wdiff            --statistics -- "$@"; }
+    else
+        diff() { wdiff --terminal --statistics -- "$@"; }
+    fi
 else
-    diff() {
-        command diff --unified --ignore-all-space -- "$@"
-    }
+    diff() { command diff --unified --ignore-all-space -- "$@"; }
 fi
 
 # some preconditions

From 46673c9f96963b238d73bd1d237a415ba4248a80 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 08:08:40 -0700
Subject: [PATCH 108/347] Polishes the tests for readability from Travis

Bats' special characters actually aren't shown correctly.
---
 .travis.yml                             | 2 +-
 test/expected-output-test.bats.template | 1 -
 test/test.sh                            | 3 ---
 3 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index eacfee640..f955b0537 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,7 +2,7 @@ language: scala
 scala:
     - "2.11.1"
 before_install:
-    - sudo apt-get install -qq make wdiff
+    - sudo apt-get install -qq wdiff
 script:
     - make test MEASURE_COVERAGE=true
 after_success:
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index cad5ac21b..c61d7ded7 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -12,7 +12,6 @@
 : ${TEST_CLASS_OR_JAR:?class name or -jar with the path to the ddlog.jar to test}
 
 # some shorthands
-cd "$BATS_TEST_DIRNAME"
 TESTDIR=${BATS_TEST_FILENAME%.bats}
 TESTDIR=${TESTDIR#$PWD/}
 TEST=${BATS_TEST_FILENAME#$PWD/}
diff --git a/test/test.sh b/test/test.sh
index 36641c621..a0317ea01 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -22,8 +22,5 @@ for t in *.bats.template; do
     done
 done
 
-# TravisCI supports colorful output
-! ${TRAVIS:-false} || set -- --pretty "$@"
-
 # run all .bats tests
 bats "$@" *.bats */*.bats

From 61e9d26f2b920a25abd9fafef29da19f40cf2acc Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 08:12:39 -0700
Subject: [PATCH 109/347] Turns Bats into a submodule

---
 .gitignore   | 1 -
 .gitmodules  | 3 +++
 test/bats    | 1 +
 test/test.sh | 2 --
 4 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 test/bats

diff --git a/.gitignore b/.gitignore
index 2fb25d6c0..60477fe8b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,5 @@
 /ddlog.jar
 target
 
-/test/bats
 /test/expected-output-test/**/*.bats
 /test/expected-output-test/**/*.actual
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 000000000..db077d414
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "test/bats"]
+	path = test/bats
+	url = https://github.com/sstephenson/bats.git
diff --git a/test/bats b/test/bats
new file mode 160000
index 000000000..955309ab9
--- /dev/null
+++ b/test/bats
@@ -0,0 +1 @@
+Subproject commit 955309ab943ea157ded0c402df98b160bb45ff92
diff --git a/test/test.sh b/test/test.sh
index a0317ea01..cf48bf7dc 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -5,8 +5,6 @@ cd "$(dirname "$0")"
 
 # make sure bats is available
 PATH="$PWD/bats/bin:$PATH"
-type bats &>/dev/null ||
-    git clone https://github.com/sstephenson/bats.git
 
 # instantiate bats tests templates under its directory
 for t in *.bats.template; do

From 9745165c47e8c6eaf54aebf7ac410e0ff80441f7 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 08:22:08 -0700
Subject: [PATCH 110/347] Polishes wdiff error: .actual instead of (null)

---
 test/expected-output-test.bats.template | 30 ++++++++++++-------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index c61d7ded7..bc6a26573 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -46,29 +46,29 @@ setup() {
 
 # check if print is idempotent
 @test "$it parses and prints what it prints (idempotent)" {
-    printed=$TESTDIR/print-idempotent.actual
+    printed=$TESTDIR/printed.actual
     ddlog print "$TESTDIR"/input.ddl >"$printed" || skip
-    ddlog print "$printed" |
-    diff "$printed" -
+    ddlog print "$printed" >"$TESTDIR"/printed-printed.actual
+    diff "$printed" "$TESTDIR"/printed-printed.actual
 }
 
 
 # compare the compiled output with what's expected
 @test "$it compiles input as expected" {
     expectedOutput=$TESTDIR/compile.expected
+    actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog compile "$TESTDIR"/input.ddl |
-    tee "${expectedOutput%.expected}.actual" |
-    diff "$expectedOutput" -
+    ddlog compile "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
 }
 
 # compare the pretty-printed output with what's expected
 @test "$it prints input as expected" {
     expectedOutput=$TESTDIR/print.expected
+    actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog print "$TESTDIR"/input.ddl |
-    tee "${expectedOutput%.expected}.actual" |
-    diff "$expectedOutput" -
+    ddlog print "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
 }
 
 
@@ -77,17 +77,17 @@ setup() {
 # compare the compiled output of the incremental version with what's expected
 @test "$it compiles --incremental input as expected" {
     expectedOutput=$TESTDIR/compile-incremental.expected
+    actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog compile --incremental "$TESTDIR"/input.ddl |
-    tee "${expectedOutput%.expected}.actual" |
-    diff "$expectedOutput" -
+    ddlog compile --incremental "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
 }
 
 # compare the pretty-printed output of the incremental version with what's expected
 @test "$it prints --incremental input as expected" {
     expectedOutput=$TESTDIR/print-incremental.expected
+    actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog print --incremental "$TESTDIR"/input.ddl |
-    tee "${expectedOutput%.expected}.actual" |
-    diff "$expectedOutput" -
+    ddlog print --incremental "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
 }

From 2fd2c978707ae5bc97854ecdef57b6dc068afa37 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 15:24:57 -0700
Subject: [PATCH 111/347] Adds tests for confirming parse errors

---
 .gitignore                                    |  4 +-
 test/bats-template.bash                       | 27 ++++++++++++
 test/expected-output-test.bats.template       | 43 ++++++-------------
 test/expected-output-test/comments/input.ddl  |  2 +-
 test/parse-error-test.bats.template           | 21 +++++++++
 .../nested_multiline_comments/input.ddl       |  1 +
 .../parse-error.expected                      |  4 ++
 7 files changed, 69 insertions(+), 33 deletions(-)
 create mode 100644 test/bats-template.bash
 create mode 100644 test/parse-error-test.bats.template
 create mode 100644 test/parse-error-test/nested_multiline_comments/input.ddl
 create mode 100644 test/parse-error-test/nested_multiline_comments/parse-error.expected

diff --git a/.gitignore b/.gitignore
index 60477fe8b..61245514c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 /ddlog.jar
 target
 
-/test/expected-output-test/**/*.bats
-/test/expected-output-test/**/*.actual
+/test/*-test/**/*.bats
+/test/*-test/**/*.actual
diff --git a/test/bats-template.bash b/test/bats-template.bash
new file mode 100644
index 000000000..319ed5004
--- /dev/null
+++ b/test/bats-template.bash
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+# Utilities for testing with Bats
+
+# required variables
+: ${TEST_CLASS_OR_JAR:?class name or -jar with the path to the ddlog.jar to test}
+
+# some shorthands
+TESTDIR=${BATS_TEST_FILENAME%.bats}
+TESTDIR=${TESTDIR#$PWD/}
+TEST=${BATS_TEST_FILENAME#$PWD/}
+it="${TEST%.bats}:"
+
+# how to invoke ddlog compiler
+ddlog() {
+    java $TEST_CLASS_OR_JAR "$@"
+}
+# how to diff (prefer wdiff)
+if type wdiff &>/dev/null; then
+    if ${TRAVIS:-false}; then
+        diff() { wdiff            --statistics -- "$@"; }
+    else
+        diff() { wdiff --terminal --statistics -- "$@"; }
+    fi
+else
+    diff() { command diff --unified --ignore-all-space -- "$@"; }
+fi
+
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index bc6a26573..59be8b438 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -1,36 +1,10 @@
 #!/usr/bin/env bats
-# Expected output test with Bats
-#
+# Expected output tests
+# 
 # These test cases compares outputs of various modes of ddlog against a .ddl example file with its expected output.
 # Tests are skipped if no expected output is found.
-#
-# This .bats.template file should be run by creating a .bats symlink to it
-# next to a directory with the same name (without .bats) that contains
-# input.ddl.
 
-# required variables
-: ${TEST_CLASS_OR_JAR:?class name or -jar with the path to the ddlog.jar to test}
-
-# some shorthands
-TESTDIR=${BATS_TEST_FILENAME%.bats}
-TESTDIR=${TESTDIR#$PWD/}
-TEST=${BATS_TEST_FILENAME#$PWD/}
-it="${TEST%.bats}:"
-
-# how to invoke ddlog compiler
-ddlog() {
-    java $TEST_CLASS_OR_JAR "$@"
-}
-# how to diff (prefer wdiff)
-if type wdiff &>/dev/null; then
-    if ${TRAVIS:-false}; then
-        diff() { wdiff            --statistics -- "$@"; }
-    else
-        diff() { wdiff --terminal --statistics -- "$@"; }
-    fi
-else
-    diff() { command diff --unified --ignore-all-space -- "$@"; }
-fi
+source bats-template.bash  # for $TESTDIR, $it, etc.
 
 # some preconditions
 setup() {
@@ -41,7 +15,16 @@ setup() {
 
 # check if example can be parsed
 @test "$it parses input" {
-    ddlog print "$TESTDIR"/input.ddl >/dev/null
+    expectedError="$TESTDIR"/parse-error.expected
+    if [ -e "$expectedError" ]; then
+        # input is expected to have parse errors
+        actualError=${expectedError%.expected}.actual
+        ! ddlog print "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+        diff "$expectedError" "$actualError"
+    else
+        # input is supposed to parse without errors
+        ddlog print "$TESTDIR"/input.ddl >/dev/null
+    fi
 }
 
 # check if print is idempotent
diff --git a/test/expected-output-test/comments/input.ddl b/test/expected-output-test/comments/input.ddl
index 147644b75..f34c68b9d 100644
--- a/test/expected-output-test/comments/input.ddl
+++ b/test/expected-output-test/comments/input.ddl
@@ -13,4 +13,4 @@ R(x) :- S(x, y, z).
 Multi
 -line
 comments
-    /* unfortunately cannot be nested */
+*/
diff --git a/test/parse-error-test.bats.template b/test/parse-error-test.bats.template
new file mode 100644
index 000000000..b15cc80d5
--- /dev/null
+++ b/test/parse-error-test.bats.template
@@ -0,0 +1,21 @@
+#!/usr/bin/env bats
+# Parse error test
+# 
+# The test case here feeds a malformed .ddl into ddlog's print command and compares whether it produces an expected error.
+
+source bats-template.bash  # for $TESTDIR, $it, etc.
+
+# some preconditions
+setup() {
+    [ -e "$TESTDIR" ]
+    expectedError="$TESTDIR"/parse-error.expected
+    [ -e "$expectedError" ]
+    actualError=${expectedError%.expected}.actual
+}
+
+# check if input produces a parse error
+@test "$it parses input" {
+    ! ddlog print "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+    diff "$expectedError" "$actualError"
+}
+
diff --git a/test/parse-error-test/nested_multiline_comments/input.ddl b/test/parse-error-test/nested_multiline_comments/input.ddl
new file mode 100644
index 000000000..82e085022
--- /dev/null
+++ b/test/parse-error-test/nested_multiline_comments/input.ddl
@@ -0,0 +1 @@
+/* Multi-line comments /* unfortunately cannot be nested */ */
diff --git a/test/parse-error-test/nested_multiline_comments/parse-error.expected b/test/parse-error-test/nested_multiline_comments/parse-error.expected
new file mode 100644
index 000000000..366b77ddc
--- /dev/null
+++ b/test/parse-error-test/nested_multiline_comments/parse-error.expected
@@ -0,0 +1,4 @@
+[error] parse-error-test/nested_multiline_comments/input.ddl[1.61] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `*' found
+
+/* Multi-line comments /* unfortunately cannot be nested */ */
+                                                            ^

From 2c4a6eddd3404856a821d8fbddf1cf122667f042 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 23 May 2015 15:52:49 -0700
Subject: [PATCH 112/347] Makes `make test-coverage` incremental by avoiding
 clean

It turns out `sbt coverage compile` takes care of rebuilding the instrumented .classes.
---
 Makefile | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index 355386c94..efb9b5f84 100644
--- a/Makefile
+++ b/Makefile
@@ -2,6 +2,7 @@
 
 SOURCE_DIR = src/main/scala/org/deepdive/ddlog
 TARGET_DIR = target/scala-2.10/classes
+COVERAGE_DIR = $(TARGET_DIR)/../scoverage-data
 TEST_CLASSPATH_CACHE = $(TARGET_DIR)/../dependency-classpath
 JAR = ddlog.jar
 
@@ -13,18 +14,22 @@ TEST_CLASS_OR_JAR=org.deepdive.ddlog.DeepDiveLog \
 test/test.sh
 $(TEST_CLASSPATH_CACHE): build.sbt $(wildcard project/*.sbt)
 	sbt "export compile:dependency-classpath" | tail -1 >$@
-$(TARGET_DIR): $(wildcard $(SOURCE_DIR)/*.scala)
+
+SOURCES = $(wildcard $(SOURCE_DIR)/*.scala)
 ifndef MEASURE_COVERAGE
+$(TARGET_DIR): $(SOURCES)
 	sbt compile
 else
+$(TARGET_DIR): $(COVERAGE_DIR)
+$(COVERAGE_DIR): $(SOURCES)
 	# enabling coverage measurement
 	sbt coverage compile
 endif
 
-# test coverage report from a clean build
+# test coverage report
 .PHONY: test-coverage coveralls
-test-coverage: clean
-	-$(MAKE) test MEASURE_COVERAGE=1
+test-coverage:
+	-$(MAKE) test MEASURE_COVERAGE=true
 	sbt coverageReport
 coveralls: test-coverage
 	# submit coverage data to https://coveralls.io/r/HazyResearch/ddlog

From 0d58a32d7630b32df7938af15452a785580edfe7 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 26 May 2015 21:57:25 -0700
Subject: [PATCH 113/347] fix bugs in test

---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  4 +-
 .../many_joins/print-incremental.expected     | 43 ++++++++++++-------
 2 files changed, 29 insertions(+), 18 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index fda08cc32..b4ac0c56c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -96,8 +96,8 @@ object DeepDiveLogDeltaDeriver{
     )
     if (!stmt.isQuery) incNewStmt = incNewStmt.copy(
       a = incNewStmt.a.copy(
-        terms = stmt.a.terms :+ Variable("dd_count", newPrefix + stmt.a.name, stmt.a.terms.length),
-        types = stmt.a.types :+ "int"
+        terms = incNewStmt.a.terms :+ Variable("dd_count", newPrefix + stmt.a.name, stmt.a.terms.length),
+        types = incNewStmt.a.types :+ "int"
       )
     )
     incrementalStatement += incNewStmt
diff --git a/test/expected-output-test/many_joins/print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
index c0e725b31..745d8e067 100644
--- a/test/expected-output-test/many_joins/print-incremental.expected
+++ b/test/expected-output-test/many_joins/print-incremental.expected
@@ -2,41 +2,52 @@ R?(x text).
 
 dd_delta_R?(x text).
 
-S(x text).
+dd_new_R?(x text).
 
-dd_delta_S(x text).
+S(x text,
+  dd_count int).
 
-dd_new_S(x text).
+dd_delta_S(x text,
+           dd_count int).
 
-dd_new_S(x) :-
-    S(x).
+dd_new_S(x text,
+         dd_count int).
 
-dd_new_S(x) :-
-    dd_delta_S(x).
+dd_new_S(x, dd_count) :-
+    S(x, dd_count);
+    dd_delta_S(x, dd_count).
 
 T(x text,
-  f text).
+  f text,
+  dd_count int).
 
 dd_delta_T(x text,
-           f text).
+           f text,
+           dd_count int).
 
 dd_new_T(x text,
-         f text).
+         f text,
+         dd_count int).
 
 dd_new_T(x, f, dd_count) :-
     T(x, f, dd_count);
     dd_delta_T(x, f, dd_count).
 
 U(x text,
-  l text).
+  l text,
+  dd_count int).
 
 dd_delta_U(x text,
-           l text).
+           l text,
+           dd_count int).
 
-R(x) :-
-    S(x),
-    T(x, f),
-    U(x, l).
+dd_new_U(x text,
+         l text,
+         dd_count int).
+
+dd_new_U(x, l, dd_count) :-
+    U(x, l, dd_count);
+    dd_delta_U(x, l, dd_count).
 
 dd_delta_R(x) :-
     dd_delta_S(x),

From 7f6a09ebfda5bf55ae409b6d1e48b5a0c619339c Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 26 May 2015 23:45:12 -0700
Subject: [PATCH 114/347] support pipeplines:   1. Add three pipelines: initdb,
 extraction, inference   2. Create tables for all schema declaration   3. For
 extraction rules, using TRUNCATE/INSERT INTO if it contains   schema,
 otherwise using DROP VIEW IF EXISTS/CREATE VIEW.   4. Change inference rule
 index to global statement index for creating   inference pipeline.

---
 examples/spouse_example.ddl                   |  20 --
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 100 ++++--
 .../compile-incremental.expected              | 315 ++++++++++++++----
 .../spouse_example/compile.expected           |  97 +++++-
 .../spouse_example/print-incremental.expected |  72 ----
 .../spouse_example/print.expected             |  17 -
 6 files changed, 404 insertions(+), 217 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 1e910528d..1e3e0304b 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -37,11 +37,6 @@ has_spouse?(relation_id text).
 people_mentions :-
   !ext_people(ext_people_input).
 
-ext_people_input(
-  sentence_id text,
-  words       text[],
-  ner_tags    text[]).
-
 ext_people_input(s, words, ner_tags) :-
   sentences(a, b, words, c, d, e, ner_tags, f, s).
 
@@ -52,13 +47,6 @@ function ext_people over like ext_people_input
 has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
 
-ext_has_spouse_input(
-  sentence_id text,
-  p1_id       text,
-  p1_text     text,
-  p2_id       text,
-  p2_text     text).
-
 ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, a, b, p1_text, p1_id),
   people_mentions(s, c, d, p2_text, p2_id).
@@ -70,14 +58,6 @@ function ext_has_spouse over like ext_has_spouse_input
 has_spouse_features :-
   !ext_has_spouse_features(ext_has_spouse_features_input).
 
-ext_has_spouse_features_input(
-  words             text[],
-  relation_id       text,
-  p1_start_position int,
-  p1_length         int,
-  p2_start_position int,
-  p2_length         int).
-
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
   has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index f8cab1cbd..4d63f391e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -96,11 +96,12 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   var isIncremental : Boolean = false
 
   // Mapping head names to the actual statements
+  var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
   var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
   var inferenceRuleGroupByHead      : Map[String, List[InferenceRule]] = new HashMap[String, List[InferenceRule]]()
   var functionCallRuleGroupByInput  : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
   var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
-  
+
   def init() = {
     // generate the statements.
     isIncremental = config.isIncremental
@@ -130,12 +131,18 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // Given a statement, resolve its name for the compiled extractor block.
   def resolveExtractorBlockName(s: Statement): String = {
     s match {
-      case s: FunctionCallRule => s"extraction_rule_${statements indexOf s}"
-      case s: ExtractionRule   => s"extraction_rule_${statements indexOf s}"
-      case s: InferenceRule    => s"extraction_rule_${s.q.head.name}"
+      case s: SchemaDeclaration => s"extraction_rule_${statements indexOf s}"
+      case s: FunctionCallRule  => s"extraction_rule_${statements indexOf s}"
+      case s: ExtractionRule    => s"extraction_rule_${statements indexOf s}"
+      case s: InferenceRule     => s"extraction_rule_${s.q.head.name}"
     }
   }
 
+  // Given an inference rule, resolve its name for the compiled inference block.
+  def resolveInferenceBlockName(s: InferenceRule): String = {
+    s"factor_${s.q.head.name}_${statements indexOf s}"
+  }
+
   // Given a variable, resolve it.  TODO: This should give a warning,
   // if we encouter a variable that is not in this map, then something
   // odd has happened.
@@ -203,20 +210,24 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // Group statements by head
   def groupByHead(statements: List[Statement]) = {
     // Compile compilation states by head name based on type
-    val extractionRuleToCompile = new ListBuffer[ExtractionRule]()
-    val inferenceRuleToCompile = new ListBuffer[InferenceRule]()
-    val functionCallRuleToCompile = new ListBuffer[FunctionCallRule]()
+    val schemaDeclarationToCompile = new ListBuffer[SchemaDeclaration]()
+    val extractionRuleToCompile    = new ListBuffer[ExtractionRule]()
+    val inferenceRuleToCompile     = new ListBuffer[InferenceRule]()
+    val functionCallRuleToCompile  = new ListBuffer[FunctionCallRule]()
+
     statements foreach (_ match {
-      case s: ExtractionRule   => extractionRuleToCompile += s
-      case s: FunctionCallRule => functionCallRuleToCompile += s
-      case s: InferenceRule    => inferenceRuleToCompile += s
-      case _                   => 
+      case s: SchemaDeclaration    => schemaDeclarationToCompile += s
+      case s: ExtractionRule       => extractionRuleToCompile += s
+      case s: FunctionCallRule     => functionCallRuleToCompile += s
+      case s: InferenceRule        => inferenceRuleToCompile += s
+      case _                       =>
     })
 
-    extractionRuleGroupByHead     = extractionRuleToCompile.toList.groupBy(_.q.head.name)
-    inferenceRuleGroupByHead      = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
-    functionCallRuleGroupByInput  = functionCallRuleToCompile.toList.groupBy(_.input)
-    functionCallRuleGroupByOutput = functionCallRuleToCompile.toList.groupBy(_.output)
+    schemaDeclarationGroupByHead   = schemaDeclarationToCompile.toList.groupBy(_.a.name)
+    extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.q.head.name)
+    inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
+    functionCallRuleGroupByInput   = functionCallRuleToCompile.toList.groupBy(_.input)
+    functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
   }
 
   // Analyze the block visibility among statements 
@@ -285,6 +296,27 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
 
+  // Generate schema for database
+  def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
+    var schemas = new ListBuffer[String]()
+    for (stmt <- stmts) {
+      val columnDecls = stmt.a.terms map {
+        case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
+      }
+      val indentation = " " * stmt.a.name.length
+      val blockName = ss.resolveExtractorBlockName(stmt)
+      schemas += s"""
+        deepdive.extraction.extractors.${blockName} {
+          sql: \"\"\" DROP TABLE IF EXISTS ${stmt.a.name} CASCADE;
+          CREATE TABLE
+          ${stmt.a.name}(${columnDecls.mkString(",\n" + indentation)})
+          \"\"\"
+          style: "sql_extractor"
+        }"""
+    }
+    schemas.toList
+  }
+
   // Generate extraction rule part for deepdive
   def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
     var inputQueries = new ListBuffer[String]()
@@ -316,10 +348,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
+    val sqlCmdForCleanUp = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) "TRUNCATE" else "DROP VIEW IF EXISTS"
+    val sqlCmdForInsert  = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) "INSERT INTO" else "CREATE VIEW"
+    val useAS            = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) "" else " AS"
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" DROP VIEW IF EXISTS ${stmts(0).q.head.name};
-        CREATE VIEW ${stmts(0).q.head.name} AS ${inputQueries.mkString(" UNION ")}
+        sql: \"\"\" ${sqlCmdForCleanUp} ${stmts(0).q.head.name};
+        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ")}
         \"\"\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
@@ -388,10 +423,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         }
       }
       val blockName = ss.resolveExtractorBlockName(zs(0))
+      val sqlCmdForCleanUp = if (ss.schemaDeclarationGroupByHead contains zs(0).q.head.name) "TRUNCATE" else "DROP VIEW IF EXISTS"
+      val sqlCmdForInsert  = if (ss.schemaDeclarationGroupByHead contains zs(0).q.head.name) "INSERT INTO" else "CREATE VIEW"
+      val useAS            = if (ss.schemaDeclarationGroupByHead contains zs(0).q.head.name) "" else " AS"
       val ext = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" DROP TABLE IF EXISTS ${zs(0).q.head.name};
-        CREATE TABLE ${zs(0).q.head.name} AS
+        sql: \"\"\" ${sqlCmdForCleanUp} ${zs(0).q.head.name};
+        ${sqlCmdForInsert} ${zs(0).q.head.name}${useAS}
         ${inputQueries.mkString(" UNION ")}
         \"\"\"
         style: "sql_extractor"
@@ -403,8 +441,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     if (ss.isQueryTerm(stmts(0).q.head.name))
       blocks :::= compileNodeRule(stmts, ss)
 
-    val inferenceRuleGroupByHead    = stmts.groupBy(_.q.head.name)
-    var stmtIndex = 0
     for (stmt <- stmts) {
       var inputQueries = new ListBuffer[String]()
       var func = ""
@@ -445,14 +481,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             }
           }
       }
+      val blockName = ss.resolveInferenceBlockName(stmt)
       blocks ::= s"""
-        deepdive.inference.factors.factor_${stmt.q.head.name}_${stmtIndex} {
+        deepdive.inference.factors.${blockName} {
           input_query: \"\"\"${inputQueries.mkString(" UNION ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
         }
       """
-      stmtIndex += 1
     }
     blocks.reverse
   }
@@ -473,6 +509,18 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   """)
   }
 
+  def compilePipelines(ss: CompilationState): CompiledBlocks = {
+    val run = "deepdive.pipeline.run: ${PIPELINE}"
+    val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
+    val initdb = s"deepdive.pipeline.pipelines.initdb: [${setup_database_pipeline}]"
+    val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
+    val extraction_pipeline = s"deepdive.pipeline.pipelines.extraction: [${extraction}]"
+    val inference = ((ss.inferenceRuleGroupByHead map (_._2)).flatten map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
+    val inference_pipeline = s"deepdive.pipeline.pipelines.inference: [${inference}]"
+
+    List(run, initdb, extraction_pipeline, inference_pipeline)
+  }
+
   // generate variable schema statements
   def compileVariableSchema(statements: DeepDiveLog.Program, ss: CompilationState): CompiledBlocks = {
     var schema = Set[String]()
@@ -498,11 +546,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       // derive and compile the program with delta rules instead for incremental version
       if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
       else parsedProgram
-
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile, config )
 
     val body = new ListBuffer[String]()
+    body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
     state.extractionRuleGroupByHead    foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
     state.functionCallRuleGroupByInput foreach {keyVal => body ++= compileFunctionCallRules(keyVal._2, state)}
     state.inferenceRuleGroupByHead     foreach {keyVal => body ++= compileInferenceRules(keyVal._2, state)}
@@ -513,7 +561,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       :::
       compileVariableSchema(programToCompile, state)
       :::
-      body.toList 
+      body.toList
+      :::
+      compilePipelines(state)
     )
 
     // emit the generated code
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 415587dc8..0ace5843d 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -15,7 +15,223 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_42 {
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+          CREATE TABLE
+          sentences(document_id text,
+         sentence text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
+         sentence_offset int,
+         sentence_id text,
+         dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+          CREATE TABLE
+          dd_delta_articles(article_id text,
+                 text text,
+                 dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_12 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+          CREATE TABLE
+          has_spouse_candidates(person1_id text,
+                     person2_id text,
+                     sentence_id text,
+                     description text,
+                     relation_id text,
+                     is_true boolean,
+                     dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_10 {
+          sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+          CREATE TABLE
+          dd_new_people_mentions(sentence_id text,
+                      start_position int,
+                      length int,
+                      text text,
+                      mention_id text,
+                      dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_20 {
+          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+          CREATE TABLE
+          has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_17 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse_features(relation_id text,
+                            feature text,
+                            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+          CREATE TABLE
+          dd_new_articles(article_id text,
+               text text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS articles CASCADE;
+          CREATE TABLE
+          articles(article_id text,
+        text text,
+        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_14 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse_candidates(person1_id text,
+                            person2_id text,
+                            sentence_id text,
+                            description text,
+                            relation_id text,
+                            is_true boolean,
+                            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_18 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse_features(relation_id text,
+                          feature text,
+                          dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_6 {
+          sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+          CREATE TABLE
+          dd_new_sentences(document_id text,
+                sentence text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
+                sentence_offset int,
+                sentence_id text,
+                dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_9 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+          CREATE TABLE
+          dd_delta_people_mentions(sentence_id text,
+                        start_position int,
+                        length int,
+                        text text,
+                        mention_id text,
+                        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_13 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse_candidates(person1_id text,
+                              person2_id text,
+                              sentence_id text,
+                              description text,
+                              relation_id text,
+                              is_true boolean,
+                              dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_16 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+          CREATE TABLE
+          has_spouse_features(relation_id text,
+                   feature text,
+                   dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+          CREATE TABLE
+          dd_delta_sentences(document_id text,
+                  sentence text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
+                  sentence_offset int,
+                  sentence_id text,
+                  dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_8 {
+          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+          CREATE TABLE
+          people_mentions(sentence_id text,
+               start_position int,
+               length int,
+               text text,
+               mention_id text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_21 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_22 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
           SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
@@ -32,13 +248,13 @@
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_11 {
-        sql: """ DROP VIEW IF EXISTS dd_new_people_mentions;
-        CREATE VIEW dd_new_people_mentions AS 
+        sql: """ TRUNCATE dd_new_people_mentions;
+        INSERT INTO dd_new_people_mentions 
           SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
           FROM people_mentions R0
          UNION 
@@ -51,24 +267,9 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_27 {
-        sql: """ DROP VIEW IF EXISTS dd_new_ext_people_input;
-        CREATE VIEW dd_new_ext_people_input AS 
-          SELECT R0.sentence_id, R0.words, R0.ner_tags, R0.dd_count
-          FROM ext_people_input R0
-         UNION 
-          SELECT R0.sentence_id, R0.words, R0.ner_tags, R0.dd_count
-          FROM dd_delta_ext_people_input R0
-        
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ]
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_3 {
-        sql: """ DROP VIEW IF EXISTS dd_new_articles;
-        CREATE VIEW dd_new_articles AS 
+        sql: """ TRUNCATE dd_new_articles;
+        INSERT INTO dd_new_articles 
           SELECT R0.article_id, R0.text, R0.dd_count
           FROM articles R0
          UNION 
@@ -81,7 +282,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_28 {
+      deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
           SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
@@ -94,8 +295,8 @@
     
 
       deepdive.extraction.extractors.extraction_rule_15 {
-        sql: """ DROP VIEW IF EXISTS dd_new_has_spouse_candidates;
-        CREATE VIEW dd_new_has_spouse_candidates AS 
+        sql: """ TRUNCATE dd_new_has_spouse_candidates;
+        INSERT INTO dd_new_has_spouse_candidates 
           SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
           FROM has_spouse_candidates R0
          UNION 
@@ -104,43 +305,13 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_41 {
-        sql: """ DROP VIEW IF EXISTS dd_new_ext_has_spouse_features_input;
-        CREATE VIEW dd_new_ext_has_spouse_features_input AS 
-          SELECT R0.words, R0.relation_id, R0.p1_start_position, R0.p1_length, R0.p2_start_position, R0.p2_length, R0.dd_count
-          FROM ext_has_spouse_features_input R0
-         UNION 
-          SELECT R0.words, R0.relation_id, R0.p1_start_position, R0.p1_length, R0.p2_start_position, R0.p2_length, R0.dd_count
-          FROM dd_delta_ext_has_spouse_features_input R0
-        
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_42" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_34 {
-        sql: """ DROP VIEW IF EXISTS dd_new_ext_has_spouse_input;
-        CREATE VIEW dd_new_ext_has_spouse_input AS 
-          SELECT R0.sentence_id, R0.p1_id, R0.p1_text, R0.p2_id, R0.p2_text, R0.dd_count
-          FROM ext_has_spouse_input R0
-         UNION 
-          SELECT R0.sentence_id, R0.p1_id, R0.p1_text, R0.p2_id, R0.p2_text, R0.dd_count
-          FROM dd_delta_ext_has_spouse_input R0
-        
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_35" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_19 {
-        sql: """ DROP VIEW IF EXISTS dd_new_has_spouse_features;
-        CREATE VIEW dd_new_has_spouse_features AS 
+        sql: """ TRUNCATE dd_new_has_spouse_features;
+        INSERT INTO dd_new_has_spouse_features 
           SELECT R0.relation_id, R0.feature, R0.dd_count
           FROM has_spouse_features R0
          UNION 
@@ -149,13 +320,13 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_37" ]
+          dependencies: [ "extraction_rule_29" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_7 {
-        sql: """ DROP VIEW IF EXISTS dd_new_sentences;
-        CREATE VIEW dd_new_sentences AS 
+        sql: """ TRUNCATE dd_new_sentences;
+        INSERT INTO dd_new_sentences 
           SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
           FROM sentences R0
          UNION 
@@ -168,7 +339,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_35 {
+      deepdive.extraction.extractors.extraction_rule_27 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
           SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
@@ -189,33 +360,33 @@
           output_relation: "dd_delta_people_mentions"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_24" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_37 {
+        deepdive.extraction.extractors.extraction_rule_29 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_42" ]
+          dependencies: [ "extraction_rule_30" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_30 {
+        deepdive.extraction.extractors.extraction_rule_26 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_35" ]
+          dependencies: [ "extraction_rule_27" ]
         }
       
 
       deepdive.extraction.extractors.extraction_rule_dd_delta_has_spouse {
-        sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse;
-        CREATE TABLE dd_delta_has_spouse AS
+        sql: """ TRUNCATE dd_delta_has_spouse;
+        INSERT INTO dd_delta_has_spouse
         SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
@@ -225,11 +396,11 @@
           
         """
         style: "sql_extractor"
-        dependencies: [ "extraction_rule_30" ,  "extraction_rule_15" ,  "extraction_rule_37" ]
+        dependencies: [ "extraction_rule_26" ,  "extraction_rule_15" ,  "extraction_rule_29" ]
       }
     
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse_0 {
+        deepdive.inference.factors.factor_dd_delta_has_spouse_32 {
           input_query: """
           SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -241,3 +412,7 @@
           weight: "?(has_spouse_features.R2.feature)"
         }
       
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_dd_delta_has_spouse, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_32]
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 2dfb73e7c..b7c45e917 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -15,7 +15,74 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_8 {
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+          CREATE TABLE
+          sentences(document_id text,
+         sentence text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
+         sentence_offset int,
+         sentence_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_3 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+          CREATE TABLE
+          has_spouse_candidates(person1_id text,
+                     person2_id text,
+                     sentence_id text,
+                     description text,
+                     relation_id text,
+                     is_true boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+          CREATE TABLE
+          has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS articles CASCADE;
+          CREATE TABLE
+          articles(article_id text,
+        text text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+          CREATE TABLE
+          has_spouse_features(relation_id text,
+                   feature text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+          CREATE TABLE
+          people_mentions(sentence_id text,
+               start_position int,
+               length int,
+               text text,
+               mention_id text)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
           SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
@@ -27,7 +94,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_16 {
+      deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
           SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
@@ -35,11 +102,11 @@
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_10" ,  "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_12 {
+      deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
           SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
@@ -57,44 +124,44 @@
           output_relation: "people_mentions"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_8" ]
+          dependencies: [ "extraction_rule_7" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_14 {
+        deepdive.extraction.extractors.extraction_rule_12 {
           input: """ SELECT * FROM ext_has_spouse_features_input
           """
           output_relation: "has_spouse_features"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_16" ]
+          dependencies: [ "extraction_rule_13" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_10 {
+        deepdive.extraction.extractors.extraction_rule_9 {
           input: """ SELECT * FROM ext_has_spouse_input
           """
           output_relation: "has_spouse_candidates"
           udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_12" ]
+          dependencies: [ "extraction_rule_10" ]
         }
       
 
       deepdive.extraction.extractors.extraction_rule_has_spouse {
-        sql: """ DROP TABLE IF EXISTS has_spouse;
-        CREATE TABLE has_spouse AS
+        sql: """ TRUNCATE has_spouse;
+        INSERT INTO has_spouse
         SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
           FROM has_spouse_candidates R0, has_spouse_features R1
         WHERE R1.relation_id = R0.relation_id 
           
         """
         style: "sql_extractor"
-        dependencies: [ "extraction_rule_10" ,  "extraction_rule_14" ]
+        dependencies: [ "extraction_rule_9" ,  "extraction_rule_12" ]
       }
     
 
-        deepdive.inference.factors.factor_has_spouse_0 {
+        deepdive.inference.factors.factor_has_spouse_15 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -103,3 +170,7 @@
           weight: "?(has_spouse_features.R2.feature)"
         }
       
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_has_spouse, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [factor_has_spouse_15]
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 0dececb3e..b9ed27b40 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -128,25 +128,6 @@ dd_new_has_spouse?(relation_id text).
 
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
-ext_people_input(sentence_id text,
-                 words text[],
-                 ner_tags text[],
-                 dd_count int).
-
-dd_delta_ext_people_input(sentence_id text,
-                          words text[],
-                          ner_tags text[],
-                          dd_count int).
-
-dd_new_ext_people_input(sentence_id text,
-                        words text[],
-                        ner_tags text[],
-                        dd_count int).
-
-dd_new_ext_people_input(sentence_id, words, ner_tags, dd_count) :-
-    ext_people_input(sentence_id, words, ner_tags, dd_count);
-    dd_delta_ext_people_input(sentence_id, words, ner_tags, dd_count).
-
 dd_delta_ext_people_input(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
@@ -158,31 +139,6 @@ function ext_people
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
-ext_has_spouse_input(sentence_id text,
-                     p1_id text,
-                     p1_text text,
-                     p2_id text,
-                     p2_text text,
-                     dd_count int).
-
-dd_delta_ext_has_spouse_input(sentence_id text,
-                              p1_id text,
-                              p1_text text,
-                              p2_id text,
-                              p2_text text,
-                              dd_count int).
-
-dd_new_ext_has_spouse_input(sentence_id text,
-                            p1_id text,
-                            p1_text text,
-                            p2_id text,
-                            p2_text text,
-                            dd_count int).
-
-dd_new_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count) :-
-    ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count);
-    dd_delta_ext_has_spouse_input(sentence_id, p1_id, p1_text, p2_id, p2_text, dd_count).
-
 dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
@@ -197,34 +153,6 @@ function ext_has_spouse
 
 dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
 
-ext_has_spouse_features_input(words text[],
-                              relation_id text,
-                              p1_start_position int,
-                              p1_length int,
-                              p2_start_position int,
-                              p2_length int,
-                              dd_count int).
-
-dd_delta_ext_has_spouse_features_input(words text[],
-                                       relation_id text,
-                                       p1_start_position int,
-                                       p1_length int,
-                                       p2_start_position int,
-                                       p2_length int,
-                                       dd_count int).
-
-dd_new_ext_has_spouse_features_input(words text[],
-                                     relation_id text,
-                                     p1_start_position int,
-                                     p1_length int,
-                                     p2_start_position int,
-                                     p2_length int,
-                                     dd_count int).
-
-dd_new_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count) :-
-    ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count);
-    dd_delta_ext_has_spouse_features_input(words, relation_id, p1_start_position, p1_length, p2_start_position, p2_length, dd_count).
-
 dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index eefd87be5..1e8829521 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -31,10 +31,6 @@ has_spouse?(relation_id text).
 
 people_mentions :- !ext_people(ext_people_input).
 
-ext_people_input(sentence_id text,
-                 words text[],
-                 ner_tags text[]).
-
 ext_people_input(s, words, ner_tags) :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
@@ -46,12 +42,6 @@ function ext_people
 
 has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
 
-ext_has_spouse_input(sentence_id text,
-                     p1_id text,
-                     p1_text text,
-                     p2_id text,
-                     p2_text text).
-
 ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
@@ -64,13 +54,6 @@ function ext_has_spouse
 
 has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
 
-ext_has_spouse_features_input(words text[],
-                              relation_id text,
-                              p1_start_position int,
-                              p1_length int,
-                              p2_start_position int,
-                              p2_length int).
-
 ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),

From a019c1a8be7e8f417c38c3ec0bd56e821d0201ff Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Wed, 27 May 2015 00:59:33 -0700
Subject: [PATCH 115/347] inline dd_count in incremental ddlog, handle dd_count
 in compile

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 11 ++-
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 22 +-----
 .../many_joins/print-incremental.expected     | 45 +++++------
 .../spouse_example/print-incremental.expected | 75 ++++++++-----------
 4 files changed, 57 insertions(+), 96 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 4d63f391e..17d3abc3d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -300,9 +300,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
     for (stmt <- stmts) {
-      val columnDecls = stmt.a.terms map {
+      var columnDecls = stmt.a.terms map {
         case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
       }
+      if (ss.isIncremental && !stmt.isQuery) columnDecls = columnDecls :+ "dd_count int"
       val indentation = " " * stmt.a.name.length
       val blockName = ss.resolveExtractorBlockName(stmt)
       schemas += s"""
@@ -327,7 +328,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val qs              = new QuerySchema( tmpCq )
         // variable columns
         // dd_new_ tale only need original column name to make sure the schema is the same with original table
-        val tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
+        var tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
         val resolveColumnFlag = tmpCqIsForNewTable match {
           case true => OriginalOnly
           case false => OriginalAndAlias
@@ -339,8 +340,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val selectStr = variableCols.mkString(", ")
         // additional dd_count column will be added in incremental version not dd_new_ table
         // dd_new_ table does not need additional dd_count column
-        val ddCount = if (ss.isIncremental && !tmpCqIsForNewTable) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-        val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
+        val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        val ddCountStr = if (ddCount.length > 0) {
+          if (!tmpCqIsForNewTable) s""", ${ddCount} AS \"dd_count\" """ else s", ${ddCount}"
+        } else ""
 
         inputQueries += s"""
           SELECT ${selectStr}${ddCountStr}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index b4ac0c56c..3ef2bca6a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -62,13 +62,7 @@ object DeepDiveLogDeltaDeriver{
   def transform(stmt: SchemaDeclaration): List[Statement] = {
     var incrementalStatement = new ListBuffer[Statement]()
     // Incremental table
-    val incStmt = if (stmt.isQuery) stmt else stmt.copy(
-      a = stmt.a.copy(
-          terms = stmt.a.terms :+ Variable("dd_count", stmt.a.name, stmt.a.terms.length),
-          types = stmt.a.types :+ "int"
-          )
-    )
-    incrementalStatement += incStmt
+    incrementalStatement += stmt
 
     // Delta table
     var incDeltaStmt = stmt.copy(
@@ -78,12 +72,6 @@ object DeepDiveLogDeltaDeriver{
         types = stmt.a.types
       )
     )
-    if (!stmt.isQuery) incDeltaStmt = incDeltaStmt.copy(
-      a = incDeltaStmt.a.copy(
-        terms = incDeltaStmt.a.terms :+ Variable("dd_count", deltaPrefix + stmt.a.name, stmt.a.terms.length),
-        types = incDeltaStmt.a.types :+ "int"
-      )
-    )    
     incrementalStatement += incDeltaStmt
 
     // New table
@@ -94,17 +82,11 @@ object DeepDiveLogDeltaDeriver{
         types = stmt.a.types
       )
     )
-    if (!stmt.isQuery) incNewStmt = incNewStmt.copy(
-      a = incNewStmt.a.copy(
-        terms = incNewStmt.a.terms :+ Variable("dd_count", newPrefix + stmt.a.name, stmt.a.terms.length),
-        types = incNewStmt.a.types :+ "int"
-      )
-    )
     incrementalStatement += incNewStmt
 
     if (!stmt.isQuery) {
       incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(incNewStmt.a.name, incNewStmt.a.terms),
-        List(List(Atom(incStmt.a.name, incStmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms)))))
+        List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms)))))
     }
     incrementalStatement.toList
   }
diff --git a/test/expected-output-test/many_joins/print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
index 745d8e067..1394144d5 100644
--- a/test/expected-output-test/many_joins/print-incremental.expected
+++ b/test/expected-output-test/many_joins/print-incremental.expected
@@ -4,50 +4,41 @@ dd_delta_R?(x text).
 
 dd_new_R?(x text).
 
-S(x text,
-  dd_count int).
+S(x text).
 
-dd_delta_S(x text,
-           dd_count int).
+dd_delta_S(x text).
 
-dd_new_S(x text,
-         dd_count int).
+dd_new_S(x text).
 
-dd_new_S(x, dd_count) :-
-    S(x, dd_count);
-    dd_delta_S(x, dd_count).
+dd_new_S(x) :-
+    S(x);
+    dd_delta_S(x).
 
 T(x text,
-  f text,
-  dd_count int).
+  f text).
 
 dd_delta_T(x text,
-           f text,
-           dd_count int).
+           f text).
 
 dd_new_T(x text,
-         f text,
-         dd_count int).
+         f text).
 
-dd_new_T(x, f, dd_count) :-
-    T(x, f, dd_count);
-    dd_delta_T(x, f, dd_count).
+dd_new_T(x, f) :-
+    T(x, f);
+    dd_delta_T(x, f).
 
 U(x text,
-  l text,
-  dd_count int).
+  l text).
 
 dd_delta_U(x text,
-           l text,
-           dd_count int).
+           l text).
 
 dd_new_U(x text,
-         l text,
-         dd_count int).
+         l text).
 
-dd_new_U(x, l, dd_count) :-
-    U(x, l, dd_count);
-    dd_delta_U(x, l, dd_count).
+dd_new_U(x, l) :-
+    U(x, l);
+    dd_delta_U(x, l).
 
 dd_delta_R(x) :-
     dd_delta_S(x),
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index b9ed27b40..a92177eaa 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -1,18 +1,15 @@
 articles(article_id text,
-         text text,
-         dd_count int).
+         text text).
 
 dd_delta_articles(article_id text,
-                  text text,
-                  dd_count int).
+                  text text).
 
 dd_new_articles(article_id text,
-                text text,
-                dd_count int).
+                text text).
 
-dd_new_articles(article_id, text, dd_count) :-
-    articles(article_id, text, dd_count);
-    dd_delta_articles(article_id, text, dd_count).
+dd_new_articles(article_id, text) :-
+    articles(article_id, text);
+    dd_delta_articles(article_id, text).
 
 sentences(document_id text,
           sentence text,
@@ -22,8 +19,7 @@ sentences(document_id text,
           dependencies text[],
           ner_tags text[],
           sentence_offset int,
-          sentence_id text,
-          dd_count int).
+          sentence_id text).
 
 dd_delta_sentences(document_id text,
                    sentence text,
@@ -33,8 +29,7 @@ dd_delta_sentences(document_id text,
                    dependencies text[],
                    ner_tags text[],
                    sentence_offset int,
-                   sentence_id text,
-                   dd_count int).
+                   sentence_id text).
 
 dd_new_sentences(document_id text,
                  sentence text,
@@ -44,81 +39,71 @@ dd_new_sentences(document_id text,
                  dependencies text[],
                  ner_tags text[],
                  sentence_offset int,
-                 sentence_id text,
-                 dd_count int).
+                 sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count) :-
-    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count);
-    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id, dd_count).
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
+    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
+    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
 people_mentions(sentence_id text,
                 start_position int,
                 length int,
                 text text,
-                mention_id text,
-                dd_count int).
+                mention_id text).
 
 dd_delta_people_mentions(sentence_id text,
                          start_position int,
                          length int,
                          text text,
-                         mention_id text,
-                         dd_count int).
+                         mention_id text).
 
 dd_new_people_mentions(sentence_id text,
                        start_position int,
                        length int,
                        text text,
-                       mention_id text,
-                       dd_count int).
+                       mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count) :-
-    people_mentions(sentence_id, start_position, length, text, mention_id, dd_count);
-    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id, dd_count).
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
+    people_mentions(sentence_id, start_position, length, text, mention_id);
+    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
 has_spouse_candidates(person1_id text,
                       person2_id text,
                       sentence_id text,
                       description text,
                       relation_id text,
-                      is_true boolean,
-                      dd_count int).
+                      is_true boolean).
 
 dd_delta_has_spouse_candidates(person1_id text,
                                person2_id text,
                                sentence_id text,
                                description text,
                                relation_id text,
-                               is_true boolean,
-                               dd_count int).
+                               is_true boolean).
 
 dd_new_has_spouse_candidates(person1_id text,
                              person2_id text,
                              sentence_id text,
                              description text,
                              relation_id text,
-                             is_true boolean,
-                             dd_count int).
+                             is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count) :-
-    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count);
-    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true, dd_count).
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
+    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
+    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
 has_spouse_features(relation_id text,
-                    feature text,
-                    dd_count int).
+                    feature text).
 
 dd_delta_has_spouse_features(relation_id text,
-                             feature text,
-                             dd_count int).
+                             feature text).
 
 dd_new_has_spouse_features(relation_id text,
-                           feature text,
-                           dd_count int).
+                           feature text).
 
-dd_new_has_spouse_features(relation_id, feature, dd_count) :-
-    has_spouse_features(relation_id, feature, dd_count);
-    dd_delta_has_spouse_features(relation_id, feature, dd_count).
+dd_new_has_spouse_features(relation_id, feature) :-
+    has_spouse_features(relation_id, feature);
+    dd_delta_has_spouse_features(relation_id, feature).
 
 has_spouse?(relation_id text).
 

From e53d90bc70fe23e0726bbfe4a7f4aa785ac791a9 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 27 May 2015 05:18:13 -0700
Subject: [PATCH 116/347] Fixes Travis config for coverage submission

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index f955b0537..e2b825e41 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,4 +6,4 @@ before_install:
 script:
     - make test MEASURE_COVERAGE=true
 after_success:
-    - sbt coveralls
+    - sbt coverageReport coveralls

From 9e1eb8a4278bda3e8f974889aa8689011319c40c Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Wed, 27 May 2015 21:55:53 -0700
Subject: [PATCH 117/347] import supervision to extraction rules for tying
 label. Let compile extraction function to handle scoping rule then remove
 node query generation in compile inference function.

---
 examples/spouse_example.ddl                   |   2 +
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 103 +++++++-----------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |   2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  13 ++-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   8 +-
 .../compile-incremental.expected              | 102 +++++++++--------
 .../spouse_example/compile.expected           |  43 ++++----
 .../spouse_example/print-incremental.expected |   5 +
 .../spouse_example/print.expected             |   5 +
 9 files changed, 134 insertions(+), 149 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 1e3e0304b..6d186b067 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -68,6 +68,8 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
 
+has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
+
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 17d3abc3d..389c19fa3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -112,7 +112,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
             schema           += { (r,i) -> n }
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
         }
-      case ExtractionRule(_) => ()
+      case ExtractionRule(_,_) => ()
       case InferenceRule(_,_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case FunctionCallRule(_,_,_) => ()
@@ -234,7 +234,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   def analyzeVisible(statements: List[Statement]) = {
     extractionRuleGroupByHead   foreach {keyVal => visible += keyVal._2(0)}
     functionCallRuleGroupByInput foreach {keyVal => visible += keyVal._2(0)}
-    inferenceRuleGroupByHead    foreach {keyVal => visible += keyVal._2(0)}
+    // inferenceRuleGroupByHead    foreach {keyVal => visible += keyVal._2(0)}
   }
 
   // Analyze the dependency between statements and construct a graph.
@@ -326,28 +326,45 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
-        // variable columns
-        // dd_new_ tale only need original column name to make sure the schema is the same with original table
-        var tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
-        val resolveColumnFlag = tmpCqIsForNewTable match {
-          case true => OriginalOnly
-          case false => OriginalAndAlias
-        }
-        val variableCols = tmpCq.head.terms flatMap {
-          case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpCq, resolveColumnFlag)
-        }
+        if (ss.inferenceRuleGroupByHead contains stmt.q.head.name) {
+          if (stmt.supervision == null) ss.error(s"Cannot find supervision for variable ${stmt.q.head.name}.\n")
+          if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
+          val headTerms = tmpCq.head.terms map {
+            case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+          }
+          val index = qs.getBodyIndex(stmt.supervision)
+          val name  = ss.resolveName(qs.getVar(stmt.supervision))
+          val labelCol = s"R${index}.${name}"
+          val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
+          val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
+          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
+          ${ ss.generateSQLBody(tmpCq) }
+          """
+        } else {
+          // variable columns
+          // dd_new_ tale only need original column name to make sure the schema is the same with original table
+          var tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
+          val resolveColumnFlag = tmpCqIsForNewTable match {
+            case true => OriginalOnly
+            case false => OriginalAndAlias
+          }
+          val variableCols = tmpCq.head.terms flatMap {
+            case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpCq, resolveColumnFlag)
+          }
 
-        val selectStr = variableCols.mkString(", ")
-        // additional dd_count column will be added in incremental version not dd_new_ table
-        // dd_new_ table does not need additional dd_count column
-        val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-        val ddCountStr = if (ddCount.length > 0) {
-          if (!tmpCqIsForNewTable) s""", ${ddCount} AS \"dd_count\" """ else s", ${ddCount}"
-        } else ""
+          val selectStr = variableCols.mkString(", ")
+          // additional dd_count column will be added in incremental version not dd_new_ table
+          // dd_new_ table does not need additional dd_count column
+          val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          val ddCountStr = if (ddCount.length > 0) {
+            if (!tmpCqIsForNewTable) s""", ${ddCount} AS \"dd_count\" """ else s", ${ddCount}"
+          } else ""
 
-        inputQueries += s"""
-          SELECT ${selectStr}${ddCountStr}
-          ${ ss.generateSQLBody(tmpCq) }"""
+          inputQueries += s"""
+            SELECT ${selectStr}${ddCountStr}
+            ${ ss.generateSQLBody(tmpCq) }"""
+        }
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
@@ -402,48 +419,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   // generate inference rule part for deepdive
   def compileInferenceRules(stmts: List[InferenceRule], ss: CompilationState): CompiledBlocks = {
     var blocks = List[String]()
-    // node query
-    // generate the node portion (V) of the factor graph
-    def compileNodeRule(zs: List[InferenceRule], ss: CompilationState) : CompiledBlocks = {
-      var inputQueries = new ListBuffer[String]()
-      for (z <- zs) {
-        for (cqBody <- z.q.bodies) {
-          val tmpCq = ConjunctiveQuery(z.q.head, List(cqBody))
-          val qs = new QuerySchema(tmpCq)
-          val headTerms = tmpCq.head.terms map {
-            case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
-          }
-          val index = qs.getBodyIndex(z.supervision)
-          val name  = ss.resolveName(qs.getVar(z.supervision))
-          val labelCol = s"R${index}.${name}"
-          val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-          val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-          val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
-
-          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
-          ${ ss.generateSQLBody(tmpCq) }
-          """
-        }
-      }
-      val blockName = ss.resolveExtractorBlockName(zs(0))
-      val sqlCmdForCleanUp = if (ss.schemaDeclarationGroupByHead contains zs(0).q.head.name) "TRUNCATE" else "DROP VIEW IF EXISTS"
-      val sqlCmdForInsert  = if (ss.schemaDeclarationGroupByHead contains zs(0).q.head.name) "INSERT INTO" else "CREATE VIEW"
-      val useAS            = if (ss.schemaDeclarationGroupByHead contains zs(0).q.head.name) "" else " AS"
-      val ext = s"""
-      deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" ${sqlCmdForCleanUp} ${zs(0).q.head.name};
-        ${sqlCmdForInsert} ${zs(0).q.head.name}${useAS}
-        ${inputQueries.mkString(" UNION ")}
-        \"\"\"
-        style: "sql_extractor"
-        ${ss.generateDependenciesOfCompiledBlockFor(zs)}
-      }
-    """
-      List(ext)
-    }
-    if (ss.isQueryTerm(stmts(0).q.head.name))
-      blocks :::= compileNodeRule(stmts, ss)
-
     for (stmt <- stmts) {
       var inputQueries = new ListBuffer[String]()
       var func = ""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 3ef2bca6a..b6af1da2d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -113,7 +113,7 @@ object DeepDiveLogDeltaDeriver{
   // Incremental extraction rule,
   // create delta rules based on original extraction rule
   def transform(stmt: ExtractionRule): List[Statement] = {
-    List(ExtractionRule(transform(stmt.q)))
+    List(ExtractionRule(transform(stmt.q), stmt.supervision))
   }
 
   // Incremental function call rule,
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 221b1cfd5..4cc5284c4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -36,9 +36,9 @@ case class RowWiseLineHandler(format: String, command: String) extends FunctionI
 trait Statement
 case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
-case class ExtractionRule(q : ConjunctiveQuery) extends Statement // Extraction rule
+case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, semantics : String = "imply") extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, semantics : String = "Imply") extends Statement // Weighted rule
 
 
 // Parser
@@ -134,8 +134,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def extractionRule : Parser[ExtractionRule] =
-    conjunctiveQuery ^^ {
-      ExtractionRule(_)
+    conjunctiveQuery ~ opt(supervision) ^^ {
+      case (q ~ supervision) =>
+        ExtractionRule(q, supervision.getOrElse(null))
     }
 
   def functionCallRule : Parser[FunctionCallRule] =
@@ -155,10 +156,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def semantics = "semantics" ~> "=" ~> semanticType
 
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ supervision ~ semantics
+    ( conjunctiveQuery ~ factorWeight ~ supervision ~ opt(semantics)
     ) ^^ {
       case (q ~ weight ~ supervision ~ semantics) =>
-        InferenceRule(q, weight, supervision, semantics)
+        InferenceRule(q, weight, supervision, semantics.getOrElse("Imply"))
     }
 
   // rules or schema elements in arbitrary order
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index f0b2a944b..2a00b38f2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -59,8 +59,10 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-    s"""${print(stmt.q)}.
-       |""".stripMargin
+    print(stmt.q) +
+    ( if (stmt.supervision == null) ""
+      else  "\n  label = " + stmt.supervision
+    ) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
@@ -81,7 +83,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     ) +
     ( if (stmt.semantics == null) ""
       else "\n  semantics = " + stmt.semantics
-    ) + "."
+    ) + ".\n"
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 0ace5843d..78d7547de 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -234,17 +234,17 @@
       deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-          SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-          FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-          SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-          FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-          SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-          FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
-          SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
-          FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
@@ -255,11 +255,11 @@
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-          SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
-          FROM people_mentions R0
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            FROM people_mentions R0
          UNION 
-          SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
-          FROM dd_delta_people_mentions R0
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
@@ -270,11 +270,11 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-          SELECT R0.article_id, R0.text, R0.dd_count
-          FROM articles R0
+            SELECT R0.article_id, R0.text, R0.dd_count
+            FROM articles R0
          UNION 
-          SELECT R0.article_id, R0.text, R0.dd_count
-          FROM dd_delta_articles R0
+            SELECT R0.article_id, R0.text, R0.dd_count
+            FROM dd_delta_articles R0
         
         """
         style: "sql_extractor"
@@ -285,8 +285,8 @@
       deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-          SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
-          FROM dd_delta_sentences R0
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -297,11 +297,11 @@
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-          SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
-          FROM has_spouse_candidates R0
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            FROM has_spouse_candidates R0
          UNION 
-          SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
-          FROM dd_delta_has_spouse_candidates R0
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
@@ -312,11 +312,11 @@
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-          SELECT R0.relation_id, R0.feature, R0.dd_count
-          FROM has_spouse_features R0
+            SELECT R0.relation_id, R0.feature, R0.dd_count
+            FROM has_spouse_features R0
          UNION 
-          SELECT R0.relation_id, R0.feature, R0.dd_count
-          FROM dd_delta_has_spouse_features R0
+            SELECT R0.relation_id, R0.feature, R0.dd_count
+            FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
@@ -327,11 +327,11 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-          SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
-          FROM sentences R0
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            FROM sentences R0
          UNION 
-          SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
-          FROM dd_delta_sentences R0
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -342,11 +342,11 @@
       deepdive.extraction.extractors.extraction_rule_27 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-          SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
-          FROM dd_delta_people_mentions R0, people_mentions R1
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id  UNION 
-          SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
-          FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
@@ -354,6 +354,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_32 {
+        sql: """ TRUNCATE dd_delta_has_spouse;
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count AS dd_count
+          FROM dd_delta_has_spouse_candidates R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_26" ]
+      }
+    
+
         deepdive.extraction.extractors.extraction_rule_23 {
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
@@ -384,23 +396,7 @@
         }
       
 
-      deepdive.extraction.extractors.extraction_rule_dd_delta_has_spouse {
-        sql: """ TRUNCATE dd_delta_has_spouse;
-        INSERT INTO dd_delta_has_spouse
-        SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-          FROM dd_delta_has_spouse_candidates R0, has_spouse_features R1
-        WHERE R1.relation_id = R0.relation_id 
-           UNION SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count * R1.dd_count AS dd_count
-          FROM dd_new_has_spouse_candidates R0, dd_delta_has_spouse_features R1
-        WHERE R1.relation_id = R0.relation_id 
-          
-        """
-        style: "sql_extractor"
-        dependencies: [ "extraction_rule_26" ,  "extraction_rule_15" ,  "extraction_rule_29" ]
-      }
-    
-
-        deepdive.inference.factors.factor_dd_delta_has_spouse_32 {
+        deepdive.inference.factors.factor_dd_delta_has_spouse_33 {
           input_query: """
           SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -414,5 +410,5 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_dd_delta_has_spouse, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_32]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index b7c45e917..1eee5f63e 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -82,11 +82,23 @@
           style: "sql_extractor"
         }
 
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ TRUNCATE has_spouse;
+        INSERT INTO has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
+          FROM has_spouse_candidates R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_9" ]
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-          SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-          FROM sentences R0
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            FROM sentences R0
         
         """
         style: "sql_extractor"
@@ -97,8 +109,8 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-          SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-          FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
@@ -109,8 +121,8 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-          SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-          FROM people_mentions R0, people_mentions R1
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
@@ -148,20 +160,7 @@
         }
       
 
-      deepdive.extraction.extractors.extraction_rule_has_spouse {
-        sql: """ TRUNCATE has_spouse;
-        INSERT INTO has_spouse
-        SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
-          FROM has_spouse_candidates R0, has_spouse_features R1
-        WHERE R1.relation_id = R0.relation_id 
-          
-        """
-        style: "sql_extractor"
-        dependencies: [ "extraction_rule_9" ,  "extraction_rule_12" ]
-      }
-    
-
-        deepdive.inference.factors.factor_has_spouse_15 {
+        deepdive.inference.factors.factor_has_spouse_16 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -172,5 +171,5 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_has_spouse, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [factor_has_spouse_15]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [factor_has_spouse_16]
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index a92177eaa..de4ffdc89 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -162,6 +162,10 @@ function ext_has_spouse_features
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
+  label = l.
+
 dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
@@ -170,3 +174,4 @@ dd_delta_has_spouse(rid) :-
   weight = f
   label = l
   semantics = imply.
+
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 1e8829521..4f6323266 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -66,9 +66,14 @@ function ext_has_spouse_features
  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l)
+  label = l.
+
 has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
   label = l
   semantics = imply.
+

From 35e657a985070197d27f04ec28c5e8b8bdd25a4e Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 01:15:17 -0700
Subject: [PATCH 118/347] support original, incremental, materialization, merge
 modes and add corrsponding test examples

---
 .../org/deepdive/ddlog/DeepDiveLog.scala      |  19 +-
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  83 +++++---
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  36 ++++
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  12 +-
 test/expected-output-test.bats.template       |  22 +++
 .../compile-materialization.expected          | 180 ++++++++++++++++++
 .../spouse_example/compile-merge.expected     |  83 ++++++++
 7 files changed, 402 insertions(+), 33 deletions(-)
 create mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
 create mode 100644 test/expected-output-test/spouse_example/compile-materialization.expected
 create mode 100644 test/expected-output-test/spouse_example/compile-merge.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index df647b932..eecb7f9a7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -2,18 +2,33 @@ package org.deepdive.ddlog
 
 // A command-line interface
 object DeepDiveLog {
+
+  object Mode extends Enumeration {
+  type Mode = Value
+  // Four modes of DDlog compilation:
+  // ORIGINAL => Generate standard application.conf
+  // INCREMENTAL => Generate incremental application.conf
+  // MATERIALIZATION => Materialize existing factor graph for incremental mode
+  // MERGE => Merge new generated data into original table
+  val ORIGINAL, INCREMENTAL, MATERIALIZATION, MERGE  = Value
+
+  }
+  import Mode._
+
   type Program = List[Statement]
 
   case class Config
   ( handler: DeepDiveLogHandler = null
   , inputFiles: List[String] = List()
-  , isIncremental: Boolean = false
+  , mode: Mode = ORIGINAL
   )
   val parser = new scopt.OptionParser[Config]("ddlogc") {
     head("ddlogc", "0.0.1")
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
-    opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(isIncremental = true)                 } text("Whether to derive delta rules")
+    opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
+    opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
+    opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
     arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
     checkConfig { c =>
       if (c.handler == null) failure("No command specified")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 389c19fa3..db85a8e66 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -61,6 +61,7 @@ Consider
 import scala.collection.immutable.HashMap
 import org.apache.commons.lang3.StringEscapeUtils
 import scala.collection.mutable.ListBuffer
+import org.deepdive.ddlog.DeepDiveLog.Mode._
 
 object AliasStyle extends Enumeration {
   type AliasStyle = Value
@@ -93,7 +94,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // The statement whether will compile or union to other statements
   var visible : Set[Statement] = Set()
 
-  var isIncremental : Boolean = false
+  var mode : Mode = ORIGINAL
+
+  var useDeltaCount : Boolean = false
 
   // Mapping head names to the actual statements
   var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
@@ -104,7 +107,11 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   def init() = {
     // generate the statements.
-    isIncremental = config.isIncremental
+    mode = config.mode
+    useDeltaCount = mode match {
+      case ORIGINAL => false
+      case _ => true
+    }
     statements.foreach {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery) =>
         terms.foreach {
@@ -303,7 +310,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var columnDecls = stmt.a.terms map {
         case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
       }
-      if (ss.isIncremental && !stmt.isQuery) columnDecls = columnDecls :+ "dd_count int"
+      if (ss.useDeltaCount && !stmt.isQuery) columnDecls = columnDecls :+ "dd_count int"
       val indentation = " " * stmt.a.name.length
       val blockName = ss.resolveExtractorBlockName(stmt)
       schemas += s"""
@@ -336,7 +343,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
           val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
-          val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          val ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
           val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
           ${ ss.generateSQLBody(tmpCq) }
@@ -344,8 +351,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         } else {
           // variable columns
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
-          var tmpCqIsForNewTable = tmpCq.head.name.startsWith("dd_new_")
-          val resolveColumnFlag = tmpCqIsForNewTable match {
+          var tmpCqUseOnlyOriginal = ss.mode match {
+            case MERGE => true
+            case _     => if (tmpCq.head.name.startsWith("dd_new_")) true else false
+          }
+          val resolveColumnFlag = tmpCqUseOnlyOriginal match {
             case true => OriginalOnly
             case false => OriginalAndAlias
           }
@@ -354,27 +364,42 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           }
 
           val selectStr = variableCols.mkString(", ")
-          // additional dd_count column will be added in incremental version not dd_new_ table
-          // dd_new_ table does not need additional dd_count column
-          val ddCount = if (ss.isIncremental) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+
+          var ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          ddCount = ss.mode match {
+            case MERGE => s"SUM(${ddCount})"
+            case _ => ddCount
+          }
           val ddCountStr = if (ddCount.length > 0) {
-            if (!tmpCqIsForNewTable) s""", ${ddCount} AS \"dd_count\" """ else s", ${ddCount}"
+            if (!tmpCqUseOnlyOriginal) s""", ${ddCount} AS \"dd_count\" """ else s", ${ddCount}"
           } else ""
-
+          val groupBy = ss.mode match {
+            case MERGE => s" GROUP BY ${selectStr}"
+            case _ => ""
+          }
           inputQueries += s"""
             SELECT ${selectStr}${ddCountStr}
-            ${ ss.generateSQLBody(tmpCq) }"""
+            ${ ss.generateSQLBody(tmpCq) }${ groupBy }"""
         }
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
-    val sqlCmdForCleanUp = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) "TRUNCATE" else "DROP VIEW IF EXISTS"
-    val sqlCmdForInsert  = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) "INSERT INTO" else "CREATE VIEW"
-    val useAS            = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) "" else " AS"
+    val createTable = ss.mode match {
+      case MERGE => true
+      case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) true else false
+    }
+    val sqlCmdForCleanUp = if (createTable) "TRUNCATE" else "DROP VIEW IF EXISTS"
+    val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
+    val useAS            = if (createTable) "" else " AS"
+    val cleanUp          = ss.mode match {
+      case MERGE => s""";
+        DELETE FROM ${stmts(0).q.head.name} WHERE dd_count = 0;"""
+      case _     => ""
+    }
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" ${sqlCmdForCleanUp} ${stmts(0).q.head.name};
-        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ")}
+        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ")}${cleanUp}
         \"\"\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
@@ -441,7 +466,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
 
-        val ddCount = if (ss.isIncremental) ( fakeCQ.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+        val ddCount = if (ss.useDeltaCount) ( fakeCQ.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
         val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
 
         // factor input query
@@ -490,13 +515,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
     val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
-    val initdb = s"deepdive.pipeline.pipelines.initdb: [${setup_database_pipeline}]"
+    val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [${setup_database_pipeline}]" else ""
     val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
-    val extraction_pipeline = s"deepdive.pipeline.pipelines.extraction: [${extraction}]"
+    val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [${extraction}]" else ""
     val inference = ((ss.inferenceRuleGroupByHead map (_._2)).flatten map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
-    val inference_pipeline = s"deepdive.pipeline.pipelines.inference: [${inference}]"
+    val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [${inference}]" else ""
 
-    List(run, initdb, extraction_pipeline, inference_pipeline)
+    List(run, initdb, extraction_pipeline, inference_pipeline).filter(_ != "")
   }
 
   // generate variable schema statements
@@ -521,9 +546,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     // determine the program to compile
     val programToCompile =
-      // derive and compile the program with delta rules instead for incremental version
-      if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
-      else parsedProgram
+      // derive and compile the program based on mode information
+      config.mode match {
+        case ORIGINAL => parsedProgram
+        case INCREMENTAL => DeepDiveLogDeltaDeriver.derive(parsedProgram)
+        case MATERIALIZATION => parsedProgram
+        case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
+      }
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile, config )
 
@@ -547,8 +576,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // emit the generated code
     blocks foreach println
 
-    if (config.isIncremental) {
-      // TODO emit extra extractor for moving rows of dd_delta_* to *
-    }
+    // if (config.isIncremental) {
+    //   // TODO emit extra extractor for moving rows of dd_delta_* to *
+    // }
   }
 }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
new file mode 100644
index 000000000..8be539d0a
--- /dev/null
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -0,0 +1,36 @@
+package org.deepdive.ddlog
+
+import scala.collection.mutable.ListBuffer
+
+object DeepDiveLogMergeDeriver{
+
+  // Default prefix for incremental tables
+  val newPrefix = "dd_new_"
+
+  // Incremental scheme declaration,
+  // keep the original scheme and create one delta scheme
+  def transform(stmt: SchemaDeclaration): Statement = {
+    // New table
+    var incNewStmt = stmt.copy(
+      a = stmt.a.copy(
+        name = newPrefix + stmt.a.name,
+        terms = stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)},
+        types = stmt.a.types
+      )
+    )
+
+    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms),
+      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms)))))
+  }
+
+  def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
+    var mergeProgram = new ListBuffer[Statement]()
+    program foreach { x =>
+      x match {
+        case x: SchemaDeclaration => if (!x.isQuery) mergeProgram += transform(x)
+        case _ =>
+      }
+    }
+    mergeProgram.toList
+  }
+}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 2a00b38f2..d9054c65c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -1,6 +1,7 @@
 package org.deepdive.ddlog
 
 import org.apache.commons.lang3.StringEscapeUtils
+import org.deepdive.ddlog.DeepDiveLog.Mode._
 
 // Pretty printer that simply prints the parsed input
 object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
@@ -88,10 +89,13 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     val programToPrint =
-      // derive the delta rules for incremental version
-      if (config.isIncremental) DeepDiveLogDeltaDeriver.derive(parsedProgram)
-      else parsedProgram
-
+      // derive the program based on mode information
+      config.mode match {
+        case ORIGINAL => parsedProgram
+        case INCREMENTAL => DeepDiveLogDeltaDeriver.derive(parsedProgram)
+        case MATERIALIZATION => parsedProgram
+        case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
+      }
     // pretty print in original syntax
     programToPrint foreach {stmt => println(print(stmt))}
   }
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index 59be8b438..d37846df3 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -74,3 +74,25 @@ setup() {
     ddlog print --incremental "$TESTDIR"/input.ddl >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
+
+## tests for --merge support
+
+# compare the compiled output of the merge version with what's expected
+@test "$it compiles --merge input as expected" {
+    expectedOutput=$TESTDIR/compile-merge.expected
+    actualOutput=${expectedOutput%.expected}.actual
+    [ -e "$expectedOutput" ] || skip
+    ddlog compile --merge "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
+}
+
+## tests for --materialization support
+
+# compare the compiled output of the merge version with what's expected
+@test "$it compiles --materialization input as expected" {
+    expectedOutput=$TESTDIR/compile-materialization.expected
+    actualOutput=${expectedOutput%.expected}.actual
+    [ -e "$expectedOutput" ] || skip
+    ddlog compile --materialization "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
+}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
new file mode 100644
index 000000000..050204c9b
--- /dev/null
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -0,0 +1,180 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  
+
+      deepdive.schema.variables {
+        has_spouse.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+          CREATE TABLE
+          sentences(document_id text,
+         sentence text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
+         sentence_offset int,
+         sentence_id text,
+         dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_3 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+          CREATE TABLE
+          has_spouse_candidates(person1_id text,
+                     person2_id text,
+                     sentence_id text,
+                     description text,
+                     relation_id text,
+                     is_true boolean,
+                     dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+          CREATE TABLE
+          has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS articles CASCADE;
+          CREATE TABLE
+          articles(article_id text,
+        text text,
+        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+          CREATE TABLE
+          has_spouse_features(relation_id text,
+                   feature text,
+                   dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+          CREATE TABLE
+          people_mentions(sentence_id text,
+               start_position int,
+               length int,
+               text text,
+               mention_id text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ TRUNCATE has_spouse;
+        INSERT INTO has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count AS dd_count
+          FROM has_spouse_candidates R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_9" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ DROP VIEW IF EXISTS ext_people_input;
+        CREATE VIEW ext_people_input AS 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            FROM sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_13 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
+        CREATE VIEW ext_has_spouse_features_input AS 
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_10 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
+        CREATE VIEW ext_has_spouse_input AS 
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_6" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_6 {
+          input: """ SELECT * FROM ext_people_input
+          """
+          output_relation: "people_mentions"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_7" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_12 {
+          input: """ SELECT * FROM ext_has_spouse_features_input
+          """
+          output_relation: "has_spouse_features"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_13" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_9 {
+          input: """ SELECT * FROM ext_has_spouse_input
+          """
+          output_relation: "has_spouse_candidates"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_10" ]
+        }
+      
+
+        deepdive.inference.factors.factor_has_spouse_16 {
+          input_query: """
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Imply(has_spouse.R0.label)"
+          weight: "?(has_spouse_features.R2.feature)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [factor_has_spouse_16]
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
new file mode 100644
index 000000000..7a071a982
--- /dev/null
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -0,0 +1,83 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_1 {
+        sql: """ TRUNCATE sentences;
+        INSERT INTO sentences 
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, SUM(R0.dd_count)
+            FROM dd_new_sentences R0
+         GROUP BY R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id;
+        DELETE FROM sentences WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE has_spouse_candidates;
+        INSERT INTO has_spouse_candidates 
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, SUM(R0.dd_count)
+            FROM dd_new_has_spouse_candidates R0
+         GROUP BY R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true;
+        DELETE FROM has_spouse_candidates WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_0 {
+        sql: """ TRUNCATE articles;
+        INSERT INTO articles 
+            SELECT R0.article_id, R0.text, SUM(R0.dd_count)
+            FROM dd_new_articles R0
+         GROUP BY R0.article_id, R0.text;
+        DELETE FROM articles WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_4 {
+        sql: """ TRUNCATE has_spouse_features;
+        INSERT INTO has_spouse_features 
+            SELECT R0.relation_id, R0.feature, SUM(R0.dd_count)
+            FROM dd_new_has_spouse_features R0
+         GROUP BY R0.relation_id, R0.feature;
+        DELETE FROM has_spouse_features WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_2 {
+        sql: """ TRUNCATE people_mentions;
+        INSERT INTO people_mentions 
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, SUM(R0.dd_count)
+            FROM dd_new_people_mentions R0
+         GROUP BY R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id;
+        DELETE FROM people_mentions WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.extraction: [extraction_rule_0, extraction_rule_3, extraction_rule_4, extraction_rule_2, extraction_rule_1]

From 1801175d244e15b23474f0a9421dc118261d43bd Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 12:17:00 -0700
Subject: [PATCH 119/347] support incremental function   add an argument in
 function declaration 'mode = inc' to specific   incremental function

---
 .../compile-incremental.expected              | 417 ++++++++++++++++++
 .../spouse_example_new_feature/input.ddl      |  79 ++++
 .../print-incremental.expected                | 178 ++++++++
 3 files changed, 674 insertions(+)
 create mode 100644 test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
 create mode 100644 test/expected-output-test/spouse_example_new_feature/input.ddl
 create mode 100644 test/expected-output-test/spouse_example_new_feature/print-incremental.expected

diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
new file mode 100644
index 000000000..7a544e25a
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -0,0 +1,417 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+  }
+  
+
+      deepdive.schema.variables {
+        dd_delta_has_spouse.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+          CREATE TABLE
+          sentences(document_id text,
+         sentence text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
+         sentence_offset int,
+         sentence_id text,
+         dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+          CREATE TABLE
+          dd_delta_articles(article_id text,
+                 text text,
+                 dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_12 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+          CREATE TABLE
+          has_spouse_candidates(person1_id text,
+                     person2_id text,
+                     sentence_id text,
+                     description text,
+                     relation_id text,
+                     is_true boolean,
+                     dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_10 {
+          sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+          CREATE TABLE
+          dd_new_people_mentions(sentence_id text,
+                      start_position int,
+                      length int,
+                      text text,
+                      mention_id text,
+                      dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_20 {
+          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+          CREATE TABLE
+          has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_17 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse_features(relation_id text,
+                            feature text,
+                            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+          CREATE TABLE
+          dd_new_articles(article_id text,
+               text text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS articles CASCADE;
+          CREATE TABLE
+          articles(article_id text,
+        text text,
+        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_14 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse_candidates(person1_id text,
+                            person2_id text,
+                            sentence_id text,
+                            description text,
+                            relation_id text,
+                            is_true boolean,
+                            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_18 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse_features(relation_id text,
+                          feature text,
+                          dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_6 {
+          sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+          CREATE TABLE
+          dd_new_sentences(document_id text,
+                sentence text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
+                sentence_offset int,
+                sentence_id text,
+                dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_9 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+          CREATE TABLE
+          dd_delta_people_mentions(sentence_id text,
+                        start_position int,
+                        length int,
+                        text text,
+                        mention_id text,
+                        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_13 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse_candidates(person1_id text,
+                              person2_id text,
+                              sentence_id text,
+                              description text,
+                              relation_id text,
+                              is_true boolean,
+                              dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_16 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+          CREATE TABLE
+          has_spouse_features(relation_id text,
+                   feature text,
+                   dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+          CREATE TABLE
+          dd_delta_sentences(document_id text,
+                  sentence text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
+                  sentence_offset int,
+                  sentence_id text,
+                  dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_8 {
+          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+          CREATE TABLE
+          people_mentions(sentence_id text,
+               start_position int,
+               length int,
+               text text,
+               mention_id text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_21 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_22 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse(relation_id text)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_30 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
+        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_11 {
+        sql: """ TRUNCATE dd_new_people_mentions;
+        INSERT INTO dd_new_people_mentions 
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            FROM people_mentions R0
+         UNION 
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            FROM dd_delta_people_mentions R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_23" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE dd_new_articles;
+        INSERT INTO dd_new_articles 
+            SELECT R0.article_id, R0.text, R0.dd_count
+            FROM articles R0
+         UNION 
+            SELECT R0.article_id, R0.text, R0.dd_count
+            FROM dd_delta_articles R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_24 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
+        CREATE VIEW dd_delta_ext_people_input AS 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            FROM sentences R0
+         UNION 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            FROM dd_delta_sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ TRUNCATE dd_new_has_spouse_candidates;
+        INSERT INTO dd_new_has_spouse_candidates 
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            FROM has_spouse_candidates R0
+         UNION 
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            FROM dd_delta_has_spouse_candidates R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_26" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ TRUNCATE dd_new_has_spouse_features;
+        INSERT INTO dd_new_has_spouse_features 
+            SELECT R0.relation_id, R0.feature, R0.dd_count
+            FROM has_spouse_features R0
+         UNION 
+            SELECT R0.relation_id, R0.feature, R0.dd_count
+            FROM dd_delta_has_spouse_features R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_29" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ TRUNCATE dd_new_sentences;
+        INSERT INTO dd_new_sentences 
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            FROM sentences R0
+         UNION 
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            FROM dd_delta_sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_27 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
+        CREATE VIEW dd_delta_ext_has_spouse_input AS 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM dd_delta_people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id  UNION 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_11" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_32 {
+        sql: """ TRUNCATE dd_delta_has_spouse;
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count AS dd_count
+          FROM dd_delta_has_spouse_candidates R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_26" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_23 {
+          input: """ SELECT * FROM dd_delta_ext_people_input
+          """
+          output_relation: "dd_delta_people_mentions"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_24" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_29 {
+          input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
+          """
+          output_relation: "dd_delta_has_spouse_features"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_30" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_26 {
+          input: """ SELECT * FROM dd_delta_ext_has_spouse_input
+          """
+          output_relation: "dd_delta_has_spouse_candidates"
+          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_27" ]
+        }
+      
+
+        deepdive.inference.factors.factor_dd_delta_has_spouse_33 {
+          input_query: """
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Imply(dd_delta_has_spouse.R0.label)"
+          weight: "?(has_spouse_features.R2.feature)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
new file mode 100644
index 000000000..0b22fabfc
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -0,0 +1,79 @@
+articles(
+  article_id text,
+  text       text).
+
+sentences(
+  document_id     text,
+  sentence        text,
+  words           text[],
+  lemma           text[],
+  pos_tags        text[],
+  dependencies    text[],
+  ner_tags        text[],
+  sentence_offset int,
+  sentence_id     text).
+
+people_mentions(
+  sentence_id    text,
+  start_position int,
+  length         int,
+  text           text,
+  mention_id     text).
+
+has_spouse_candidates(
+  person1_id  text,
+  person2_id  text,
+  sentence_id text,
+  description text,
+  relation_id text,
+  is_true boolean).
+
+has_spouse_features(
+  relation_id text,
+  feature     text).
+
+has_spouse?(relation_id text).
+
+people_mentions :-
+  !ext_people(ext_people_input).
+
+ext_people_input(s, words, ner_tags) :-
+  sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people over like ext_people_input
+                 returns like people_mentions
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines
+  mode = inc.
+
+has_spouse_candidates :-
+  !ext_has_spouse(ext_has_spouse_input).
+
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, a, b, p1_text, p1_id),
+  people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse over like ext_has_spouse_input
+                     returns like has_spouse_candidates
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
+
+has_spouse_features :-
+  !ext_has_spouse_features(ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(a, b, words, c, d, e, f, g, s),
+  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+  people_mentions(s, p1idx, p1len, k, person1_id),
+  people_mentions(s, p2idx, p2len, l, person2_id).
+  
+function ext_has_spouse_features over like ext_has_spouse_features_input
+                              returns like has_spouse_features
+  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
+
+has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
+
+has_spouse(rid) :-
+  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_features(rid, f)
+weight = f
+label = l
+semantics = imply.
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
new file mode 100644
index 000000000..0e3b00bc6
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -0,0 +1,178 @@
+articles(article_id text,
+         text text).
+
+dd_delta_articles(article_id text,
+                  text text).
+
+dd_new_articles(article_id text,
+                text text).
+
+dd_new_articles(article_id, text) :-
+    articles(article_id, text);
+    dd_delta_articles(article_id, text).
+
+sentences(document_id text,
+          sentence text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
+          sentence_offset int,
+          sentence_id text).
+
+dd_delta_sentences(document_id text,
+                   sentence text,
+                   words text[],
+                   lemma text[],
+                   pos_tags text[],
+                   dependencies text[],
+                   ner_tags text[],
+                   sentence_offset int,
+                   sentence_id text).
+
+dd_new_sentences(document_id text,
+                 sentence text,
+                 words text[],
+                 lemma text[],
+                 pos_tags text[],
+                 dependencies text[],
+                 ner_tags text[],
+                 sentence_offset int,
+                 sentence_id text).
+
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
+    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
+    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
+
+people_mentions(sentence_id text,
+                start_position int,
+                length int,
+                text text,
+                mention_id text).
+
+dd_delta_people_mentions(sentence_id text,
+                         start_position int,
+                         length int,
+                         text text,
+                         mention_id text).
+
+dd_new_people_mentions(sentence_id text,
+                       start_position int,
+                       length int,
+                       text text,
+                       mention_id text).
+
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
+    people_mentions(sentence_id, start_position, length, text, mention_id);
+    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
+
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text,
+                      is_true boolean).
+
+dd_delta_has_spouse_candidates(person1_id text,
+                               person2_id text,
+                               sentence_id text,
+                               description text,
+                               relation_id text,
+                               is_true boolean).
+
+dd_new_has_spouse_candidates(person1_id text,
+                             person2_id text,
+                             sentence_id text,
+                             description text,
+                             relation_id text,
+                             is_true boolean).
+
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
+    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
+    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
+
+has_spouse_features(relation_id text,
+                    feature text).
+
+dd_delta_has_spouse_features(relation_id text,
+                             feature text).
+
+dd_new_has_spouse_features(relation_id text,
+                           feature text).
+
+dd_new_has_spouse_features(relation_id, feature) :-
+    has_spouse_features(relation_id, feature);
+    dd_delta_has_spouse_features(relation_id, feature).
+
+has_spouse?(relation_id text).
+
+dd_delta_has_spouse?(relation_id text).
+
+dd_new_has_spouse?(relation_id text).
+
+dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
+
+dd_delta_ext_people_input(s, words, ner_tags) :-
+    sentences(a, b, words, c, d, e, ner_tags, f, s);
+    dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people
+    over like dd_delta_ext_people_input
+ returns like dd_delta_people_mentions
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+        handles tsv lines mode = inc.
+
+dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
+
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
+    people_mentions(s, c, d, p2_text, p2_id);
+    dd_new_people_mentions(s, a, b, p1_text, p1_id),
+    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse
+    over like dd_delta_ext_has_spouse_input
+ returns like dd_delta_has_spouse_candidates
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+        handles tsv lines.
+
+dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id);
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id);
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id);
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+function ext_has_spouse_features
+    over like dd_delta_ext_has_spouse_features_input
+ returns like dd_delta_has_spouse_features
+ implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+        handles tsv lines.
+
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
+  label = l.
+
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_features(rid, f);
+    dd_new_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_features(rid, f)
+  weight = f
+  label = l
+  semantics = imply.
+

From 1d2a6e0c95175018e71b4248ef1bf998ddd9b6b9 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 12:39:51 -0700
Subject: [PATCH 120/347] add modified files for support incremental function

---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 20 ++++++++++++++++++-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 16 +++++++--------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  3 ++-
 3 files changed, 29 insertions(+), 10 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index b6af1da2d..db3964570 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -8,6 +8,8 @@ object DeepDiveLogDeltaDeriver{
   val deltaPrefix = "dd_delta_"
   val newPrefix = "dd_new_"
 
+  var incrementalFunctionInput = new ListBuffer[String]()
+
   def transform(stmt: Statement): List[Statement] = stmt match {
     case s: SchemaDeclaration   => transform(s)
     case s: FunctionDeclaration => transform(s)
@@ -41,7 +43,8 @@ object DeepDiveLogDeltaDeriver{
       }
       var i = 0
       var j = 0
-      for (i <- 0 to (body.length - 1)) {
+      var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
+      for (i <- index to (body.length - 1)) {
         var newBody = new ListBuffer[Atom]()
         for (j <- 0 to (body.length - 1)) {
           if (j > i)
@@ -128,8 +131,23 @@ object DeepDiveLogDeltaDeriver{
     List(InferenceRule(transform(stmt.q), stmt.weights, stmt.supervision, stmt.semantics))
   }
 
+  def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
+    program.foreach {
+      case x:FunctionDeclaration => if (x.mode == "inc") {
+        x.inputType match {
+          case inTy: RelationTypeAlias => incrementalFunctionInput += deltaPrefix + inTy.likeRelationName
+          case _ =>
+        }
+      }
+      case _ =>
+    }
+  }
+
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
     var incrementalProgram = new ListBuffer[Statement]()
+
+    generateIncrementalFunctionInputList(program)
+
     for (x <- program) {
       incrementalProgram = incrementalProgram ++ transform(x)
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 4cc5284c4..dfd1ef9be 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -5,6 +5,7 @@ package org.deepdive.ddlog
 
 import scala.util.parsing.combinator._
 import org.apache.commons.lang3.StringEscapeUtils
+import scala.util.Try
 
 // ***************************************
 // * The union types for for the parser. *
@@ -35,7 +36,7 @@ case class RowWiseLineHandler(format: String, command: String) extends FunctionI
 // Statements that will be parsed and compiled
 trait Statement
 case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
-case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration]) extends Statement
+case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
 case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, semantics : String = "Imply") extends Statement // Weighted rule
@@ -65,6 +66,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def variableName = ident
   def functionName = ident
   def semanticType = ident
+  def functionModeType = ident
 
   def columnDeclaration: Parser[Column] =
     columnName ~ columnType ^^ {
@@ -103,10 +105,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
     cqHead ~ ":-" ~ rep1sep(cqBody, ";") ^^ {
       case (headatom ~ ":-" ~ disjunctiveBodies) =>
-        // TODO handle all disjunctiveBodies
-        // XXX only compiling the first body
-        // val bodyatoms = disjunctiveBodies(0)
-        // ConjunctiveQuery(headatom, bodyatoms.toList)
         ConjunctiveQuery(headatom, disjunctiveBodies)
     }
 
@@ -117,6 +115,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
+  def functionMode = "mode" ~> "=" ~> functionModeType
+
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
     "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
       case (_ ~ command ~ _ ~ format ~ _) => RowWiseLineHandler(command=command, format=format)
@@ -125,12 +125,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def functionDeclaration : Parser[FunctionDeclaration] =
     ( "function" ~ functionName ~ "over" ~ relationType
                              ~ "returns" ~ relationType
-                 ~ (functionImplementation+)
+                 ~ (functionImplementation+) ~ opt(functionMode)
     ) ^^ {
       case ("function" ~ a ~ "over" ~ inTy
                            ~ "returns" ~ outTy
-                       ~ implementationDecls) =>
-             FunctionDeclaration(a, inTy, outTy, implementationDecls)
+                       ~ implementationDecls ~ mode) =>
+             FunctionDeclaration(a, inTy, outTy, implementationDecls, mode.getOrElse(null))
     }
 
   def extractionRule : Parser[ExtractionRule] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index d9054c65c..56f7249bb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -40,10 +40,11 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" +
         s"\n        handles ${impl.format} lines"
     }
+    val modeStr = if (stmt.mode == null) "" else s" mode = ${stmt.mode}"
     s"""function ${stmt.functionName}
        |    over ${inputType}
        | returns ${outputType}
-       | ${(impls map {"implementation " + _}).mkString("\n ")}.
+       | ${(impls map {"implementation " + _}).mkString("\n ")}${modeStr}.
        |""".stripMargin
   }
 

From 9d65baa4571ad07b6b999f66e90c33823fc4b842 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 15:47:31 -0700
Subject: [PATCH 121/347] add cleanup incremental tables in INCREMENTAL mode
 for supporting adding new data

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 21 +++++++++++++++----
 .../compile-incremental.expected              | 19 +++++++++++++++++
 .../compile-incremental.expected              | 19 +++++++++++++++++
 3 files changed, 55 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index db85a8e66..77ef7c509 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -241,7 +241,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   def analyzeVisible(statements: List[Statement]) = {
     extractionRuleGroupByHead   foreach {keyVal => visible += keyVal._2(0)}
     functionCallRuleGroupByInput foreach {keyVal => visible += keyVal._2(0)}
-    // inferenceRuleGroupByHead    foreach {keyVal => visible += keyVal._2(0)}
   }
 
   // Analyze the dependency between statements and construct a graph.
@@ -303,7 +302,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
 
-  // Generate schema for database
+  // Generate schema and cleanup part for database
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
     for (stmt <- stmts) {
@@ -322,6 +321,17 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           style: "sql_extractor"
         }"""
     }
+    // Cleanup incremental table extractor
+    val truncateTableList = (stmts map (x => if (x.a.name.startsWith("dd_")) s"TRUNCATE ${x.a.name};" else "")).filter(_ != "")
+    if (truncateTableList.length > 0) {
+      schemas += s"""
+        deepdive.extraction.extractors.cleanup {
+          sql: \"\"\"
+          ${truncateTableList.mkString("\n          ")}
+          \"\"\"
+          style: "sql_extractor"
+        }"""
+    }
     schemas.toList
   }
 
@@ -520,8 +530,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [${extraction}]" else ""
     val inference = ((ss.inferenceRuleGroupByHead map (_._2)).flatten map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [${inference}]" else ""
-
-    List(run, initdb, extraction_pipeline, inference_pipeline).filter(_ != "")
+    val cleanup_pipeline = ss.mode match {
+      case INCREMENTAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [cleanup]" else ""
+      case _ => ""
+    }
+    List(run, initdb, extraction_pipeline, inference_pipeline, cleanup_pipeline).filter(_ != "")
   }
 
   // generate variable schema statements
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 78d7547de..e8292ef3e 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -231,6 +231,24 @@
           style: "sql_extractor"
         }
 
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_articles;
+          TRUNCATE dd_new_people_mentions;
+          TRUNCATE dd_delta_has_spouse_features;
+          TRUNCATE dd_new_articles;
+          TRUNCATE dd_new_has_spouse_candidates;
+          TRUNCATE dd_new_has_spouse_features;
+          TRUNCATE dd_new_sentences;
+          TRUNCATE dd_delta_people_mentions;
+          TRUNCATE dd_delta_has_spouse_candidates;
+          TRUNCATE dd_delta_sentences;
+          TRUNCATE dd_delta_has_spouse;
+          TRUNCATE dd_new_has_spouse;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
@@ -412,3 +430,4 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 7a544e25a..2febacca8 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -231,6 +231,24 @@
           style: "sql_extractor"
         }
 
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_articles;
+          TRUNCATE dd_new_people_mentions;
+          TRUNCATE dd_delta_has_spouse_features;
+          TRUNCATE dd_new_articles;
+          TRUNCATE dd_new_has_spouse_candidates;
+          TRUNCATE dd_new_has_spouse_features;
+          TRUNCATE dd_new_sentences;
+          TRUNCATE dd_delta_people_mentions;
+          TRUNCATE dd_delta_has_spouse_candidates;
+          TRUNCATE dd_delta_sentences;
+          TRUNCATE dd_delta_has_spouse;
+          TRUNCATE dd_new_has_spouse;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
@@ -415,3 +433,4 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
+deepdive.pipeline.pipelines.cleanup: [cleanup]

From 28de580690615c7efdc7288eb09070ef846507f6 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 16:20:05 -0700
Subject: [PATCH 122/347] fix bugs in creating variable table schema: add id,
 label, (dd_count) column, reorder column order(move user specify column to
 the first column instead of id column. GreenPlum will distributed by the
 first column which might cause an issue by using id column)

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala    |  5 +++--
 .../spouse_example/compile-incremental.expected | 17 +++++++++++++----
 .../compile-materialization.expected            |  7 +++++--
 .../spouse_example/compile.expected             |  6 ++++--
 .../compile-incremental.expected                | 17 +++++++++++++----
 5 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 77ef7c509..596b54adb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -309,7 +309,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var columnDecls = stmt.a.terms map {
         case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
       }
-      if (ss.useDeltaCount && !stmt.isQuery) columnDecls = columnDecls :+ "dd_count int"
+      if (stmt.isQuery) columnDecls = columnDecls :+ "id bigint" :+ "label boolean"
+      if (ss.useDeltaCount) columnDecls = columnDecls :+ "dd_count int"
       val indentation = " " * stmt.a.name.length
       val blockName = ss.resolveExtractorBlockName(stmt)
       schemas += s"""
@@ -352,7 +353,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
-          val headTermsStr = ( "0 as id"  :: headTerms ).mkString(", ")
+          val headTermsStr = ( headTerms :+ "0 as id" ).mkString(", ")
           val ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
           val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index e8292ef3e..8bfcb6bfb 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -72,7 +72,10 @@
         deepdive.extraction.extractors.extraction_rule_20 {
           sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
           CREATE TABLE
-          has_spouse(relation_id text)
+          has_spouse(relation_id text,
+          id bigint,
+          label boolean,
+          dd_count int)
           """
           style: "sql_extractor"
         }
@@ -218,7 +221,10 @@
         deepdive.extraction.extractors.extraction_rule_21 {
           sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
           CREATE TABLE
-          dd_delta_has_spouse(relation_id text)
+          dd_delta_has_spouse(relation_id text,
+                   id bigint,
+                   label boolean,
+                   dd_count int)
           """
           style: "sql_extractor"
         }
@@ -226,7 +232,10 @@
         deepdive.extraction.extractors.extraction_rule_22 {
           sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
           CREATE TABLE
-          dd_new_has_spouse(relation_id text)
+          dd_new_has_spouse(relation_id text,
+                 id bigint,
+                 label boolean,
+                 dd_count int)
           """
           style: "sql_extractor"
         }
@@ -374,7 +383,7 @@
 
       deepdive.extraction.extractors.extraction_rule_32 {
         sql: """ TRUNCATE dd_delta_has_spouse;
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
         
           
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 050204c9b..dffdaf9b1 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -49,7 +49,10 @@
         deepdive.extraction.extractors.extraction_rule_5 {
           sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
           CREATE TABLE
-          has_spouse(relation_id text)
+          has_spouse(relation_id text,
+          id bigint,
+          label boolean,
+          dd_count int)
           """
           style: "sql_extractor"
         }
@@ -89,7 +92,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE has_spouse;
-        INSERT INTO has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM has_spouse_candidates R0
         
           
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 1eee5f63e..92d41bd89 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -47,7 +47,9 @@
         deepdive.extraction.extractors.extraction_rule_5 {
           sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
           CREATE TABLE
-          has_spouse(relation_id text)
+          has_spouse(relation_id text,
+          id bigint,
+          label boolean)
           """
           style: "sql_extractor"
         }
@@ -84,7 +86,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE has_spouse;
-        INSERT INTO has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label 
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label 
           FROM has_spouse_candidates R0
         
           
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 2febacca8..7c6d1e0c0 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -72,7 +72,10 @@
         deepdive.extraction.extractors.extraction_rule_20 {
           sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
           CREATE TABLE
-          has_spouse(relation_id text)
+          has_spouse(relation_id text,
+          id bigint,
+          label boolean,
+          dd_count int)
           """
           style: "sql_extractor"
         }
@@ -218,7 +221,10 @@
         deepdive.extraction.extractors.extraction_rule_21 {
           sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
           CREATE TABLE
-          dd_delta_has_spouse(relation_id text)
+          dd_delta_has_spouse(relation_id text,
+                   id bigint,
+                   label boolean,
+                   dd_count int)
           """
           style: "sql_extractor"
         }
@@ -226,7 +232,10 @@
         deepdive.extraction.extractors.extraction_rule_22 {
           sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
           CREATE TABLE
-          dd_new_has_spouse(relation_id text)
+          dd_new_has_spouse(relation_id text,
+                 id bigint,
+                 label boolean,
+                 dd_count int)
           """
           style: "sql_extractor"
         }
@@ -377,7 +386,7 @@
 
       deepdive.extraction.extractors.extraction_rule_32 {
         sql: """ TRUNCATE dd_delta_has_spouse;
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT 0 as id, R0.relation_id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
         
           

From 04aafc0c3416e175dfe3b60378976be4f24edfc5 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 18:01:42 -0700
Subject: [PATCH 123/347] fix bugs   1. remove create original tables in
 INCREMENTAL mode. (We assume first   run MATERIALIZATION mode)   2. reslove
 whether DDlog compiler need TRUNCATE table in extractors

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 17 +++-
 .../compile-incremental.expected              | 79 +------------------
 .../compile-materialization.expected          |  2 +-
 .../spouse_example/compile.expected           |  2 +-
 .../compile-incremental.expected              | 79 +------------------
 5 files changed, 20 insertions(+), 159 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 596b54adb..20f812063 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -230,7 +230,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case _                       =>
     })
 
-    schemaDeclarationGroupByHead   = schemaDeclarationToCompile.toList.groupBy(_.a.name)
+    schemaDeclarationGroupByHead = mode match {
+      case INCREMENTAL => schemaDeclarationToCompile.toList.filter(_.a.name.startsWith("dd_")).groupBy(_.a.name)
+      case _           => schemaDeclarationToCompile.toList.groupBy(_.a.name)
+    }
     extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.q.head.name)
     inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
     functionCallRuleGroupByInput   = functionCallRuleToCompile.toList.groupBy(_.input)
@@ -395,11 +398,19 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
+    // val createTable = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) true else false
+    val sqlCmdForCleanUp = ss.mode match {
+      case MERGE => s"TRUNCATE ${stmts(0).q.head.name};"
+      case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) {
+        if (stmts(0).q.head.name.startsWith("dd_new_"))
+          s"TRUNCATE ${stmts(0).q.head.name};"
+        else ""
+      } else s"DROP VIEW IF EXISTS ${stmts(0).q.head.name};"
+    }
     val createTable = ss.mode match {
       case MERGE => true
       case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) true else false
     }
-    val sqlCmdForCleanUp = if (createTable) "TRUNCATE" else "DROP VIEW IF EXISTS"
     val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
     val useAS            = if (createTable) "" else " AS"
     val cleanUp          = ss.mode match {
@@ -409,7 +420,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     }
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" ${sqlCmdForCleanUp} ${stmts(0).q.head.name};
+        sql: \"\"\" ${sqlCmdForCleanUp}
         ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ")}${cleanUp}
         \"\"\"
         style: "sql_extractor"
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 8bfcb6bfb..a3d44b221 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -15,23 +15,6 @@
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-          CREATE TABLE
-          sentences(document_id text,
-         sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
-         sentence_offset int,
-         sentence_id text,
-         dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_1 {
           sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
           CREATE TABLE
@@ -42,20 +25,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_12 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-          CREATE TABLE
-          has_spouse_candidates(person1_id text,
-                     person2_id text,
-                     sentence_id text,
-                     description text,
-                     relation_id text,
-                     is_true boolean,
-                     dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_10 {
           sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
           CREATE TABLE
@@ -69,17 +38,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_20 {
-          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-          CREATE TABLE
-          has_spouse(relation_id text,
-          id bigint,
-          label boolean,
-          dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_17 {
           sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
           CREATE TABLE
@@ -100,16 +58,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS articles CASCADE;
-          CREATE TABLE
-          articles(article_id text,
-        text text,
-        dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_14 {
           sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
           CREATE TABLE
@@ -178,16 +126,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_16 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-          CREATE TABLE
-          has_spouse_features(relation_id text,
-                   feature text,
-                   dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_5 {
           sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
           CREATE TABLE
@@ -205,19 +143,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_8 {
-          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-          CREATE TABLE
-          people_mentions(sentence_id text,
-               start_position int,
-               length int,
-               text text,
-               mention_id text,
-               dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_21 {
           sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
           CREATE TABLE
@@ -382,7 +307,7 @@
     
 
       deepdive.extraction.extractors.extraction_rule_32 {
-        sql: """ TRUNCATE dd_delta_has_spouse;
+        sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
         
@@ -436,7 +361,7 @@
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index dffdaf9b1..6aae96223 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -91,7 +91,7 @@
         }
 
       deepdive.extraction.extractors.extraction_rule_15 {
-        sql: """ TRUNCATE has_spouse;
+        sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM has_spouse_candidates R0
         
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 92d41bd89..ec2e5abbf 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -85,7 +85,7 @@
         }
 
       deepdive.extraction.extractors.extraction_rule_15 {
-        sql: """ TRUNCATE has_spouse;
+        sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label 
           FROM has_spouse_candidates R0
         
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 7c6d1e0c0..2387e8a23 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -15,23 +15,6 @@
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-          CREATE TABLE
-          sentences(document_id text,
-         sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
-         sentence_offset int,
-         sentence_id text,
-         dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_1 {
           sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
           CREATE TABLE
@@ -42,20 +25,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_12 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-          CREATE TABLE
-          has_spouse_candidates(person1_id text,
-                     person2_id text,
-                     sentence_id text,
-                     description text,
-                     relation_id text,
-                     is_true boolean,
-                     dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_10 {
           sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
           CREATE TABLE
@@ -69,17 +38,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_20 {
-          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-          CREATE TABLE
-          has_spouse(relation_id text,
-          id bigint,
-          label boolean,
-          dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_17 {
           sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
           CREATE TABLE
@@ -100,16 +58,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS articles CASCADE;
-          CREATE TABLE
-          articles(article_id text,
-        text text,
-        dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_14 {
           sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
           CREATE TABLE
@@ -178,16 +126,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_16 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-          CREATE TABLE
-          has_spouse_features(relation_id text,
-                   feature text,
-                   dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_5 {
           sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
           CREATE TABLE
@@ -205,19 +143,6 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_8 {
-          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-          CREATE TABLE
-          people_mentions(sentence_id text,
-               start_position int,
-               length int,
-               text text,
-               mention_id text,
-               dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.extraction.extractors.extraction_rule_21 {
           sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
           CREATE TABLE
@@ -385,7 +310,7 @@
     
 
       deepdive.extraction.extractors.extraction_rule_32 {
-        sql: """ TRUNCATE dd_delta_has_spouse;
+        sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
         
@@ -439,7 +364,7 @@
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_4, extraction_rule_1, extraction_rule_12, extraction_rule_10, extraction_rule_20, extraction_rule_17, extraction_rule_2, extraction_rule_0, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_16, extraction_rule_5, extraction_rule_8, extraction_rule_21, extraction_rule_22]
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
 deepdive.pipeline.pipelines.cleanup: [cleanup]

From 2a1f2ded925276bde540b2fe372a87fe497c76f9 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 18:26:58 -0700
Subject: [PATCH 124/347] update inference rule naming, from global index to
 local index in order to match inference name between MATERIALIZAION and
 INCREMENTAL mode

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala   | 2 +-
 .../spouse_example/compile-incremental.expected               | 4 ++--
 .../spouse_example/compile-materialization.expected           | 4 ++--
 test/expected-output-test/spouse_example/compile.expected     | 4 ++--
 .../spouse_example_new_feature/compile-incremental.expected   | 4 ++--
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 20f812063..ce8a4fb46 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -147,7 +147,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
-    s"factor_${s.q.head.name}_${statements indexOf s}"
+    s"${s.q.head.name}_${(inferenceRuleGroupByHead map (_._2)).flatten.toList indexOf s}"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index a3d44b221..a8f90345f 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -348,7 +348,7 @@
         }
       
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse_33 {
+        deepdive.inference.factors.dd_delta_has_spouse_0 {
           input_query: """
           SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -363,5 +363,5 @@
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
+deepdive.pipeline.pipelines.inference: [dd_delta_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 6aae96223..dd9d06ed1 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -168,7 +168,7 @@
         }
       
 
-        deepdive.inference.factors.factor_has_spouse_16 {
+        deepdive.inference.factors.has_spouse_0 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -180,4 +180,4 @@
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [factor_has_spouse_16]
+deepdive.pipeline.pipelines.inference: [has_spouse_0]
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index ec2e5abbf..09686a2d0 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -162,7 +162,7 @@
         }
       
 
-        deepdive.inference.factors.factor_has_spouse_16 {
+        deepdive.inference.factors.has_spouse_0 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -174,4 +174,4 @@
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [factor_has_spouse_16]
+deepdive.pipeline.pipelines.inference: [has_spouse_0]
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 2387e8a23..5ca1442c2 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -351,7 +351,7 @@
         }
       
 
-        deepdive.inference.factors.factor_dd_delta_has_spouse_33 {
+        deepdive.inference.factors.dd_delta_has_spouse_0 {
           input_query: """
           SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -366,5 +366,5 @@
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [factor_dd_delta_has_spouse_33]
+deepdive.pipeline.pipelines.inference: [dd_delta_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]

From 28b73e7cdb1514abe35d4799d151b051ddc98ad6 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 18:39:12 -0700
Subject: [PATCH 125/347] add incremental_mode in dbsettings

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala  | 15 +++++++++++----
 .../spouse_example/compile-incremental.expected   |  5 +++--
 .../compile-materialization.expected              |  5 +++--
 .../spouse_example/compile-merge.expected         |  5 +++--
 .../spouse_example/compile.expected               |  5 +++--
 .../compile-incremental.expected                  |  5 +++--
 6 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index ce8a4fb46..1bc5c5f67 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -519,8 +519,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   }
 
 
-  def compileUserSettings(): CompiledBlocks = {
+  def compileUserSettings(ss: CompilationState): CompiledBlocks = {
     // TODO read user's proto-application.conf and augment it
+    val mode = ss.mode match {
+      case ORIGINAL        => "ORIGINAL"
+      case INCREMENTAL     => "INCREMENTAL"
+      case MATERIALIZATION => "MATERIALIZATION"
+      case MERGE           => "MERGE"
+    }
     List("""
   deepdive.db.default {
     driver: "org.postgresql.Driver"
@@ -530,8 +536,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     dbname: ${DBNAME}
     host: ${PGHOST}
     port: ${PGPORT}
-  }
-  """)
+    incremental_mode: """ + s"""${mode}
+    }
+    """)
   }
 
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
@@ -589,7 +596,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     
     // compile the program into blocks of application.conf
     val blocks = (
-      compileUserSettings
+      compileUserSettings(state)
       :::
       compileVariableSchema(programToCompile, state)
       :::
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index a8f90345f..eed01bc17 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -7,8 +7,9 @@
     dbname: ${DBNAME}
     host: ${PGHOST}
     port: ${PGPORT}
-  }
-  
+    incremental_mode: INCREMENTAL
+    }
+    
 
       deepdive.schema.variables {
         dd_delta_has_spouse.label: Boolean
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index dd9d06ed1..5197ed894 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -7,8 +7,9 @@
     dbname: ${DBNAME}
     host: ${PGHOST}
     port: ${PGPORT}
-  }
-  
+    incremental_mode: MATERIALIZATION
+    }
+    
 
       deepdive.schema.variables {
         has_spouse.label: Boolean
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index 7a071a982..f65265b3a 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -7,8 +7,9 @@
     dbname: ${DBNAME}
     host: ${PGHOST}
     port: ${PGPORT}
-  }
-  
+    incremental_mode: MERGE
+    }
+    
 
       deepdive.schema.variables {
         
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 09686a2d0..f83b1ac08 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -7,8 +7,9 @@
     dbname: ${DBNAME}
     host: ${PGHOST}
     port: ${PGPORT}
-  }
-  
+    incremental_mode: ORIGINAL
+    }
+    
 
       deepdive.schema.variables {
         has_spouse.label: Boolean
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 5ca1442c2..3ad61910a 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -7,8 +7,9 @@
     dbname: ${DBNAME}
     host: ${PGHOST}
     port: ${PGPORT}
-  }
-  
+    incremental_mode: INCREMENTAL
+    }
+    
 
       deepdive.schema.variables {
         dd_delta_has_spouse.label: Boolean

From 369f5f9a3cfa0a87f8ae997945fa1f3c143ff16d Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Thu, 28 May 2015 19:22:05 -0700
Subject: [PATCH 126/347] add variable keys for INCREMENTAL mode to recognize
 unique keys

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 19 +++++++++++++++++++
 .../compile-incremental.expected              |  5 +++++
 .../compile-materialization.expected          |  1 +
 .../spouse_example/compile-merge.expected     |  1 +
 .../spouse_example/compile.expected           |  1 +
 .../compile-incremental.expected              |  5 +++++
 6 files changed, 32 insertions(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 1bc5c5f67..d5943d6d2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -541,6 +541,23 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     """)
   }
 
+  def compileVariableKey(ss: CompilationState): CompiledBlocks = {
+    var keys = new ListBuffer[String]()
+    for (stmt <- (ss.schemaDeclarationGroupByHead map (_._2)).flatten) {
+      var columnNames = stmt.a.terms map {
+        case Variable(name, _, i) => name
+      }
+      if (stmt.isQuery) keys += s"""${stmt.a.name} : [${columnNames.mkString(", ")}]"""
+    }
+    ss.mode match {
+      case INCREMENTAL => List(s"""
+      deepdive.schema.keys {
+        ${keys.mkString("\n        ")}
+      }""")
+      case _ => List("")
+    }
+  }
+
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
     val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
@@ -598,6 +615,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val blocks = (
       compileUserSettings(state)
       :::
+      compileVariableKey(state)
+      :::
       compileVariableSchema(programToCompile, state)
       :::
       body.toList
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index eed01bc17..feaf6c418 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -11,6 +11,11 @@
     }
     
 
+      deepdive.schema.keys {
+        dd_delta_has_spouse : [relation_id]
+        dd_new_has_spouse : [relation_id]
+      }
+
       deepdive.schema.variables {
         dd_delta_has_spouse.label: Boolean
       }
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 5197ed894..126d3cf68 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -11,6 +11,7 @@
     }
     
 
+
       deepdive.schema.variables {
         has_spouse.label: Boolean
       }
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index f65265b3a..b0dfc4a2f 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -11,6 +11,7 @@
     }
     
 
+
       deepdive.schema.variables {
         
       }
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index f83b1ac08..674f5d9f6 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -11,6 +11,7 @@
     }
     
 
+
       deepdive.schema.variables {
         has_spouse.label: Boolean
       }
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 3ad61910a..69b1e1425 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -11,6 +11,11 @@
     }
     
 
+      deepdive.schema.keys {
+        dd_delta_has_spouse : [relation_id]
+        dd_new_has_spouse : [relation_id]
+      }
+
       deepdive.schema.variables {
         dd_delta_has_spouse.label: Boolean
       }

From fb1d0fe1a91ce452f3c113ea68229e67eb3027b5 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 29 May 2015 00:34:38 -0700
Subject: [PATCH 127/347] support inference rule with more than one variable

---
 examples/smoke.ddl                            |  35 +++
 examples/spouse_example.ddl                   |   2 +-
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  24 +-
 .../compile-incremental.expected              | 268 ++++++++++++++++++
 .../compile-materialization.expected          | 118 ++++++++
 .../smoke_example/compile-merge.expected      |  72 +++++
 .../smoke_example/compile.expected            | 112 ++++++++
 .../smoke_example/input.ddl                   |  35 +++
 .../smoke_example/print-incremental.expected  |  81 ++++++
 .../smoke_example/print.expected              |  31 ++
 .../spouse_example/print-incremental.expected |   2 +-
 .../spouse_example/print.expected             |   2 +-
 .../spouse_example_new_feature/input.ddl      |   2 +-
 .../print-incremental.expected                |   2 +-
 14 files changed, 778 insertions(+), 8 deletions(-)
 create mode 100644 examples/smoke.ddl
 create mode 100644 test/expected-output-test/smoke_example/compile-incremental.expected
 create mode 100644 test/expected-output-test/smoke_example/compile-materialization.expected
 create mode 100644 test/expected-output-test/smoke_example/compile-merge.expected
 create mode 100644 test/expected-output-test/smoke_example/compile.expected
 create mode 100644 test/expected-output-test/smoke_example/input.ddl
 create mode 100644 test/expected-output-test/smoke_example/print-incremental.expected
 create mode 100644 test/expected-output-test/smoke_example/print.expected

diff --git a/examples/smoke.ddl b/examples/smoke.ddl
new file mode 100644
index 000000000..7371f2885
--- /dev/null
+++ b/examples/smoke.ddl
@@ -0,0 +1,35 @@
+person (
+    person_id bigint,
+    name text
+).
+
+person_has_cancer (
+    person_id bigint,
+    has_cancer boolean
+).
+
+person_smokes (
+    person_id bigint,
+    smokes boolean
+).
+
+friends (
+    person_id bigint,
+    friend_id bigint
+).
+
+smoke? (
+    person_id bigint
+).
+
+cancer? (
+    person_id bigint
+).
+
+smoke(pid)  :- person_smokes(pid, l)     label = l.
+cancer(pid) :- person_has_cancer(pid, l) label = l.
+
+cancer(pid) :- smoke(pid), person_smokes(pid, l)
+    weight = 3
+    label = l.
+
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 6d186b067..ca340bcab 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -75,4 +75,4 @@ has_spouse(rid) :-
   has_spouse_features(rid, f)
 weight = f
 label = l
-semantics = imply.
+semantics = Imply.
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d5943d6d2..9fb793c7d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -94,6 +94,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // The statement whether will compile or union to other statements
   var visible : Set[Statement] = Set()
 
+  var variableTableNames : Set[String] = Set()
+
   var mode : Mode = ORIGINAL
 
   var useDeltaCount : Boolean = false
@@ -113,12 +115,14 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case _ => true
     }
     statements.foreach {
-      case SchemaDeclaration(Attribute(r, terms, types), isQuery) =>
+      case SchemaDeclaration(Attribute(r, terms, types), isQuery) => {
         terms.foreach {
           case Variable(n,r,i) =>
             schema           += { (r,i) -> n }
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
         }
+        if (isQuery) variableTableNames += r
+      }
       case ExtractionRule(_,_) => ()
       case InferenceRule(_,_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
@@ -478,7 +482,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         val index = cqBody.length + 1
         val qs2 = new QuerySchema( fakeCQ )
-        val variableIdsStr = Some(s"""R0.id AS "${stmt.q.head.name}.R0.id" """)
+        val varInBody = (fakeBody map {x =>
+          if (ss.variableTableNames contains x.name)
+            s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """
+          else ""
+          }).filter(_ != "")
+
+        val variableIdsStr = Some(varInBody.mkString(", "))
 
         // weight string
         val uwStr = stmt.weights match {
@@ -496,7 +506,15 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           SELECT ${selectStr} ${ddCountStr}
           ${ ss.generateSQLBody(fakeCQ) }"""
         // factor function
-        func = s"""Imply(${stmt.q.head.name}.R0.label)"""
+        if (func.length == 0) {
+          val funcBody = (fakeBody map {x =>
+          if (ss.variableTableNames contains x.name)
+            s"""${x.name}.R${fakeBody indexOf x}.label"""
+          else ""
+          }).filter(_ != "")
+          val firstFunc = funcBody(0)
+          func = s"""${stmt.semantics}(${(funcBody.tail :+ firstFunc).mkString(", ")})"""
+        }
         // weight
         if (weight.length == 0)
           weight = stmt.weights match {
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
new file mode 100644
index 000000000..a1eebd935
--- /dev/null
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -0,0 +1,268 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: INCREMENTAL
+    }
+    
+
+      deepdive.schema.keys {
+        dd_delta_smoke : [person_id]
+        dd_new_smoke : [person_id]
+        dd_delta_cancer : [person_id]
+        dd_new_cancer : [person_id]
+      }
+
+      deepdive.schema.variables {
+        dd_delta_cancer.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_13 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
+          CREATE TABLE
+          dd_delta_friends(person_id bigint,
+                friend_id bigint,
+                dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_17 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
+          CREATE TABLE
+          dd_delta_smoke(person_id bigint,
+              id bigint,
+              label boolean,
+              dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_6 {
+          sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
+          CREATE TABLE
+          dd_new_person_has_cancer(person_id bigint,
+                        has_cancer boolean,
+                        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
+          CREATE TABLE
+          dd_delta_person(person_id bigint,
+               name text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
+          CREATE TABLE
+          dd_new_person(person_id bigint,
+             name text,
+             dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
+          CREATE TABLE
+          dd_delta_person_has_cancer(person_id bigint,
+                          has_cancer boolean,
+                          dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_18 {
+          sql: """ DROP TABLE IF EXISTS dd_new_smoke CASCADE;
+          CREATE TABLE
+          dd_new_smoke(person_id bigint,
+            id bigint,
+            label boolean,
+            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_20 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
+          CREATE TABLE
+          dd_delta_cancer(person_id bigint,
+               id bigint,
+               label boolean,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_21 {
+          sql: """ DROP TABLE IF EXISTS dd_new_cancer CASCADE;
+          CREATE TABLE
+          dd_new_cancer(person_id bigint,
+             id bigint,
+             label boolean,
+             dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_9 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
+          CREATE TABLE
+          dd_delta_person_smokes(person_id bigint,
+                      smokes boolean,
+                      dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_10 {
+          sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
+          CREATE TABLE
+          dd_new_person_smokes(person_id bigint,
+                    smokes boolean,
+                    dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_14 {
+          sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
+          CREATE TABLE
+          dd_new_friends(person_id bigint,
+              friend_id bigint,
+              dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_friends;
+          TRUNCATE dd_delta_smoke;
+          TRUNCATE dd_new_person_has_cancer;
+          TRUNCATE dd_delta_person;
+          TRUNCATE dd_new_person;
+          TRUNCATE dd_delta_person_has_cancer;
+          TRUNCATE dd_new_smoke;
+          TRUNCATE dd_delta_cancer;
+          TRUNCATE dd_new_cancer;
+          TRUNCATE dd_delta_person_smokes;
+          TRUNCATE dd_new_person_smokes;
+          TRUNCATE dd_new_friends;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_22 {
+        sql: """ 
+        INSERT INTO dd_delta_smoke 
+            SELECT R0.person_id AS "dd_delta_person_smokes.R0.person_id" , R0.dd_count AS "dd_count" 
+            FROM dd_delta_person_smokes R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ TRUNCATE dd_new_person_has_cancer;
+        INSERT INTO dd_new_person_has_cancer 
+            SELECT R0.person_id, R0.has_cancer, R0.dd_count
+            FROM person_has_cancer R0
+         UNION 
+            SELECT R0.person_id, R0.has_cancer, R0.dd_count
+            FROM dd_delta_person_has_cancer R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE dd_new_person;
+        INSERT INTO dd_new_person 
+            SELECT R0.person_id, R0.name, R0.dd_count
+            FROM person R0
+         UNION 
+            SELECT R0.person_id, R0.name, R0.dd_count
+            FROM dd_delta_person R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ 
+        INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label , R0.dd_count AS dd_count
+          FROM dd_delta_person_has_cancer R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_11 {
+        sql: """ TRUNCATE dd_new_person_smokes;
+        INSERT INTO dd_new_person_smokes 
+            SELECT R0.person_id, R0.smokes, R0.dd_count
+            FROM person_smokes R0
+         UNION 
+            SELECT R0.person_id, R0.smokes, R0.dd_count
+            FROM dd_delta_person_smokes R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ TRUNCATE dd_new_friends;
+        INSERT INTO dd_new_friends 
+            SELECT R0.person_id, R0.friend_id, R0.dd_count
+            FROM friends R0
+         UNION 
+            SELECT R0.person_id, R0.friend_id, R0.dd_count
+            FROM dd_delta_friends R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.dd_delta_cancer_0 {
+          input_query: """
+          SELECT R0.id AS "dd_delta_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_cancer R0, dd_delta_smoke R1, person_smokes R2
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION 
+          SELECT R0.id AS "dd_delta_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+          function: "Imply(dd_delta_smoke.R1.label, dd_delta_cancer.R0.label)"
+          weight: "3.0"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_20, extraction_rule_21, extraction_rule_9, extraction_rule_10, extraction_rule_14]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_22, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_delta_cancer_0]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
new file mode 100644
index 000000000..82710e1cd
--- /dev/null
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -0,0 +1,118 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: MATERIALIZATION
+    }
+    
+
+
+      deepdive.schema.variables {
+        cancer.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
+          CREATE TABLE
+          person_smokes(person_id bigint,
+             smokes boolean,
+             dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS smoke CASCADE;
+          CREATE TABLE
+          smoke(person_id bigint,
+     id bigint,
+     label boolean,
+     dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS cancer CASCADE;
+          CREATE TABLE
+          cancer(person_id bigint,
+      id bigint,
+      label boolean,
+      dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_3 {
+          sql: """ DROP TABLE IF EXISTS friends CASCADE;
+          CREATE TABLE
+          friends(person_id bigint,
+       friend_id bigint,
+       dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
+          CREATE TABLE
+          person_has_cancer(person_id bigint,
+                 has_cancer boolean,
+                 dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS person CASCADE;
+          CREATE TABLE
+          person(person_id bigint,
+      name text,
+      dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ 
+        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label , R0.dd_count AS dd_count
+          FROM person_has_cancer R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ 
+        INSERT INTO smoke 
+            SELECT R0.person_id AS "person_smokes.R0.person_id" , R0.dd_count AS "dd_count" 
+            FROM person_smokes R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.cancer_0 {
+          input_query: """
+          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM cancer R0, smoke R1, person_smokes R2
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+          function: "Imply(smoke.R1.label, cancer.R0.label)"
+          weight: "3.0"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [cancer_0]
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
new file mode 100644
index 000000000..10a177f1e
--- /dev/null
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -0,0 +1,72 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: MERGE
+    }
+    
+
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_2 {
+        sql: """ TRUNCATE person_smokes;
+        INSERT INTO person_smokes 
+            SELECT R0.person_id, R0.smokes, SUM(R0.dd_count)
+            FROM dd_new_person_smokes R0
+         GROUP BY R0.person_id, R0.smokes;
+        DELETE FROM person_smokes WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE friends;
+        INSERT INTO friends 
+            SELECT R0.person_id, R0.friend_id, SUM(R0.dd_count)
+            FROM dd_new_friends R0
+         GROUP BY R0.person_id, R0.friend_id;
+        DELETE FROM friends WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_1 {
+        sql: """ TRUNCATE person_has_cancer;
+        INSERT INTO person_has_cancer 
+            SELECT R0.person_id, R0.has_cancer, SUM(R0.dd_count)
+            FROM dd_new_person_has_cancer R0
+         GROUP BY R0.person_id, R0.has_cancer;
+        DELETE FROM person_has_cancer WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_0 {
+        sql: """ TRUNCATE person;
+        INSERT INTO person 
+            SELECT R0.person_id, R0.name, SUM(R0.dd_count)
+            FROM dd_new_person R0
+         GROUP BY R0.person_id, R0.name;
+        DELETE FROM person WHERE dd_count = 0;
+        """
+        style: "sql_extractor"
+          
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_3, extraction_rule_1, extraction_rule_0]
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
new file mode 100644
index 000000000..6d4c87891
--- /dev/null
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -0,0 +1,112 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        cancer.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
+          CREATE TABLE
+          person_smokes(person_id bigint,
+             smokes boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS smoke CASCADE;
+          CREATE TABLE
+          smoke(person_id bigint,
+     id bigint,
+     label boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS cancer CASCADE;
+          CREATE TABLE
+          cancer(person_id bigint,
+      id bigint,
+      label boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_3 {
+          sql: """ DROP TABLE IF EXISTS friends CASCADE;
+          CREATE TABLE
+          friends(person_id bigint,
+       friend_id bigint)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
+          CREATE TABLE
+          person_has_cancer(person_id bigint,
+                 has_cancer boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS person CASCADE;
+          CREATE TABLE
+          person(person_id bigint,
+      name text)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ 
+        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label 
+          FROM person_has_cancer R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ 
+        INSERT INTO smoke 
+            SELECT R0.person_id AS "person_smokes.R0.person_id" 
+            FROM person_smokes R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.cancer_0 {
+          input_query: """
+          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id"  
+          FROM cancer R0, smoke R1, person_smokes R2
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+          function: "Imply(smoke.R1.label, cancer.R0.label)"
+          weight: "3.0"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [cancer_0]
diff --git a/test/expected-output-test/smoke_example/input.ddl b/test/expected-output-test/smoke_example/input.ddl
new file mode 100644
index 000000000..7371f2885
--- /dev/null
+++ b/test/expected-output-test/smoke_example/input.ddl
@@ -0,0 +1,35 @@
+person (
+    person_id bigint,
+    name text
+).
+
+person_has_cancer (
+    person_id bigint,
+    has_cancer boolean
+).
+
+person_smokes (
+    person_id bigint,
+    smokes boolean
+).
+
+friends (
+    person_id bigint,
+    friend_id bigint
+).
+
+smoke? (
+    person_id bigint
+).
+
+cancer? (
+    person_id bigint
+).
+
+smoke(pid)  :- person_smokes(pid, l)     label = l.
+cancer(pid) :- person_has_cancer(pid, l) label = l.
+
+cancer(pid) :- smoke(pid), person_smokes(pid, l)
+    weight = 3
+    label = l.
+
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
new file mode 100644
index 000000000..def3b989b
--- /dev/null
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -0,0 +1,81 @@
+person(person_id bigint,
+       name text).
+
+dd_delta_person(person_id bigint,
+                name text).
+
+dd_new_person(person_id bigint,
+              name text).
+
+dd_new_person(person_id, name) :-
+    person(person_id, name);
+    dd_delta_person(person_id, name).
+
+person_has_cancer(person_id bigint,
+                  has_cancer boolean).
+
+dd_delta_person_has_cancer(person_id bigint,
+                           has_cancer boolean).
+
+dd_new_person_has_cancer(person_id bigint,
+                         has_cancer boolean).
+
+dd_new_person_has_cancer(person_id, has_cancer) :-
+    person_has_cancer(person_id, has_cancer);
+    dd_delta_person_has_cancer(person_id, has_cancer).
+
+person_smokes(person_id bigint,
+              smokes boolean).
+
+dd_delta_person_smokes(person_id bigint,
+                       smokes boolean).
+
+dd_new_person_smokes(person_id bigint,
+                     smokes boolean).
+
+dd_new_person_smokes(person_id, smokes) :-
+    person_smokes(person_id, smokes);
+    dd_delta_person_smokes(person_id, smokes).
+
+friends(person_id bigint,
+        friend_id bigint).
+
+dd_delta_friends(person_id bigint,
+                 friend_id bigint).
+
+dd_new_friends(person_id bigint,
+               friend_id bigint).
+
+dd_new_friends(person_id, friend_id) :-
+    friends(person_id, friend_id);
+    dd_delta_friends(person_id, friend_id).
+
+smoke?(person_id bigint).
+
+dd_delta_smoke?(person_id bigint).
+
+dd_new_smoke?(person_id bigint).
+
+cancer?(person_id bigint).
+
+dd_delta_cancer?(person_id bigint).
+
+dd_new_cancer?(person_id bigint).
+
+dd_delta_smoke(pid) :-
+    dd_delta_person_smokes(pid, l)
+  label = l.
+
+dd_delta_cancer(pid) :-
+    dd_delta_person_has_cancer(pid, l)
+  label = l.
+
+dd_delta_cancer(pid) :-
+    dd_delta_smoke(pid),
+    person_smokes(pid, l);
+    dd_new_smoke(pid),
+    dd_delta_person_smokes(pid, l)
+  weight = 3.0
+  label = l
+  semantics = Imply.
+
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
new file mode 100644
index 000000000..d3e06c9c8
--- /dev/null
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -0,0 +1,31 @@
+person(person_id bigint,
+       name text).
+
+person_has_cancer(person_id bigint,
+                  has_cancer boolean).
+
+person_smokes(person_id bigint,
+              smokes boolean).
+
+friends(person_id bigint,
+        friend_id bigint).
+
+smoke?(person_id bigint).
+
+cancer?(person_id bigint).
+
+smoke(pid) :-
+    person_smokes(pid, l)
+  label = l.
+
+cancer(pid) :-
+    person_has_cancer(pid, l)
+  label = l.
+
+cancer(pid) :-
+    smoke(pid),
+    person_smokes(pid, l)
+  weight = 3.0
+  label = l
+  semantics = Imply.
+
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index de4ffdc89..0a053b167 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -173,5 +173,5 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l
-  semantics = imply.
+  semantics = Imply.
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 4f6323266..b0260f557 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -75,5 +75,5 @@ has_spouse(rid) :-
     has_spouse_features(rid, f)
   weight = f
   label = l
-  semantics = imply.
+  semantics = Imply.
 
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 0b22fabfc..aff904191 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -76,4 +76,4 @@ has_spouse(rid) :-
   has_spouse_features(rid, f)
 weight = f
 label = l
-semantics = imply.
+semantics = Imply.
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 0e3b00bc6..1ae89f64e 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -174,5 +174,5 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_features(rid, f)
   weight = f
   label = l
-  semantics = imply.
+  semantics = Imply.
 

From fef8086cceffd776236097dacd1d39b4bd768567 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 29 May 2015 14:36:42 -0700
Subject: [PATCH 128/347] remove label indicator in inference rules

---
 examples/spouse_example.ddl                               | 4 +---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 4 ++--
 .../org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala      | 2 +-
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 8 ++++----
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala     | 3 ---
 test/expected-output-test/semantics/input.ddl             | 1 -
 test/expected-output-test/smoke_example/input.ddl         | 4 +---
 .../smoke_example/print-incremental.expected              | 1 -
 test/expected-output-test/smoke_example/print.expected    | 1 -
 .../spouse_example/print-incremental.expected             | 1 -
 test/expected-output-test/spouse_example/print.expected   | 1 -
 .../compile-incremental.expected                          | 2 +-
 .../spouse_example_new_feature/input.ddl                  | 3 +--
 .../spouse_example_new_feature/print-incremental.expected | 3 +--
 14 files changed, 12 insertions(+), 26 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index ca340bcab..4df11a8af 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -73,6 +73,4 @@ has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
-weight = f
-label = l
-semantics = Imply.
+weight = f.
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9fb793c7d..8a11cb126 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -124,7 +124,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         if (isQuery) variableTableNames += r
       }
       case ExtractionRule(_,_) => ()
-      case InferenceRule(_,_,_,_) => ()
+      case InferenceRule(_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case FunctionCallRule(_,_,_) => ()
     }
@@ -596,7 +596,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
-      case InferenceRule(q, weights, supervision, rule) =>
+      case InferenceRule(q, weights, rule) =>
         val qs = new QuerySchema(q)
         schema += s"${q.head.name}.label: Boolean"
       case _ => ()
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index db3964570..bd2b15738 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -128,7 +128,7 @@ object DeepDiveLogDeltaDeriver{
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(InferenceRule(transform(stmt.q), stmt.weights, stmt.supervision, stmt.semantics))
+    List(InferenceRule(transform(stmt.q), stmt.weights, stmt.semantics))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index dfd1ef9be..d238dfa54 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -39,7 +39,7 @@ case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statem
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, supervision : String, semantics : String = "Imply") extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, semantics : String = "Imply") extends Statement // Weighted rule
 
 
 // Parser
@@ -156,10 +156,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def semantics = "semantics" ~> "=" ~> semanticType
 
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ supervision ~ opt(semantics)
+    ( conjunctiveQuery ~ factorWeight ~ opt(semantics)
     ) ^^ {
-      case (q ~ weight ~ supervision ~ semantics) =>
-        InferenceRule(q, weight, supervision, semantics.getOrElse("Imply"))
+      case (q ~ weight ~ semantics) =>
+        InferenceRule(q, weight, semantics.getOrElse("Imply"))
     }
 
   // rules or schema elements in arbitrary order
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 56f7249bb..2d3c300eb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -80,9 +80,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         case UnknownFactorWeight(vs) => vs.mkString(", ")
       })
     ) +
-    ( if (stmt.supervision == null) ""
-      else "\n  label = " + stmt.supervision
-    ) +
     ( if (stmt.semantics == null) ""
       else "\n  semantics = " + stmt.semantics
     ) + ".\n"
diff --git a/test/expected-output-test/semantics/input.ddl b/test/expected-output-test/semantics/input.ddl
index 3de8d36d1..f18e77c06 100644
--- a/test/expected-output-test/semantics/input.ddl
+++ b/test/expected-output-test/semantics/input.ddl
@@ -5,5 +5,4 @@ Q?(x int).
 
 Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w)
 weight = y
-label   = z
 semantics = imply.
diff --git a/test/expected-output-test/smoke_example/input.ddl b/test/expected-output-test/smoke_example/input.ddl
index 7371f2885..10da92bed 100644
--- a/test/expected-output-test/smoke_example/input.ddl
+++ b/test/expected-output-test/smoke_example/input.ddl
@@ -30,6 +30,4 @@ smoke(pid)  :- person_smokes(pid, l)     label = l.
 cancer(pid) :- person_has_cancer(pid, l) label = l.
 
 cancer(pid) :- smoke(pid), person_smokes(pid, l)
-    weight = 3
-    label = l.
-
+    weight = 3.0.
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index def3b989b..51a3a7443 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -76,6 +76,5 @@ dd_delta_cancer(pid) :-
     dd_new_smoke(pid),
     dd_delta_person_smokes(pid, l)
   weight = 3.0
-  label = l
   semantics = Imply.
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index d3e06c9c8..48f4d4b4f 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -26,6 +26,5 @@ cancer(pid) :-
     smoke(pid),
     person_smokes(pid, l)
   weight = 3.0
-  label = l
   semantics = Imply.
 
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 0a053b167..edc1c0271 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -172,6 +172,5 @@ dd_delta_has_spouse(rid) :-
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
-  label = l
   semantics = Imply.
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index b0260f557..55dbaeaf7 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -74,6 +74,5 @@ has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
-  label = l
   semantics = Imply.
 
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 69b1e1425..09f9c2a25 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -365,7 +365,7 @@
           SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
+          function: "Linear(dd_delta_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index aff904191..4761caf9c 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -75,5 +75,4 @@ has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
-label = l
-semantics = Imply.
+semantics = Linear.
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 1ae89f64e..b18dc4339 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -173,6 +173,5 @@ dd_delta_has_spouse(rid) :-
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
-  label = l
-  semantics = Imply.
+  semantics = Linear.
 

From f9c874cd423ccb7b2cf6714cbc17668aa4750f0d Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 29 May 2015 21:05:00 -0700
Subject: [PATCH 129/347] correct column type in spouse example

---
 examples/spouse_example.ddl                   | 13 ++++----
 .../compile-incremental.expected              | 20 ++++++-------
 .../compile-materialization.expected          | 10 +++----
 .../spouse_example/compile.expected           | 10 +++----
 .../spouse_example/print-incremental.expected | 30 +++++++++----------
 .../spouse_example/print.expected             | 10 +++----
 .../compile-incremental.expected              | 20 ++++++-------
 .../spouse_example_new_feature/input.ddl      | 10 +++----
 .../print-incremental.expected                | 30 +++++++++----------
 9 files changed, 77 insertions(+), 76 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 4df11a8af..e27850501 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -5,11 +5,11 @@ articles(
 sentences(
   document_id     text,
   sentence        text,
-  words           text[],
-  lemma           text[],
-  pos_tags        text[],
-  dependencies    text[],
-  ner_tags        text[],
+  words           text,
+  lemma           text,
+  pos_tags        text,
+  dependencies    text,
+  ner_tags        text,
   sentence_offset int,
   sentence_id     text).
 
@@ -73,4 +73,5 @@ has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
-weight = f.
+weight = f
+semantics = Imply.
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index feaf6c418..3fdead7cc 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -93,11 +93,11 @@
           CREATE TABLE
           dd_new_sentences(document_id text,
                 sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
+                words text,
+                lemma text,
+                pos_tags text,
+                dependencies text,
+                ner_tags text,
                 sentence_offset int,
                 sentence_id text,
                 dd_count int)
@@ -137,11 +137,11 @@
           CREATE TABLE
           dd_delta_sentences(document_id text,
                   sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
+                  words text,
+                  lemma text,
+                  pos_tags text,
+                  dependencies text,
+                  ner_tags text,
                   sentence_offset int,
                   sentence_id text,
                   dd_count int)
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 126d3cf68..2781a6e18 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -22,11 +22,11 @@
           CREATE TABLE
           sentences(document_id text,
          sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
+         words text,
+         lemma text,
+         pos_tags text,
+         dependencies text,
+         ner_tags text,
          sentence_offset int,
          sentence_id text,
          dd_count int)
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 674f5d9f6..4ffb7f909 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -22,11 +22,11 @@
           CREATE TABLE
           sentences(document_id text,
          sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
+         words text,
+         lemma text,
+         pos_tags text,
+         dependencies text,
+         ner_tags text,
          sentence_offset int,
          sentence_id text)
           """
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index edc1c0271..b3446d979 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -13,31 +13,31 @@ dd_new_articles(article_id, text) :-
 
 sentences(document_id text,
           sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
+          words text,
+          lemma text,
+          pos_tags text,
+          dependencies text,
+          ner_tags text,
           sentence_offset int,
           sentence_id text).
 
 dd_delta_sentences(document_id text,
                    sentence text,
-                   words text[],
-                   lemma text[],
-                   pos_tags text[],
-                   dependencies text[],
-                   ner_tags text[],
+                   words text,
+                   lemma text,
+                   pos_tags text,
+                   dependencies text,
+                   ner_tags text,
                    sentence_offset int,
                    sentence_id text).
 
 dd_new_sentences(document_id text,
                  sentence text,
-                 words text[],
-                 lemma text[],
-                 pos_tags text[],
-                 dependencies text[],
-                 ner_tags text[],
+                 words text,
+                 lemma text,
+                 pos_tags text,
+                 dependencies text,
+                 ner_tags text,
                  sentence_offset int,
                  sentence_id text).
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 55dbaeaf7..786573805 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -3,11 +3,11 @@ articles(article_id text,
 
 sentences(document_id text,
           sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
+          words text,
+          lemma text,
+          pos_tags text,
+          dependencies text,
+          ner_tags text,
           sentence_offset int,
           sentence_id text).
 
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 09f9c2a25..47ef761b5 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -93,11 +93,11 @@
           CREATE TABLE
           dd_new_sentences(document_id text,
                 sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
+                words text,
+                lemma text,
+                pos_tags text,
+                dependencies text,
+                ner_tags text,
                 sentence_offset int,
                 sentence_id text,
                 dd_count int)
@@ -137,11 +137,11 @@
           CREATE TABLE
           dd_delta_sentences(document_id text,
                   sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
+                  words text,
+                  lemma text,
+                  pos_tags text,
+                  dependencies text,
+                  ner_tags text,
                   sentence_offset int,
                   sentence_id text,
                   dd_count int)
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 4761caf9c..e932cbf3d 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -5,11 +5,11 @@ articles(
 sentences(
   document_id     text,
   sentence        text,
-  words           text[],
-  lemma           text[],
-  pos_tags        text[],
-  dependencies    text[],
-  ner_tags        text[],
+  words           text,
+  lemma           text,
+  pos_tags        text,
+  dependencies    text,
+  ner_tags        text,
   sentence_offset int,
   sentence_id     text).
 
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index b18dc4339..7aeaacf7b 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -13,31 +13,31 @@ dd_new_articles(article_id, text) :-
 
 sentences(document_id text,
           sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
+          words text,
+          lemma text,
+          pos_tags text,
+          dependencies text,
+          ner_tags text,
           sentence_offset int,
           sentence_id text).
 
 dd_delta_sentences(document_id text,
                    sentence text,
-                   words text[],
-                   lemma text[],
-                   pos_tags text[],
-                   dependencies text[],
-                   ner_tags text[],
+                   words text,
+                   lemma text,
+                   pos_tags text,
+                   dependencies text,
+                   ner_tags text,
                    sentence_offset int,
                    sentence_id text).
 
 dd_new_sentences(document_id text,
                  sentence text,
-                 words text[],
-                 lemma text[],
-                 pos_tags text[],
-                 dependencies text[],
-                 ner_tags text[],
+                 words text,
+                 lemma text,
+                 pos_tags text,
+                 dependencies text,
+                 ner_tags text,
                  sentence_offset int,
                  sentence_id text).
 

From e829e944cc7ab81264a42c7020e378c3433eeec4 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Tue, 9 Jun 2015 15:40:28 -0700
Subject: [PATCH 130/347] clean up the udf directory in spouse example, add
 ${APP_HOME} prefix in compiler for udf directory

---
 examples/spouse_example.ddl                                 | 6 +++---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 3 ++-
 .../spouse_example/compile-incremental.expected             | 6 +++---
 .../spouse_example/compile-materialization.expected         | 6 +++---
 test/expected-output-test/spouse_example/compile.expected   | 6 +++---
 .../spouse_example/print-incremental.expected               | 6 +++---
 test/expected-output-test/spouse_example/print.expected     | 6 +++---
 .../spouse_example_new_feature/compile-incremental.expected | 6 +++---
 .../spouse_example_new_feature/input.ddl                    | 6 +++---
 .../spouse_example_new_feature/print-incremental.expected   | 6 +++---
 10 files changed, 29 insertions(+), 28 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index e27850501..b6fd72021 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -42,7 +42,7 @@ ext_people_input(s, words, ner_tags) :-
 
 function ext_people over like ext_people_input
                  returns like people_mentions
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines.
+  implementation "/udf/ext_people.py" handles tsv lines.
 
 has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
@@ -53,7 +53,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
+  implementation "/udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
   !ext_has_spouse_features(ext_has_spouse_features_input).
@@ -66,7 +66,7 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
+  implementation "/udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 8a11cb126..1b2fce6d6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -444,7 +444,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val function = ss.resolveFunctionName(stmt.function)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
-          s"""udf: \"${StringEscapeUtils.escapeJava(impl.command)}\"
+          s"""udf: $${APP_HOME}\"${StringEscapeUtils.escapeJava(impl.command)}\"
           style: \"${impl.format}_extractor\" """
       })
 
@@ -576,6 +576,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     }
   }
 
+  // generate application.conf pipelines
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
     val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 3fdead7cc..657fbcb45 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -328,7 +328,7 @@
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_24" ]
         }
@@ -338,7 +338,7 @@
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_30" ]
         }
@@ -348,7 +348,7 @@
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_27" ]
         }
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 2781a6e18..7f90239da 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -144,7 +144,7 @@
           input: """ SELECT * FROM ext_people_input
           """
           output_relation: "people_mentions"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_7" ]
         }
@@ -154,7 +154,7 @@
           input: """ SELECT * FROM ext_has_spouse_features_input
           """
           output_relation: "has_spouse_features"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_13" ]
         }
@@ -164,7 +164,7 @@
           input: """ SELECT * FROM ext_has_spouse_input
           """
           output_relation: "has_spouse_candidates"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_10" ]
         }
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 4ffb7f909..0a290eff3 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -138,7 +138,7 @@
           input: """ SELECT * FROM ext_people_input
           """
           output_relation: "people_mentions"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_7" ]
         }
@@ -148,7 +148,7 @@
           input: """ SELECT * FROM ext_has_spouse_features_input
           """
           output_relation: "has_spouse_features"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_13" ]
         }
@@ -158,7 +158,7 @@
           input: """ SELECT * FROM ext_has_spouse_input
           """
           output_relation: "has_spouse_candidates"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_10" ]
         }
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index b3446d979..aa6d787db 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -119,7 +119,7 @@ dd_delta_ext_people_input(s, words, ner_tags) :-
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+ implementation "/udf/ext_people.py"
         handles tsv lines.
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
@@ -133,7 +133,7 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
  returns like dd_delta_has_spouse_candidates
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+ implementation "/udf/ext_has_spouse.py"
         handles tsv lines.
 
 dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
@@ -159,7 +159,7 @@ dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :
 function ext_has_spouse_features
     over like dd_delta_ext_has_spouse_features_input
  returns like dd_delta_has_spouse_features
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+ implementation "/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
 dd_delta_has_spouse(rid) :-
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 786573805..0827f99cf 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -37,7 +37,7 @@ ext_people_input(s, words, ner_tags) :-
 function ext_people
     over like ext_people_input
  returns like people_mentions
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+ implementation "/udf/ext_people.py"
         handles tsv lines.
 
 has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
@@ -49,7 +49,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 function ext_has_spouse
     over like ext_has_spouse_input
  returns like has_spouse_candidates
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+ implementation "/udf/ext_has_spouse.py"
         handles tsv lines.
 
 has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
@@ -63,7 +63,7 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
 function ext_has_spouse_features
     over like ext_has_spouse_features_input
  returns like has_spouse_features
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+ implementation "/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
 has_spouse(rid) :-
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 47ef761b5..7de09941f 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -331,7 +331,7 @@
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+          udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_24" ]
         }
@@ -341,7 +341,7 @@
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_30" ]
         }
@@ -351,7 +351,7 @@
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
-          udf: "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "extraction_rule_27" ]
         }
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index e932cbf3d..f5c1bf625 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -42,7 +42,7 @@ ext_people_input(s, words, ner_tags) :-
 
 function ext_people over like ext_people_input
                  returns like people_mentions
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py" handles tsv lines
+  implementation "/udf/ext_people.py" handles tsv lines
   mode = inc.
 
 has_spouse_candidates :-
@@ -54,7 +54,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py" handles tsv lines.
+  implementation "/udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
   !ext_has_spouse_features(ext_has_spouse_features_input).
@@ -67,7 +67,7 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
-  implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py" handles tsv lines.
+  implementation "/udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 7aeaacf7b..3edd6b253 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -120,7 +120,7 @@ dd_delta_ext_people_input(s, words, ner_tags) :-
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_people.py"
+ implementation "/udf/ext_people.py"
         handles tsv lines mode = inc.
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
@@ -134,7 +134,7 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
  returns like dd_delta_has_spouse_candidates
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse.py"
+ implementation "/udf/ext_has_spouse.py"
         handles tsv lines.
 
 dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
@@ -160,7 +160,7 @@ dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :
 function ext_has_spouse_features
     over like dd_delta_ext_has_spouse_features_input
  returns like dd_delta_has_spouse_features
- implementation "/Users/feiran/workspace/release/deepdive/app/spouse_datalog/udf/ext_has_spouse_features.py"
+ implementation "/udf/ext_has_spouse_features.py"
         handles tsv lines.
 
 dd_delta_has_spouse(rid) :-

From 9676719be8af0b762ea69cfd082db419233918ad Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Wed, 10 Jun 2015 12:06:45 -0700
Subject: [PATCH 131/347] add support for new inference rule

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |   4 +-
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |   8 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  10 +-
 .../compile-incremental.expected              | 376 ++++++++++++++++++
 .../spouse_example_new_inference/input.ddl    |  78 ++++
 .../print-incremental.expected                | 178 +++++++++
 .../print.expected                            |  78 ++++
 7 files changed, 722 insertions(+), 10 deletions(-)
 create mode 100644 test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
 create mode 100644 test/expected-output-test/spouse_example_new_inference/input.ddl
 create mode 100644 test/expected-output-test/spouse_example_new_inference/print-incremental.expected
 create mode 100644 test/expected-output-test/spouse_example_new_inference/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 1b2fce6d6..c78fa031a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -124,7 +124,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         if (isQuery) variableTableNames += r
       }
       case ExtractionRule(_,_) => ()
-      case InferenceRule(_,_,_) => ()
+      case InferenceRule(_,_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case FunctionCallRule(_,_,_) => ()
     }
@@ -597,7 +597,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
-      case InferenceRule(q, weights, rule) =>
+      case InferenceRule(q, weights, rule, mode) =>
         val qs = new QuerySchema(q)
         schema += s"${q.head.name}.label: Boolean"
       case _ => ()
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index bd2b15738..cb24223d8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -18,7 +18,7 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
-  def transform(cq: ConjunctiveQuery): ConjunctiveQuery = {
+  def transform(cq: ConjunctiveQuery, mode: String): ConjunctiveQuery = {
     // New head
     val incCqHead = cq.head.copy(
       name = deltaPrefix + cq.head.name,
@@ -43,7 +43,7 @@ object DeepDiveLogDeltaDeriver{
       }
       var i = 0
       var j = 0
-      var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
+      var index = if ((incrementalFunctionInput contains incCqHead.name) || (mode == "inc")) -1 else 0
       for (i <- index to (body.length - 1)) {
         var newBody = new ListBuffer[Atom]()
         for (j <- 0 to (body.length - 1)) {
@@ -116,7 +116,7 @@ object DeepDiveLogDeltaDeriver{
   // Incremental extraction rule,
   // create delta rules based on original extraction rule
   def transform(stmt: ExtractionRule): List[Statement] = {
-    List(ExtractionRule(transform(stmt.q), stmt.supervision))
+    List(ExtractionRule(transform(stmt.q, null), stmt.supervision))
   }
 
   // Incremental function call rule,
@@ -128,7 +128,7 @@ object DeepDiveLogDeltaDeriver{
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(InferenceRule(transform(stmt.q), stmt.weights, stmt.semantics))
+    List(InferenceRule(transform(stmt.q, stmt.mode), stmt.weights, stmt.semantics))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index d238dfa54..10cc1caac 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -39,7 +39,7 @@ case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statem
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, semantics : String = "Imply") extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, semantics : String = "Imply", mode: String = null) extends Statement // Weighted rule
 
 
 // Parser
@@ -67,6 +67,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def functionName = ident
   def semanticType = ident
   def functionModeType = ident
+  def inferenceModeType = ident
 
   def columnDeclaration: Parser[Column] =
     columnName ~ columnType ^^ {
@@ -116,6 +117,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     )
 
   def functionMode = "mode" ~> "=" ~> functionModeType
+  def inferenceMode = "mode" ~> "=" ~> inferenceModeType
 
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
     "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
@@ -156,10 +158,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def semantics = "semantics" ~> "=" ~> semanticType
 
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ opt(semantics)
+    ( conjunctiveQuery ~ factorWeight ~ opt(semantics) ~ opt(inferenceMode)
     ) ^^ {
-      case (q ~ weight ~ semantics) =>
-        InferenceRule(q, weight, semantics.getOrElse("Imply"))
+      case (q ~ weight ~ semantics ~ mode) =>
+        InferenceRule(q, weight, semantics.getOrElse("Imply"), mode.getOrElse(null))
     }
 
   // rules or schema elements in arbitrary order
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
new file mode 100644
index 000000000..56f8f4fd3
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -0,0 +1,376 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: INCREMENTAL
+    }
+    
+
+      deepdive.schema.keys {
+        dd_delta_has_spouse : [relation_id]
+        dd_new_has_spouse : [relation_id]
+      }
+
+      deepdive.schema.variables {
+        dd_delta_has_spouse.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+          CREATE TABLE
+          dd_delta_articles(article_id text,
+                 text text,
+                 dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_10 {
+          sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+          CREATE TABLE
+          dd_new_people_mentions(sentence_id text,
+                      start_position int,
+                      length int,
+                      text text,
+                      mention_id text,
+                      dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_17 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse_features(relation_id text,
+                            feature text,
+                            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+          CREATE TABLE
+          dd_new_articles(article_id text,
+               text text,
+               dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_14 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse_candidates(person1_id text,
+                            person2_id text,
+                            sentence_id text,
+                            description text,
+                            relation_id text,
+                            is_true boolean,
+                            dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_18 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse_features(relation_id text,
+                          feature text,
+                          dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_6 {
+          sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+          CREATE TABLE
+          dd_new_sentences(document_id text,
+                sentence text,
+                words text,
+                lemma text,
+                pos_tags text,
+                dependencies text,
+                ner_tags text,
+                sentence_offset int,
+                sentence_id text,
+                dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_9 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+          CREATE TABLE
+          dd_delta_people_mentions(sentence_id text,
+                        start_position int,
+                        length int,
+                        text text,
+                        mention_id text,
+                        dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_13 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse_candidates(person1_id text,
+                              person2_id text,
+                              sentence_id text,
+                              description text,
+                              relation_id text,
+                              is_true boolean,
+                              dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+          CREATE TABLE
+          dd_delta_sentences(document_id text,
+                  sentence text,
+                  words text,
+                  lemma text,
+                  pos_tags text,
+                  dependencies text,
+                  ner_tags text,
+                  sentence_offset int,
+                  sentence_id text,
+                  dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_21 {
+          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+          CREATE TABLE
+          dd_delta_has_spouse(relation_id text,
+                   id bigint,
+                   label boolean,
+                   dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_22 {
+          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
+          CREATE TABLE
+          dd_new_has_spouse(relation_id text,
+                 id bigint,
+                 label boolean,
+                 dd_count int)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_articles;
+          TRUNCATE dd_new_people_mentions;
+          TRUNCATE dd_delta_has_spouse_features;
+          TRUNCATE dd_new_articles;
+          TRUNCATE dd_new_has_spouse_candidates;
+          TRUNCATE dd_new_has_spouse_features;
+          TRUNCATE dd_new_sentences;
+          TRUNCATE dd_delta_people_mentions;
+          TRUNCATE dd_delta_has_spouse_candidates;
+          TRUNCATE dd_delta_sentences;
+          TRUNCATE dd_delta_has_spouse;
+          TRUNCATE dd_new_has_spouse;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_30 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
+        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_11 {
+        sql: """ TRUNCATE dd_new_people_mentions;
+        INSERT INTO dd_new_people_mentions 
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            FROM people_mentions R0
+         UNION 
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            FROM dd_delta_people_mentions R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_23" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE dd_new_articles;
+        INSERT INTO dd_new_articles 
+            SELECT R0.article_id, R0.text, R0.dd_count
+            FROM articles R0
+         UNION 
+            SELECT R0.article_id, R0.text, R0.dd_count
+            FROM dd_delta_articles R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_24 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
+        CREATE VIEW dd_delta_ext_people_input AS 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            FROM dd_delta_sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ TRUNCATE dd_new_has_spouse_candidates;
+        INSERT INTO dd_new_has_spouse_candidates 
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            FROM has_spouse_candidates R0
+         UNION 
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            FROM dd_delta_has_spouse_candidates R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_26" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ TRUNCATE dd_new_has_spouse_features;
+        INSERT INTO dd_new_has_spouse_features 
+            SELECT R0.relation_id, R0.feature, R0.dd_count
+            FROM has_spouse_features R0
+         UNION 
+            SELECT R0.relation_id, R0.feature, R0.dd_count
+            FROM dd_delta_has_spouse_features R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_29" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ TRUNCATE dd_new_sentences;
+        INSERT INTO dd_new_sentences 
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            FROM sentences R0
+         UNION 
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            FROM dd_delta_sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_27 {
+        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
+        CREATE VIEW dd_delta_ext_has_spouse_input AS 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM dd_delta_people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id  UNION 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_23" ,  "extraction_rule_11" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_32 {
+        sql: """ 
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
+          FROM dd_delta_has_spouse_candidates R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_26" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_23 {
+          input: """ SELECT * FROM dd_delta_ext_people_input
+          """
+          output_relation: "dd_delta_people_mentions"
+          udf: ${APP_HOME}"/udf/ext_people.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_24" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_29 {
+          input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
+          """
+          output_relation: "dd_delta_has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_30" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_26 {
+          input: """ SELECT * FROM dd_delta_ext_has_spouse_input
+          """
+          output_relation: "dd_delta_has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_27" ]
+        }
+      
+
+        deepdive.inference.factors.dd_delta_has_spouse_0 {
+          input_query: """
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Linear(dd_delta_has_spouse.R0.label)"
+          weight: "?(has_spouse_features.R2.feature)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_delta_has_spouse_0]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
new file mode 100644
index 000000000..db34f0d16
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -0,0 +1,78 @@
+articles(
+  article_id text,
+  text       text).
+
+sentences(
+  document_id     text,
+  sentence        text,
+  words           text,
+  lemma           text,
+  pos_tags        text,
+  dependencies    text,
+  ner_tags        text,
+  sentence_offset int,
+  sentence_id     text).
+
+people_mentions(
+  sentence_id    text,
+  start_position int,
+  length         int,
+  text           text,
+  mention_id     text).
+
+has_spouse_candidates(
+  person1_id  text,
+  person2_id  text,
+  sentence_id text,
+  description text,
+  relation_id text,
+  is_true boolean).
+
+has_spouse_features(
+  relation_id text,
+  feature     text).
+
+has_spouse?(relation_id text).
+
+people_mentions :-
+  !ext_people(ext_people_input).
+
+ext_people_input(s, words, ner_tags) :-
+  sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people over like ext_people_input
+                 returns like people_mentions
+  implementation "/udf/ext_people.py" handles tsv lines.
+
+has_spouse_candidates :-
+  !ext_has_spouse(ext_has_spouse_input).
+
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, a, b, p1_text, p1_id),
+  people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse over like ext_has_spouse_input
+                     returns like has_spouse_candidates
+  implementation "/udf/ext_has_spouse.py" handles tsv lines.
+
+has_spouse_features :-
+  !ext_has_spouse_features(ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(a, b, words, c, d, e, f, g, s),
+  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+  people_mentions(s, p1idx, p1len, k, person1_id),
+  people_mentions(s, p2idx, p2len, l, person2_id).
+  
+function ext_has_spouse_features over like ext_has_spouse_features_input
+                              returns like has_spouse_features
+  implementation "/udf/ext_has_spouse_features.py" handles tsv lines.
+
+has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
+
+has_spouse(rid) :-
+  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_features(rid, f)
+weight = f
+semantics = Linear
+mode = inc.
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
new file mode 100644
index 000000000..7619f98cd
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -0,0 +1,178 @@
+articles(article_id text,
+         text text).
+
+dd_delta_articles(article_id text,
+                  text text).
+
+dd_new_articles(article_id text,
+                text text).
+
+dd_new_articles(article_id, text) :-
+    articles(article_id, text);
+    dd_delta_articles(article_id, text).
+
+sentences(document_id text,
+          sentence text,
+          words text,
+          lemma text,
+          pos_tags text,
+          dependencies text,
+          ner_tags text,
+          sentence_offset int,
+          sentence_id text).
+
+dd_delta_sentences(document_id text,
+                   sentence text,
+                   words text,
+                   lemma text,
+                   pos_tags text,
+                   dependencies text,
+                   ner_tags text,
+                   sentence_offset int,
+                   sentence_id text).
+
+dd_new_sentences(document_id text,
+                 sentence text,
+                 words text,
+                 lemma text,
+                 pos_tags text,
+                 dependencies text,
+                 ner_tags text,
+                 sentence_offset int,
+                 sentence_id text).
+
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
+    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
+    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
+
+people_mentions(sentence_id text,
+                start_position int,
+                length int,
+                text text,
+                mention_id text).
+
+dd_delta_people_mentions(sentence_id text,
+                         start_position int,
+                         length int,
+                         text text,
+                         mention_id text).
+
+dd_new_people_mentions(sentence_id text,
+                       start_position int,
+                       length int,
+                       text text,
+                       mention_id text).
+
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
+    people_mentions(sentence_id, start_position, length, text, mention_id);
+    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
+
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text,
+                      is_true boolean).
+
+dd_delta_has_spouse_candidates(person1_id text,
+                               person2_id text,
+                               sentence_id text,
+                               description text,
+                               relation_id text,
+                               is_true boolean).
+
+dd_new_has_spouse_candidates(person1_id text,
+                             person2_id text,
+                             sentence_id text,
+                             description text,
+                             relation_id text,
+                             is_true boolean).
+
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
+    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
+    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
+
+has_spouse_features(relation_id text,
+                    feature text).
+
+dd_delta_has_spouse_features(relation_id text,
+                             feature text).
+
+dd_new_has_spouse_features(relation_id text,
+                           feature text).
+
+dd_new_has_spouse_features(relation_id, feature) :-
+    has_spouse_features(relation_id, feature);
+    dd_delta_has_spouse_features(relation_id, feature).
+
+has_spouse?(relation_id text).
+
+dd_delta_has_spouse?(relation_id text).
+
+dd_new_has_spouse?(relation_id text).
+
+dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
+
+dd_delta_ext_people_input(s, words, ner_tags) :-
+    dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people
+    over like dd_delta_ext_people_input
+ returns like dd_delta_people_mentions
+ implementation "/udf/ext_people.py"
+        handles tsv lines.
+
+dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
+
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
+    people_mentions(s, c, d, p2_text, p2_id);
+    dd_new_people_mentions(s, a, b, p1_text, p1_id),
+    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse
+    over like dd_delta_ext_has_spouse_input
+ returns like dd_delta_has_spouse_candidates
+ implementation "/udf/ext_has_spouse.py"
+        handles tsv lines.
+
+dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
+
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id);
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id);
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id);
+    dd_new_sentences(a, b, words, c, d, e, f, g, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+
+function ext_has_spouse_features
+    over like dd_delta_ext_has_spouse_features_input
+ returns like dd_delta_has_spouse_features
+ implementation "/udf/ext_has_spouse_features.py"
+        handles tsv lines.
+
+dd_delta_has_spouse(rid) :-
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
+  label = l.
+
+dd_delta_has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_features(rid, f);
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_features(rid, f);
+    dd_new_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_features(rid, f)
+  weight = f
+  semantics = Linear.
+
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
new file mode 100644
index 000000000..abcb22144
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -0,0 +1,78 @@
+articles(article_id text,
+         text text).
+
+sentences(document_id text,
+          sentence text,
+          words text,
+          lemma text,
+          pos_tags text,
+          dependencies text,
+          ner_tags text,
+          sentence_offset int,
+          sentence_id text).
+
+people_mentions(sentence_id text,
+                start_position int,
+                length int,
+                text text,
+                mention_id text).
+
+has_spouse_candidates(person1_id text,
+                      person2_id text,
+                      sentence_id text,
+                      description text,
+                      relation_id text,
+                      is_true boolean).
+
+has_spouse_features(relation_id text,
+                    feature text).
+
+has_spouse?(relation_id text).
+
+people_mentions :- !ext_people(ext_people_input).
+
+ext_people_input(s, words, ner_tags) :-
+    sentences(a, b, words, c, d, e, ner_tags, f, s).
+
+function ext_people
+    over like ext_people_input
+ returns like people_mentions
+ implementation "/udf/ext_people.py"
+        handles tsv lines.
+
+has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
+
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+    people_mentions(s, a, b, p1_text, p1_id),
+    people_mentions(s, c, d, p2_text, p2_id).
+
+function ext_has_spouse
+    over like ext_has_spouse_input
+ returns like has_spouse_candidates
+ implementation "/udf/ext_has_spouse.py"
+        handles tsv lines.
+
+has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
+
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(a, b, words, c, d, e, f, g, s),
+    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
+    people_mentions(s, p1idx, p1len, k, person1_id),
+    people_mentions(s, p2idx, p2len, l, person2_id).
+
+function ext_has_spouse_features
+    over like ext_has_spouse_features_input
+ returns like has_spouse_features
+ implementation "/udf/ext_has_spouse_features.py"
+        handles tsv lines.
+
+has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l)
+  label = l.
+
+has_spouse(rid) :-
+    has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_features(rid, f)
+  weight = f
+  semantics = Linear.
+

From 4d57821c2f67d2d833a871161b6d5ce39d2bc627 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 12 Jun 2015 01:35:13 -0700
Subject: [PATCH 132/347] fix bugs

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  24 ++-
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  59 ++++--
 .../many_joins/print-incremental.expected     |   4 +
 .../compile-incremental.expected              |  70 +++++--
 .../compile-materialization.expected          |   9 +-
 .../smoke_example/compile.expected            |   9 +-
 .../smoke_example/print-incremental.expected  |  10 +-
 .../compile-incremental.expected              |  68 ++++---
 .../spouse_example/print-incremental.expected |   6 +-
 .../compile-incremental.expected              |  68 ++++---
 .../print-incremental.expected                |   6 +-
 .../compile-incremental.expected              |  81 +++++---
 .../compile.expected                          | 189 ++++++++++++++++++
 .../spouse_example_new_inference/input.ddl    |   9 +-
 .../print-incremental.expected                |  17 +-
 .../print.expected                            |   9 +-
 16 files changed, 497 insertions(+), 141 deletions(-)
 create mode 100644 test/expected-output-test/spouse_example_new_inference/compile.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index c78fa031a..acf4676e4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -351,8 +351,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
-        if (ss.inferenceRuleGroupByHead contains stmt.q.head.name) {
-          if (stmt.supervision == null) ss.error(s"Cannot find supervision for variable ${stmt.q.head.name}.\n")
+        if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
           val headTerms = tmpCq.head.terms map {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
@@ -366,6 +365,16 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
           ${ ss.generateSQLBody(tmpCq) }
           """
+        } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
+          val headTerms = tmpCq.head.terms map {
+            case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+          }
+          val headTermsStr = ( headTerms :+ "0 as id" ).mkString(", ")
+          val ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
+          val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
+          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label ${ddCountStr}
+          ${ ss.generateSQLBody(tmpCq) }
+          """
         } else {
           // variable columns
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
@@ -589,7 +598,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       case INCREMENTAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [cleanup]" else ""
       case _ => ""
     }
-    List(run, initdb, extraction_pipeline, inference_pipeline, cleanup_pipeline).filter(_ != "")
+    val base_dir = ss.mode match {
+      case INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
+      case _ => ""
+    }
+    List(run, initdb, extraction_pipeline, inference_pipeline, cleanup_pipeline, base_dir).filter(_ != "")
   }
 
   // generate variable schema statements
@@ -597,9 +610,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
-      case InferenceRule(q, weights, rule, mode) =>
-        val qs = new QuerySchema(q)
-        schema += s"${q.head.name}.label: Boolean"
+      case SchemaDeclaration(a, isQuery) =>
+        if (isQuery) schema += s"${a.name}.label: Boolean"
       case _ => ()
     }
     val ddSchema = s"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index cb24223d8..16564f6fc 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -18,12 +18,20 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
-  def transform(cq: ConjunctiveQuery, mode: String): ConjunctiveQuery = {
+  def transform(cq: ConjunctiveQuery, isInference: Boolean, mode: String): ConjunctiveQuery = {
     // New head
-    val incCqHead = cq.head.copy(
-      name = deltaPrefix + cq.head.name,
-      terms = cq.head.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
-    )
+    val incCqHead = if (isInference) {
+      cq.head.copy(
+        name = newPrefix + cq.head.name,
+        terms = cq.head.terms map {term => term.copy(relName = newPrefix + term.relName)}
+      )
+    } else {
+      cq.head.copy(
+        name = deltaPrefix + cq.head.name,
+        terms = cq.head.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
+      )
+    }
+
     var incCqBodies = new ListBuffer[List[Atom]]()
     // New incremental bodies
     for (body <- cq.bodies) {
@@ -43,18 +51,22 @@ object DeepDiveLogDeltaDeriver{
       }
       var i = 0
       var j = 0
-      var index = if ((incrementalFunctionInput contains incCqHead.name) || (mode == "inc")) -1 else 0
-      for (i <- index to (body.length - 1)) {
-        var newBody = new ListBuffer[Atom]()
-        for (j <- 0 to (body.length - 1)) {
-          if (j > i)
-            newBody += body(j)
-          else if (j < i)
-            newBody += incNewBody(j)
-          else if (j == i)
-            newBody += incDeltaBody(j)
+      var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
+      if (mode == "inc") {
+        incCqBodies += incNewBody
+      } else {
+        for (i <- index to (body.length - 1)) {
+          var newBody = new ListBuffer[Atom]()
+          for (j <- 0 to (body.length - 1)) {
+            if (j > i)
+              newBody += body(j)
+            else if (j < i)
+              newBody += incNewBody(j)
+            else if (j == i)
+              newBody += incDeltaBody(j)
+          }
+          incCqBodies += newBody.toList
         }
-        incCqBodies += newBody.toList
       }
     }
     ConjunctiveQuery(incCqHead, incCqBodies.toList)
@@ -87,10 +99,10 @@ object DeepDiveLogDeltaDeriver{
     )
     incrementalStatement += incNewStmt
 
-    if (!stmt.isQuery) {
-      incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(incNewStmt.a.name, incNewStmt.a.terms),
-        List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms)))))
-    }
+    // if (!stmt.isQuery) {
+    incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(incNewStmt.a.name, incNewStmt.a.terms),
+      List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms)))))
+    // }
     incrementalStatement.toList
   }
 
@@ -116,7 +128,10 @@ object DeepDiveLogDeltaDeriver{
   // Incremental extraction rule,
   // create delta rules based on original extraction rule
   def transform(stmt: ExtractionRule): List[Statement] = {
-    List(ExtractionRule(transform(stmt.q, null), stmt.supervision))
+    // if (stmt.supervision != null)
+      // List(ExtractionRule(transform(stmt.q, true, null), stmt.supervision))
+    // else
+      List(ExtractionRule(transform(stmt.q, false, null), stmt.supervision))
   }
 
   // Incremental function call rule,
@@ -128,7 +143,7 @@ object DeepDiveLogDeltaDeriver{
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(InferenceRule(transform(stmt.q, stmt.mode), stmt.weights, stmt.semantics))
+    List(InferenceRule(transform(stmt.q, true, stmt.mode), stmt.weights, stmt.semantics))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
diff --git a/test/expected-output-test/many_joins/print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
index 1394144d5..6edb3d0f8 100644
--- a/test/expected-output-test/many_joins/print-incremental.expected
+++ b/test/expected-output-test/many_joins/print-incremental.expected
@@ -4,6 +4,10 @@ dd_delta_R?(x text).
 
 dd_new_R?(x text).
 
+dd_new_R(x) :-
+    R(x);
+    dd_delta_R(x).
+
 S(x text).
 
 dd_delta_S(x text).
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index a1eebd935..475317479 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -19,7 +19,12 @@
       }
 
       deepdive.schema.variables {
-        dd_delta_cancer.label: Boolean
+        dd_new_smoke.label: Boolean
+smoke.label: Boolean
+cancer.label: Boolean
+dd_delta_cancer.label: Boolean
+dd_new_cancer.label: Boolean
+dd_delta_smoke.label: Boolean
       }
     
 
@@ -95,7 +100,7 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_20 {
+        deepdive.extraction.extractors.extraction_rule_21 {
           sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
           CREATE TABLE
           dd_delta_cancer(person_id bigint,
@@ -106,7 +111,7 @@
           style: "sql_extractor"
         }
 
-        deepdive.extraction.extractors.extraction_rule_21 {
+        deepdive.extraction.extractors.extraction_rule_22 {
           sql: """ DROP TABLE IF EXISTS dd_new_cancer CASCADE;
           CREATE TABLE
           dd_new_cancer(person_id bigint,
@@ -165,12 +170,12 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_22 {
+      deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ 
-        INSERT INTO dd_delta_smoke 
-            SELECT R0.person_id AS "dd_delta_person_smokes.R0.person_id" , R0.dd_count AS "dd_count" 
-            FROM dd_delta_person_smokes R0
+        INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label , R0.dd_count AS dd_count
+          FROM dd_delta_person_smokes R0
         
+          
         """
         style: "sql_extractor"
           
@@ -207,7 +212,22 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ TRUNCATE dd_new_smoke;
+        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM smoke R0
+        
+           UNION SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM dd_delta_smoke R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_24" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ 
         INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label , R0.dd_count AS dd_count
           FROM dd_delta_person_has_cancer R0
@@ -219,6 +239,21 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ TRUNCATE dd_new_cancer;
+        INSERT INTO dd_new_cancer SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM cancer R0
+        
+           UNION SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM dd_delta_cancer R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_25" ]
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_person_smokes;
         INSERT INTO dd_new_person_smokes 
@@ -249,20 +284,21 @@
       }
     
 
-        deepdive.inference.factors.dd_delta_cancer_0 {
+        deepdive.inference.factors.dd_new_cancer_0 {
           input_query: """
-          SELECT R0.id AS "dd_delta_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_cancer R0, dd_delta_smoke R1, person_smokes R2
+          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION 
-          SELECT R0.id AS "dd_delta_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
+          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(dd_delta_smoke.R1.label, dd_delta_cancer.R0.label)"
+          function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
           weight: "3.0"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_20, extraction_rule_21, extraction_rule_9, extraction_rule_10, extraction_rule_14]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_22, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_cancer_0]
+deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_new_cancer_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 82710e1cd..6296be46d 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -13,7 +13,8 @@
 
 
       deepdive.schema.variables {
-        cancer.label: Boolean
+        smoke.label: Boolean
+cancer.label: Boolean
       }
     
 
@@ -93,10 +94,10 @@
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO smoke 
-            SELECT R0.person_id AS "person_smokes.R0.person_id" , R0.dd_count AS "dd_count" 
-            FROM person_smokes R0
+        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label , R0.dd_count AS dd_count
+          FROM person_smokes R0
         
+          
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 6d4c87891..16c907851 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -13,7 +13,8 @@
 
 
       deepdive.schema.variables {
-        cancer.label: Boolean
+        smoke.label: Boolean
+cancer.label: Boolean
       }
     
 
@@ -87,10 +88,10 @@
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO smoke 
-            SELECT R0.person_id AS "person_smokes.R0.person_id" 
-            FROM person_smokes R0
+        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label 
+          FROM person_smokes R0
         
+          
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index 51a3a7443..5046bbaf3 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -56,12 +56,20 @@ dd_delta_smoke?(person_id bigint).
 
 dd_new_smoke?(person_id bigint).
 
+dd_new_smoke(person_id) :-
+    smoke(person_id);
+    dd_delta_smoke(person_id).
+
 cancer?(person_id bigint).
 
 dd_delta_cancer?(person_id bigint).
 
 dd_new_cancer?(person_id bigint).
 
+dd_new_cancer(person_id) :-
+    cancer(person_id);
+    dd_delta_cancer(person_id).
+
 dd_delta_smoke(pid) :-
     dd_delta_person_smokes(pid, l)
   label = l.
@@ -70,7 +78,7 @@ dd_delta_cancer(pid) :-
     dd_delta_person_has_cancer(pid, l)
   label = l.
 
-dd_delta_cancer(pid) :-
+dd_new_cancer(pid) :-
     dd_delta_smoke(pid),
     person_smokes(pid, l);
     dd_new_smoke(pid),
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 657fbcb45..439b69a1b 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -17,7 +17,9 @@
       }
 
       deepdive.schema.variables {
-        dd_delta_has_spouse.label: Boolean
+        has_spouse.label: Boolean
+dd_delta_has_spouse.label: Boolean
+dd_new_has_spouse.label: Boolean
       }
     
 
@@ -189,7 +191,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_30 {
+      deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
             SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
@@ -206,7 +208,7 @@
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
       }
     
 
@@ -221,7 +223,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ]
+          dependencies: [ "extraction_rule_24" ]
       }
     
 
@@ -240,7 +242,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_24 {
+      deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
             SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
@@ -263,7 +265,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -278,7 +280,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_29" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
@@ -297,7 +299,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_27 {
+      deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
             SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
@@ -308,11 +310,11 @@
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_32 {
+      deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
@@ -320,54 +322,70 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ TRUNCATE dd_new_has_spouse;
+        INSERT INTO dd_new_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM has_spouse R0
+        
+           UNION SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM dd_delta_has_spouse R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_33" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_24 {
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "extraction_rule_25" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_29 {
+        deepdive.extraction.extractors.extraction_rule_30 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_31" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_26 {
+        deepdive.extraction.extractors.extraction_rule_27 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_28" ]
         }
       
 
-        deepdive.inference.factors.dd_delta_has_spouse_0 {
+        deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_delta_has_spouse.R0.label)"
+          function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_has_spouse_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index aa6d787db..d552faf9f 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -111,6 +111,10 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
+dd_new_has_spouse(relation_id) :-
+    has_spouse(relation_id);
+    dd_delta_has_spouse(relation_id).
+
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
 dd_delta_ext_people_input(s, words, ner_tags) :-
@@ -166,7 +170,7 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-dd_delta_has_spouse(rid) :-
+dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 7de09941f..52adc16f4 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -17,7 +17,9 @@
       }
 
       deepdive.schema.variables {
-        dd_delta_has_spouse.label: Boolean
+        has_spouse.label: Boolean
+dd_delta_has_spouse.label: Boolean
+dd_new_has_spouse.label: Boolean
       }
     
 
@@ -189,7 +191,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_30 {
+      deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
             SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
@@ -206,7 +208,7 @@
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
       }
     
 
@@ -221,7 +223,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ]
+          dependencies: [ "extraction_rule_24" ]
       }
     
 
@@ -240,7 +242,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_24 {
+      deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
             SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
@@ -266,7 +268,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -281,7 +283,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_29" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
@@ -300,7 +302,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_27 {
+      deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
             SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
@@ -311,11 +313,11 @@
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_32 {
+      deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
@@ -323,54 +325,70 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ TRUNCATE dd_new_has_spouse;
+        INSERT INTO dd_new_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM has_spouse R0
+        
+           UNION SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM dd_delta_has_spouse R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_33" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_24 {
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "extraction_rule_25" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_29 {
+        deepdive.extraction.extractors.extraction_rule_30 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_31" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_26 {
+        deepdive.extraction.extractors.extraction_rule_27 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_28" ]
         }
       
 
-        deepdive.inference.factors.dd_delta_has_spouse_0 {
+        deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Linear(dd_delta_has_spouse.R0.label)"
+          function: "Linear(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_has_spouse_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 3edd6b253..edc9e85c5 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -111,6 +111,10 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
+dd_new_has_spouse(relation_id) :-
+    has_spouse(relation_id);
+    dd_delta_has_spouse(relation_id).
+
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
 dd_delta_ext_people_input(s, words, ner_tags) :-
@@ -167,7 +171,7 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-dd_delta_has_spouse(rid) :-
+dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 56f8f4fd3..c3391a893 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -17,7 +17,9 @@
       }
 
       deepdive.schema.variables {
-        dd_delta_has_spouse.label: Boolean
+        has_spouse.label: Boolean
+dd_delta_has_spouse.label: Boolean
+dd_new_has_spouse.label: Boolean
       }
     
 
@@ -189,7 +191,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_30 {
+      deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
             SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
@@ -206,7 +208,7 @@
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
       }
     
 
@@ -221,7 +223,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ]
+          dependencies: [ "extraction_rule_24" ]
       }
     
 
@@ -240,7 +242,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_24 {
+      deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
             SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
@@ -263,7 +265,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -278,7 +280,7 @@
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_29" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
@@ -297,7 +299,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_27 {
+      deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
             SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
@@ -308,11 +310,11 @@
         WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_23" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_32 {
+      deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse_candidates R0
@@ -320,57 +322,80 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ TRUNCATE dd_new_has_spouse;
+        INSERT INTO dd_new_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM has_spouse R0
+        
+           UNION SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+          FROM dd_delta_has_spouse R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_33" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_23 {
+        deepdive.extraction.extractors.extraction_rule_24 {
           input: """ SELECT * FROM dd_delta_ext_people_input
           """
           output_relation: "dd_delta_people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "extraction_rule_25" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_29 {
+        deepdive.extraction.extractors.extraction_rule_30 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_31" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_26 {
+        deepdive.extraction.extractors.extraction_rule_27 {
           input: """ SELECT * FROM dd_delta_ext_has_spouse_input
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_28" ]
         }
       
 
-        deepdive.inference.factors.dd_delta_has_spouse_0 {
+        deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
-          SELECT R0.id AS "dd_delta_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
-          FROM dd_delta_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Linear(dd_delta_has_spouse.R0.label)"
+          function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
       
+
+        deepdive.inference.factors.dd_new_has_spouse_1 {
+          input_query: """
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+          FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
+        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
+          function: "Imply(dd_new_has_spouse.R1.label, dd_new_has_spouse.R0.label)"
+          weight: "3.0"
+        }
+      
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_19, extraction_rule_32, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_has_spouse_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0, dd_new_has_spouse_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
new file mode 100644
index 000000000..981f3cee2
--- /dev/null
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -0,0 +1,189 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        has_spouse.label: Boolean
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_1 {
+          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+          CREATE TABLE
+          sentences(document_id text,
+         sentence text,
+         words text,
+         lemma text,
+         pos_tags text,
+         dependencies text,
+         ner_tags text,
+         sentence_offset int,
+         sentence_id text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_3 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+          CREATE TABLE
+          has_spouse_candidates(person1_id text,
+                     person2_id text,
+                     sentence_id text,
+                     description text,
+                     relation_id text,
+                     is_true boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+          CREATE TABLE
+          has_spouse(relation_id text,
+          id bigint,
+          label boolean)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_0 {
+          sql: """ DROP TABLE IF EXISTS articles CASCADE;
+          CREATE TABLE
+          articles(article_id text,
+        text text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_4 {
+          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+          CREATE TABLE
+          has_spouse_features(relation_id text,
+                   feature text)
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.extraction.extractors.extraction_rule_2 {
+          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+          CREATE TABLE
+          people_mentions(sentence_id text,
+               start_position int,
+               length int,
+               text text,
+               mention_id text)
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ 
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label 
+          FROM has_spouse_candidates R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_9" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ DROP VIEW IF EXISTS ext_people_input;
+        CREATE VIEW ext_people_input AS 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            FROM sentences R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_13 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
+        CREATE VIEW ext_has_spouse_features_input AS 
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_10 {
+        sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
+        CREATE VIEW ext_has_spouse_input AS 
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            FROM people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_6" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_6 {
+          input: """ SELECT * FROM ext_people_input
+          """
+          output_relation: "people_mentions"
+          udf: ${APP_HOME}"/udf/ext_people.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_7" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_12 {
+          input: """ SELECT * FROM ext_has_spouse_features_input
+          """
+          output_relation: "has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_13" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_9 {
+          input: """ SELECT * FROM ext_has_spouse_input
+          """
+          output_relation: "has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_10" ]
+        }
+      
+
+        deepdive.inference.factors.has_spouse_0 {
+          input_query: """
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
+          FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+          function: "Imply(has_spouse.R0.label)"
+          weight: "?(has_spouse_features.R2.feature)"
+        }
+      
+
+        deepdive.inference.factors.has_spouse_1 {
+          input_query: """
+          SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id"  
+          FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
+        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
+          function: "Imply(has_spouse.R1.label, has_spouse.R0.label)"
+          weight: "3.0"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [has_spouse_0, has_spouse_1]
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index db34f0d16..e6eb50fce 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -73,6 +73,11 @@ has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
-weight = f
-semantics = Linear
+weight = f.
+
+has_spouse(rid) :-
+  has_spouse(rid2),
+  has_spouse_candidates(a1, b1, c1, d1, rid, l1),
+  has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
+weight = 3.0
 mode = inc.
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 7619f98cd..baab6b961 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -111,6 +111,10 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
+dd_new_has_spouse(relation_id) :-
+    has_spouse(relation_id);
+    dd_delta_has_spouse(relation_id).
+
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
 dd_delta_ext_people_input(s, words, ner_tags) :-
@@ -166,13 +170,18 @@ dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-dd_delta_has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l),
-    has_spouse_features(rid, f);
+dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
-  semantics = Linear.
+  semantics = Imply.
+
+dd_new_has_spouse(rid) :-
+    dd_new_has_spouse(rid2),
+    dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
+    dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
+  weight = 3.0
+  semantics = Imply.
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index abcb22144..4e8b107bd 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -74,5 +74,12 @@ has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
-  semantics = Linear.
+  semantics = Imply.
+
+has_spouse(rid) :-
+    has_spouse(rid2),
+    has_spouse_candidates(a1, b1, c1, d1, rid, l1),
+    has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
+  weight = 3.0
+  semantics = Imply.
 

From abeb61b389727b067cd4c5ae04414b4850165b21 Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 12 Jun 2015 04:37:45 -0700
Subject: [PATCH 133/347] fix bugs, use view for dd_new_ variable tables

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  45 ++--
 .../compile-incremental.expected              | 186 ++++++++---------
 .../compile-materialization.expected          |  91 ++++----
 .../smoke_example/compile.expected            |  90 ++++----
 .../compile-incremental.expected              | 192 ++++++++---------
 .../compile-materialization.expected          | 101 +++++----
 .../spouse_example/compile.expected           | 100 +++++----
 .../compile-incremental.expected              | 194 ++++++++----------
 .../compile-incremental.expected              | 192 ++++++++---------
 .../compile.expected                          | 100 +++++----
 10 files changed, 654 insertions(+), 637 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index acf4676e4..e2b1dc3e7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -313,24 +313,27 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
     for (stmt <- stmts) {
-      var columnDecls = stmt.a.terms map {
-        case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
+      if ((stmt.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains stmt.a.name)) {
+      } else {
+        var columnDecls = stmt.a.terms map {
+          case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
+        }
+        if (stmt.isQuery) columnDecls = columnDecls :+ "id bigint" :+ "label boolean"
+        if (ss.useDeltaCount) columnDecls = columnDecls :+ "dd_count int"
+        val indentation = " " * stmt.a.name.length
+        val blockName = ss.resolveExtractorBlockName(stmt)
+        schemas += s"""
+          deepdive.extraction.extractors.${blockName} {
+            sql: \"\"\" DROP TABLE IF EXISTS ${stmt.a.name} CASCADE;
+            CREATE TABLE
+            ${stmt.a.name}(${columnDecls.mkString(",\n" + indentation)})
+            \"\"\"
+            style: "sql_extractor"
+          }"""
       }
-      if (stmt.isQuery) columnDecls = columnDecls :+ "id bigint" :+ "label boolean"
-      if (ss.useDeltaCount) columnDecls = columnDecls :+ "dd_count int"
-      val indentation = " " * stmt.a.name.length
-      val blockName = ss.resolveExtractorBlockName(stmt)
-      schemas += s"""
-        deepdive.extraction.extractors.${blockName} {
-          sql: \"\"\" DROP TABLE IF EXISTS ${stmt.a.name} CASCADE;
-          CREATE TABLE
-          ${stmt.a.name}(${columnDecls.mkString(",\n" + indentation)})
-          \"\"\"
-          style: "sql_extractor"
-        }"""
     }
     // Cleanup incremental table extractor
-    val truncateTableList = (stmts map (x => if (x.a.name.startsWith("dd_")) s"TRUNCATE ${x.a.name};" else "")).filter(_ != "")
+    val truncateTableList = (stmts map (x => if ((x.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains x.a.name)) "" else s"TRUNCATE ${x.a.name};")).filter(_ != "")
     if (truncateTableList.length > 0) {
       schemas += s"""
         deepdive.extraction.extractors.cleanup {
@@ -369,7 +372,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val headTerms = tmpCq.head.terms map {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
           }
-          val headTermsStr = ( headTerms :+ "0 as id" ).mkString(", ")
+          val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           val ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
           val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label ${ddCountStr}
@@ -415,14 +418,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val sqlCmdForCleanUp = ss.mode match {
       case MERGE => s"TRUNCATE ${stmts(0).q.head.name};"
       case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) {
-        if (stmts(0).q.head.name.startsWith("dd_new_"))
+        if (stmts(0).q.head.name.startsWith("dd_new_") && !(ss.inferenceRuleGroupByHead contains stmts(0).q.head.name))
           s"TRUNCATE ${stmts(0).q.head.name};"
         else ""
       } else s"DROP VIEW IF EXISTS ${stmts(0).q.head.name};"
     }
     val createTable = ss.mode match {
       case MERGE => true
-      case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) true else false
+      case _ => if ((!(stmts(0).q.head.name startsWith "dd_new_") && (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name)) || ((stmts(0).q.head.name startsWith "dd_new_") && !(ss.inferenceRuleGroupByHead contains stmts(0).q.head.name))) true else false
     }
     val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
     val useAS            = if (createTable) "" else " AS"
@@ -434,7 +437,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" ${sqlCmdForCleanUp}
-        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ")}${cleanUp}
+        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ALL ")}${cleanUp}
         \"\"\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
@@ -536,7 +539,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val blockName = ss.resolveInferenceBlockName(stmt)
       blocks ::= s"""
         deepdive.inference.factors.${blockName} {
-          input_query: \"\"\"${inputQueries.mkString(" UNION ")}\"\"\"
+          input_query: \"\"\"${inputQueries.mkString(" UNION ALL ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
         }
@@ -599,7 +602,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       case _ => ""
     }
     val base_dir = ss.mode match {
-      case INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
+      case MATERIALIZATION | INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
       case _ => ""
     }
     List(run, initdb, extraction_pipeline, inference_pipeline, cleanup_pipeline, base_dir).filter(_ != "")
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 475317479..08154a6ce 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -28,129 +28,118 @@ dd_delta_smoke.label: Boolean
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_13 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
-          CREATE TABLE
-          dd_delta_friends(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_13 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
+            CREATE TABLE
+            dd_delta_friends(person_id bigint,
                 friend_id bigint,
                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_17 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
-          CREATE TABLE
-          dd_delta_smoke(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_17 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
+            CREATE TABLE
+            dd_delta_smoke(person_id bigint,
               id bigint,
               label boolean,
               dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
-          CREATE TABLE
-          dd_new_person_has_cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_6 {
+            sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
+            CREATE TABLE
+            dd_new_person_has_cancer(person_id bigint,
                         has_cancer boolean,
                         dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
-          CREATE TABLE
-          dd_delta_person(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
+            CREATE TABLE
+            dd_delta_person(person_id bigint,
                name text,
                dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
-          CREATE TABLE
-          dd_new_person(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
+            CREATE TABLE
+            dd_new_person(person_id bigint,
              name text,
              dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
-          CREATE TABLE
-          dd_delta_person_has_cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
+            CREATE TABLE
+            dd_delta_person_has_cancer(person_id bigint,
                           has_cancer boolean,
                           dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_18 {
-          sql: """ DROP TABLE IF EXISTS dd_new_smoke CASCADE;
-          CREATE TABLE
-          dd_new_smoke(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_18 {
+            sql: """ DROP TABLE IF EXISTS dd_new_smoke CASCADE;
+            CREATE TABLE
+            dd_new_smoke(person_id bigint,
             id bigint,
             label boolean,
             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_21 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
-          CREATE TABLE
-          dd_delta_cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_21 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
+            CREATE TABLE
+            dd_delta_cancer(person_id bigint,
                id bigint,
                label boolean,
                dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_22 {
-          sql: """ DROP TABLE IF EXISTS dd_new_cancer CASCADE;
-          CREATE TABLE
-          dd_new_cancer(person_id bigint,
-             id bigint,
-             label boolean,
-             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
-          CREATE TABLE
-          dd_delta_person_smokes(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_9 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
+            CREATE TABLE
+            dd_delta_person_smokes(person_id bigint,
                       smokes boolean,
                       dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
-          CREATE TABLE
-          dd_new_person_smokes(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_10 {
+            sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
+            CREATE TABLE
+            dd_new_person_smokes(person_id bigint,
                     smokes boolean,
                     dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_14 {
-          sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
-          CREATE TABLE
-          dd_new_friends(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_14 {
+            sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
+            CREATE TABLE
+            dd_new_friends(person_id bigint,
               friend_id bigint,
               dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
         deepdive.extraction.extractors.cleanup {
           sql: """
@@ -162,7 +151,6 @@ dd_delta_smoke.label: Boolean
           TRUNCATE dd_delta_person_has_cancer;
           TRUNCATE dd_new_smoke;
           TRUNCATE dd_delta_cancer;
-          TRUNCATE dd_new_cancer;
           TRUNCATE dd_delta_person_smokes;
           TRUNCATE dd_new_person_smokes;
           TRUNCATE dd_new_friends;
@@ -187,7 +175,7 @@ dd_delta_smoke.label: Boolean
         INSERT INTO dd_new_person_has_cancer 
             SELECT R0.person_id, R0.has_cancer, R0.dd_count
             FROM person_has_cancer R0
-         UNION 
+         UNION ALL 
             SELECT R0.person_id, R0.has_cancer, R0.dd_count
             FROM dd_delta_person_has_cancer R0
         
@@ -202,7 +190,7 @@ dd_delta_smoke.label: Boolean
         INSERT INTO dd_new_person 
             SELECT R0.person_id, R0.name, R0.dd_count
             FROM person R0
-         UNION 
+         UNION ALL 
             SELECT R0.person_id, R0.name, R0.dd_count
             FROM dd_delta_person R0
         
@@ -214,10 +202,10 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_smoke;
-        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
           FROM smoke R0
         
-           UNION SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
           FROM dd_delta_smoke R0
         
           
@@ -240,11 +228,11 @@ dd_delta_smoke.label: Boolean
     
 
       deepdive.extraction.extractors.extraction_rule_23 {
-        sql: """ TRUNCATE dd_new_cancer;
-        INSERT INTO dd_new_cancer SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+        sql: """ 
+        CREATE VIEW dd_new_cancer AS SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
           FROM cancer R0
         
-           UNION SELECT DISTINCT R0.person_id, 0 as id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
           FROM dd_delta_cancer R0
         
           
@@ -259,7 +247,7 @@ dd_delta_smoke.label: Boolean
         INSERT INTO dd_new_person_smokes 
             SELECT R0.person_id, R0.smokes, R0.dd_count
             FROM person_smokes R0
-         UNION 
+         UNION ALL 
             SELECT R0.person_id, R0.smokes, R0.dd_count
             FROM dd_delta_person_smokes R0
         
@@ -274,7 +262,7 @@ dd_delta_smoke.label: Boolean
         INSERT INTO dd_new_friends 
             SELECT R0.person_id, R0.friend_id, R0.dd_count
             FROM friends R0
-         UNION 
+         UNION ALL 
             SELECT R0.person_id, R0.friend_id, R0.dd_count
             FROM dd_delta_friends R0
         
@@ -288,7 +276,7 @@ dd_delta_smoke.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION 
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION ALL 
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 6296be46d..1c050a73a 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -18,64 +18,76 @@ cancer.label: Boolean
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
-          CREATE TABLE
-          person_smokes(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
+            CREATE TABLE
+            person_smokes(person_id bigint,
              smokes boolean,
              dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS smoke CASCADE;
-          CREATE TABLE
-          smoke(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS smoke CASCADE;
+            CREATE TABLE
+            smoke(person_id bigint,
      id bigint,
      label boolean,
      dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS cancer CASCADE;
-          CREATE TABLE
-          cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS cancer CASCADE;
+            CREATE TABLE
+            cancer(person_id bigint,
       id bigint,
       label boolean,
       dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_3 {
-          sql: """ DROP TABLE IF EXISTS friends CASCADE;
-          CREATE TABLE
-          friends(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS friends CASCADE;
+            CREATE TABLE
+            friends(person_id bigint,
        friend_id bigint,
        dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
-          CREATE TABLE
-          person_has_cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
+            CREATE TABLE
+            person_has_cancer(person_id bigint,
                  has_cancer boolean,
                  dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS person CASCADE;
-          CREATE TABLE
-          person(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS person CASCADE;
+            CREATE TABLE
+            person(person_id bigint,
       name text,
       dd_count int)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE person_smokes;
+          TRUNCATE smoke;
+          TRUNCATE cancer;
+          TRUNCATE friends;
+          TRUNCATE person_has_cancer;
+          TRUNCATE person;
           """
           style: "sql_extractor"
         }
@@ -117,3 +129,4 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [cancer_0]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 16c907851..c5147d90d 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -18,58 +18,70 @@ cancer.label: Boolean
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
-          CREATE TABLE
-          person_smokes(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
+            CREATE TABLE
+            person_smokes(person_id bigint,
              smokes boolean)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS smoke CASCADE;
-          CREATE TABLE
-          smoke(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS smoke CASCADE;
+            CREATE TABLE
+            smoke(person_id bigint,
      id bigint,
      label boolean)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS cancer CASCADE;
-          CREATE TABLE
-          cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS cancer CASCADE;
+            CREATE TABLE
+            cancer(person_id bigint,
       id bigint,
       label boolean)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_3 {
-          sql: """ DROP TABLE IF EXISTS friends CASCADE;
-          CREATE TABLE
-          friends(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS friends CASCADE;
+            CREATE TABLE
+            friends(person_id bigint,
        friend_id bigint)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
-          CREATE TABLE
-          person_has_cancer(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
+            CREATE TABLE
+            person_has_cancer(person_id bigint,
                  has_cancer boolean)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS person CASCADE;
-          CREATE TABLE
-          person(person_id bigint,
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS person CASCADE;
+            CREATE TABLE
+            person(person_id bigint,
       name text)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE person_smokes;
+          TRUNCATE smoke;
+          TRUNCATE cancer;
+          TRUNCATE friends;
+          TRUNCATE person_has_cancer;
+          TRUNCATE person;
           """
           style: "sql_extractor"
         }
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 439b69a1b..bcbd12095 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -23,77 +23,77 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-          CREATE TABLE
-          dd_delta_articles(article_id text,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+            CREATE TABLE
+            dd_delta_articles(article_id text,
                  text text,
                  dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-          CREATE TABLE
-          dd_new_people_mentions(sentence_id text,
+          deepdive.extraction.extractors.extraction_rule_10 {
+            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+            CREATE TABLE
+            dd_new_people_mentions(sentence_id text,
                       start_position int,
                       length int,
                       text text,
                       mention_id text,
                       dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_17 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse_features(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_17 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_features(relation_id text,
                             feature text,
                             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-          CREATE TABLE
-          dd_new_articles(article_id text,
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+            CREATE TABLE
+            dd_new_articles(article_id text,
                text text,
                dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_14 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse_candidates(person1_id text,
+          deepdive.extraction.extractors.extraction_rule_14 {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_candidates(person1_id text,
                             person2_id text,
                             sentence_id text,
                             description text,
                             relation_id text,
                             is_true boolean,
                             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_18 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse_features(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_18 {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_features(relation_id text,
                           feature text,
                           dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-          CREATE TABLE
-          dd_new_sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_6 {
+            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+            CREATE TABLE
+            dd_new_sentences(document_id text,
                 sentence text,
                 words text,
                 lemma text,
@@ -103,41 +103,41 @@ dd_new_has_spouse.label: Boolean
                 sentence_offset int,
                 sentence_id text,
                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-          CREATE TABLE
-          dd_delta_people_mentions(sentence_id text,
+          deepdive.extraction.extractors.extraction_rule_9 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+            CREATE TABLE
+            dd_delta_people_mentions(sentence_id text,
                         start_position int,
                         length int,
                         text text,
                         mention_id text,
                         dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_13 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse_candidates(person1_id text,
+          deepdive.extraction.extractors.extraction_rule_13 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_candidates(person1_id text,
                               person2_id text,
                               sentence_id text,
                               description text,
                               relation_id text,
                               is_true boolean,
                               dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-          CREATE TABLE
-          dd_delta_sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+            CREATE TABLE
+            dd_delta_sentences(document_id text,
                   sentence text,
                   words text,
                   lemma text,
@@ -147,31 +147,20 @@ dd_new_has_spouse.label: Boolean
                   sentence_offset int,
                   sentence_id text,
                   dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_21 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_21 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse(relation_id text,
                    id bigint,
                    label boolean,
                    dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_22 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse(relation_id text,
-                 id bigint,
-                 label boolean,
-                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
         deepdive.extraction.extractors.cleanup {
           sql: """
@@ -186,7 +175,6 @@ dd_new_has_spouse.label: Boolean
           TRUNCATE dd_delta_has_spouse_candidates;
           TRUNCATE dd_delta_sentences;
           TRUNCATE dd_delta_has_spouse;
-          TRUNCATE dd_new_has_spouse;
           """
           style: "sql_extractor"
         }
@@ -196,13 +184,13 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
             SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -217,7 +205,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_people_mentions 
             SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
             FROM people_mentions R0
-         UNION 
+         UNION ALL 
             SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
             FROM dd_delta_people_mentions R0
         
@@ -232,7 +220,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_articles 
             SELECT R0.article_id, R0.text, R0.dd_count
             FROM articles R0
-         UNION 
+         UNION ALL 
             SELECT R0.article_id, R0.text, R0.dd_count
             FROM dd_delta_articles R0
         
@@ -259,7 +247,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_has_spouse_candidates 
             SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
             FROM has_spouse_candidates R0
-         UNION 
+         UNION ALL 
             SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
             FROM dd_delta_has_spouse_candidates R0
         
@@ -274,7 +262,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_has_spouse_features 
             SELECT R0.relation_id, R0.feature, R0.dd_count
             FROM has_spouse_features R0
-         UNION 
+         UNION ALL 
             SELECT R0.relation_id, R0.feature, R0.dd_count
             FROM dd_delta_has_spouse_features R0
         
@@ -289,7 +277,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_sentences 
             SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
             FROM sentences R0
-         UNION 
+         UNION ALL 
             SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
             FROM dd_delta_sentences R0
         
@@ -304,7 +292,7 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
             SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
             SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -327,11 +315,11 @@ dd_new_has_spouse.label: Boolean
     
 
       deepdive.extraction.extractors.extraction_rule_23 {
-        sql: """ TRUNCATE dd_new_has_spouse;
-        INSERT INTO dd_new_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+        sql: """ 
+        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
           FROM has_spouse R0
         
-           UNION SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse R0
         
           
@@ -375,7 +363,7 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 7f90239da..b3e0309c9 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -17,10 +17,10 @@
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-          CREATE TABLE
-          sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+            CREATE TABLE
+            sentences(document_id text,
          sentence text,
          words text,
          lemma text,
@@ -30,64 +30,76 @@
          sentence_offset int,
          sentence_id text,
          dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_3 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-          CREATE TABLE
-          has_spouse_candidates(person1_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+            CREATE TABLE
+            has_spouse_candidates(person1_id text,
                      person2_id text,
                      sentence_id text,
                      description text,
                      relation_id text,
                      is_true boolean,
                      dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-          CREATE TABLE
-          has_spouse(relation_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+            CREATE TABLE
+            has_spouse(relation_id text,
           id bigint,
           label boolean,
           dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS articles CASCADE;
-          CREATE TABLE
-          articles(article_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS articles CASCADE;
+            CREATE TABLE
+            articles(article_id text,
         text text,
         dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-          CREATE TABLE
-          has_spouse_features(relation_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+            CREATE TABLE
+            has_spouse_features(relation_id text,
                    feature text,
                    dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-          CREATE TABLE
-          people_mentions(sentence_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+            CREATE TABLE
+            people_mentions(sentence_id text,
                start_position int,
                length int,
                text text,
                mention_id text,
                dd_count int)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE sentences;
+          TRUNCATE has_spouse_candidates;
+          TRUNCATE has_spouse;
+          TRUNCATE articles;
+          TRUNCATE has_spouse_features;
+          TRUNCATE people_mentions;
           """
           style: "sql_extractor"
         }
@@ -183,3 +195,4 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [has_spouse_0]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 0a290eff3..ee490fafe 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -17,10 +17,10 @@
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-          CREATE TABLE
-          sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+            CREATE TABLE
+            sentences(document_id text,
          sentence text,
          words text,
          lemma text,
@@ -29,59 +29,71 @@
          ner_tags text,
          sentence_offset int,
          sentence_id text)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_3 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-          CREATE TABLE
-          has_spouse_candidates(person1_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+            CREATE TABLE
+            has_spouse_candidates(person1_id text,
                      person2_id text,
                      sentence_id text,
                      description text,
                      relation_id text,
                      is_true boolean)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-          CREATE TABLE
-          has_spouse(relation_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+            CREATE TABLE
+            has_spouse(relation_id text,
           id bigint,
           label boolean)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS articles CASCADE;
-          CREATE TABLE
-          articles(article_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS articles CASCADE;
+            CREATE TABLE
+            articles(article_id text,
         text text)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-          CREATE TABLE
-          has_spouse_features(relation_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+            CREATE TABLE
+            has_spouse_features(relation_id text,
                    feature text)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-          CREATE TABLE
-          people_mentions(sentence_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+            CREATE TABLE
+            people_mentions(sentence_id text,
                start_position int,
                length int,
                text text,
                mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE sentences;
+          TRUNCATE has_spouse_candidates;
+          TRUNCATE has_spouse;
+          TRUNCATE articles;
+          TRUNCATE has_spouse_features;
+          TRUNCATE people_mentions;
           """
           style: "sql_extractor"
         }
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 52adc16f4..028b2ae9a 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -23,77 +23,77 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-          CREATE TABLE
-          dd_delta_articles(article_id text,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+            CREATE TABLE
+            dd_delta_articles(article_id text,
                  text text,
                  dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-          CREATE TABLE
-          dd_new_people_mentions(sentence_id text,
+          deepdive.extraction.extractors.extraction_rule_10 {
+            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+            CREATE TABLE
+            dd_new_people_mentions(sentence_id text,
                       start_position int,
                       length int,
                       text text,
                       mention_id text,
                       dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_17 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse_features(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_17 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_features(relation_id text,
                             feature text,
                             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-          CREATE TABLE
-          dd_new_articles(article_id text,
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+            CREATE TABLE
+            dd_new_articles(article_id text,
                text text,
                dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_14 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse_candidates(person1_id text,
+          deepdive.extraction.extractors.extraction_rule_14 {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_candidates(person1_id text,
                             person2_id text,
                             sentence_id text,
                             description text,
                             relation_id text,
                             is_true boolean,
                             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_18 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse_features(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_18 {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_features(relation_id text,
                           feature text,
                           dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-          CREATE TABLE
-          dd_new_sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_6 {
+            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+            CREATE TABLE
+            dd_new_sentences(document_id text,
                 sentence text,
                 words text,
                 lemma text,
@@ -103,41 +103,41 @@ dd_new_has_spouse.label: Boolean
                 sentence_offset int,
                 sentence_id text,
                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-          CREATE TABLE
-          dd_delta_people_mentions(sentence_id text,
+          deepdive.extraction.extractors.extraction_rule_9 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+            CREATE TABLE
+            dd_delta_people_mentions(sentence_id text,
                         start_position int,
                         length int,
                         text text,
                         mention_id text,
                         dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_13 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse_candidates(person1_id text,
+          deepdive.extraction.extractors.extraction_rule_13 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_candidates(person1_id text,
                               person2_id text,
                               sentence_id text,
                               description text,
                               relation_id text,
                               is_true boolean,
                               dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-          CREATE TABLE
-          dd_delta_sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+            CREATE TABLE
+            dd_delta_sentences(document_id text,
                   sentence text,
                   words text,
                   lemma text,
@@ -147,31 +147,20 @@ dd_new_has_spouse.label: Boolean
                   sentence_offset int,
                   sentence_id text,
                   dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_21 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_21 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse(relation_id text,
                    id bigint,
                    label boolean,
                    dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_22 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse(relation_id text,
-                 id bigint,
-                 label boolean,
-                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
         deepdive.extraction.extractors.cleanup {
           sql: """
@@ -186,7 +175,6 @@ dd_new_has_spouse.label: Boolean
           TRUNCATE dd_delta_has_spouse_candidates;
           TRUNCATE dd_delta_sentences;
           TRUNCATE dd_delta_has_spouse;
-          TRUNCATE dd_new_has_spouse;
           """
           style: "sql_extractor"
         }
@@ -196,13 +184,13 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
             SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -217,7 +205,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_people_mentions 
             SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
             FROM people_mentions R0
-         UNION 
+         UNION ALL 
             SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
             FROM dd_delta_people_mentions R0
         
@@ -232,7 +220,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_articles 
             SELECT R0.article_id, R0.text, R0.dd_count
             FROM articles R0
-         UNION 
+         UNION ALL 
             SELECT R0.article_id, R0.text, R0.dd_count
             FROM dd_delta_articles R0
         
@@ -247,7 +235,7 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_people_input AS 
             SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
             FROM sentences R0
-         UNION 
+         UNION ALL 
             SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
             FROM dd_delta_sentences R0
         
@@ -262,7 +250,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_has_spouse_candidates 
             SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
             FROM has_spouse_candidates R0
-         UNION 
+         UNION ALL 
             SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
             FROM dd_delta_has_spouse_candidates R0
         
@@ -277,7 +265,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_has_spouse_features 
             SELECT R0.relation_id, R0.feature, R0.dd_count
             FROM has_spouse_features R0
-         UNION 
+         UNION ALL 
             SELECT R0.relation_id, R0.feature, R0.dd_count
             FROM dd_delta_has_spouse_features R0
         
@@ -292,7 +280,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_sentences 
             SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
             FROM sentences R0
-         UNION 
+         UNION ALL 
             SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
             FROM dd_delta_sentences R0
         
@@ -307,7 +295,7 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
             SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
             SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -330,11 +318,11 @@ dd_new_has_spouse.label: Boolean
     
 
       deepdive.extraction.extractors.extraction_rule_23 {
-        sql: """ TRUNCATE dd_new_has_spouse;
-        INSERT INTO dd_new_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+        sql: """ 
+        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
           FROM has_spouse R0
         
-           UNION SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse R0
         
           
@@ -378,7 +366,7 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index c3391a893..d6ed9c2e6 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -23,77 +23,77 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-          CREATE TABLE
-          dd_delta_articles(article_id text,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+            CREATE TABLE
+            dd_delta_articles(article_id text,
                  text text,
                  dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-          CREATE TABLE
-          dd_new_people_mentions(sentence_id text,
+          deepdive.extraction.extractors.extraction_rule_10 {
+            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+            CREATE TABLE
+            dd_new_people_mentions(sentence_id text,
                       start_position int,
                       length int,
                       text text,
                       mention_id text,
                       dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_17 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse_features(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_17 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_features(relation_id text,
                             feature text,
                             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-          CREATE TABLE
-          dd_new_articles(article_id text,
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+            CREATE TABLE
+            dd_new_articles(article_id text,
                text text,
                dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_14 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse_candidates(person1_id text,
+          deepdive.extraction.extractors.extraction_rule_14 {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_candidates(person1_id text,
                             person2_id text,
                             sentence_id text,
                             description text,
                             relation_id text,
                             is_true boolean,
                             dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_18 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse_features(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_18 {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_features(relation_id text,
                           feature text,
                           dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-          CREATE TABLE
-          dd_new_sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_6 {
+            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+            CREATE TABLE
+            dd_new_sentences(document_id text,
                 sentence text,
                 words text,
                 lemma text,
@@ -103,41 +103,41 @@ dd_new_has_spouse.label: Boolean
                 sentence_offset int,
                 sentence_id text,
                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-          CREATE TABLE
-          dd_delta_people_mentions(sentence_id text,
+          deepdive.extraction.extractors.extraction_rule_9 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+            CREATE TABLE
+            dd_delta_people_mentions(sentence_id text,
                         start_position int,
                         length int,
                         text text,
                         mention_id text,
                         dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_13 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse_candidates(person1_id text,
+          deepdive.extraction.extractors.extraction_rule_13 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_candidates(person1_id text,
                               person2_id text,
                               sentence_id text,
                               description text,
                               relation_id text,
                               is_true boolean,
                               dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-          CREATE TABLE
-          dd_delta_sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+            CREATE TABLE
+            dd_delta_sentences(document_id text,
                   sentence text,
                   words text,
                   lemma text,
@@ -147,31 +147,20 @@ dd_new_has_spouse.label: Boolean
                   sentence_offset int,
                   sentence_id text,
                   dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
-        deepdive.extraction.extractors.extraction_rule_21 {
-          sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-          CREATE TABLE
-          dd_delta_has_spouse(relation_id text,
+          deepdive.extraction.extractors.extraction_rule_21 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse(relation_id text,
                    id bigint,
                    label boolean,
                    dd_count int)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_22 {
-          sql: """ DROP TABLE IF EXISTS dd_new_has_spouse CASCADE;
-          CREATE TABLE
-          dd_new_has_spouse(relation_id text,
-                 id bigint,
-                 label boolean,
-                 dd_count int)
-          """
-          style: "sql_extractor"
-        }
+            """
+            style: "sql_extractor"
+          }
 
         deepdive.extraction.extractors.cleanup {
           sql: """
@@ -186,7 +175,6 @@ dd_new_has_spouse.label: Boolean
           TRUNCATE dd_delta_has_spouse_candidates;
           TRUNCATE dd_delta_sentences;
           TRUNCATE dd_delta_has_spouse;
-          TRUNCATE dd_new_has_spouse;
           """
           style: "sql_extractor"
         }
@@ -196,13 +184,13 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
             SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
             SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -217,7 +205,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_people_mentions 
             SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
             FROM people_mentions R0
-         UNION 
+         UNION ALL 
             SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
             FROM dd_delta_people_mentions R0
         
@@ -232,7 +220,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_articles 
             SELECT R0.article_id, R0.text, R0.dd_count
             FROM articles R0
-         UNION 
+         UNION ALL 
             SELECT R0.article_id, R0.text, R0.dd_count
             FROM dd_delta_articles R0
         
@@ -259,7 +247,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_has_spouse_candidates 
             SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
             FROM has_spouse_candidates R0
-         UNION 
+         UNION ALL 
             SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
             FROM dd_delta_has_spouse_candidates R0
         
@@ -274,7 +262,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_has_spouse_features 
             SELECT R0.relation_id, R0.feature, R0.dd_count
             FROM has_spouse_features R0
-         UNION 
+         UNION ALL 
             SELECT R0.relation_id, R0.feature, R0.dd_count
             FROM dd_delta_has_spouse_features R0
         
@@ -289,7 +277,7 @@ dd_new_has_spouse.label: Boolean
         INSERT INTO dd_new_sentences 
             SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
             FROM sentences R0
-         UNION 
+         UNION ALL 
             SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
             FROM dd_delta_sentences R0
         
@@ -304,7 +292,7 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
             SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION 
+        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
             SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -327,11 +315,11 @@ dd_new_has_spouse.label: Boolean
     
 
       deepdive.extraction.extractors.extraction_rule_23 {
-        sql: """ TRUNCATE dd_new_has_spouse;
-        INSERT INTO dd_new_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+        sql: """ 
+        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
           FROM has_spouse R0
         
-           UNION SELECT DISTINCT R0.relation_id, 0 as id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
           FROM dd_delta_has_spouse R0
         
           
@@ -375,7 +363,7 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 981f3cee2..d516477b9 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -17,10 +17,10 @@
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_1 {
-          sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-          CREATE TABLE
-          sentences(document_id text,
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS sentences CASCADE;
+            CREATE TABLE
+            sentences(document_id text,
          sentence text,
          words text,
          lemma text,
@@ -29,59 +29,71 @@
          ner_tags text,
          sentence_offset int,
          sentence_id text)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_3 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-          CREATE TABLE
-          has_spouse_candidates(person1_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
+            CREATE TABLE
+            has_spouse_candidates(person1_id text,
                      person2_id text,
                      sentence_id text,
                      description text,
                      relation_id text,
                      is_true boolean)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_5 {
-          sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-          CREATE TABLE
-          has_spouse(relation_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
+            CREATE TABLE
+            has_spouse(relation_id text,
           id bigint,
           label boolean)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_0 {
-          sql: """ DROP TABLE IF EXISTS articles CASCADE;
-          CREATE TABLE
-          articles(article_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS articles CASCADE;
+            CREATE TABLE
+            articles(article_id text,
         text text)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_4 {
-          sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-          CREATE TABLE
-          has_spouse_features(relation_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
+            CREATE TABLE
+            has_spouse_features(relation_id text,
                    feature text)
-          """
-          style: "sql_extractor"
-        }
-
-        deepdive.extraction.extractors.extraction_rule_2 {
-          sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-          CREATE TABLE
-          people_mentions(sentence_id text,
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
+            CREATE TABLE
+            people_mentions(sentence_id text,
                start_position int,
                length int,
                text text,
                mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE sentences;
+          TRUNCATE has_spouse_candidates;
+          TRUNCATE has_spouse;
+          TRUNCATE articles;
+          TRUNCATE has_spouse_features;
+          TRUNCATE people_mentions;
           """
           style: "sql_extractor"
         }

From 6dab902da9dab5e7044ca420502caba31300dcff Mon Sep 17 00:00:00 2001
From: senwu <senwu@stanford.edu>
Date: Fri, 12 Jun 2015 17:57:27 -0700
Subject: [PATCH 134/347] get rid of dd_count

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 48 ++---------
 .../compile-incremental.expected              | 65 +++++++--------
 .../compile-materialization.expected          | 24 +++---
 .../smoke_example/compile-merge.expected      | 20 ++---
 .../compile-incremental.expected              | 77 ++++++++----------
 .../compile-materialization.expected          | 28 +++----
 .../spouse_example/compile-merge.expected     | 25 +++---
 .../spouse_example/compile.expected           |  4 +-
 .../compile-incremental.expected              | 79 ++++++++-----------
 .../compile-incremental.expected              | 79 ++++++++-----------
 .../compile.expected                          |  6 +-
 11 files changed, 177 insertions(+), 278 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index e2b1dc3e7..289c1bfbe 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -98,8 +98,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   var mode : Mode = ORIGINAL
 
-  var useDeltaCount : Boolean = false
-
   // Mapping head names to the actual statements
   var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
   var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
@@ -110,10 +108,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   def init() = {
     // generate the statements.
     mode = config.mode
-    useDeltaCount = mode match {
-      case ORIGINAL => false
-      case _ => true
-    }
     statements.foreach {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery) => {
         terms.foreach {
@@ -319,7 +313,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
         }
         if (stmt.isQuery) columnDecls = columnDecls :+ "id bigint" :+ "label boolean"
-        if (ss.useDeltaCount) columnDecls = columnDecls :+ "dd_count int"
         val indentation = " " * stmt.a.name.length
         val blockName = ss.resolveExtractorBlockName(stmt)
         schemas += s"""
@@ -363,9 +356,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
           val headTermsStr = ( headTerms :+ "0 as id" ).mkString(", ")
-          val ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-          val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
-          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label ${ddCountStr}
+          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
@@ -373,9 +364,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
           }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
-          val ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-          val ddCountStr = if (ddCount.length > 0) s", ${ddCount} AS dd_count" else ""
-          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label ${ddCountStr}
+          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else {
@@ -395,21 +384,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
           val selectStr = variableCols.mkString(", ")
 
-          var ddCount = if (ss.useDeltaCount) ( tmpCq.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-          ddCount = ss.mode match {
-            case MERGE => s"SUM(${ddCount})"
-            case _ => ddCount
-          }
-          val ddCountStr = if (ddCount.length > 0) {
-            if (!tmpCqUseOnlyOriginal) s""", ${ddCount} AS \"dd_count\" """ else s", ${ddCount}"
-          } else ""
-          val groupBy = ss.mode match {
-            case MERGE => s" GROUP BY ${selectStr}"
-            case _ => ""
-          }
           inputQueries += s"""
-            SELECT ${selectStr}${ddCountStr}
-            ${ ss.generateSQLBody(tmpCq) }${ groupBy }"""
+            SELECT ${selectStr}
+            ${ ss.generateSQLBody(tmpCq) }"""
         }
       }
     }
@@ -429,15 +406,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     }
     val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
     val useAS            = if (createTable) "" else " AS"
-    val cleanUp          = ss.mode match {
-      case MERGE => s""";
-        DELETE FROM ${stmts(0).q.head.name} WHERE dd_count = 0;"""
-      case _     => ""
-    }
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" ${sqlCmdForCleanUp}
-        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ALL ")}${cleanUp}
+        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ALL ")}
         \"\"\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
@@ -489,7 +461,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       for (cqBody <- stmt.q.bodies) {
         // edge query
         val fakeBody        = stmt.q.head +: cqBody
-        // val fakeBody        = stmt.q.bodies +: List(stmt.q.head)
         val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody)) // we will just use the fakeBody below.
 
         val index = cqBody.length + 1
@@ -510,12 +481,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
 
-        val ddCount = if (ss.useDeltaCount) ( fakeCQ.bodies(0).zipWithIndex map { case(x,i) => s"R${i}.dd_count"}).mkString(" * ") else ""
-        val ddCountStr = if (ddCount.length > 0) s""", ${ddCount} AS \"dd_count\" """ else ""
-
         // factor input query
         inputQueries += s"""
-          SELECT ${selectStr} ${ddCountStr}
+          SELECT ${selectStr}
           ${ ss.generateSQLBody(fakeCQ) }"""
         // factor function
         if (func.length == 0) {
@@ -660,9 +628,5 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
     // emit the generated code
     blocks foreach println
-
-    // if (config.isIncremental) {
-    //   // TODO emit extra extractor for moving rows of dd_delta_* to *
-    // }
   }
 }
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 08154a6ce..b547dc8df 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -32,8 +32,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
             CREATE TABLE
             dd_delta_friends(person_id bigint,
-                friend_id bigint,
-                dd_count int)
+                friend_id bigint)
             """
             style: "sql_extractor"
           }
@@ -43,8 +42,7 @@ dd_delta_smoke.label: Boolean
             CREATE TABLE
             dd_delta_smoke(person_id bigint,
               id bigint,
-              label boolean,
-              dd_count int)
+              label boolean)
             """
             style: "sql_extractor"
           }
@@ -53,8 +51,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
             CREATE TABLE
             dd_new_person_has_cancer(person_id bigint,
-                        has_cancer boolean,
-                        dd_count int)
+                        has_cancer boolean)
             """
             style: "sql_extractor"
           }
@@ -63,8 +60,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
             CREATE TABLE
             dd_delta_person(person_id bigint,
-               name text,
-               dd_count int)
+               name text)
             """
             style: "sql_extractor"
           }
@@ -73,8 +69,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
             CREATE TABLE
             dd_new_person(person_id bigint,
-             name text,
-             dd_count int)
+             name text)
             """
             style: "sql_extractor"
           }
@@ -83,8 +78,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
             CREATE TABLE
             dd_delta_person_has_cancer(person_id bigint,
-                          has_cancer boolean,
-                          dd_count int)
+                          has_cancer boolean)
             """
             style: "sql_extractor"
           }
@@ -94,8 +88,7 @@ dd_delta_smoke.label: Boolean
             CREATE TABLE
             dd_new_smoke(person_id bigint,
             id bigint,
-            label boolean,
-            dd_count int)
+            label boolean)
             """
             style: "sql_extractor"
           }
@@ -105,8 +98,7 @@ dd_delta_smoke.label: Boolean
             CREATE TABLE
             dd_delta_cancer(person_id bigint,
                id bigint,
-               label boolean,
-               dd_count int)
+               label boolean)
             """
             style: "sql_extractor"
           }
@@ -115,8 +107,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
             CREATE TABLE
             dd_delta_person_smokes(person_id bigint,
-                      smokes boolean,
-                      dd_count int)
+                      smokes boolean)
             """
             style: "sql_extractor"
           }
@@ -125,8 +116,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
             CREATE TABLE
             dd_new_person_smokes(person_id bigint,
-                    smokes boolean,
-                    dd_count int)
+                    smokes boolean)
             """
             style: "sql_extractor"
           }
@@ -135,8 +125,7 @@ dd_delta_smoke.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
             CREATE TABLE
             dd_new_friends(person_id bigint,
-              friend_id bigint,
-              dd_count int)
+              friend_id bigint)
             """
             style: "sql_extractor"
           }
@@ -160,7 +149,7 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ 
-        INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label
           FROM dd_delta_person_smokes R0
         
           
@@ -173,10 +162,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_person_has_cancer;
         INSERT INTO dd_new_person_has_cancer 
-            SELECT R0.person_id, R0.has_cancer, R0.dd_count
+            SELECT R0.person_id, R0.has_cancer
             FROM person_has_cancer R0
          UNION ALL 
-            SELECT R0.person_id, R0.has_cancer, R0.dd_count
+            SELECT R0.person_id, R0.has_cancer
             FROM dd_delta_person_has_cancer R0
         
         """
@@ -188,10 +177,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_person;
         INSERT INTO dd_new_person 
-            SELECT R0.person_id, R0.name, R0.dd_count
+            SELECT R0.person_id, R0.name
             FROM person R0
          UNION ALL 
-            SELECT R0.person_id, R0.name, R0.dd_count
+            SELECT R0.person_id, R0.name
             FROM dd_delta_person R0
         
         """
@@ -202,10 +191,10 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_smoke;
-        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
+        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id, id, label
           FROM smoke R0
         
-           UNION ALL SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.person_id, id, label
           FROM dd_delta_smoke R0
         
           
@@ -217,7 +206,7 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ 
-        INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label
           FROM dd_delta_person_has_cancer R0
         
           
@@ -229,10 +218,10 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ 
-        CREATE VIEW dd_new_cancer AS SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
+        CREATE VIEW dd_new_cancer AS SELECT DISTINCT R0.person_id, id, label
           FROM cancer R0
         
-           UNION ALL SELECT DISTINCT R0.person_id,  id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.person_id, id, label
           FROM dd_delta_cancer R0
         
           
@@ -245,10 +234,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_person_smokes;
         INSERT INTO dd_new_person_smokes 
-            SELECT R0.person_id, R0.smokes, R0.dd_count
+            SELECT R0.person_id, R0.smokes
             FROM person_smokes R0
          UNION ALL 
-            SELECT R0.person_id, R0.smokes, R0.dd_count
+            SELECT R0.person_id, R0.smokes
             FROM dd_delta_person_smokes R0
         
         """
@@ -260,10 +249,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_friends;
         INSERT INTO dd_new_friends 
-            SELECT R0.person_id, R0.friend_id, R0.dd_count
+            SELECT R0.person_id, R0.friend_id
             FROM friends R0
          UNION ALL 
-            SELECT R0.person_id, R0.friend_id, R0.dd_count
+            SELECT R0.person_id, R0.friend_id
             FROM dd_delta_friends R0
         
         """
@@ -274,10 +263,10 @@ dd_delta_smoke.label: Boolean
 
         deepdive.inference.factors.dd_new_cancer_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION ALL 
-          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 1c050a73a..6ed2190ad 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -22,8 +22,7 @@ cancer.label: Boolean
             sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
             CREATE TABLE
             person_smokes(person_id bigint,
-             smokes boolean,
-             dd_count int)
+             smokes boolean)
             """
             style: "sql_extractor"
           }
@@ -33,8 +32,7 @@ cancer.label: Boolean
             CREATE TABLE
             smoke(person_id bigint,
      id bigint,
-     label boolean,
-     dd_count int)
+     label boolean)
             """
             style: "sql_extractor"
           }
@@ -44,8 +42,7 @@ cancer.label: Boolean
             CREATE TABLE
             cancer(person_id bigint,
       id bigint,
-      label boolean,
-      dd_count int)
+      label boolean)
             """
             style: "sql_extractor"
           }
@@ -54,8 +51,7 @@ cancer.label: Boolean
             sql: """ DROP TABLE IF EXISTS friends CASCADE;
             CREATE TABLE
             friends(person_id bigint,
-       friend_id bigint,
-       dd_count int)
+       friend_id bigint)
             """
             style: "sql_extractor"
           }
@@ -64,8 +60,7 @@ cancer.label: Boolean
             sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
             CREATE TABLE
             person_has_cancer(person_id bigint,
-                 has_cancer boolean,
-                 dd_count int)
+                 has_cancer boolean)
             """
             style: "sql_extractor"
           }
@@ -74,8 +69,7 @@ cancer.label: Boolean
             sql: """ DROP TABLE IF EXISTS person CASCADE;
             CREATE TABLE
             person(person_id bigint,
-      name text,
-      dd_count int)
+      name text)
             """
             style: "sql_extractor"
           }
@@ -94,7 +88,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ 
-        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label , R0.dd_count AS dd_count
+        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
           
@@ -106,7 +100,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label , R0.dd_count AS dd_count
+        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label
           FROM person_smokes R0
         
           
@@ -118,7 +112,7 @@ cancer.label: Boolean
 
         deepdive.inference.factors.cancer_0 {
           input_query: """
-          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
index 10a177f1e..487fc94a3 100644
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -20,10 +20,9 @@
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE person_smokes;
         INSERT INTO person_smokes 
-            SELECT R0.person_id, R0.smokes, SUM(R0.dd_count)
+            SELECT R0.person_id, R0.smokes
             FROM dd_new_person_smokes R0
-         GROUP BY R0.person_id, R0.smokes;
-        DELETE FROM person_smokes WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -33,10 +32,9 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE friends;
         INSERT INTO friends 
-            SELECT R0.person_id, R0.friend_id, SUM(R0.dd_count)
+            SELECT R0.person_id, R0.friend_id
             FROM dd_new_friends R0
-         GROUP BY R0.person_id, R0.friend_id;
-        DELETE FROM friends WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -46,10 +44,9 @@
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE person_has_cancer;
         INSERT INTO person_has_cancer 
-            SELECT R0.person_id, R0.has_cancer, SUM(R0.dd_count)
+            SELECT R0.person_id, R0.has_cancer
             FROM dd_new_person_has_cancer R0
-         GROUP BY R0.person_id, R0.has_cancer;
-        DELETE FROM person_has_cancer WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -59,10 +56,9 @@
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE person;
         INSERT INTO person 
-            SELECT R0.person_id, R0.name, SUM(R0.dd_count)
+            SELECT R0.person_id, R0.name
             FROM dd_new_person R0
-         GROUP BY R0.person_id, R0.name;
-        DELETE FROM person WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index bcbd12095..beee5b073 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -27,8 +27,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
             CREATE TABLE
             dd_delta_articles(article_id text,
-                 text text,
-                 dd_count int)
+                 text text)
             """
             style: "sql_extractor"
           }
@@ -40,8 +39,7 @@ dd_new_has_spouse.label: Boolean
                       start_position int,
                       length int,
                       text text,
-                      mention_id text,
-                      dd_count int)
+                      mention_id text)
             """
             style: "sql_extractor"
           }
@@ -50,8 +48,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_features(relation_id text,
-                            feature text,
-                            dd_count int)
+                            feature text)
             """
             style: "sql_extractor"
           }
@@ -60,8 +57,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
             CREATE TABLE
             dd_new_articles(article_id text,
-               text text,
-               dd_count int)
+               text text)
             """
             style: "sql_extractor"
           }
@@ -74,8 +70,7 @@ dd_new_has_spouse.label: Boolean
                             sentence_id text,
                             description text,
                             relation_id text,
-                            is_true boolean,
-                            dd_count int)
+                            is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -84,8 +79,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
             CREATE TABLE
             dd_new_has_spouse_features(relation_id text,
-                          feature text,
-                          dd_count int)
+                          feature text)
             """
             style: "sql_extractor"
           }
@@ -101,8 +95,7 @@ dd_new_has_spouse.label: Boolean
                 dependencies text,
                 ner_tags text,
                 sentence_offset int,
-                sentence_id text,
-                dd_count int)
+                sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -114,8 +107,7 @@ dd_new_has_spouse.label: Boolean
                         start_position int,
                         length int,
                         text text,
-                        mention_id text,
-                        dd_count int)
+                        mention_id text)
             """
             style: "sql_extractor"
           }
@@ -128,8 +120,7 @@ dd_new_has_spouse.label: Boolean
                               sentence_id text,
                               description text,
                               relation_id text,
-                              is_true boolean,
-                              dd_count int)
+                              is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -145,8 +136,7 @@ dd_new_has_spouse.label: Boolean
                   dependencies text,
                   ner_tags text,
                   sentence_offset int,
-                  sentence_id text,
-                  dd_count int)
+                  sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -156,8 +146,7 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_delta_has_spouse(relation_id text,
                    id bigint,
-                   label boolean,
-                   dd_count int)
+                   label boolean)
             """
             style: "sql_extractor"
           }
@@ -182,16 +171,16 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
@@ -203,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -218,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text, R0.dd_count
+            SELECT R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT R0.article_id, R0.text, R0.dd_count
+            SELECT R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -233,7 +222,7 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -245,10 +234,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -260,10 +249,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature, R0.dd_count
+            SELECT R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT R0.relation_id, R0.feature, R0.dd_count
+            SELECT R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -275,10 +264,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -290,10 +279,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
@@ -304,7 +293,7 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
           
@@ -316,10 +305,10 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ 
-        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
+        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
-           UNION ALL SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
           
@@ -361,10 +350,10 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index b3e0309c9..706b2bbac 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -28,8 +28,7 @@
          dependencies text,
          ner_tags text,
          sentence_offset int,
-         sentence_id text,
-         dd_count int)
+         sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -42,8 +41,7 @@
                      sentence_id text,
                      description text,
                      relation_id text,
-                     is_true boolean,
-                     dd_count int)
+                     is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -53,8 +51,7 @@
             CREATE TABLE
             has_spouse(relation_id text,
           id bigint,
-          label boolean,
-          dd_count int)
+          label boolean)
             """
             style: "sql_extractor"
           }
@@ -63,8 +60,7 @@
             sql: """ DROP TABLE IF EXISTS articles CASCADE;
             CREATE TABLE
             articles(article_id text,
-        text text,
-        dd_count int)
+        text text)
             """
             style: "sql_extractor"
           }
@@ -73,8 +69,7 @@
             sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
             CREATE TABLE
             has_spouse_features(relation_id text,
-                   feature text,
-                   dd_count int)
+                   feature text)
             """
             style: "sql_extractor"
           }
@@ -86,8 +81,7 @@
                start_position int,
                length int,
                text text,
-               mention_id text,
-               dd_count int)
+               mention_id text)
             """
             style: "sql_extractor"
           }
@@ -106,7 +100,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           
@@ -119,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -131,7 +125,7 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
@@ -143,7 +137,7 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
@@ -184,7 +178,7 @@
 
         deepdive.inference.factors.has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index b0dfc4a2f..9a972542f 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -20,10 +20,9 @@
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE sentences;
         INSERT INTO sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, SUM(R0.dd_count)
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_new_sentences R0
-         GROUP BY R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id;
-        DELETE FROM sentences WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -33,10 +32,9 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE has_spouse_candidates;
         INSERT INTO has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, SUM(R0.dd_count)
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_new_has_spouse_candidates R0
-         GROUP BY R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true;
-        DELETE FROM has_spouse_candidates WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -46,10 +44,9 @@
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE articles;
         INSERT INTO articles 
-            SELECT R0.article_id, R0.text, SUM(R0.dd_count)
+            SELECT R0.article_id, R0.text
             FROM dd_new_articles R0
-         GROUP BY R0.article_id, R0.text;
-        DELETE FROM articles WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -59,10 +56,9 @@
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ TRUNCATE has_spouse_features;
         INSERT INTO has_spouse_features 
-            SELECT R0.relation_id, R0.feature, SUM(R0.dd_count)
+            SELECT R0.relation_id, R0.feature
             FROM dd_new_has_spouse_features R0
-         GROUP BY R0.relation_id, R0.feature;
-        DELETE FROM has_spouse_features WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
@@ -72,10 +68,9 @@
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE people_mentions;
         INSERT INTO people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, SUM(R0.dd_count)
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_new_people_mentions R0
-         GROUP BY R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id;
-        DELETE FROM people_mentions WHERE dd_count = 0;
+        
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index ee490fafe..87d478af8 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -100,7 +100,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label 
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           
@@ -178,7 +178,7 @@
 
         deepdive.inference.factors.has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 028b2ae9a..ca8c73cb5 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -27,8 +27,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
             CREATE TABLE
             dd_delta_articles(article_id text,
-                 text text,
-                 dd_count int)
+                 text text)
             """
             style: "sql_extractor"
           }
@@ -40,8 +39,7 @@ dd_new_has_spouse.label: Boolean
                       start_position int,
                       length int,
                       text text,
-                      mention_id text,
-                      dd_count int)
+                      mention_id text)
             """
             style: "sql_extractor"
           }
@@ -50,8 +48,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_features(relation_id text,
-                            feature text,
-                            dd_count int)
+                            feature text)
             """
             style: "sql_extractor"
           }
@@ -60,8 +57,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
             CREATE TABLE
             dd_new_articles(article_id text,
-               text text,
-               dd_count int)
+               text text)
             """
             style: "sql_extractor"
           }
@@ -74,8 +70,7 @@ dd_new_has_spouse.label: Boolean
                             sentence_id text,
                             description text,
                             relation_id text,
-                            is_true boolean,
-                            dd_count int)
+                            is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -84,8 +79,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
             CREATE TABLE
             dd_new_has_spouse_features(relation_id text,
-                          feature text,
-                          dd_count int)
+                          feature text)
             """
             style: "sql_extractor"
           }
@@ -101,8 +95,7 @@ dd_new_has_spouse.label: Boolean
                 dependencies text,
                 ner_tags text,
                 sentence_offset int,
-                sentence_id text,
-                dd_count int)
+                sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -114,8 +107,7 @@ dd_new_has_spouse.label: Boolean
                         start_position int,
                         length int,
                         text text,
-                        mention_id text,
-                        dd_count int)
+                        mention_id text)
             """
             style: "sql_extractor"
           }
@@ -128,8 +120,7 @@ dd_new_has_spouse.label: Boolean
                               sentence_id text,
                               description text,
                               relation_id text,
-                              is_true boolean,
-                              dd_count int)
+                              is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -145,8 +136,7 @@ dd_new_has_spouse.label: Boolean
                   dependencies text,
                   ner_tags text,
                   sentence_offset int,
-                  sentence_id text,
-                  dd_count int)
+                  sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -156,8 +146,7 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_delta_has_spouse(relation_id text,
                    id bigint,
-                   label boolean,
-                   dd_count int)
+                   label boolean)
             """
             style: "sql_extractor"
           }
@@ -182,16 +171,16 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
@@ -203,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -218,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text, R0.dd_count
+            SELECT R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT R0.article_id, R0.text, R0.dd_count
+            SELECT R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -233,10 +222,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
          UNION ALL 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -248,10 +237,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -263,10 +252,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature, R0.dd_count
+            SELECT R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT R0.relation_id, R0.feature, R0.dd_count
+            SELECT R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -278,10 +267,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -293,10 +282,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
@@ -307,7 +296,7 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
           
@@ -319,10 +308,10 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ 
-        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
+        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
-           UNION ALL SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
           
@@ -364,10 +353,10 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Linear(dd_new_has_spouse.R0.label)"
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index d6ed9c2e6..3baea1486 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -27,8 +27,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
             CREATE TABLE
             dd_delta_articles(article_id text,
-                 text text,
-                 dd_count int)
+                 text text)
             """
             style: "sql_extractor"
           }
@@ -40,8 +39,7 @@ dd_new_has_spouse.label: Boolean
                       start_position int,
                       length int,
                       text text,
-                      mention_id text,
-                      dd_count int)
+                      mention_id text)
             """
             style: "sql_extractor"
           }
@@ -50,8 +48,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_features(relation_id text,
-                            feature text,
-                            dd_count int)
+                            feature text)
             """
             style: "sql_extractor"
           }
@@ -60,8 +57,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
             CREATE TABLE
             dd_new_articles(article_id text,
-               text text,
-               dd_count int)
+               text text)
             """
             style: "sql_extractor"
           }
@@ -74,8 +70,7 @@ dd_new_has_spouse.label: Boolean
                             sentence_id text,
                             description text,
                             relation_id text,
-                            is_true boolean,
-                            dd_count int)
+                            is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -84,8 +79,7 @@ dd_new_has_spouse.label: Boolean
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
             CREATE TABLE
             dd_new_has_spouse_features(relation_id text,
-                          feature text,
-                          dd_count int)
+                          feature text)
             """
             style: "sql_extractor"
           }
@@ -101,8 +95,7 @@ dd_new_has_spouse.label: Boolean
                 dependencies text,
                 ner_tags text,
                 sentence_offset int,
-                sentence_id text,
-                dd_count int)
+                sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -114,8 +107,7 @@ dd_new_has_spouse.label: Boolean
                         start_position int,
                         length int,
                         text text,
-                        mention_id text,
-                        dd_count int)
+                        mention_id text)
             """
             style: "sql_extractor"
           }
@@ -128,8 +120,7 @@ dd_new_has_spouse.label: Boolean
                               sentence_id text,
                               description text,
                               relation_id text,
-                              is_true boolean,
-                              dd_count int)
+                              is_true boolean)
             """
             style: "sql_extractor"
           }
@@ -145,8 +136,7 @@ dd_new_has_spouse.label: Boolean
                   dependencies text,
                   ner_tags text,
                   sentence_offset int,
-                  sentence_id text,
-                  dd_count int)
+                  sentence_id text)
             """
             style: "sql_extractor"
           }
@@ -156,8 +146,7 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_delta_has_spouse(relation_id text,
                    id bigint,
-                   label boolean,
-                   dd_count int)
+                   label boolean)
             """
             style: "sql_extractor"
           }
@@ -182,16 +171,16 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
@@ -203,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id, R0.dd_count
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -218,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text, R0.dd_count
+            SELECT R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT R0.article_id, R0.text, R0.dd_count
+            SELECT R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -233,7 +222,7 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" , R0.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -245,10 +234,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true, R0.dd_count
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -260,10 +249,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature, R0.dd_count
+            SELECT R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT R0.relation_id, R0.feature, R0.dd_count
+            SELECT R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -275,10 +264,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id, R0.dd_count
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -290,10 +279,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" , R0.dd_count * R1.dd_count AS "dd_count" 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
         """
@@ -304,7 +293,7 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label , R0.dd_count AS dd_count
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
           
@@ -316,10 +305,10 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ 
-        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
+        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
-           UNION ALL SELECT DISTINCT R0.relation_id,  id, label , R0.dd_count AS dd_count
+           UNION ALL SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
           
@@ -361,10 +350,10 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature"  , R0.dd_count * R1.dd_count * R2.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
@@ -374,7 +363,7 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_1 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id"  , R0.dd_count * R1.dd_count * R2.dd_count * R3.dd_count AS "dd_count" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
         WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
           function: "Imply(dd_new_has_spouse.R1.label, dd_new_has_spouse.R0.label)"
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index d516477b9..d184ea219 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -100,7 +100,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label 
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           
@@ -178,7 +178,7 @@
 
         deepdive.inference.factors.has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature"  
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
@@ -188,7 +188,7 @@
 
         deepdive.inference.factors.has_spouse_1 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id"  
+          SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
         WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
           function: "Imply(has_spouse.R1.label, has_spouse.R0.label)"

From f390c460b71389b4c7716e8d0e0f0a43bb756e3f Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 1 Jul 2015 16:02:25 -0700
Subject: [PATCH 135/347] update smoke example

---
 .../compile-incremental.expected              | 32 ++++++++++---------
 .../compile-materialization.expected          | 14 ++++++--
 .../smoke_example/compile.expected            | 14 ++++++--
 .../smoke_example/input.ddl                   |  5 ++-
 .../smoke_example/print-incremental.expected  | 10 +++++-
 .../smoke_example/print.expected              |  8 ++++-
 6 files changed, 61 insertions(+), 22 deletions(-)

diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index b547dc8df..042e044f4 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -83,16 +83,6 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_18 {
-            sql: """ DROP TABLE IF EXISTS dd_new_smoke CASCADE;
-            CREATE TABLE
-            dd_new_smoke(person_id bigint,
-            id bigint,
-            label boolean)
-            """
-            style: "sql_extractor"
-          }
-
           deepdive.extraction.extractors.extraction_rule_21 {
             sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
             CREATE TABLE
@@ -138,7 +128,6 @@ dd_delta_smoke.label: Boolean
           TRUNCATE dd_delta_person;
           TRUNCATE dd_new_person;
           TRUNCATE dd_delta_person_has_cancer;
-          TRUNCATE dd_new_smoke;
           TRUNCATE dd_delta_cancer;
           TRUNCATE dd_delta_person_smokes;
           TRUNCATE dd_new_person_smokes;
@@ -190,8 +179,8 @@ dd_delta_smoke.label: Boolean
     
 
       deepdive.extraction.extractors.extraction_rule_19 {
-        sql: """ TRUNCATE dd_new_smoke;
-        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id, id, label
+        sql: """ 
+        CREATE VIEW dd_new_smoke AS SELECT DISTINCT R0.person_id, id, label
           FROM smoke R0
         
            UNION ALL SELECT DISTINCT R0.person_id, id, label
@@ -270,12 +259,25 @@ dd_delta_smoke.label: Boolean
           FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
-          weight: "3.0"
+          weight: "0.5"
+        }
+      
+
+        deepdive.inference.factors.dd_new_smoke_1 {
+          input_query: """
+          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
+          FROM dd_new_smoke R0, dd_delta_smoke R1, friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id  UNION ALL 
+          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
+          FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          function: "Imply(dd_delta_smoke.R1.label, dd_new_smoke.R0.label)"
+          weight: "0.4"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_cancer_0]
+deepdive.pipeline.pipelines.inference: [dd_new_cancer_0, dd_new_smoke_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 6ed2190ad..295dfd0a7 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -116,11 +116,21 @@ cancer.label: Boolean
           FROM cancer R0, smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
-          weight: "3.0"
+          weight: "0.5"
+        }
+      
+
+        deepdive.inference.factors.smoke_1 {
+          input_query: """
+          SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
+          FROM smoke R0, smoke R1, friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          function: "Imply(smoke.R1.label, smoke.R0.label)"
+          weight: "0.4"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [cancer_0]
+deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index c5147d90d..60b6e3112 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -116,10 +116,20 @@ cancer.label: Boolean
           FROM cancer R0, smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
-          weight: "3.0"
+          weight: "0.5"
+        }
+
+
+        deepdive.inference.factors.smoke_1 {
+          input_query: """
+          SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
+          FROM smoke R0, smoke R1, friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          function: "Imply(smoke.R1.label, smoke.R0.label)"
+          weight: "0.4"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [cancer_0]
+deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
diff --git a/test/expected-output-test/smoke_example/input.ddl b/test/expected-output-test/smoke_example/input.ddl
index 10da92bed..25e5ee7cf 100644
--- a/test/expected-output-test/smoke_example/input.ddl
+++ b/test/expected-output-test/smoke_example/input.ddl
@@ -30,4 +30,7 @@ smoke(pid)  :- person_smokes(pid, l)     label = l.
 cancer(pid) :- person_has_cancer(pid, l) label = l.
 
 cancer(pid) :- smoke(pid), person_smokes(pid, l)
-    weight = 3.0.
+    weight = 0.5.
+
+smoke(pid)  :- smoke(pid1), friend(pid1, pid)
+    weight = 0.4.
\ No newline at end of file
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index 5046bbaf3..7a52fb60d 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -83,6 +83,14 @@ dd_new_cancer(pid) :-
     person_smokes(pid, l);
     dd_new_smoke(pid),
     dd_delta_person_smokes(pid, l)
-  weight = 3.0
+  weight = 0.5
+  semantics = Imply.
+
+dd_new_smoke(pid) :-
+    dd_delta_smoke(pid1),
+    friend(pid1, pid);
+    dd_new_smoke(pid1),
+    dd_delta_friend(pid1, pid)
+  weight = 0.4
   semantics = Imply.
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index 48f4d4b4f..bef8589bc 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -25,6 +25,12 @@ cancer(pid) :-
 cancer(pid) :-
     smoke(pid),
     person_smokes(pid, l)
-  weight = 3.0
+  weight = 0.5
+  semantics = Imply.
+
+smoke(pid) :-
+    smoke(pid1),
+    friend(pid1, pid)
+  weight = 0.4
   semantics = Imply.
 

From fade27892182f936d5ef5e2d3c9f449808cf75f5 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 1 Jul 2015 16:06:57 -0700
Subject: [PATCH 136/347] add ocr example

---
 .../ocr_example/compile-incremental.expected  | 246 ++++++++++++++++++
 .../compile-materialization.expected          | 128 +++++++++
 .../ocr_example/compile-merge.expected        |  56 ++++
 .../ocr_example/compile.expected              | 127 +++++++++
 .../ocr_example/input.ddl                     |  25 ++
 .../ocr_example/print-incremental.expected    |  83 ++++++
 .../ocr_example/print.expected                |  33 +++
 7 files changed, 698 insertions(+)
 create mode 100644 test/expected-output-test/ocr_example/compile-incremental.expected
 create mode 100644 test/expected-output-test/ocr_example/compile-materialization.expected
 create mode 100644 test/expected-output-test/ocr_example/compile-merge.expected
 create mode 100644 test/expected-output-test/ocr_example/compile.expected
 create mode 100644 test/expected-output-test/ocr_example/input.ddl
 create mode 100644 test/expected-output-test/ocr_example/print-incremental.expected
 create mode 100644 test/expected-output-test/ocr_example/print.expected

diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
new file mode 100644
index 000000000..c7da34686
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -0,0 +1,246 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: INCREMENTAL
+    }
+    
+
+      deepdive.schema.keys {
+        dd_new_q1 : [wid]
+        dd_delta_q2 : [wid]
+        dd_delta_q1 : [wid]
+        dd_new_q2 : [wid]
+      }
+
+      deepdive.schema.variables {
+        dd_delta_q1.label: Boolean
+dd_new_q2.label: Boolean
+dd_new_q1.label: Boolean
+q2.label: Boolean
+dd_delta_q2.label: Boolean
+q1.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_10 {
+            sql: """ DROP TABLE IF EXISTS dd_new_label2 CASCADE;
+            CREATE TABLE
+            dd_new_label2(wid INT,
+             val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_label1 CASCADE;
+            CREATE TABLE
+            dd_delta_label1(wid INT,
+               val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_6 {
+            sql: """ DROP TABLE IF EXISTS dd_new_label1 CASCADE;
+            CREATE TABLE
+            dd_new_label1(wid INT,
+             val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_features CASCADE;
+            CREATE TABLE
+            dd_delta_features(id BIGSERIAL,
+                 word_id INT,
+                 feature_id INT,
+                 feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_17 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_q2 CASCADE;
+            CREATE TABLE
+            dd_delta_q2(wid INT,
+           id bigint,
+           label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_9 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_label2 CASCADE;
+            CREATE TABLE
+            dd_delta_label2(wid INT,
+               val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_features CASCADE;
+            CREATE TABLE
+            dd_new_features(id BIGSERIAL,
+               word_id INT,
+               feature_id INT,
+               feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_13 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_q1 CASCADE;
+            CREATE TABLE
+            dd_delta_q1(wid INT,
+           id bigint,
+           label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_new_label2;
+          TRUNCATE dd_delta_label1;
+          TRUNCATE dd_new_label1;
+          TRUNCATE dd_delta_features;
+          TRUNCATE dd_delta_q2;
+          TRUNCATE dd_delta_label2;
+          TRUNCATE dd_new_features;
+          TRUNCATE dd_delta_q1;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_11 {
+        sql: """ TRUNCATE dd_new_label2;
+        INSERT INTO dd_new_label2 
+            SELECT R0.wid, R0.val
+            FROM label2 R0
+         UNION ALL 
+            SELECT R0.wid, R0.val
+            FROM dd_delta_label2 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ 
+        CREATE VIEW dd_new_q1 AS SELECT DISTINCT R0.wid, id, label
+          FROM q1 R0
+        
+           UNION ALL SELECT DISTINCT R0.wid, id, label
+          FROM dd_delta_q1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_20" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ TRUNCATE dd_new_label1;
+        INSERT INTO dd_new_label1 
+            SELECT R0.wid, R0.val
+            FROM label1 R0
+         UNION ALL 
+            SELECT R0.wid, R0.val
+            FROM dd_delta_label1 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_21 {
+        sql: """ 
+        INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM dd_delta_label2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE dd_new_features;
+        INSERT INTO dd_new_features 
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            FROM features R0
+         UNION ALL 
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            FROM dd_delta_features R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_20 {
+        sql: """ 
+        INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM dd_delta_label1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ 
+        CREATE VIEW dd_new_q2 AS SELECT DISTINCT R0.wid, id, label
+          FROM q2 R0
+        
+           UNION ALL SELECT DISTINCT R0.wid, id, label
+          FROM dd_delta_q2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_21" ]
+      }
+    
+
+        deepdive.inference.factors.dd_new_q2_0 {
+          input_query: """
+          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
+          FROM dd_new_q2 R0, dd_delta_features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(dd_new_q2.R0.label)"
+          weight: "?(dd_delta_features.R1.feature_id)"
+        }
+      
+
+        deepdive.inference.factors.dd_new_q1_1 {
+          input_query: """
+          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
+          FROM dd_new_q1 R0, dd_delta_features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(dd_new_q1.R0.label)"
+          weight: "?(dd_delta_features.R1.feature_id)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_10, extraction_rule_5, extraction_rule_14, extraction_rule_6, extraction_rule_1, extraction_rule_17, extraction_rule_9, extraction_rule_2, extraction_rule_13, extraction_rule_18]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_new_q2_0, dd_new_q1_1]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
new file mode 100644
index 000000000..1fc5c659c
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -0,0 +1,128 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: MATERIALIZATION
+    }
+    
+
+
+      deepdive.schema.variables {
+        q1.label: Boolean
+q2.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS label1 CASCADE;
+            CREATE TABLE
+            label1(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS features CASCADE;
+            CREATE TABLE
+            features(id BIGSERIAL,
+        word_id INT,
+        feature_id INT,
+        feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS label2 CASCADE;
+            CREATE TABLE
+            label2(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS q1 CASCADE;
+            CREATE TABLE
+            q1(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS q2 CASCADE;
+            CREATE TABLE
+            q2(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE label1;
+          TRUNCATE features;
+          TRUNCATE label2;
+          TRUNCATE q1;
+          TRUNCATE q2;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_5 {
+        sql: """ 
+        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ 
+        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.q1_0 {
+          input_query: """
+          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q1 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q1.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+
+        deepdive.inference.factors.q2_1 {
+          input_query: """
+          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q2 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q2.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
new file mode 100644
index 000000000..d45ec8193
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -0,0 +1,56 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: MERGE
+    }
+    
+
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_2 {
+        sql: """ TRUNCATE label2;
+        INSERT INTO label2 
+            SELECT R0.wid, R0.val
+            FROM dd_new_label2 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_1 {
+        sql: """ TRUNCATE label1;
+        INSERT INTO label1 
+            SELECT R0.wid, R0.val
+            FROM dd_new_label1 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_0 {
+        sql: """ TRUNCATE features;
+        INSERT INTO features 
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            FROM dd_new_features R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_1, extraction_rule_0]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
new file mode 100644
index 000000000..e41c42804
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -0,0 +1,127 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        q1.label: Boolean
+q2.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS label1 CASCADE;
+            CREATE TABLE
+            label1(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS features CASCADE;
+            CREATE TABLE
+            features(id BIGSERIAL,
+        word_id INT,
+        feature_id INT,
+        feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS label2 CASCADE;
+            CREATE TABLE
+            label2(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS q1 CASCADE;
+            CREATE TABLE
+            q1(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS q2 CASCADE;
+            CREATE TABLE
+            q2(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE label1;
+          TRUNCATE features;
+          TRUNCATE label2;
+          TRUNCATE q1;
+          TRUNCATE q2;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_5 {
+        sql: """ 
+        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ 
+        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.q1_0 {
+          input_query: """
+          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q1 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q1.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+
+        deepdive.inference.factors.q2_1 {
+          input_query: """
+          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q2 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q2.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
diff --git a/test/expected-output-test/ocr_example/input.ddl b/test/expected-output-test/ocr_example/input.ddl
new file mode 100644
index 000000000..dba9cec58
--- /dev/null
+++ b/test/expected-output-test/ocr_example/input.ddl
@@ -0,0 +1,25 @@
+features(
+  id          BIGSERIAL, 
+  word_id     INT, 
+  feature_id  INT, 
+  feature_val BOOLEAN).
+
+label1(
+  wid   INT, 
+  val   BOOLEAN).
+
+label2(
+  wid   INT, 
+  val   BOOLEAN).
+
+q1?(wid INT).
+q2?(wid INT).
+
+q1(wid) :- label1(wid, val) label = val.
+q2(wid) :- label2(wid, val) label = val.
+
+q1(wid) :- features(id, wid, fid, fval)
+weight = fid.
+
+q2(wid) :- features(id, wid, fid, fval)
+weight = fid.
\ No newline at end of file
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
new file mode 100644
index 000000000..e8ed0bbf8
--- /dev/null
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -0,0 +1,83 @@
+features(id BIGSERIAL,
+         word_id INT,
+         feature_id INT,
+         feature_val BOOLEAN).
+
+dd_delta_features(id BIGSERIAL,
+                  word_id INT,
+                  feature_id INT,
+                  feature_val BOOLEAN).
+
+dd_new_features(id BIGSERIAL,
+                word_id INT,
+                feature_id INT,
+                feature_val BOOLEAN).
+
+dd_new_features(id, word_id, feature_id, feature_val) :-
+    features(id, word_id, feature_id, feature_val);
+    dd_delta_features(id, word_id, feature_id, feature_val).
+
+label1(wid INT,
+       val BOOLEAN).
+
+dd_delta_label1(wid INT,
+                val BOOLEAN).
+
+dd_new_label1(wid INT,
+              val BOOLEAN).
+
+dd_new_label1(wid, val) :-
+    label1(wid, val);
+    dd_delta_label1(wid, val).
+
+label2(wid INT,
+       val BOOLEAN).
+
+dd_delta_label2(wid INT,
+                val BOOLEAN).
+
+dd_new_label2(wid INT,
+              val BOOLEAN).
+
+dd_new_label2(wid, val) :-
+    label2(wid, val);
+    dd_delta_label2(wid, val).
+
+q1?(wid INT).
+
+dd_delta_q1?(wid INT).
+
+dd_new_q1?(wid INT).
+
+dd_new_q1(wid) :-
+    q1(wid);
+    dd_delta_q1(wid).
+
+q2?(wid INT).
+
+dd_delta_q2?(wid INT).
+
+dd_new_q2?(wid INT).
+
+dd_new_q2(wid) :-
+    q2(wid);
+    dd_delta_q2(wid).
+
+dd_delta_q1(wid) :-
+    dd_delta_label1(wid, val)
+  label = val.
+
+dd_delta_q2(wid) :-
+    dd_delta_label2(wid, val)
+  label = val.
+
+dd_new_q1(wid) :-
+    dd_delta_features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
+dd_new_q2(wid) :-
+    dd_delta_features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
new file mode 100644
index 000000000..da66f1d67
--- /dev/null
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -0,0 +1,33 @@
+features(id BIGSERIAL,
+         word_id INT,
+         feature_id INT,
+         feature_val BOOLEAN).
+
+label1(wid INT,
+       val BOOLEAN).
+
+label2(wid INT,
+       val BOOLEAN).
+
+q1?(wid INT).
+
+q2?(wid INT).
+
+q1(wid) :-
+    label1(wid, val)
+  label = val.
+
+q2(wid) :-
+    label2(wid, val)
+  label = val.
+
+q1(wid) :-
+    features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
+q2(wid) :-
+    features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+

From 1ff0e953dd3ac3b137bd594eb3b24d96d8750a91 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 1 Jul 2015 16:02:25 -0700
Subject: [PATCH 137/347] add ocr and smoke example

---
 examples/ocr.ddl                              |  28 ++
 examples/smoke.ddl                            |   8 +-
 .../ocr_example/compile-incremental.expected  | 246 ++++++++++++++++++
 .../compile-materialization.expected          | 128 +++++++++
 .../ocr_example/compile-merge.expected        |  56 ++++
 .../ocr_example/compile.expected              | 127 +++++++++
 .../ocr_example/input.ddl                     |   1 +
 .../ocr_example/print-incremental.expected    |  83 ++++++
 .../ocr_example/print.expected                |  33 +++
 .../compile-incremental.expected              |  32 +--
 .../compile-materialization.expected          |  14 +-
 .../smoke_example/compile.expected            |  14 +-
 .../smoke_example/input.ddl                   |  34 +--
 .../smoke_example/print-incremental.expected  |  10 +-
 .../smoke_example/print.expected              |   8 +-
 15 files changed, 766 insertions(+), 56 deletions(-)
 create mode 100644 examples/ocr.ddl
 create mode 100644 test/expected-output-test/ocr_example/compile-incremental.expected
 create mode 100644 test/expected-output-test/ocr_example/compile-materialization.expected
 create mode 100644 test/expected-output-test/ocr_example/compile-merge.expected
 create mode 100644 test/expected-output-test/ocr_example/compile.expected
 create mode 120000 test/expected-output-test/ocr_example/input.ddl
 create mode 100644 test/expected-output-test/ocr_example/print-incremental.expected
 create mode 100644 test/expected-output-test/ocr_example/print.expected
 mode change 100644 => 120000 test/expected-output-test/smoke_example/input.ddl

diff --git a/examples/ocr.ddl b/examples/ocr.ddl
new file mode 100644
index 000000000..0960ecaf4
--- /dev/null
+++ b/examples/ocr.ddl
@@ -0,0 +1,28 @@
+// ocr example from deepdive
+// https://github.com/HazyResearch/deepdive/tree/master/examples/ocr
+
+features(
+  id          BIGSERIAL, 
+  word_id     INT, 
+  feature_id  INT, 
+  feature_val BOOLEAN).
+
+label1(
+  wid   INT, 
+  val   BOOLEAN).
+
+label2(
+  wid   INT, 
+  val   BOOLEAN).
+
+q1?(wid INT).
+q2?(wid INT).
+
+q1(wid) :- label1(wid, val) label = val.
+q2(wid) :- label2(wid, val) label = val.
+
+q1(wid) :- features(id, wid, fid, fval)
+weight = fid.
+
+q2(wid) :- features(id, wid, fid, fval)
+weight = fid.
\ No newline at end of file
diff --git a/examples/smoke.ddl b/examples/smoke.ddl
index 7371f2885..26f28fd37 100644
--- a/examples/smoke.ddl
+++ b/examples/smoke.ddl
@@ -1,3 +1,6 @@
+// smoke example from deepdive
+// https://github.com/HazyResearch/deepdive/tree/master/examples/smoke
+
 person (
     person_id bigint,
     name text
@@ -30,6 +33,7 @@ smoke(pid)  :- person_smokes(pid, l)     label = l.
 cancer(pid) :- person_has_cancer(pid, l) label = l.
 
 cancer(pid) :- smoke(pid), person_smokes(pid, l)
-    weight = 3
-    label = l.
+    weight = 0.5.
 
+smoke(pid)  :- smoke(pid1), friend(pid1, pid)
+    weight = 0.4.
\ No newline at end of file
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
new file mode 100644
index 000000000..c7da34686
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -0,0 +1,246 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: INCREMENTAL
+    }
+    
+
+      deepdive.schema.keys {
+        dd_new_q1 : [wid]
+        dd_delta_q2 : [wid]
+        dd_delta_q1 : [wid]
+        dd_new_q2 : [wid]
+      }
+
+      deepdive.schema.variables {
+        dd_delta_q1.label: Boolean
+dd_new_q2.label: Boolean
+dd_new_q1.label: Boolean
+q2.label: Boolean
+dd_delta_q2.label: Boolean
+q1.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_10 {
+            sql: """ DROP TABLE IF EXISTS dd_new_label2 CASCADE;
+            CREATE TABLE
+            dd_new_label2(wid INT,
+             val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_label1 CASCADE;
+            CREATE TABLE
+            dd_delta_label1(wid INT,
+               val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_6 {
+            sql: """ DROP TABLE IF EXISTS dd_new_label1 CASCADE;
+            CREATE TABLE
+            dd_new_label1(wid INT,
+             val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_features CASCADE;
+            CREATE TABLE
+            dd_delta_features(id BIGSERIAL,
+                 word_id INT,
+                 feature_id INT,
+                 feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_17 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_q2 CASCADE;
+            CREATE TABLE
+            dd_delta_q2(wid INT,
+           id bigint,
+           label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_9 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_label2 CASCADE;
+            CREATE TABLE
+            dd_delta_label2(wid INT,
+               val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_features CASCADE;
+            CREATE TABLE
+            dd_new_features(id BIGSERIAL,
+               word_id INT,
+               feature_id INT,
+               feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_13 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_q1 CASCADE;
+            CREATE TABLE
+            dd_delta_q1(wid INT,
+           id bigint,
+           label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_new_label2;
+          TRUNCATE dd_delta_label1;
+          TRUNCATE dd_new_label1;
+          TRUNCATE dd_delta_features;
+          TRUNCATE dd_delta_q2;
+          TRUNCATE dd_delta_label2;
+          TRUNCATE dd_new_features;
+          TRUNCATE dd_delta_q1;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_11 {
+        sql: """ TRUNCATE dd_new_label2;
+        INSERT INTO dd_new_label2 
+            SELECT R0.wid, R0.val
+            FROM label2 R0
+         UNION ALL 
+            SELECT R0.wid, R0.val
+            FROM dd_delta_label2 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ 
+        CREATE VIEW dd_new_q1 AS SELECT DISTINCT R0.wid, id, label
+          FROM q1 R0
+        
+           UNION ALL SELECT DISTINCT R0.wid, id, label
+          FROM dd_delta_q1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_20" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ TRUNCATE dd_new_label1;
+        INSERT INTO dd_new_label1 
+            SELECT R0.wid, R0.val
+            FROM label1 R0
+         UNION ALL 
+            SELECT R0.wid, R0.val
+            FROM dd_delta_label1 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_21 {
+        sql: """ 
+        INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM dd_delta_label2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ TRUNCATE dd_new_features;
+        INSERT INTO dd_new_features 
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            FROM features R0
+         UNION ALL 
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            FROM dd_delta_features R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_20 {
+        sql: """ 
+        INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM dd_delta_label1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ 
+        CREATE VIEW dd_new_q2 AS SELECT DISTINCT R0.wid, id, label
+          FROM q2 R0
+        
+           UNION ALL SELECT DISTINCT R0.wid, id, label
+          FROM dd_delta_q2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_21" ]
+      }
+    
+
+        deepdive.inference.factors.dd_new_q2_0 {
+          input_query: """
+          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
+          FROM dd_new_q2 R0, dd_delta_features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(dd_new_q2.R0.label)"
+          weight: "?(dd_delta_features.R1.feature_id)"
+        }
+      
+
+        deepdive.inference.factors.dd_new_q1_1 {
+          input_query: """
+          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
+          FROM dd_new_q1 R0, dd_delta_features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(dd_new_q1.R0.label)"
+          weight: "?(dd_delta_features.R1.feature_id)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_10, extraction_rule_5, extraction_rule_14, extraction_rule_6, extraction_rule_1, extraction_rule_17, extraction_rule_9, extraction_rule_2, extraction_rule_13, extraction_rule_18]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_new_q2_0, dd_new_q1_1]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
new file mode 100644
index 000000000..1fc5c659c
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -0,0 +1,128 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: MATERIALIZATION
+    }
+    
+
+
+      deepdive.schema.variables {
+        q1.label: Boolean
+q2.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS label1 CASCADE;
+            CREATE TABLE
+            label1(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS features CASCADE;
+            CREATE TABLE
+            features(id BIGSERIAL,
+        word_id INT,
+        feature_id INT,
+        feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS label2 CASCADE;
+            CREATE TABLE
+            label2(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS q1 CASCADE;
+            CREATE TABLE
+            q1(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS q2 CASCADE;
+            CREATE TABLE
+            q2(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE label1;
+          TRUNCATE features;
+          TRUNCATE label2;
+          TRUNCATE q1;
+          TRUNCATE q2;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_5 {
+        sql: """ 
+        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ 
+        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.q1_0 {
+          input_query: """
+          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q1 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q1.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+
+        deepdive.inference.factors.q2_1 {
+          input_query: """
+          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q2 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q2.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
new file mode 100644
index 000000000..d45ec8193
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -0,0 +1,56 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: MERGE
+    }
+    
+
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_2 {
+        sql: """ TRUNCATE label2;
+        INSERT INTO label2 
+            SELECT R0.wid, R0.val
+            FROM dd_new_label2 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_1 {
+        sql: """ TRUNCATE label1;
+        INSERT INTO label1 
+            SELECT R0.wid, R0.val
+            FROM dd_new_label1 R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_0 {
+        sql: """ TRUNCATE features;
+        INSERT INTO features 
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            FROM dd_new_features R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_1, extraction_rule_0]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
new file mode 100644
index 000000000..e41c42804
--- /dev/null
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -0,0 +1,127 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        q1.label: Boolean
+q2.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS label1 CASCADE;
+            CREATE TABLE
+            label1(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS features CASCADE;
+            CREATE TABLE
+            features(id BIGSERIAL,
+        word_id INT,
+        feature_id INT,
+        feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS label2 CASCADE;
+            CREATE TABLE
+            label2(wid INT,
+      val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS q1 CASCADE;
+            CREATE TABLE
+            q1(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS q2 CASCADE;
+            CREATE TABLE
+            q2(wid INT,
+  id bigint,
+  label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE label1;
+          TRUNCATE features;
+          TRUNCATE label2;
+          TRUNCATE q1;
+          TRUNCATE q2;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_5 {
+        sql: """ 
+        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label1 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ 
+        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+          FROM label2 R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.inference.factors.q1_0 {
+          input_query: """
+          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q1 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q1.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+
+        deepdive.inference.factors.q2_1 {
+          input_query: """
+          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          FROM q2 R0, features R1
+        WHERE R1.word_id = R0.wid """
+          function: "Imply(q2.R0.label)"
+          weight: "?(features.R1.feature_id)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
+deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
diff --git a/test/expected-output-test/ocr_example/input.ddl b/test/expected-output-test/ocr_example/input.ddl
new file mode 120000
index 000000000..69125ec70
--- /dev/null
+++ b/test/expected-output-test/ocr_example/input.ddl
@@ -0,0 +1 @@
+../../../examples/ocr.ddl
\ No newline at end of file
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
new file mode 100644
index 000000000..e8ed0bbf8
--- /dev/null
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -0,0 +1,83 @@
+features(id BIGSERIAL,
+         word_id INT,
+         feature_id INT,
+         feature_val BOOLEAN).
+
+dd_delta_features(id BIGSERIAL,
+                  word_id INT,
+                  feature_id INT,
+                  feature_val BOOLEAN).
+
+dd_new_features(id BIGSERIAL,
+                word_id INT,
+                feature_id INT,
+                feature_val BOOLEAN).
+
+dd_new_features(id, word_id, feature_id, feature_val) :-
+    features(id, word_id, feature_id, feature_val);
+    dd_delta_features(id, word_id, feature_id, feature_val).
+
+label1(wid INT,
+       val BOOLEAN).
+
+dd_delta_label1(wid INT,
+                val BOOLEAN).
+
+dd_new_label1(wid INT,
+              val BOOLEAN).
+
+dd_new_label1(wid, val) :-
+    label1(wid, val);
+    dd_delta_label1(wid, val).
+
+label2(wid INT,
+       val BOOLEAN).
+
+dd_delta_label2(wid INT,
+                val BOOLEAN).
+
+dd_new_label2(wid INT,
+              val BOOLEAN).
+
+dd_new_label2(wid, val) :-
+    label2(wid, val);
+    dd_delta_label2(wid, val).
+
+q1?(wid INT).
+
+dd_delta_q1?(wid INT).
+
+dd_new_q1?(wid INT).
+
+dd_new_q1(wid) :-
+    q1(wid);
+    dd_delta_q1(wid).
+
+q2?(wid INT).
+
+dd_delta_q2?(wid INT).
+
+dd_new_q2?(wid INT).
+
+dd_new_q2(wid) :-
+    q2(wid);
+    dd_delta_q2(wid).
+
+dd_delta_q1(wid) :-
+    dd_delta_label1(wid, val)
+  label = val.
+
+dd_delta_q2(wid) :-
+    dd_delta_label2(wid, val)
+  label = val.
+
+dd_new_q1(wid) :-
+    dd_delta_features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
+dd_new_q2(wid) :-
+    dd_delta_features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
new file mode 100644
index 000000000..da66f1d67
--- /dev/null
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -0,0 +1,33 @@
+features(id BIGSERIAL,
+         word_id INT,
+         feature_id INT,
+         feature_val BOOLEAN).
+
+label1(wid INT,
+       val BOOLEAN).
+
+label2(wid INT,
+       val BOOLEAN).
+
+q1?(wid INT).
+
+q2?(wid INT).
+
+q1(wid) :-
+    label1(wid, val)
+  label = val.
+
+q2(wid) :-
+    label2(wid, val)
+  label = val.
+
+q1(wid) :-
+    features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
+q2(wid) :-
+    features(id, wid, fid, fval)
+  weight = fid
+  semantics = Imply.
+
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index b547dc8df..042e044f4 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -83,16 +83,6 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_18 {
-            sql: """ DROP TABLE IF EXISTS dd_new_smoke CASCADE;
-            CREATE TABLE
-            dd_new_smoke(person_id bigint,
-            id bigint,
-            label boolean)
-            """
-            style: "sql_extractor"
-          }
-
           deepdive.extraction.extractors.extraction_rule_21 {
             sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
             CREATE TABLE
@@ -138,7 +128,6 @@ dd_delta_smoke.label: Boolean
           TRUNCATE dd_delta_person;
           TRUNCATE dd_new_person;
           TRUNCATE dd_delta_person_has_cancer;
-          TRUNCATE dd_new_smoke;
           TRUNCATE dd_delta_cancer;
           TRUNCATE dd_delta_person_smokes;
           TRUNCATE dd_new_person_smokes;
@@ -190,8 +179,8 @@ dd_delta_smoke.label: Boolean
     
 
       deepdive.extraction.extractors.extraction_rule_19 {
-        sql: """ TRUNCATE dd_new_smoke;
-        INSERT INTO dd_new_smoke SELECT DISTINCT R0.person_id, id, label
+        sql: """ 
+        CREATE VIEW dd_new_smoke AS SELECT DISTINCT R0.person_id, id, label
           FROM smoke R0
         
            UNION ALL SELECT DISTINCT R0.person_id, id, label
@@ -270,12 +259,25 @@ dd_delta_smoke.label: Boolean
           FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
-          weight: "3.0"
+          weight: "0.5"
+        }
+      
+
+        deepdive.inference.factors.dd_new_smoke_1 {
+          input_query: """
+          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
+          FROM dd_new_smoke R0, dd_delta_smoke R1, friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id  UNION ALL 
+          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
+          FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          function: "Imply(dd_delta_smoke.R1.label, dd_new_smoke.R0.label)"
+          weight: "0.4"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_cancer_0]
+deepdive.pipeline.pipelines.inference: [dd_new_cancer_0, dd_new_smoke_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 6ed2190ad..295dfd0a7 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -116,11 +116,21 @@ cancer.label: Boolean
           FROM cancer R0, smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
-          weight: "3.0"
+          weight: "0.5"
+        }
+      
+
+        deepdive.inference.factors.smoke_1 {
+          input_query: """
+          SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
+          FROM smoke R0, smoke R1, friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          function: "Imply(smoke.R1.label, smoke.R0.label)"
+          weight: "0.4"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [cancer_0]
+deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index c5147d90d..60b6e3112 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -116,10 +116,20 @@ cancer.label: Boolean
           FROM cancer R0, smoke R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
-          weight: "3.0"
+          weight: "0.5"
+        }
+
+
+        deepdive.inference.factors.smoke_1 {
+          input_query: """
+          SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
+          FROM smoke R0, smoke R1, friend R2
+        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          function: "Imply(smoke.R1.label, smoke.R0.label)"
+          weight: "0.4"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [cancer_0]
+deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
diff --git a/test/expected-output-test/smoke_example/input.ddl b/test/expected-output-test/smoke_example/input.ddl
deleted file mode 100644
index 10da92bed..000000000
--- a/test/expected-output-test/smoke_example/input.ddl
+++ /dev/null
@@ -1,33 +0,0 @@
-person (
-    person_id bigint,
-    name text
-).
-
-person_has_cancer (
-    person_id bigint,
-    has_cancer boolean
-).
-
-person_smokes (
-    person_id bigint,
-    smokes boolean
-).
-
-friends (
-    person_id bigint,
-    friend_id bigint
-).
-
-smoke? (
-    person_id bigint
-).
-
-cancer? (
-    person_id bigint
-).
-
-smoke(pid)  :- person_smokes(pid, l)     label = l.
-cancer(pid) :- person_has_cancer(pid, l) label = l.
-
-cancer(pid) :- smoke(pid), person_smokes(pid, l)
-    weight = 3.0.
diff --git a/test/expected-output-test/smoke_example/input.ddl b/test/expected-output-test/smoke_example/input.ddl
new file mode 120000
index 000000000..5c2cf2d32
--- /dev/null
+++ b/test/expected-output-test/smoke_example/input.ddl
@@ -0,0 +1 @@
+../../../examples/smoke.ddl
\ No newline at end of file
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index 5046bbaf3..7a52fb60d 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -83,6 +83,14 @@ dd_new_cancer(pid) :-
     person_smokes(pid, l);
     dd_new_smoke(pid),
     dd_delta_person_smokes(pid, l)
-  weight = 3.0
+  weight = 0.5
+  semantics = Imply.
+
+dd_new_smoke(pid) :-
+    dd_delta_smoke(pid1),
+    friend(pid1, pid);
+    dd_new_smoke(pid1),
+    dd_delta_friend(pid1, pid)
+  weight = 0.4
   semantics = Imply.
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index 48f4d4b4f..bef8589bc 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -25,6 +25,12 @@ cancer(pid) :-
 cancer(pid) :-
     smoke(pid),
     person_smokes(pid, l)
-  weight = 3.0
+  weight = 0.5
+  semantics = Imply.
+
+smoke(pid) :-
+    smoke(pid1),
+    friend(pid1, pid)
+  weight = 0.4
   semantics = Imply.
 

From 7c04a0a1dc411ebf8c43ff84f3f9df5508277549 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 1 Jul 2015 19:36:41 -0700
Subject: [PATCH 138/347] add support for multinomial

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 30 +++++++++++++++----
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 28 ++++++++++++++---
 2 files changed, 49 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 289c1bfbe..88575c0f6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -86,6 +86,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
 
+  // map relation name -> variable type
+  var variableType : Map[String, VariableType]   = new HashMap[String, VariableType]()
+
   var function_schema : Map[String, FunctionDeclaration] = new HashMap[ String, FunctionDeclaration]()
 
   // The dependency graph between statements.
@@ -109,11 +112,12 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // generate the statements.
     mode = config.mode
     statements.foreach {
-      case SchemaDeclaration(Attribute(r, terms, types), isQuery) => {
+      case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
         terms.foreach {
           case Variable(n,r,i) =>
             schema           += { (r,i) -> n }
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
+            if (isQuery) variableType += { r -> vType.get }
         }
         if (isQuery) variableTableNames += r
       }
@@ -312,7 +316,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         var columnDecls = stmt.a.terms map {
           case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
         }
-        if (stmt.isQuery) columnDecls = columnDecls :+ "id bigint" :+ "label boolean"
+        if (stmt.isQuery) {
+          val labelColumn = stmt.variableType match {
+            case Some(BooleanType)        => "label boolean"
+            case Some(MultinomialType(_)) => "label int"
+          }
+          columnDecls = columnDecls :+ "id bigint" :+ labelColumn
+        }
         val indentation = " " * stmt.a.name.length
         val blockName = ss.resolveExtractorBlockName(stmt)
         schemas += s"""
@@ -493,7 +503,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           else ""
           }).filter(_ != "")
           val firstFunc = funcBody(0)
-          func = s"""${stmt.semantics}(${(funcBody.tail :+ firstFunc).mkString(", ")})"""
+          val function  = ss.variableType get stmt.q.head.name match {
+            case Some(BooleanType)        => stmt.semantics
+            case Some(MultinomialType(_)) => "Multinomial"
+          }
+          func = s"""${function}(${(funcBody.tail :+ firstFunc).mkString(", ")})"""
         }
         // weight
         if (weight.length == 0)
@@ -581,8 +595,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
-      case SchemaDeclaration(a, isQuery) =>
-        if (isQuery) schema += s"${a.name}.label: Boolean"
+      case SchemaDeclaration(a, isQuery, variableType) =>
+        if (isQuery) {
+          val variableTypeDecl = variableType match {
+            case Some(BooleanType)        => "Boolean"
+            case Some(MultinomialType(x)) => s"Categorical(${x})"
+          }
+          schema += s"${a.name}.label: ${variableTypeDecl}"
+        }
       case _ => ()
     }
     val ddSchema = s"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 10cc1caac..65ce612d7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -17,6 +17,17 @@ case class Attribute(name : String, terms : List[Variable], types : List[String]
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]])
 case class Column(name : String, t : String)
 
+// variable type
+sealed trait VariableType {
+  def cardinality: Long
+}
+case object BooleanType extends VariableType {
+  def cardinality = 2
+}
+case class MultinomialType(numCategories: Int) extends VariableType {
+  def cardinality = numCategories
+}
+
 sealed trait FactorWeight {
   def variables : List[String]
 }
@@ -35,7 +46,7 @@ case class RowWiseLineHandler(format: String, command: String) extends FunctionI
 
 // Statements that will be parsed and compiled
 trait Statement
-case class SchemaDeclaration( a : Attribute , isQuery : Boolean ) extends Statement // atom and whether this is a query relation.
+case class SchemaDeclaration( a : Attribute , isQuery : Boolean, variableType : Option[VariableType] = None) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
@@ -73,12 +84,21 @@ class DeepDiveLogParser extends JavaTokenParsers {
     columnName ~ columnType ^^ {
       case(name ~ ty) => Column(name, ty)
     }
+
+  def CategoricalParser = "Categorical" ~> "(" ~> """\d+""".r <~ ")" ^^ { n => MultinomialType(n.toInt) }
+  def BooleanParser = "Boolean" ^^ { s => BooleanType }
+  def dataType = CategoricalParser | BooleanParser
+
   def schemaDeclaration: Parser[SchemaDeclaration] =
-    relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ^^ {
-      case (r ~ isQuery ~ "(" ~ attrs ~ ")") => {
+    relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
+      case (r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
         val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
         var types = attrs map { case(x) => x.t }
-        SchemaDeclaration(Attribute(r, vars, types), (isQuery != None))
+        val variableType = vType match {
+          case None => if (isQuery != None) Some(BooleanType) else None
+          case Some(s) => Some(s)
+        }
+        SchemaDeclaration(Attribute(r, vars, types), (isQuery != None), variableType)
       }
     }
 

From 0fe09eb9810c20f4441cb144a251d3eac878e4f5 Mon Sep 17 00:00:00 2001
From: feiranwang <feiran.wang1@gmail.com>
Date: Wed, 1 Jul 2015 19:59:07 -0700
Subject: [PATCH 139/347] add chunking example

---
 examples/chunking.ddl                         |  43 ++++++
 .../chunking_example/compile.expected         | 128 ++++++++++++++++++
 .../chunking_example/input.ddl                |   1 +
 3 files changed, 172 insertions(+)
 create mode 100644 examples/chunking.ddl
 create mode 100644 test/expected-output-test/chunking_example/compile.expected
 create mode 120000 test/expected-output-test/chunking_example/input.ddl

diff --git a/examples/chunking.ddl b/examples/chunking.ddl
new file mode 100644
index 000000000..1ef26623d
--- /dev/null
+++ b/examples/chunking.ddl
@@ -0,0 +1,43 @@
+// chunking example
+// https://github.com/HazyResearch/deepdive/tree/master/examples/chunking
+
+words_raw(
+  word_id bigserial,
+  word text,
+  pos text,
+  tag text).
+
+words(
+  sent_id bigint,
+  word_id bigint,
+  word text,
+  pos text,
+  true_tag text).
+
+word_features(
+  word_id bigint,
+  feature text).
+
+tag?(word_id bigint) Categorical(13).
+
+function ext_training 
+  over like words_raw
+  returns like words
+  implementation "/udf/ext_training.py" handles tsv lines.
+
+words :- !ext_training(words_raw).
+
+ext_features_input(word_id1, word1, pos1, word2, pos2) :-
+  words(sent_id, word_id1, word1, pos1, tag1),
+  words(sent_id, word_id2, word2, pos2, tag2).
+
+function ext_features
+  over like ext_features_input
+  returns like word_features
+  implementation "/udf/ext_features.py" handles tsv lines.
+
+word_features :- !ext_features(ext_features_input).
+
+tag(word_id) :- words(word_id, a, b, c, tag) label = tag.
+
+tag(word_id) :- word_features(word_id, f) weight = f.
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
new file mode 100644
index 000000000..1288f1873
--- /dev/null
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -0,0 +1,128 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        tag.label: Categorical(13)
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS words_raw CASCADE;
+            CREATE TABLE
+            words_raw(word_id bigserial,
+         word text,
+         pos text,
+         tag text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS words CASCADE;
+            CREATE TABLE
+            words(sent_id bigint,
+     word_id bigint,
+     word text,
+     pos text,
+     true_tag text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS tag CASCADE;
+            CREATE TABLE
+            tag(word_id bigint,
+   id bigint,
+   label int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS word_features CASCADE;
+            CREATE TABLE
+            word_features(word_id bigint,
+             feature text)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE words_raw;
+          TRUNCATE words;
+          TRUNCATE tag;
+          TRUNCATE word_features;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ DROP VIEW IF EXISTS ext_features_input;
+        CREATE VIEW ext_features_input AS 
+            SELECT R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
+            FROM words R0, words R1
+        WHERE R1.sent_id = R0.sent_id 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_5" ]
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_9 {
+        sql: """ 
+        INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 as id, R0.true_tag AS label
+          FROM words R0
+        
+          
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_5" ]
+      }
+    
+
+        deepdive.extraction.extractors.extraction_rule_8 {
+          input: """ SELECT * FROM ext_features_input
+          """
+          output_relation: "word_features"
+          udf: ${APP_HOME}"/udf/ext_features.py"
+          style: "tsv_extractor" 
+          dependencies: [ "extraction_rule_6" ]
+        }
+      
+
+        deepdive.extraction.extractors.extraction_rule_5 {
+          input: """ SELECT * FROM words_raw
+          """
+          output_relation: "words"
+          udf: ${APP_HOME}"/udf/ext_training.py"
+          style: "tsv_extractor" 
+          
+        }
+      
+
+        deepdive.inference.factors.tag_0 {
+          input_query: """
+          SELECT R0.id AS "tag.R0.id" , R1.feature AS "word_features.R1.feature" 
+          FROM tag R0, word_features R1
+        WHERE R1.word_id = R0.word_id """
+          function: "Multinomial(tag.R0.label)"
+          weight: "?(word_features.R1.feature)"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_0, extraction_rule_1, extraction_rule_3, extraction_rule_2]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_6, extraction_rule_9, extraction_rule_8, extraction_rule_5]
+deepdive.pipeline.pipelines.inference: [tag_0]
diff --git a/test/expected-output-test/chunking_example/input.ddl b/test/expected-output-test/chunking_example/input.ddl
new file mode 120000
index 000000000..64139b0ef
--- /dev/null
+++ b/test/expected-output-test/chunking_example/input.ddl
@@ -0,0 +1 @@
+../../../examples/chunking.ddl
\ No newline at end of file

From b495f8dc9fa9a6abea75b7f97b6aee8c5c9efd52 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 3 Jul 2015 22:01:26 -0700
Subject: [PATCH 140/347] initial support for constants, conditions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 35 +++++++++++--
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 24 ++++++---
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 51 +++++++++++++++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 10 +++-
 .../conditions/compile.expected               |  0
 .../expected-output-test/conditions/input.ddl |  5 ++
 7 files changed, 105 insertions(+), 22 deletions(-)
 create mode 100644 test/expected-output-test/conditions/compile.expected
 create mode 100644 test/expected-output-test/conditions/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 88575c0f6..3ea56435c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -194,8 +194,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    val whereClause = z.bodies(0).zipWithIndex flatMap {
-      case (Atom(relName, terms),body_index) =>
+    var whereClause = z.bodies(0).zipWithIndex flatMap {
+      case (Atom(relName, terms),body_index) => {
         terms flatMap {
           case Variable(varName, relName, index) =>
             val canonical_body_index = qs.getBodyIndex(varName)
@@ -205,9 +205,30 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
               val real_attr_name2 = resolveName( qs.getVar(varName))
               Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
             } else { None }
+          // a constant in body means a equality condition
+          case Constant(value, r, i) => {
+            val attr = schema(relName, i)
+            Some(s"R${body_index}.${attr} = ${value}")
+          }
         }
+      }
+    }
+    println(whereClause)
+
+    // resolve conditions
+    val conditions = z.conditions(0) flatMap { case Condition(lhs, op, rhs, isRhsValue) =>
+      val resolvedLhs = resolveColumn(lhs, qs, z, OriginalOnly)
+      val resolvedRhs = isRhsValue match {
+        case true  => Some(rhs)
+        case false => resolveColumn(rhs, qs, z, OriginalOnly)
+      }
+      Some(s"${resolvedLhs.get} ${op} ${resolvedRhs.get}")
     }
-    val whereClauseStr = whereClause match {
+    println(conditions)
+    
+    whereClause = whereClause ++ conditions
+
+    var whereClauseStr = whereClause match {
       case Nil => ""
       case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
     }
@@ -290,6 +311,7 @@ class QuerySchema(q : ConjunctiveQuery) {
           case Variable(v, r, i) =>
             if( ! (query_schema contains v) )
               query_schema += { v -> (index, Variable(v,r,i) ) }
+          case _ =>
         }
       }
     }
@@ -354,13 +376,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
       for (cqBody <- stmt.q.bodies) {
-        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody))
+        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions)
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
           val headTerms = tmpCq.head.terms map {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+            case Constant(v,r,i) => Some(v)
           }
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
@@ -372,6 +395,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
           val headTerms = tmpCq.head.terms map {
             case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
+            case Constant(v,r,i) => Some(v)
           }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
@@ -390,6 +414,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           }
           val variableCols = tmpCq.head.terms flatMap {
             case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpCq, resolveColumnFlag)
+            case Constant(v,rr,i)  => Some(v)
           }
 
           val selectStr = variableCols.mkString(", ")
@@ -471,7 +496,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       for (cqBody <- stmt.q.bodies) {
         // edge query
         val fakeBody        = stmt.q.head +: cqBody
-        val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody)) // we will just use the fakeBody below.
+        val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody), stmt.q.conditions) // we will just use the fakeBody below.
 
         val index = cqBody.length + 1
         val qs2 = new QuerySchema( fakeCQ )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 16564f6fc..874582076 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -23,12 +23,18 @@ object DeepDiveLogDeltaDeriver{
     val incCqHead = if (isInference) {
       cq.head.copy(
         name = newPrefix + cq.head.name,
-        terms = cq.head.terms map {term => term.copy(relName = newPrefix + term.relName)}
+        terms = cq.head.terms map {
+          case term: Variable => term.copy(relName = newPrefix + term.relName)
+          case term: Constant => term
+        }
       )
     } else {
       cq.head.copy(
         name = deltaPrefix + cq.head.name,
-        terms = cq.head.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
+        terms = cq.head.terms map {
+          case term: Variable => term.copy(relName = deltaPrefix + term.relName)
+          case term: Constant => term
+        }
       )
     }
 
@@ -39,14 +45,20 @@ object DeepDiveLogDeltaDeriver{
       val incDeltaBody = body map {
         a => a.copy(
           name = deltaPrefix + a.name,
-          terms = a.terms map {term => term.copy(relName = deltaPrefix + term.relName)}
+          terms = a.terms map {
+            case term: Variable => term.copy(relName = deltaPrefix + term.relName)
+            case term: Constant => term
+          }
         )
       }
       // New body
       val incNewBody = body map {
         a => a.copy(
           name = newPrefix + a.name,
-          terms = a.terms map {term => term.copy(relName = newPrefix + term.relName)}
+          terms = a.terms map {
+            case term: Variable => term.copy(relName = newPrefix + term.relName)
+            case term: Constant => term
+          }
         )
       }
       var i = 0
@@ -69,7 +81,7 @@ object DeepDiveLogDeltaDeriver{
         }
       }
     }
-    ConjunctiveQuery(incCqHead, incCqBodies.toList)
+    ConjunctiveQuery(incCqHead, incCqBodies.toList, Nil)
   }
 
   // Incremental scheme declaration,
@@ -101,7 +113,7 @@ object DeepDiveLogDeltaDeriver{
 
     // if (!stmt.isQuery) {
     incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(incNewStmt.a.name, incNewStmt.a.terms),
-      List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms)))))
+      List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms))), Nil))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index 8be539d0a..b34555547 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -20,7 +20,7 @@ object DeepDiveLogMergeDeriver{
     )
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms),
-      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms)))))
+      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms))), Nil))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 65ce612d7..a3111cee3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -10,13 +10,21 @@ import scala.util.Try
 // ***************************************
 // * The union types for for the parser. *
 // ***************************************
-case class Variable(varName : String, relName : String, index : Int )
+// case class Variable(varName : String, relName : String, index : Int )
 // TODO make Atom a trait, and have multiple case classes, e.g., RelationAtom and CondExprAtom
-case class Atom(name : String, terms : List[Variable])
+// ddlog column variable type: constant or variable
+sealed trait ColumnVariable
+case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
+case class Constant(value : String, relName: String, index: Int) extends ColumnVariable
+case class Atom(name : String, terms : List[ColumnVariable])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]])
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[List[Condition]])
 case class Column(name : String, t : String)
 
+// condition
+case class Condition(lhs: String, op: String, rhs: String, isRhsValue: Boolean)
+case class BodyWithConditions(body: List[Atom], conditions: List[Condition])
+
 // variable type
 sealed trait VariableType {
   def cardinality: Long
@@ -63,6 +71,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
     s => StringEscapeUtils.unescapeJava(
       s.stripPrefix("\"").stripSuffix("\""))
   }
+  def stringLiteralAsSqlString = stringLiteral ^^ { s =>
+    s"""'${s.stripPrefix("\"").stripSuffix("\"")}'"""
+  }
+  def constant = stringLiteralAsSqlString | wholeNumber
 
   // C/Java/Scala-style as well as shell script-style comments are supported
   // by treating them as whiteSpace
@@ -102,31 +114,52 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
+  def variable = variableName ^^ { Variable(_, "", 0) }
+  def columnConstant = constant ^^ { Constant(_, "", 0) }
+  def column = columnConstant | variable
 
   // TODO support aggregate function syntax somehow
-  def cqHead = relationName ~ "(" ~ repsep(variableName, ",") ~ ")" ^^ {
+  def cqHead = relationName ~ "(" ~ repsep(column, ",") ~ ")" ^^ {
       case (r ~ "(" ~ variableUses ~ ")") =>
         Atom(r, variableUses.zipWithIndex map {
-          case(name,i) => Variable(name, r, i)
+          case(Variable(name,_,_),i) => Variable(name, r, i)
+          case(Constant(name,_,_),i) => Constant(name, r, i)
         })
     }
 
   // TODO add conditional expressions for where clause
   def cqConditionalExpr = failure("No conditional expression supported yet")
   def cqBodyAtom: Parser[Atom] =
-    ( relationName ~ "(" ~ repsep(variableName, ",") ~ ")" ^^ {
+    ( relationName ~ "(" ~ repsep(column, ",") ~ ")" ^^ {
         case (r ~ "(" ~ variableBindings ~ ")") =>
           Atom(r, variableBindings.zipWithIndex map {
-            case(name,i) => Variable(name, r, i)
+            case(Variable(name,_,_),i) => Variable(name, r, i)
+            case(Constant(name,_,_),i) => Constant(name, r, i)
           })
       }
     | cqConditionalExpr
     )
   def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
+
+  // conditions
+  def convertOperator = "||" | "::"
+  def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "="
+  def conditionWithConstant = variableName ~ filterOperator ~ constant ^^ {
+    case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs, true)
+  }
+  def conditionWithVariable = variableName ~ filterOperator ~ variableName ^^ {
+    case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs, false)
+  }
+  def condition = conditionWithVariable | conditionWithConstant
+  def cqCondition: Parser[List[Condition]] = repsep(condition, ",")
+  def cqBodyWithCondition = cqBody ~ opt(",") ~ cqCondition ^^ {
+    case (b ~ o ~ c) => BodyWithConditions(b, c)
+  }
+
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
-    cqHead ~ ":-" ~ rep1sep(cqBody, ";") ^^ {
+    cqHead ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
       case (headatom ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(headatom, disjunctiveBodies)
+        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.conditions))
     }
 
   def relationType: Parser[RelationType] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 2d3c300eb..1e8643cd3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -50,7 +50,15 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(cq: ConjunctiveQuery): String = {
     val printAtom = {a:Atom =>
-      val vars = a.terms map { _.varName }
+      val vars = a.terms map { 
+        case x: Variable => x.varName
+        case x: Constant => {
+          if (x.value.startsWith("'"))
+            s""" "${x.value.stripPrefix("'").stripSuffix("'")}" """
+          else
+            x.value
+        }
+      }
       s"${a.name}(${vars.mkString(", ")})"
     }
     val printListAtom = {a:List[Atom] =>
diff --git a/test/expected-output-test/conditions/compile.expected b/test/expected-output-test/conditions/compile.expected
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/expected-output-test/conditions/input.ddl b/test/expected-output-test/conditions/input.ddl
new file mode 100644
index 000000000..050cb0f7d
--- /dev/null
+++ b/test/expected-output-test/conditions/input.ddl
@@ -0,0 +1,5 @@
+a(k int).
+b(k int, p text, q text, r int).
+c(s text, n int, t text).
+
+Q("test", 123, id) :- a(id), b(id, x,y,z), c("foo", 10, t), z>100.
\ No newline at end of file

From db4f5517e84fe8256f8f8a1201719c77645fc587 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sat, 4 Jul 2015 21:34:37 -0700
Subject: [PATCH 141/347] expressions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 109 ++++++++++++------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  41 ++++---
 .../ddlog/DeepDiveLogMergeDeriver.scala       |   8 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  59 +++++++---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  23 ++--
 .../expected-output-test/conditions/input.ddl |   2 +-
 6 files changed, 167 insertions(+), 75 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 3ea56435c..0ac6d9122 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -194,26 +194,58 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
+    // def resolveVarOrConst(variable: ColumnVariable, bodyIndex: Int) = {
+    //   variable match {
+    //     case Variable(varName,relName,index) => {
+    //       val canonical_body_index = qs.getBodyIndex(varName)
+    //       if (canonical_body_index != bodyIndex) {
+    //         val real_attr_name1 = resolveName( Variable(varName, relName, index) )
+    //         val real_attr_name2 = resolveName( qs.getVar(varName))
+    //         Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+    //       } else { None }
+    //     }
+    //     case Constant(v,relName,i) => {
+    //       val attr = schema(relName, i)
+    //       Some(s"R${bodyIndex}.${attr} = ${v}")
+    //     }
+    //   }
+    // }
+
+    def resolveVarOrConst(variable: ColumnVariable, bodyIndex: Int) : String = {
+      variable match {
+        case Variable(varName,relName,index) => resolveColumn(varName, qs, z, OriginalOnly).get
+        case Constant(v,relName,i) => "v"
+      }
+    }
+
     var whereClause = z.bodies(0).zipWithIndex flatMap {
-      case (Atom(relName, terms),body_index) => {
-        terms flatMap {
-          case Variable(varName, relName, index) =>
-            val canonical_body_index = qs.getBodyIndex(varName)
-
-            if (canonical_body_index != body_index) {
-              val real_attr_name1 = resolveName( Variable(varName, relName, index) )
-              val real_attr_name2 = resolveName( qs.getVar(varName))
-              Some(s"R${ body_index }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
-            } else { None }
-          // a constant in body means a equality condition
-          case Constant(value, r, i) => {
-            val attr = schema(relName, i)
-            Some(s"R${body_index}.${attr} = ${value}")
+      case (Atom(relName, terms),bodyIndex) => {
+        terms flatMap { case Expression(vars, ops, relName, index) =>
+          // simple variable name or constant 
+          if (ops isEmpty) {
+            vars(0) match {
+              case Variable(varName,relName,index) => {
+                val canonical_body_index = qs.getBodyIndex(varName)
+                if (canonical_body_index != bodyIndex) {
+                  val real_attr_name1 = resolveName( Variable(varName, relName, index) )
+                  val real_attr_name2 = resolveName( qs.getVar(varName))
+                  Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+                } else { None }
+              }
+              case Constant(v,relName,i) => {
+                val attr = schema(relName, i)
+                Some(s"R${bodyIndex}.${attr} = ${v}")
+              }
+            }
+          } else { // expression
+            val resolvedVars = vars map (resolveVarOrConst(_, bodyIndex))
+            val expr = resolvedVars(0) + " " + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
+            val attr = schema(relName, index)
+            Some(s"${expr} = R${bodyIndex}.${attr}")
           }
         }
       }
     }
-    println(whereClause)
 
     // resolve conditions
     val conditions = z.conditions(0) flatMap { case Condition(lhs, op, rhs, isRhsValue) =>
@@ -224,7 +256,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       }
       Some(s"${resolvedLhs.get} ${op} ${resolvedRhs.get}")
     }
-    println(conditions)
     
     whereClause = whereClause ++ conditions
 
@@ -307,11 +338,15 @@ class QuerySchema(q : ConjunctiveQuery) {
   def generateCanonicalVar()  = {
     q.bodies(0).zipWithIndex.foreach {
       case (Atom(relName,terms),index) =>  {
-        terms.foreach {
-          case Variable(v, r, i) =>
-            if( ! (query_schema contains v) )
-              query_schema += { v -> (index, Variable(v,r,i) ) }
-          case _ =>
+        terms.foreach { case Expression(c, op, r, i) =>
+          if (op.isEmpty) {
+            c(0) match {
+              case Variable(v,r,i) =>
+                if (! (query_schema contains v) )
+                  query_schema += { v -> (index, Variable(v,r,i) ) }
+              case _ =>
+            }
+          }
         }
       }
     }
@@ -379,12 +414,26 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions)
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
+
+        // map head terms to sql
+        def mapHeadTerms(terms: List[Expression], alias: AliasStyle = OriginalOnly) = {
+          terms map { case Expression(v, ops, _, _) =>
+            val resolvedVars = v map (resolveVarOrConst(_))
+            val expr = resolvedVars(0) + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
+            expr
+          }
+        }
+
+        def resolveVarOrConst(v: ColumnVariable, alias: AliasStyle = OriginalOnly) = {
+          v match {
+            case Variable(v,r,i) => ss.resolveColumn(v, qs, tmpCq, alias).get
+            case Constant(v,r,i) => v
+          }
+        }
+
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = tmpCq.head.terms map {
-            case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
-            case Constant(v,r,i) => Some(v)
-          }
+          val headTerms = mapHeadTerms(tmpCq.head.terms)
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
@@ -393,10 +442,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = tmpCq.head.terms map {
-            case Variable(v,r,i) => s"R${i}.${ss.resolveName(qs.getVar(v)) }"
-            case Constant(v,r,i) => Some(v)
-          }
+          val headTerms = mapHeadTerms(tmpCq.head.terms)
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
           ${ ss.generateSQLBody(tmpCq) }
@@ -412,10 +458,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case true => OriginalOnly
             case false => OriginalAndAlias
           }
-          val variableCols = tmpCq.head.terms flatMap {
-            case(Variable(v,rr,i)) => ss.resolveColumn(v, qs, tmpCq, resolveColumnFlag)
-            case Constant(v,rr,i)  => Some(v)
-          }
+          val variableCols = mapHeadTerms(tmpCq.head.terms, resolveColumnFlag)
 
           val selectStr = variableCols.mkString(", ")
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 874582076..25dfc318b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -19,22 +19,25 @@ object DeepDiveLogDeltaDeriver{
   }
 
   def transform(cq: ConjunctiveQuery, isInference: Boolean, mode: String): ConjunctiveQuery = {
+    // transform an expression
+    def transformExpression(expr: Expression, prefix: String) = {
+      val newVars = expr.variables map {
+        case term: Variable => term.copy(relName = prefix + term.relName)
+        case term: Constant => term
+      }
+      Expression(newVars, expr.ops, expr.relName, expr.index)
+    }
+
     // New head
     val incCqHead = if (isInference) {
       cq.head.copy(
         name = newPrefix + cq.head.name,
-        terms = cq.head.terms map {
-          case term: Variable => term.copy(relName = newPrefix + term.relName)
-          case term: Constant => term
-        }
+        terms = cq.head.terms map (transformExpression(_, newPrefix))
       )
     } else {
       cq.head.copy(
         name = deltaPrefix + cq.head.name,
-        terms = cq.head.terms map {
-          case term: Variable => term.copy(relName = deltaPrefix + term.relName)
-          case term: Constant => term
-        }
+        terms = cq.head.terms map (transformExpression(_, deltaPrefix))
       )
     }
 
@@ -45,20 +48,14 @@ object DeepDiveLogDeltaDeriver{
       val incDeltaBody = body map {
         a => a.copy(
           name = deltaPrefix + a.name,
-          terms = a.terms map {
-            case term: Variable => term.copy(relName = deltaPrefix + term.relName)
-            case term: Constant => term
-          }
+          terms = a.terms map (transformExpression(_, deltaPrefix))
         )
       }
       // New body
       val incNewBody = body map {
         a => a.copy(
           name = newPrefix + a.name,
-          terms = a.terms map {
-            case term: Variable => term.copy(relName = newPrefix + term.relName)
-            case term: Constant => term
-          }
+          terms = a.terms map (transformExpression(_, newPrefix))
         )
       }
       var i = 0
@@ -111,9 +108,17 @@ object DeepDiveLogDeltaDeriver{
     )
     incrementalStatement += incNewStmt
 
+    // from schema declaration to expressions
+    def variableToExpr(v: Variable) = Expression(List(v), List(), v.relName, v.index)
+    val originalExpr = stmt.a.terms map (variableToExpr(_))
+    val incDeltaExpr = incDeltaStmt.a.terms map (variableToExpr(_))
+    val incNewExpr = incNewStmt.a.terms map (variableToExpr(_))
+
     // if (!stmt.isQuery) {
-    incrementalStatement += ExtractionRule(ConjunctiveQuery(Atom(incNewStmt.a.name, incNewStmt.a.terms),
-      List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms))), Nil))
+    incrementalStatement += ExtractionRule(ConjunctiveQuery(
+      Atom(incNewStmt.a.name, incNewExpr),
+      List(List(Atom(stmt.a.name, originalExpr)), List(Atom(incDeltaStmt.a.name, incDeltaExpr))), 
+      List()))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index b34555547..8b581d42f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -19,8 +19,12 @@ object DeepDiveLogMergeDeriver{
       )
     )
 
-    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms),
-      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms))), Nil))
+    def variableToExpr(v: Variable) = Expression(List(v), List(), v.relName, v.index)
+    val originalExpr = stmt.a.terms map (variableToExpr(_))
+    val incNewExpr = incNewStmt.a.terms map (variableToExpr(_))
+
+    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, originalExpr),
+      List(List(Atom(incNewStmt.a.name, incNewExpr))), Nil))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index a3111cee3..eaab4a531 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -16,7 +16,15 @@ import scala.util.Try
 sealed trait ColumnVariable
 case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
 case class Constant(value : String, relName: String, index: Int) extends ColumnVariable
-case class Atom(name : String, terms : List[ColumnVariable])
+case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int) {
+  def print(resolve: ColumnVariable => String) = {
+    val resolvedVars = variables map (resolve(_))
+    resolvedVars(0) + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
+  }
+}
+case class Operator(operator: String, operand: ColumnVariable)
+
+case class Atom(name : String, terms : List[Expression])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[List[Condition]])
 case class Column(name : String, t : String)
@@ -54,7 +62,7 @@ case class RowWiseLineHandler(format: String, command: String) extends FunctionI
 
 // Statements that will be parsed and compiled
 trait Statement
-case class SchemaDeclaration( a : Attribute , isQuery : Boolean, variableType : Option[VariableType] = None) extends Statement // atom and whether this is a query relation.
+case class SchemaDeclaration( a : Attribute , isQuery : Boolean, variableType : Option[VariableType]) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
@@ -74,7 +82,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def stringLiteralAsSqlString = stringLiteral ^^ { s =>
     s"""'${s.stripPrefix("\"").stripSuffix("\"")}'"""
   }
-  def constant = stringLiteralAsSqlString | wholeNumber
+  def constant = stringLiteralAsSqlString | wholeNumber | "TRUE" | "FALSE" | "TEXT" | "INT" | "BOOLEAN"
 
   // C/Java/Scala-style as well as shell script-style comments are supported
   // by treating them as whiteSpace
@@ -102,8 +110,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def dataType = CategoricalParser | BooleanParser
 
   def schemaDeclaration: Parser[SchemaDeclaration] =
-    relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
-      case (r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
+    relationName ~ opt("?") ~ opt("!") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
+      case (r ~ isQuery ~ isDistinct ~ "(" ~ attrs ~ ")" ~ vType) => {
         val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
         var types = attrs map { case(x) => x.t }
         val variableType = vType match {
@@ -114,35 +122,58 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
+  def operator = "||" | "+" | "-" | "*" | "/"
+  def castOp = "::"
+
   def variable = variableName ^^ { Variable(_, "", 0) }
   def columnConstant = constant ^^ { Constant(_, "", 0) }
-  def column = columnConstant | variable
+  def variableOrConstant = columnConstant | variable
+  def operateOn = operator ~ variableOrConstant ^^ { case (v ~ o) => Operator(v,o) }
+  def typecast = castOp ~ columnConstant ^^ { case (v ~ o) => Operator(v,o) }
+  def operatorAndOperand = operateOn | typecast
+  def expression = variableOrConstant ~ rep(operatorAndOperand) ^^ {
+    case (v ~ opList) => {
+      val variables = List(v) ++ (opList map (_.operand))
+      val ops = opList map (_.operator)
+      Expression(variables, ops, "", 0)
+    }
+  }
 
   // TODO support aggregate function syntax somehow
-  def cqHead = relationName ~ "(" ~ repsep(column, ",") ~ ")" ^^ {
+  def cqHead = relationName ~ "(" ~ repsep(expression, ",") ~ ")" ^^ {
       case (r ~ "(" ~ variableUses ~ ")") =>
         Atom(r, variableUses.zipWithIndex map {
-          case(Variable(name,_,_),i) => Variable(name, r, i)
-          case(Constant(name,_,_),i) => Constant(name, r, i)
+          case (Expression(v,op,_,_),i) => {
+            val vars = v map {
+              case Variable(x,_,_) => Variable(x,r,i)
+              case Constant(x,_,_) => Constant(x,r,i)
+            }
+            Expression(vars, op, r, i)
+          }
         })
     }
 
   // TODO add conditional expressions for where clause
   def cqConditionalExpr = failure("No conditional expression supported yet")
   def cqBodyAtom: Parser[Atom] =
-    ( relationName ~ "(" ~ repsep(column, ",") ~ ")" ^^ {
+    ( relationName ~ "(" ~ repsep(expression, ",") ~ ")" ^^ {
         case (r ~ "(" ~ variableBindings ~ ")") =>
           Atom(r, variableBindings.zipWithIndex map {
-            case(Variable(name,_,_),i) => Variable(name, r, i)
-            case(Constant(name,_,_),i) => Constant(name, r, i)
-          })
+          case (Expression(v,op,_,_),i) => {
+            val vars = v map {
+              case Variable(x,_,_) => Variable(x,r,i)
+              case Constant(x,_,_) => Constant(x,r,i)
+            }
+            // println(Expression(vars, op, r, i))
+            Expression(vars, op, r, i)
+          }
+        })
       }
     | cqConditionalExpr
     )
   def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
 
   // conditions
-  def convertOperator = "||" | "::"
   def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "="
   def conditionWithConstant = variableName ~ filterOperator ~ constant ^^ {
     case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs, true)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 1e8643cd3..e680951ba 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -48,22 +48,31 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
        |""".stripMargin
   }
 
+  def printVarOrConst(x: ColumnVariable) = {
+    x match {
+      case x: Variable => x.varName
+      case x: Constant => {
+        if (x.value.startsWith("'"))
+          s""" "${x.value.stripPrefix("'").stripSuffix("'")}" """
+        else
+          x.value
+      }
+    }
+  }
+
   def print(cq: ConjunctiveQuery): String = {
     val printAtom = {a:Atom =>
       val vars = a.terms map { 
-        case x: Variable => x.varName
-        case x: Constant => {
-          if (x.value.startsWith("'"))
-            s""" "${x.value.stripPrefix("'").stripSuffix("'")}" """
-          else
-            x.value
-        }
+        case e => e.print(printVarOrConst)
       }
       s"${a.name}(${vars.mkString(", ")})"
     }
     val printListAtom = {a:List[Atom] =>
       s"${(a map printAtom).mkString(",\n    ")}"
     }
+    val printCondition = {a: List[Condition] =>
+      (a map { case Condition(lhs, op, rhs, _) => s"${lhs} ${op} ${rhs}" }).mkString(",")
+    }
     s"""${printAtom(cq.head)} :-
        |    ${(cq.bodies map printListAtom).mkString(";\n    ")}""".stripMargin
   }
diff --git a/test/expected-output-test/conditions/input.ddl b/test/expected-output-test/conditions/input.ddl
index 050cb0f7d..6c14b88d1 100644
--- a/test/expected-output-test/conditions/input.ddl
+++ b/test/expected-output-test/conditions/input.ddl
@@ -2,4 +2,4 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q("test", 123, id) :- a(id), b(id, x,y,z), c("foo", 10, t), z>100.
\ No newline at end of file
+Q("test" :: TEXT, 123, id) :- a(id), b(id, x,y,z), c(x || y,10,"foo"), z>100.
\ No newline at end of file

From 4acacde0230546bd28e3babdf1a82b15482185ec Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sat, 4 Jul 2015 22:59:12 -0700
Subject: [PATCH 142/347] add support for compound conditions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 54 ++++++--------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 24 +++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  6 +-
 .../conditions/compile.expected               |  0
 .../expressions/compile.expected              | 71 +++++++++++++++++++
 .../{conditions => expressions}/input.ddl     |  2 +-
 test/test.sh                                  |  3 +-
 7 files changed, 109 insertions(+), 51 deletions(-)
 delete mode 100644 test/expected-output-test/conditions/compile.expected
 create mode 100644 test/expected-output-test/expressions/compile.expected
 rename test/expected-output-test/{conditions => expressions}/input.ddl (81%)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 0ac6d9122..eb725b9b3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -194,30 +194,20 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    // def resolveVarOrConst(variable: ColumnVariable, bodyIndex: Int) = {
-    //   variable match {
-    //     case Variable(varName,relName,index) => {
-    //       val canonical_body_index = qs.getBodyIndex(varName)
-    //       if (canonical_body_index != bodyIndex) {
-    //         val real_attr_name1 = resolveName( Variable(varName, relName, index) )
-    //         val real_attr_name2 = resolveName( qs.getVar(varName))
-    //         Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
-    //       } else { None }
-    //     }
-    //     case Constant(v,relName,i) => {
-    //       val attr = schema(relName, i)
-    //       Some(s"R${bodyIndex}.${attr} = ${v}")
-    //     }
-    //   }
-    // }
-
-    def resolveVarOrConst(variable: ColumnVariable, bodyIndex: Int) : String = {
+    def resolveVarOrConst(variable: ColumnVariable) : String = {
       variable match {
         case Variable(varName,relName,index) => resolveColumn(varName, qs, z, OriginalOnly).get
-        case Constant(v,relName,i) => "v"
+        case Constant(v,relName,i) => v
       }
     }
 
+    // // resolve an expression
+    // def resolveExpression(e: Expression) = {
+    //   val resolvedVars = e.variables map (resolveVarOrConst(_))
+    //   resolvedVars(0) + " " + ((e.ops zip resolvedVars.drop(1)).map { 
+    //     case (a,b) => s"${a} ${b}" }).mkString      
+    // }
+
     var whereClause = z.bodies(0).zipWithIndex flatMap {
       case (Atom(relName, terms),bodyIndex) => {
         terms flatMap { case Expression(vars, ops, relName, index) =>
@@ -238,8 +228,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
               }
             }
           } else { // expression
-            val resolvedVars = vars map (resolveVarOrConst(_, bodyIndex))
-            val expr = resolvedVars(0) + " " + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
+            val expr = Expression(vars, ops, relName, index).print(resolveVarOrConst)
             val attr = schema(relName, index)
             Some(s"${expr} = R${bodyIndex}.${attr}")
           }
@@ -248,20 +237,17 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
 
     // resolve conditions
-    val conditions = z.conditions(0) flatMap { case Condition(lhs, op, rhs, isRhsValue) =>
-      val resolvedLhs = resolveColumn(lhs, qs, z, OriginalOnly)
-      val resolvedRhs = isRhsValue match {
-        case true  => Some(rhs)
-        case false => resolveColumn(rhs, qs, z, OriginalOnly)
-      }
-      Some(s"${resolvedLhs.get} ${op} ${resolvedRhs.get}")
-    }
-    
-    whereClause = whereClause ++ conditions
-
+    val conditions = ((z.conditions(0).conditions map { case x: List[Condition] =>
+      (x map { case Condition(lhs, op, rhs) =>
+        val lhsExpr = lhs.print(resolveVarOrConst)
+        val rhsExpr = rhs.print(resolveVarOrConst)
+        s"${lhsExpr} ${op} ${rhsExpr}"
+      }).mkString(" AND ")
+    }) map(v => s"(${v})")).mkString(" OR ")
+  
     var whereClauseStr = whereClause match {
-      case Nil => ""
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")}"""
+      case Nil => if (conditions == "") "" else s"WHERE ${conditions}"
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditions == "") "" else s" AND (${conditions})"}"""
     }
 
     s"""FROM ${ bodyNames }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index eaab4a531..f87e22469 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -26,12 +26,14 @@ case class Operator(operator: String, operand: ColumnVariable)
 
 case class Atom(name : String, terms : List[Expression])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[List[Condition]])
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[CompoundCondition])
 case class Column(name : String, t : String)
 
 // condition
-case class Condition(lhs: String, op: String, rhs: String, isRhsValue: Boolean)
-case class BodyWithConditions(body: List[Atom], conditions: List[Condition])
+case class BodyWithConditions(body: List[Atom], conditions: CompoundCondition)
+
+case class Condition(lhs: Expression, op: String, rhs: Expression)
+case class CompoundCondition(conditions: List[List[Condition]])
 
 // variable type
 sealed trait VariableType {
@@ -175,16 +177,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // conditions
   def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "="
-  def conditionWithConstant = variableName ~ filterOperator ~ constant ^^ {
-    case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs, true)
-  }
-  def conditionWithVariable = variableName ~ filterOperator ~ variableName ^^ {
-    case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs, false)
+  def condition = expression ~ filterOperator ~ expression ^^ {
+    case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs)
   }
-  def condition = conditionWithVariable | conditionWithConstant
-  def cqCondition: Parser[List[Condition]] = repsep(condition, ",")
-  def cqBodyWithCondition = cqBody ~ opt(",") ~ cqCondition ^^ {
-    case (b ~ o ~ c) => BodyWithConditions(b, c)
+  def conjunctiveCondition = repsep(condition, ",")
+  def compoundCondition = repsep(conjunctiveCondition, ";") ^^ { CompoundCondition(_) }
+  // def cqCondition: Parser[List[Condition]] = repsep(condition, ",")
+  def cqBodyWithCondition = cqBody ~ opt(",") ~ opt("[") ~ compoundCondition ~ opt("]") ^^ {
+    case (b ~ _ ~ _ ~ c ~ _) => BodyWithConditions(b, c)
   }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index e680951ba..1cb3111d0 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -70,9 +70,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val printListAtom = {a:List[Atom] =>
       s"${(a map printAtom).mkString(",\n    ")}"
     }
-    val printCondition = {a: List[Condition] =>
-      (a map { case Condition(lhs, op, rhs, _) => s"${lhs} ${op} ${rhs}" }).mkString(",")
-    }
+    // val printCondition = {a: List[Condition] =>
+    //   (a map { case Condition(lhs, op, rhs, _) => s"${lhs} ${op} ${rhs}" }).mkString(",")
+    // }
     s"""${printAtom(cq.head)} :-
        |    ${(cq.bodies map printListAtom).mkString(";\n    ")}""".stripMargin
   }
diff --git a/test/expected-output-test/conditions/compile.expected b/test/expected-output-test/conditions/compile.expected
deleted file mode 100644
index e69de29bb..000000000
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
new file mode 100644
index 000000000..2b90c3a5d
--- /dev/null
+++ b/test/expected-output-test/expressions/compile.expected
@@ -0,0 +1,71 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS b CASCADE;
+            CREATE TABLE
+            b(k int,
+ p text,
+ q text,
+ r int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS a CASCADE;
+            CREATE TABLE
+            a(k int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS c CASCADE;
+            CREATE TABLE
+            c(s text,
+ n int,
+ t text)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE b;
+          TRUNCATE a;
+          TRUNCATE c;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ DROP VIEW IF EXISTS Q;
+        CREATE VIEW Q AS 
+            SELECT 'test':: TEXT, 123, R0.k
+            FROM a R0, b R1, c R2
+        WHERE R1.k = R0.k  AND R1.p|| R1.q = R2.s AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
+        """
+        style: "sql_extractor"
+          
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_3]
diff --git a/test/expected-output-test/conditions/input.ddl b/test/expected-output-test/expressions/input.ddl
similarity index 81%
rename from test/expected-output-test/conditions/input.ddl
rename to test/expected-output-test/expressions/input.ddl
index 6c14b88d1..df231a530 100644
--- a/test/expected-output-test/conditions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -2,4 +2,4 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q("test" :: TEXT, 123, id) :- a(id), b(id, x,y,z), c(x || y,10,"foo"), z>100.
\ No newline at end of file
+Q("test" :: TEXT, 123, id) :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
\ No newline at end of file
diff --git a/test/test.sh b/test/test.sh
index cf48bf7dc..a466452b5 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -21,4 +21,5 @@ for t in *.bats.template; do
 done
 
 # run all .bats tests
-bats "$@" *.bats */*.bats
+# bats "$@" *.bats */*.bats
+bats "$@" expected*/expressions.bats

From 313bb8cd956cbdb4818d106470b6eef581bb8ea4 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 5 Jul 2015 18:32:36 -0700
Subject: [PATCH 143/347] fixes conflict in parsing compound conditions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 38 ++++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  5 ++-
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 16 ++++----
 .../expressions/compile.expected              |  2 +-
 5 files changed, 34 insertions(+), 29 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index eb725b9b3..1d5286e88 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -201,13 +201,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       }
     }
 
-    // // resolve an expression
-    // def resolveExpression(e: Expression) = {
-    //   val resolvedVars = e.variables map (resolveVarOrConst(_))
-    //   resolvedVars(0) + " " + ((e.ops zip resolvedVars.drop(1)).map { 
-    //     case (a,b) => s"${a} ${b}" }).mkString      
-    // }
-
     var whereClause = z.bodies(0).zipWithIndex flatMap {
       case (Atom(relName, terms),bodyIndex) => {
         terms flatMap { case Expression(vars, ops, relName, index) =>
@@ -237,17 +230,24 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
 
     // resolve conditions
-    val conditions = ((z.conditions(0).conditions map { case x: List[Condition] =>
-      (x map { case Condition(lhs, op, rhs) =>
-        val lhsExpr = lhs.print(resolveVarOrConst)
-        val rhsExpr = rhs.print(resolveVarOrConst)
-        s"${lhsExpr} ${op} ${rhsExpr}"
-      }).mkString(" AND ")
-    }) map(v => s"(${v})")).mkString(" OR ")
+    val conditionList = z.conditions(0) match {
+      case Some(c) => c.conditions map { case x: List[Condition] =>
+        val inner = x map { case Condition(lhs, op, rhs) =>
+          val lhsExpr = lhs.print(resolveVarOrConst)
+          val rhsExpr = rhs.print(resolveVarOrConst)
+          s"${lhsExpr} ${op} ${rhsExpr}"
+        }
+        inner.mkString(" AND ")
+      }
+      case None => List("")
+    }
+
+    val conditions = conditionList flatMap ( v => if (v != "") Some(s"(${v})") else None)
+    val conditionStr = conditions.mkString(" OR ")
   
     var whereClauseStr = whereClause match {
-      case Nil => if (conditions == "") "" else s"WHERE ${conditions}"
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditions == "") "" else s" AND (${conditions})"}"""
+      case Nil => if (conditionStr == "") "" else s"WHERE ${conditionStr}"
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditionStr == "") "" else s" AND (${conditionStr})"}"""
     }
 
     s"""FROM ${ bodyNames }
@@ -396,6 +396,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
+      // println(DeepDiveLogPrettyPrinter.print(stmt))
       for (cqBody <- stmt.q.bodies) {
         val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions)
         // Generate the body of the query.
@@ -404,7 +405,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // map head terms to sql
         def mapHeadTerms(terms: List[Expression], alias: AliasStyle = OriginalOnly) = {
           terms map { case Expression(v, ops, _, _) =>
-            val resolvedVars = v map (resolveVarOrConst(_))
+            val resolvedVars = v map (resolveVarOrConst(_, alias))
             val expr = resolvedVars(0) + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
             expr
           }
@@ -445,7 +446,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case false => OriginalAndAlias
           }
           val variableCols = mapHeadTerms(tmpCq.head.terms, resolveColumnFlag)
-
           val selectStr = variableCols.mkString(", ")
 
           inputQueries += s"""
@@ -681,6 +681,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile, config )
 
+    // programToCompile foreach {stmt => println(DeepDiveLogPrettyPrinter.print(stmt))}
+
     val body = new ListBuffer[String]()
     body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
     state.extractionRuleGroupByHead    foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 25dfc318b..735074f95 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -78,7 +78,8 @@ object DeepDiveLogDeltaDeriver{
         }
       }
     }
-    ConjunctiveQuery(incCqHead, incCqBodies.toList, Nil)
+    // TODO fix conditions
+    ConjunctiveQuery(incCqHead, incCqBodies.toList, cq.conditions)
   }
 
   // Incremental scheme declaration,
@@ -118,7 +119,7 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
       Atom(incNewStmt.a.name, incNewExpr),
       List(List(Atom(stmt.a.name, originalExpr)), List(Atom(incDeltaStmt.a.name, incDeltaExpr))), 
-      List()))
+      List(None)))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index 8b581d42f..d79654968 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -24,7 +24,7 @@ object DeepDiveLogMergeDeriver{
     val incNewExpr = incNewStmt.a.terms map (variableToExpr(_))
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, originalExpr),
-      List(List(Atom(incNewStmt.a.name, incNewExpr))), Nil))
+      List(List(Atom(incNewStmt.a.name, incNewExpr))), List(None)))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index f87e22469..6a8192e0d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -26,11 +26,11 @@ case class Operator(operator: String, operand: ColumnVariable)
 
 case class Atom(name : String, terms : List[Expression])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[CompoundCondition])
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[CompoundCondition]])
 case class Column(name : String, t : String)
 
 // condition
-case class BodyWithConditions(body: List[Atom], conditions: CompoundCondition)
+case class BodyWithConditions(body: List[Atom], conditions: Option[CompoundCondition])
 
 case class Condition(lhs: Expression, op: String, rhs: Expression)
 case class CompoundCondition(conditions: List[List[Condition]])
@@ -137,6 +137,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     case (v ~ opList) => {
       val variables = List(v) ++ (opList map (_.operand))
       val ops = opList map (_.operator)
+      // println(Expression(variables, ops, "", 0))
       Expression(variables, ops, "", 0)
     }
   }
@@ -178,13 +179,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
   // conditions
   def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "="
   def condition = expression ~ filterOperator ~ expression ^^ {
-    case (lhs ~ op ~ rhs) => Condition(lhs, op, rhs)
+    case (lhs ~ op ~ rhs) => {
+      Condition(lhs, op, rhs)
+    }
   }
   def conjunctiveCondition = repsep(condition, ",")
-  def compoundCondition = repsep(conjunctiveCondition, ";") ^^ { CompoundCondition(_) }
-  // def cqCondition: Parser[List[Condition]] = repsep(condition, ",")
-  def cqBodyWithCondition = cqBody ~ opt(",") ~ opt("[") ~ compoundCondition ~ opt("]") ^^ {
-    case (b ~ _ ~ _ ~ c ~ _) => BodyWithConditions(b, c)
+  def compoundCondition = "[" ~> repsep(conjunctiveCondition, ";") <~ "]" ^^ { CompoundCondition(_) }
+  def cqBodyWithCondition = cqBody ~ ("," ~> compoundCondition).? ^^ {
+    case (b ~ c) => BodyWithConditions(b, c)
   }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 2b90c3a5d..bb0710e7a 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -58,7 +58,7 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
-            SELECT 'test':: TEXT, 123, R0.k
+            SELECT 'test':: TEXT, 123, R0.k AS "a.R0.k" 
             FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R1.p|| R1.q = R2.s AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
         """

From 3f32cff295972008e066d27c127e92f9c46ad3f9 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 6 Jul 2015 00:28:56 -0700
Subject: [PATCH 144/347] Fix delta deriver with conditions

Match conditions with bodies when deriving delta rule
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  6 ++--
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  9 +++--
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  7 +---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 36 ++++++++++++++++---
 4 files changed, 41 insertions(+), 17 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 1d5286e88..88a97184f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -221,7 +221,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
               }
             }
           } else { // expression
-            val expr = Expression(vars, ops, relName, index).print(resolveVarOrConst)
+            val expr = DeepDiveLogPrettyPrinter.printExpr(Expression(vars, ops, relName, index), resolveVarOrConst)
             val attr = schema(relName, index)
             Some(s"${expr} = R${bodyIndex}.${attr}")
           }
@@ -233,8 +233,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     val conditionList = z.conditions(0) match {
       case Some(c) => c.conditions map { case x: List[Condition] =>
         val inner = x map { case Condition(lhs, op, rhs) =>
-          val lhsExpr = lhs.print(resolveVarOrConst)
-          val rhsExpr = rhs.print(resolveVarOrConst)
+          val lhsExpr = DeepDiveLogPrettyPrinter.printExpr(lhs, resolveVarOrConst)
+          val rhsExpr = DeepDiveLogPrettyPrinter.printExpr(rhs, resolveVarOrConst)
           s"${lhsExpr} ${op} ${rhsExpr}"
         }
         inner.mkString(" AND ")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 735074f95..3ad56dfb9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -42,8 +42,9 @@ object DeepDiveLogDeltaDeriver{
     }
 
     var incCqBodies = new ListBuffer[List[Atom]]()
+    var incCqConditions = new ListBuffer[Option[CompoundCondition]]()
     // New incremental bodies
-    for (body <- cq.bodies) {
+    cq.bodies zip cq.conditions foreach { case (body, cond) =>
       // Delta body
       val incDeltaBody = body map {
         a => a.copy(
@@ -63,6 +64,7 @@ object DeepDiveLogDeltaDeriver{
       var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
       if (mode == "inc") {
         incCqBodies += incNewBody
+        incCqConditions += cond
       } else {
         for (i <- index to (body.length - 1)) {
           var newBody = new ListBuffer[Atom]()
@@ -73,13 +75,14 @@ object DeepDiveLogDeltaDeriver{
               newBody += incNewBody(j)
             else if (j == i)
               newBody += incDeltaBody(j)
+            incCqConditions += cond
           }
           incCqBodies += newBody.toList
         }
       }
     }
     // TODO fix conditions
-    ConjunctiveQuery(incCqHead, incCqBodies.toList, cq.conditions)
+    ConjunctiveQuery(incCqHead, incCqBodies.toList, incCqConditions.toList)
   }
 
   // Incremental scheme declaration,
@@ -119,7 +122,7 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
       Atom(incNewStmt.a.name, incNewExpr),
       List(List(Atom(stmt.a.name, originalExpr)), List(Atom(incDeltaStmt.a.name, incDeltaExpr))), 
-      List(None)))
+      List(None, None)))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 6a8192e0d..91ba31410 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -16,12 +16,7 @@ import scala.util.Try
 sealed trait ColumnVariable
 case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
 case class Constant(value : String, relName: String, index: Int) extends ColumnVariable
-case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int) {
-  def print(resolve: ColumnVariable => String) = {
-    val resolvedVars = variables map (resolve(_))
-    resolvedVars(0) + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
-  }
-}
+case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int)
 case class Operator(operator: String, operand: ColumnVariable)
 
 case class Atom(name : String, terms : List[Expression])
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 1cb3111d0..e66a8cc14 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -60,21 +60,47 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     }
   }
 
+  def printExpr(e: Expression, resolve: ColumnVariable => String) = {
+    val resolvedVars = e.variables map (resolve(_))
+    resolvedVars(0) + ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
+  }
+
   def print(cq: ConjunctiveQuery): String = {
     val printAtom = {a:Atom =>
       val vars = a.terms map { 
-        case e => e.print(printVarOrConst)
+        case e => printExpr(e, printVarOrConst)
       }
       s"${a.name}(${vars.mkString(", ")})"
     }
     val printListAtom = {a:List[Atom] =>
       s"${(a map printAtom).mkString(",\n    ")}"
     }
-    // val printCondition = {a: List[Condition] =>
-    //   (a map { case Condition(lhs, op, rhs, _) => s"${lhs} ${op} ${rhs}" }).mkString(",")
-    // }
+
+    def printVar(x: ColumnVariable) = { x match {
+        case Variable(v,_,_) => v
+        case Constant(v,_,_) => v 
+      }
+    }
+    val printConjunctiveCondition = {a: List[Condition] =>
+      (a map { case Condition(lhs, op, rhs) => 
+        val lhsExpr = printExpr(lhs, printVar)
+        val rhsExpr = printExpr(rhs, printVar)
+        s"${lhsExpr} ${op} ${rhsExpr}" }).mkString(", ")
+    }
+    val conditionList = cq.conditions map {
+      case Some(x) => Some(x.conditions map printConjunctiveCondition mkString("; "))
+      case None    => None
+    }
+    val bodyList = cq.bodies map printListAtom
+    val bodyWithCondition = (bodyList zip conditionList map { case(a,b) => 
+      b match {
+        case Some(c) => s"${a}, [ ${c} ]" 
+        case None    => a
+      }
+    }).mkString(";\n    ")
+
     s"""${printAtom(cq.head)} :-
-       |    ${(cq.bodies map printListAtom).mkString(";\n    ")}""".stripMargin
+       |    ${bodyWithCondition}""".stripMargin
   }
 
   def print(stmt: ExtractionRule): String = {

From d15a3b5fa37efb9c39060d1284170035d70c4c58 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 6 Jul 2015 02:16:44 -0700
Subject: [PATCH 145/347] functions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 75 ++++++++++---------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 17 ++++-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 24 +++---
 .../expressions/compile.expected              |  4 +-
 .../expressions/input.ddl                     |  2 +-
 .../expressions/print.expected                | 16 ++++
 test/test.sh                                  |  3 +-
 7 files changed, 87 insertions(+), 54 deletions(-)
 create mode 100644 test/expected-output-test/expressions/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 88a97184f..00e72fea2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -186,6 +186,24 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
   }
 
+  def resolveColumnVar(v: ColumnVariable, cq: ConjunctiveQuery, alias: AliasStyle = OriginalOnly) = {
+    val qs = new QuerySchema(cq)
+    def resolveVarOrConst(x: ColumnVariable, alias: AliasStyle) = {
+      x match {
+        case Variable(v,r,i) => resolveColumn(v, qs, cq, alias).get
+        case Constant(v,r,i) => v
+        case _ => ""
+      }
+    }
+    v match {
+      case InlineFunction(name, args) => {
+        val resolvedArgs = args map (resolveVarOrConst(_, OriginalOnly))
+        s"${name}(${resolvedArgs.mkString(", ")})"
+      }
+      case _ => resolveVarOrConst(v, alias)
+    }
+  }
+
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
   def generateSQLBody(z : ConjunctiveQuery) : String = {
@@ -194,18 +212,15 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    def resolveVarOrConst(variable: ColumnVariable) : String = {
-      variable match {
-        case Variable(varName,relName,index) => resolveColumn(varName, qs, z, OriginalOnly).get
-        case Constant(v,relName,i) => v
-      }
-    }
-
     var whereClause = z.bodies(0).zipWithIndex flatMap {
       case (Atom(relName, terms),bodyIndex) => {
         terms flatMap { case Expression(vars, ops, relName, index) =>
-          // simple variable name or constant 
-          if (ops isEmpty) {
+          // simple variable
+          val simpleVar = (ops isEmpty) && (vars(0) match {
+            case x: Variable => true
+            case _ => false
+          })
+          if (simpleVar) {
             vars(0) match {
               case Variable(varName,relName,index) => {
                 val canonical_body_index = qs.getBodyIndex(varName)
@@ -215,15 +230,12 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
               }
-              case Constant(v,relName,i) => {
-                val attr = schema(relName, i)
-                Some(s"R${bodyIndex}.${attr} = ${v}")
-              }
+              case _ => None
             }
           } else { // expression
-            val expr = DeepDiveLogPrettyPrinter.printExpr(Expression(vars, ops, relName, index), resolveVarOrConst)
+            val expr = DeepDiveLogPrettyPrinter.printExpr(Expression(vars, ops, relName, index), resolveColumnVar(_,z))
             val attr = schema(relName, index)
-            Some(s"${expr} = R${bodyIndex}.${attr}")
+            Some(s"R${bodyIndex}.${attr} = ${expr}")
           }
         }
       }
@@ -233,8 +245,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     val conditionList = z.conditions(0) match {
       case Some(c) => c.conditions map { case x: List[Condition] =>
         val inner = x map { case Condition(lhs, op, rhs) =>
-          val lhsExpr = DeepDiveLogPrettyPrinter.printExpr(lhs, resolveVarOrConst)
-          val rhsExpr = DeepDiveLogPrettyPrinter.printExpr(rhs, resolveVarOrConst)
+          val lhsExpr = DeepDiveLogPrettyPrinter.printExpr(lhs, resolveColumnVar(_,z))
+          val rhsExpr = DeepDiveLogPrettyPrinter.printExpr(rhs, resolveColumnVar(_,z))
           s"${lhsExpr} ${op} ${rhsExpr}"
         }
         inner.mkString(" AND ")
@@ -392,6 +404,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     schemas.toList
   }
 
+
   // Generate extraction rule part for deepdive
   def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
     var inputQueries = new ListBuffer[String]()
@@ -402,25 +415,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
 
-        // map head terms to sql
-        def mapHeadTerms(terms: List[Expression], alias: AliasStyle = OriginalOnly) = {
-          terms map { case Expression(v, ops, _, _) =>
-            val resolvedVars = v map (resolveVarOrConst(_, alias))
-            val expr = resolvedVars(0) + ((ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
-            expr
-          }
-        }
-
-        def resolveVarOrConst(v: ColumnVariable, alias: AliasStyle = OriginalOnly) = {
-          v match {
-            case Variable(v,r,i) => ss.resolveColumn(v, qs, tmpCq, alias).get
-            case Constant(v,r,i) => v
-          }
-        }
-
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = mapHeadTerms(tmpCq.head.terms)
+          val headTerms = tmpCq.head.terms map { x => 
+            DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, OriginalOnly))
+          }
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
@@ -429,7 +428,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = mapHeadTerms(tmpCq.head.terms)
+          val headTerms = tmpCq.head.terms map { x => 
+            DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, OriginalOnly))
+          }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
           ${ ss.generateSQLBody(tmpCq) }
@@ -445,7 +446,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case true => OriginalOnly
             case false => OriginalAndAlias
           }
-          val variableCols = mapHeadTerms(tmpCq.head.terms, resolveColumnFlag)
+          val variableCols = tmpCq.head.terms map { x => 
+            DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, resolveColumnFlag))
+          }
           val selectStr = variableCols.mkString(", ")
 
           inputQueries += s"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 91ba31410..cc801cb51 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -16,6 +16,7 @@ import scala.util.Try
 sealed trait ColumnVariable
 case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
 case class Constant(value : String, relName: String, index: Int) extends ColumnVariable
+case class InlineFunction(functionName: String, args: List[ColumnVariable]) extends ColumnVariable
 case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int)
 case class Operator(operator: String, operand: ColumnVariable)
 
@@ -125,14 +126,20 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def variable = variableName ^^ { Variable(_, "", 0) }
   def columnConstant = constant ^^ { Constant(_, "", 0) }
   def variableOrConstant = columnConstant | variable
-  def operateOn = operator ~ variableOrConstant ^^ { case (v ~ o) => Operator(v,o) }
+  def inlineFunction = "!" ~> functionName ~ "(" ~ rep1sep(variableOrConstant, ",") ~ ")" ^^ {
+    case (name ~ _ ~ args ~ _) => {
+      InlineFunction(name, args)
+    }
+  }
+  def columnVariable = columnConstant | variable | inlineFunction
+  def operateOn = operator ~ columnVariable ^^ { case (v ~ o) => Operator(v,o) }
   def typecast = castOp ~ columnConstant ^^ { case (v ~ o) => Operator(v,o) }
   def operatorAndOperand = operateOn | typecast
-  def expression = variableOrConstant ~ rep(operatorAndOperand) ^^ {
+  def expression = columnVariable ~ rep(operatorAndOperand) ^^ {
     case (v ~ opList) => {
       val variables = List(v) ++ (opList map (_.operand))
       val ops = opList map (_.operator)
-      // println(Expression(variables, ops, "", 0))
+      // println(variables.mkString)
       Expression(variables, ops, "", 0)
     }
   }
@@ -145,6 +152,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             val vars = v map {
               case Variable(x,_,_) => Variable(x,r,i)
               case Constant(x,_,_) => Constant(x,r,i)
+              case InlineFunction(x, args) => InlineFunction(x, args)
             }
             Expression(vars, op, r, i)
           }
@@ -161,6 +169,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             val vars = v map {
               case Variable(x,_,_) => Variable(x,r,i)
               case Constant(x,_,_) => Constant(x,r,i)
+              case InlineFunction(x, args) => InlineFunction(x, args)
             }
             // println(Expression(vars, op, r, i))
             Expression(vars, op, r, i)
@@ -179,7 +188,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   }
   def conjunctiveCondition = repsep(condition, ",")
-  def compoundCondition = "[" ~> repsep(conjunctiveCondition, ";") <~ "]" ^^ { CompoundCondition(_) }
+  def compoundCondition = opt("[") ~> repsep(conjunctiveCondition, ";") <~ opt("]") ^^ { CompoundCondition(_) }
   def cqBodyWithCondition = cqBody ~ ("," ~> compoundCondition).? ^^ {
     case (b ~ c) => BodyWithConditions(b, c)
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index e66a8cc14..a56a67525 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -57,18 +57,29 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         else
           x.value
       }
+      case _ => ""
+    }
+  }
+
+  def printColumnVar(x: ColumnVariable) = {
+    x match {
+      case InlineFunction(name, args) => {
+        val resolvedArgs = args map printVarOrConst
+        s"!${name}(${resolvedArgs.mkString(", ")})"
+      }
+      case _ => printVarOrConst(x)
     }
   }
 
   def printExpr(e: Expression, resolve: ColumnVariable => String) = {
     val resolvedVars = e.variables map (resolve(_))
-    resolvedVars(0) + ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString
+    resolvedVars(0) + " " + ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString(" ")
   }
 
   def print(cq: ConjunctiveQuery): String = {
     val printAtom = {a:Atom =>
       val vars = a.terms map { 
-        case e => printExpr(e, printVarOrConst)
+        case e => printExpr(e, printColumnVar)
       }
       s"${a.name}(${vars.mkString(", ")})"
     }
@@ -76,15 +87,10 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       s"${(a map printAtom).mkString(",\n    ")}"
     }
 
-    def printVar(x: ColumnVariable) = { x match {
-        case Variable(v,_,_) => v
-        case Constant(v,_,_) => v 
-      }
-    }
     val printConjunctiveCondition = {a: List[Condition] =>
       (a map { case Condition(lhs, op, rhs) => 
-        val lhsExpr = printExpr(lhs, printVar)
-        val rhsExpr = printExpr(rhs, printVar)
+        val lhsExpr = printExpr(lhs, printColumnVar)
+        val rhsExpr = printExpr(rhs, printColumnVar)
         s"${lhsExpr} ${op} ${rhsExpr}" }).mkString(", ")
     }
     val conditionList = cq.conditions map {
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index bb0710e7a..20de75800 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -58,9 +58,9 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
-            SELECT 'test':: TEXT, 123, R0.k AS "a.R0.k" 
+            SELECT 'test':: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
             FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R1.p|| R1.q = R2.s AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
+        WHERE R1.k = R0.k  AND R2.s = R1.p|| R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index df231a530..2580789a9 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -2,4 +2,4 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q("test" :: TEXT, 123, id) :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
\ No newline at end of file
+Q("test" :: TEXT, 123, id, !unnest(y)) :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
new file mode 100644
index 000000000..b68126f98
--- /dev/null
+++ b/test/expected-output-test/expressions/print.expected
@@ -0,0 +1,16 @@
+a(k int).
+
+b(k int,
+  p text,
+  q text,
+  r int).
+
+c(s text,
+  n int,
+  t text).
+
+Q( "test" :: TEXT, 123, id, !unnest(y)) :-
+    a(id),
+    b(id, x, y, z),
+    c(x || y, 10,  "foo" ), [ z > 100; z < 20, z > 10 ].
+
diff --git a/test/test.sh b/test/test.sh
index a466452b5..cf48bf7dc 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -21,5 +21,4 @@ for t in *.bats.template; do
 done
 
 # run all .bats tests
-# bats "$@" *.bats */*.bats
-bats "$@" expected*/expressions.bats
+bats "$@" *.bats */*.bats

From 1296274bc34321f4525e68749aae9c9e98bd3f3b Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 6 Jul 2015 02:34:02 -0700
Subject: [PATCH 146/347] Add distinct

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 8 ++++----
 .../org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala      | 5 +++--
 .../org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala      | 2 +-
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 8 ++++----
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala     | 2 +-
 test/expected-output-test/expressions/compile.expected    | 2 +-
 test/expected-output-test/expressions/input.ddl           | 2 +-
 test/expected-output-test/expressions/print.expected      | 2 +-
 8 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 00e72fea2..261f42b7b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -411,7 +411,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     for (stmt <- stmts) {
       // println(DeepDiveLogPrettyPrinter.print(stmt))
       for (cqBody <- stmt.q.bodies) {
-        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions)
+        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions, stmt.q.isDistinct)
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
 
@@ -450,9 +450,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, resolveColumnFlag))
           }
           val selectStr = variableCols.mkString(", ")
-
+          val distinctStr = if (tmpCq.isDistinct) " DISTINCT " else ""
           inputQueries += s"""
-            SELECT ${selectStr}
+            SELECT ${distinctStr} ${selectStr}
             ${ ss.generateSQLBody(tmpCq) }"""
         }
       }
@@ -528,7 +528,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       for (cqBody <- stmt.q.bodies) {
         // edge query
         val fakeBody        = stmt.q.head +: cqBody
-        val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody), stmt.q.conditions) // we will just use the fakeBody below.
+        val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody), stmt.q.conditions, stmt.q.isDistinct) // we will just use the fakeBody below.
 
         val index = cqBody.length + 1
         val qs2 = new QuerySchema( fakeCQ )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 3ad56dfb9..1aa958c7e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -24,6 +24,7 @@ object DeepDiveLogDeltaDeriver{
       val newVars = expr.variables map {
         case term: Variable => term.copy(relName = prefix + term.relName)
         case term: Constant => term
+        case term: InlineFunction => term
       }
       Expression(newVars, expr.ops, expr.relName, expr.index)
     }
@@ -82,7 +83,7 @@ object DeepDiveLogDeltaDeriver{
       }
     }
     // TODO fix conditions
-    ConjunctiveQuery(incCqHead, incCqBodies.toList, incCqConditions.toList)
+    ConjunctiveQuery(incCqHead, incCqBodies.toList, incCqConditions.toList, cq.isDistinct)
   }
 
   // Incremental scheme declaration,
@@ -122,7 +123,7 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
       Atom(incNewStmt.a.name, incNewExpr),
       List(List(Atom(stmt.a.name, originalExpr)), List(Atom(incDeltaStmt.a.name, incDeltaExpr))), 
-      List(None, None)))
+      List(None, None), false))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index d79654968..6ab4d6666 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -24,7 +24,7 @@ object DeepDiveLogMergeDeriver{
     val incNewExpr = incNewStmt.a.terms map (variableToExpr(_))
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, originalExpr),
-      List(List(Atom(incNewStmt.a.name, incNewExpr))), List(None)))
+      List(List(Atom(incNewStmt.a.name, incNewExpr))), List(None), false))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index cc801cb51..194b56e86 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -22,7 +22,7 @@ case class Operator(operator: String, operand: ColumnVariable)
 
 case class Atom(name : String, terms : List[Expression])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[CompoundCondition]])
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[CompoundCondition]], isDistinct: Boolean)
 case class Column(name : String, t : String)
 
 // condition
@@ -194,9 +194,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
-    cqHead ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
-      case (headatom ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.conditions))
+    cqHead ~ opt("*") ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
+      case (headatom ~ isDistinct ~ ":-" ~ disjunctiveBodies) =>
+        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.conditions), isDistinct != None)
     }
 
   def relationType: Parser[RelationType] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index a56a67525..67c51c557 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -105,7 +105,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
     }).mkString(";\n    ")
 
-    s"""${printAtom(cq.head)} :-
+    s"""${printAtom(cq.head)} ${if (cq.isDistinct) "*" else ""} :-
        |    ${bodyWithCondition}""".stripMargin
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 20de75800..106dad5b5 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -58,7 +58,7 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
-            SELECT 'test':: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
+            SELECT  DISTINCT  'test':: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
             FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = R1.p|| R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
         """
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 2580789a9..cf6827dc5 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -2,4 +2,4 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q("test" :: TEXT, 123, id, !unnest(y)) :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
\ No newline at end of file
+Q("test" :: TEXT, 123, id, !unnest(y)) * :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index b68126f98..b37bf8a4b 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -9,7 +9,7 @@ c(s text,
   n int,
   t text).
 
-Q( "test" :: TEXT, 123, id, !unnest(y)) :-
+Q( "test" :: TEXT, 123, id, !unnest(y)) * :-
     a(id),
     b(id, x, y, z),
     c(x || y, 10,  "foo" ), [ z > 100; z < 20, z > 10 ].

From e5bd6753be4af14691b3cbf04cff0dbe9e3b62f0 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 6 Jul 2015 13:04:42 -0700
Subject: [PATCH 147/347] adjust whitespaces

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala   | 3 ++-
 .../scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala   | 3 ++-
 test/expected-output-test/expressions/compile.expected        | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 261f42b7b..99c8b7678 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -420,6 +420,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val headTerms = tmpCq.head.terms map { x => 
             DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, OriginalOnly))
           }
+          // println(headTerms)
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
@@ -450,7 +451,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, resolveColumnFlag))
           }
           val selectStr = variableCols.mkString(", ")
-          val distinctStr = if (tmpCq.isDistinct) " DISTINCT " else ""
+          val distinctStr = if (tmpCq.isDistinct) "DISTINCT" else ""
           inputQueries += s"""
             SELECT ${distinctStr} ${selectStr}
             ${ ss.generateSQLBody(tmpCq) }"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 67c51c557..34d17a8ca 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -73,7 +73,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def printExpr(e: Expression, resolve: ColumnVariable => String) = {
     val resolvedVars = e.variables map (resolve(_))
-    resolvedVars(0) + " " + ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString(" ")
+    val rest = ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString(" ")
+    resolvedVars(0) + (if (rest != "") " " + rest else "")
   }
 
   def print(cq: ConjunctiveQuery): String = {
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 106dad5b5..31b040301 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -58,9 +58,9 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
-            SELECT  DISTINCT  'test':: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
+            SELECT DISTINCT 'test' :: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
             FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p|| R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
         """
         style: "sql_extractor"
           

From 3013fa187a138c2c70d58af632c637c50ae688b4 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 6 Jul 2015 20:43:30 -0700
Subject: [PATCH 148/347] Fix alias with expressions in head

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 13 +++++++++++--
 .../org/deepdive/ddlog/DeepDiveLogParser.scala      |  2 +-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 99c8b7678..02ffb4884 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -204,6 +204,15 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
   }
 
+  def resolveExpr(e: Expression, cq: ConjunctiveQuery, alias: AliasStyle) = {
+    val resolvedVars = e.ops isEmpty match {
+      case true  => e.variables map (resolveColumnVar(_, cq, alias))
+      case false => e.variables map (resolveColumnVar(_, cq, OriginalOnly))
+    }
+    val rest = ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString(" ")
+    resolvedVars(0) + (if (rest != "") " " + rest else "")
+  }
+
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
   def generateSQLBody(z : ConjunctiveQuery) : String = {
@@ -233,7 +242,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
               case _ => None
             }
           } else { // expression
-            val expr = DeepDiveLogPrettyPrinter.printExpr(Expression(vars, ops, relName, index), resolveColumnVar(_,z))
+            val expr = resolveExpr(Expression(vars, ops, relName, index), z, OriginalOnly)
             val attr = schema(relName, index)
             Some(s"R${bodyIndex}.${attr} = ${expr}")
           }
@@ -448,7 +457,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case false => OriginalAndAlias
           }
           val variableCols = tmpCq.head.terms map { x => 
-            DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, resolveColumnFlag))
+            ss.resolveExpr(x, tmpCq, resolveColumnFlag)
           }
           val selectStr = variableCols.mkString(", ")
           val distinctStr = if (tmpCq.isDistinct) "DISTINCT" else ""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 194b56e86..3ccd9d4da 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -80,7 +80,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def stringLiteralAsSqlString = stringLiteral ^^ { s =>
     s"""'${s.stripPrefix("\"").stripSuffix("\"")}'"""
   }
-  def constant = stringLiteralAsSqlString | wholeNumber | "TRUE" | "FALSE" | "TEXT" | "INT" | "BOOLEAN"
+  def constant = stringLiteralAsSqlString | wholeNumber | "TRUE" | "FALSE" | "NULL" | "TEXT" | "INT" | "BOOLEAN"
 
   // C/Java/Scala-style as well as shell script-style comments are supported
   // by treating them as whiteSpace

From 6190e9bfd783229018f4cf597b7c68b3adf20c91 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 6 Jul 2015 22:06:42 -0700
Subject: [PATCH 149/347] cleanup debug printing

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 4 ----
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala   | 2 --
 2 files changed, 6 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 02ffb4884..159a143e8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -418,7 +418,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
-      // println(DeepDiveLogPrettyPrinter.print(stmt))
       for (cqBody <- stmt.q.bodies) {
         val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions, stmt.q.isDistinct)
         // Generate the body of the query.
@@ -429,7 +428,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val headTerms = tmpCq.head.terms map { x => 
             DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, OriginalOnly))
           }
-          // println(headTerms)
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
           val labelCol = s"R${index}.${name}"
@@ -694,8 +692,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile, config )
 
-    // programToCompile foreach {stmt => println(DeepDiveLogPrettyPrinter.print(stmt))}
-
     val body = new ListBuffer[String]()
     body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
     state.extractionRuleGroupByHead    foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 3ccd9d4da..2f81d7c03 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -139,7 +139,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     case (v ~ opList) => {
       val variables = List(v) ++ (opList map (_.operand))
       val ops = opList map (_.operator)
-      // println(variables.mkString)
       Expression(variables, ops, "", 0)
     }
   }
@@ -171,7 +170,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
               case Constant(x,_,_) => Constant(x,r,i)
               case InlineFunction(x, args) => InlineFunction(x, args)
             }
-            // println(Expression(vars, op, r, i))
             Expression(vars, op, r, i)
           }
         })

From fd4369aff737e1ddf7ff456a8b11ad3fa569585c Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 7 Jul 2015 16:21:14 -0700
Subject: [PATCH 150/347] Add a semantic checker

The following checks are performed
1. if a relation is defined
2. if a function is defined
3. if the number of columns of a relation match that in the schema
4. if variable relations use reserved columns (id, label)
---
 examples/smoke.ddl                            |   2 +-
 .../org/deepdive/ddlog/DeepDiveLog.scala      |   2 +-
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |   2 +
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 126 ++++++++++++++++++
 .../compile-incremental.expected              |   8 +-
 .../compile-materialization.expected          |   4 +-
 .../smoke_example/compile.expected            |   4 +-
 .../smoke_example/print-incremental.expected  |   4 +-
 .../smoke_example/print.expected              |   2 +-
 9 files changed, 141 insertions(+), 13 deletions(-)
 create mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala

diff --git a/examples/smoke.ddl b/examples/smoke.ddl
index 26f28fd37..c3aa5cdd4 100644
--- a/examples/smoke.ddl
+++ b/examples/smoke.ddl
@@ -35,5 +35,5 @@ cancer(pid) :- person_has_cancer(pid, l) label = l.
 cancer(pid) :- smoke(pid), person_smokes(pid, l)
     weight = 0.5.
 
-smoke(pid)  :- smoke(pid1), friend(pid1, pid)
+smoke(pid)  :- smoke(pid1), friends(pid1, pid)
     weight = 0.4.
\ No newline at end of file
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index eecb7f9a7..db5ad3101 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -26,6 +26,7 @@ object DeepDiveLog {
     head("ddlogc", "0.0.1")
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
+    cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) }
     opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
     opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
     opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
@@ -53,7 +54,6 @@ trait DeepDiveLogHandler {
   def run(config: DeepDiveLog.Config): Unit = try {
     // parse each file into a single program
     val parsedProgram = parseFiles(config.inputFiles)
-
     // run handler with the parsed program
     run(parsedProgram, config)
   } catch {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 159a143e8..9666a20a8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -680,6 +680,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    // semantic checking
+    DeepDiveLogSemanticChecker.run(parsedProgram, config)
     // determine the program to compile
     val programToCompile =
       // derive and compile the program based on mode information
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
new file mode 100644
index 000000000..7468979dc
--- /dev/null
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -0,0 +1,126 @@
+package org.deepdive.ddlog
+
+import scala.collection.immutable.HashMap
+import scala.collection.immutable.HashSet
+
+// semantic checker for ddlog
+object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
+  
+  // initialize the checker
+  def init(program: DeepDiveLog.Program) {
+    program foreach {
+      case s: SchemaDeclaration => {
+        heads += s.a.name
+        schemaDeclaration += { s.a.name -> s }
+      }
+      case ExtractionRule(q, supervision) => {
+        heads += q.head.name
+      }
+      case InferenceRule(q, weight, semantic, mode) => {
+        heads += q.head.name
+      }
+      case f: FunctionDeclaration => {
+        functionDeclaration += { f.functionName -> f }
+      }
+      case FunctionCallRule(input, output, function) => {
+        heads += output
+      }
+    }
+  }
+
+  // check a statement
+  def check(stmt: Statement) {
+    checkRelationDefined(stmt)
+    checkFunctionDefined(stmt)
+    checkVariableRelationSchema(stmt)
+    checkNumberOfColumns(stmt)
+  }
+
+  // check if relations in the body are defined
+  def checkRelationDefined(stmt: Statement) {
+    val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
+    def checkRelation(name: String) {
+      if (!(heads contains name))
+        error(stmt, s"""relation "${name}" is not defined""")
+    }
+    stmt match {
+      case s: ExtractionRule => {
+        s.q.bodies foreach { x => 
+          x foreach { a => checkRelation(a.name) }
+        }
+      }
+      case s: InferenceRule => {
+        s.q.bodies foreach { x => 
+          x foreach { a => checkRelation(a.name) }
+        }
+      }
+      case s: FunctionCallRule => checkRelation(s.input)
+      case _ => 
+    }
+  }
+
+  // check if a function is defined when it's called
+  def checkFunctionDefined(stmt: Statement) {
+    stmt match {
+      case s: FunctionCallRule => {
+        if (!(functionDeclaration.keySet contains s.function))
+          error(stmt, s"""function "${s.function}" is not defined""")
+      }
+      case _ => 
+    }
+  }
+
+  // check if the user use reserved column names
+  def checkVariableRelationSchema(stmt: Statement) {
+    val reservedSet = Set("id", "label")
+    stmt match {
+      case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
+        if (isQuery) {
+          terms.foreach { x => 
+            if (reservedSet contains x.varName) 
+              error(stmt, s"""variable relation contains reserved column "${x.varName}" """)
+          }
+        }
+      }
+      case _ => 
+    }
+  }
+
+  // check if the number of columns match schema declaration
+  def checkNumberOfColumns(stmt: Statement) {
+    def checkAtom(a: Atom) {
+      if ((schemaDeclaration.keySet contains a.name) &&
+        (a.terms.size != schemaDeclaration(a.name).a.terms.size))
+        error(stmt, s""""${a.name}": number of columns in the query does not match number of columns in the schema""")
+    }
+    def checkCq(cq: ConjunctiveQuery) {
+      checkAtom(cq.head)
+      cq.bodies foreach { x => x foreach checkAtom }
+    }
+    stmt match {
+      case s: ExtractionRule => checkCq(s.q)
+      case s: InferenceRule  => checkCq(s.q)
+      case _ => 
+    }
+  }
+
+  // throw exception 
+  def error(stmt: Statement, message: String) {
+    val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
+    throw new RuntimeException(message + s"\n${stmtStr}")
+  }
+
+  // run the checker
+  override def run(program: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    init(program)
+    program foreach check
+  }
+
+  // schema declaration
+  var heads  : Set[String]                       = new HashSet[String]() 
+  // schema
+  var schemaDeclaration : Map[String, SchemaDeclaration] = new HashMap[String, SchemaDeclaration]()
+  // function declaration
+  var functionDeclaration : Map[String, FunctionDeclaration] = new HashMap[String, FunctionDeclaration]()
+
+}
\ No newline at end of file
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 042e044f4..7853ad847 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -266,11 +266,11 @@ dd_delta_smoke.label: Boolean
         deepdive.inference.factors.dd_new_smoke_1 {
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
-          FROM dd_new_smoke R0, dd_delta_smoke R1, friend R2
-        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id  UNION ALL 
+          FROM dd_new_smoke R0, dd_delta_smoke R1, friends R2
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  UNION ALL 
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
-          FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friend R2
-        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_smoke.R0.label)"
           weight: "0.4"
         }
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 295dfd0a7..47ab03e5d 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -123,8 +123,8 @@ cancer.label: Boolean
         deepdive.inference.factors.smoke_1 {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
-          FROM smoke R0, smoke R1, friend R2
-        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          FROM smoke R0, smoke R1, friends R2
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
           function: "Imply(smoke.R1.label, smoke.R0.label)"
           weight: "0.4"
         }
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 60b6e3112..8a52c5346 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -123,8 +123,8 @@ cancer.label: Boolean
         deepdive.inference.factors.smoke_1 {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
-          FROM smoke R0, smoke R1, friend R2
-        WHERE R2.pid1 = R1.person_id  AND R2.pid = R0.person_id """
+          FROM smoke R0, smoke R1, friends R2
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
           function: "Imply(smoke.R1.label, smoke.R0.label)"
           weight: "0.4"
         }
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index 7a52fb60d..3ed640bfc 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -88,9 +88,9 @@ dd_new_cancer(pid) :-
 
 dd_new_smoke(pid) :-
     dd_delta_smoke(pid1),
-    friend(pid1, pid);
+    friends(pid1, pid);
     dd_new_smoke(pid1),
-    dd_delta_friend(pid1, pid)
+    dd_delta_friends(pid1, pid)
   weight = 0.4
   semantics = Imply.
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index bef8589bc..eccbb0b6f 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -30,7 +30,7 @@ cancer(pid) :-
 
 smoke(pid) :-
     smoke(pid1),
-    friend(pid1, pid)
+    friends(pid1, pid)
   weight = 0.4
   semantics = Imply.
 

From dc57357885723196a9c5017ec52589cf902cbe69 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 7 Jul 2015 17:37:24 -0700
Subject: [PATCH 151/347] Add support for aggregation

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 28 ++++++++++++++++---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 18 ++++++------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  4 +--
 .../expressions/compile.expected              |  6 +++-
 .../expressions/input.ddl                     |  4 ++-
 .../expressions/print.expected                |  6 +++-
 6 files changed, 49 insertions(+), 17 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9666a20a8..9eacbb297 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -196,7 +196,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       }
     }
     v match {
-      case InlineFunction(name, args) => {
+      case InlineFunction(name, args, _) => {
         val resolvedArgs = args map (resolveVarOrConst(_, OriginalOnly))
         s"${name}(${resolvedArgs.mkString(", ")})"
       }
@@ -265,10 +265,30 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
     val conditions = conditionList flatMap ( v => if (v != "") Some(s"(${v})") else None)
     val conditionStr = conditions.mkString(" OR ")
-  
+    
+    // handle group by
+    // map head terms, leaving out aggregation functions
+    val groupbyTerms = z.head.terms flatMap { case Expression(vars, ops, relName, index) =>
+      if (ops isEmpty) {
+        vars(0) match {
+          case InlineFunction(name, args, a) => if (a) None else Some("")
+          case Variable(v,r,i) => resolveColumn(v, qs, z, OriginalOnly)
+          case _ => Some("")
+        }
+      } else {
+        Some("")
+      }
+    }
+
+    val groupbyStr = if (groupbyTerms.size == z.head.terms.size) {
+      ""
+    } else {
+      s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
+    }
+
     var whereClauseStr = whereClause match {
-      case Nil => if (conditionStr == "") "" else s"WHERE ${conditionStr}"
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditionStr == "") "" else s" AND (${conditionStr})"}"""
+      case Nil => if (conditionStr == "") "" else s"WHERE ${conditionStr}${groupbyStr}"
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditionStr == "") "" else s" AND (${conditionStr})"}${groupbyStr}"""
     }
 
     s"""FROM ${ bodyNames }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 2f81d7c03..c0873cff4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -16,7 +16,7 @@ import scala.util.Try
 sealed trait ColumnVariable
 case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
 case class Constant(value : String, relName: String, index: Int) extends ColumnVariable
-case class InlineFunction(functionName: String, args: List[ColumnVariable]) extends ColumnVariable
+case class InlineFunction(functionName: String, args: List[ColumnVariable], isAggregation: Boolean) extends ColumnVariable
 case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int)
 case class Operator(operator: String, operand: ColumnVariable)
 
@@ -108,8 +108,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def dataType = CategoricalParser | BooleanParser
 
   def schemaDeclaration: Parser[SchemaDeclaration] =
-    relationName ~ opt("?") ~ opt("!") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
-      case (r ~ isQuery ~ isDistinct ~ "(" ~ attrs ~ ")" ~ vType) => {
+    relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
+      case (r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
         val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
         var types = attrs map { case(x) => x.t }
         val variableType = vType match {
@@ -126,12 +126,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def variable = variableName ^^ { Variable(_, "", 0) }
   def columnConstant = constant ^^ { Constant(_, "", 0) }
   def variableOrConstant = columnConstant | variable
-  def inlineFunction = "!" ~> functionName ~ "(" ~ rep1sep(variableOrConstant, ",") ~ ")" ^^ {
+  val aggregationFunctions = Set("MAX", "SUM", "MIN")
+  def inlineFunction = functionName ~ "(" ~ rep1sep(variableOrConstant, ",") ~ ")" ^^ {
     case (name ~ _ ~ args ~ _) => {
-      InlineFunction(name, args)
+      if (aggregationFunctions contains name) InlineFunction(name, args, true)
+      else InlineFunction(name, args, false)
     }
   }
-  def columnVariable = columnConstant | variable | inlineFunction
+  def columnVariable = columnConstant | inlineFunction | variable
   def operateOn = operator ~ columnVariable ^^ { case (v ~ o) => Operator(v,o) }
   def typecast = castOp ~ columnConstant ^^ { case (v ~ o) => Operator(v,o) }
   def operatorAndOperand = operateOn | typecast
@@ -151,7 +153,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             val vars = v map {
               case Variable(x,_,_) => Variable(x,r,i)
               case Constant(x,_,_) => Constant(x,r,i)
-              case InlineFunction(x, args) => InlineFunction(x, args)
+              case InlineFunction(x, args, a) => InlineFunction(x, args, a)
             }
             Expression(vars, op, r, i)
           }
@@ -168,7 +170,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             val vars = v map {
               case Variable(x,_,_) => Variable(x,r,i)
               case Constant(x,_,_) => Constant(x,r,i)
-              case InlineFunction(x, args) => InlineFunction(x, args)
+              case InlineFunction(x, args, _) => InlineFunction(x, args, false)
             }
             Expression(vars, op, r, i)
           }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 34d17a8ca..fe04a460c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -63,9 +63,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def printColumnVar(x: ColumnVariable) = {
     x match {
-      case InlineFunction(name, args) => {
+      case InlineFunction(name, args, _) => {
         val resolvedArgs = args map printVarOrConst
-        s"!${name}(${resolvedArgs.mkString(", ")})"
+        s"${name}(${resolvedArgs.mkString(", ")})"
       }
       case _ => printVarOrConst(x)
     }
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 31b040301..9ff5adfe6 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -60,7 +60,11 @@
         CREATE VIEW Q AS 
             SELECT DISTINCT 'test' :: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
             FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10))
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10)) UNION ALL 
+            SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r)
+            FROM a R0, b R1
+        WHERE R1.k = R0.k  
+        GROUP BY R1.p, R1.q
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index cf6827dc5..0795e99bb 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -2,4 +2,6 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q("test" :: TEXT, 123, id, !unnest(y)) * :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
\ No newline at end of file
+Q("test" :: TEXT, 123, id, unnest(y)) * :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
+
+Q(y, z, MAX(w)) :- a(x), b(x,y,z,w).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index b37bf8a4b..f6312d0b2 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -9,8 +9,12 @@ c(s text,
   n int,
   t text).
 
-Q( "test" :: TEXT, 123, id, !unnest(y)) * :-
+Q( "test"  :: TEXT, 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
     c(x || y, 10,  "foo" ), [ z > 100; z < 20, z > 10 ].
 
+Q(y, z, MAX(w))  :-
+    a(x),
+    b(x, y, z, w).
+

From 68ba0999f254e24f217753e6699896ba9656d491 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 7 Jul 2015 21:25:41 -0700
Subject: [PATCH 152/347] Add test for semantic checker

---
 test/compile-error-test.bats.template         | 21 +++++++++++++++++++
 .../column_dismatch/compile-error.expected    |  5 +++++
 .../column_dismatch/input.ddl                 |  5 +++++
 .../compile-error.expected                    |  6 ++++++
 .../invalid_variable_schema/input.ddl         |  5 +++++
 .../undefined_function/compile-error.expected |  3 +++
 .../undefined_function/input.ddl              |  5 +++++
 .../undefined_relation/compile-error.expected |  5 +++++
 .../undefined_relation/input.ddl              |  5 +++++
 9 files changed, 60 insertions(+)
 create mode 100644 test/compile-error-test.bats.template
 create mode 100644 test/compile-error-test/column_dismatch/compile-error.expected
 create mode 100644 test/compile-error-test/column_dismatch/input.ddl
 create mode 100644 test/compile-error-test/invalid_variable_schema/compile-error.expected
 create mode 100644 test/compile-error-test/invalid_variable_schema/input.ddl
 create mode 100644 test/compile-error-test/undefined_function/compile-error.expected
 create mode 100644 test/compile-error-test/undefined_function/input.ddl
 create mode 100644 test/compile-error-test/undefined_relation/compile-error.expected
 create mode 100644 test/compile-error-test/undefined_relation/input.ddl

diff --git a/test/compile-error-test.bats.template b/test/compile-error-test.bats.template
new file mode 100644
index 000000000..f9af002cc
--- /dev/null
+++ b/test/compile-error-test.bats.template
@@ -0,0 +1,21 @@
+#!/usr/bin/env bats
+# Compile error test
+# 
+# The test case here feeds a malformed .ddl into ddlog's print command and compares whether it produces an expected error.
+
+source bats-template.bash  # for $TESTDIR, $it, etc.
+
+# some preconditions
+setup() {
+    [ -e "$TESTDIR" ]
+    expectedError="$TESTDIR"/compile-error.expected
+    [ -e "$expectedError" ]
+    actualError=${expectedError%.expected}.actual
+}
+
+# check if input produces a compile error
+@test "$it compiles input" {
+    ! ddlog compile "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+    diff "$expectedError" "$actualError"
+}
+
diff --git a/test/compile-error-test/column_dismatch/compile-error.expected b/test/compile-error-test/column_dismatch/compile-error.expected
new file mode 100644
index 000000000..06dd1101f
--- /dev/null
+++ b/test/compile-error-test/column_dismatch/compile-error.expected
@@ -0,0 +1,5 @@
+[error] "c": number of columns in the query does not match number of columns in the schema
+Q(y, z)  :-
+    a(x),
+    c(x, y, z, w).
+
diff --git a/test/compile-error-test/column_dismatch/input.ddl b/test/compile-error-test/column_dismatch/input.ddl
new file mode 100644
index 000000000..cf2b01ec4
--- /dev/null
+++ b/test/compile-error-test/column_dismatch/input.ddl
@@ -0,0 +1,5 @@
+a(k int).
+b(k int, p text, q text, r int).
+c(s text, n int, t text).
+
+Q(y, z) :- a(x), c(x,y,z,w).
\ No newline at end of file
diff --git a/test/compile-error-test/invalid_variable_schema/compile-error.expected b/test/compile-error-test/invalid_variable_schema/compile-error.expected
new file mode 100644
index 000000000..6086a2b35
--- /dev/null
+++ b/test/compile-error-test/invalid_variable_schema/compile-error.expected
@@ -0,0 +1,6 @@
+[error] variable relation contains reserved column "id" 
+c?(id int,
+  s text,
+  n int,
+  t text).
+
diff --git a/test/compile-error-test/invalid_variable_schema/input.ddl b/test/compile-error-test/invalid_variable_schema/input.ddl
new file mode 100644
index 000000000..d9254a628
--- /dev/null
+++ b/test/compile-error-test/invalid_variable_schema/input.ddl
@@ -0,0 +1,5 @@
+a(k int).
+b(k int, p text, q text, r int).
+c?(id int, s text, n int, t text).
+
+Q(y, z) :- a(x), d(x,y,z,w).
\ No newline at end of file
diff --git a/test/compile-error-test/undefined_function/compile-error.expected b/test/compile-error-test/undefined_function/compile-error.expected
new file mode 100644
index 000000000..90ffa0742
--- /dev/null
+++ b/test/compile-error-test/undefined_function/compile-error.expected
@@ -0,0 +1,3 @@
+[error] function "ext" is not defined
+Q :- !ext(a).
+    
diff --git a/test/compile-error-test/undefined_function/input.ddl b/test/compile-error-test/undefined_function/input.ddl
new file mode 100644
index 000000000..27a2a045a
--- /dev/null
+++ b/test/compile-error-test/undefined_function/input.ddl
@@ -0,0 +1,5 @@
+a(k int).
+b(k int, p text, q text, r int).
+c(s text, n int, t text).
+
+Q :- !ext(a).
\ No newline at end of file
diff --git a/test/compile-error-test/undefined_relation/compile-error.expected b/test/compile-error-test/undefined_relation/compile-error.expected
new file mode 100644
index 000000000..b8e721de4
--- /dev/null
+++ b/test/compile-error-test/undefined_relation/compile-error.expected
@@ -0,0 +1,5 @@
+[error] relation "d" is not defined
+Q(y, z)  :-
+    a(x),
+    d(x, y, z, w).
+
diff --git a/test/compile-error-test/undefined_relation/input.ddl b/test/compile-error-test/undefined_relation/input.ddl
new file mode 100644
index 000000000..dde018a26
--- /dev/null
+++ b/test/compile-error-test/undefined_relation/input.ddl
@@ -0,0 +1,5 @@
+a(k int).
+b(k int, p text, q text, r int).
+c(s text, n int, t text).
+
+Q(y, z) :- a(x), d(x,y,z,w).
\ No newline at end of file

From b5beb82bd7b9d7755d1be3c7258ff3b0e00a8ad4 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 7 Jul 2015 23:31:06 -0700
Subject: [PATCH 153/347] add endtoend and cleanup pipeline

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 10 ++--
 .../chunking_example/compile.expected         |  8 +--
 .../expressions/compile.expected              |  2 +
 .../ocr_example/compile-incremental.expected  | 17 +++---
 .../compile-materialization.expected          |  5 +-
 .../ocr_example/compile-merge.expected        |  7 +--
 .../ocr_example/compile.expected              |  6 ++-
 .../compile-incremental.expected              | 25 ++++-----
 .../compile-materialization.expected          |  5 +-
 .../smoke_example/compile-merge.expected      |  9 ++--
 .../smoke_example/compile.expected            | 14 ++---
 .../compile-incremental.expected              | 51 +++++++++---------
 .../compile-materialization.expected          | 13 ++---
 .../spouse_example/compile-merge.expected     | 11 ++--
 .../spouse_example/compile.expected           | 14 ++---
 .../compile-incremental.expected              | 53 ++++++++++---------
 .../compile-incremental.expected              | 53 ++++++++++---------
 .../compile.expected                          | 16 +++---
 18 files changed, 173 insertions(+), 146 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9eacbb297..38470eea4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -420,7 +420,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       }
     }
     // Cleanup incremental table extractor
-    val truncateTableList = (stmts map (x => if ((x.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains x.a.name)) "" else s"TRUNCATE ${x.a.name};")).filter(_ != "")
+    val truncateTableList = (stmts map (x => 
+      if ((x.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains x.a.name)) "" 
+      else s"TRUNCATE ${x.a.name};")).filter(_ != "")
     if (truncateTableList.length > 0) {
       schemas += s"""
         deepdive.extraction.extractors.cleanup {
@@ -664,15 +666,17 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [${extraction}]" else ""
     val inference = ((ss.inferenceRuleGroupByHead map (_._2)).flatten map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [${inference}]" else ""
+    val endtoend = List(extraction, inference).filter(_ != "").mkString(", ")
+    val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [${endtoend}]" else ""
     val cleanup_pipeline = ss.mode match {
-      case INCREMENTAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [cleanup]" else ""
+      case INCREMENTAL | ORIGINAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [cleanup]" else ""
       case _ => ""
     }
     val base_dir = ss.mode match {
       case MATERIALIZATION | INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
       case _ => ""
     }
-    List(run, initdb, extraction_pipeline, inference_pipeline, cleanup_pipeline, base_dir).filter(_ != "")
+    List(run, initdb, extraction_pipeline, inference_pipeline, endtoend_pipeline, cleanup_pipeline, base_dir).filter(_ != "")
   }
 
   // generate variable schema statements
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 1288f1873..2afd5affe 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -72,9 +72,9 @@
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS ext_features_input;
         CREATE VIEW ext_features_input AS 
-            SELECT R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
+            SELECT  R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
             FROM words R0, words R1
-        WHERE R1.sent_id = R0.sent_id 
+        WHERE R1.sent_id = R0.sent_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_5" ]
@@ -117,7 +117,7 @@
           input_query: """
           SELECT R0.id AS "tag.R0.id" , R1.feature AS "word_features.R1.feature" 
           FROM tag R0, word_features R1
-        WHERE R1.word_id = R0.word_id """
+        WHERE R1.word_id = R0.word_id  """
           function: "Multinomial(tag.R0.label)"
           weight: "?(word_features.R1.feature)"
         }
@@ -126,3 +126,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_0, extraction_rule_1, extraction_rule_3, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_6, extraction_rule_9, extraction_rule_8, extraction_rule_5]
 deepdive.pipeline.pipelines.inference: [tag_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_6, extraction_rule_9, extraction_rule_8, extraction_rule_5, tag_0]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 9ff5adfe6..88d756923 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -73,3 +73,5 @@
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_3]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_3]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index c7da34686..1939614bf 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -123,10 +123,10 @@ q1.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_label2;
         INSERT INTO dd_new_label2 
-            SELECT R0.wid, R0.val
+            SELECT  R0.wid, R0.val
             FROM label2 R0
          UNION ALL 
-            SELECT R0.wid, R0.val
+            SELECT  R0.wid, R0.val
             FROM dd_delta_label2 R0
         
         """
@@ -153,10 +153,10 @@ q1.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_label1;
         INSERT INTO dd_new_label1 
-            SELECT R0.wid, R0.val
+            SELECT  R0.wid, R0.val
             FROM label1 R0
          UNION ALL 
-            SELECT R0.wid, R0.val
+            SELECT  R0.wid, R0.val
             FROM dd_delta_label1 R0
         
         """
@@ -180,10 +180,10 @@ q1.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_features;
         INSERT INTO dd_new_features 
-            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            SELECT  R0.id, R0.word_id, R0.feature_id, R0.feature_val
             FROM features R0
          UNION ALL 
-            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            SELECT  R0.id, R0.word_id, R0.feature_id, R0.feature_val
             FROM dd_delta_features R0
         
         """
@@ -223,7 +223,7 @@ q1.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
           FROM dd_new_q2 R0, dd_delta_features R1
-        WHERE R1.word_id = R0.wid """
+        WHERE R1.word_id = R0.wid  """
           function: "Imply(dd_new_q2.R0.label)"
           weight: "?(dd_delta_features.R1.feature_id)"
         }
@@ -233,7 +233,7 @@ q1.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
           FROM dd_new_q1 R0, dd_delta_features R1
-        WHERE R1.word_id = R0.wid """
+        WHERE R1.word_id = R0.wid  """
           function: "Imply(dd_new_q1.R0.label)"
           weight: "?(dd_delta_features.R1.feature_id)"
         }
@@ -242,5 +242,6 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_10, extraction_rule_5, extraction_rule_14, extraction_rule_6, extraction_rule_1, extraction_rule_17, extraction_rule_9, extraction_rule_2, extraction_rule_13, extraction_rule_18]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_q2_0, dd_new_q1_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15, dd_new_q2_0, dd_new_q1_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index 1fc5c659c..79b41870d 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -106,7 +106,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q1 R0, features R1
-        WHERE R1.word_id = R0.wid """
+        WHERE R1.word_id = R0.wid  """
           function: "Imply(q1.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
@@ -116,7 +116,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q2 R0, features R1
-        WHERE R1.word_id = R0.wid """
+        WHERE R1.word_id = R0.wid  """
           function: "Imply(q2.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
@@ -125,4 +125,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, q1_0, q2_1]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
index d45ec8193..a6ffd7d42 100644
--- a/test/expected-output-test/ocr_example/compile-merge.expected
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -20,7 +20,7 @@
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE label2;
         INSERT INTO label2 
-            SELECT R0.wid, R0.val
+            SELECT  R0.wid, R0.val
             FROM dd_new_label2 R0
         
         """
@@ -32,7 +32,7 @@
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE label1;
         INSERT INTO label1 
-            SELECT R0.wid, R0.val
+            SELECT  R0.wid, R0.val
             FROM dd_new_label1 R0
         
         """
@@ -44,7 +44,7 @@
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE features;
         INSERT INTO features 
-            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            SELECT  R0.id, R0.word_id, R0.feature_id, R0.feature_val
             FROM dd_new_features R0
         
         """
@@ -54,3 +54,4 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_1, extraction_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_2, extraction_rule_1, extraction_rule_0]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index e41c42804..05d770f85 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -106,7 +106,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q1 R0, features R1
-        WHERE R1.word_id = R0.wid """
+        WHERE R1.word_id = R0.wid  """
           function: "Imply(q1.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
@@ -116,7 +116,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q2 R0, features R1
-        WHERE R1.word_id = R0.wid """
+        WHERE R1.word_id = R0.wid  """
           function: "Imply(q2.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
@@ -125,3 +125,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, q1_0, q2_1]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 7853ad847..1e0b6a07c 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -151,10 +151,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_person_has_cancer;
         INSERT INTO dd_new_person_has_cancer 
-            SELECT R0.person_id, R0.has_cancer
+            SELECT  R0.person_id, R0.has_cancer
             FROM person_has_cancer R0
          UNION ALL 
-            SELECT R0.person_id, R0.has_cancer
+            SELECT  R0.person_id, R0.has_cancer
             FROM dd_delta_person_has_cancer R0
         
         """
@@ -166,10 +166,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_person;
         INSERT INTO dd_new_person 
-            SELECT R0.person_id, R0.name
+            SELECT  R0.person_id, R0.name
             FROM person R0
          UNION ALL 
-            SELECT R0.person_id, R0.name
+            SELECT  R0.person_id, R0.name
             FROM dd_delta_person R0
         
         """
@@ -223,10 +223,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_person_smokes;
         INSERT INTO dd_new_person_smokes 
-            SELECT R0.person_id, R0.smokes
+            SELECT  R0.person_id, R0.smokes
             FROM person_smokes R0
          UNION ALL 
-            SELECT R0.person_id, R0.smokes
+            SELECT  R0.person_id, R0.smokes
             FROM dd_delta_person_smokes R0
         
         """
@@ -238,10 +238,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_friends;
         INSERT INTO dd_new_friends 
-            SELECT R0.person_id, R0.friend_id
+            SELECT  R0.person_id, R0.friend_id
             FROM friends R0
          UNION ALL 
-            SELECT R0.person_id, R0.friend_id
+            SELECT  R0.person_id, R0.friend_id
             FROM dd_delta_friends R0
         
         """
@@ -254,10 +254,10 @@ dd_delta_smoke.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION ALL 
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id   UNION ALL 
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
           weight: "0.5"
         }
@@ -267,10 +267,10 @@ dd_delta_smoke.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_delta_smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  UNION ALL 
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id   UNION ALL 
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_smoke.R0.label)"
           weight: "0.4"
         }
@@ -279,5 +279,6 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_cancer_0, dd_new_smoke_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_cancer_0, dd_new_smoke_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 47ab03e5d..b9908b20d 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -114,7 +114,7 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
           weight: "0.5"
         }
@@ -124,7 +124,7 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  """
           function: "Imply(smoke.R1.label, smoke.R0.label)"
           weight: "0.4"
         }
@@ -133,4 +133,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, cancer_0, smoke_1]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
index 487fc94a3..12622b100 100644
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -20,7 +20,7 @@
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE person_smokes;
         INSERT INTO person_smokes 
-            SELECT R0.person_id, R0.smokes
+            SELECT  R0.person_id, R0.smokes
             FROM dd_new_person_smokes R0
         
         """
@@ -32,7 +32,7 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE friends;
         INSERT INTO friends 
-            SELECT R0.person_id, R0.friend_id
+            SELECT  R0.person_id, R0.friend_id
             FROM dd_new_friends R0
         
         """
@@ -44,7 +44,7 @@
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE person_has_cancer;
         INSERT INTO person_has_cancer 
-            SELECT R0.person_id, R0.has_cancer
+            SELECT  R0.person_id, R0.has_cancer
             FROM dd_new_person_has_cancer R0
         
         """
@@ -56,7 +56,7 @@
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE person;
         INSERT INTO person 
-            SELECT R0.person_id, R0.name
+            SELECT  R0.person_id, R0.name
             FROM dd_new_person R0
         
         """
@@ -66,3 +66,4 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_3, extraction_rule_1, extraction_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_2, extraction_rule_3, extraction_rule_1, extraction_rule_0]
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 8a52c5346..7f33cc14f 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -88,7 +88,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ 
-        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label 
+        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
           
@@ -100,7 +100,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label 
+        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label
           FROM person_smokes R0
         
           
@@ -112,19 +112,19 @@ cancer.label: Boolean
 
         deepdive.inference.factors.cancer_0 {
           input_query: """
-          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id"  
+          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
           weight: "0.5"
         }
-
+      
 
         deepdive.inference.factors.smoke_1 {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  """
           function: "Imply(smoke.R1.label, smoke.R0.label)"
           weight: "0.4"
         }
@@ -133,3 +133,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, cancer_0, smoke_1]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index beee5b073..ae12889c9 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -171,18 +171,18 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT  R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
@@ -192,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -207,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -222,7 +222,7 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -234,10 +234,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -249,10 +249,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -264,10 +264,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -279,12 +279,12 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT  R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
+        WHERE R1.sentence_id = R0.sentence_id   UNION ALL 
+            SELECT  R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
+        WHERE R1.sentence_id = R0.sentence_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
@@ -352,10 +352,10 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id   UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -364,5 +364,6 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 706b2bbac..224d48c47 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -113,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -125,9 +125,9 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT  R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
@@ -137,9 +137,9 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT  R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
+        WHERE R1.sentence_id = R0.sentence_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_6" ]
@@ -180,7 +180,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -189,4 +189,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6, has_spouse_0]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index 9a972542f..632d934f0 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -20,7 +20,7 @@
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE sentences;
         INSERT INTO sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_new_sentences R0
         
         """
@@ -32,7 +32,7 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE has_spouse_candidates;
         INSERT INTO has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_new_has_spouse_candidates R0
         
         """
@@ -44,7 +44,7 @@
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE articles;
         INSERT INTO articles 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM dd_new_articles R0
         
         """
@@ -56,7 +56,7 @@
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ TRUNCATE has_spouse_features;
         INSERT INTO has_spouse_features 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM dd_new_has_spouse_features R0
         
         """
@@ -68,7 +68,7 @@
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE people_mentions;
         INSERT INTO people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_new_people_mentions R0
         
         """
@@ -78,3 +78,4 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [extraction_rule_0, extraction_rule_3, extraction_rule_4, extraction_rule_2, extraction_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_0, extraction_rule_3, extraction_rule_4, extraction_rule_2, extraction_rule_1]
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 87d478af8..25024387e 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -113,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -125,9 +125,9 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT  R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
@@ -137,9 +137,9 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT  R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
+        WHERE R1.sentence_id = R0.sentence_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_6" ]
@@ -180,7 +180,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -189,3 +189,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6, has_spouse_0]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index ca8c73cb5..9b0c86453 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -171,18 +171,18 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT  R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
@@ -192,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -207,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -222,10 +222,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
          UNION ALL 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -237,10 +237,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -252,10 +252,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -267,10 +267,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -282,12 +282,12 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT  R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
+        WHERE R1.sentence_id = R0.sentence_id   UNION ALL 
+            SELECT  R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
+        WHERE R1.sentence_id = R0.sentence_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
@@ -355,10 +355,10 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id   UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
           function: "Linear(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -367,5 +367,6 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 3baea1486..be999877f 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -171,18 +171,18 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT  R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
+            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
@@ -192,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -207,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT R0.article_id, R0.text
+            SELECT  R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -222,7 +222,7 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -234,10 +234,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -249,10 +249,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT R0.relation_id, R0.feature
+            SELECT  R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -264,10 +264,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -279,12 +279,12 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT  R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
+        WHERE R1.sentence_id = R0.sentence_id   UNION ALL 
+            SELECT  R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
+        WHERE R1.sentence_id = R0.sentence_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
@@ -352,10 +352,10 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id   UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -365,7 +365,7 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
-        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
+        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id  """
           function: "Imply(dd_new_has_spouse.R1.label, dd_new_has_spouse.R0.label)"
           weight: "3.0"
         }
@@ -374,5 +374,6 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0, dd_new_has_spouse_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0, dd_new_has_spouse_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index d184ea219..8b7469360 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -113,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -125,9 +125,9 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT  R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
@@ -137,9 +137,9 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT  R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
+        WHERE R1.sentence_id = R0.sentence_id  
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_6" ]
@@ -180,7 +180,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -190,7 +190,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
-        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
+        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id  """
           function: "Imply(has_spouse.R1.label, has_spouse.R0.label)"
           weight: "3.0"
         }
@@ -199,3 +199,5 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.inference: [has_spouse_0, has_spouse_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6, has_spouse_0, has_spouse_1]
+deepdive.pipeline.pipelines.cleanup: [cleanup]

From 7c19a8c7637445aaef6c2e77ea0e1df9dc96d7cc Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 8 Jul 2015 14:03:04 -0700
Subject: [PATCH 154/347] add alias for aggregation column

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala   | 9 +++++++--
 test/expected-output-test/expressions/compile.expected   | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 38470eea4..a00195b37 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -196,9 +196,14 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       }
     }
     v match {
-      case InlineFunction(name, args, _) => {
+      case InlineFunction(name, args, agg) => {
         val resolvedArgs = args map (resolveVarOrConst(_, OriginalOnly))
-        s"${name}(${resolvedArgs.mkString(", ")})"
+        val resolved = s"${name}(${resolvedArgs.mkString(", ")})"
+        val aggAlias = if (agg) { args(0) match {
+          case Variable(v,r,i) => s""" AS "${name}_${resolveColumn(v, qs, cq, OriginalOnly).get}"""" // "
+          case _ => ""
+        }} else ""
+        resolved + aggAlias
       }
       case _ => resolveVarOrConst(v, alias)
     }
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 88d756923..090108a90 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -61,7 +61,7 @@
             SELECT DISTINCT 'test' :: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
             FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10)) UNION ALL 
-            SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r)
+            SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS "MAX_R1.r"
             FROM a R0, b R1
         WHERE R1.k = R0.k  
         GROUP BY R1.p, R1.q

From fa12a6bd3b26972454e744360fe7f1266ca2d1cf Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 8 Jul 2015 16:28:04 -0700
Subject: [PATCH 155/347] Add bitwise and, is

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index c0873cff4..b192669d2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -120,7 +120,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
-  def operator = "||" | "+" | "-" | "*" | "/"
+  def operator = "||" | "+" | "-" | "*" | "/" | "&"
   def castOp = "::"
 
   def variable = variableName ^^ { Variable(_, "", 0) }
@@ -181,7 +181,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
 
   // conditions
-  def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "="
+  def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
   def condition = expression ~ filterOperator ~ expression ^^ {
     case (lhs ~ op ~ rhs) => {
       Condition(lhs, op, rhs)

From f22bb145d2728a80539e45adc409ea7cefcf4a05 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 9 Jul 2015 11:54:59 -0700
Subject: [PATCH 156/347] Fix group by. Add more aggregation functions. Support
 unknown weight that only depends on inference rule

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala     | 12 +++++++-----
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala |  2 +-
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a00195b37..dd5614c8a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -291,10 +291,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
     }
 
-    var whereClauseStr = whereClause match {
-      case Nil => if (conditionStr == "") "" else s"WHERE ${conditionStr}${groupbyStr}"
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditionStr == "") "" else s" AND (${conditionStr})"}${groupbyStr}"""
-    }
+    var whereClauseStr = (whereClause match {
+      case Nil => if (conditionStr == "") "" else s"WHERE ${conditionStr}"
+      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditionStr == "") "" else s" AND (${conditionStr})"}"""
+    }) + groupbyStr
 
     s"""FROM ${ bodyNames }
         ${ whereClauseStr }"""
@@ -606,7 +606,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              s"""?(${w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasOnly)).mkString(", ")})"""
+              val weightVar = w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasOnly)).mkString(", ")
+              if (weightVar == "") "?"
+              else s"?(${weightVar})"
             }
           }
       }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index b192669d2..4d09d5c7e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -126,7 +126,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def variable = variableName ^^ { Variable(_, "", 0) }
   def columnConstant = constant ^^ { Constant(_, "", 0) }
   def variableOrConstant = columnConstant | variable
-  val aggregationFunctions = Set("MAX", "SUM", "MIN")
+  val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG")
   def inlineFunction = functionName ~ "(" ~ rep1sep(variableOrConstant, ",") ~ ")" ^^ {
     case (name ~ _ ~ args ~ _) => {
       if (aggregationFunctions contains name) InlineFunction(name, args, true)

From 7423bc6d6a9e389514d3b377753665e601a19f01 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 9 Jul 2015 14:25:34 -0700
Subject: [PATCH 157/347] Fix function call rule in extraction pipeline

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 5 +++--
 test/expected-output-test/chunking_example/compile.expected | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index dd5614c8a..8c3cfe542 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -107,6 +107,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   var inferenceRuleGroupByHead      : Map[String, List[InferenceRule]] = new HashMap[String, List[InferenceRule]]()
   var functionCallRuleGroupByInput  : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
   var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
+  var functionCallList              : ListBuffer[FunctionCallRule] = new ListBuffer[FunctionCallRule]()
 
   def init() = {
     // generate the statements.
@@ -124,7 +125,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case ExtractionRule(_,_) => ()
       case InferenceRule(_,_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
-      case FunctionCallRule(_,_,_) => ()
+      case f: FunctionCallRule => functionCallList += f
     }
     groupByHead(statements)
     analyzeVisible(statements)
@@ -329,7 +330,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // Analyze the block visibility among statements 
   def analyzeVisible(statements: List[Statement]) = {
     extractionRuleGroupByHead   foreach {keyVal => visible += keyVal._2(0)}
-    functionCallRuleGroupByInput foreach {keyVal => visible += keyVal._2(0)}
+    functionCallList foreach { stmt => visible += stmt }
   }
 
   // Analyze the dependency between statements and construct a graph.
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 2afd5affe..f456ed25f 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -124,7 +124,7 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_0, extraction_rule_1, extraction_rule_3, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_6, extraction_rule_9, extraction_rule_8, extraction_rule_5]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_6, extraction_rule_9, extraction_rule_5, extraction_rule_8]
 deepdive.pipeline.pipelines.inference: [tag_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_6, extraction_rule_9, extraction_rule_8, extraction_rule_5, tag_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_6, extraction_rule_9, extraction_rule_5, extraction_rule_8, tag_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]

From 3d47ee13b7535ee561e34d4d91eed8e766a5ad6c Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 9 Jul 2015 14:30:46 -0700
Subject: [PATCH 158/347] Add example for debugging

---
 test.ddl | 107 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100644 test.ddl

diff --git a/test.ddl b/test.ddl
new file mode 100644
index 000000000..1fae812df
--- /dev/null
+++ b/test.ddl
@@ -0,0 +1,107 @@
+/*sentences(docid text, sentid text, wordidxs text[], words text[], poses text[], ners text[], lemmas text[], dep_paths text[], dep_parents text[], bounding_boxes text[]).
+ 
+sentences_serialized(docid text, sentid text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
+ 
+documents(docid text, sentids text[], wordidxs text[], words text[], poses text[], ners text[], lemmas text[], dep_paths text[], dep_parents text[], bounding_boxes text[]).
+ 
+documents_serialized(docid text, sentids text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
+ 
+entity_formation_candidate_local (docid text, type text, eid text, entity text, prov text).
+ 
+entity_formation_candidate (docid text, type text, eid text, entity text, prov text).
+ 
+entity_taxon_candidate_local (docid text, type text, eid text, entity text, author_year text, prov text).
+ 
+entity_taxon_candidate (docid text, type text, eid text, entity text, author_year text, prov text).
+ 
+entity_location_candidate (docid text, type text, eid text, entity text, prov text).
+ 
+entity_temporal_candidate (docid text, type text, eid text, entity text, prov text).
+ 
+entity_formation? (docid text, type text, eid text, entity text, prov text).
+ 
+entity_taxon? (docid text, type text, eid text, entity text, author_year text, prov text).
+ 
+entity_location? (docid text, type text, eid text, entity text, prov text).
+ 
+entity_temporal? (docid text, type text, eid text, entity text, prov text).
+ 
+relation_candidates (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text, features text).
+ 
+relation_formation? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_formationtemporal? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_formationlocation? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_taxonomy? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_formation_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_formationtemporal_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_formationlocation_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+relation_taxonomy_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
+ 
+ddtables (docid text, tableid text, type text, sentid text).
+ 
+interval_containments (formation text, child text, parent text).
+ 
+interval_not_that_possible(formation text, interval1 text, interval2 text).
+ 
+formation_per_doc(docid text, entity text[], type text[]).
+ 
+taxon_per_doc(docid text, entity text[], type text[]).
+ 
+document_with_formation_entities(docid text, entities text, types text, sentids text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
+ 
+document_with_taxon_entities(docid text, entities text, types text, sentids text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
+ 
+ 
+// Each word in sentence is separated with @@@@@
+sentences_serialized(
+  docid, 
+  sentid, 
+  array_to_string(wordidxs, "@@@@@"), 
+  array_to_string(words, "@@@@@"), 
+  array_to_string(poses, "@@@@@"), 
+  array_to_string(ners, "@@@@@"), 
+  array_to_string(lemmas, "@@@@@"), 
+  array_to_string(dep_paths, "@@@@@"), 
+  array_to_string(dep_parents, "@@@@@"), 
+  array_to_string(bounding_boxes, "@@@@@")) *
+  :- sentences(docid, sentid, wordidxs, words, poses, ners, lemmas, dep_paths, dep_parents, bounding_boxes).
+ 
+// Intermidate table to generate `documents_serialized`.
+documents(
+  docid,
+  ARRAY_AGG(sentid),
+  ARRAY_AGG(wordidxs), 
+  ARRAY_AGG(words), 
+  ARRAY_AGG(poses),
+  ARRAY_AGG(ners), 
+  ARRAY_AGG(lemmas), 
+  ARRAY_AGG(dep_paths),
+  ARRAY_AGG(dep_parents), 
+  ARRAY_AGG(bounding_boxes)) *
+  :- sentences_serialized(docid, sentid, wordidxs, words, poses, ners, lemmas, dep_paths, dep_parents, bounding_boxes).
+ 
+ 
+// Each sentence is separated with |||||, Each word in sentence is separated with @@@@@
+documents_serialized(
+  docid,
+  array_to_string(sentids, "|||||"),
+  array_to_string(wordidxs, "|||||"),
+  array_to_string(words, "|||||"),
+  array_to_string(poses, "|||||"),
+  array_to_string(ners, "|||||"),
+  array_to_string(lemmas, "|||||"),
+  array_to_string(dep_paths, "|||||"),
+  array_to_string(dep_parents, "|||||"),
+  array_to_string(bounding_boxes, "|||||")) 
+  :- documents(docid, sentids, wordidxs, words, poses, ners, lemmas, dep_paths, dep_parents, bounding_boxes).
+ 
+/**
+ * Formation that can be decided by only looking at the phrase itself.
+ **/

From c803ba78bfeded57445154ed0113d4c5b0afd256 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 9 Jul 2015 17:37:21 -0700
Subject: [PATCH 159/347] Drops support for multi-line /* */ style comments

due to causing StackOverflow and having no easy way to fix it.

Closes #31
---
 .../deepdive/ddlog/DeepDiveLogParser.scala    |   6 +-
 test.ddl                                      | 107 ------------------
 test/expected-output-test/comments/input.ddl  |  61 ++++++++--
 .../nested_multiline_comments/input.ddl       |   2 +-
 .../parse-error.expected                      |   6 +-
 5 files changed, 61 insertions(+), 121 deletions(-)
 delete mode 100644 test.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 10cc1caac..34842221c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -53,9 +53,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
       s.stripPrefix("\"").stripSuffix("\""))
   }
 
-  // C/Java/Scala-style as well as shell script-style comments are supported
-  // by treating them as whiteSpace
-  protected override val whiteSpace = """(?:(?:^|\s+)#.*|//.*|(?m)/\*(\*(?!/)|[^*])*\*/|\s)+""".r
+  // Single-line comments beginning with # or // are supported by treating them as whiteSpace
+  // C/Java/Scala style multi-line comments cannot be easily supported with RegexParsers unless we introduce a dedicated lexer.
+  protected override val whiteSpace = """(?:(?:^|\s+)#.*|//.*|\s)+""".r
 
   // We just use Java identifiers to parse various names
   def relationName = ident
diff --git a/test.ddl b/test.ddl
deleted file mode 100644
index 1fae812df..000000000
--- a/test.ddl
+++ /dev/null
@@ -1,107 +0,0 @@
-/*sentences(docid text, sentid text, wordidxs text[], words text[], poses text[], ners text[], lemmas text[], dep_paths text[], dep_parents text[], bounding_boxes text[]).
- 
-sentences_serialized(docid text, sentid text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
- 
-documents(docid text, sentids text[], wordidxs text[], words text[], poses text[], ners text[], lemmas text[], dep_paths text[], dep_parents text[], bounding_boxes text[]).
- 
-documents_serialized(docid text, sentids text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
- 
-entity_formation_candidate_local (docid text, type text, eid text, entity text, prov text).
- 
-entity_formation_candidate (docid text, type text, eid text, entity text, prov text).
- 
-entity_taxon_candidate_local (docid text, type text, eid text, entity text, author_year text, prov text).
- 
-entity_taxon_candidate (docid text, type text, eid text, entity text, author_year text, prov text).
- 
-entity_location_candidate (docid text, type text, eid text, entity text, prov text).
- 
-entity_temporal_candidate (docid text, type text, eid text, entity text, prov text).
- 
-entity_formation? (docid text, type text, eid text, entity text, prov text).
- 
-entity_taxon? (docid text, type text, eid text, entity text, author_year text, prov text).
- 
-entity_location? (docid text, type text, eid text, entity text, prov text).
- 
-entity_temporal? (docid text, type text, eid text, entity text, prov text).
- 
-relation_candidates (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text, features text).
- 
-relation_formation? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_formationtemporal? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_formationlocation? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_taxonomy? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_formation_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_formationtemporal_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_formationlocation_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-relation_taxonomy_global? (docid text, type text, eid1 text, eid2 text, entity1 text, entity2 text).
- 
-ddtables (docid text, tableid text, type text, sentid text).
- 
-interval_containments (formation text, child text, parent text).
- 
-interval_not_that_possible(formation text, interval1 text, interval2 text).
- 
-formation_per_doc(docid text, entity text[], type text[]).
- 
-taxon_per_doc(docid text, entity text[], type text[]).
- 
-document_with_formation_entities(docid text, entities text, types text, sentids text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
- 
-document_with_taxon_entities(docid text, entities text, types text, sentids text, wordidxs text, words text, poses text, ners text, lemmas text, dep_paths text, dep_parents text, bounding_boxes text).
- 
- 
-// Each word in sentence is separated with @@@@@
-sentences_serialized(
-  docid, 
-  sentid, 
-  array_to_string(wordidxs, "@@@@@"), 
-  array_to_string(words, "@@@@@"), 
-  array_to_string(poses, "@@@@@"), 
-  array_to_string(ners, "@@@@@"), 
-  array_to_string(lemmas, "@@@@@"), 
-  array_to_string(dep_paths, "@@@@@"), 
-  array_to_string(dep_parents, "@@@@@"), 
-  array_to_string(bounding_boxes, "@@@@@")) *
-  :- sentences(docid, sentid, wordidxs, words, poses, ners, lemmas, dep_paths, dep_parents, bounding_boxes).
- 
-// Intermidate table to generate `documents_serialized`.
-documents(
-  docid,
-  ARRAY_AGG(sentid),
-  ARRAY_AGG(wordidxs), 
-  ARRAY_AGG(words), 
-  ARRAY_AGG(poses),
-  ARRAY_AGG(ners), 
-  ARRAY_AGG(lemmas), 
-  ARRAY_AGG(dep_paths),
-  ARRAY_AGG(dep_parents), 
-  ARRAY_AGG(bounding_boxes)) *
-  :- sentences_serialized(docid, sentid, wordidxs, words, poses, ners, lemmas, dep_paths, dep_parents, bounding_boxes).
- 
- 
-// Each sentence is separated with |||||, Each word in sentence is separated with @@@@@
-documents_serialized(
-  docid,
-  array_to_string(sentids, "|||||"),
-  array_to_string(wordidxs, "|||||"),
-  array_to_string(words, "|||||"),
-  array_to_string(poses, "|||||"),
-  array_to_string(ners, "|||||"),
-  array_to_string(lemmas, "|||||"),
-  array_to_string(dep_paths, "|||||"),
-  array_to_string(dep_parents, "|||||"),
-  array_to_string(bounding_boxes, "|||||")) 
-  :- documents(docid, sentids, wordidxs, words, poses, ners, lemmas, dep_paths, dep_parents, bounding_boxes).
- 
-/**
- * Formation that can be decided by only looking at the phrase itself.
- **/
diff --git a/test/expected-output-test/comments/input.ddl b/test/expected-output-test/comments/input.ddl
index f34c68b9d..fddd68683 100644
--- a/test/expected-output-test/comments/input.ddl
+++ b/test/expected-output-test/comments/input.ddl
@@ -3,14 +3,61 @@
 
 R(a int).
 S( a int   # this is an integer field
- , b text  // seond one is a text field
- , c /* third one is a float field */ float
+ , b text  // second one is a text field
+ , c float#this_isnt_a_comment
 ).
 
 R(x) :- S(x, y, z).
 
-/*
-Multi
--line
-comments
-*/
+# Long block of comments (generated from http://www.lipsum.com/feed)
+#
+# Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum ut
+# elementum nisi, eget blandit ex. Donec dictum quam porta dolor commodo, sed
+# porta ipsum pretium. Donec egestas iaculis lacinia. Pellentesque ultricies
+# enim eget viverra iaculis. Praesent auctor erat id sem suscipit, quis feugiat
+# nulla volutpat. Vestibulum faucibus interdum enim, sed ornare mi iaculis sit
+# amet. Sed viverra pellentesque metus nec finibus. Morbi et turpis augue.
+# Curabitur luctus, lacus egestas pharetra rutrum, mi velit vestibulum nulla,
+# ut porta sem diam et nibh. Nulla finibus felis vel sem elementum pulvinar.
+# Morbi congue ante ut elit dapibus, sed sodales diam aliquam. Cras justo
+# nulla, dignissim sed justo maximus, aliquam dapibus ex. Donec feugiat
+# suscipit arcu eu tempor.
+#
+# Maecenas lacinia lacus nec nibh tristique, ac vestibulum sem rutrum. Proin
+# interdum ex risus, euismod sodales nulla interdum non. Vivamus lectus massa,
+# tristique eu convallis id, hendrerit sed quam. Nulla ullamcorper dapibus sem
+# id tempus. In imperdiet lacus et odio mattis cursus. Proin a sapien sit amet
+# metus cursus finibus eu et elit. Sed ac vehicula nibh. Nam eleifend nunc eget
+# magna malesuada, vel accumsan ligula mollis. Maecenas tristique a justo ac
+# pulvinar. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices
+# posuere cubilia Curae; Suspendisse laoreet a nulla at pellentesque. Sed
+# aliquet sapien elit, at vulputate lorem dictum nec. Pellentesque orci ante,
+# maximus id ex sed, placerat dignissim erat. Suspendisse id ullamcorper enim.
+#
+# Praesent cursus auctor laoreet. Nullam vehicula volutpat odio, vitae pulvinar
+# elit venenatis in. Aliquam vel maximus lectus, ac commodo velit. Fusce
+# consectetur blandit bibendum. Proin elementum ultricies metus sed viverra.
+# Aenean vel orci eu metus mattis maximus id quis ipsum. Nullam a velit risus.
+# Cras tempus vel massa ut facilisis. Cras semper, velit id euismod lacinia,
+# turpis nisl tincidunt ex, eu varius sapien lorem vitae odio. Vivamus sed
+# mauris nunc. Etiam et libero at metus aliquet dignissim. Quisque dui velit,
+# bibendum eget imperdiet in, sagittis et lorem. Nullam blandit tempor felis et
+# congue. Cras nec vehicula ante.
+#
+# Phasellus ac bibendum purus. Quisque lobortis lobortis porttitor. Fusce ut
+# magna lobortis, aliquam ipsum at, venenatis diam. Nullam at egestas risus, ac
+# consectetur ante. Integer commodo gravida libero eu ultricies. Mauris justo
+# lectus, rutrum ac magna eget, condimentum suscipit nisi. Sed aliquam lacus
+# eget ligula convallis, a accumsan turpis interdum. Pellentesque et turpis
+# feugiat, elementum justo id, efficitur sem.
+#
+# Etiam massa orci, placerat quis dui eget, sollicitudin posuere nulla. Lorem
+# ipsum dolor sit amet, consectetur adipiscing elit. Vivamus elementum euismod
+# erat in rutrum. Nullam ut magna velit. In aliquet eros a venenatis efficitur.
+# Ut dignissim nibh non lectus gravida, id maximus ligula luctus. Pellentesque
+# vitae euismod est, at viverra felis. Donec faucibus nisl non nulla tincidunt
+# dapibus. Nunc venenatis molestie vulputate. Cum sociis natoque penatibus et
+# magnis dis parturient montes, nascetur ridiculus mus. Cras auctor faucibus
+# enim nec venenatis. Nulla varius diam mi, egestas luctus sem gravida ac.
+# Phasellus hendrerit enim augue, sagittis consequat turpis elementum ac. Nam
+# sapien velit, gravida quis sem at, auctor laoreet ex.
diff --git a/test/parse-error-test/nested_multiline_comments/input.ddl b/test/parse-error-test/nested_multiline_comments/input.ddl
index 82e085022..ea73e476a 100644
--- a/test/parse-error-test/nested_multiline_comments/input.ddl
+++ b/test/parse-error-test/nested_multiline_comments/input.ddl
@@ -1 +1 @@
-/* Multi-line comments /* unfortunately cannot be nested */ */
+/* Multi-line comments are not supported */
diff --git a/test/parse-error-test/nested_multiline_comments/parse-error.expected b/test/parse-error-test/nested_multiline_comments/parse-error.expected
index 366b77ddc..cf167b1ef 100644
--- a/test/parse-error-test/nested_multiline_comments/parse-error.expected
+++ b/test/parse-error-test/nested_multiline_comments/parse-error.expected
@@ -1,4 +1,4 @@
-[error] parse-error-test/nested_multiline_comments/input.ddl[1.61] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `*' found
+[error] parse-error-test/nested_multiline_comments/input.ddl[1.1] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `/' found
 
-/* Multi-line comments /* unfortunately cannot be nested */ */
-                                                            ^
+/* Multi-line comments are not supported */
+^

From d9b17cd17c76f4afab76b9871b48b5d9648eb22b Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 9 Jul 2015 17:59:08 -0700
Subject: [PATCH 160/347] Switches Travis settings to use container-based infra

---
 .travis.yml | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index e2b825e41..9d3dd9d73 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,8 +1,16 @@
 language: scala
 scala:
     - "2.11.1"
-before_install:
-    - sudo apt-get install -qq wdiff
+
+sudo: false  # to use container-based infrastructure
+addons:
+    apt:
+        packages:
+            - wdiff
+cache:
+    directories:
+        - $HOME/.ivy2/cache
+
 script:
     - make test MEASURE_COVERAGE=true
 after_success:

From aa9300084848d3a7a914f0ea64f95d5e7ba4f9de Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 9 Jul 2015 19:36:56 -0700
Subject: [PATCH 161/347] Rewrites Makefile for running individual tests

with ONLY= and EXCEPT= make arguments.

Rewrites Makefile and test scripts, refactoring SBT targets to scala.mk
and BATS part to test/bats.mk
---
 .travis.yml                                   |  4 +-
 Makefile                                      | 83 +++++++++----------
 scala.mk                                      | 69 +++++++++++++++
 test/bats-template.bash                       |  6 +-
 test/bats.mk                                  | 37 +++++++++
 test/{test.sh => enumerate-tests.sh}          | 16 ++--
 test/expected-output-test.bats.template       |  2 +-
 test/parse-error-test.bats.template           |  2 +-
 .../parse-error.expected                      |  2 +-
 9 files changed, 159 insertions(+), 62 deletions(-)
 create mode 100644 scala.mk
 create mode 100644 test/bats.mk
 rename test/{test.sh => enumerate-tests.sh} (62%)

diff --git a/.travis.yml b/.travis.yml
index 9d3dd9d73..25f64fbe8 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,7 +11,9 @@ cache:
     directories:
         - $HOME/.ivy2/cache
 
+install:
+    - make test-build
 script:
-    - make test MEASURE_COVERAGE=true
+    - make test
 after_success:
     - sbt coverageReport coveralls
diff --git a/Makefile b/Makefile
index efb9b5f84..a2aa295f5 100644
--- a/Makefile
+++ b/Makefile
@@ -1,59 +1,50 @@
-# Makefile for DeepDiveLogCompiler
+# Makefile for DDlog compiler
 
-SOURCE_DIR = src/main/scala/org/deepdive/ddlog
-TARGET_DIR = target/scala-2.10/classes
-COVERAGE_DIR = $(TARGET_DIR)/../scoverage-data
-TEST_CLASSPATH_CACHE = $(TARGET_DIR)/../dependency-classpath
+
+### Build & Clean #############################################################
+
+# build a standalone jar
 JAR = ddlog.jar
+.PHONY: package
+package: $(JAR)
+$(JAR): scala-assembly-jar
+	ln -sfn $(SCALA_ASSEMBLY_JAR) $@
+	touch $@
+
+.PHONY: clean
+clean: scala-clean
+	# clean test artifacts
+	rm -f $(JAR) $(wildcard test/*/*/*.actual)
+	find test/ -name '*.bats' -type l -exec rm -f {} +
+
+include scala.mk  # defines scala-build, scala-test-build, scala-assembly-jar, scala-clean targets
+
 
-# test
-.PHONY: test
-test: $(TARGET_DIR) $(TEST_CLASSPATH_CACHE)
-	CLASSPATH=$(realpath $<):$(shell cat $(TEST_CLASSPATH_CACHE)) \
-TEST_CLASS_OR_JAR=org.deepdive.ddlog.DeepDiveLog \
-test/test.sh
-$(TEST_CLASSPATH_CACHE): build.sbt $(wildcard project/*.sbt)
-	sbt "export compile:dependency-classpath" | tail -1 >$@
-
-SOURCES = $(wildcard $(SOURCE_DIR)/*.scala)
-ifndef MEASURE_COVERAGE
-$(TARGET_DIR): $(SOURCES)
-	sbt compile
-else
-$(TARGET_DIR): $(COVERAGE_DIR)
-$(COVERAGE_DIR): $(SOURCES)
-	# enabling coverage measurement
-	sbt coverage compile
-endif
+
+### Test ######################################################################
+
+# test prep for built classes or assembly jar
+test-package: $(JAR)
+	$(MAKE) test TEST_JAR=1
+ifndef TEST_JAR
+test-build: scala-test-build
+test: export CLASSPATH = $(shell cat $(SCALA_TEST_CLASSPATH_EXPORTED))
+
+else # ifdef TEST_JAR
+.PHONY: test-package
+test-build: $(JAR)
+test: export CLASSPATH = $(realpath $(JAR))
+
+endif # TEST_JAR
 
 # test coverage report
 .PHONY: test-coverage coveralls
 test-coverage:
-	-$(MAKE) test MEASURE_COVERAGE=true
+	-$(MAKE) test
 	sbt coverageReport
 coveralls: test-coverage
 	# submit coverage data to https://coveralls.io/r/HazyResearch/ddlog
 	# (Make sure you have set COVERALLS_REPO_TOKEN=...)
 	sbt coveralls
 
-# test standalone package
-.PHONY: test-package
-test-package: $(JAR)
-	CLASSPATH= \
-TEST_CLASS_OR_JAR="-jar $(realpath $(JAR))" \
-test/test.sh
-
-# build standalone jar
-.PHONY: package
-package: $(JAR)
-$(JAR): $(wildcard $(SOURCE_DIR)/*.scala)
-	sbt clean assembly
-	ln -sfn $$(ls -t target/scala-*/*-assembly-*.jar | head -1) $@
-	touch $@
-
-.PHONY: clean
-clean:
-	sbt clean
-	# clean test artifacts
-	rm -f $(JAR) $(TEST_CLASSPATH_CACHE) $(wildcard test/*/*/*.actual)
-	find test/ -name '*.bats' -type l -exec rm -f {} +
+include test/bats.mk  # defines test, test-build, test-list targets
diff --git a/scala.mk b/scala.mk
new file mode 100644
index 000000000..f9737debd
--- /dev/null
+++ b/scala.mk
@@ -0,0 +1,69 @@
+# Makefile for Scala ##########################################################
+
+# Why do we use Makefile instead of SBT?
+# - Makefile can build components written in any language.  We use it anyway
+#   for handling dependency and installation.
+# - It's much easier to run integration tests with non-Scala components outside
+#   SBT or ScalaTest.
+# - SBT is slow.
+#
+# How can Makefile build and test Scala code?
+# - By exporting the CLASSPATH and running java directly instead, we can avoid
+#   SBT's poor command-line interface performance.  Note that we try to invoke
+#   SBT as least as possible through out the Makefile, duplicating some commands.
+# - Since there are test-specific classes and dependencies, there has to be two
+#   CLASSPATHs.
+# - When built for tests, the classes are instrumented such that coverage can
+#   be measured.
+
+# Some path names for Scala
+SCALA_BUILD_FILES             = build.sbt $(wildcard project/*.*)
+SCALA_MAIN_SOURCES            = $(shell find src/main/scala -name '*.scala' 2>/dev/null)
+SCALA_MAIN_CLASSES_DIR        = target/scala-2.10/classes
+SCALA_MAIN_CLASSPATH_EXPORTED = target/scala-2.10/classpath
+SCALA_TEST_SOURCES            = $(shell find src/test/scala -name '*.scala' 2>/dev/null)
+SCALA_TEST_CLASSES_DIR        = target/scala-2.10/test-classes
+SCALA_TEST_CLASSPATH_EXPORTED = target/scala-2.10/test-classpath
+SCALA_COVERAGE_DIR            = target/scala-2.10/scoverage-data
+SCALA_ASSEMBLY_JAR            = target/scala-2.10/*-assembly-*.jar
+
+# SBT settings
+PATH := $(PATH):$(shell pwd)/sbt
+SBT_OPTS ?= -Xmx4g -XX:MaxHeapSize=4g -XX:MaxPermSize=4g
+export SBT_OPTS
+
+.PHONY: scala-build
+scala-build: $(SCALA_MAIN_CLASSES_DIR) $(SCALA_MAIN_CLASSPATH_EXPORTED)
+# How to build main Scala code and export main CLASSPATH
+$(SCALA_MAIN_CLASSES_DIR): $(SCALA_MAIN_SOURCES) $(SCALA_BUILD_FILES)
+	# Compiling Scala code
+	sbt compile
+	touch $(SCALA_MAIN_CLASSES_DIR)
+$(SCALA_MAIN_CLASSPATH_EXPORTED): $(SCALA_BUILD_FILES)
+	# Exporting CLASSPATH
+	sbt --error "export compile:full-classpath" | tee /dev/stderr | \
+	    tail -1 >$@
+
+# How to build test Scala code with coverage and export test CLASSPATH
+.PHONY: scala-test-build
+scala-test-build: $(SCALA_COVERAGE_DIR) $(SCALA_TEST_CLASSES_DIR) $(SCALA_TEST_CLASSPATH_EXPORTED)
+$(SCALA_COVERAGE_DIR) $(SCALA_TEST_CLASSES_DIR): $(SCALA_MAIN_SOURCES) $(SCALA_TEST_SOURCES) $(SCALA_BUILD_FILES)
+	# Compiling Scala code for test with coverage
+	sbt coverage compile test:compile
+	touch $(SCALA_COVERAGE_DIR) $(SCALA_TEST_CLASSES_DIR)
+$(SCALA_TEST_CLASSPATH_EXPORTED): $(SCALA_BUILD_FILES)
+	# Exporting CLASSPATH for tests
+	sbt --error coverage "export test:full-classpath" | tee /dev/stderr | \
+	    tail -1 | tee $(SCALA_MAIN_CLASSPATH_EXPORTED) >$@
+
+# How to build an assembly jar
+.PHONY: scala-assembly-jar
+scala-assembly-jar: $(SCALA_ASSEMBLY_JAR)
+$(SCALA_ASSEMBLY_JAR): $(SCALA_MAIN_SOURCES) $(SCALA_BUILD_FILES)
+	sbt clean assembly
+
+# How to clean
+.PHONY: scala-clean
+scala-clean:
+	sbt clean
+	rm -f $(SCALA_MAIN_CLASSPATH_EXPORTED) $(SCALA_TEST_CLASSPATH_EXPORTED) $(SCALA_ASSEMBLY_JAR)
diff --git a/test/bats-template.bash b/test/bats-template.bash
index 319ed5004..698afa401 100644
--- a/test/bats-template.bash
+++ b/test/bats-template.bash
@@ -1,9 +1,6 @@
 #!/usr/bin/env bash
 # Utilities for testing with Bats
 
-# required variables
-: ${TEST_CLASS_OR_JAR:?class name or -jar with the path to the ddlog.jar to test}
-
 # some shorthands
 TESTDIR=${BATS_TEST_FILENAME%.bats}
 TESTDIR=${TESTDIR#$PWD/}
@@ -12,8 +9,9 @@ it="${TEST%.bats}:"
 
 # how to invoke ddlog compiler
 ddlog() {
-    java $TEST_CLASS_OR_JAR "$@"
+    java org.deepdive.ddlog.DeepDiveLog "$@"
 }
+
 # how to diff (prefer wdiff)
 if type wdiff &>/dev/null; then
     if ${TRAVIS:-false}; then
diff --git a/test/bats.mk b/test/bats.mk
new file mode 100644
index 000000000..36f2bb906
--- /dev/null
+++ b/test/bats.mk
@@ -0,0 +1,37 @@
+# A Makefile fragment for running tests with BATS
+#
+# Author: Jaeho Shin <netj@cs.stanford.edu>
+# Created: 2015-07-09
+
+# some default locations
+TEST_ROOT = test
+TEST_LIST_COMMAND = $(TEST_ROOT)/enumerate-tests.sh
+BATS_ROOT = $(TEST_ROOT)/bats
+export TEST_ROOT
+
+.PHONY: test test-build test-list
+# One can fine-tune the list of tests by setting environment variables
+# TEST_ONLY and TEST_EXCEPT, or passing the same glob patterns as Make
+# arguments ONLY and EXCEPT, e.g.:
+#   $ make test ONLY+=$(TEST_ROOT)/foo/*.bats EXCEPT+=$(TEST_ROOT)/*/unit_tests.bats
+#   $ TEST_ONLY=$(TEST_ROOT)/foo/*.bats  make test EXCEPT+=$(TEST_ROOT)/*/unit_tests.bats
+#   $ TEST_ONLY=$(TEST_ROOT)/foo/*.bats TEST_EXCEPT=$(TEST_ROOT)/*/unit_tests.bats   make test
+TEST_ONLY ?= $(shell $(TEST_LIST_COMMAND))
+TEST_EXCEPT ?=
+test: ONLY = $(TEST_ONLY)
+test: EXCEPT = $(TEST_EXCEPT)
+test: BATS_FILES = $(filter-out $(wildcard $(EXCEPT)),$(wildcard $(ONLY)))
+test: $(BATS_ROOT)/bin/bats $(BATS_FILES) test-build
+	# Running $(shell $(TEST_ROOT)/bats/bin/bats -c $(BATS_FILES)) tests defined in $(words $(BATS_FILES)) .bats files
+	#  To test selectively, run:  make test   ONLY+=/path/to/bats/files
+	#  To exclude certain tests:  make test EXCEPT+=/path/to/bats/files
+	#  For a list of tests, run:  make test-list
+	$(BATS_ROOT)/bin/bats  $(BATS_FILES)
+test-build:
+$(BATS_ROOT)/bin/bats:
+	git submodule update --init $(BATS_ROOT)
+test-list:
+	@echo "make test \\"
+	@$(TEST_LIST_COMMAND) | sed 's/$$/ \\/; s/^/   ONLY+=/p; s/^   ONLY+=/ EXCEPT+=/'
+	@echo " #"
+
diff --git a/test/test.sh b/test/enumerate-tests.sh
similarity index 62%
rename from test/test.sh
rename to test/enumerate-tests.sh
index cf48bf7dc..7baf9b6c8 100755
--- a/test/test.sh
+++ b/test/enumerate-tests.sh
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash
+# A script for enumerating all .bats files after instantiating any templates
 set -eu
-shopt -s nullglob
-cd "$(dirname "$0")"
 
-# make sure bats is available
-PATH="$PWD/bats/bin:$PATH"
+: ${TEST_ROOT:=test}
+
+( cd "$(dirname "$0")"
 
 # instantiate bats tests templates under its directory
 for t in *.bats.template; do
@@ -14,11 +14,11 @@ for t in *.bats.template; do
     # create a .bats symlink for each test specification
     for testSpec in "$testSpecDir"/*; do
         [[ -d "$testSpec" ]] || continue
-        testSpec=${testSpec%/input.ddl}
         batsFile="$testSpec".bats
-        ln -sfn ../"$t" "$batsFile"
+        ln -sfn ../"$(basename "$t")" "$batsFile"
+        echo "$TEST_ROOT/$batsFile"
     done
 done
+)
 
-# run all .bats tests
-bats "$@" *.bats */*.bats
+ls "$TEST_ROOT"/*.bats 2>/dev/null
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index d37846df3..2f83395c8 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -4,7 +4,7 @@
 # These test cases compares outputs of various modes of ddlog against a .ddl example file with its expected output.
 # Tests are skipped if no expected output is found.
 
-source bats-template.bash  # for $TESTDIR, $it, etc.
+source "$BATS_TEST_DIRNAME"/../bats-template.bash  # for $TESTDIR, $it, etc.
 
 # some preconditions
 setup() {
diff --git a/test/parse-error-test.bats.template b/test/parse-error-test.bats.template
index b15cc80d5..35b9020b8 100644
--- a/test/parse-error-test.bats.template
+++ b/test/parse-error-test.bats.template
@@ -3,7 +3,7 @@
 # 
 # The test case here feeds a malformed .ddl into ddlog's print command and compares whether it produces an expected error.
 
-source bats-template.bash  # for $TESTDIR, $it, etc.
+source "$BATS_TEST_DIRNAME"/../bats-template.bash  # for $TESTDIR, $it, etc.
 
 # some preconditions
 setup() {
diff --git a/test/parse-error-test/nested_multiline_comments/parse-error.expected b/test/parse-error-test/nested_multiline_comments/parse-error.expected
index cf167b1ef..39ddabdaf 100644
--- a/test/parse-error-test/nested_multiline_comments/parse-error.expected
+++ b/test/parse-error-test/nested_multiline_comments/parse-error.expected
@@ -1,4 +1,4 @@
-[error] parse-error-test/nested_multiline_comments/input.ddl[1.1] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `/' found
+[error] test/parse-error-test/nested_multiline_comments/input.ddl[1.1] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `/' found
 
 /* Multi-line comments are not supported */
 ^

From b10019c21fcfc99ee0542f69c20abd6f34d8c268 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 9 Jul 2015 20:43:52 -0700
Subject: [PATCH 162/347] Refactor expressions and conditions

Allow recursive and nested expressions/conditions
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 157 ++++++++----------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  27 +--
 .../ddlog/DeepDiveLogMergeDeriver.scala       |   6 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 142 ++++++++--------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  55 +++---
 .../expressions/compile.expected              |  24 ++-
 .../expressions/input.ddl                     |   4 +-
 .../expressions/print.expected                |   4 +-
 8 files changed, 201 insertions(+), 218 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 8c3cfe542..cdb9521ac 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -176,7 +176,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // Resolve a column name with alias
-  def resolveColumn(s: String, qs: QuerySchema, q : ConjunctiveQuery, alias: AliasStyle) : Option[String] = {
+  def resolveColumn(s: String, q : ConjunctiveQuery, alias: AliasStyle) : Option[String] = {
+    val qs = new QuerySchema(q)
     val index = qs.getBodyIndex(s)
     val name  = resolveName(qs.getVar(s))
     val relation = q.bodies(0)(index).name
@@ -187,36 +188,44 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
   }
 
-  def resolveColumnVar(v: ColumnVariable, cq: ConjunctiveQuery, alias: AliasStyle = OriginalOnly) = {
-    val qs = new QuerySchema(cq)
-    def resolveVarOrConst(x: ColumnVariable, alias: AliasStyle) = {
-      x match {
-        case Variable(v,r,i) => resolveColumn(v, qs, cq, alias).get
-        case Constant(v,r,i) => v
-        case _ => ""
-      }
-    }
-    v match {
-      case InlineFunction(name, args, agg) => {
-        val resolvedArgs = args map (resolveVarOrConst(_, OriginalOnly))
-        val resolved = s"${name}(${resolvedArgs.mkString(", ")})"
-        val aggAlias = if (agg) { args(0) match {
-          case Variable(v,r,i) => s""" AS "${name}_${resolveColumn(v, qs, cq, OriginalOnly).get}"""" // "
-          case _ => ""
-        }} else ""
-        resolved + aggAlias
+  // resolve an expression
+  def resolveExpr(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle, index : Int, isHead: Boolean) : String = {
+    def recurse(e: Expr, alias: AliasStyle, depth: Int) : String = {
+      // for columns without a name (constant, function call, binary operator), add an column index alias if necessary
+      val columnAlias = if (depth == 0 && isHead) s" AS column_${index}" else ""
+      e match {
+        case VarExpr(name) => resolveColumn(name, cq, alias).get
+        case ConstExpr(value) => value + columnAlias
+        case FuncExpr(function, args, agg) => {
+          val resolvedArgs = args map (x => recurse(x, OriginalOnly, depth + 1))
+          val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
+          resolved + columnAlias
+        }
+        case BinaryOpExpr(lhs, op, rhs) => {
+          val resovledLhs = recurse(lhs, OriginalOnly, depth + 1)
+          val resovledRhs = recurse(rhs, OriginalOnly, depth + 1)
+          s"${resovledLhs} ${op} ${resovledRhs}${columnAlias}"
+        }
       }
-      case _ => resolveVarOrConst(v, alias)
     }
+    recurse(e, alias, 0)
   }
 
-  def resolveExpr(e: Expression, cq: ConjunctiveQuery, alias: AliasStyle) = {
-    val resolvedVars = e.ops isEmpty match {
-      case true  => e.variables map (resolveColumnVar(_, cq, alias))
-      case false => e.variables map (resolveColumnVar(_, cq, OriginalOnly))
+  // resolve a condition
+  def resolveCond(cond: Cond, cq: ConjunctiveQuery) : String = {
+    cond match {
+      case ComparisonCond(lhs, op, rhs) => 
+        s"${resolveExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${resolveExpr(rhs, cq, OriginalOnly, 0, false)}"
+      case NegationCond(c) => s"NOT (${resolveCond(c, cq)})"
+      case BinaryOpCond(lhs, op, rhs) => {
+        val resolvedLhs = s"${resolveCond(lhs, cq)}"
+        val resolvedRhs = s"${resolveCond(rhs, cq)}"
+        op match {
+          case LogicOperator.AND => s"(${resolvedLhs}) AND (${resolvedRhs})" 
+          case LogicOperator.OR  => s"(${resolvedLhs}) OR (${resolvedRhs})"
+        }
+      }
     }
-    val rest = ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString(" ")
-    resolvedVars(0) + (if (rest != "") " " + rest else "")
   }
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
@@ -229,60 +238,40 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
     var whereClause = z.bodies(0).zipWithIndex flatMap {
       case (Atom(relName, terms),bodyIndex) => {
-        terms flatMap { case Expression(vars, ops, relName, index) =>
-          // simple variable
-          val simpleVar = (ops isEmpty) && (vars(0) match {
-            case x: Variable => true
-            case _ => false
-          })
-          if (simpleVar) {
-            vars(0) match {
-              case Variable(varName,relName,index) => {
-                val canonical_body_index = qs.getBodyIndex(varName)
-                if (canonical_body_index != bodyIndex) {
-                  val real_attr_name1 = resolveName( Variable(varName, relName, index) )
-                  val real_attr_name2 = resolveName( qs.getVar(varName))
-                  Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
-                } else { None }
-              }
-              case _ => None
+        terms flatMap { case ColumnExpr(expr, relName, index) =>
+          expr match {
+            // a simple variable
+            case VarExpr(varName) => {
+              val canonical_body_index = qs.getBodyIndex(varName)
+              if (canonical_body_index != bodyIndex) {
+                val real_attr_name1 = resolveName( Variable(varName, relName, index) )
+                val real_attr_name2 = resolveName( qs.getVar(varName))
+                Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+              } else { None }
+            }
+            // other expressions
+            case _ => {
+              val resolved = resolveExpr(expr, z, OriginalOnly, index, false)
+              val attr = schema(relName, index)
+              Some(s"R${bodyIndex}.${attr} = ${resolved}")
             }
-          } else { // expression
-            val expr = resolveExpr(Expression(vars, ops, relName, index), z, OriginalOnly)
-            val attr = schema(relName, index)
-            Some(s"R${bodyIndex}.${attr} = ${expr}")
           }
         }
       }
     }
 
     // resolve conditions
-    val conditionList = z.conditions(0) match {
-      case Some(c) => c.conditions map { case x: List[Condition] =>
-        val inner = x map { case Condition(lhs, op, rhs) =>
-          val lhsExpr = DeepDiveLogPrettyPrinter.printExpr(lhs, resolveColumnVar(_,z))
-          val rhsExpr = DeepDiveLogPrettyPrinter.printExpr(rhs, resolveColumnVar(_,z))
-          s"${lhsExpr} ${op} ${rhsExpr}"
-        }
-        inner.mkString(" AND ")
-      }
-      case None => List("")
+    val conditionStr = z.conditions(0) match {
+      case Some(c) => resolveCond(c, z)
+      case None    => ""
     }
 
-    val conditions = conditionList flatMap ( v => if (v != "") Some(s"(${v})") else None)
-    val conditionStr = conditions.mkString(" OR ")
-    
     // handle group by
     // map head terms, leaving out aggregation functions
-    val groupbyTerms = z.head.terms flatMap { case Expression(vars, ops, relName, index) =>
-      if (ops isEmpty) {
-        vars(0) match {
-          case InlineFunction(name, args, a) => if (a) None else Some("")
-          case Variable(v,r,i) => resolveColumn(v, qs, z, OriginalOnly)
-          case _ => Some("")
-        }
-      } else {
-        Some("")
+    val groupbyTerms = z.head.terms map { case ColumnExpr(expr, relName, index) =>
+      expr match {
+        case FuncExpr(f, args, agg) => if (agg) None else Some("")
+        case _ => Some(resolveExpr(expr, z, OriginalOnly, index, false))
       }
     }
 
@@ -371,14 +360,12 @@ class QuerySchema(q : ConjunctiveQuery) {
   def generateCanonicalVar()  = {
     q.bodies(0).zipWithIndex.foreach {
       case (Atom(relName,terms),index) =>  {
-        terms.foreach { case Expression(c, op, r, i) =>
-          if (op.isEmpty) {
-            c(0) match {
-              case Variable(v,r,i) =>
-                if (! (query_schema contains v) )
-                  query_schema += { v -> (index, Variable(v,r,i) ) }
-              case _ =>
-            }
+        terms.foreach { case ColumnExpr(expr, r, i) =>
+          expr match {
+            case VarExpr(v) => 
+              if (! (query_schema contains v) )
+                query_schema += { v -> (index, Variable(v,r,i) ) }
+            case _ =>
           }
         }
       }
@@ -453,8 +440,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = tmpCq.head.terms map { x => 
-            DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, OriginalOnly))
+          val headTerms = tmpCq.head.terms map { case ColumnExpr(expr, _, index) => 
+            ss.resolveExpr(expr, tmpCq, OriginalOnly, index, true)
           }
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
@@ -464,8 +451,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = tmpCq.head.terms map { x => 
-            DeepDiveLogPrettyPrinter.printExpr(x, ss.resolveColumnVar(_, tmpCq, OriginalOnly))
+          val headTerms = tmpCq.head.terms map { case ColumnExpr(expr, _, index) => 
+            ss.resolveExpr(expr, tmpCq, OriginalOnly, index, true)
           }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
@@ -482,8 +469,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case true => OriginalOnly
             case false => OriginalAndAlias
           }
-          val variableCols = tmpCq.head.terms map { x => 
-            ss.resolveExpr(x, tmpCq, resolveColumnFlag)
+          val variableCols = tmpCq.head.terms map { case ColumnExpr(expr, _, index) => 
+            ss.resolveExpr(expr, tmpCq, resolveColumnFlag, index, true)
           }
           val selectStr = variableCols.mkString(", ")
           val distinctStr = if (tmpCq.isDistinct) "DISTINCT" else ""
@@ -579,7 +566,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // weight string
         val uwStr = stmt.weights match {
           case KnownFactorWeight(x) => None
-          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, OriginalAndAlias)).mkString(", "))
+          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, fakeCQ, OriginalAndAlias)).mkString(", "))
         }
 
         val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
@@ -607,7 +594,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              val weightVar = w.flatMap(s => ss.resolveColumn(s, qs2, fakeCQ, AliasOnly)).mkString(", ")
+              val weightVar = w.flatMap(s => ss.resolveColumn(s, fakeCQ, AliasOnly)).mkString(", ")
               if (weightVar == "") "?"
               else s"?(${weightVar})"
             }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 1aa958c7e..d250fcbc2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -19,45 +19,36 @@ object DeepDiveLogDeltaDeriver{
   }
 
   def transform(cq: ConjunctiveQuery, isInference: Boolean, mode: String): ConjunctiveQuery = {
-    // transform an expression
-    def transformExpression(expr: Expression, prefix: String) = {
-      val newVars = expr.variables map {
-        case term: Variable => term.copy(relName = prefix + term.relName)
-        case term: Constant => term
-        case term: InlineFunction => term
-      }
-      Expression(newVars, expr.ops, expr.relName, expr.index)
-    }
 
     // New head
     val incCqHead = if (isInference) {
       cq.head.copy(
         name = newPrefix + cq.head.name,
-        terms = cq.head.terms map (transformExpression(_, newPrefix))
+        terms = cq.head.terms
       )
     } else {
       cq.head.copy(
         name = deltaPrefix + cq.head.name,
-        terms = cq.head.terms map (transformExpression(_, deltaPrefix))
+        terms = cq.head.terms
       )
     }
 
     var incCqBodies = new ListBuffer[List[Atom]]()
-    var incCqConditions = new ListBuffer[Option[CompoundCondition]]()
+    var incCqConditions = new ListBuffer[Option[Cond]]()
     // New incremental bodies
     cq.bodies zip cq.conditions foreach { case (body, cond) =>
       // Delta body
       val incDeltaBody = body map {
         a => a.copy(
           name = deltaPrefix + a.name,
-          terms = a.terms map (transformExpression(_, deltaPrefix))
+          terms = a.terms
         )
       }
       // New body
       val incNewBody = body map {
         a => a.copy(
           name = newPrefix + a.name,
-          terms = a.terms map (transformExpression(_, newPrefix))
+          terms = a.terms
         )
       }
       var i = 0
@@ -114,10 +105,10 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement += incNewStmt
 
     // from schema declaration to expressions
-    def variableToExpr(v: Variable) = Expression(List(v), List(), v.relName, v.index)
-    val originalExpr = stmt.a.terms map (variableToExpr(_))
-    val incDeltaExpr = incDeltaStmt.a.terms map (variableToExpr(_))
-    val incNewExpr = incNewStmt.a.terms map (variableToExpr(_))
+    def variableToExpr(v: Variable) = ColumnExpr(VarExpr(v.varName), v.relName, v.index)
+    val originalExpr = stmt.a.terms map variableToExpr
+    val incDeltaExpr = incDeltaStmt.a.terms map variableToExpr
+    val incNewExpr = incNewStmt.a.terms map variableToExpr
 
     // if (!stmt.isQuery) {
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index 6ab4d6666..cbc73c0c3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -19,9 +19,9 @@ object DeepDiveLogMergeDeriver{
       )
     )
 
-    def variableToExpr(v: Variable) = Expression(List(v), List(), v.relName, v.index)
-    val originalExpr = stmt.a.terms map (variableToExpr(_))
-    val incNewExpr = incNewStmt.a.terms map (variableToExpr(_))
+    def variableToExpr(v: Variable) = ColumnExpr(VarExpr(v.varName), v.relName, v.index)
+    val originalExpr = stmt.a.terms map variableToExpr
+    val incNewExpr = incNewStmt.a.terms map variableToExpr
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, originalExpr),
       List(List(Atom(incNewStmt.a.name, incNewExpr))), List(None), false))
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 4d09d5c7e..88beb4d0b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -15,21 +15,34 @@ import scala.util.Try
 // ddlog column variable type: constant or variable
 sealed trait ColumnVariable
 case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
-case class Constant(value : String, relName: String, index: Int) extends ColumnVariable
-case class InlineFunction(functionName: String, args: List[ColumnVariable], isAggregation: Boolean) extends ColumnVariable
+
 case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int)
+case class ColumnExpr(expr: Expr, relName: String, index: Int)
 case class Operator(operator: String, operand: ColumnVariable)
 
-case class Atom(name : String, terms : List[Expression])
+sealed trait Expr
+case class VarExpr(name: String) extends Expr
+case class ConstExpr(value: String) extends Expr
+case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
+case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
+
+case class Atom(name : String, terms : List[ColumnExpr])
 case class Attribute(name : String, terms : List[Variable], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[CompoundCondition]], isDistinct: Boolean)
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], isDistinct: Boolean)
 case class Column(name : String, t : String)
+case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 
 // condition
-case class BodyWithConditions(body: List[Atom], conditions: Option[CompoundCondition])
-
-case class Condition(lhs: Expression, op: String, rhs: Expression)
-case class CompoundCondition(conditions: List[List[Condition]])
+sealed trait Cond
+case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
+case class NegationCond(cond: Cond) extends Cond
+case class BinaryOpCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
+
+// logic operators
+object LogicOperator extends Enumeration {
+  type LogicOperator = Value
+  val  AND, OR = Value
+}
 
 // variable type
 sealed trait VariableType {
@@ -66,7 +79,6 @@ case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) exte
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
 case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, semantics : String = "Imply", mode: String = null) extends Statement // Weighted rule
 
-
 // Parser
 class DeepDiveLogParser extends JavaTokenParsers {
 
@@ -120,84 +132,74 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
-  def operator = "||" | "+" | "-" | "*" | "/" | "&"
-  def castOp = "::"
-
-  def variable = variableName ^^ { Variable(_, "", 0) }
-  def columnConstant = constant ^^ { Constant(_, "", 0) }
-  def variableOrConstant = columnConstant | variable
+  def operator = "||" | "+" | "-" | "*" | "/" | "&" | "::"
   val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG")
-  def inlineFunction = functionName ~ "(" ~ rep1sep(variableOrConstant, ",") ~ ")" ^^ {
-    case (name ~ _ ~ args ~ _) => {
-      if (aggregationFunctions contains name) InlineFunction(name, args, true)
-      else InlineFunction(name, args, false)
-    }
-  }
-  def columnVariable = columnConstant | inlineFunction | variable
-  def operateOn = operator ~ columnVariable ^^ { case (v ~ o) => Operator(v,o) }
-  def typecast = castOp ~ columnConstant ^^ { case (v ~ o) => Operator(v,o) }
-  def operatorAndOperand = operateOn | typecast
-  def expression = columnVariable ~ rep(operatorAndOperand) ^^ {
-    case (v ~ opList) => {
-      val variables = List(v) ++ (opList map (_.operand))
-      val ops = opList map (_.operator)
-      Expression(variables, ops, "", 0)
-    }
-  }
+
+  // expressions
+  def expr : Parser[Expr] =
+    ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    | lexpr
+    )
+
+  def lexpr : Parser[Expr] =
+    ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ { 
+        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
+      }
+    | constant ^^ { ConstExpr(_) }
+    | variableName ^^ { VarExpr(_) }
+    | "(" ~> expr <~ ")" 
+    )
 
   // TODO support aggregate function syntax somehow
-  def cqHead = relationName ~ "(" ~ repsep(expression, ",") ~ ")" ^^ {
+  def cqHead = relationName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
       case (r ~ "(" ~ variableUses ~ ")") =>
         Atom(r, variableUses.zipWithIndex map {
-          case (Expression(v,op,_,_),i) => {
-            val vars = v map {
-              case Variable(x,_,_) => Variable(x,r,i)
-              case Constant(x,_,_) => Constant(x,r,i)
-              case InlineFunction(x, args, a) => InlineFunction(x, args, a)
-            }
-            Expression(vars, op, r, i)
-          }
+          case (e,i) => ColumnExpr(e, r, i)
         })
     }
 
-  // TODO add conditional expressions for where clause
-  def cqConditionalExpr = failure("No conditional expression supported yet")
-  def cqBodyAtom: Parser[Atom] =
-    ( relationName ~ "(" ~ repsep(expression, ",") ~ ")" ^^ {
-        case (r ~ "(" ~ variableBindings ~ ")") =>
-          Atom(r, variableBindings.zipWithIndex map {
-          case (Expression(v,op,_,_),i) => {
-            val vars = v map {
-              case Variable(x,_,_) => Variable(x,r,i)
-              case Constant(x,_,_) => Constant(x,r,i)
-              case InlineFunction(x, args, _) => InlineFunction(x, args, false)
-            }
-            Expression(vars, op, r, i)
-          }
-        })
+  // conditional expressions
+  def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
+  def cond : Parser[Cond] = 
+    ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
+        BinaryOpCond(lhs, LogicOperator.OR, rhs)
       }
-    | cqConditionalExpr
+    | acond
+    )
+  def acond : Parser[Cond] = 
+    ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => BinaryOpCond(lhs, LogicOperator.AND, rhs) }
+    | lcond
+    )
+  // ! has higher priority...
+  def lcond : Parser[Cond] = 
+    ( "!" ~> bcond ^^ { NegationCond(_) }
+    | bcond
+    )
+  def bcond : Parser[Cond] = 
+    ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) =>
+        ComparisonCond(lhs, op, rhs)
+      }
+    | "[" ~> cond <~ "]"
     )
-  def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
 
-  // conditions
-  def filterOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
-  def condition = expression ~ filterOperator ~ expression ^^ {
-    case (lhs ~ op ~ rhs) => {
-      Condition(lhs, op, rhs)
+  def cqBodyAtom: Parser[Atom] =
+    relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
+      case (r ~ "(" ~ variableBindings ~ ")") =>
+        Atom(r, variableBindings.zipWithIndex map {
+        case (e,i) => ColumnExpr(e, r, i)
+      })
     }
-  }
-  def conjunctiveCondition = repsep(condition, ",")
-  def compoundCondition = opt("[") ~> repsep(conjunctiveCondition, ";") <~ opt("]") ^^ { CompoundCondition(_) }
-  def cqBodyWithCondition = cqBody ~ ("," ~> compoundCondition).? ^^ {
-    case (b ~ c) => BodyWithConditions(b, c)
+  def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
+
+  def cqBodyWithCondition = cqBody ~ ("," ~> cond).? ^^ {
+    case (b ~ c) => BodyWithCondition(b, c)
   }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
     cqHead ~ opt("*") ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
       case (headatom ~ isDistinct ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.conditions), isDistinct != None)
-    }
+        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.condition), isDistinct != None)
+  }
 
   def relationType: Parser[RelationType] =
     ( "like" ~> relationName ^^ { RelationTypeAlias(_) }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index fe04a460c..a3c41ca23 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -48,39 +48,40 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
        |""".stripMargin
   }
 
-  def printVarOrConst(x: ColumnVariable) = {
-    x match {
-      case x: Variable => x.varName
-      case x: Constant => {
-        if (x.value.startsWith("'"))
-          s""" "${x.value.stripPrefix("'").stripSuffix("'")}" """
-        else
-          x.value
+  // print an expression
+  def printExpr(e: Expr) : String = {
+    e match {
+      case VarExpr(name) => name
+      case ConstExpr(value) => {
+        if (value.startsWith("'")) s""" "${value.stripPrefix("'").stripSuffix("'")}" """
+        else value
       }
-      case _ => ""
+      case FuncExpr(function, args, agg) => {
+        val resolvedArgs = args map (x => printExpr(x))
+        s"${function}(${resolvedArgs.mkString(", ")})"
+      }
+      case BinaryOpExpr(lhs, op, rhs) => s"${printExpr(lhs)} ${op} ${printExpr(rhs)}"
     }
   }
 
-  def printColumnVar(x: ColumnVariable) = {
-    x match {
-      case InlineFunction(name, args, _) => {
-        val resolvedArgs = args map printVarOrConst
-        s"${name}(${resolvedArgs.mkString(", ")})"
+  // print a condition
+  def printCond(cond: Cond) : String = {
+    cond match {
+      case ComparisonCond(lhs, op, rhs) => s"${printExpr(lhs)} ${op} ${printExpr(rhs)}"
+      case NegationCond(c) => s"![${printCond(c)}]"
+      case BinaryOpCond(lhs, op, rhs) => {
+        op match {
+          case LogicOperator.AND => s"[${printCond(lhs)}], [${printCond(rhs)}]" 
+          case LogicOperator.OR  => s"[${printCond(lhs)}]; [${printCond(rhs)}]"
+        }
       }
-      case _ => printVarOrConst(x)
     }
   }
 
-  def printExpr(e: Expression, resolve: ColumnVariable => String) = {
-    val resolvedVars = e.variables map (resolve(_))
-    val rest = ((e.ops zip resolvedVars.drop(1)).map { case (a,b) => s"${a} ${b}" }).mkString(" ")
-    resolvedVars(0) + (if (rest != "") " " + rest else "")
-  }
-
   def print(cq: ConjunctiveQuery): String = {
     val printAtom = {a:Atom =>
       val vars = a.terms map { 
-        case e => printExpr(e, printColumnVar)
+        case e => printExpr(e.expr)
       }
       s"${a.name}(${vars.mkString(", ")})"
     }
@@ -88,20 +89,14 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       s"${(a map printAtom).mkString(",\n    ")}"
     }
 
-    val printConjunctiveCondition = {a: List[Condition] =>
-      (a map { case Condition(lhs, op, rhs) => 
-        val lhsExpr = printExpr(lhs, printColumnVar)
-        val rhsExpr = printExpr(rhs, printColumnVar)
-        s"${lhsExpr} ${op} ${rhsExpr}" }).mkString(", ")
-    }
     val conditionList = cq.conditions map {
-      case Some(x) => Some(x.conditions map printConjunctiveCondition mkString("; "))
+      case Some(x) => Some(printCond(x))
       case None    => None
     }
     val bodyList = cq.bodies map printListAtom
     val bodyWithCondition = (bodyList zip conditionList map { case(a,b) => 
       b match {
-        case Some(c) => s"${a}, [ ${c} ]" 
+        case Some(c) => s"${a}, ${c}" 
         case None    => a
       }
     }).mkString(";\n    ")
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 090108a90..3ce87caa8 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -55,16 +55,24 @@
           style: "sql_extractor"
         }
 
+      deepdive.extraction.extractors.extraction_rule_4 {
+        sql: """ DROP VIEW IF EXISTS P;
+        CREATE VIEW P AS 
+            SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS column_2
+            FROM a R0, b R1
+        WHERE R1.k = R0.k  
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
-            SELECT DISTINCT 'test' :: TEXT, 123, R0.k AS "a.R0.k" , unnest(R1.q)
+            SELECT DISTINCT 'test' :: TEXT AS column_0, 123 AS column_1, R0.k AS "a.R0.k" , unnest(R1.q) AS column_3
             FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR (R1.r < 20 AND R1.r > 10)) UNION ALL 
-            SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS "MAX_R1.r"
-            FROM a R0, b R1
-        WHERE R1.k = R0.k  
-        GROUP BY R1.p, R1.q
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR ((NOT (R1.r < 20)) AND (R1.r < 50)))
         """
         style: "sql_extractor"
           
@@ -72,6 +80,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_3]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_3]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_4, extraction_rule_3]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_4, extraction_rule_3]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 0795e99bb..f0ba156c5 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -2,6 +2,6 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q("test" :: TEXT, 123, id, unnest(y)) * :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; z < 20, z > 10].
+Q("test" :: TEXT, 123, id, unnest(y)) * :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; !z < 20, z < 50].
 
-Q(y, z, MAX(w)) :- a(x), b(x,y,z,w).
\ No newline at end of file
+P(y, z, MAX(w)) :- a(x), b(x,y,z,w).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index f6312d0b2..97d9a9859 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -12,9 +12,9 @@ c(s text,
 Q( "test"  :: TEXT, 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c(x || y, 10,  "foo" ), [ z > 100; z < 20, z > 10 ].
+    c(x || y, 10,  "foo" ), [z > 100]; [[![z < 20]], [z < 50]].
 
-Q(y, z, MAX(w))  :-
+P(y, z, MAX(w))  :-
     a(x),
     b(x, y, z, w).
 

From 199b7e30cc6be3e1a4d1cc03dccb04095eaa033b Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 10 Jul 2015 14:30:12 -0700
Subject: [PATCH 163/347] Add traling "/" to ${APP_HOME}, remove leading "/" in
 udf

---
 examples/chunking.ddl                         |  4 +--
 examples/spouse_example.ddl                   |  6 ++--
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  2 +-
 .../spouse_example/print-incremental.expected | 28 ++++++++---------
 .../spouse_example/print.expected             | 16 +++++-----
 .../spouse_example_new_feature/input.ddl      |  6 ++--
 .../print-incremental.expected                | 28 ++++++++---------
 .../spouse_example_new_inference/input.ddl    |  6 ++--
 .../print-incremental.expected                | 30 +++++++++----------
 .../print.expected                            | 18 +++++------
 10 files changed, 72 insertions(+), 72 deletions(-)

diff --git a/examples/chunking.ddl b/examples/chunking.ddl
index 1ef26623d..f73307681 100644
--- a/examples/chunking.ddl
+++ b/examples/chunking.ddl
@@ -23,7 +23,7 @@ tag?(word_id bigint) Categorical(13).
 function ext_training 
   over like words_raw
   returns like words
-  implementation "/udf/ext_training.py" handles tsv lines.
+  implementation "udf/ext_training.py" handles tsv lines.
 
 words :- !ext_training(words_raw).
 
@@ -34,7 +34,7 @@ ext_features_input(word_id1, word1, pos1, word2, pos2) :-
 function ext_features
   over like ext_features_input
   returns like word_features
-  implementation "/udf/ext_features.py" handles tsv lines.
+  implementation "udf/ext_features.py" handles tsv lines.
 
 word_features :- !ext_features(ext_features_input).
 
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index b6fd72021..040545fce 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -42,7 +42,7 @@ ext_people_input(s, words, ner_tags) :-
 
 function ext_people over like ext_people_input
                  returns like people_mentions
-  implementation "/udf/ext_people.py" handles tsv lines.
+  implementation "udf/ext_people.py" handles tsv lines.
 
 has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
@@ -53,7 +53,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
-  implementation "/udf/ext_has_spouse.py" handles tsv lines.
+  implementation "udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
   !ext_has_spouse_features(ext_has_spouse_features_input).
@@ -66,7 +66,7 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
-  implementation "/udf/ext_has_spouse_features.py" handles tsv lines.
+  implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index cdb9521ac..cf90af4a7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -518,7 +518,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val function = ss.resolveFunctionName(stmt.function)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
-          s"""udf: $${APP_HOME}\"${StringEscapeUtils.escapeJava(impl.command)}\"
+          s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
           style: \"${impl.format}_extractor\" """
       })
 
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index d552faf9f..08a87f0a6 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_articles(article_id text,
 dd_new_articles(article_id text,
                 text text).
 
-dd_new_articles(article_id, text) :-
+dd_new_articles(article_id, text)  :-
     articles(article_id, text);
     dd_delta_articles(article_id, text).
 
@@ -41,7 +41,7 @@ dd_new_sentences(document_id text,
                  sentence_offset int,
                  sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)  :-
     sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
@@ -63,7 +63,7 @@ dd_new_people_mentions(sentence_id text,
                        text text,
                        mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id)  :-
     people_mentions(sentence_id, start_position, length, text, mention_id);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
@@ -88,7 +88,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              relation_id text,
                              is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true)  :-
     has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
@@ -101,7 +101,7 @@ dd_delta_has_spouse_features(relation_id text,
 dd_new_has_spouse_features(relation_id text,
                            feature text).
 
-dd_new_has_spouse_features(relation_id, feature) :-
+dd_new_has_spouse_features(relation_id, feature)  :-
     has_spouse_features(relation_id, feature);
     dd_delta_has_spouse_features(relation_id, feature).
 
@@ -111,24 +111,24 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
-dd_new_has_spouse(relation_id) :-
+dd_new_has_spouse(relation_id)  :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
-dd_delta_ext_people_input(s, words, ner_tags) :-
+dd_delta_ext_people_input(s, words, ner_tags)  :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
- implementation "/udf/ext_people.py"
+ implementation "udf/ext_people.py"
         handles tsv lines.
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -137,12 +137,12 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
  returns like dd_delta_has_spouse_candidates
- implementation "/udf/ext_has_spouse.py"
+ implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
 dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
 
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -163,14 +163,14 @@ dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :
 function ext_has_spouse_features
     over like dd_delta_ext_has_spouse_features_input
  returns like dd_delta_has_spouse_features
- implementation "/udf/ext_has_spouse_features.py"
+ implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-dd_new_has_spouse(rid) :-
+dd_new_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 0827f99cf..db505c038 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -31,30 +31,30 @@ has_spouse?(relation_id text).
 
 people_mentions :- !ext_people(ext_people_input).
 
-ext_people_input(s, words, ner_tags) :-
+ext_people_input(s, words, ner_tags)  :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
     over like ext_people_input
  returns like people_mentions
- implementation "/udf/ext_people.py"
+ implementation "udf/ext_people.py"
         handles tsv lines.
 
 has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
 
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse
     over like ext_has_spouse_input
  returns like has_spouse_candidates
- implementation "/udf/ext_has_spouse.py"
+ implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
 has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
 
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -63,14 +63,14 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
 function ext_has_spouse_features
     over like ext_has_spouse_features_input
  returns like has_spouse_features
- implementation "/udf/ext_has_spouse_features.py"
+ implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-has_spouse(rid) :-
+has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-has_spouse(rid) :-
+has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index f5c1bf625..4e5711eea 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -42,7 +42,7 @@ ext_people_input(s, words, ner_tags) :-
 
 function ext_people over like ext_people_input
                  returns like people_mentions
-  implementation "/udf/ext_people.py" handles tsv lines
+  implementation "udf/ext_people.py" handles tsv lines
   mode = inc.
 
 has_spouse_candidates :-
@@ -54,7 +54,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
-  implementation "/udf/ext_has_spouse.py" handles tsv lines.
+  implementation "udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
   !ext_has_spouse_features(ext_has_spouse_features_input).
@@ -67,7 +67,7 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
-  implementation "/udf/ext_has_spouse_features.py" handles tsv lines.
+  implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index edc9e85c5..8ebd7d939 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_articles(article_id text,
 dd_new_articles(article_id text,
                 text text).
 
-dd_new_articles(article_id, text) :-
+dd_new_articles(article_id, text)  :-
     articles(article_id, text);
     dd_delta_articles(article_id, text).
 
@@ -41,7 +41,7 @@ dd_new_sentences(document_id text,
                  sentence_offset int,
                  sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)  :-
     sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
@@ -63,7 +63,7 @@ dd_new_people_mentions(sentence_id text,
                        text text,
                        mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id)  :-
     people_mentions(sentence_id, start_position, length, text, mention_id);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
@@ -88,7 +88,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              relation_id text,
                              is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true)  :-
     has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
@@ -101,7 +101,7 @@ dd_delta_has_spouse_features(relation_id text,
 dd_new_has_spouse_features(relation_id text,
                            feature text).
 
-dd_new_has_spouse_features(relation_id, feature) :-
+dd_new_has_spouse_features(relation_id, feature)  :-
     has_spouse_features(relation_id, feature);
     dd_delta_has_spouse_features(relation_id, feature).
 
@@ -111,25 +111,25 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
-dd_new_has_spouse(relation_id) :-
+dd_new_has_spouse(relation_id)  :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
-dd_delta_ext_people_input(s, words, ner_tags) :-
+dd_delta_ext_people_input(s, words, ner_tags)  :-
     sentences(a, b, words, c, d, e, ner_tags, f, s);
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
- implementation "/udf/ext_people.py"
+ implementation "udf/ext_people.py"
         handles tsv lines mode = inc.
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -138,12 +138,12 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
  returns like dd_delta_has_spouse_candidates
- implementation "/udf/ext_has_spouse.py"
+ implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
 dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
 
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -164,14 +164,14 @@ dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :
 function ext_has_spouse_features
     over like dd_delta_ext_has_spouse_features_input
  returns like dd_delta_has_spouse_features
- implementation "/udf/ext_has_spouse_features.py"
+ implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-dd_new_has_spouse(rid) :-
+dd_new_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index e6eb50fce..08e9b910e 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -42,7 +42,7 @@ ext_people_input(s, words, ner_tags) :-
 
 function ext_people over like ext_people_input
                  returns like people_mentions
-  implementation "/udf/ext_people.py" handles tsv lines.
+  implementation "udf/ext_people.py" handles tsv lines.
 
 has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
@@ -53,7 +53,7 @@ ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
-  implementation "/udf/ext_has_spouse.py" handles tsv lines.
+  implementation "udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_features :-
   !ext_has_spouse_features(ext_has_spouse_features_input).
@@ -66,7 +66,7 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
   
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
-  implementation "/udf/ext_has_spouse_features.py" handles tsv lines.
+  implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index baab6b961..3f1ab2e4a 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_articles(article_id text,
 dd_new_articles(article_id text,
                 text text).
 
-dd_new_articles(article_id, text) :-
+dd_new_articles(article_id, text)  :-
     articles(article_id, text);
     dd_delta_articles(article_id, text).
 
@@ -41,7 +41,7 @@ dd_new_sentences(document_id text,
                  sentence_offset int,
                  sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)  :-
     sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
@@ -63,7 +63,7 @@ dd_new_people_mentions(sentence_id text,
                        text text,
                        mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id)  :-
     people_mentions(sentence_id, start_position, length, text, mention_id);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
@@ -88,7 +88,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              relation_id text,
                              is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true)  :-
     has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
@@ -101,7 +101,7 @@ dd_delta_has_spouse_features(relation_id text,
 dd_new_has_spouse_features(relation_id text,
                            feature text).
 
-dd_new_has_spouse_features(relation_id, feature) :-
+dd_new_has_spouse_features(relation_id, feature)  :-
     has_spouse_features(relation_id, feature);
     dd_delta_has_spouse_features(relation_id, feature).
 
@@ -111,24 +111,24 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
-dd_new_has_spouse(relation_id) :-
+dd_new_has_spouse(relation_id)  :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
 dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
 
-dd_delta_ext_people_input(s, words, ner_tags) :-
+dd_delta_ext_people_input(s, words, ner_tags)  :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
- implementation "/udf/ext_people.py"
+ implementation "udf/ext_people.py"
         handles tsv lines.
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -137,12 +137,12 @@ dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
 function ext_has_spouse
     over like dd_delta_ext_has_spouse_input
  returns like dd_delta_has_spouse_candidates
- implementation "/udf/ext_has_spouse.py"
+ implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
 dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
 
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -163,14 +163,14 @@ dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :
 function ext_has_spouse_features
     over like dd_delta_ext_has_spouse_features_input
  returns like dd_delta_has_spouse_features
- implementation "/udf/ext_has_spouse_features.py"
+ implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-dd_new_has_spouse(rid) :-
+dd_new_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
@@ -178,7 +178,7 @@ dd_new_has_spouse(rid) :-
   weight = f
   semantics = Imply.
 
-dd_new_has_spouse(rid) :-
+dd_new_has_spouse(rid)  :-
     dd_new_has_spouse(rid2),
     dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 4e8b107bd..3aefbc215 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -31,30 +31,30 @@ has_spouse?(relation_id text).
 
 people_mentions :- !ext_people(ext_people_input).
 
-ext_people_input(s, words, ner_tags) :-
+ext_people_input(s, words, ner_tags)  :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
     over like ext_people_input
  returns like people_mentions
- implementation "/udf/ext_people.py"
+ implementation "udf/ext_people.py"
         handles tsv lines.
 
 has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
 
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
 function ext_has_spouse
     over like ext_has_spouse_input
  returns like has_spouse_candidates
- implementation "/udf/ext_has_spouse.py"
+ implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
 has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
 
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -63,20 +63,20 @@ ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
 function ext_has_spouse_features
     over like ext_has_spouse_features_input
  returns like has_spouse_features
- implementation "/udf/ext_has_spouse_features.py"
+ implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
-has_spouse(rid) :-
+has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l)
   label = l.
 
-has_spouse(rid) :-
+has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
   weight = f
   semantics = Imply.
 
-has_spouse(rid) :-
+has_spouse(rid)  :-
     has_spouse(rid2),
     has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     has_spouse_candidates(b1, a1, c2, d2, rid2, l2)

From 0088ddcffce269e26b9c38d8bf67eecd4798036b Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 10 Jul 2015 16:00:54 -0700
Subject: [PATCH 164/347] Refactoring

1. Rename some functions, classes and variables
2. Remove unused code in parser
3. Change bracket style
4. Better where clause generation
5. Use unified expression in statements
6. Type cast
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 69 ++++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 30 +++-----
 .../ddlog/DeepDiveLogMergeDeriver.scala       | 12 +---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 35 ++++------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 14 ++--
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  6 +-
 test/compile-error-test.bats.template         |  4 +-
 .../expressions/compile.expected              |  2 +-
 .../expressions/print.expected                |  2 +-
 9 files changed, 72 insertions(+), 102 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index cf90af4a7..374145b86 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -114,8 +114,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     mode = config.mode
     statements.foreach {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
-        terms.foreach {
-          case Variable(n,r,i) =>
+        terms.zipWithIndex.foreach { 
+          case (VarExpr(n), i) =>
             schema           += { (r,i) -> n }
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
             if (isQuery) variableType += { r -> vType.get }
@@ -189,7 +189,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // resolve an expression
-  def resolveExpr(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle, index : Int, isHead: Boolean) : String = {
+  def compileExpr(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle, index : Int, isHead: Boolean) : String = {
     def recurse(e: Expr, alias: AliasStyle, depth: Int) : String = {
       // for columns without a name (constant, function call, binary operator), add an column index alias if necessary
       val columnAlias = if (depth == 0 && isHead) s" AS column_${index}" else ""
@@ -212,17 +212,17 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // resolve a condition
-  def resolveCond(cond: Cond, cq: ConjunctiveQuery) : String = {
+  def compileCond(cond: Cond, cq: ConjunctiveQuery) : String = {
     cond match {
       case ComparisonCond(lhs, op, rhs) => 
-        s"${resolveExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${resolveExpr(rhs, cq, OriginalOnly, 0, false)}"
-      case NegationCond(c) => s"NOT (${resolveCond(c, cq)})"
-      case BinaryOpCond(lhs, op, rhs) => {
-        val resolvedLhs = s"${resolveCond(lhs, cq)}"
-        val resolvedRhs = s"${resolveCond(rhs, cq)}"
+        s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${compileExpr(rhs, cq, OriginalOnly, 0, false)}"
+      case NegationCond(c) => s"NOT (${compileCond(c, cq)})"
+      case CompoundCond(lhs, op, rhs) => {
+        val resolvedLhs = s"${compileCond(lhs, cq)}"
+        val resolvedRhs = s"${compileCond(rhs, cq)}"
         op match {
-          case LogicOperator.AND => s"(${resolvedLhs}) AND (${resolvedRhs})" 
-          case LogicOperator.OR  => s"(${resolvedLhs}) OR (${resolvedRhs})"
+          case LogicOperator.AND => s"(${resolvedLhs} AND ${resolvedRhs})" 
+          case LogicOperator.OR  => s"(${resolvedLhs} OR ${resolvedRhs})"
         }
       }
     }
@@ -238,9 +238,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
     var whereClause = z.bodies(0).zipWithIndex flatMap {
       case (Atom(relName, terms),bodyIndex) => {
-        terms flatMap { case ColumnExpr(expr, relName, index) =>
+        terms.zipWithIndex flatMap { case (expr, index) =>
           expr match {
-            // a simple variable
+            // a simple variable indicates a join condition with other columns having the same variable name
             case VarExpr(varName) => {
               val canonical_body_index = qs.getBodyIndex(varName)
               if (canonical_body_index != bodyIndex) {
@@ -249,9 +249,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
                 Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
               } else { None }
             }
-            // other expressions
+            // other expressions indicate a filter condition on the column
             case _ => {
-              val resolved = resolveExpr(expr, z, OriginalOnly, index, false)
+              val resolved = compileExpr(expr, z, OriginalOnly, index, false)
               val attr = schema(relName, index)
               Some(s"R${bodyIndex}.${attr} = ${resolved}")
             }
@@ -262,16 +262,16 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
     // resolve conditions
     val conditionStr = z.conditions(0) match {
-      case Some(c) => resolveCond(c, z)
+      case Some(c) => compileCond(c, z)
       case None    => ""
     }
 
     // handle group by
     // map head terms, leaving out aggregation functions
-    val groupbyTerms = z.head.terms map { case ColumnExpr(expr, relName, index) =>
+    val groupbyTerms = z.head.terms.zipWithIndex map { case (expr, index) =>
       expr match {
         case FuncExpr(f, args, agg) => if (agg) None else Some("")
-        case _ => Some(resolveExpr(expr, z, OriginalOnly, index, false))
+        case _ => Some(compileExpr(expr, z, OriginalOnly, index, false))
       }
     }
 
@@ -281,9 +281,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
     }
 
-    var whereClauseStr = (whereClause match {
-      case Nil => if (conditionStr == "") "" else s"WHERE ${conditionStr}"
-      case _ => s"""WHERE ${whereClause.mkString(" AND ")} ${if (conditionStr == "") "" else s" AND (${conditionStr})"}"""
+    val whereClauseStrBody = List(whereClause.mkString(" AND "), conditionStr).filter(_ != "").mkString(" AND ")
+    val whereClauseStr = (whereClauseStrBody match {
+      case "" => ""
+      case _  => "WHERE " + whereClauseStrBody
     }) + groupbyStr
 
     s"""FROM ${ bodyNames }
@@ -318,8 +319,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Analyze the block visibility among statements 
   def analyzeVisible(statements: List[Statement]) = {
-    extractionRuleGroupByHead   foreach {keyVal => visible += keyVal._2(0)}
-    functionCallList foreach { stmt => visible += stmt }
+    extractionRuleGroupByHead.values foreach { value => visible += value(0) }
+    functionCallList foreach { visible += _ }
   }
 
   // Analyze the dependency between statements and construct a graph.
@@ -360,11 +361,11 @@ class QuerySchema(q : ConjunctiveQuery) {
   def generateCanonicalVar()  = {
     q.bodies(0).zipWithIndex.foreach {
       case (Atom(relName,terms),index) =>  {
-        terms.foreach { case ColumnExpr(expr, r, i) =>
+        terms.zipWithIndex.foreach { case (expr, i) =>
           expr match {
             case VarExpr(v) => 
               if (! (query_schema contains v) )
-                query_schema += { v -> (index, Variable(v,r,i) ) }
+                query_schema += { v -> (index, Variable(v,relName,i) ) }
             case _ =>
           }
         }
@@ -390,8 +391,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     for (stmt <- stmts) {
       if ((stmt.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains stmt.a.name)) {
       } else {
-        var columnDecls = stmt.a.terms map {
-          case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
+        var columnDecls = stmt.a.terms.zipWithIndex map {
+          case (VarExpr(name),i) => s"${name} ${stmt.a.types(i)}"
         }
         if (stmt.isQuery) {
           val labelColumn = stmt.variableType match {
@@ -440,8 +441,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = tmpCq.head.terms map { case ColumnExpr(expr, _, index) => 
-            ss.resolveExpr(expr, tmpCq, OriginalOnly, index, true)
+          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) => 
+            ss.compileExpr(expr, tmpCq, OriginalOnly, index, true)
           }
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
@@ -451,8 +452,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = tmpCq.head.terms map { case ColumnExpr(expr, _, index) => 
-            ss.resolveExpr(expr, tmpCq, OriginalOnly, index, true)
+          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) => 
+            ss.compileExpr(expr, tmpCq, OriginalOnly, index, true)
           }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
@@ -469,8 +470,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case true => OriginalOnly
             case false => OriginalAndAlias
           }
-          val variableCols = tmpCq.head.terms map { case ColumnExpr(expr, _, index) => 
-            ss.resolveExpr(expr, tmpCq, resolveColumnFlag, index, true)
+          val variableCols = tmpCq.head.terms.zipWithIndex map { case (expr, index) => 
+            ss.compileExpr(expr, tmpCq, resolveColumnFlag, index, true)
           }
           val selectStr = variableCols.mkString(", ")
           val distinctStr = if (tmpCq.isDistinct) "DISTINCT" else ""
@@ -639,7 +640,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var keys = new ListBuffer[String]()
     for (stmt <- (ss.schemaDeclarationGroupByHead map (_._2)).flatten) {
       var columnNames = stmt.a.terms map {
-        case Variable(name, _, i) => name
+        case VarExpr(name) => name
       }
       if (stmt.isQuery) keys += s"""${stmt.a.name} : [${columnNames.mkString(", ")}]"""
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index d250fcbc2..ad96f33d3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -23,13 +23,11 @@ object DeepDiveLogDeltaDeriver{
     // New head
     val incCqHead = if (isInference) {
       cq.head.copy(
-        name = newPrefix + cq.head.name,
-        terms = cq.head.terms
+        name = newPrefix + cq.head.name
       )
     } else {
       cq.head.copy(
-        name = deltaPrefix + cq.head.name,
-        terms = cq.head.terms
+        name = deltaPrefix + cq.head.name
       )
     }
 
@@ -40,15 +38,13 @@ object DeepDiveLogDeltaDeriver{
       // Delta body
       val incDeltaBody = body map {
         a => a.copy(
-          name = deltaPrefix + a.name,
-          terms = a.terms
+          name = deltaPrefix + a.name
         )
       }
       // New body
       val incNewBody = body map {
         a => a.copy(
-          name = newPrefix + a.name,
-          terms = a.terms
+          name = newPrefix + a.name
         )
       }
       var i = 0
@@ -87,9 +83,7 @@ object DeepDiveLogDeltaDeriver{
     // Delta table
     var incDeltaStmt = stmt.copy(
       a = stmt.a.copy(
-        name = deltaPrefix + stmt.a.name,
-        terms = stmt.a.terms map {term => term.copy(relName = deltaPrefix + term.relName)},
-        types = stmt.a.types
+        name = deltaPrefix + stmt.a.name
       )
     )
     incrementalStatement += incDeltaStmt
@@ -97,23 +91,15 @@ object DeepDiveLogDeltaDeriver{
     // New table
     var incNewStmt = stmt.copy(
       a = stmt.a.copy(
-        name = newPrefix + stmt.a.name,
-        terms = stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)},
-        types = stmt.a.types
+        name = newPrefix + stmt.a.name
       )
     )
     incrementalStatement += incNewStmt
 
-    // from schema declaration to expressions
-    def variableToExpr(v: Variable) = ColumnExpr(VarExpr(v.varName), v.relName, v.index)
-    val originalExpr = stmt.a.terms map variableToExpr
-    val incDeltaExpr = incDeltaStmt.a.terms map variableToExpr
-    val incNewExpr = incNewStmt.a.terms map variableToExpr
-
     // if (!stmt.isQuery) {
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
-      Atom(incNewStmt.a.name, incNewExpr),
-      List(List(Atom(stmt.a.name, originalExpr)), List(Atom(incDeltaStmt.a.name, incDeltaExpr))), 
+      Atom(incNewStmt.a.name, incNewStmt.a.terms),
+      List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms))), 
       List(None, None), false))
     // }
     incrementalStatement.toList
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index cbc73c0c3..3a8567688 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -13,18 +13,12 @@ object DeepDiveLogMergeDeriver{
     // New table
     var incNewStmt = stmt.copy(
       a = stmt.a.copy(
-        name = newPrefix + stmt.a.name,
-        terms = stmt.a.terms map {term => term.copy(relName = newPrefix + term.relName)},
-        types = stmt.a.types
+        name = newPrefix + stmt.a.name
       )
     )
 
-    def variableToExpr(v: Variable) = ColumnExpr(VarExpr(v.varName), v.relName, v.index)
-    val originalExpr = stmt.a.terms map variableToExpr
-    val incNewExpr = incNewStmt.a.terms map variableToExpr
-
-    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, originalExpr),
-      List(List(Atom(incNewStmt.a.name, incNewExpr))), List(None), false))
+    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms),
+      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms))), List(None), false))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 90e70b950..1593d3665 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -13,12 +13,7 @@ import scala.util.Try
 // case class Variable(varName : String, relName : String, index : Int )
 // TODO make Atom a trait, and have multiple case classes, e.g., RelationAtom and CondExprAtom
 // ddlog column variable type: constant or variable
-sealed trait ColumnVariable
-case class Variable(varName : String, relName : String, index : Int ) extends ColumnVariable
-
-case class Expression(variables: List[ColumnVariable], ops: List[String], relName: String, index: Int)
-case class ColumnExpr(expr: Expr, relName: String, index: Int)
-case class Operator(operator: String, operand: ColumnVariable)
+case class Variable(varName : String, relName : String, index : Int )
 
 sealed trait Expr
 case class VarExpr(name: String) extends Expr
@@ -26,8 +21,8 @@ case class ConstExpr(value: String) extends Expr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 
-case class Atom(name : String, terms : List[ColumnExpr])
-case class Attribute(name : String, terms : List[Variable], types : List[String])
+case class Atom(name : String, terms : List[Expr])
+case class Attribute(name : String, terms : List[VarExpr], types : List[String])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], isDistinct: Boolean)
 case class Column(name : String, t : String)
 case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
@@ -36,7 +31,7 @@ case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 sealed trait Cond
 case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
 case class NegationCond(cond: Cond) extends Cond
-case class BinaryOpCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
+case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
 
 // logic operators
 object LogicOperator extends Enumeration {
@@ -122,7 +117,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def schemaDeclaration: Parser[SchemaDeclaration] =
     relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
       case (r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
-        val vars = attrs.zipWithIndex map { case(x, i) => Variable(x.name, r, i) }
+        val vars = attrs map { case(x) => VarExpr(x.name) }
         var types = attrs map { case(x) => x.t }
         val variableType = vType match {
           case None => if (isQuery != None) Some(BooleanType) else None
@@ -132,12 +127,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
-  def operator = "||" | "+" | "-" | "*" | "/" | "&" | "::"
+  def operator = "||" | "+" | "-" | "*" | "/" | "&"
+  def typeOperator = "::"
   val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG")
 
   // expressions
   def expr : Parser[Expr] =
     ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    | lexpr ~ typeOperator ~ constant ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, ConstExpr(rhs)) }
     | lexpr
     )
 
@@ -152,22 +149,19 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // TODO support aggregate function syntax somehow
   def cqHead = relationName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
-      case (r ~ "(" ~ variableUses ~ ")") =>
-        Atom(r, variableUses.zipWithIndex map {
-          case (e,i) => ColumnExpr(e, r, i)
-        })
-    }
+    case (r ~ "(" ~ expressions ~ ")") => Atom(r, expressions)
+  }
 
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
   def cond : Parser[Cond] = 
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
-        BinaryOpCond(lhs, LogicOperator.OR, rhs)
+        CompoundCond(lhs, LogicOperator.OR, rhs)
       }
     | acond
     )
   def acond : Parser[Cond] = 
-    ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => BinaryOpCond(lhs, LogicOperator.AND, rhs) }
+    ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND, rhs) }
     | lcond
     )
   // ! has higher priority...
@@ -184,10 +178,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def cqBodyAtom: Parser[Atom] =
     relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
-      case (r ~ "(" ~ variableBindings ~ ")") =>
-        Atom(r, variableBindings.zipWithIndex map {
-        case (e,i) => ColumnExpr(e, r, i)
-      })
+      case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
     }
   def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index a3c41ca23..b61619026 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -16,8 +16,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: SchemaDeclaration): String = {
-    val columnDecls = stmt.a.terms map {
-      case Variable(name, _, i) => s"${name} ${stmt.a.types(i)}"
+    val columnDecls = stmt.a.terms.zipWithIndex map {
+      case (VarExpr(name),i) => s"${name} ${stmt.a.types(i)}"
     }
     val prefix = s"${stmt.a.name}${if (stmt.isQuery) "?" else ""}("
     val indentation = " " * prefix.length
@@ -69,10 +69,10 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     cond match {
       case ComparisonCond(lhs, op, rhs) => s"${printExpr(lhs)} ${op} ${printExpr(rhs)}"
       case NegationCond(c) => s"![${printCond(c)}]"
-      case BinaryOpCond(lhs, op, rhs) => {
+      case CompoundCond(lhs, op, rhs) => {
         op match {
-          case LogicOperator.AND => s"[${printCond(lhs)}], [${printCond(rhs)}]" 
-          case LogicOperator.OR  => s"[${printCond(lhs)}]; [${printCond(rhs)}]"
+          case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]" 
+          case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
         }
       }
     }
@@ -80,9 +80,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(cq: ConjunctiveQuery): String = {
     val printAtom = {a:Atom =>
-      val vars = a.terms map { 
-        case e => printExpr(e.expr)
-      }
+      val vars = a.terms map printExpr
       s"${a.name}(${vars.mkString(", ")})"
     }
     val printListAtom = {a:List[Atom] =>
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 7468979dc..ca2f7fc36 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -76,9 +76,9 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
         if (isQuery) {
-          terms.foreach { x => 
-            if (reservedSet contains x.varName) 
-              error(stmt, s"""variable relation contains reserved column "${x.varName}" """)
+          terms.foreach { case VarExpr(name) => 
+            if (reservedSet contains name) 
+              error(stmt, s"""variable relation contains reserved column "${name}" """)
           }
         }
       }
diff --git a/test/compile-error-test.bats.template b/test/compile-error-test.bats.template
index 1a8d59d76..2488fa915 100644
--- a/test/compile-error-test.bats.template
+++ b/test/compile-error-test.bats.template
@@ -1,7 +1,7 @@
 #!/usr/bin/env bats
 # Compile error test
 # 
-# The test case here feeds a malformed .ddl into ddlog's print command and compares whether it produces an expected error.
+# The test case here feeds a malformed .ddl into ddlog's check command and compares whether it produces an expected error.
 
 source "$BATS_TEST_DIRNAME"/../bats-template.bash  # for $TESTDIR, $it, etc.
 
@@ -15,7 +15,7 @@ setup() {
 
 # check if input produces a compile error
 @test "$it compiles input" {
-    ! ddlog compile "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+    ! ddlog check "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
     diff "$expectedError" "$actualError"
 }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 3ce87caa8..b24266301 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -72,7 +72,7 @@
         CREATE VIEW Q AS 
             SELECT DISTINCT 'test' :: TEXT AS column_0, 123 AS column_1, R0.k AS "a.R0.k" , unnest(R1.q) AS column_3
             FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo'  AND ((R1.r > 100) OR ((NOT (R1.r < 20)) AND (R1.r < 50)))
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR (NOT (R1.r < 20) AND R1.r < 50))
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 97d9a9859..c858e7f0a 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -12,7 +12,7 @@ c(s text,
 Q( "test"  :: TEXT, 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c(x || y, 10,  "foo" ), [z > 100]; [[![z < 20]], [z < 50]].
+    c(x || y, 10,  "foo" ), [z > 100; [![z < 20], z < 50]].
 
 P(y, z, MAX(w))  :-
     a(x),

From ecb4d6fbeefcfaf2c67a2d51760322f08933953f Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 10 Jul 2015 16:52:31 -0700
Subject: [PATCH 165/347] Add parenthesis to expressions, add more tests

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |   2 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   2 +-
 .../expressions/compile.expected              | 150 ++++++++++++++++--
 .../expressions/input.ddl                     |  28 +++-
 .../expressions/print.expected                |  37 ++++-
 5 files changed, 205 insertions(+), 14 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 374145b86..7e6e7ebc0 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -204,7 +204,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         case BinaryOpExpr(lhs, op, rhs) => {
           val resovledLhs = recurse(lhs, OriginalOnly, depth + 1)
           val resovledRhs = recurse(rhs, OriginalOnly, depth + 1)
-          s"${resovledLhs} ${op} ${resovledRhs}${columnAlias}"
+          s"(${resovledLhs} ${op} ${resovledRhs})${columnAlias}"
         }
       }
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index b61619026..582c9d82a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -60,7 +60,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         val resolvedArgs = args map (x => printExpr(x))
         s"${function}(${resolvedArgs.mkString(", ")})"
       }
-      case BinaryOpExpr(lhs, op, rhs) => s"${printExpr(lhs)} ${op} ${printExpr(rhs)}"
+      case BinaryOpExpr(lhs, op, rhs) => s"(${printExpr(lhs)} ${op} ${printExpr(rhs)})"
     }
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index b24266301..88958c3b8 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -55,24 +55,156 @@
           style: "sql_extractor"
         }
 
+      deepdive.extraction.extractors.extraction_rule_9 {
+        sql: """ DROP VIEW IF EXISTS E;
+        CREATE VIEW E AS 
+            SELECT  (R0.k :: INT) AS column_0
+            FROM b R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_14 {
+        sql: """ DROP VIEW IF EXISTS J;
+        CREATE VIEW J AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE ((R0.k + R0.r) = 100 OR NOT (R0.k > 50))
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_10 {
+        sql: """ DROP VIEW IF EXISTS F;
+        CREATE VIEW F AS 
+            SELECT  ((R0.k :: INT) + (R0.r :: INT)) AS column_0
+            FROM b R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_5 {
+        sql: """ DROP VIEW IF EXISTS A;
+        CREATE VIEW A AS 
+            SELECT  (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
+            FROM b R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_13 {
+        sql: """ DROP VIEW IF EXISTS I;
+        CREATE VIEW I AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_11 {
+        sql: """ DROP VIEW IF EXISTS G;
+        CREATE VIEW G AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE (R0.k + R0.r) = 100
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_3 {
+        sql: """ DROP VIEW IF EXISTS Q;
+        CREATE VIEW Q AS 
+            SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS "a.R0.k" , unnest(R1.q) AS column_3
+            FROM a R0, b R1, c R2
+        WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR (NOT (R1.r < 20) AND R1.r < 50))
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_6 {
+        sql: """ DROP VIEW IF EXISTS B;
+        CREATE VIEW B AS 
+            SELECT  func((R0.k + (R0.r + R0.k))) AS column_0
+            FROM b R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ DROP VIEW IF EXISTS P;
         CREATE VIEW P AS 
             SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS column_2
             FROM a R0, b R1
-        WHERE R1.k = R0.k  
+        WHERE R1.k = R0.k 
         """
         style: "sql_extractor"
           
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
-        sql: """ DROP VIEW IF EXISTS Q;
-        CREATE VIEW Q AS 
-            SELECT DISTINCT 'test' :: TEXT AS column_0, 123 AS column_1, R0.k AS "a.R0.k" , unnest(R1.q) AS column_3
-            FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR (NOT (R1.r < 20) AND R1.r < 50))
+      deepdive.extraction.extractors.extraction_rule_7 {
+        sql: """ DROP VIEW IF EXISTS C;
+        CREATE VIEW C AS 
+            SELECT  func(func(func(R0.k))) AS column_0
+            FROM b R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_12 {
+        sql: """ DROP VIEW IF EXISTS H;
+        CREATE VIEW H AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_15 {
+        sql: """ DROP VIEW IF EXISTS K;
+        CREATE VIEW K AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE ((R0.k + R0.r) = 100 AND (NOT (R0.k > 50) OR R0.k = 40))
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_8 {
+        sql: """ DROP VIEW IF EXISTS D;
+        CREATE VIEW D AS 
+            SELECT  (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
+            FROM b R0
+        
         """
         style: "sql_extractor"
           
@@ -80,6 +212,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_4, extraction_rule_3]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_4, extraction_rule_3]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index f0ba156c5..51c046b1d 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -2,6 +2,32 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
+# comprehensive
 Q("test" :: TEXT, 123, id, unnest(y)) * :- a(id), b(id, x,y,z), c(x || y,10,"foo"), [z>100; !z < 20, z < 50].
 
-P(y, z, MAX(w)) :- a(x), b(x,y,z,w).
\ No newline at end of file
+# group by
+P(y, z, MAX(w)) :- a(x), b(x,y,z,w).
+
+# expressions
+A( x + (w * (x + w)) ) :- b(x,y,z,w).
+
+B( func(x + w + x) ) :- b(x,y,z,w).
+
+C( func(func(func(x))) ) :- b(x,y,z,w).
+
+D( func(x * func2(w + x)) + x ) :- b(x,y,z,w).
+
+E( x :: INT) :- b(x,y,z,w).
+
+F( (x :: INT) + (w :: INT) ) :- b(x,y,z,w).
+
+# conditions
+G(x) :- b(x,y,z,w), x + w = 100.
+
+H(x) :- b(x,y,z,w), [x + w = 100, x > 50].
+
+I(x) :- b(x,y,z,w), [x + w = 100; [x > 50, w < 10]].
+
+J(x) :- b(x,y,z,w), [x + w = 100; !x > 50].
+
+K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index c858e7f0a..2598ef85a 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -9,12 +9,45 @@ c(s text,
   n int,
   t text).
 
-Q( "test"  :: TEXT, 123, id, unnest(y)) * :-
+Q(( "test"  :: TEXT), 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c(x || y, 10,  "foo" ), [z > 100; [![z < 20], z < 50]].
+    c((x || y), 10,  "foo" ), [z > 100; [![z < 20], z < 50]].
 
 P(y, z, MAX(w))  :-
     a(x),
     b(x, y, z, w).
 
+A((x + (w * (x + w))))  :-
+    b(x, y, z, w).
+
+B(func((x + (w + x))))  :-
+    b(x, y, z, w).
+
+C(func(func(func(x))))  :-
+    b(x, y, z, w).
+
+D((func((x * func2((w + x)))) + x))  :-
+    b(x, y, z, w).
+
+E((x :: INT))  :-
+    b(x, y, z, w).
+
+F(((x :: INT) + (w :: INT)))  :-
+    b(x, y, z, w).
+
+G(x)  :-
+    b(x, y, z, w), (x + w) = 100.
+
+H(x)  :-
+    b(x, y, z, w), [(x + w) = 100, x > 50].
+
+I(x)  :-
+    b(x, y, z, w), [(x + w) = 100; [x > 50, w < 10]].
+
+J(x)  :-
+    b(x, y, z, w), [(x + w) = 100; ![x > 50]].
+
+K(x)  :-
+    b(x, y, z, w), [(x + w) = 100, [![x > 50]; x = 40]].
+

From 11a3c3177cfd757ce160275323a0c662cfd90f60 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 10 Jul 2015 19:00:15 -0700
Subject: [PATCH 166/347] Further refactoring

1. Redo typecast
2. Change type of terms in schema declaration
3. Simplify compileExpr and generateSQLBody
4. Correct bracketing for conditions
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 57 ++++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  5 +-
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  5 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 14 ++---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  5 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  2 +-
 .../expressions/compile.expected              |  6 +-
 .../expressions/input.ddl                     |  2 +-
 .../expressions/print.expected                |  6 +-
 9 files changed, 52 insertions(+), 50 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 7e6e7ebc0..32ea7de9b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -115,7 +115,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     statements.foreach {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
         terms.zipWithIndex.foreach { 
-          case (VarExpr(n), i) =>
+          case (n, i) =>
             schema           += { (r,i) -> n }
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
             if (isQuery) variableType += { r -> vType.get }
@@ -190,25 +190,35 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // resolve an expression
   def compileExpr(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle, index : Int, isHead: Boolean) : String = {
-    def recurse(e: Expr, alias: AliasStyle, depth: Int) : String = {
-      // for columns without a name (constant, function call, binary operator), add an column index alias if necessary
-      val columnAlias = if (depth == 0 && isHead) s" AS column_${index}" else ""
+    // recursively compile an expression
+    def compileExprInner(e: Expr, alias: AliasStyle) : String = {
       e match {
         case VarExpr(name) => resolveColumn(name, cq, alias).get
-        case ConstExpr(value) => value + columnAlias
+        case ConstExpr(value) => value
         case FuncExpr(function, args, agg) => {
-          val resolvedArgs = args map (x => recurse(x, OriginalOnly, depth + 1))
+          // note alias is overriden with OriginalOnly, because when an expression appears in 
+          // the function, we only need it's column name, without " AS ..." aliasing, same below
+          val resolvedArgs = args map (x => compileExprInner(x, OriginalOnly))
           val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
-          resolved + columnAlias
+          resolved
         }
         case BinaryOpExpr(lhs, op, rhs) => {
-          val resovledLhs = recurse(lhs, OriginalOnly, depth + 1)
-          val resovledRhs = recurse(rhs, OriginalOnly, depth + 1)
-          s"(${resovledLhs} ${op} ${resovledRhs})${columnAlias}"
+          val resovledLhs = compileExprInner(lhs, OriginalOnly)
+          val resovledRhs = compileExprInner(rhs, OriginalOnly)
+          s"(${resovledLhs} ${op} ${resovledRhs})"
+        }
+        case TypecastExpr(lhs, rhs) => {
+          val resovledLhs = compileExprInner(lhs, OriginalOnly)
+          s"(${resovledLhs} :: ${rhs})"
         }
       }
     }
-    recurse(e, alias, 0)
+    // for columns without a name (constant, function call, binary operator), add an column index alias if necessary
+    val columnAlias = e match {
+      case x: VarExpr => ""
+      case _ => if (isHead) s" AS column_${index}" else ""
+    }
+    compileExprInner(e, alias) + columnAlias
   }
 
   // resolve a condition
@@ -216,7 +226,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     cond match {
       case ComparisonCond(lhs, op, rhs) => 
         s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${compileExpr(rhs, cq, OriginalOnly, 0, false)}"
-      case NegationCond(c) => s"NOT (${compileCond(c, cq)})"
+      case NegationCond(c) => s"(NOT ${compileCond(c, cq)})"
       case CompoundCond(lhs, op, rhs) => {
         val resolvedLhs = s"${compileCond(lhs, cq)}"
         val resolvedRhs = s"${compileCond(rhs, cq)}"
@@ -261,10 +271,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
 
     // resolve conditions
-    val conditionStr = z.conditions(0) match {
-      case Some(c) => compileCond(c, z)
-      case None    => ""
-    }
+    val conditionStr = z.conditions(0) map (compileCond(_, z))
 
     // handle group by
     // map head terms, leaving out aggregation functions
@@ -281,14 +288,11 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
     }
 
-    val whereClauseStrBody = List(whereClause.mkString(" AND "), conditionStr).filter(_ != "").mkString(" AND ")
-    val whereClauseStr = (whereClauseStrBody match {
-      case "" => ""
-      case _  => "WHERE " + whereClauseStrBody
-    }) + groupbyStr
+    val whereClauseConds = whereClause ++ conditionStr
+    val whereClauseStr = if (whereClauseConds isEmpty) "" else whereClauseConds.mkString("WHERE ", " AND ", "")
 
     s"""FROM ${ bodyNames }
-        ${ whereClauseStr }"""
+        ${ whereClauseStr }${groupbyStr}"""
   }
 
   // Group statements by head
@@ -319,7 +323,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Analyze the block visibility among statements 
   def analyzeVisible(statements: List[Statement]) = {
-    extractionRuleGroupByHead.values foreach { value => visible += value(0) }
+    extractionRuleGroupByHead.values foreach { visible += _(0) }
     functionCallList foreach { visible += _ }
   }
 
@@ -392,7 +396,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       if ((stmt.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains stmt.a.name)) {
       } else {
         var columnDecls = stmt.a.terms.zipWithIndex map {
-          case (VarExpr(name),i) => s"${name} ${stmt.a.types(i)}"
+          case (name,i) => s"${name} ${stmt.a.types(i)}"
         }
         if (stmt.isQuery) {
           val labelColumn = stmt.variableType match {
@@ -639,10 +643,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileVariableKey(ss: CompilationState): CompiledBlocks = {
     var keys = new ListBuffer[String]()
     for (stmt <- (ss.schemaDeclarationGroupByHead map (_._2)).flatten) {
-      var columnNames = stmt.a.terms map {
-        case VarExpr(name) => name
-      }
-      if (stmt.isQuery) keys += s"""${stmt.a.name} : [${columnNames.mkString(", ")}]"""
+      if (stmt.isQuery) keys += s"""${stmt.a.name} : [${stmt.a.terms.mkString(", ")}]"""
     }
     ss.mode match {
       case INCREMENTAL => List(s"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index ad96f33d3..0207f2e00 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -98,8 +98,9 @@ object DeepDiveLogDeltaDeriver{
 
     // if (!stmt.isQuery) {
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
-      Atom(incNewStmt.a.name, incNewStmt.a.terms),
-      List(List(Atom(stmt.a.name, stmt.a.terms)), List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms))), 
+      Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
+      List(List(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) })),
+        List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarExpr(_) }))), 
       List(None, None), false))
     // }
     incrementalStatement.toList
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index 3a8567688..77a942459 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -17,8 +17,9 @@ object DeepDiveLogMergeDeriver{
       )
     )
 
-    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms),
-      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms))), List(None), false))
+    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
+      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) }))),
+      List(None), false))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 1593d3665..8cc7b2e77 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -10,9 +10,6 @@ import scala.util.Try
 // ***************************************
 // * The union types for for the parser. *
 // ***************************************
-// case class Variable(varName : String, relName : String, index : Int )
-// TODO make Atom a trait, and have multiple case classes, e.g., RelationAtom and CondExprAtom
-// ddlog column variable type: constant or variable
 case class Variable(varName : String, relName : String, index : Int )
 
 sealed trait Expr
@@ -20,9 +17,10 @@ case class VarExpr(name: String) extends Expr
 case class ConstExpr(value: String) extends Expr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
+case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 
 case class Atom(name : String, terms : List[Expr])
-case class Attribute(name : String, terms : List[VarExpr], types : List[String])
+case class Attribute(name : String, terms : List[String], types : List[String])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], isDistinct: Boolean)
 case class Column(name : String, t : String)
 case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
@@ -87,7 +85,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def stringLiteralAsSqlString = stringLiteral ^^ { s =>
     s"""'${s.stripPrefix("\"").stripSuffix("\"")}'"""
   }
-  def constant = stringLiteralAsSqlString | wholeNumber | "TRUE" | "FALSE" | "NULL" | "TEXT" | "INT" | "BOOLEAN"
+  def constant = stringLiteralAsSqlString | wholeNumber | "TRUE" | "FALSE" | "NULL"
 
   // Single-line comments beginning with # or // are supported by treating them as whiteSpace
   // C/Java/Scala style multi-line comments cannot be easily supported with RegexParsers unless we introduce a dedicated lexer.
@@ -117,8 +115,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def schemaDeclaration: Parser[SchemaDeclaration] =
     relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
       case (r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
-        val vars = attrs map { case(x) => VarExpr(x.name) }
-        var types = attrs map { case(x) => x.t }
+        val vars = attrs map (_.name)
+        var types = attrs map (_.t)
         val variableType = vType match {
           case None => if (isQuery != None) Some(BooleanType) else None
           case Some(s) => Some(s)
@@ -134,7 +132,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   // expressions
   def expr : Parser[Expr] =
     ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
-    | lexpr ~ typeOperator ~ constant ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, ConstExpr(rhs)) }
+    | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
     )
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 582c9d82a..0d33cc5c1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -17,7 +17,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(stmt: SchemaDeclaration): String = {
     val columnDecls = stmt.a.terms.zipWithIndex map {
-      case (VarExpr(name),i) => s"${name} ${stmt.a.types(i)}"
+      case (name,i) => s"${name} ${stmt.a.types(i)}"
     }
     val prefix = s"${stmt.a.name}${if (stmt.isQuery) "?" else ""}("
     val indentation = " " * prefix.length
@@ -61,6 +61,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         s"${function}(${resolvedArgs.mkString(", ")})"
       }
       case BinaryOpExpr(lhs, op, rhs) => s"(${printExpr(lhs)} ${op} ${printExpr(rhs)})"
+      case TypecastExpr(lhs, rhs) => s"(${printExpr(lhs)} :: ${rhs})"
     }
   }
 
@@ -68,7 +69,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   def printCond(cond: Cond) : String = {
     cond match {
       case ComparisonCond(lhs, op, rhs) => s"${printExpr(lhs)} ${op} ${printExpr(rhs)}"
-      case NegationCond(c) => s"![${printCond(c)}]"
+      case NegationCond(c) => s"[!${printCond(c)}]"
       case CompoundCond(lhs, op, rhs) => {
         op match {
           case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]" 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index ca2f7fc36..13fc3ed87 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -76,7 +76,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
         if (isQuery) {
-          terms.foreach { case VarExpr(name) => 
+          terms.foreach { case name => 
             if (reservedSet contains name) 
               error(stmt, s"""variable relation contains reserved column "${name}" """)
           }
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 88958c3b8..b2f3f249e 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -72,7 +72,7 @@
         CREATE VIEW J AS 
             SELECT  R0.k AS "b.R0.k" 
             FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR NOT (R0.k > 50))
+        WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
         """
         style: "sql_extractor"
           
@@ -132,7 +132,7 @@
         CREATE VIEW Q AS 
             SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS "a.R0.k" , unnest(R1.q) AS column_3
             FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR (NOT (R1.r < 20) AND R1.r < 50))
+        WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
         """
         style: "sql_extractor"
           
@@ -192,7 +192,7 @@
         CREATE VIEW K AS 
             SELECT  R0.k AS "b.R0.k" 
             FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND (NOT (R0.k > 50) OR R0.k = 40))
+        WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 51c046b1d..092889b4a 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -24,7 +24,7 @@ F( (x :: INT) + (w :: INT) ) :- b(x,y,z,w).
 # conditions
 G(x) :- b(x,y,z,w), x + w = 100.
 
-H(x) :- b(x,y,z,w), [x + w = 100, x > 50].
+H(x) :- b(x,y,z,w), x + w = 100, x > 50.
 
 I(x) :- b(x,y,z,w), [x + w = 100; [x > 50, w < 10]].
 
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 2598ef85a..10bb024d5 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -12,7 +12,7 @@ c(s text,
 Q(( "test"  :: TEXT), 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c((x || y), 10,  "foo" ), [z > 100; [![z < 20], z < 50]].
+    c((x || y), 10,  "foo" ), [z > 100; [[!z < 20], z < 50]].
 
 P(y, z, MAX(w))  :-
     a(x),
@@ -46,8 +46,8 @@ I(x)  :-
     b(x, y, z, w), [(x + w) = 100; [x > 50, w < 10]].
 
 J(x)  :-
-    b(x, y, z, w), [(x + w) = 100; ![x > 50]].
+    b(x, y, z, w), [(x + w) = 100; [!x > 50]].
 
 K(x)  :-
-    b(x, y, z, w), [(x + w) = 100, [![x > 50]; x = 40]].
+    b(x, y, z, w), [(x + w) = 100, [[!x > 50]; x = 40]].
 

From 34339f094fb4eecca2e78fcce2173b2da12491b4 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 12 Jul 2015 03:32:32 -0700
Subject: [PATCH 167/347] Add support for limit

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala | 11 ++++++++---
 .../deepdive/ddlog/DeepDiveLogDeltaDeriver.scala |  4 ++--
 .../deepdive/ddlog/DeepDiveLogMergeDeriver.scala |  2 +-
 .../org/deepdive/ddlog/DeepDiveLogParser.scala   | 10 ++++++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala         |  8 +++++++-
 .../expressions/compile.expected                 | 16 ++++++++++++++--
 test/expected-output-test/expressions/input.ddl  |  5 ++++-
 .../expressions/print.expected                   |  3 +++
 8 files changed, 45 insertions(+), 14 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 32ea7de9b..7c4c5df09 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -291,8 +291,13 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     val whereClauseConds = whereClause ++ conditionStr
     val whereClauseStr = if (whereClauseConds isEmpty) "" else whereClauseConds.mkString("WHERE ", " AND ", "")
 
+    val limitStr = z.limit match {
+      case Some(s) => s" LIMIT ${s}"
+      case None => ""
+    }
+
     s"""FROM ${ bodyNames }
-        ${ whereClauseStr }${groupbyStr}"""
+        ${ whereClauseStr }${groupbyStr}${limitStr}"""
   }
 
   // Group statements by head
@@ -439,7 +444,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
       for (cqBody <- stmt.q.bodies) {
-        val tmpCq = ConjunctiveQuery(stmt.q.head, List(cqBody), stmt.q.conditions, stmt.q.isDistinct)
+        val tmpCq = stmt.q.copy(bodies = List(cqBody))
         // Generate the body of the query.
         val qs              = new QuerySchema( tmpCq )
 
@@ -556,7 +561,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       for (cqBody <- stmt.q.bodies) {
         // edge query
         val fakeBody        = stmt.q.head +: cqBody
-        val fakeCQ          = ConjunctiveQuery(stmt.q.head, List(fakeBody), stmt.q.conditions, stmt.q.isDistinct) // we will just use the fakeBody below.
+        val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
 
         val index = cqBody.length + 1
         val qs2 = new QuerySchema( fakeCQ )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 0207f2e00..71b647c92 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -70,7 +70,7 @@ object DeepDiveLogDeltaDeriver{
       }
     }
     // TODO fix conditions
-    ConjunctiveQuery(incCqHead, incCqBodies.toList, incCqConditions.toList, cq.isDistinct)
+    ConjunctiveQuery(incCqHead, incCqBodies.toList, incCqConditions.toList, cq.isDistinct, cq.limit)
   }
 
   // Incremental scheme declaration,
@@ -101,7 +101,7 @@ object DeepDiveLogDeltaDeriver{
       Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
       List(List(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) })),
         List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarExpr(_) }))), 
-      List(None, None), false))
+      List(None, None), false, None))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index 77a942459..f9eea977a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -19,7 +19,7 @@ object DeepDiveLogMergeDeriver{
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
       List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) }))),
-      List(None), false))
+      List(None), false, None))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 8cc7b2e77..2d4cd1786 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -21,7 +21,8 @@ case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 
 case class Atom(name : String, terms : List[Expr])
 case class Attribute(name : String, terms : List[String], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], isDistinct: Boolean)
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], 
+  isDistinct: Boolean, limit: Option[Int])
 case class Column(name : String, t : String)
 case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 
@@ -185,9 +186,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
-    cqHead ~ opt("*") ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
-      case (headatom ~ isDistinct ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.condition), isDistinct != None)
+    cqHead ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
+      case (headatom ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
+        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.condition), 
+          isDistinct != None, limit map (_.toInt))
   }
 
   def relationType: Parser[RelationType] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 0d33cc5c1..dd19c0ebe 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -100,7 +100,13 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
     }).mkString(";\n    ")
 
-    s"""${printAtom(cq.head)} ${if (cq.isDistinct) "*" else ""} :-
+    val distinctStr = if (cq.isDistinct) "*" else ""
+    val limitStr = cq.limit match {
+      case Some(s) => s" | ${s}"
+      case None => ""
+    }
+
+    s"""${printAtom(cq.head)} ${distinctStr}${limitStr} :-
        |    ${bodyWithCondition}""".stripMargin
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index b2f3f249e..556d415b8 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -139,6 +139,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_16 {
+        sql: """ DROP VIEW IF EXISTS L;
+        CREATE VIEW L AS 
+            SELECT DISTINCT R0.k AS "b.R0.k" 
+            FROM b R0
+         LIMIT 100
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS B;
         CREATE VIEW B AS 
@@ -212,6 +224,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 092889b4a..7e1bd8597 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -30,4 +30,7 @@ I(x) :- b(x,y,z,w), [x + w = 100; [x > 50, w < 10]].
 
 J(x) :- b(x,y,z,w), [x + w = 100; !x > 50].
 
-K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
\ No newline at end of file
+K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
+
+# limit
+L(x) * | 100 :- b(x, y, z, w).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 10bb024d5..7a29b3a82 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -51,3 +51,6 @@ J(x)  :-
 K(x)  :-
     b(x, y, z, w), [(x + w) = 100, [[!x > 50]; x = 40]].
 
+L(x) * | 100 :-
+    b(x, y, z, w).
+

From e183e70f95ddce46502ecb2fc889a666a3e67129 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 12 Jul 2015 17:36:13 -0700
Subject: [PATCH 168/347] Add support for plpy extractor

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala     |  2 +-
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 12 ++++++++----
 .../deepdive/ddlog/DeepDiveLogPrettyPrinter.scala    |  8 +++++---
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 7c4c5df09..d3cc3b256 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -529,7 +529,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
           s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
-          style: \"${impl.format}_extractor\" """
+          style: \"${impl.style}_extractor\" """
       })
 
       if (udfDetails.isEmpty)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 2d4cd1786..b04fb5b35 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -63,7 +63,7 @@ case class RelationTypeDeclaration(names: List[String], types: List[String]) ext
 case class RelationTypeAlias(likeRelationName: String) extends RelationType
 
 trait FunctionImplementationDeclaration
-case class RowWiseLineHandler(format: String, command: String) extends FunctionImplementationDeclaration
+case class RowWiseLineHandler(style: String, command: String) extends FunctionImplementationDeclaration
 
 // Statements that will be parsed and compiled
 trait Statement
@@ -203,9 +203,13 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def inferenceMode = "mode" ~> "=" ~> inferenceModeType
 
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
-    "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
-      case (_ ~ command ~ _ ~ format ~ _) => RowWiseLineHandler(command=command, format=format)
-    }
+    ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
+        case (_ ~ command ~ _ ~ style ~ _) => RowWiseLineHandler(command=command, style=style)
+      }
+    | "implementation" ~ stringLiteralAsString ~ "runs" ~ "as" ~ "plpy" ^^ {
+        case (_ ~ command ~ _ ~ _ ~ style) => RowWiseLineHandler(command=command, style=style)
+      }
+    )
 
   def functionDeclaration : Parser[FunctionDeclaration] =
     ( "function" ~ functionName ~ "over" ~ relationType
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index dd19c0ebe..a0b3f8f65 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -36,9 +36,11 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val inputType = print(stmt.inputType)
     val outputType = print(stmt.outputType)
     val impls = stmt.implementations map {
-      case impl: RowWiseLineHandler =>
-        "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" +
-        s"\n        handles ${impl.format} lines"
+      case impl: RowWiseLineHandler => {
+        val styleStr = if (impl.style == "plpy") s"\n        runs as plpy"
+        else s"\n        handles ${impl.style} lines"
+        "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" + styleStr
+      }
     }
     val modeStr = if (stmt.mode == null) "" else s" mode = ${stmt.mode}"
     s"""function ${stmt.functionName}

From 0830c30718800dc88f8253a268aa27044c88bbf1 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 12 Jul 2015 18:27:06 -0700
Subject: [PATCH 169/347] Add support for specifying factor functions. Change
 semantics specification

---
 examples/spouse_example.ddl                   |  3 +--
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 10 ++++---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 11 ++++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  6 +++--
 .../ocr_example/print-incremental.expected    | 24 ++++++++---------
 .../ocr_example/print.expected                | 14 +++++-----
 test/expected-output-test/semantics/input.ddl |  2 +-
 .../smoke_example/print-incremental.expected  | 26 +++++++++----------
 .../smoke_example/print.expected              | 14 +++++-----
 .../spouse_example/print-incremental.expected |  3 +--
 .../spouse_example/print.expected             |  3 +--
 .../spouse_example_new_feature/input.ddl      |  2 +-
 .../print-incremental.expected                |  2 +-
 .../print-incremental.expected                |  6 ++---
 .../print.expected                            |  6 ++---
 16 files changed, 63 insertions(+), 71 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 040545fce..1aaa9703f 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -73,5 +73,4 @@ has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
-weight = f
-semantics = Imply.
+weight = f.
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d3cc3b256..4cac69c5d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -593,9 +593,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           else ""
           }).filter(_ != "")
           val firstFunc = funcBody(0)
-          val function  = ss.variableType get stmt.q.head.name match {
-            case Some(BooleanType)        => stmt.semantics
-            case Some(MultinomialType(_)) => "Multinomial"
+          // if function is not specified, use Imply for boolean, and Multinomial for multinomial variables
+          val function  = stmt.function match {
+            case Some(f) => f
+            case None => ss.variableType get stmt.q.head.name match {
+              case Some(BooleanType)        => "Imply"
+              case Some(MultinomialType(_)) => "Multinomial"
+            }
           }
           func = s"""${function}(${(funcBody.tail :+ firstFunc).mkString(", ")})"""
         }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 71b647c92..e2176fb46 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -143,7 +143,7 @@ object DeepDiveLogDeltaDeriver{
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(InferenceRule(transform(stmt.q, true, stmt.mode), stmt.weights, stmt.semantics))
+    List(stmt.copy(q = transform(stmt.q, true, stmt.mode), mode = null))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index b04fb5b35..6a39de807 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -71,7 +71,7 @@ case class SchemaDeclaration( a : Attribute , isQuery : Boolean, variableType :
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, semantics : String = "Imply", mode: String = null) extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: String = null) extends Statement // Weighted rule
 
 // Parser
 class DeepDiveLogParser extends JavaTokenParsers {
@@ -242,13 +242,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def supervision = "label" ~> "=" ~> variableName
 
-  def semantics = "semantics" ~> "=" ~> semanticType
+  def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
+  def factorFunction = "function" ~> "=" ~> factorFunctionName
 
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ opt(semantics) ~ opt(inferenceMode)
+    ( conjunctiveQuery ~ factorWeight ~ opt(factorFunction) ~ opt(inferenceMode)
     ) ^^ {
-      case (q ~ weight ~ semantics ~ mode) =>
-        InferenceRule(q, weight, semantics.getOrElse("Imply"), mode.getOrElse(null))
+      case (q ~ weight ~ function ~ mode) =>
+        InferenceRule(q, weight, function, mode.getOrElse(null))
     }
 
   // rules or schema elements in arbitrary order
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index a0b3f8f65..a291fc8ab 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -132,8 +132,10 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         case UnknownFactorWeight(vs) => vs.mkString(", ")
       })
     ) +
-    ( if (stmt.semantics == null) ""
-      else "\n  semantics = " + stmt.semantics
+    ( stmt.function match {
+        case Some(f) => s"\n  function = ${f}"
+        case None => ""
+      }
     ) + ".\n"
   }
 
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
index e8ed0bbf8..fc4e69079 100644
--- a/test/expected-output-test/ocr_example/print-incremental.expected
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -13,7 +13,7 @@ dd_new_features(id BIGSERIAL,
                 feature_id INT,
                 feature_val BOOLEAN).
 
-dd_new_features(id, word_id, feature_id, feature_val) :-
+dd_new_features(id, word_id, feature_id, feature_val)  :-
     features(id, word_id, feature_id, feature_val);
     dd_delta_features(id, word_id, feature_id, feature_val).
 
@@ -26,7 +26,7 @@ dd_delta_label1(wid INT,
 dd_new_label1(wid INT,
               val BOOLEAN).
 
-dd_new_label1(wid, val) :-
+dd_new_label1(wid, val)  :-
     label1(wid, val);
     dd_delta_label1(wid, val).
 
@@ -39,7 +39,7 @@ dd_delta_label2(wid INT,
 dd_new_label2(wid INT,
               val BOOLEAN).
 
-dd_new_label2(wid, val) :-
+dd_new_label2(wid, val)  :-
     label2(wid, val);
     dd_delta_label2(wid, val).
 
@@ -49,7 +49,7 @@ dd_delta_q1?(wid INT).
 
 dd_new_q1?(wid INT).
 
-dd_new_q1(wid) :-
+dd_new_q1(wid)  :-
     q1(wid);
     dd_delta_q1(wid).
 
@@ -59,25 +59,23 @@ dd_delta_q2?(wid INT).
 
 dd_new_q2?(wid INT).
 
-dd_new_q2(wid) :-
+dd_new_q2(wid)  :-
     q2(wid);
     dd_delta_q2(wid).
 
-dd_delta_q1(wid) :-
+dd_delta_q1(wid)  :-
     dd_delta_label1(wid, val)
   label = val.
 
-dd_delta_q2(wid) :-
+dd_delta_q2(wid)  :-
     dd_delta_label2(wid, val)
   label = val.
 
-dd_new_q1(wid) :-
+dd_new_q1(wid)  :-
     dd_delta_features(id, wid, fid, fval)
-  weight = fid
-  semantics = Imply.
+  weight = fid.
 
-dd_new_q2(wid) :-
+dd_new_q2(wid)  :-
     dd_delta_features(id, wid, fid, fval)
-  weight = fid
-  semantics = Imply.
+  weight = fid.
 
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
index da66f1d67..d3ff92171 100644
--- a/test/expected-output-test/ocr_example/print.expected
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -13,21 +13,19 @@ q1?(wid INT).
 
 q2?(wid INT).
 
-q1(wid) :-
+q1(wid)  :-
     label1(wid, val)
   label = val.
 
-q2(wid) :-
+q2(wid)  :-
     label2(wid, val)
   label = val.
 
-q1(wid) :-
+q1(wid)  :-
     features(id, wid, fid, fval)
-  weight = fid
-  semantics = Imply.
+  weight = fid.
 
-q2(wid) :-
+q2(wid)  :-
     features(id, wid, fid, fval)
-  weight = fid
-  semantics = Imply.
+  weight = fid.
 
diff --git a/test/expected-output-test/semantics/input.ddl b/test/expected-output-test/semantics/input.ddl
index f18e77c06..6f3a9f36c 100644
--- a/test/expected-output-test/semantics/input.ddl
+++ b/test/expected-output-test/semantics/input.ddl
@@ -5,4 +5,4 @@ Q?(x int).
 
 Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w)
 weight = y
-semantics = imply.
+function = Linear.
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index 3ed640bfc..3a17e8fba 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_person(person_id bigint,
 dd_new_person(person_id bigint,
               name text).
 
-dd_new_person(person_id, name) :-
+dd_new_person(person_id, name)  :-
     person(person_id, name);
     dd_delta_person(person_id, name).
 
@@ -20,7 +20,7 @@ dd_delta_person_has_cancer(person_id bigint,
 dd_new_person_has_cancer(person_id bigint,
                          has_cancer boolean).
 
-dd_new_person_has_cancer(person_id, has_cancer) :-
+dd_new_person_has_cancer(person_id, has_cancer)  :-
     person_has_cancer(person_id, has_cancer);
     dd_delta_person_has_cancer(person_id, has_cancer).
 
@@ -33,7 +33,7 @@ dd_delta_person_smokes(person_id bigint,
 dd_new_person_smokes(person_id bigint,
                      smokes boolean).
 
-dd_new_person_smokes(person_id, smokes) :-
+dd_new_person_smokes(person_id, smokes)  :-
     person_smokes(person_id, smokes);
     dd_delta_person_smokes(person_id, smokes).
 
@@ -46,7 +46,7 @@ dd_delta_friends(person_id bigint,
 dd_new_friends(person_id bigint,
                friend_id bigint).
 
-dd_new_friends(person_id, friend_id) :-
+dd_new_friends(person_id, friend_id)  :-
     friends(person_id, friend_id);
     dd_delta_friends(person_id, friend_id).
 
@@ -56,7 +56,7 @@ dd_delta_smoke?(person_id bigint).
 
 dd_new_smoke?(person_id bigint).
 
-dd_new_smoke(person_id) :-
+dd_new_smoke(person_id)  :-
     smoke(person_id);
     dd_delta_smoke(person_id).
 
@@ -66,31 +66,29 @@ dd_delta_cancer?(person_id bigint).
 
 dd_new_cancer?(person_id bigint).
 
-dd_new_cancer(person_id) :-
+dd_new_cancer(person_id)  :-
     cancer(person_id);
     dd_delta_cancer(person_id).
 
-dd_delta_smoke(pid) :-
+dd_delta_smoke(pid)  :-
     dd_delta_person_smokes(pid, l)
   label = l.
 
-dd_delta_cancer(pid) :-
+dd_delta_cancer(pid)  :-
     dd_delta_person_has_cancer(pid, l)
   label = l.
 
-dd_new_cancer(pid) :-
+dd_new_cancer(pid)  :-
     dd_delta_smoke(pid),
     person_smokes(pid, l);
     dd_new_smoke(pid),
     dd_delta_person_smokes(pid, l)
-  weight = 0.5
-  semantics = Imply.
+  weight = 0.5.
 
-dd_new_smoke(pid) :-
+dd_new_smoke(pid)  :-
     dd_delta_smoke(pid1),
     friends(pid1, pid);
     dd_new_smoke(pid1),
     dd_delta_friends(pid1, pid)
-  weight = 0.4
-  semantics = Imply.
+  weight = 0.4.
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index eccbb0b6f..f9e81e54d 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -14,23 +14,21 @@ smoke?(person_id bigint).
 
 cancer?(person_id bigint).
 
-smoke(pid) :-
+smoke(pid)  :-
     person_smokes(pid, l)
   label = l.
 
-cancer(pid) :-
+cancer(pid)  :-
     person_has_cancer(pid, l)
   label = l.
 
-cancer(pid) :-
+cancer(pid)  :-
     smoke(pid),
     person_smokes(pid, l)
-  weight = 0.5
-  semantics = Imply.
+  weight = 0.5.
 
-smoke(pid) :-
+smoke(pid)  :-
     smoke(pid1),
     friends(pid1, pid)
-  weight = 0.4
-  semantics = Imply.
+  weight = 0.4.
 
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 08a87f0a6..90523ea59 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -175,6 +175,5 @@ dd_new_has_spouse(rid)  :-
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
-  weight = f
-  semantics = Imply.
+  weight = f.
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index db505c038..5e07df218 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -73,6 +73,5 @@ has_spouse(rid)  :-
 has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
-  weight = f
-  semantics = Imply.
+  weight = f.
 
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 4e5711eea..0b1563441 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -75,4 +75,4 @@ has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f)
 weight = f
-semantics = Linear.
+function = Linear.
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 8ebd7d939..7575d31f3 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -177,5 +177,5 @@ dd_new_has_spouse(rid)  :-
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
   weight = f
-  semantics = Linear.
+  function = Linear.
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 3f1ab2e4a..71b4f119d 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -175,13 +175,11 @@ dd_new_has_spouse(rid)  :-
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f)
-  weight = f
-  semantics = Imply.
+  weight = f.
 
 dd_new_has_spouse(rid)  :-
     dd_new_has_spouse(rid2),
     dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
-  weight = 3.0
-  semantics = Imply.
+  weight = 3.0.
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 3aefbc215..742839292 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -73,13 +73,11 @@ has_spouse(rid)  :-
 has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f)
-  weight = f
-  semantics = Imply.
+  weight = f.
 
 has_spouse(rid)  :-
     has_spouse(rid2),
     has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
-  weight = 3.0
-  semantics = Imply.
+  weight = 3.0.
 

From 6927e14e986a38c76745a01ffaf389c6f62c9cfd Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 13 Jul 2015 00:54:52 -0700
Subject: [PATCH 170/347] Add support for IN, EXISTS, ANY, ALL

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  7 +++++
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 13 +++++++--
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  3 ++
 .../expressions/compile.expected              | 28 +++++++++++++++++--
 .../expressions/input.ddl                     |  6 +++-
 .../expressions/print.expected                |  6 ++++
 6 files changed, 58 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 4cac69c5d..d75ccffc1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -235,6 +235,13 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
           case LogicOperator.OR  => s"(${resolvedLhs} OR ${resolvedRhs})"
         }
       }
+      case InCond(lhs, rhs) => {
+        s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} IN (SELECT * FROM ${rhs})"
+      }
+      case ExistCond(rhs) => s"EXISTS (SELECT * FROM ${rhs})"
+      case QuantifiedCond(lhs, op, quan, rhs) => {
+        s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${quan} (SELECT * FROM ${rhs})"
+      }
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 6a39de807..4f97e8268 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -31,6 +31,9 @@ sealed trait Cond
 case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
 case class NegationCond(cond: Cond) extends Cond
 case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
+case class InCond(lhs: Expr, relName: String) extends Cond
+case class ExistCond(relName: String) extends Cond
+case class QuantifiedCond(lhs: Expr, op: String, quantifier: String, relName: String) extends Cond
 
 // logic operators
 object LogicOperator extends Enumeration {
@@ -153,6 +156,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
+  def inOperator = "IN"
+  def quantifierOperator = "ANY" | "ALL"
+
   def cond : Parser[Cond] = 
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
         CompoundCond(lhs, LogicOperator.OR, rhs)
@@ -169,9 +175,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | bcond
     )
   def bcond : Parser[Cond] = 
-    ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) =>
-        ComparisonCond(lhs, op, rhs)
+    ( expr ~ compareOperator ~ quantifierOperator ~ relationName ^^ { case (lhs ~ op ~ quan ~ rhs) => 
+        QuantifiedCond(lhs, op, quan, rhs) 
       }
+    | expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => ComparisonCond(lhs, op, rhs) }
+    | expr ~ inOperator ~ relationName ^^ { case (lhs ~ _ ~ rhs) => InCond(lhs, rhs) } 
+    | "EXISTS" ~> relationName ^^ { ExistCond(_) }
     | "[" ~> cond <~ "]"
     )
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index a291fc8ab..ce7d79a65 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -78,6 +78,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
           case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
         }
       }
+      case InCond(lhs, rhs) => s"${printExpr(lhs)} IN ${rhs}"
+      case ExistCond(rhs) => s"EXISTS ${rhs}"
+      case QuantifiedCond(lhs, op, quan, rhs) => s"${printExpr(lhs)} ${op} ${quan} ${rhs}"
     }
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 556d415b8..427f95c91 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -67,6 +67,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_18 {
+        sql: """ DROP VIEW IF EXISTS N;
+        CREATE VIEW N AS 
+            SELECT  R0.k AS "a.R0.k" 
+            FROM a R0
+        WHERE R0.k > ANY (SELECT * FROM G)
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
         CREATE VIEW J AS 
@@ -103,6 +115,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_17 {
+        sql: """ DROP VIEW IF EXISTS M;
+        CREATE VIEW M AS 
+            SELECT  R0.k AS "a.R0.k" 
+            FROM a R0
+        WHERE R0.k IN (SELECT * FROM G)
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS I;
         CREATE VIEW I AS 
@@ -224,6 +248,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 7e1bd8597..74070c3a8 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -33,4 +33,8 @@ J(x) :- b(x,y,z,w), [x + w = 100; !x > 50].
 K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
 
 # limit
-L(x) * | 100 :- b(x, y, z, w).
\ No newline at end of file
+L(x) * | 100 :- b(x, y, z, w).
+
+M(x) :- a(x), x IN G.
+
+N(x) :- a(x), x > ANY G.
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 7a29b3a82..a1a72da16 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -54,3 +54,9 @@ K(x)  :-
 L(x) * | 100 :-
     b(x, y, z, w).
 
+M(x)  :-
+    a(x), x IN G.
+
+N(x)  :-
+    a(x), x > ANY G.
+

From 36b87db405f0e5e30c9f2e1443b6f6d67217ae1e Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 13 Jul 2015 02:17:43 -0700
Subject: [PATCH 171/347] Add support for left outer join

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 21 ++++++++++++++++---
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  7 ++++++-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  1 +
 .../expressions/compile.expected              | 16 ++++++++++++--
 .../expressions/input.ddl                     |  4 +++-
 .../expressions/print.expected                |  4 ++++
 6 files changed, 46 insertions(+), 7 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d75ccffc1..1d6a15c4a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -242,13 +242,13 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case QuantifiedCond(lhs, op, quan, rhs) => {
         s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${quan} (SELECT * FROM ${rhs})"
       }
+      case _ => ""
     }
   }
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause (equating all variables)
   def generateSQLBody(z : ConjunctiveQuery) : String = {
-    val bodyNames = ( z.bodies(0).zipWithIndex map { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
     // Simple logic for the where clause, first find every first occurence of a
     // and stick it in a map.
     val qs = new QuerySchema(z)
@@ -278,7 +278,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
 
     // resolve conditions
-    val conditionStr = z.conditions(0) map (compileCond(_, z))
+    val conditionStr = z.conditions(0).flatMap {
+      case x: OuterJoinCond => None
+      case x: Cond => Some(compileCond(x, z))
+    }
 
     // handle group by
     // map head terms, leaving out aggregation functions
@@ -303,7 +306,19 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case None => ""
     }
 
-    s"""FROM ${ bodyNames }
+    // compile outer join
+    val bodyNames = z.bodies(0) map (_.name)
+    val outerJoins = z.conditions(0).collect { case x: OuterJoinCond => x }
+    val outerRelations = outerJoins map (_.relName) toSet
+    val outerJoinStr = (outerJoins map { case OuterJoinCond(name, cond) =>
+      s" LEFT OUTER JOIN ${name} R${bodyNames.indexOf(name)} ON ${compileCond(cond, z)} "
+    }).mkString
+
+    val fromBodyNames = (z.bodies(0).filterNot(outerRelations contains _.name).zipWithIndex map 
+      { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
+    val fromClause = fromBodyNames + outerJoinStr
+
+    s"""FROM ${ fromClause }
         ${ whereClauseStr }${groupbyStr}${limitStr}"""
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 4f97e8268..07f953ef0 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -34,6 +34,7 @@ case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) e
 case class InCond(lhs: Expr, relName: String) extends Cond
 case class ExistCond(relName: String) extends Cond
 case class QuantifiedCond(lhs: Expr, op: String, quantifier: String, relName: String) extends Cond
+case class OuterJoinCond(relName: String, cond: Cond) extends Cond
 
 // logic operators
 object LogicOperator extends Enumeration {
@@ -158,9 +159,13 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
   def inOperator = "IN"
   def quantifierOperator = "ANY" | "ALL"
+  def outerJoinOperator = "OUTER"
 
   def cond : Parser[Cond] = 
-    ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
+    ( outerJoinOperator ~> "(" ~> relationName ~ ":" ~ cond <~ ")" ^^ { case (relName ~ _ ~ cond) =>
+        OuterJoinCond(relName, cond)
+      }
+    | acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
         CompoundCond(lhs, LogicOperator.OR, rhs)
       }
     | acond
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index ce7d79a65..ef68c1616 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -81,6 +81,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case InCond(lhs, rhs) => s"${printExpr(lhs)} IN ${rhs}"
       case ExistCond(rhs) => s"EXISTS ${rhs}"
       case QuantifiedCond(lhs, op, quan, rhs) => s"${printExpr(lhs)} ${op} ${quan} ${rhs}"
+      case OuterJoinCond(relName, c) => s"OUTER(${relName}: ${printCond(c)})"
     }
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 427f95c91..e65b2a16b 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -235,6 +235,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ DROP VIEW IF EXISTS O;
+        CREATE VIEW O AS 
+            SELECT  R0.k AS "a.R0.k" 
+            FROM a R0 LEFT OUTER JOIN b R1 ON R0.k = R1.k 
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
         CREATE VIEW D AS 
@@ -248,6 +260,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 74070c3a8..e883b3f57 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -37,4 +37,6 @@ L(x) * | 100 :- b(x, y, z, w).
 
 M(x) :- a(x), x IN G.
 
-N(x) :- a(x), x > ANY G.
\ No newline at end of file
+N(x) :- a(x), x > ANY G.
+
+O(x) :- a(x), b(q,w,e,r), OUTER(b: x = q).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index a1a72da16..52ef4df1c 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -60,3 +60,7 @@ M(x)  :-
 N(x)  :-
     a(x), x > ANY G.
 
+O(x)  :-
+    a(x),
+    b(q, w, e, r), OUTER(b: x = q).
+

From df5bc238870ba53a6a3e9782ef86e2573eb4496c Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 13 Jul 2015 21:47:20 -0700
Subject: [PATCH 172/347] Add support for binding weight to a constant

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala     |  6 +++---
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 12 +++++-------
 .../deepdive/ddlog/DeepDiveLogPrettyPrinter.scala    |  1 +
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 1d6a15c4a..ece92d94b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -597,8 +597,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         // weight string
         val uwStr = stmt.weights match {
-          case KnownFactorWeight(x) => None
           case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, fakeCQ, OriginalAndAlias)).mkString(", "))
+          case _ => None
         }
 
         val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
@@ -631,9 +631,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
               val weightVar = w.flatMap(s => ss.resolveColumn(s, fakeCQ, AliasOnly)).mkString(", ")
-              if (weightVar == "") "?"
-              else s"?(${weightVar})"
+              s"?(${weightVar})"
             }
+            case UnknownFactorWeightBindingToConst(w) => "?"
           }
       }
       val blockName = ss.resolveInferenceBlockName(stmt)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 07f953ef0..1159533a7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -53,14 +53,11 @@ case class MultinomialType(numCategories: Int) extends VariableType {
   def cardinality = numCategories
 }
 
-sealed trait FactorWeight {
-  def variables : List[String]
-}
+sealed trait FactorWeight
 
-case class KnownFactorWeight(value: Double) extends FactorWeight {
-  def variables = Nil
-}
+case class KnownFactorWeight(value: Double) extends FactorWeight
 case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
+case class UnknownFactorWeightBindingToConst(value: String) extends FactorWeight
 
 trait RelationType
 case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
@@ -252,7 +249,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def constantWeight = floatingPointNumberAsDouble ^^ {   KnownFactorWeight(_) }
   def unknownWeight  = repsep(variableName, ",")   ^^ { UnknownFactorWeight(_) }
-  def factorWeight = "weight" ~> "=" ~> (constantWeight | unknownWeight)
+  def unknownWeightBindingToConst = stringLiteralAsString ^^ { UnknownFactorWeightBindingToConst(_) }
+  def factorWeight = "weight" ~> "=" ~> (constantWeight | unknownWeightBindingToConst | unknownWeight)
 
   def supervision = "label" ~> "=" ~> variableName
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index ef68c1616..92227fbc1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -134,6 +134,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       else "\n  weight = " + (stmt.weights match {
         case KnownFactorWeight(w) => w.toString
         case UnknownFactorWeight(vs) => vs.mkString(", ")
+        case UnknownFactorWeightBindingToConst(vs) => "\"" + vs + "\""
       })
     ) +
     ( stmt.function match {

From 8d38f48ace149c8a4f27e9815773c7fa22b135ae Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 13 Jul 2015 23:53:23 -0700
Subject: [PATCH 173/347] Fix aggregation in nested expressions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 21 ++++++++++++++-----
 .../expressions/compile.expected              |  1 +
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index ece92d94b..59aebf410 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -283,15 +283,26 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case x: Cond => Some(compileCond(x, z))
     }
 
-    // handle group by
-    // map head terms, leaving out aggregation functions
-    val groupbyTerms = z.head.terms.zipWithIndex map { case (expr, index) =>
+    // check if an expression contains an aggregation function
+    def containsAggregation(expr: Expr) : Boolean = {
       expr match {
-        case FuncExpr(f, args, agg) => if (agg) None else Some("")
-        case _ => Some(compileExpr(expr, z, OriginalOnly, index, false))
+        case VarExpr(name) => false
+        case ConstExpr(value) => false
+        case FuncExpr(function, args, agg) => if (agg) agg else {
+          args.map(containsAggregation).foldLeft(false)(_ || _)
+        }
+        case BinaryOpExpr(lhs, op, rhs) => containsAggregation(lhs) || containsAggregation(rhs)
+        case TypecastExpr(lhs, rhs) => containsAggregation(lhs)
       }
     }
 
+    // handle group by
+    // map head terms, leaving out aggregation functions
+    val groupbyTerms = z.head.terms.zipWithIndex flatMap { case (expr, index) =>
+      if (containsAggregation(expr)) None
+      else Some(compileExpr(expr, z, OriginalOnly, index, false))
+    }
+
     val groupbyStr = if (groupbyTerms.size == z.head.terms.size) {
       ""
     } else {
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index e65b2a16b..dbfb402bf 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -193,6 +193,7 @@
             SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS column_2
             FROM a R0, b R1
         WHERE R1.k = R0.k 
+        GROUP BY R1.p, R1.q
         """
         style: "sql_extractor"
           

From 7cfd485be11ffa6d1b9947c43ff9bb7312f44d2f Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 14 Jul 2015 11:55:52 -0700
Subject: [PATCH 174/347] Fix outer join

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  5 ++--
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 10 ++++---
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 22 +++++++++-------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 26 ++++++++++++-------
 .../expressions/compile.expected              |  2 +-
 .../expressions/input.ddl                     |  2 +-
 .../expressions/print.expected                |  2 +-
 8 files changed, 42 insertions(+), 29 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 59aebf410..efbb7b180 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -319,9 +319,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
     // compile outer join
     val bodyNames = z.bodies(0) map (_.name)
-    val outerJoins = z.conditions(0).collect { case x: OuterJoinCond => x }
-    val outerRelations = outerJoins map (_.relName) toSet
-    val outerJoinStr = (outerJoins map { case OuterJoinCond(name, cond) =>
+    val outerRelations = z.outerJoinConds(0) map (_.relName) toSet
+    val outerJoinStr = (z.outerJoinConds(0) map { case OuterJoinCond(name, cond) =>
       s" LEFT OUTER JOIN ${name} R${bodyNames.indexOf(name)} ON ${compileCond(cond, z)} "
     }).mkString
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index e2176fb46..4da0a9d63 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -33,6 +33,7 @@ object DeepDiveLogDeltaDeriver{
 
     var incCqBodies = new ListBuffer[List[Atom]]()
     var incCqConditions = new ListBuffer[Option[Cond]]()
+    var incCqOuterConditions = new ListBuffer[List[OuterJoinCond]]()
     // New incremental bodies
     cq.bodies zip cq.conditions foreach { case (body, cond) =>
       // Delta body
@@ -53,6 +54,7 @@ object DeepDiveLogDeltaDeriver{
       if (mode == "inc") {
         incCqBodies += incNewBody
         incCqConditions += cond
+        incCqOuterConditions += List()
       } else {
         for (i <- index to (body.length - 1)) {
           var newBody = new ListBuffer[Atom]()
@@ -64,13 +66,15 @@ object DeepDiveLogDeltaDeriver{
             else if (j == i)
               newBody += incDeltaBody(j)
             incCqConditions += cond
+            // NOTE we don't support outer join in derivation
+            incCqOuterConditions += List()
           }
           incCqBodies += newBody.toList
         }
       }
     }
-    // TODO fix conditions
-    ConjunctiveQuery(incCqHead, incCqBodies.toList, incCqConditions.toList, cq.isDistinct, cq.limit)
+    cq.copy(head = incCqHead, bodies = incCqBodies.toList, conditions = incCqConditions.toList,
+      outerJoinConds = incCqOuterConditions.toList)
   }
 
   // Incremental scheme declaration,
@@ -101,7 +105,7 @@ object DeepDiveLogDeltaDeriver{
       Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
       List(List(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) })),
         List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarExpr(_) }))), 
-      List(None, None), false, None))
+      List(None, None), false, None, List(List(), List())))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index f9eea977a..ee86ae479 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -19,7 +19,7 @@ object DeepDiveLogMergeDeriver{
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
       List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) }))),
-      List(None), false, None))
+      List(None), false, None, List(List())))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 1159533a7..e02d3915a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -22,9 +22,9 @@ case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 case class Atom(name : String, terms : List[Expr])
 case class Attribute(name : String, terms : List[String], types : List[String])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], 
-  isDistinct: Boolean, limit: Option[Int])
+  isDistinct: Boolean, limit: Option[Int], outerJoinConds: List[List[OuterJoinCond]])
 case class Column(name : String, t : String)
-case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
+case class BodyWithCondition(body: List[Atom], condition: Option[Cond], outerJoinCond: List[OuterJoinCond])
 
 // condition
 sealed trait Cond
@@ -34,7 +34,7 @@ case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) e
 case class InCond(lhs: Expr, relName: String) extends Cond
 case class ExistCond(relName: String) extends Cond
 case class QuantifiedCond(lhs: Expr, op: String, quantifier: String, relName: String) extends Cond
-case class OuterJoinCond(relName: String, cond: Cond) extends Cond
+case class OuterJoinCond(relName: String, cond: Cond)
 
 // logic operators
 object LogicOperator extends Enumeration {
@@ -159,10 +159,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def outerJoinOperator = "OUTER"
 
   def cond : Parser[Cond] = 
-    ( outerJoinOperator ~> "(" ~> relationName ~ ":" ~ cond <~ ")" ^^ { case (relName ~ _ ~ cond) =>
-        OuterJoinCond(relName, cond)
-      }
-    | acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
+    ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
         CompoundCond(lhs, LogicOperator.OR, rhs)
       }
     | acond
@@ -186,21 +183,26 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "[" ~> cond <~ "]"
     )
 
+  def outerJoinCond = 
+    outerJoinOperator ~> "(" ~> relationName ~ ":" ~ cond <~ ")" ^^ { case (relName ~ _ ~ cond) =>
+      OuterJoinCond(relName, cond)
+    }
+
   def cqBodyAtom: Parser[Atom] =
     relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
       case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
     }
   def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
 
-  def cqBodyWithCondition = cqBody ~ ("," ~> cond).? ^^ {
-    case (b ~ c) => BodyWithCondition(b, c)
+  def cqBodyWithCondition = cqBody ~ opt("," ~> rep1sep(outerJoinCond, ",")) ~ ("," ~> cond).? ^^ {
+    case (b ~ o ~ c) => BodyWithCondition(b, c, o.getOrElse(List()))
   }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
     cqHead ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
       case (headatom ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
         ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.condition), 
-          isDistinct != None, limit map (_.toInt))
+          isDistinct != None, limit map (_.toInt), disjunctiveBodies.map(_.outerJoinCond))
   }
 
   def relationType: Parser[RelationType] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 92227fbc1..98060f740 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -81,7 +81,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case InCond(lhs, rhs) => s"${printExpr(lhs)} IN ${rhs}"
       case ExistCond(rhs) => s"EXISTS ${rhs}"
       case QuantifiedCond(lhs, op, quan, rhs) => s"${printExpr(lhs)} ${op} ${quan} ${rhs}"
-      case OuterJoinCond(relName, c) => s"OUTER(${relName}: ${printCond(c)})"
     }
   }
 
@@ -94,16 +93,25 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       s"${(a map printAtom).mkString(",\n    ")}"
     }
 
-    val conditionList = cq.conditions map {
-      case Some(x) => Some(printCond(x))
-      case None    => None
+    var conditionList = cq.conditions map {
+      case Some(x) => printCond(x)
+      case None    => ""
     }
+
+    def printOuter(cond: OuterJoinCond) = {
+      s"OUTER(${cond.relName}: ${printCond(cond.cond)})"
+    }
+
+    def printOuterList(conds: List[OuterJoinCond]) : String = {
+      s"${(conds map printOuter).mkString(",\n    ")}"
+    }
+
+    val outerList = cq.outerJoinConds map (printOuterList(_))
+
+    // conditionList = outerList ++ conditionList
     val bodyList = cq.bodies map printListAtom
-    val bodyWithCondition = (bodyList zip conditionList map { case(a,b) => 
-      b match {
-        case Some(c) => s"${a}, ${c}" 
-        case None    => a
-      }
+    val bodyWithCondition = ((bodyList, outerList, conditionList).zipped.toList map { case(a,b,c) => 
+      List(a,b,c).filter(_ != "").mkString(", ")
     }).mkString(";\n    ")
 
     val distinctStr = if (cq.isDistinct) "*" else ""
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index dbfb402bf..d8788e85f 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -241,7 +241,7 @@
         CREATE VIEW O AS 
             SELECT  R0.k AS "a.R0.k" 
             FROM a R0 LEFT OUTER JOIN b R1 ON R0.k = R1.k 
-        
+        WHERE R0.k = R1.r
         """
         style: "sql_extractor"
           
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index e883b3f57..fcf87cfea 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -39,4 +39,4 @@ M(x) :- a(x), x IN G.
 
 N(x) :- a(x), x > ANY G.
 
-O(x) :- a(x), b(q,w,e,r), OUTER(b: x = q).
\ No newline at end of file
+O(x) :- a(x), b(q,w,e,r), OUTER(b: x = q), x = r.
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 52ef4df1c..88df9d43b 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -62,5 +62,5 @@ N(x)  :-
 
 O(x)  :-
     a(x),
-    b(q, w, e, r), OUTER(b: x = q).
+    b(q, w, e, r), OUTER(b: x = q), x = r.
 

From 6ee7d965a1344b0d0d0819daf0de67c01f3f9264 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 16 Jul 2015 01:05:07 -0700
Subject: [PATCH 175/347] Embeds SBT

---
 Makefile                   |   6 ++++++
 project/sbt/sbt            |   3 +++
 project/sbt/sbt-launch.jar | Bin 0 -> 1132093 bytes
 3 files changed, 9 insertions(+)
 create mode 100755 project/sbt/sbt
 create mode 100644 project/sbt/sbt-launch.jar

diff --git a/Makefile b/Makefile
index a2aa295f5..91e440c6a 100644
--- a/Makefile
+++ b/Makefile
@@ -17,6 +17,12 @@ clean: scala-clean
 	rm -f $(JAR) $(wildcard test/*/*/*.actual)
 	find test/ -name '*.bats' -type l -exec rm -f {} +
 
+PATH += :$(shell pwd)/project/sbt
+export PATH
+ifeq ($(shell uname),Darwin)
+SHELL := /bin/bash  # Mac requires SHELL to be forced to bash
+endif
+
 include scala.mk  # defines scala-build, scala-test-build, scala-assembly-jar, scala-clean targets
 
 
diff --git a/project/sbt/sbt b/project/sbt/sbt
new file mode 100755
index 000000000..be43b76e8
--- /dev/null
+++ b/project/sbt/sbt
@@ -0,0 +1,3 @@
+#!/bin/bash
+SBT_OPTS="-Xms512M -Xmx1536M -Xss1M -XX:+CMSClassUnloadingEnabled -XX:MaxPermSize=256M"
+java $SBT_OPTS -jar `dirname $0`/sbt-launch.jar "$@"
diff --git a/project/sbt/sbt-launch.jar b/project/sbt/sbt-launch.jar
new file mode 100644
index 0000000000000000000000000000000000000000..76342c66822d832bd88a4630c50274c24d539252
GIT binary patch
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HcmV?d00001


From 8c7723a55c4c0840084988a4637352df32e9b867 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 16 Jul 2015 03:47:56 -0700
Subject: [PATCH 176/347] Adds schema annotation syntax and export-schema mode

---
 .../org/deepdive/ddlog/DeepDiveLog.scala      |  1 +
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 21 +++----
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 57 ++++++++++++++-----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 29 ++++++++--
 .../ddlog/DeepDiveLogSchemaExporter.scala     | 40 +++++++++++++
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  6 +-
 test/expected-output-test.bats.template       |  9 +++
 .../annotations/export-schema.expected        |  1 +
 .../annotations/input.ddl                     | 18 ++++++
 .../annotations/print.expected                | 14 +++++
 .../annotations/printed.expected              |  7 +++
 11 files changed, 173 insertions(+), 30 deletions(-)
 create mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
 create mode 100644 test/expected-output-test/annotations/export-schema.expected
 create mode 100644 test/expected-output-test/annotations/input.ddl
 create mode 100644 test/expected-output-test/annotations/print.expected
 create mode 100644 test/expected-output-test/annotations/printed.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index db5ad3101..b47c5102f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -27,6 +27,7 @@ object DeepDiveLog {
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
     cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) }
+    cmd("export-schema")               required() action { (_, c) => c.copy(handler = DeepDiveLogSchemaExporter)  }
     opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
     opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
     opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 32ea7de9b..ba03fa72b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -113,14 +113,15 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // generate the statements.
     mode = config.mode
     statements.foreach {
-      case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
-        terms.zipWithIndex.foreach { 
+      case decl: SchemaDeclaration => {
+        val r = decl.a.name
+        decl.a.terms.zipWithIndex.foreach {
           case (n, i) =>
-            schema           += { (r,i) -> n }
-            ground_relations += { r -> !isQuery } // record whether a query or a ground term.
-            if (isQuery) variableType += { r -> vType.get }
+            schema           += { (r, i) -> n }
+            ground_relations += { r -> !decl.isQuery } // record whether a query or a ground term.
+            if (decl.isQuery) variableType += { r -> decl.variableType.get }
         }
-        if (isQuery) variableTableNames += r
+        if (decl.isQuery) variableTableNames += r
       }
       case ExtractionRule(_,_) => ()
       case InferenceRule(_,_,_,_) => ()
@@ -681,13 +682,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     var schema = Set[String]()
     // generate the statements.
     statements.foreach {
-      case SchemaDeclaration(a, isQuery, variableType) =>
-        if (isQuery) {
-          val variableTypeDecl = variableType match {
+      case decl: SchemaDeclaration =>
+        if (decl.isQuery) {
+          val variableTypeDecl = decl.variableType match {
             case Some(BooleanType)        => "Boolean"
             case Some(MultinomialType(x)) => s"Categorical(${x})"
           }
-          schema += s"${a.name}.label: ${variableTypeDecl}"
+          schema += s"${decl.a.name}.label: ${variableTypeDecl}"
         }
       case _ => ()
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 8cc7b2e77..1a867f2b3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -20,11 +20,18 @@ case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 
 case class Atom(name : String, terms : List[Expr])
-case class Attribute(name : String, terms : List[String], types : List[String])
+case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], isDistinct: Boolean)
-case class Column(name : String, t : String)
+case class Column(name : String // name of the column
+                 , t : String // type of the column
+                 , annotation: List[Annotation] = List.empty // optional annotation
+                 )
 case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 
+case class Annotation( name : String // name of the annotation
+                     , args : Map[String, Any] = Map.empty // optional, named arguments
+                     )
+
 // condition
 sealed trait Cond
 case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
@@ -66,7 +73,11 @@ case class RowWiseLineHandler(format: String, command: String) extends FunctionI
 
 // Statements that will be parsed and compiled
 trait Statement
-case class SchemaDeclaration( a : Attribute , isQuery : Boolean, variableType : Option[VariableType]) extends Statement // atom and whether this is a query relation.
+case class SchemaDeclaration( a : Attribute
+                            , isQuery : Boolean
+                            , variableType : Option[VariableType]
+                            , annotation : List[Annotation] = List.empty // optional annotation
+                            ) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
@@ -76,8 +87,10 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, semantics
 class DeepDiveLogParser extends JavaTokenParsers {
 
   // JavaTokenParsers provides several useful number parsers:
-  //   wholeNumber, decimalNumber, floatingPointNumber 
+  //   wholeNumber, decimalNumber, floatingPointNumber
   def floatingPointNumberAsDouble = floatingPointNumber ^^ { _.toDouble }
+  def wholeNumberAsInt = wholeNumber ^^ { _.toInt }
+  def wholeNumberAsLong = wholeNumber ^^ { _.toLong }
   def stringLiteralAsString = stringLiteral ^^ {
     s => StringEscapeUtils.unescapeJava(
       s.stripPrefix("\"").stripSuffix("\""))
@@ -102,10 +115,26 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def semanticType = ident
   def functionModeType = ident
   def inferenceModeType = ident
+  def annotationName = ident
+  def annotationArgumentName = ident
+
+  def annotation: Parser[Annotation] =
+    "@" ~ annotationName ~ opt("(" ~> repsep(annotationArgument, ",") <~ ")") ^^ {
+      case (_ ~ name ~ optArgs) =>
+        Annotation(name, optArgs getOrElse { List.empty } toMap)
+    }
+
+  def annotationArgument: Parser[(String, Any)] =
+    annotationArgumentName ~ "=" ~ annotationArgumentValue ^^ {
+      case name ~ _ ~ value => name -> value
+    }
+  def annotationArgumentValue: Parser[Any] =
+    stringLiteralAsString | floatingPointNumberAsDouble | wholeNumberAsInt
 
   def columnDeclaration: Parser[Column] =
+    rep(annotation) ~
     columnName ~ columnType ^^ {
-      case(name ~ ty) => Column(name, ty)
+      case(anno ~ name ~ ty) => Column(name, ty, anno)
     }
 
   def CategoricalParser = "Categorical" ~> "(" ~> """\d+""".r <~ ")" ^^ { n => MultinomialType(n.toInt) }
@@ -113,15 +142,17 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def dataType = CategoricalParser | BooleanParser
 
   def schemaDeclaration: Parser[SchemaDeclaration] =
+    rep(annotation) ~
     relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
-      case (r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
+      case (anno ~ r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
         val vars = attrs map (_.name)
         var types = attrs map (_.t)
+        val annos = attrs map (_.annotation)
         val variableType = vType match {
           case None => if (isQuery != None) Some(BooleanType) else None
           case Some(s) => Some(s)
         }
-        SchemaDeclaration(Attribute(r, vars, types), (isQuery != None), variableType)
+        SchemaDeclaration(Attribute(r, vars, types, annos), (isQuery != None), variableType, anno)
       }
     }
 
@@ -137,12 +168,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
     )
 
   def lexpr : Parser[Expr] =
-    ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ { 
+    ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
     | constant ^^ { ConstExpr(_) }
     | variableName ^^ { VarExpr(_) }
-    | "(" ~> expr <~ ")" 
+    | "(" ~> expr <~ ")"
     )
 
   // TODO support aggregate function syntax somehow
@@ -152,22 +183,22 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
-  def cond : Parser[Cond] = 
+  def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
         CompoundCond(lhs, LogicOperator.OR, rhs)
       }
     | acond
     )
-  def acond : Parser[Cond] = 
+  def acond : Parser[Cond] =
     ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND, rhs) }
     | lcond
     )
   // ! has higher priority...
-  def lcond : Parser[Cond] = 
+  def lcond : Parser[Cond] =
     ( "!" ~> bcond ^^ { NegationCond(_) }
     | bcond
     )
-  def bcond : Parser[Cond] = 
+  def bcond : Parser[Cond] =
     ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) =>
         ComparisonCond(lhs, op, rhs)
       }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 0d33cc5c1..fa7f0ce4b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -15,12 +15,27 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     case s: InferenceRule       => print(s)
   }
 
+  def printAnnotations(annos: List[Annotation], indentation: String = ""): String =
+    annos map {
+      case anno =>
+        s"@${anno.name}${
+          if (anno.args isEmpty) ""
+          else s"(${anno.args map {
+            case (name, value) => s"${name}=${printLiteral(value)}"
+          } mkString(", ")})"
+        }" + ("\n" + indentation)
+    } mkString
+
+
   def print(stmt: SchemaDeclaration): String = {
-    val columnDecls = stmt.a.terms.zipWithIndex map {
-      case (name,i) => s"${name} ${stmt.a.types(i)}"
-    }
     val prefix = s"${stmt.a.name}${if (stmt.isQuery) "?" else ""}("
     val indentation = " " * prefix.length
+    val columnDecls = stmt.a.terms.zipWithIndex map {
+      case (name,i) =>
+        printAnnotations(stmt.a.annotations(i), indentation) +
+        s"${name} ${stmt.a.types(i)}"
+    }
+    printAnnotations(stmt.annotation) +
     s"""${prefix}${columnDecls.mkString(",\n" + indentation)}).
        |""".stripMargin
   }
@@ -37,7 +52,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val outputType = print(stmt.outputType)
     val impls = stmt.implementations map {
       case impl: RowWiseLineHandler =>
-        "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" +
+        printLiteral(impl.command) +
         s"\n        handles ${impl.format} lines"
     }
     val modeStr = if (stmt.mode == null) "" else s" mode = ${stmt.mode}"
@@ -48,11 +63,17 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
        |""".stripMargin
   }
 
+  def printLiteral(value: Any): String = value match {
+    case s: String => "\"" + StringEscapeUtils.escapeJava(s) + "\""
+    case _ => value toString
+  }
+
   // print an expression
   def printExpr(e: Expr) : String = {
     e match {
       case VarExpr(name) => name
       case ConstExpr(value) => {
+        // TODO use distinct class for different types
         if (value.startsWith("'")) s""" "${value.stripPrefix("'").stripSuffix("'")}" """
         else value
       }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
new file mode 100644
index 000000000..6ddcfd0e4
--- /dev/null
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -0,0 +1,40 @@
+package org.deepdive.ddlog
+
+import org.apache.commons.lang3.StringEscapeUtils
+import org.deepdive.ddlog.DeepDiveLog.Mode._
+
+import scala.util.parsing.json.{JSONArray, JSONObject}
+
+// Schema exporter that dumps column names and types of every relation as well as their annotations
+object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
+
+  def export(decl: SchemaDeclaration): (String, JSONObject) = {
+    val schema = JSONObject(Map(
+      "columns" -> JSONObject(Map() ++ decl.a.terms.zipWithIndex map {
+        case (name, i) => (name, JSONObject(Map(
+          "type" -> decl.a.types(i),
+          "annotations" -> exportAnnotations(decl.a.annotations(i))
+        )))
+      }),
+      "annotations" -> exportAnnotations(decl.annotation)
+    ))
+    (decl.a.name, schema)
+  }
+
+  def exportAnnotations(annos: Seq[Annotation]): JSONArray =
+    JSONArray(annos map export toList)
+
+  def export(anno: Annotation): JSONObject =
+    JSONObject(Map(
+        "name" -> anno.name,
+        "args" -> JSONObject(anno.args)
+      ))
+
+  override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
+    val program = parsedProgram  // TODO derive the program based on config.mode?
+    val relations = program collect {
+      case decl: SchemaDeclaration => export(decl)
+    }
+    println(JSONObject(Map() ++ relations))
+  }
+}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 13fc3ed87..26d64fc9b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -74,9 +74,9 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkVariableRelationSchema(stmt: Statement) {
     val reservedSet = Set("id", "label")
     stmt match {
-      case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
-        if (isQuery) {
-          terms.foreach { case name => 
+      case decl: SchemaDeclaration => {
+        if (decl.isQuery) {
+          decl.a.terms.foreach { case name =>
             if (reservedSet contains name) 
               error(stmt, s"""variable relation contains reserved column "${name}" """)
           }
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index 2f83395c8..ba628fd47 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -54,6 +54,15 @@ setup() {
     diff "$expectedOutput" "$actualOutput"
 }
 
+# compare the export-schema output with what's expected
+@test "$it exports schema and annotations as expected" {
+    expectedOutput=$TESTDIR/export-schema.expected
+    actualOutput=${expectedOutput%.expected}.actual
+    [ -e "$expectedOutput" ] || skip
+    ddlog export-schema "$TESTDIR"/input.ddl >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
+}
+
 
 ## tests for --incremental support
 
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
new file mode 100644
index 000000000..33e139d71
--- /dev/null
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -0,0 +1 @@
+{"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text", "annotations" : []}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start", "args" : {}}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length", "args" : {}}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text", "annotations" : []}, "q" : {"type" : "int", "annotations" : []}, "r" : {"type" : "float", "annotations" : []}}, "annotations" : [{"name" : "foo", "args" : {}}, {"name" : "bar", "args" : {"x" : 1.0}}, {"name" : "qux", "args" : {"y" : 2.345}}]}}
diff --git a/test/expected-output-test/annotations/input.ddl b/test/expected-output-test/annotations/input.ddl
new file mode 100644
index 000000000..4124b63b5
--- /dev/null
+++ b/test/expected-output-test/annotations/input.ddl
@@ -0,0 +1,18 @@
+@textspan(from="start_pos", length="len")
+mention_candidate(
+  doc_id text,
+
+  @textspan_start
+  start_pos int,
+
+  @textspan_length
+  len int
+).
+
+
+@foo @bar(x=1) @qux(y=2.345)
+R(
+    p text,
+    q int,
+    r float
+).
diff --git a/test/expected-output-test/annotations/print.expected b/test/expected-output-test/annotations/print.expected
new file mode 100644
index 000000000..640cece52
--- /dev/null
+++ b/test/expected-output-test/annotations/print.expected
@@ -0,0 +1,14 @@
+@textspan(from="start_pos", length="len")
+mention_candidate(doc_id text,
+                  @textspan_start
+                  start_pos int,
+                  @textspan_length
+                  len int).
+
+@foo
+@bar(x=1.0)
+@qux(y=2.345)
+R(p text,
+  q int,
+  r float).
+
diff --git a/test/expected-output-test/annotations/printed.expected b/test/expected-output-test/annotations/printed.expected
new file mode 100644
index 000000000..8a34c9821
--- /dev/null
+++ b/test/expected-output-test/annotations/printed.expected
@@ -0,0 +1,7 @@
+@textspan(from="start_pos", length="len")
+mention_candidate(doc_id text,
+                  @textspan_start
+                  start_pos int,
+                  @textspan_length
+                  len int).
+

From 8a6bd94fc45229697280e578f67f54e903b7bc4a Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 16 Jul 2015 04:16:31 -0700
Subject: [PATCH 177/347] Enhances export-schema to avoid producing empty
 fields

e.g., empty annotations, empty args for annotations

Closes #35
---
 .../ddlog/DeepDiveLogSchemaExporter.scala     | 58 +++++++++++++------
 .../annotations/export-schema.expected        |  2 +-
 2 files changed, 40 insertions(+), 20 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 6ddcfd0e4..59fd44796 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -8,33 +8,53 @@ import scala.util.parsing.json.{JSONArray, JSONObject}
 // Schema exporter that dumps column names and types of every relation as well as their annotations
 object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
 
+  def jsonMap(kvs: (String, Any)*): Map[String, Any] = kvs toMap
+
   def export(decl: SchemaDeclaration): (String, JSONObject) = {
-    val schema = JSONObject(Map(
-      "columns" -> JSONObject(Map() ++ decl.a.terms.zipWithIndex map {
-        case (name, i) => (name, JSONObject(Map(
-          "type" -> decl.a.types(i),
-          "annotations" -> exportAnnotations(decl.a.annotations(i))
-        )))
-      }),
-      "annotations" -> exportAnnotations(decl.annotation)
-    ))
-    (decl.a.name, schema)
+    var schema = jsonMap(
+//      "name" -> decl.a.name // XXX redundant but potentially useful
+    )
+    // column names with types and annotations
+    schema += "columns" -> JSONObject(
+      decl.a.terms.zipWithIndex map {
+        case (name, i) =>
+          var columnSchema = jsonMap(
+//              "name" -> name, // XXX redundant but potentially useful
+              "type" -> decl.a.types(i)
+          )
+          // column annotations are omitted when not present
+          val annos = decl.a.annotations(i)
+          if (annos nonEmpty)
+            columnSchema += "annotations" -> exportAnnotations(annos)
+
+          (name, JSONObject(columnSchema))
+      } toMap)
+    // relation annotations are omitted when not present
+    if (decl.annotation nonEmpty)
+      schema += "annotations" -> exportAnnotations(decl.annotation)
+
+    (decl.a.name, JSONObject(schema))
   }
 
   def exportAnnotations(annos: Seq[Annotation]): JSONArray =
     JSONArray(annos map export toList)
 
-  def export(anno: Annotation): JSONObject =
-    JSONObject(Map(
-        "name" -> anno.name,
-        "args" -> JSONObject(anno.args)
-      ))
+  def export(anno: Annotation): JSONObject = {
+    var a = jsonMap(
+      "name" -> anno.name
+    )
+    if (anno.args nonEmpty)
+      a += "args" -> JSONObject(anno.args)
+    JSONObject(a)
+  }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     val program = parsedProgram  // TODO derive the program based on config.mode?
-    val relations = program collect {
-      case decl: SchemaDeclaration => export(decl)
-    }
-    println(JSONObject(Map() ++ relations))
+
+    println(JSONObject(Map(
+      "relations" -> JSONObject(program collect {
+          case decl: SchemaDeclaration => export(decl)
+        } toMap)
+    )))
   }
 }
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
index 33e139d71..dde7a42cd 100644
--- a/test/expected-output-test/annotations/export-schema.expected
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -1 +1 @@
-{"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text", "annotations" : []}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start", "args" : {}}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length", "args" : {}}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text", "annotations" : []}, "q" : {"type" : "int", "annotations" : []}, "r" : {"type" : "float", "annotations" : []}}, "annotations" : [{"name" : "foo", "args" : {}}, {"name" : "bar", "args" : {"x" : 1.0}}, {"name" : "qux", "args" : {"y" : 2.345}}]}}
+{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float"}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1.0}}, {"name" : "qux", "args" : {"y" : 2.345}}]}}}

From ac37c2bd7efa9cd11fb90aa2c372aad663093a1f Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 01:49:59 -0700
Subject: [PATCH 178/347] Unify atom and condition

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 82 ++++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 50 ++++++-----
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 48 ++++-------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 32 +++-----
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 17 +++-
 .../expressions/compile.expected              | 40 +--------
 .../expressions/input.ddl                     |  6 +-
 .../expressions/print.expected                | 28 +++----
 9 files changed, 124 insertions(+), 181 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index efbb7b180..183119ebd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -180,7 +180,11 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     val qs = new QuerySchema(q)
     val index = qs.getBodyIndex(s)
     val name  = resolveName(qs.getVar(s))
-    val relation = q.bodies(0)(index).name
+    // TODO better way to get relation
+    val relation = q.bodies(0)(index) match {
+      case x: Atom => x.name
+      case _  => error("Wrong index")
+    }
     alias match {
       case OriginalOnly => Some(s"R${index}.${name}")
       case AliasOnly => Some(s"${relation}.R${index}.${name}")
@@ -196,7 +200,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         case VarExpr(name) => resolveColumn(name, cq, alias).get
         case ConstExpr(value) => value
         case FuncExpr(function, args, agg) => {
-          // note alias is overriden with OriginalOnly, because when an expression appears in 
+          // note alias is overriden with OriginalOnly, because when an expression appears in
           // the function, we only need it's column name, without " AS ..." aliasing, same below
           val resolvedArgs = args map (x => compileExprInner(x, OriginalOnly))
           val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
@@ -239,9 +243,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} IN (SELECT * FROM ${rhs})"
       }
       case ExistCond(rhs) => s"EXISTS (SELECT * FROM ${rhs})"
-      case QuantifiedCond(lhs, op, quan, rhs) => {
-        s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${quan} (SELECT * FROM ${rhs})"
-      }
       case _ => ""
     }
   }
@@ -275,12 +276,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
           }
         }
       }
-    }
-
-    // resolve conditions
-    val conditionStr = z.conditions(0).flatMap {
-      case x: OuterJoinCond => None
-      case x: Cond => Some(compileCond(x, z))
+      case (x: Cond, i) => Some(compileCond(x, z))
     }
 
     // check if an expression contains an aggregation function
@@ -303,30 +299,24 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       else Some(compileExpr(expr, z, OriginalOnly, index, false))
     }
 
-    val groupbyStr = if (groupbyTerms.size == z.head.terms.size) {
+    val groupbyStr = if (groupbyTerms.size == z.head.terms.size || groupbyTerms.isEmpty) {
       ""
     } else {
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
     }
 
-    val whereClauseConds = whereClause ++ conditionStr
-    val whereClauseStr = if (whereClauseConds isEmpty) "" else whereClauseConds.mkString("WHERE ", " AND ", "")
+    val whereClauseStr = if (whereClause.isEmpty) "" else whereClause.mkString("WHERE ", " AND ", "")
 
     val limitStr = z.limit match {
       case Some(s) => s" LIMIT ${s}"
       case None => ""
     }
 
-    // compile outer join
-    val bodyNames = z.bodies(0) map (_.name)
-    val outerRelations = z.outerJoinConds(0) map (_.relName) toSet
-    val outerJoinStr = (z.outerJoinConds(0) map { case OuterJoinCond(name, cond) =>
-      s" LEFT OUTER JOIN ${name} R${bodyNames.indexOf(name)} ON ${compileCond(cond, z)} "
-    }).mkString
-
-    val fromBodyNames = (z.bodies(0).filterNot(outerRelations contains _.name).zipWithIndex map 
-      { case(x,i) => s"${x.name} R${i}"}).mkString(", ")
-    val fromClause = fromBodyNames + outerJoinStr
+    val fromBodyNames = (z.bodies(0).zipWithIndex flatMap {
+      case(x:Atom,i) => Some(s"${x.name} R${i}")
+      case _ => None
+    }).mkString(", ")
+    val fromClause = fromBodyNames
 
     s"""FROM ${ fromClause }
         ${ whereClauseStr }${groupbyStr}${limitStr}"""
@@ -358,7 +348,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
   }
 
-  // Analyze the block visibility among statements 
+  // Analyze the block visibility among statements
   def analyzeVisible(statements: List[Statement]) = {
     extractionRuleGroupByHead.values foreach { visible += _(0) }
     functionCallList foreach { visible += _ }
@@ -366,13 +356,19 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Analyze the dependency between statements and construct a graph.
   def analyzeDependency(statements: List[Statement]) = {
-    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++ functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
+    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++
+      functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
     // Look at the body of each statement to construct a dependency graph
     statements foreach {
-      case f : FunctionCallRule => dependencies += { f -> ((        Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case e : ExtractionRule   => dependencies += { e -> ((e.q.bodies.flatten map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case w : InferenceRule    => dependencies += { w -> ((w.q.bodies.flatten map (_.name) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case f : FunctionCallRule => dependencies += {
+        f -> (( Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case e : ExtractionRule   => dependencies += {
+        e -> (((e.q.bodies.flatten collect { case x: Atom => x.name })
+          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case w : InferenceRule    => dependencies += {
+        w -> (((w.q.bodies.flatten collect { case x: Atom => x.name })
+          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case _ =>
     }
   }
@@ -404,13 +400,14 @@ class QuerySchema(q : ConjunctiveQuery) {
       case (Atom(relName,terms),index) =>  {
         terms.zipWithIndex.foreach { case (expr, i) =>
           expr match {
-            case VarExpr(v) => 
+            case VarExpr(v) =>
               if (! (query_schema contains v) )
                 query_schema += { v -> (index, Variable(v,relName,i) ) }
             case _ =>
           }
         }
       }
+      case _ =>
     }
   }
   generateCanonicalVar() // initialize
@@ -482,7 +479,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) => 
+          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) =>
             ss.compileExpr(expr, tmpCq, OriginalOnly, index, true)
           }
           val index = qs.getBodyIndex(stmt.supervision)
@@ -493,7 +490,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) => 
+          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) =>
             ss.compileExpr(expr, tmpCq, OriginalOnly, index, true)
           }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
@@ -511,7 +508,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case true => OriginalOnly
             case false => OriginalAndAlias
           }
-          val variableCols = tmpCq.head.terms.zipWithIndex map { case (expr, index) => 
+          val variableCols = tmpCq.head.terms.zipWithIndex map { case (expr, index) =>
             ss.compileExpr(expr, tmpCq, resolveColumnFlag, index, true)
           }
           val selectStr = variableCols.mkString(", ")
@@ -594,14 +591,19 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // edge query
         val fakeBody        = stmt.q.head +: cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
+        val fakeBodyAtoms   = fakeBody.collect { case x: Atom => x }
 
         val index = cqBody.length + 1
         val qs2 = new QuerySchema( fakeCQ )
-        val varInBody = (fakeBody map {x =>
-          if (ss.variableTableNames contains x.name)
-            s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """
-          else ""
-          }).filter(_ != "")
+        // TODO self-join?
+        val varInBody = (fakeBody.zipWithIndex flatMap {
+          case (x: Atom, i) =>
+            if (ss.variableTableNames contains x.name)
+              Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
+            else
+              None
+          case _ => None
+        })
 
         val variableIdsStr = Some(varInBody.mkString(", "))
 
@@ -619,7 +621,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(fakeCQ) }"""
         // factor function
         if (func.length == 0) {
-          val funcBody = (fakeBody map {x =>
+          val funcBody = (fakeBodyAtoms map {x =>
           if (ss.variableTableNames contains x.name)
             s"""${x.name}.R${fakeBody indexOf x}.label"""
           else ""
@@ -761,7 +763,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     state.extractionRuleGroupByHead    foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
     state.functionCallRuleGroupByInput foreach {keyVal => body ++= compileFunctionCallRules(keyVal._2, state)}
     state.inferenceRuleGroupByHead     foreach {keyVal => body ++= compileInferenceRules(keyVal._2, state)}
-    
+
     // compile the program into blocks of application.conf
     val blocks = (
       compileUserSettings(state)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 4da0a9d63..26a4e221a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -31,50 +31,46 @@ object DeepDiveLogDeltaDeriver{
       )
     }
 
-    var incCqBodies = new ListBuffer[List[Atom]]()
-    var incCqConditions = new ListBuffer[Option[Cond]]()
-    var incCqOuterConditions = new ListBuffer[List[OuterJoinCond]]()
+    var incCqBodies = new ListBuffer[List[Body]]()
     // New incremental bodies
-    cq.bodies zip cq.conditions foreach { case (body, cond) =>
+    cq.bodies foreach { bodies =>
       // Delta body
-      val incDeltaBody = body map {
-        a => a.copy(
-          name = deltaPrefix + a.name
-        )
+      val incDeltaBody = bodies map { 
+        case a: Atom => a.copy(name = deltaPrefix + a.name)
+        case a: Cond => a
       }
       // New body
-      val incNewBody = body map {
-        a => a.copy(
-          name = newPrefix + a.name
-        )
+      val incNewBody = bodies map {
+        case a: Atom => a.copy(name = newPrefix + a.name)
+        case a: Cond => a
       }
+      val bodyAtoms         = bodies       collect { case a: Atom => a }
+      val bodyConds         = bodies       collect { case a: Cond => a }
+      val incDeltaBodyAtoms = incDeltaBody collect { case a: Atom => a }
+      val incNewBodyAtoms   = incNewBody   collect { case a: Atom => a }
+
       var i = 0
       var j = 0
       var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
       if (mode == "inc") {
         incCqBodies += incNewBody
-        incCqConditions += cond
-        incCqOuterConditions += List()
       } else {
-        for (i <- index to (body.length - 1)) {
-          var newBody = new ListBuffer[Atom]()
-          for (j <- 0 to (body.length - 1)) {
+        for (i <- index to (bodyAtoms.length - 1)) {
+          var newBody = new ListBuffer[Body]()
+          for (j <- 0 to (bodyAtoms.length - 1)) {
             if (j > i)
-              newBody += body(j)
+              newBody += bodyAtoms(j)
             else if (j < i)
-              newBody += incNewBody(j)
+              newBody += incNewBodyAtoms(j)
             else if (j == i)
-              newBody += incDeltaBody(j)
-            incCqConditions += cond
-            // NOTE we don't support outer join in derivation
-            incCqOuterConditions += List()
+              newBody += incDeltaBodyAtoms(j)
           }
+          newBody = newBody ++ bodyConds
           incCqBodies += newBody.toList
         }
       }
     }
-    cq.copy(head = incCqHead, bodies = incCqBodies.toList, conditions = incCqConditions.toList,
-      outerJoinConds = incCqOuterConditions.toList)
+    cq.copy(head = incCqHead, bodies = incCqBodies.toList)
   }
 
   // Incremental scheme declaration,
@@ -104,8 +100,8 @@ object DeepDiveLogDeltaDeriver{
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
       Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
       List(List(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) })),
-        List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarExpr(_) }))), 
-      List(None, None), false, None, List(List(), List())))
+        List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarExpr(_) }))),
+      false, None))
     // }
     incrementalStatement.toList
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index ee86ae479..b2d2ce509 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -19,7 +19,7 @@ object DeepDiveLogMergeDeriver{
 
     ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
       List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) }))),
-      List(None), false, None, List(List())))
+      false, None))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index e02d3915a..6774a82ec 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -19,22 +19,20 @@ case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean)
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 
-case class Atom(name : String, terms : List[Expr])
+sealed trait Body
+case class Atom(name : String, terms : List[Expr]) extends Body
 case class Attribute(name : String, terms : List[String], types : List[String])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Atom]], conditions: List[Option[Cond]], 
-  isDistinct: Boolean, limit: Option[Int], outerJoinConds: List[List[OuterJoinCond]])
+case class ConjunctiveQuery(head: Atom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
 case class Column(name : String, t : String)
-case class BodyWithCondition(body: List[Atom], condition: Option[Cond], outerJoinCond: List[OuterJoinCond])
+case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 
 // condition
-sealed trait Cond
+sealed trait Cond extends Body
 case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
 case class NegationCond(cond: Cond) extends Cond
 case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
 case class InCond(lhs: Expr, relName: String) extends Cond
 case class ExistCond(relName: String) extends Cond
-case class QuantifiedCond(lhs: Expr, op: String, quantifier: String, relName: String) extends Cond
-case class OuterJoinCond(relName: String, cond: Cond)
 
 // logic operators
 object LogicOperator extends Enumeration {
@@ -129,9 +127,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def operator = "||" | "+" | "-" | "*" | "/" | "&"
   def typeOperator = "::"
-  val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG")
+  val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG", "COUNT")
 
-  // expressions
+  // expression
   def expr : Parser[Expr] =
     ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
@@ -156,7 +154,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
   def inOperator = "IN"
   def quantifierOperator = "ANY" | "ALL"
-  def outerJoinOperator = "OUTER"
 
   def cond : Parser[Cond] = 
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
@@ -174,35 +171,24 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | bcond
     )
   def bcond : Parser[Cond] = 
-    ( expr ~ compareOperator ~ quantifierOperator ~ relationName ^^ { case (lhs ~ op ~ quan ~ rhs) => 
-        QuantifiedCond(lhs, op, quan, rhs) 
-      }
-    | expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => ComparisonCond(lhs, op, rhs) }
+    ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => ComparisonCond(lhs, op, rhs) }
     | expr ~ inOperator ~ relationName ^^ { case (lhs ~ _ ~ rhs) => InCond(lhs, rhs) } 
     | "EXISTS" ~> relationName ^^ { ExistCond(_) }
     | "[" ~> cond <~ "]"
     )
 
-  def outerJoinCond = 
-    outerJoinOperator ~> "(" ~> relationName ~ ":" ~ cond <~ ")" ^^ { case (relName ~ _ ~ cond) =>
-      OuterJoinCond(relName, cond)
-    }
-
-  def cqBodyAtom: Parser[Atom] =
-    relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
-      case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
-    }
-  def cqBody: Parser[List[Atom]] = rep1sep(cqBodyAtom, ",")
-
-  def cqBodyWithCondition = cqBody ~ opt("," ~> rep1sep(outerJoinCond, ",")) ~ ("," ~> cond).? ^^ {
-    case (b ~ o ~ c) => BodyWithCondition(b, c, o.getOrElse(List()))
-  }
+  def cqBody: Parser[Body] =
+    ( relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
+        case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
+      }
+    | cond
+    )
+  def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
-    cqHead ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqBodyWithCondition, ";") ^^ {
+    cqHead ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
       case (headatom ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(headatom, disjunctiveBodies.map(_.body), disjunctiveBodies.map(_.condition), 
-          isDistinct != None, limit map (_.toInt), disjunctiveBodies.map(_.outerJoinCond))
+        ConjunctiveQuery(headatom, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
   }
 
   def relationType: Parser[RelationType] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 98060f740..5df383ec7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -80,39 +80,27 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
       case InCond(lhs, rhs) => s"${printExpr(lhs)} IN ${rhs}"
       case ExistCond(rhs) => s"EXISTS ${rhs}"
-      case QuantifiedCond(lhs, op, quan, rhs) => s"${printExpr(lhs)} ${op} ${quan} ${rhs}"
     }
   }
 
   def print(cq: ConjunctiveQuery): String = {
-    val printAtom = {a:Atom =>
+    def printAtom(a: Atom) = {
       val vars = a.terms map printExpr
       s"${a.name}(${vars.mkString(", ")})"
     }
-    val printListAtom = {a:List[Atom] =>
-      s"${(a map printAtom).mkString(",\n    ")}"
-    }
-
-    var conditionList = cq.conditions map {
-      case Some(x) => printCond(x)
-      case None    => ""
-    }
 
-    def printOuter(cond: OuterJoinCond) = {
-      s"OUTER(${cond.relName}: ${printCond(cond.cond)})"
+    def printBody(b: Body) = {
+      b match {
+        case b: Atom => printAtom(b)
+        case b: Cond => printCond(b)
+      }
     }
 
-    def printOuterList(conds: List[OuterJoinCond]) : String = {
-      s"${(conds map printOuter).mkString(",\n    ")}"
+    def printBodyList(b: List[Body]) = {
+      s"${(b map printBody).mkString(",\n    ")}"
     }
 
-    val outerList = cq.outerJoinConds map (printOuterList(_))
-
-    // conditionList = outerList ++ conditionList
-    val bodyList = cq.bodies map printListAtom
-    val bodyWithCondition = ((bodyList, outerList, conditionList).zipped.toList map { case(a,b,c) => 
-      List(a,b,c).filter(_ != "").mkString(", ")
-    }).mkString(";\n    ")
+    val bodyStr = (cq.bodies map printBodyList).mkString(";\n    ")
 
     val distinctStr = if (cq.isDistinct) "*" else ""
     val limitStr = cq.limit match {
@@ -121,7 +109,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     }
 
     s"""${printAtom(cq.head)} ${distinctStr}${limitStr} :-
-       |    ${bodyWithCondition}""".stripMargin
+       |    ${bodyStr}""".stripMargin
   }
 
   def print(stmt: ExtractionRule): String = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 13fc3ed87..b256bce8b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -46,12 +46,18 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case s: ExtractionRule => {
         s.q.bodies foreach { x => 
-          x foreach { a => checkRelation(a.name) }
+          x foreach {
+            case a: Atom => checkRelation(a.name)
+            case _ =>
+          }
         }
       }
       case s: InferenceRule => {
         s.q.bodies foreach { x => 
-          x foreach { a => checkRelation(a.name) }
+          x foreach {
+            case a: Atom => checkRelation(a.name)
+            case _ =>
+          }
         }
       }
       case s: FunctionCallRule => checkRelation(s.input)
@@ -95,7 +101,12 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
     def checkCq(cq: ConjunctiveQuery) {
       checkAtom(cq.head)
-      cq.bodies foreach { x => x foreach checkAtom }
+      cq.bodies foreach { x =>
+        x foreach {
+          case a: Atom => checkAtom(a)
+          case _ =>
+        }
+      }
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index d8788e85f..49591e797 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -67,18 +67,6 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_18 {
-        sql: """ DROP VIEW IF EXISTS N;
-        CREATE VIEW N AS 
-            SELECT  R0.k AS "a.R0.k" 
-            FROM a R0
-        WHERE R0.k > ANY (SELECT * FROM G)
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
         CREATE VIEW J AS 
@@ -115,18 +103,6 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_17 {
-        sql: """ DROP VIEW IF EXISTS M;
-        CREATE VIEW M AS 
-            SELECT  R0.k AS "a.R0.k" 
-            FROM a R0
-        WHERE R0.k IN (SELECT * FROM G)
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS I;
         CREATE VIEW I AS 
@@ -236,18 +212,6 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
-        sql: """ DROP VIEW IF EXISTS O;
-        CREATE VIEW O AS 
-            SELECT  R0.k AS "a.R0.k" 
-            FROM a R0 LEFT OUTER JOIN b R1 ON R0.k = R1.k 
-        WHERE R0.k = R1.r
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
         CREATE VIEW D AS 
@@ -261,6 +225,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index fcf87cfea..79c8599fe 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -35,8 +35,8 @@ K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
 # limit
 L(x) * | 100 :- b(x, y, z, w).
 
-M(x) :- a(x), x IN G.
+# M(x) :- a(x), x IN G.
 
-N(x) :- a(x), x > ANY G.
+# N(x) :- a(x), x > ANY G.
 
-O(x) :- a(x), b(q,w,e,r), OUTER(b: x = q), x = r.
\ No newline at end of file
+# O(x) :- a(x), b(q,w,e,r), OUTER(b: x = q), x = r.
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 88df9d43b..95533eaa1 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -12,7 +12,8 @@ c(s text,
 Q(( "test"  :: TEXT), 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c((x || y), 10,  "foo" ), [z > 100; [[!z < 20], z < 50]].
+    c((x || y), 10,  "foo" ),
+    [z > 100; [[!z < 20], z < 50]].
 
 P(y, z, MAX(w))  :-
     a(x),
@@ -37,30 +38,25 @@ F(((x :: INT) + (w :: INT)))  :-
     b(x, y, z, w).
 
 G(x)  :-
-    b(x, y, z, w), (x + w) = 100.
+    b(x, y, z, w),
+    (x + w) = 100.
 
 H(x)  :-
-    b(x, y, z, w), [(x + w) = 100, x > 50].
+    b(x, y, z, w),
+    [(x + w) = 100, x > 50].
 
 I(x)  :-
-    b(x, y, z, w), [(x + w) = 100; [x > 50, w < 10]].
+    b(x, y, z, w),
+    [(x + w) = 100; [x > 50, w < 10]].
 
 J(x)  :-
-    b(x, y, z, w), [(x + w) = 100; [!x > 50]].
+    b(x, y, z, w),
+    [(x + w) = 100; [!x > 50]].
 
 K(x)  :-
-    b(x, y, z, w), [(x + w) = 100, [[!x > 50]; x = 40]].
+    b(x, y, z, w),
+    [(x + w) = 100, [[!x > 50]; x = 40]].
 
 L(x) * | 100 :-
     b(x, y, z, w).
 
-M(x)  :-
-    a(x), x IN G.
-
-N(x)  :-
-    a(x), x > ANY G.
-
-O(x)  :-
-    a(x),
-    b(q, w, e, r), OUTER(b: x = q), x = r.
-

From 723d28f3f489276f0ad182f27b186da76f95ffd9 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 01:51:45 -0700
Subject: [PATCH 179/347] Remove trailing whitespaces

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 10 ++++-----
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  6 ++---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 16 +++++++-------
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 22 +++++++++----------
 4 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 183119ebd..d38328d7e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -114,7 +114,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     mode = config.mode
     statements.foreach {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
-        terms.zipWithIndex.foreach { 
+        terms.zipWithIndex.foreach {
           case (n, i) =>
             schema           += { (r,i) -> n }
             ground_relations += { r -> !isQuery } // record whether a query or a ground term.
@@ -228,14 +228,14 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // resolve a condition
   def compileCond(cond: Cond, cq: ConjunctiveQuery) : String = {
     cond match {
-      case ComparisonCond(lhs, op, rhs) => 
+      case ComparisonCond(lhs, op, rhs) =>
         s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${compileExpr(rhs, cq, OriginalOnly, 0, false)}"
       case NegationCond(c) => s"(NOT ${compileCond(c, cq)})"
       case CompoundCond(lhs, op, rhs) => {
         val resolvedLhs = s"${compileCond(lhs, cq)}"
         val resolvedRhs = s"${compileCond(rhs, cq)}"
         op match {
-          case LogicOperator.AND => s"(${resolvedLhs} AND ${resolvedRhs})" 
+          case LogicOperator.AND => s"(${resolvedLhs} AND ${resolvedRhs})"
           case LogicOperator.OR  => s"(${resolvedLhs} OR ${resolvedRhs})"
         }
       }
@@ -452,8 +452,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       }
     }
     // Cleanup incremental table extractor
-    val truncateTableList = (stmts map (x => 
-      if ((x.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains x.a.name)) "" 
+    val truncateTableList = (stmts map (x =>
+      if ((x.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains x.a.name)) ""
       else s"TRUNCATE ${x.a.name};")).filter(_ != "")
     if (truncateTableList.length > 0) {
       schemas += s"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 26a4e221a..80150a741 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -35,7 +35,7 @@ object DeepDiveLogDeltaDeriver{
     // New incremental bodies
     cq.bodies foreach { bodies =>
       // Delta body
-      val incDeltaBody = bodies map { 
+      val incDeltaBody = bodies map {
         case a: Atom => a.copy(name = deltaPrefix + a.name)
         case a: Cond => a
       }
@@ -111,9 +111,9 @@ object DeepDiveLogDeltaDeriver{
   def transform(stmt: FunctionDeclaration): List[Statement] = {
     List(stmt.copy(
       inputType = stmt.inputType match {
-        case inTy: RelationTypeDeclaration => 
+        case inTy: RelationTypeDeclaration =>
           inTy.copy(names = inTy.names map {name => deltaPrefix + name})
-        case inTy: RelationTypeAlias => 
+        case inTy: RelationTypeAlias =>
           inTy.copy(likeRelationName = deltaPrefix + inTy.likeRelationName)
       },
       outputType = stmt.outputType match {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 6774a82ec..764074fce 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -76,7 +76,7 @@ case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function
 class DeepDiveLogParser extends JavaTokenParsers {
 
   // JavaTokenParsers provides several useful number parsers:
-  //   wholeNumber, decimalNumber, floatingPointNumber 
+  //   wholeNumber, decimalNumber, floatingPointNumber
   def floatingPointNumberAsDouble = floatingPointNumber ^^ { _.toDouble }
   def stringLiteralAsString = stringLiteral ^^ {
     s => StringEscapeUtils.unescapeJava(
@@ -137,12 +137,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
     )
 
   def lexpr : Parser[Expr] =
-    ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ { 
+    ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
     | constant ^^ { ConstExpr(_) }
     | variableName ^^ { VarExpr(_) }
-    | "(" ~> expr <~ ")" 
+    | "(" ~> expr <~ ")"
     )
 
   // TODO support aggregate function syntax somehow
@@ -155,24 +155,24 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def inOperator = "IN"
   def quantifierOperator = "ANY" | "ALL"
 
-  def cond : Parser[Cond] = 
+  def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
         CompoundCond(lhs, LogicOperator.OR, rhs)
       }
     | acond
     )
-  def acond : Parser[Cond] = 
+  def acond : Parser[Cond] =
     ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND, rhs) }
     | lcond
     )
   // ! has higher priority...
-  def lcond : Parser[Cond] = 
+  def lcond : Parser[Cond] =
     ( "!" ~> bcond ^^ { NegationCond(_) }
     | bcond
     )
-  def bcond : Parser[Cond] = 
+  def bcond : Parser[Cond] =
     ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => ComparisonCond(lhs, op, rhs) }
-    | expr ~ inOperator ~ relationName ^^ { case (lhs ~ _ ~ rhs) => InCond(lhs, rhs) } 
+    | expr ~ inOperator ~ relationName ^^ { case (lhs ~ _ ~ rhs) => InCond(lhs, rhs) }
     | "EXISTS" ~> relationName ^^ { ExistCond(_) }
     | "[" ~> cond <~ "]"
     )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index b256bce8b..e0a92d0a9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -5,7 +5,7 @@ import scala.collection.immutable.HashSet
 
 // semantic checker for ddlog
 object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
-  
+
   // initialize the checker
   def init(program: DeepDiveLog.Program) {
     program foreach {
@@ -45,7 +45,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
     stmt match {
       case s: ExtractionRule => {
-        s.q.bodies foreach { x => 
+        s.q.bodies foreach { x =>
           x foreach {
             case a: Atom => checkRelation(a.name)
             case _ =>
@@ -53,7 +53,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         }
       }
       case s: InferenceRule => {
-        s.q.bodies foreach { x => 
+        s.q.bodies foreach { x =>
           x foreach {
             case a: Atom => checkRelation(a.name)
             case _ =>
@@ -61,7 +61,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         }
       }
       case s: FunctionCallRule => checkRelation(s.input)
-      case _ => 
+      case _ =>
     }
   }
 
@@ -72,7 +72,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         if (!(functionDeclaration.keySet contains s.function))
           error(stmt, s"""function "${s.function}" is not defined""")
       }
-      case _ => 
+      case _ =>
     }
   }
 
@@ -82,13 +82,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case SchemaDeclaration(Attribute(r, terms, types), isQuery, vType) => {
         if (isQuery) {
-          terms.foreach { case name => 
-            if (reservedSet contains name) 
+          terms.foreach { case name =>
+            if (reservedSet contains name)
               error(stmt, s"""variable relation contains reserved column "${name}" """)
           }
         }
       }
-      case _ => 
+      case _ =>
     }
   }
 
@@ -111,11 +111,11 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
       case s: InferenceRule  => checkCq(s.q)
-      case _ => 
+      case _ =>
     }
   }
 
-  // throw exception 
+  // throw exception
   def error(stmt: Statement, message: String) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
     throw new RuntimeException(message + s"\n${stmtStr}")
@@ -128,7 +128,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   // schema declaration
-  var heads  : Set[String]                       = new HashSet[String]() 
+  var heads  : Set[String]                       = new HashSet[String]()
   // schema
   var schemaDeclaration : Map[String, SchemaDeclaration] = new HashMap[String, SchemaDeclaration]()
   // function declaration

From f71d72af3b4e28a7b90ca4434e70fbb8e6cd7744 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 03:52:18 -0700
Subject: [PATCH 180/347] Refactor compiling expression and alias

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 100 ++++++++++--------
 1 file changed, 53 insertions(+), 47 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d38328d7e..464139832 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -66,10 +66,10 @@ import org.deepdive.ddlog.DeepDiveLog.Mode._
 object AliasStyle extends Enumeration {
   type AliasStyle = Value
   // Three kinds of column expressions:
-  // OriginalOnly => use column name for dd_new_ tables
-  // AliasOnly => use alias for unknown weight in inference
-  // OriginalAndAlias => use column name and alias for normal extraction rule
-  val OriginalOnly, AliasOnly, OriginalAndAlias = Value
+  // NoAlias => use column name for dd_new_ tables
+  // WeightAlias => use alias for unknown weight in inference
+  // HeadAlias => use column name and alias for normal extraction rule
+  val NoAlias, WeightAlias, HeadAlias = Value
 
 }
 import AliasStyle._
@@ -175,61 +175,66 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     if( ground_relations contains relName ) !ground_relations(relName) else true
   }
 
-  // Resolve a column name with alias
-  def resolveColumn(s: String, q : ConjunctiveQuery, alias: AliasStyle) : Option[String] = {
-    val qs = new QuerySchema(q)
-    val index = qs.getBodyIndex(s)
-    val name  = resolveName(qs.getVar(s))
-    // TODO better way to get relation
-    val relation = q.bodies(0)(index) match {
-      case x: Atom => x.name
-      case _  => error("Wrong index")
-    }
-    alias match {
-      case OriginalOnly => Some(s"R${index}.${name}")
-      case AliasOnly => Some(s"${relation}.R${index}.${name}")
-      case OriginalAndAlias => Some(s"""R${index}.${name} AS "${relation}.R${index}.${name}" """)
+  // compile a variable name to its canonical relation and column in R{index}.{name} style
+  def compileVariable(v: String, cq: ConjunctiveQuery) = {
+    val qs = new QuerySchema(cq)
+    val index = qs.getBodyIndex(v)
+    val name  = resolveName(qs.getVar(v))
+    s"R${index}.${name}"
+  }
+
+  // compile alias, only used for head
+  def compileAlias(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle) = {
+    e match {
+      case VarExpr(v) => {
+        val qs = new QuerySchema(cq)
+        val index = qs.getBodyIndex(v)
+        val name  = resolveName(qs.getVar(v))
+        val relation = cq.bodies(0)(index) match {
+          case x: Atom => x.name
+          case _ => error("Wrong index when compiling alias")
+        }
+        alias match {
+          case NoAlias => ""
+          case HeadAlias => s""" AS "${relation}.R${index}.${name}" """
+          case WeightAlias => s"${relation}.R${index}.${name}"
+        }
+      }
+      case _ => s" AS column_${cq.head.terms indexOf e}"
     }
   }
 
   // resolve an expression
-  def compileExpr(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle, index : Int, isHead: Boolean) : String = {
+  def compileExpr(e: Expr, cq: ConjunctiveQuery, generateAlias: Expr => String = e => "") = {
     // recursively compile an expression
-    def compileExprInner(e: Expr, alias: AliasStyle) : String = {
+    def compileExprInner(e: Expr) : String = {
       e match {
-        case VarExpr(name) => resolveColumn(name, cq, alias).get
+        case VarExpr(name) => compileVariable(name, cq)
         case ConstExpr(value) => value
         case FuncExpr(function, args, agg) => {
-          // note alias is overriden with OriginalOnly, because when an expression appears in
-          // the function, we only need it's column name, without " AS ..." aliasing, same below
-          val resolvedArgs = args map (x => compileExprInner(x, OriginalOnly))
+          val resolvedArgs = args map (x => compileExprInner(x))
           val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
           resolved
         }
         case BinaryOpExpr(lhs, op, rhs) => {
-          val resovledLhs = compileExprInner(lhs, OriginalOnly)
-          val resovledRhs = compileExprInner(rhs, OriginalOnly)
+          val resovledLhs = compileExprInner(lhs)
+          val resovledRhs = compileExprInner(rhs)
           s"(${resovledLhs} ${op} ${resovledRhs})"
         }
         case TypecastExpr(lhs, rhs) => {
-          val resovledLhs = compileExprInner(lhs, OriginalOnly)
+          val resovledLhs = compileExprInner(lhs)
           s"(${resovledLhs} :: ${rhs})"
         }
       }
     }
-    // for columns without a name (constant, function call, binary operator), add an column index alias if necessary
-    val columnAlias = e match {
-      case x: VarExpr => ""
-      case _ => if (isHead) s" AS column_${index}" else ""
-    }
-    compileExprInner(e, alias) + columnAlias
+    compileExprInner(e) + generateAlias(e)
   }
 
   // resolve a condition
   def compileCond(cond: Cond, cq: ConjunctiveQuery) : String = {
     cond match {
       case ComparisonCond(lhs, op, rhs) =>
-        s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} ${op} ${compileExpr(rhs, cq, OriginalOnly, 0, false)}"
+        s"${compileExpr(lhs, cq)} ${op} ${compileExpr(rhs, cq)}"
       case NegationCond(c) => s"(NOT ${compileCond(c, cq)})"
       case CompoundCond(lhs, op, rhs) => {
         val resolvedLhs = s"${compileCond(lhs, cq)}"
@@ -240,7 +245,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         }
       }
       case InCond(lhs, rhs) => {
-        s"${compileExpr(lhs, cq, OriginalOnly, 0, false)} IN (SELECT * FROM ${rhs})"
+        s"${compileExpr(lhs, cq)} IN (SELECT * FROM ${rhs})"
       }
       case ExistCond(rhs) => s"EXISTS (SELECT * FROM ${rhs})"
       case _ => ""
@@ -269,7 +274,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
             }
             // other expressions indicate a filter condition on the column
             case _ => {
-              val resolved = compileExpr(expr, z, OriginalOnly, index, false)
+              val resolved = compileExpr(expr, z)
               val attr = schema(relName, index)
               Some(s"R${bodyIndex}.${attr} = ${resolved}")
             }
@@ -296,7 +301,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // map head terms, leaving out aggregation functions
     val groupbyTerms = z.head.terms.zipWithIndex flatMap { case (expr, index) =>
       if (containsAggregation(expr)) None
-      else Some(compileExpr(expr, z, OriginalOnly, index, false))
+      else Some(compileExpr(expr, z))
     }
 
     val groupbyStr = if (groupbyTerms.size == z.head.terms.size || groupbyTerms.isEmpty) {
@@ -479,8 +484,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) =>
-            ss.compileExpr(expr, tmpCq, OriginalOnly, index, true)
+          val headTerms = tmpCq.head.terms map { expr =>
+            ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, NoAlias))
           }
           val index = qs.getBodyIndex(stmt.supervision)
           val name  = ss.resolveName(qs.getVar(stmt.supervision))
@@ -490,8 +495,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           ${ ss.generateSQLBody(tmpCq) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = tmpCq.head.terms.zipWithIndex map { case (expr, index) =>
-            ss.compileExpr(expr, tmpCq, OriginalOnly, index, true)
+          val headTerms = tmpCq.head.terms map { expr =>
+            ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, NoAlias))
           }
           val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
@@ -505,11 +510,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case _     => if (tmpCq.head.name.startsWith("dd_new_")) true else false
           }
           val resolveColumnFlag = tmpCqUseOnlyOriginal match {
-            case true => OriginalOnly
-            case false => OriginalAndAlias
+            case true => NoAlias
+            case false => HeadAlias
           }
-          val variableCols = tmpCq.head.terms.zipWithIndex map { case (expr, index) =>
-            ss.compileExpr(expr, tmpCq, resolveColumnFlag, index, true)
+          val variableCols = tmpCq.head.terms map { expr =>
+            ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, resolveColumnFlag))
           }
           val selectStr = variableCols.mkString(", ")
           val distinctStr = if (tmpCq.isDistinct) "DISTINCT" else ""
@@ -609,7 +614,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         // weight string
         val uwStr = stmt.weights match {
-          case UnknownFactorWeight(w) => Some(w.flatMap(s => ss.resolveColumn(s, fakeCQ, OriginalAndAlias)).mkString(", "))
+          case UnknownFactorWeight(w) => Some(w.map(s =>
+            ss.compileExpr(VarExpr(s), fakeCQ, ss.compileAlias(_, fakeCQ, HeadAlias))).mkString(", "))
           case _ => None
         }
 
@@ -642,7 +648,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              val weightVar = w.flatMap(s => ss.resolveColumn(s, fakeCQ, AliasOnly)).mkString(", ")
+              val weightVar = w.map(s => ss.compileAlias(VarExpr(s), fakeCQ, WeightAlias)).mkString(", ")
               s"?(${weightVar})"
             }
             case UnknownFactorWeightBindingToConst(w) => "?"

From db0d6b23dbeba3e0249eec44f094ba3cb256404d Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 05:21:19 -0700
Subject: [PATCH 181/347] Add support for atom modifier. Support EXIST

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 73 +++++++++++--------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  9 ++-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 29 +++++---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 21 ++++--
 .../expressions/compile.expected              | 28 ++++++-
 .../expressions/input.ddl                     |  6 +-
 .../expressions/print.expected                |  8 ++
 7 files changed, 122 insertions(+), 52 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 464139832..0722a2099 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -253,37 +253,50 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
-  // and the corresponding WHERE clause (equating all variables)
+  // and the corresponding WHERE clause
   def generateSQLBody(z : ConjunctiveQuery) : String = {
     // Simple logic for the where clause, first find every first occurence of a
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    var whereClause = z.bodies(0).zipWithIndex flatMap {
-      case (Atom(relName, terms),bodyIndex) => {
-        terms.zipWithIndex flatMap { case (expr, index) =>
-          expr match {
-            // a simple variable indicates a join condition with other columns having the same variable name
-            case VarExpr(varName) => {
-              val canonical_body_index = qs.getBodyIndex(varName)
-              if (canonical_body_index != bodyIndex) {
-                val real_attr_name1 = resolveName( Variable(varName, relName, index) )
-                val real_attr_name2 = resolveName( qs.getVar(varName))
-                Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
-              } else { None }
-            }
-            // other expressions indicate a filter condition on the column
-            case _ => {
-              val resolved = compileExpr(expr, z)
-              val attr = schema(relName, index)
-              Some(s"R${bodyIndex}.${attr} = ${resolved}")
+    def generateWhereClause(body: Body, bodyIndex: Int) : List[String] = {
+      body match {
+        case Atom(relName, terms) => {
+          terms.zipWithIndex flatMap { case (expr, index) =>
+            expr match {
+              // a simple variable indicates a join condition with other columns having the same variable name
+              case VarExpr(varName) => {
+                val canonical_body_index = qs.getBodyIndex(varName)
+                if (canonical_body_index != bodyIndex) {
+                  val real_attr_name1 = resolveName( Variable(varName, relName, index) )
+                  val real_attr_name2 = resolveName( qs.getVar(varName))
+                  Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+                } else { None }
+              }
+              // other expressions indicate a filter condition on the column
+              case _ => {
+                val resolved = compileExpr(expr, z)
+                val attr = schema(relName, index)
+                Some(s"R${bodyIndex}.${attr} = ${resolved}")
+              }
             }
           }
         }
+        case x: Cond => List(compileCond(x, z))
+        case x: ModifierAtom => {
+          val unification = generateWhereClause(x.atom, bodyIndex)
+          val condition = x.condition map { c => compileCond(c, z) }
+          val subqueryWhereStr = (unification ++ condition).mkString(" AND ")
+          x.modifier match {
+            case ExistModifier() => List(s"EXISTS (SELECT 1 FROM ${x.atom.name} WHERE ${subqueryWhereStr})")
+            case _ => List() // TODO
+          }
+        }
       }
-      case (x: Cond, i) => Some(compileCond(x, z))
     }
 
+    val whereClause = z.bodies(0).zipWithIndex flatMap { case (x,i) => generateWhereClause(x,i) }
+
     // check if an expression contains an aggregation function
     def containsAggregation(expr: Expr) : Boolean = {
       expr match {
@@ -401,17 +414,19 @@ class QuerySchema(q : ConjunctiveQuery) {
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
   def generateCanonicalVar()  = {
-    q.bodies(0).zipWithIndex.foreach {
-      case (Atom(relName,terms),index) =>  {
-        terms.zipWithIndex.foreach { case (expr, i) =>
-          expr match {
-            case VarExpr(v) =>
-              if (! (query_schema contains v) )
-                query_schema += { v -> (index, Variable(v,relName,i) ) }
-            case _ =>
-          }
+    def generateCanonicalVarFromAtom(a: Atom, index: Int) {
+      a.terms.zipWithIndex.foreach { case (expr, i) =>
+        expr match {
+          case VarExpr(v) =>
+            if (! (query_schema contains v) )
+              query_schema += { v -> (index, Variable(v,a.name,i) ) }
+          case _ =>
         }
       }
+    }
+    q.bodies(0).zipWithIndex.foreach {
+      case (a: Atom, index) => generateCanonicalVarFromAtom(a, index)
+      case (a: ModifierAtom, index) => generateCanonicalVarFromAtom(a.atom, index)
       case _ =>
     }
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 80150a741..2678ed886 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -34,13 +34,18 @@ object DeepDiveLogDeltaDeriver{
     var incCqBodies = new ListBuffer[List[Body]]()
     // New incremental bodies
     cq.bodies foreach { bodies =>
+      // We don't support deriving delta rules for modifiers
+      bodies foreach {
+        case x: ModifierAtom => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
+        case _ =>
+      }
       // Delta body
-      val incDeltaBody = bodies map {
+      val incDeltaBody = bodies collect {
         case a: Atom => a.copy(name = deltaPrefix + a.name)
         case a: Cond => a
       }
       // New body
-      val incNewBody = bodies map {
+      val incNewBody = bodies collect {
         case a: Atom => a.copy(name = newPrefix + a.name)
         case a: Cond => a
       }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 764074fce..58bfe74d8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -21,10 +21,15 @@ case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 
 sealed trait Body
 case class Atom(name : String, terms : List[Expr]) extends Body
+case class ModifierAtom(modifier: AtomModifier, atom: Atom, condition: Option[Cond]) extends Body
+
+sealed trait AtomModifier
+case class ExistModifier extends AtomModifier
+case class OuterModifier extends AtomModifier
+
 case class Attribute(name : String, terms : List[String], types : List[String])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
 case class Column(name : String, t : String)
-case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 
 // condition
 sealed trait Cond extends Body
@@ -145,15 +150,13 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "(" ~> expr <~ ")"
     )
 
-  // TODO support aggregate function syntax somehow
   def cqHead = relationName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
     case (r ~ "(" ~ expressions ~ ")") => Atom(r, expressions)
   }
 
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
-  def inOperator = "IN"
-  def quantifierOperator = "ANY" | "ALL"
+  def atomModifier = "EXIST" | "OUTER"
 
   def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
@@ -172,16 +175,22 @@ class DeepDiveLogParser extends JavaTokenParsers {
     )
   def bcond : Parser[Cond] =
     ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => ComparisonCond(lhs, op, rhs) }
-    | expr ~ inOperator ~ relationName ^^ { case (lhs ~ _ ~ rhs) => InCond(lhs, rhs) }
-    | "EXISTS" ~> relationName ^^ { ExistCond(_) }
     | "[" ~> cond <~ "]"
     )
 
+  def atom = relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
+    case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
+  }
+  def modifierAtom = ("EXIST") ~ "[" ~ atom ~ opt(":" ~> cond) ~ "]" ^^ { case (m ~ _ ~ a ~ c ~ _) =>
+    val modifier = m match {
+      case "EXIST" => new ExistModifier
+    }
+    ModifierAtom(modifier, a, c)
+  }
   def cqBody: Parser[Body] =
-    ( relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
-        case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
-      }
-    | cond
+    ( cond
+    | modifierAtom
+    | atom
     )
   def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 5df383ec7..dc85e5105 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -74,7 +74,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case NegationCond(c) => s"[!${printCond(c)}]"
       case CompoundCond(lhs, op, rhs) => {
         op match {
-          case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]" 
+          case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]"
           case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
         }
       }
@@ -83,16 +83,27 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     }
   }
 
-  def print(cq: ConjunctiveQuery): String = {
-    def printAtom(a: Atom) = {
-      val vars = a.terms map printExpr
-      s"${a.name}(${vars.mkString(", ")})"
+  def printAtom(a: Atom) = {
+    val vars = a.terms map printExpr
+    s"${a.name}(${vars.mkString(", ")})"
+  }
+
+  def printModifierAtom(a: ModifierAtom) = {
+    val modifier = a.modifier match {
+      case ExistModifier() => "EXIST"
+      case OuterModifier() => "OUTER"
     }
+    val conditionStr = (a.condition map { c => s": ${printCond(c)}" }).getOrElse("")
+    s"${modifier}[${printAtom(a.atom)}${conditionStr}]"
+  }
+
+  def print(cq: ConjunctiveQuery): String = {
 
     def printBody(b: Body) = {
       b match {
         case b: Atom => printAtom(b)
         case b: Cond => printCond(b)
+        case b: ModifierAtom => printModifierAtom(b)
       }
     }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 49591e797..abae6e0e4 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -67,6 +67,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_18 {
+        sql: """ DROP VIEW IF EXISTS N;
+        CREATE VIEW N AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE EXISTS (SELECT 1 FROM c WHERE R1.n = R0.k  AND R1.s > 'a')
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
         CREATE VIEW J AS 
@@ -103,6 +115,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_17 {
+        sql: """ DROP VIEW IF EXISTS M;
+        CREATE VIEW M AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE EXISTS (SELECT 1 FROM c WHERE R1.n = R0.k )
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS I;
         CREATE VIEW I AS 
@@ -225,6 +249,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 79c8599fe..02f7e5c3a 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -35,8 +35,6 @@ K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
 # limit
 L(x) * | 100 :- b(x, y, z, w).
 
-# M(x) :- a(x), x IN G.
+M(x) :- b(x,y,z,w), EXIST[c(a,x,b)].
 
-# N(x) :- a(x), x > ANY G.
-
-# O(x) :- a(x), b(q,w,e,r), OUTER(b: x = q), x = r.
\ No newline at end of file
+N(x) :- b(x,y,z,w), EXIST[c(a,x,b): a > "a"].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 95533eaa1..4e960d617 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -60,3 +60,11 @@ K(x)  :-
 L(x) * | 100 :-
     b(x, y, z, w).
 
+M(x)  :-
+    b(x, y, z, w),
+    EXIST[c(a, x, b)].
+
+N(x)  :-
+    b(x, y, z, w),
+    EXIST[c(a, x, b): a >  "a" ].
+

From 3889e5df4c8120f6db1d878560b5c17e043279ea Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 16:26:21 -0700
Subject: [PATCH 182/347] Add support for unified body in modifier atom

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 65 ++++++++++---------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 15 ++---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 22 +++----
 .../expressions/compile.expected              | 20 ++++--
 .../expressions/input.ddl                     |  4 +-
 .../expressions/print.expected                |  6 +-
 6 files changed, 78 insertions(+), 54 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 0722a2099..69d8a29b8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -189,11 +189,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case VarExpr(v) => {
         val qs = new QuerySchema(cq)
         val index = qs.getBodyIndex(v)
-        val name  = resolveName(qs.getVar(v))
-        val relation = cq.bodies(0)(index) match {
-          case x: Atom => x.name
-          case _ => error("Wrong index when compiling alias")
-        }
+        val variable = qs.getVar(v)
+        val name  = resolveName(variable)
+        val relation = variable.relName
         alias match {
           case NoAlias => ""
           case HeadAlias => s""" AS "${relation}.R${index}.${name}" """
@@ -259,16 +257,17 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    def generateWhereClause(body: Body, bodyIndex: Int) : List[String] = {
-      body match {
-        case Atom(relName, terms) => {
-          terms.zipWithIndex flatMap { case (expr, index) =>
+    def generateWhereClause(bodies: List[Body], indexPrefix: String) : List[String] = {
+      bodies.zipWithIndex.flatMap {
+        case (Atom(relName, terms), index) => {
+          val bodyIndex = s"${indexPrefix}${index}"
+          terms.zipWithIndex flatMap { case (expr, atomIndex) =>
             expr match {
               // a simple variable indicates a join condition with other columns having the same variable name
               case VarExpr(varName) => {
                 val canonical_body_index = qs.getBodyIndex(varName)
                 if (canonical_body_index != bodyIndex) {
-                  val real_attr_name1 = resolveName( Variable(varName, relName, index) )
+                  val real_attr_name1 = resolveName( Variable(varName, relName, atomIndex) )
                   val real_attr_name2 = resolveName( qs.getVar(varName))
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
@@ -276,26 +275,31 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
               // other expressions indicate a filter condition on the column
               case _ => {
                 val resolved = compileExpr(expr, z)
-                val attr = schema(relName, index)
+                val attr = schema(relName, atomIndex)
                 Some(s"R${bodyIndex}.${attr} = ${resolved}")
               }
             }
           }
         }
-        case x: Cond => List(compileCond(x, z))
-        case x: ModifierAtom => {
-          val unification = generateWhereClause(x.atom, bodyIndex)
-          val condition = x.condition map { c => compileCond(c, z) }
-          val subqueryWhereStr = (unification ++ condition).mkString(" AND ")
+        case (x: Cond, _) => List(compileCond(x, z))
+        case (x: ModifierAtom, index) => {
+          val newIndexPrefix = s"${indexPrefix}${index}_"
+          val subqueryWhereStr = generateWhereClause(x.bodies, newIndexPrefix).mkString(" AND ")
+          val subqueryFromStr  = getnerateFromClauseStr(x.bodies, newIndexPrefix)
           x.modifier match {
-            case ExistModifier() => List(s"EXISTS (SELECT 1 FROM ${x.atom.name} WHERE ${subqueryWhereStr})")
-            case _ => List() // TODO
+            case ExistModifier() => List(s"EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE ${subqueryWhereStr})")
+            case _ => List()
           }
         }
       }
     }
 
-    val whereClause = z.bodies(0).zipWithIndex flatMap { case (x,i) => generateWhereClause(x,i) }
+    def getnerateFromClauseStr(bodies: List[Body], indexPrefix: String) = (bodies.zipWithIndex flatMap {
+      case(x:Atom,i) => Some(s"${x.name} R${indexPrefix}${i}")
+      case _ => None
+    }).mkString(", ")
+
+    val whereClause = generateWhereClause(z.bodies(0), "")
 
     // check if an expression contains an aggregation function
     def containsAggregation(expr: Expr) : Boolean = {
@@ -408,13 +412,13 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 // mentioned in the body. This is useful to translate to SQL (join
 // conditions, select, etc.)
 class QuerySchema(q : ConjunctiveQuery) {
-    var query_schema = new HashMap[ String, Tuple2[Int,Variable] ]()
+  var query_schema = new HashMap[ String, Tuple2[String,Variable] ]()
 
   // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
   def generateCanonicalVar()  = {
-    def generateCanonicalVarFromAtom(a: Atom, index: Int) {
+    def generateCanonicalVarFromAtom(a: Atom, index: String) {
       a.terms.zipWithIndex.foreach { case (expr, i) =>
         expr match {
           case VarExpr(v) =>
@@ -424,16 +428,21 @@ class QuerySchema(q : ConjunctiveQuery) {
         }
       }
     }
-    q.bodies(0).zipWithIndex.foreach {
-      case (a: Atom, index) => generateCanonicalVarFromAtom(a, index)
-      case (a: ModifierAtom, index) => generateCanonicalVarFromAtom(a.atom, index)
-      case _ =>
+
+    def generateCanonicalVarFromBodies(bodies: List[Body], indexPrefix: String) {
+      bodies.zipWithIndex.foreach {
+        case (a: Atom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
+        case (a: ModifierAtom, index) => generateCanonicalVarFromBodies(a.bodies, s"${indexPrefix}${index}_")
+        case _ =>
+      }
     }
+
+    generateCanonicalVarFromBodies(q.bodies(0), "")
   }
   generateCanonicalVar() // initialize
 
   // accessors
-  def getBodyIndex( varName : String ) : Int = { query_schema(varName)._1 }
+  def getBodyIndex( varName : String )       = { query_schema(varName)._1 }
   def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
 }
 
@@ -502,9 +511,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           val headTerms = tmpCq.head.terms map { expr =>
             ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, NoAlias))
           }
-          val index = qs.getBodyIndex(stmt.supervision)
-          val name  = ss.resolveName(qs.getVar(stmt.supervision))
-          val labelCol = s"R${index}.${name}"
+          val labelCol = ss.compileVariable(stmt.supervision, tmpCq)
           val headTermsStr = ( headTerms :+ "0 as id" ).mkString(", ")
           inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
           ${ ss.generateSQLBody(tmpCq) }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 58bfe74d8..b1908488c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -21,7 +21,7 @@ case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
 
 sealed trait Body
 case class Atom(name : String, terms : List[Expr]) extends Body
-case class ModifierAtom(modifier: AtomModifier, atom: Atom, condition: Option[Cond]) extends Body
+case class ModifierAtom(modifier: AtomModifier, bodies: List[Body]) extends Body
 
 sealed trait AtomModifier
 case class ExistModifier extends AtomModifier
@@ -181,17 +181,16 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def atom = relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
     case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
   }
-  def modifierAtom = ("EXIST") ~ "[" ~ atom ~ opt(":" ~> cond) ~ "]" ^^ { case (m ~ _ ~ a ~ c ~ _) =>
+  def modifierAtom = ("EXIST" | "OUTER") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
       case "EXIST" => new ExistModifier
+      case "OUTER" => new OuterModifier
     }
-    ModifierAtom(modifier, a, c)
+    ModifierAtom(modifier, b)
   }
-  def cqBody: Parser[Body] =
-    ( cond
-    | modifierAtom
-    | atom
-    )
+
+  def cqBody: Parser[Body] = cond | modifierAtom | atom
+
   def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index dc85e5105..6adc60c96 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -88,24 +88,24 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     s"${a.name}(${vars.mkString(", ")})"
   }
 
-  def printModifierAtom(a: ModifierAtom) = {
+  def printModifierAtom(a: ModifierAtom) : String = {
     val modifier = a.modifier match {
       case ExistModifier() => "EXIST"
       case OuterModifier() => "OUTER"
     }
-    val conditionStr = (a.condition map { c => s": ${printCond(c)}" }).getOrElse("")
-    s"${modifier}[${printAtom(a.atom)}${conditionStr}]"
+    val bodyStr = (a.bodies map printBody).mkString(", ")
+    s"${modifier}[${bodyStr}]"
   }
 
-  def print(cq: ConjunctiveQuery): String = {
-
-    def printBody(b: Body) = {
-      b match {
-        case b: Atom => printAtom(b)
-        case b: Cond => printCond(b)
-        case b: ModifierAtom => printModifierAtom(b)
-      }
+  def printBody(b: Body) = {
+    b match {
+      case b: Atom => printAtom(b)
+      case b: Cond => printCond(b)
+      case b: ModifierAtom => printModifierAtom(b)
     }
+  }
+
+  def print(cq: ConjunctiveQuery): String = {
 
     def printBodyList(b: List[Body]) = {
       s"${(b map printBody).mkString(",\n    ")}"
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index abae6e0e4..67ff98e41 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -72,7 +72,7 @@
         CREATE VIEW N AS 
             SELECT  R0.k AS "b.R0.k" 
             FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c WHERE R1.n = R0.k  AND R1.s > 'a')
+        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
         """
         style: "sql_extractor"
           
@@ -120,7 +120,7 @@
         CREATE VIEW M AS 
             SELECT  R0.k AS "b.R0.k" 
             FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c WHERE R1.n = R0.k )
+        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
         """
         style: "sql_extractor"
           
@@ -236,6 +236,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_19 {
+        sql: """ DROP VIEW IF EXISTS O;
+        CREATE VIEW O AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0
+        WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
         CREATE VIEW D AS 
@@ -249,6 +261,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 02f7e5c3a..393fbd501 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -37,4 +37,6 @@ L(x) * | 100 :- b(x, y, z, w).
 
 M(x) :- b(x,y,z,w), EXIST[c(a,x,b)].
 
-N(x) :- b(x,y,z,w), EXIST[c(a,x,b): a > "a"].
\ No newline at end of file
+N(x) :- b(x,y,z,w), EXIST[c(a,x,b), a > "a"].
+
+O(x) :- b(x,y,z,w), EXIST[c(a,x,b), a(x)].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 4e960d617..cc2cedff6 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -66,5 +66,9 @@ M(x)  :-
 
 N(x)  :-
     b(x, y, z, w),
-    EXIST[c(a, x, b): a >  "a" ].
+    EXIST[c(a, x, b), a >  "a" ].
+
+O(x)  :-
+    b(x, y, z, w),
+    EXIST[c(a, x, b), a(x)].
 

From 0075ae375c60b3428556aab077fa9da99acd78dc Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 16:31:44 -0700
Subject: [PATCH 183/347] Add suport for not exist

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 2 +-
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala   | 6 +++---
 .../scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 69d8a29b8..a99bcd43b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -287,7 +287,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
           val subqueryWhereStr = generateWhereClause(x.bodies, newIndexPrefix).mkString(" AND ")
           val subqueryFromStr  = getnerateFromClauseStr(x.bodies, newIndexPrefix)
           x.modifier match {
-            case ExistModifier() => List(s"EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE ${subqueryWhereStr})")
+            case ExistModifier(negated) => List(s"${if (negated) "NOT " else ""}EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE ${subqueryWhereStr})")
             case _ => List()
           }
         }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index b1908488c..e0da97e58 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -24,7 +24,7 @@ case class Atom(name : String, terms : List[Expr]) extends Body
 case class ModifierAtom(modifier: AtomModifier, bodies: List[Body]) extends Body
 
 sealed trait AtomModifier
-case class ExistModifier extends AtomModifier
+case class ExistModifier(negated: Boolean) extends AtomModifier
 case class OuterModifier extends AtomModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String])
@@ -181,9 +181,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def atom = relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
     case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
   }
-  def modifierAtom = ("EXIST" | "OUTER") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
+  def modifierAtom = (opt("NOT") ~ "EXIST" | "OUTER") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
-      case "EXIST" => new ExistModifier
+      case (not ~ "EXIST") => new ExistModifier(not != None)
       case "OUTER" => new OuterModifier
     }
     ModifierAtom(modifier, b)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 6adc60c96..46aaa98be 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -90,7 +90,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def printModifierAtom(a: ModifierAtom) : String = {
     val modifier = a.modifier match {
-      case ExistModifier() => "EXIST"
+      case ExistModifier(negated) => if(negated) "NOT " else "" + "EXIST"
       case OuterModifier() => "OUTER"
     }
     val bodyStr = (a.bodies map printBody).mkString(", ")

From 9dbe92595763536cd9eb10e591cde71c1ff784da Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 17:45:33 -0700
Subject: [PATCH 184/347] Add support for outer join modifier

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 58 ++++++++++++-------
 .../expressions/compile.expected              | 40 ++++++++++++-
 .../expressions/input.ddl                     |  8 ++-
 .../expressions/print.expected                | 13 +++++
 4 files changed, 96 insertions(+), 23 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a99bcd43b..a8c9d5e8b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -257,8 +257,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // and stick it in a map.
     val qs = new QuerySchema(z)
 
-    def generateWhereClause(bodies: List[Body], indexPrefix: String) : List[String] = {
-      bodies.zipWithIndex.flatMap {
+    def generateWhereClause(bodies: List[Body], indexPrefix: String) : String = {
+      val conditions = bodies.zipWithIndex.flatMap {
         case (Atom(relName, terms), index) => {
           val bodyIndex = s"${indexPrefix}${index}"
           terms.zipWithIndex flatMap { case (expr, atomIndex) =>
@@ -281,25 +281,50 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
             }
           }
         }
-        case (x: Cond, _) => List(compileCond(x, z))
+        case (x: Cond, _) => Some(compileCond(x, z))
         case (x: ModifierAtom, index) => {
           val newIndexPrefix = s"${indexPrefix}${index}_"
-          val subqueryWhereStr = generateWhereClause(x.bodies, newIndexPrefix).mkString(" AND ")
-          val subqueryFromStr  = getnerateFromClauseStr(x.bodies, newIndexPrefix)
+          val subqueryWhereStr = generateWhereClause(x.bodies, newIndexPrefix)
+          val subqueryFromStr  = generateFromClause(x.bodies, newIndexPrefix)
           x.modifier match {
-            case ExistModifier(negated) => List(s"${if (negated) "NOT " else ""}EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE ${subqueryWhereStr})")
-            case _ => List()
+            case ExistModifier(negated) => Some(s"${if (negated) "NOT " else ""}EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE ${subqueryWhereStr})")
+            case _ => None
           }
         }
       }
+      conditions.mkString(" AND ")
     }
 
-    def getnerateFromClauseStr(bodies: List[Body], indexPrefix: String) = (bodies.zipWithIndex flatMap {
-      case(x:Atom,i) => Some(s"${x.name} R${indexPrefix}${i}")
-      case _ => None
-    }).mkString(", ")
+    def generateFromClause(bodies: List[Body], indexPrefix: String) : String = {
+      val atoms = bodies.zipWithIndex flatMap {
+        case (x:Atom,i) => Some(s"${x.name} R${indexPrefix}${i}")
+        case _ => None
+      }
+      val outers = bodies.zipWithIndex flatMap {
+        case (x:ModifierAtom,i) => {
+          val newIndexPrefix = s"${indexPrefix}${i}_"
+          x.modifier match {
+            case OuterModifier() => {
+              val from = generateFromClause(x.bodies, newIndexPrefix)
+              val joinCond = generateWhereClause(x.bodies, newIndexPrefix)
+              Some(s"${from} ON ${joinCond}")
+            }
+            case _ => None
+          }
+        }
+        case _ => None
+      }
+      // full outer join
+      if (atoms isEmpty) {
+        outers.mkString(" FULL OUTER JOIN ")
+      } else {
+        (atoms.mkString(", ") +: outers).mkString(" LEFT OUTER JOIN ")
+      }
+    }
 
     val whereClause = generateWhereClause(z.bodies(0), "")
+    val whereClauseStr = if (whereClause.isEmpty) "" else "WHERE " + whereClause
+    val fromClauseStr = generateFromClause(z.bodies(0), "")
 
     // check if an expression contains an aggregation function
     def containsAggregation(expr: Expr) : Boolean = {
@@ -327,20 +352,13 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
     }
 
-    val whereClauseStr = if (whereClause.isEmpty) "" else whereClause.mkString("WHERE ", " AND ", "")
-
+    // limit clause
     val limitStr = z.limit match {
       case Some(s) => s" LIMIT ${s}"
       case None => ""
     }
 
-    val fromBodyNames = (z.bodies(0).zipWithIndex flatMap {
-      case(x:Atom,i) => Some(s"${x.name} R${i}")
-      case _ => None
-    }).mkString(", ")
-    val fromClause = fromBodyNames
-
-    s"""FROM ${ fromClause }
+    s"""FROM ${ fromClauseStr }
         ${ whereClauseStr }${groupbyStr}${limitStr}"""
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 67ff98e41..8acbe0e49 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -79,6 +79,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_21 {
+        sql: """ DROP VIEW IF EXISTS T;
+        CREATE VIEW T AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
+        WHERE R1_0.s > R0.p
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
         CREATE VIEW J AS 
@@ -91,6 +103,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_22 {
+        sql: """ DROP VIEW IF EXISTS U;
+        CREATE VIEW U AS 
+            SELECT  R0_0.k AS "b.R0_0.k" 
+            FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS F;
         CREATE VIEW F AS 
@@ -259,8 +283,20 @@
           
       }
     
+
+      deepdive.extraction.extractors.extraction_rule_20 {
+        sql: """ DROP VIEW IF EXISTS S;
+        CREATE VIEW S AS 
+            SELECT  R0.k AS "b.R0.k" 
+            FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_16, extraction_rule_19, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 393fbd501..b738e4aab 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -39,4 +39,10 @@ M(x) :- b(x,y,z,w), EXIST[c(a,x,b)].
 
 N(x) :- b(x,y,z,w), EXIST[c(a,x,b), a > "a"].
 
-O(x) :- b(x,y,z,w), EXIST[c(a,x,b), a(x)].
\ No newline at end of file
+O(x) :- b(x,y,z,w), EXIST[c(a,x,b), a(x)].
+
+S(x) :- b(x,y,z,w), OUTER[c(a,x,b)].
+
+T(x) :- b(x,y,z,w), OUTER[c(a,x,b), a > y], a > y.
+
+U(x) :- OUTER[b(x,y,z,w)], OUTER[c(a,x,b)].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index cc2cedff6..bb70ff63d 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -72,3 +72,16 @@ O(x)  :-
     b(x, y, z, w),
     EXIST[c(a, x, b), a(x)].
 
+S(x)  :-
+    b(x, y, z, w),
+    OUTER[c(a, x, b)].
+
+T(x)  :-
+    b(x, y, z, w),
+    OUTER[c(a, x, b), a > y],
+    a > y.
+
+U(x)  :-
+    OUTER[b(x, y, z, w)],
+    OUTER[c(a, x, b)].
+

From 2a8a79f4b2f959bc33954581a2402107f0719e37 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 19 Jul 2015 23:34:11 -0700
Subject: [PATCH 185/347] Support placeholder

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala |  3 +++
 .../org/deepdive/ddlog/DeepDiveLogParser.scala   |  4 +++-
 .../ddlog/DeepDiveLogPrettyPrinter.scala         |  1 +
 .../expressions/compile.expected                 | 16 ++++++++++++++--
 test/expected-output-test/expressions/input.ddl  |  6 +++++-
 .../expressions/print.expected                   |  4 ++++
 6 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a8c9d5e8b..557883683 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -223,6 +223,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
           val resovledLhs = compileExprInner(lhs)
           s"(${resovledLhs} :: ${rhs})"
         }
+        case Placeholder() => ""
       }
     }
     compileExprInner(e) + generateAlias(e)
@@ -272,6 +273,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
               }
+              case Placeholder() => None
               // other expressions indicate a filter condition on the column
               case _ => {
                 val resolved = compileExpr(expr, z)
@@ -336,6 +338,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         }
         case BinaryOpExpr(lhs, op, rhs) => containsAggregation(lhs) || containsAggregation(rhs)
         case TypecastExpr(lhs, rhs) => containsAggregation(lhs)
+        case Placeholder() => false
       }
     }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index e0da97e58..17d66fe89 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -18,6 +18,7 @@ case class ConstExpr(value: String) extends Expr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
+case class Placeholder extends Expr
 
 sealed trait Body
 case class Atom(name : String, terms : List[Expr]) extends Body
@@ -136,7 +137,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // expression
   def expr : Parser[Expr] =
-    ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    ( "_" ^^ { case _ => Placeholder() }
+    | lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
     )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 46aaa98be..3f79cf040 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -64,6 +64,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
       case BinaryOpExpr(lhs, op, rhs) => s"(${printExpr(lhs)} ${op} ${printExpr(rhs)})"
       case TypecastExpr(lhs, rhs) => s"(${printExpr(lhs)} :: ${rhs})"
+      case Placeholder() => "_"
     }
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 8acbe0e49..572377cad 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -175,6 +175,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ DROP VIEW IF EXISTS V;
+        CREATE VIEW V AS 
+            SELECT  R0.n AS "c.R0.n" 
+            FROM c R0, a R1
+        WHERE R1.k = R0.n 
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
@@ -297,6 +309,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index b738e4aab..800aa782c 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -35,6 +35,7 @@ K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
 # limit
 L(x) * | 100 :- b(x, y, z, w).
 
+# modifiers
 M(x) :- b(x,y,z,w), EXIST[c(a,x,b)].
 
 N(x) :- b(x,y,z,w), EXIST[c(a,x,b), a > "a"].
@@ -45,4 +46,7 @@ S(x) :- b(x,y,z,w), OUTER[c(a,x,b)].
 
 T(x) :- b(x,y,z,w), OUTER[c(a,x,b), a > y], a > y.
 
-U(x) :- OUTER[b(x,y,z,w)], OUTER[c(a,x,b)].
\ No newline at end of file
+U(x) :- OUTER[b(x,y,z,w)], OUTER[c(a,x,b)].
+
+# placeholder
+V(x) :- c(_,x,_), a(x).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index bb70ff63d..197c45e21 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -85,3 +85,7 @@ U(x)  :-
     OUTER[b(x, y, z, w)],
     OUTER[c(a, x, b)].
 
+V(x)  :-
+    c(_, x, _),
+    a(x).
+

From 25413a0e6f77b30a4ec03bf319a9a66ff5fb7f11 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 20 Jul 2015 20:11:41 -0700
Subject: [PATCH 186/347] Refactoring

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 373 +++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |   4 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  23 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  11 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  65 +--
 .../chunking_example/compile.expected         |   8 +-
 .../expressions/compile.expected              |  40 +-
 .../expressions/input.ddl                     |  12 +-
 .../expressions/print.expected                |  14 +-
 .../ocr_example/compile-incremental.expected  |  20 +-
 .../compile-materialization.expected          |   8 +-
 .../ocr_example/compile.expected              |   8 +-
 .../compile-incremental.expected              |  28 +-
 .../compile-materialization.expected          |   8 +-
 .../smoke_example/compile.expected            |   8 +-
 .../compile-incremental.expected              |  52 +--
 .../compile-materialization.expected          |  14 +-
 .../spouse_example/compile.expected           |  14 +-
 .../compile-incremental.expected              |  54 +--
 .../compile-incremental.expected              |  54 +--
 .../compile.expected                          |  16 +-
 21 files changed, 411 insertions(+), 423 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index cb30201ea..65db4dc05 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -62,6 +62,7 @@ import scala.collection.immutable.HashMap
 import org.apache.commons.lang3.StringEscapeUtils
 import scala.collection.mutable.ListBuffer
 import org.deepdive.ddlog.DeepDiveLog.Mode._
+import scala.language.postfixOps
 
 object AliasStyle extends Enumeration {
   type AliasStyle = Value
@@ -176,22 +177,123 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     if( ground_relations contains relName ) !ground_relations(relName) else true
   }
 
+  // Group statements by head
+  def groupByHead(statements: List[Statement]) = {
+    // Compile compilation states by head name based on type
+    val schemaDeclarationToCompile = new ListBuffer[SchemaDeclaration]()
+    val extractionRuleToCompile    = new ListBuffer[ExtractionRule]()
+    val inferenceRuleToCompile     = new ListBuffer[InferenceRule]()
+    val functionCallRuleToCompile  = new ListBuffer[FunctionCallRule]()
+
+    statements foreach (_ match {
+      case s: SchemaDeclaration    => schemaDeclarationToCompile += s
+      case s: ExtractionRule       => extractionRuleToCompile += s
+      case s: FunctionCallRule     => functionCallRuleToCompile += s
+      case s: InferenceRule        => inferenceRuleToCompile += s
+      case _                       =>
+    })
+
+    schemaDeclarationGroupByHead = mode match {
+      case INCREMENTAL => schemaDeclarationToCompile.toList.filter(_.a.name.startsWith("dd_")).groupBy(_.a.name)
+      case _           => schemaDeclarationToCompile.toList.groupBy(_.a.name)
+    }
+    extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.q.head.name)
+    inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
+    functionCallRuleGroupByInput   = functionCallRuleToCompile.toList.groupBy(_.input)
+    functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
+  }
+
+  // Analyze the block visibility among statements
+  def analyzeVisible(statements: List[Statement]) = {
+    extractionRuleGroupByHead.values foreach { visible += _(0) }
+    functionCallList foreach { visible += _ }
+  }
+
+  // Analyze the dependency between statements and construct a graph.
+  def analyzeDependency(statements: List[Statement]) = {
+    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++
+      functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
+
+    // Look at the body of each statement to construct a dependency graph
+    statements foreach {
+      case f : FunctionCallRule => dependencies += {
+        f -> (( Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case e : ExtractionRule   => dependencies += {
+        e -> (((e.q.bodies.flatten collect { case x: Atom => x.name })
+          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case w : InferenceRule    => dependencies += {
+        w -> (((w.q.bodies.flatten collect { case x: Atom => x.name })
+          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+      case _ =>
+    }
+  }
+  // Generates a "dependencies" value for a compiled block of given statement.
+  def generateDependenciesOfCompiledBlockFor(statements: List[Statement]): String = {
+    var dependentExtractorBlockNames = Set[String]()
+    for (statement <- statements) {
+      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & visible) map resolveExtractorBlockName
+    }
+    if (dependentExtractorBlockNames.size == 0) "" else {
+      val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")
+      s"dependencies: [${depStr}]"
+    }
+  }
+}
+
+// This is responsible for compiling a single conjunctive query
+class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
+  // This is responsible for schema elements within a given query, e.g.,
+  // what is the canonical version of x? (i.e., the first time it is
+  // mentioned in the body. This is useful to translate to SQL (join
+  // conditions, select, etc.)
+  var query_schema = new HashMap[ String, Tuple2[String,Variable] ]()
+
+  // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
+  // index is the index of the subgoal/atom this variable is found in the body.
+  // variable is the complete Variable type for the found variable.
+  def generateCanonicalVar()  = {
+    def generateCanonicalVarFromAtom(a: Atom, index: String) {
+      a.terms.zipWithIndex.foreach { case (expr, i) =>
+        expr match {
+          case VarExpr(v) =>
+            if (! (query_schema contains v) )
+              query_schema += { v -> (index, Variable(v,a.name,i) ) }
+          case _ =>
+        }
+      }
+    }
+    // For quantified body, we need to recursively add variables from the atoms inside the quantified body
+    def generateCanonicalVarFromBodies(bodies: List[Body], indexPrefix: String) {
+      bodies.zipWithIndex.foreach {
+        case (a: Atom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
+        // we need to recursively handle the atoms inside the modifier
+        case (a: QuantifiedBody, index) => generateCanonicalVarFromBodies(a.bodies, s"${indexPrefix}${index}_")
+        case _ =>
+      }
+    }
+
+    generateCanonicalVarFromBodies(cq.bodies(0), "")
+  }
+  generateCanonicalVar() // initialize
+
+  // accessors
+  def getBodyIndex( varName : String )       = { query_schema(varName)._1 }
+  def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
+
   // compile a variable name to its canonical relation and column in R{index}.{name} style
-  def compileVariable(v: String, cq: ConjunctiveQuery) = {
-    val qs = new QuerySchema(cq)
-    val index = qs.getBodyIndex(v)
-    val name  = resolveName(qs.getVar(v))
+  def compileVariable(v: String) = {
+    val index = getBodyIndex(v)
+    val name  = ss.resolveName(getVar(v))
     s"R${index}.${name}"
   }
 
-  // compile alias, only used for head
-  def compileAlias(e: Expr, cq: ConjunctiveQuery, alias: AliasStyle) = {
+  // compile alias
+  def compileAlias(e: Expr, alias: AliasStyle) = {
     e match {
       case VarExpr(v) => {
-        val qs = new QuerySchema(cq)
-        val index = qs.getBodyIndex(v)
-        val variable = qs.getVar(v)
-        val name  = resolveName(variable)
+        val index = getBodyIndex(v)
+        val variable = getVar(v)
+        val name  = ss.resolveName(variable)
         val relation = variable.relName
         alias match {
           case NoAlias => ""
@@ -203,62 +305,62 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
   }
 
+  // compile expression with alias, only used for head
+  def compileExprWithAlias(e: Expr, alias: AliasStyle) = {
+    compileExpr(e) + compileAlias(e, alias)
+  }
+
   // resolve an expression
-  def compileExpr(e: Expr, cq: ConjunctiveQuery, generateAlias: Expr => String = e => "") = {
-    // recursively compile an expression
-    def compileExprInner(e: Expr) : String = {
-      e match {
-        case VarExpr(name) => compileVariable(name, cq)
-        case ConstExpr(value) => value
-        case FuncExpr(function, args, agg) => {
-          val resolvedArgs = args map (x => compileExprInner(x))
-          val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
-          resolved
-        }
-        case BinaryOpExpr(lhs, op, rhs) => {
-          val resovledLhs = compileExprInner(lhs)
-          val resovledRhs = compileExprInner(rhs)
-          s"(${resovledLhs} ${op} ${resovledRhs})"
-        }
-        case TypecastExpr(lhs, rhs) => {
-          val resovledLhs = compileExprInner(lhs)
-          s"(${resovledLhs} :: ${rhs})"
-        }
-        case Placeholder() => ""
+  def compileExpr(e: Expr) : String = {
+    e match {
+      case VarExpr(name) => compileVariable(name)
+      case ConstExpr(value) => value
+      case FuncExpr(function, args, agg) => {
+        val resolvedArgs = args map (x => compileExpr(x))
+        val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
+        resolved
+      }
+      case BinaryOpExpr(lhs, op, rhs) => {
+        val resovledLhs = compileExpr(lhs)
+        val resovledRhs = compileExpr(rhs)
+        s"(${resovledLhs} ${op} ${resovledRhs})"
+      }
+      case TypecastExpr(lhs, rhs) => {
+        val resovledLhs = compileExpr(lhs)
+        s"(${resovledLhs} :: ${rhs})"
       }
     }
-    compileExprInner(e) + generateAlias(e)
   }
 
   // resolve a condition
-  def compileCond(cond: Cond, cq: ConjunctiveQuery) : String = {
+  def compileCond(cond: Cond) : String = {
     cond match {
       case ComparisonCond(lhs, op, rhs) =>
-        s"${compileExpr(lhs, cq)} ${op} ${compileExpr(rhs, cq)}"
-      case NegationCond(c) => s"(NOT ${compileCond(c, cq)})"
+        s"${compileExpr(lhs)} ${op} ${compileExpr(rhs)}"
+      case NegationCond(c) => s"(NOT ${compileCond(c)})"
       case CompoundCond(lhs, op, rhs) => {
-        val resolvedLhs = s"${compileCond(lhs, cq)}"
-        val resolvedRhs = s"${compileCond(rhs, cq)}"
+        val resolvedLhs = s"${compileCond(lhs)}"
+        val resolvedRhs = s"${compileCond(rhs)}"
         op match {
           case LogicOperator.AND => s"(${resolvedLhs} AND ${resolvedRhs})"
           case LogicOperator.OR  => s"(${resolvedLhs} OR ${resolvedRhs})"
         }
       }
-      case InCond(lhs, rhs) => {
-        s"${compileExpr(lhs, cq)} IN (SELECT * FROM ${rhs})"
-      }
-      case ExistCond(rhs) => s"EXISTS (SELECT * FROM ${rhs})"
       case _ => ""
     }
   }
 
+  // generate SQL SELECT cluase
+  def generateSQLHead(alias: AliasStyle) = {
+    val head = (cq.head.terms map { expr => compileExprWithAlias(expr, alias) }).mkString(", ")
+    val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
+    s"${distinctStr}${head}"
+  }
+
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause
-  def generateSQLBody(z : ConjunctiveQuery) : String = {
-    // Simple logic for the where clause, first find every first occurence of a
-    // and stick it in a map.
-    val qs = new QuerySchema(z)
-
+  def generateSQLBody() : String = {
+    // generate where clause from unification and conditions
     def generateWhereClause(bodies: List[Body], indexPrefix: String) : String = {
       val conditions = bodies.zipWithIndex.flatMap {
         case (Atom(relName, terms), index) => {
@@ -267,25 +369,24 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
             expr match {
               // a simple variable indicates a join condition with other columns having the same variable name
               case VarExpr(varName) => {
-                val canonical_body_index = qs.getBodyIndex(varName)
+                val canonical_body_index = getBodyIndex(varName)
                 if (canonical_body_index != bodyIndex) {
-                  val real_attr_name1 = resolveName( Variable(varName, relName, atomIndex) )
-                  val real_attr_name2 = resolveName( qs.getVar(varName))
+                  val real_attr_name1 = ss.resolveName( Variable(varName, relName, atomIndex) )
+                  val real_attr_name2 = ss.resolveName( getVar(varName))
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
               }
-              case Placeholder() => None
               // other expressions indicate a filter condition on the column
               case _ => {
-                val resolved = compileExpr(expr, z)
-                val attr = schema(relName, atomIndex)
+                val resolved = compileExpr(expr)
+                val attr = ss.schema(relName, atomIndex)
                 Some(s"R${bodyIndex}.${attr} = ${resolved}")
               }
             }
           }
         }
-        case (x: Cond, _) => Some(compileCond(x, z))
-        case (x: ModifierAtom, index) => {
+        case (x: Cond, _) => Some(compileCond(x))
+        case (x: QuantifiedBody, index) => {
           val newIndexPrefix = s"${indexPrefix}${index}_"
           val subqueryWhereStr = generateWhereClause(x.bodies, newIndexPrefix)
           val subqueryFromStr  = generateFromClause(x.bodies, newIndexPrefix)
@@ -304,7 +405,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         case _ => None
       }
       val outers = bodies.zipWithIndex flatMap {
-        case (x:ModifierAtom,i) => {
+        case (x:QuantifiedBody,i) => {
           val newIndexPrefix = s"${indexPrefix}${i}_"
           x.modifier match {
             case OuterModifier() => {
@@ -325,9 +426,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       }
     }
 
-    val whereClause = generateWhereClause(z.bodies(0), "")
-    val whereClauseStr = if (whereClause.isEmpty) "" else "WHERE " + whereClause
-    val fromClauseStr = generateFromClause(z.bodies(0), "")
+    def optionalClause(prefix: String, clause: String): String =
+      if (clause.isEmpty) "" else prefix + " " + clause
 
     // check if an expression contains an aggregation function
     def containsAggregation(expr: Expr) : Boolean = {
@@ -339,133 +439,26 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         }
         case BinaryOpExpr(lhs, op, rhs) => containsAggregation(lhs) || containsAggregation(rhs)
         case TypecastExpr(lhs, rhs) => containsAggregation(lhs)
-        case Placeholder() => false
       }
     }
 
     // handle group by
     // map head terms, leaving out aggregation functions
-    val groupbyTerms = z.head.terms.zipWithIndex flatMap { case (expr, index) =>
-      if (containsAggregation(expr)) None
-      else Some(compileExpr(expr, z))
-    }
+    val groupbyTerms = cq.head.terms.filterNot(containsAggregation) map (compileExpr(_))
 
-    val groupbyStr = if (groupbyTerms.size == z.head.terms.size || groupbyTerms.isEmpty) {
+    val groupbyStr = if (groupbyTerms.size == cq.head.terms.size || groupbyTerms.isEmpty) {
       ""
     } else {
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
     }
 
     // limit clause
-    val limitStr = z.limit match {
-      case Some(s) => s" LIMIT ${s}"
-      case None => ""
-    }
+    val limitStr = optionalClause("LIMIT", cq.limit.getOrElse("").toString)
 
-    s"""FROM ${ fromClauseStr }
-        ${ whereClauseStr }${groupbyStr}${limitStr}"""
+    s"""FROM ${ generateFromClause(cq.bodies(0), "") }
+        ${ optionalClause("WHERE", generateWhereClause(cq.bodies(0), "")) }${groupbyStr}${limitStr}"""
   }
 
-  // Group statements by head
-  def groupByHead(statements: List[Statement]) = {
-    // Compile compilation states by head name based on type
-    val schemaDeclarationToCompile = new ListBuffer[SchemaDeclaration]()
-    val extractionRuleToCompile    = new ListBuffer[ExtractionRule]()
-    val inferenceRuleToCompile     = new ListBuffer[InferenceRule]()
-    val functionCallRuleToCompile  = new ListBuffer[FunctionCallRule]()
-
-    statements foreach (_ match {
-      case s: SchemaDeclaration    => schemaDeclarationToCompile += s
-      case s: ExtractionRule       => extractionRuleToCompile += s
-      case s: FunctionCallRule     => functionCallRuleToCompile += s
-      case s: InferenceRule        => inferenceRuleToCompile += s
-      case _                       =>
-    })
-
-    schemaDeclarationGroupByHead = mode match {
-      case INCREMENTAL => schemaDeclarationToCompile.toList.filter(_.a.name.startsWith("dd_")).groupBy(_.a.name)
-      case _           => schemaDeclarationToCompile.toList.groupBy(_.a.name)
-    }
-    extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.q.head.name)
-    inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
-    functionCallRuleGroupByInput   = functionCallRuleToCompile.toList.groupBy(_.input)
-    functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
-  }
-
-  // Analyze the block visibility among statements
-  def analyzeVisible(statements: List[Statement]) = {
-    extractionRuleGroupByHead.values foreach { visible += _(0) }
-    functionCallList foreach { visible += _ }
-  }
-
-  // Analyze the dependency between statements and construct a graph.
-  def analyzeDependency(statements: List[Statement]) = {
-    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++
-      functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
-
-    // Look at the body of each statement to construct a dependency graph
-    statements foreach {
-      case f : FunctionCallRule => dependencies += {
-        f -> (( Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case e : ExtractionRule   => dependencies += {
-        e -> (((e.q.bodies.flatten collect { case x: Atom => x.name })
-          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case w : InferenceRule    => dependencies += {
-        w -> (((w.q.bodies.flatten collect { case x: Atom => x.name })
-          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case _ =>
-    }
-  }
-  // Generates a "dependencies" value for a compiled block of given statement.
-  def generateDependenciesOfCompiledBlockFor(statements: List[Statement]): String = {
-    var dependentExtractorBlockNames = Set[String]()
-    for (statement <- statements) {
-      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & visible) map resolveExtractorBlockName
-    }
-    if (dependentExtractorBlockNames.size == 0) "" else {
-      val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")
-      s"dependencies: [${depStr}]"
-    }
-  }
-}
-
-// This is responsible for schema elements within a given query, e.g.,
-// what is the canonical version of x? (i.e., the first time it is
-// mentioned in the body. This is useful to translate to SQL (join
-// conditions, select, etc.)
-class QuerySchema(q : ConjunctiveQuery) {
-  var query_schema = new HashMap[ String, Tuple2[String,Variable] ]()
-
-  // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
-  // index is the index of the subgoal/atom this variable is found in the body.
-  // variable is the complete Variable type for the found variable.
-  def generateCanonicalVar()  = {
-    def generateCanonicalVarFromAtom(a: Atom, index: String) {
-      a.terms.zipWithIndex.foreach { case (expr, i) =>
-        expr match {
-          case VarExpr(v) =>
-            if (! (query_schema contains v) )
-              query_schema += { v -> (index, Variable(v,a.name,i) ) }
-          case _ =>
-        }
-      }
-    }
-
-    def generateCanonicalVarFromBodies(bodies: List[Body], indexPrefix: String) {
-      bodies.zipWithIndex.foreach {
-        case (a: Atom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
-        case (a: ModifierAtom, index) => generateCanonicalVarFromBodies(a.bodies, s"${indexPrefix}${index}_")
-        case _ =>
-      }
-    }
-
-    generateCanonicalVarFromBodies(q.bodies(0), "")
-  }
-  generateCanonicalVar() // initialize
-
-  // accessors
-  def getBodyIndex( varName : String )       = { query_schema(varName)._1 }
-  def getVar(varName : String ) : Variable   = { query_schema(varName)._2 }
 }
 
 
@@ -526,25 +519,19 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       for (cqBody <- stmt.q.bodies) {
         val tmpCq = stmt.q.copy(bodies = List(cqBody))
         // Generate the body of the query.
-        val qs              = new QuerySchema( tmpCq )
+        val qc              = new QueryCompiler(tmpCq, ss)
 
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headTerms = tmpCq.head.terms map { expr =>
-            ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, NoAlias))
-          }
-          val labelCol = ss.compileVariable(stmt.supervision, tmpCq)
-          val headTermsStr = ( headTerms :+ "0 as id" ).mkString(", ")
-          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, ${labelCol} AS label
-          ${ ss.generateSQLBody(tmpCq) }
+          val headStr = qc.generateSQLHead(NoAlias)
+          val labelCol = qc.compileVariable(stmt.supervision)
+          inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
+          ${ qc.generateSQLBody() }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headTerms = tmpCq.head.terms map { expr =>
-            ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, NoAlias))
-          }
-          val headTermsStr = ( headTerms :+ "id" ).mkString(", ")
-          inputQueries += s"""SELECT DISTINCT ${ headTermsStr }, label
-          ${ ss.generateSQLBody(tmpCq) }
+          val headStr = qc.generateSQLHead(NoAlias)
+          inputQueries += s"""SELECT DISTINCT ${ headStr }, id, label
+          ${ qc.generateSQLBody() }
           """
         } else {
           // variable columns
@@ -557,14 +544,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case true => NoAlias
             case false => HeadAlias
           }
-          val variableCols = tmpCq.head.terms map { expr =>
-            ss.compileExpr(expr, tmpCq, ss.compileAlias(_, tmpCq, resolveColumnFlag))
-          }
-          val selectStr = variableCols.mkString(", ")
-          val distinctStr = if (tmpCq.isDistinct) "DISTINCT" else ""
+          val headStr = qc.generateSQLHead(resolveColumnFlag)
           inputQueries += s"""
-            SELECT ${distinctStr} ${selectStr}
-            ${ ss.generateSQLBody(tmpCq) }"""
+            SELECT ${headStr}
+            ${ qc.generateSQLBody() }"""
         }
       }
     }
@@ -643,7 +626,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val fakeBodyAtoms   = fakeBody.collect { case x: Atom => x }
 
         val index = cqBody.length + 1
-        val qs2 = new QuerySchema( fakeCQ )
+        val qc = new QueryCompiler(fakeCQ, ss)
         // TODO self-join?
         val varInBody = (fakeBody.zipWithIndex flatMap {
           case (x: Atom, i) =>
@@ -659,7 +642,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // weight string
         val uwStr = stmt.weights match {
           case UnknownFactorWeight(w) => Some(w.map(s =>
-            ss.compileExpr(VarExpr(s), fakeCQ, ss.compileAlias(_, fakeCQ, HeadAlias))).mkString(", "))
+            qc.compileExprWithAlias(VarExpr(s), HeadAlias)).mkString(", "))
           case _ => None
         }
 
@@ -668,7 +651,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // factor input query
         inputQueries += s"""
           SELECT ${selectStr}
-          ${ ss.generateSQLBody(fakeCQ) }"""
+          ${ qc.generateSQLBody() }"""
         // factor function
         if (func.length == 0) {
           val funcBody = (fakeBodyAtoms map {x =>
@@ -692,7 +675,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              val weightVar = w.map(s => ss.compileAlias(VarExpr(s), fakeCQ, WeightAlias)).mkString(", ")
+              val weightVar = w.map(s => qc.compileAlias(VarExpr(s), WeightAlias)).mkString(", ")
               s"?(${weightVar})"
             }
             case UnknownFactorWeightBindingToConst(w) => "?"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 2678ed886..00be21e49 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -36,8 +36,8 @@ object DeepDiveLogDeltaDeriver{
     cq.bodies foreach { bodies =>
       // We don't support deriving delta rules for modifiers
       bodies foreach {
-        case x: ModifierAtom => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
-        case _ =>
+        case _: Cond | _: Atom => // supported
+        case _: QuantifiedBody => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
       }
       // Delta body
       val incDeltaBody = bodies collect {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 3936dec39..79019ac8f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -18,15 +18,14 @@ case class ConstExpr(value: String) extends Expr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
-case class Placeholder extends Expr
 
 sealed trait Body
 case class Atom(name : String, terms : List[Expr]) extends Body
-case class ModifierAtom(modifier: AtomModifier, bodies: List[Body]) extends Body
+case class QuantifiedBody(modifier: BodyModifier, bodies: List[Body]) extends Body
 
-sealed trait AtomModifier
-case class ExistModifier(negated: Boolean) extends AtomModifier
-case class OuterModifier extends AtomModifier
+sealed trait BodyModifier
+case class ExistModifier(negated: Boolean) extends BodyModifier
+case class OuterModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
@@ -45,8 +44,6 @@ sealed trait Cond extends Body
 case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
 case class NegationCond(cond: Cond) extends Cond
 case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
-case class InCond(lhs: Expr, relName: String) extends Cond
-case class ExistCond(relName: String) extends Cond
 
 // logic operators
 object LogicOperator extends Enumeration {
@@ -169,8 +166,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // expression
   def expr : Parser[Expr] =
-    ( "_" ^^ { case _ => Placeholder() }
-    | lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
     )
@@ -190,7 +186,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
-  def atomModifier = "EXIST" | "OUTER"
 
   def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
@@ -217,12 +212,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def atom = relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
     case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
   }
-  def modifierAtom = (opt("NOT") ~ "EXIST" | "OUTER") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
+  def modifierAtom = (opt("!") ~ "EXISTS" | "OPTIONAL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
-      case (not ~ "EXIST") => new ExistModifier(not != None)
-      case "OUTER" => new OuterModifier
+      case (not ~ "EXISTS") => new ExistModifier(not != None)
+      case "OPTIONAL" => new OuterModifier
     }
-    ModifierAtom(modifier, b)
+    QuantifiedBody(modifier, b)
   }
 
   def cqBody: Parser[Body] = cond | modifierAtom | atom
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index ad559e847..3534edc12 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -85,7 +85,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
       case BinaryOpExpr(lhs, op, rhs) => s"(${printExpr(lhs)} ${op} ${printExpr(rhs)})"
       case TypecastExpr(lhs, rhs) => s"(${printExpr(lhs)} :: ${rhs})"
-      case Placeholder() => "_"
     }
   }
 
@@ -100,8 +99,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
           case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
         }
       }
-      case InCond(lhs, rhs) => s"${printExpr(lhs)} IN ${rhs}"
-      case ExistCond(rhs) => s"EXISTS ${rhs}"
     }
   }
 
@@ -110,10 +107,10 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     s"${a.name}(${vars.mkString(", ")})"
   }
 
-  def printModifierAtom(a: ModifierAtom) : String = {
+  def printQuantifiedBody(a: QuantifiedBody) : String = {
     val modifier = a.modifier match {
-      case ExistModifier(negated) => if(negated) "NOT " else "" + "EXIST"
-      case OuterModifier() => "OUTER"
+      case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
+      case OuterModifier() => "OPTIONAL"
     }
     val bodyStr = (a.bodies map printBody).mkString(", ")
     s"${modifier}[${bodyStr}]"
@@ -123,7 +120,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     b match {
       case b: Atom => printAtom(b)
       case b: Cond => printCond(b)
-      case b: ModifierAtom => printModifierAtom(b)
+      case b: QuantifiedBody => printQuantifiedBody(b)
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 3b131c751..69d721df6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -36,31 +36,26 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkNumberOfColumns(stmt)
   }
 
+  // iterate over all atoms contained in the body list and apply the checker
+  def checkBodyAtoms(bodies: List[Body], checker: Atom => Unit) : Unit = {
+    bodies foreach {
+      case a: Atom => checker(a)
+      case a: QuantifiedBody => checkBodyAtoms(a.bodies, checker)
+      case _ =>
+    }
+  }
+
   // check if relations in the body are defined
   def checkRelationDefined(stmt: Statement) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
-    def checkRelation(name: String) {
-      if (!(heads contains name))
-        error(stmt, s"""relation "${name}" is not defined""")
+    def checkRelation(a: Atom) {
+      if (!(heads contains a.name))
+        error(stmt, s"""relation "${a.name}" is not defined""")
     }
     stmt match {
-      case s: ExtractionRule => {
-        s.q.bodies foreach { x =>
-          x foreach {
-            case a: Atom => checkRelation(a.name)
-            case _ =>
-          }
-        }
-      }
-      case s: InferenceRule => {
-        s.q.bodies foreach { x =>
-          x foreach {
-            case a: Atom => checkRelation(a.name)
-            case _ =>
-          }
-        }
-      }
-      case s: FunctionCallRule => checkRelation(s.input)
+      case s: ExtractionRule => checkBodyAtoms(s.q.bodies.flatten, checkRelation)
+      case s: InferenceRule => checkBodyAtoms(s.q.bodies.flatten, checkRelation)
+      case s: FunctionCallRule => checkRelation(Atom(s.input, Nil))
       case _ =>
     }
   }
@@ -101,12 +96,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
     def checkCq(cq: ConjunctiveQuery) {
       checkAtom(cq.head)
-      cq.bodies foreach { x =>
-        x foreach {
-          case a: Atom => checkAtom(a)
-          case _ =>
-        }
-      }
+      checkBodyAtoms(cq.bodies.flatten, checkAtom)
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
@@ -115,6 +105,29 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
+  // check if outer join body contains one atom
+  def checkOuterJoin(stmt: Statement) {
+    def checkOuterJoinBodies(bodies: List[Body]) {
+      bodies.foreach {
+        case b: QuantifiedBody => {
+          b.modifier match {
+            case OuterModifier() =>
+              if ((b.bodies collect { case x: Atom => 1 }).size != 1) {
+                error(stmt, s"One and only one atom should be supplied in OPTIONAL modifier")
+              }
+            case _ =>
+          }
+        }
+        case _ =>
+      }
+    }
+    stmt match {
+      case s: ExtractionRule => checkOuterJoinBodies(s.q.bodies.flatten)
+      case s: InferenceRule => checkOuterJoinBodies(s.q.bodies.flatten)
+      case _ =>
+    }
+  }
+
   // throw exception
   def error(stmt: Statement, message: String) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index f456ed25f..d8c429231 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -72,9 +72,9 @@
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS ext_features_input;
         CREATE VIEW ext_features_input AS 
-            SELECT  R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
+            SELECT R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
             FROM words R0, words R1
-        WHERE R1.sent_id = R0.sent_id  
+        WHERE R1.sent_id = R0.sent_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_5" ]
@@ -83,7 +83,7 @@
 
       deepdive.extraction.extractors.extraction_rule_9 {
         sql: """ 
-        INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 as id, R0.true_tag AS label
+        INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
           FROM words R0
         
           
@@ -117,7 +117,7 @@
           input_query: """
           SELECT R0.id AS "tag.R0.id" , R1.feature AS "word_features.R1.feature" 
           FROM tag R0, word_features R1
-        WHERE R1.word_id = R0.word_id  """
+        WHERE R1.word_id = R0.word_id """
           function: "Multinomial(tag.R0.label)"
           weight: "?(word_features.R1.feature)"
         }
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 572377cad..2abcc46b4 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -58,7 +58,7 @@
       deepdive.extraction.extractors.extraction_rule_9 {
         sql: """ DROP VIEW IF EXISTS E;
         CREATE VIEW E AS 
-            SELECT  (R0.k :: INT) AS column_0
+            SELECT (R0.k :: INT) AS column_0
             FROM b R0
         
         """
@@ -70,7 +70,7 @@
       deepdive.extraction.extractors.extraction_rule_18 {
         sql: """ DROP VIEW IF EXISTS N;
         CREATE VIEW N AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
         """
@@ -82,7 +82,7 @@
       deepdive.extraction.extractors.extraction_rule_21 {
         sql: """ DROP VIEW IF EXISTS T;
         CREATE VIEW T AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         WHERE R1_0.s > R0.p
         """
@@ -94,7 +94,7 @@
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
         CREATE VIEW J AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
         """
@@ -106,7 +106,7 @@
       deepdive.extraction.extractors.extraction_rule_22 {
         sql: """ DROP VIEW IF EXISTS U;
         CREATE VIEW U AS 
-            SELECT  R0_0.k AS "b.R0_0.k" 
+            SELECT R0_0.k AS "b.R0_0.k" 
             FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
         
         """
@@ -118,7 +118,7 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS F;
         CREATE VIEW F AS 
-            SELECT  ((R0.k :: INT) + (R0.r :: INT)) AS column_0
+            SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
             FROM b R0
         
         """
@@ -130,7 +130,7 @@
       deepdive.extraction.extractors.extraction_rule_5 {
         sql: """ DROP VIEW IF EXISTS A;
         CREATE VIEW A AS 
-            SELECT  (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
+            SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
             FROM b R0
         
         """
@@ -142,7 +142,7 @@
       deepdive.extraction.extractors.extraction_rule_17 {
         sql: """ DROP VIEW IF EXISTS M;
         CREATE VIEW M AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
         """
@@ -154,7 +154,7 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS I;
         CREATE VIEW I AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
         """
@@ -166,7 +166,7 @@
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ DROP VIEW IF EXISTS G;
         CREATE VIEW G AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE (R0.k + R0.r) = 100
         """
@@ -178,7 +178,7 @@
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ DROP VIEW IF EXISTS V;
         CREATE VIEW V AS 
-            SELECT  R0.n AS "c.R0.n" 
+            SELECT R0.n AS "c.R0.n" 
             FROM c R0, a R1
         WHERE R1.k = R0.n 
         """
@@ -204,7 +204,7 @@
         CREATE VIEW L AS 
             SELECT DISTINCT R0.k AS "b.R0.k" 
             FROM b R0
-         LIMIT 100
+        LIMIT 100
         """
         style: "sql_extractor"
           
@@ -214,7 +214,7 @@
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS B;
         CREATE VIEW B AS 
-            SELECT  func((R0.k + (R0.r + R0.k))) AS column_0
+            SELECT func((R0.k + (R0.r + R0.k))) AS column_0
             FROM b R0
         
         """
@@ -226,7 +226,7 @@
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ DROP VIEW IF EXISTS P;
         CREATE VIEW P AS 
-            SELECT  R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS column_2
+            SELECT R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS column_2
             FROM a R0, b R1
         WHERE R1.k = R0.k 
         GROUP BY R1.p, R1.q
@@ -239,7 +239,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS C;
         CREATE VIEW C AS 
-            SELECT  func(func(func(R0.k))) AS column_0
+            SELECT func(func(func(R0.k))) AS column_0
             FROM b R0
         
         """
@@ -251,7 +251,7 @@
       deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ DROP VIEW IF EXISTS H;
         CREATE VIEW H AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
         """
@@ -263,7 +263,7 @@
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ DROP VIEW IF EXISTS K;
         CREATE VIEW K AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
         """
@@ -275,7 +275,7 @@
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ DROP VIEW IF EXISTS O;
         CREATE VIEW O AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
         """
@@ -287,7 +287,7 @@
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
         CREATE VIEW D AS 
-            SELECT  (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
+            SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
             FROM b R0
         
         """
@@ -299,7 +299,7 @@
       deepdive.extraction.extractors.extraction_rule_20 {
         sql: """ DROP VIEW IF EXISTS S;
         CREATE VIEW S AS 
-            SELECT  R0.k AS "b.R0.k" 
+            SELECT R0.k AS "b.R0.k" 
             FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
         
         """
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index 800aa782c..f8b4fb3d4 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -36,17 +36,17 @@ K(x) :- b(x,y,z,w), [x + w = 100, [!x > 50; x = 40]].
 L(x) * | 100 :- b(x, y, z, w).
 
 # modifiers
-M(x) :- b(x,y,z,w), EXIST[c(a,x,b)].
+M(x) :- b(x,y,z,w), EXISTS[c(a,x,b)].
 
-N(x) :- b(x,y,z,w), EXIST[c(a,x,b), a > "a"].
+N(x) :- b(x,y,z,w), EXISTS[c(a,x,b), a > "a"].
 
-O(x) :- b(x,y,z,w), EXIST[c(a,x,b), a(x)].
+O(x) :- b(x,y,z,w), EXISTS[c(a,x,b), a(x)].
 
-S(x) :- b(x,y,z,w), OUTER[c(a,x,b)].
+S(x) :- b(x,y,z,w), OPTIONAL[c(a,x,b)].
 
-T(x) :- b(x,y,z,w), OUTER[c(a,x,b), a > y], a > y.
+T(x) :- b(x,y,z,w), OPTIONAL[c(a,x,b), a > y], a > y.
 
-U(x) :- OUTER[b(x,y,z,w)], OUTER[c(a,x,b)].
+U(x) :- OPTIONAL[b(x,y,z,w)], OPTIONAL[c(a,x,b)].
 
 # placeholder
 V(x) :- c(_,x,_), a(x).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 197c45e21..beeb5876b 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -62,28 +62,28 @@ L(x) * | 100 :-
 
 M(x)  :-
     b(x, y, z, w),
-    EXIST[c(a, x, b)].
+    EXISTS[c(a, x, b)].
 
 N(x)  :-
     b(x, y, z, w),
-    EXIST[c(a, x, b), a >  "a" ].
+    EXISTS[c(a, x, b), a >  "a" ].
 
 O(x)  :-
     b(x, y, z, w),
-    EXIST[c(a, x, b), a(x)].
+    EXISTS[c(a, x, b), a(x)].
 
 S(x)  :-
     b(x, y, z, w),
-    OUTER[c(a, x, b)].
+    OPTIONAL[c(a, x, b)].
 
 T(x)  :-
     b(x, y, z, w),
-    OUTER[c(a, x, b), a > y],
+    OPTIONAL[c(a, x, b), a > y],
     a > y.
 
 U(x)  :-
-    OUTER[b(x, y, z, w)],
-    OUTER[c(a, x, b)].
+    OPTIONAL[b(x, y, z, w)],
+    OPTIONAL[c(a, x, b)].
 
 V(x)  :-
     c(_, x, _),
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index 1939614bf..c06a83f8c 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -123,10 +123,10 @@ q1.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_label2;
         INSERT INTO dd_new_label2 
-            SELECT  R0.wid, R0.val
+            SELECT R0.wid, R0.val
             FROM label2 R0
          UNION ALL 
-            SELECT  R0.wid, R0.val
+            SELECT R0.wid, R0.val
             FROM dd_delta_label2 R0
         
         """
@@ -153,10 +153,10 @@ q1.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_label1;
         INSERT INTO dd_new_label1 
-            SELECT  R0.wid, R0.val
+            SELECT R0.wid, R0.val
             FROM label1 R0
          UNION ALL 
-            SELECT  R0.wid, R0.val
+            SELECT R0.wid, R0.val
             FROM dd_delta_label1 R0
         
         """
@@ -167,7 +167,7 @@ q1.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_21 {
         sql: """ 
-        INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+        INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM dd_delta_label2 R0
         
           
@@ -180,10 +180,10 @@ q1.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_features;
         INSERT INTO dd_new_features 
-            SELECT  R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
             FROM features R0
          UNION ALL 
-            SELECT  R0.id, R0.word_id, R0.feature_id, R0.feature_val
+            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
             FROM dd_delta_features R0
         
         """
@@ -194,7 +194,7 @@ q1.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_20 {
         sql: """ 
-        INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+        INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM dd_delta_label1 R0
         
           
@@ -223,7 +223,7 @@ q1.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
           FROM dd_new_q2 R0, dd_delta_features R1
-        WHERE R1.word_id = R0.wid  """
+        WHERE R1.word_id = R0.wid """
           function: "Imply(dd_new_q2.R0.label)"
           weight: "?(dd_delta_features.R1.feature_id)"
         }
@@ -233,7 +233,7 @@ q1.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
           FROM dd_new_q1 R0, dd_delta_features R1
-        WHERE R1.word_id = R0.wid  """
+        WHERE R1.word_id = R0.wid """
           function: "Imply(dd_new_q1.R0.label)"
           weight: "?(dd_delta_features.R1.feature_id)"
         }
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index 79b41870d..ab23cf330 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -80,7 +80,7 @@ q2.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_5 {
         sql: """ 
-        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label1 R0
         
           
@@ -92,7 +92,7 @@ q2.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label2 R0
         
           
@@ -106,7 +106,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q1 R0, features R1
-        WHERE R1.word_id = R0.wid  """
+        WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
@@ -116,7 +116,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q2 R0, features R1
-        WHERE R1.word_id = R0.wid  """
+        WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 05d770f85..76468eafa 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -80,7 +80,7 @@ q2.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_5 {
         sql: """ 
-        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label1 R0
         
           
@@ -92,7 +92,7 @@ q2.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 as id, R0.val AS label
+        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label2 R0
         
           
@@ -106,7 +106,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q1 R0, features R1
-        WHERE R1.word_id = R0.wid  """
+        WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
@@ -116,7 +116,7 @@ q2.label: Boolean
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
           FROM q2 R0, features R1
-        WHERE R1.word_id = R0.wid  """
+        WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
           weight: "?(features.R1.feature_id)"
         }
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 1e0b6a07c..31b12e7f5 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -138,7 +138,7 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ 
-        INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label
+        INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM dd_delta_person_smokes R0
         
           
@@ -151,10 +151,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_person_has_cancer;
         INSERT INTO dd_new_person_has_cancer 
-            SELECT  R0.person_id, R0.has_cancer
+            SELECT R0.person_id, R0.has_cancer
             FROM person_has_cancer R0
          UNION ALL 
-            SELECT  R0.person_id, R0.has_cancer
+            SELECT R0.person_id, R0.has_cancer
             FROM dd_delta_person_has_cancer R0
         
         """
@@ -166,10 +166,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_person;
         INSERT INTO dd_new_person 
-            SELECT  R0.person_id, R0.name
+            SELECT R0.person_id, R0.name
             FROM person R0
          UNION ALL 
-            SELECT  R0.person_id, R0.name
+            SELECT R0.person_id, R0.name
             FROM dd_delta_person R0
         
         """
@@ -195,7 +195,7 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ 
-        INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label
+        INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM dd_delta_person_has_cancer R0
         
           
@@ -223,10 +223,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_person_smokes;
         INSERT INTO dd_new_person_smokes 
-            SELECT  R0.person_id, R0.smokes
+            SELECT R0.person_id, R0.smokes
             FROM person_smokes R0
          UNION ALL 
-            SELECT  R0.person_id, R0.smokes
+            SELECT R0.person_id, R0.smokes
             FROM dd_delta_person_smokes R0
         
         """
@@ -238,10 +238,10 @@ dd_delta_smoke.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_friends;
         INSERT INTO dd_new_friends 
-            SELECT  R0.person_id, R0.friend_id
+            SELECT R0.person_id, R0.friend_id
             FROM friends R0
          UNION ALL 
-            SELECT  R0.person_id, R0.friend_id
+            SELECT R0.person_id, R0.friend_id
             FROM dd_delta_friends R0
         
         """
@@ -254,10 +254,10 @@ dd_delta_smoke.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id   UNION ALL 
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION ALL 
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  """
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
           weight: "0.5"
         }
@@ -267,10 +267,10 @@ dd_delta_smoke.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_delta_smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id   UNION ALL 
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  UNION ALL 
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  """
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
           function: "Imply(dd_delta_smoke.R1.label, dd_new_smoke.R0.label)"
           weight: "0.4"
         }
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index b9908b20d..0081014f5 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -88,7 +88,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ 
-        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label
+        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
           
@@ -100,7 +100,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label
+        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM person_smokes R0
         
           
@@ -114,7 +114,7 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  """
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
           weight: "0.5"
         }
@@ -124,7 +124,7 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  """
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
           function: "Imply(smoke.R1.label, smoke.R0.label)"
           weight: "0.4"
         }
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 7f33cc14f..109c667d8 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -88,7 +88,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ 
-        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 as id, R0.has_cancer AS label
+        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
           
@@ -100,7 +100,7 @@ cancer.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ 
-        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 as id, R0.smokes AS label
+        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM person_smokes R0
         
           
@@ -114,7 +114,7 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  """
+        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R1.label, cancer.R0.label)"
           weight: "0.5"
         }
@@ -124,7 +124,7 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  """
+        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
           function: "Imply(smoke.R1.label, smoke.R0.label)"
           weight: "0.4"
         }
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index ae12889c9..80491a2eb 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -171,18 +171,18 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT  R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
@@ -192,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -207,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT  R0.article_id, R0.text
+            SELECT R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT  R0.article_id, R0.text
+            SELECT R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -222,7 +222,7 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT  R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -234,10 +234,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -249,10 +249,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT  R0.relation_id, R0.feature
+            SELECT R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT  R0.relation_id, R0.feature
+            SELECT R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -264,10 +264,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -279,12 +279,12 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT  R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id   UNION ALL 
-            SELECT  R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
+        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  
+        WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
@@ -293,7 +293,7 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
           
@@ -352,10 +352,10 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id   UNION ALL 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 224d48c47..185550e95 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -100,7 +100,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           
@@ -113,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -125,9 +125,9 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT  R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
@@ -137,9 +137,9 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT  R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  
+        WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_6" ]
@@ -180,7 +180,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 25024387e..86fb5a642 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -100,7 +100,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           
@@ -113,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -125,9 +125,9 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT  R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
@@ -137,9 +137,9 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT  R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  
+        WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_6" ]
@@ -180,7 +180,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 9b0c86453..21a2237ec 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -171,18 +171,18 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT  R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
@@ -192,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -207,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT  R0.article_id, R0.text
+            SELECT R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT  R0.article_id, R0.text
+            SELECT R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -222,10 +222,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
          UNION ALL 
-            SELECT  R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -237,10 +237,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -252,10 +252,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT  R0.relation_id, R0.feature
+            SELECT R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT  R0.relation_id, R0.feature
+            SELECT R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -267,10 +267,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -282,12 +282,12 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT  R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id   UNION ALL 
-            SELECT  R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
+        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  
+        WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
@@ -296,7 +296,7 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
           
@@ -355,10 +355,10 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id   UNION ALL 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Linear(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index be999877f..5834ec14c 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -171,18 +171,18 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_31 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
         CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT  R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id   UNION ALL 
-            SELECT  R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
+            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
             FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
@@ -192,10 +192,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM people_mentions R0
          UNION ALL 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
             FROM dd_delta_people_mentions R0
         
         """
@@ -207,10 +207,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles 
-            SELECT  R0.article_id, R0.text
+            SELECT R0.article_id, R0.text
             FROM articles R0
          UNION ALL 
-            SELECT  R0.article_id, R0.text
+            SELECT R0.article_id, R0.text
             FROM dd_delta_articles R0
         
         """
@@ -222,7 +222,7 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
         CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT  R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
             FROM dd_delta_sentences R0
         
         """
@@ -234,10 +234,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM has_spouse_candidates R0
          UNION ALL 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
             FROM dd_delta_has_spouse_candidates R0
         
         """
@@ -249,10 +249,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features 
-            SELECT  R0.relation_id, R0.feature
+            SELECT R0.relation_id, R0.feature
             FROM has_spouse_features R0
          UNION ALL 
-            SELECT  R0.relation_id, R0.feature
+            SELECT R0.relation_id, R0.feature
             FROM dd_delta_has_spouse_features R0
         
         """
@@ -264,10 +264,10 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM sentences R0
          UNION ALL 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
             FROM dd_delta_sentences R0
         
         """
@@ -279,12 +279,12 @@ dd_new_has_spouse.label: Boolean
       deepdive.extraction.extractors.extraction_rule_28 {
         sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
         CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT  R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id   UNION ALL 
-            SELECT  R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
+        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
+            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
             FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  
+        WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
@@ -293,7 +293,7 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_33 {
         sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
+        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
           
@@ -352,10 +352,10 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id   UNION ALL 
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -365,7 +365,7 @@ dd_new_has_spouse.label: Boolean
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
-        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id  """
+        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
           function: "Imply(dd_new_has_spouse.R1.label, dd_new_has_spouse.R0.label)"
           weight: "3.0"
         }
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 8b7469360..2cde7eac4 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -100,7 +100,7 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 as id, R0.is_true AS label
+        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           
@@ -113,7 +113,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS ext_people_input;
         CREATE VIEW ext_people_input AS 
-            SELECT  R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
             FROM sentences R0
         
         """
@@ -125,9 +125,9 @@
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
         CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT  R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
             FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
@@ -137,9 +137,9 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
         CREATE VIEW ext_has_spouse_input AS 
-            SELECT  R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
             FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  
+        WHERE R1.sentence_id = R0.sentence_id 
         """
         style: "sql_extractor"
           dependencies: [ "extraction_rule_6" ]
@@ -180,7 +180,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  """
+        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(has_spouse_features.R2.feature)"
         }
@@ -190,7 +190,7 @@
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
-        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id  """
+        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
           function: "Imply(has_spouse.R1.label, has_spouse.R0.label)"
           weight: "3.0"
         }

From 59101282de7316ef5b79cbff4ca16b1d41d4a393 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 20 Jul 2015 21:10:10 -0700
Subject: [PATCH 187/347] Add All modifier

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala   |  1 +
 .../org/deepdive/ddlog/DeepDiveLogParser.scala |  4 +++-
 .../ddlog/DeepDiveLogPrettyPrinter.scala       |  1 +
 .../expressions/compile.expected               | 18 +++++++++++++++---
 .../expected-output-test/expressions/input.ddl |  2 ++
 .../expressions/print.expected                 |  4 ++++
 6 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 65db4dc05..69a50b8a5 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -392,6 +392,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
           val subqueryFromStr  = generateFromClause(x.bodies, newIndexPrefix)
           x.modifier match {
             case ExistModifier(negated) => Some(s"${if (negated) "NOT " else ""}EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE ${subqueryWhereStr})")
+            case AllModifier() => Some(s"NOT EXISTS (SELECT 1 FROM ${subqueryFromStr} WHERE NOT (${subqueryWhereStr}))")
             case _ => None
           }
         }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 79019ac8f..3ae63f968 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -26,6 +26,7 @@ case class QuantifiedBody(modifier: BodyModifier, bodies: List[Body]) extends Bo
 sealed trait BodyModifier
 case class ExistModifier(negated: Boolean) extends BodyModifier
 case class OuterModifier extends BodyModifier
+case class AllModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
 case class ConjunctiveQuery(head: Atom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
@@ -212,10 +213,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def atom = relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
     case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
   }
-  def modifierAtom = (opt("!") ~ "EXISTS" | "OPTIONAL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
+  def modifierAtom = (opt("!") ~ "EXISTS" | "OPTIONAL" | "ALL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
       case (not ~ "EXISTS") => new ExistModifier(not != None)
       case "OPTIONAL" => new OuterModifier
+      case "ALL" => new AllModifier
     }
     QuantifiedBody(modifier, b)
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 3534edc12..5ddbb60d3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -111,6 +111,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val modifier = a.modifier match {
       case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
       case OuterModifier() => "OPTIONAL"
+      case AllModifier() => "ALL"
     }
     val bodyStr = (a.bodies map printBody).mkString(", ")
     s"${modifier}[${bodyStr}]"
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 2abcc46b4..53513d50a 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -175,7 +175,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ DROP VIEW IF EXISTS V;
         CREATE VIEW V AS 
             SELECT R0.n AS "c.R0.n" 
@@ -260,6 +260,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_23 {
+        sql: """ DROP VIEW IF EXISTS W;
+        CREATE VIEW W AS 
+            SELECT R0.k AS "a.R0.k" 
+            FROM a R0
+        WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ DROP VIEW IF EXISTS K;
         CREATE VIEW K AS 
@@ -309,6 +321,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index f8b4fb3d4..ee376dd7f 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -48,5 +48,7 @@ T(x) :- b(x,y,z,w), OPTIONAL[c(a,x,b), a > y], a > y.
 
 U(x) :- OPTIONAL[b(x,y,z,w)], OPTIONAL[c(a,x,b)].
 
+W(x) :- a(x), ALL[c(_,y,_), y < x].
+
 # placeholder
 V(x) :- c(_,x,_), a(x).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index beeb5876b..89508d817 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -85,6 +85,10 @@ U(x)  :-
     OPTIONAL[b(x, y, z, w)],
     OPTIONAL[c(a, x, b)].
 
+W(x)  :-
+    a(x),
+    ALL[c(_, y, _), y < x].
+
 V(x)  :-
     c(_, x, _),
     a(x).

From 72895b7d5c4260b8eaea8ff5b836272223fcbdbd Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 20 Jul 2015 23:47:14 -0700
Subject: [PATCH 188/347] Further refactoring

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 67 ++++++-----------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  2 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 74 +++++++++----------
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 14 ++--
 .../optional_modifier/compile-error.expected  |  5 ++
 .../optional_modifier/input.ddl               |  5 ++
 .../expressions/compile.expected              | 16 ++--
 7 files changed, 83 insertions(+), 100 deletions(-)
 create mode 100644 test/compile-error-test/optional_modifier/compile-error.expected
 create mode 100644 test/compile-error-test/optional_modifier/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 69a50b8a5..3d10d96f7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -64,17 +64,6 @@ import scala.collection.mutable.ListBuffer
 import org.deepdive.ddlog.DeepDiveLog.Mode._
 import scala.language.postfixOps
 
-object AliasStyle extends Enumeration {
-  type AliasStyle = Value
-  // Three kinds of column expressions:
-  // NoAlias => use column name for dd_new_ tables
-  // WeightAlias => use alias for unknown weight in inference
-  // HeadAlias => use column name and alias for normal extraction rule
-  val NoAlias, WeightAlias, HeadAlias = Value
-
-}
-import AliasStyle._
-
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
@@ -288,28 +277,19 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // compile alias
-  def compileAlias(e: Expr, alias: AliasStyle) = {
+  def compileAlias(e: Expr) = {
     e match {
       case VarExpr(v) => {
         val index = getBodyIndex(v)
         val variable = getVar(v)
         val name  = ss.resolveName(variable)
         val relation = variable.relName
-        alias match {
-          case NoAlias => ""
-          case HeadAlias => s""" AS "${relation}.R${index}.${name}" """
-          case WeightAlias => s"${relation}.R${index}.${name}"
-        }
+        s"${relation}.R${index}.${name}"
       }
-      case _ => s" AS column_${cq.head.terms indexOf e}"
+      case _ => s"column_${cq.head.terms indexOf e}"
     }
   }
 
-  // compile expression with alias, only used for head
-  def compileExprWithAlias(e: Expr, alias: AliasStyle) = {
-    compileExpr(e) + compileAlias(e, alias)
-  }
-
   // resolve an expression
   def compileExpr(e: Expr) : String = {
     e match {
@@ -351,15 +331,17 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // generate SQL SELECT cluase
-  def generateSQLHead(alias: AliasStyle) = {
-    val head = (cq.head.terms map { expr => compileExprWithAlias(expr, alias) }).mkString(", ")
+  def generateSQLHead(useAlias: Boolean) = {
+    val head = (cq.head.terms map { expr =>
+      compileExpr(expr) + (if (useAlias) s""" AS "${compileAlias(expr)}" """ else "")
+    }).mkString(", ")
     val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
     s"${distinctStr}${head}"
   }
 
   // This is generic code that generates the FROM with positional aliasing R0, R1, etc.
   // and the corresponding WHERE clause
-  def generateSQLBody() : String = {
+  def generateSQLBody(body: List[Body]) : String = {
     // generate where clause from unification and conditions
     def generateWhereClause(bodies: List[Body], indexPrefix: String) : String = {
       val conditions = bodies.zipWithIndex.flatMap {
@@ -456,8 +438,8 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
     // limit clause
     val limitStr = optionalClause("LIMIT", cq.limit.getOrElse("").toString)
 
-    s"""FROM ${ generateFromClause(cq.bodies(0), "") }
-        ${ optionalClause("WHERE", generateWhereClause(cq.bodies(0), "")) }${groupbyStr}${limitStr}"""
+    s"""FROM ${ generateFromClause(body, "") }
+        ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${limitStr}"""
   }
 
 }
@@ -524,31 +506,26 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         if (stmt.supervision != null) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headStr = qc.generateSQLHead(NoAlias)
+          val headStr = qc.generateSQLHead(false)
           val labelCol = qc.compileVariable(stmt.supervision)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
-          ${ qc.generateSQLBody() }
+          ${ qc.generateSQLBody(cqBody) }
           """
         } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
-          val headStr = qc.generateSQLHead(NoAlias)
+          val headStr = qc.generateSQLHead(false)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, id, label
-          ${ qc.generateSQLBody() }
+          ${ qc.generateSQLBody(cqBody) }
           """
         } else {
           // variable columns
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
-          var tmpCqUseOnlyOriginal = ss.mode match {
-            case MERGE => true
-            case _     => if (tmpCq.head.name.startsWith("dd_new_")) true else false
-          }
-          val resolveColumnFlag = tmpCqUseOnlyOriginal match {
-            case true => NoAlias
-            case false => HeadAlias
+          var useAlias = ss.mode match {
+            case MERGE => false
+            case _     => if (tmpCq.head.name.startsWith("dd_new_")) false else true
           }
-          val headStr = qc.generateSQLHead(resolveColumnFlag)
           inputQueries += s"""
-            SELECT ${headStr}
-            ${ qc.generateSQLBody() }"""
+            SELECT ${qc.generateSQLHead(useAlias)}
+            ${ qc.generateSQLBody(cqBody) }"""
         }
       }
     }
@@ -643,7 +620,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // weight string
         val uwStr = stmt.weights match {
           case UnknownFactorWeight(w) => Some(w.map(s =>
-            qc.compileExprWithAlias(VarExpr(s), HeadAlias)).mkString(", "))
+            qc.compileExpr(VarExpr(s)) + s""" AS "${qc.compileAlias(VarExpr(s))}" """ ).mkString(", "))
           case _ => None
         }
 
@@ -652,7 +629,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // factor input query
         inputQueries += s"""
           SELECT ${selectStr}
-          ${ qc.generateSQLBody() }"""
+          ${ qc.generateSQLBody(fakeBody) }"""
         // factor function
         if (func.length == 0) {
           val funcBody = (fakeBodyAtoms map {x =>
@@ -676,7 +653,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              val weightVar = w.map(s => qc.compileAlias(VarExpr(s), WeightAlias)).mkString(", ")
+              val weightVar = w.map(s => qc.compileAlias(VarExpr(s))).mkString(", ")
               s"?(${weightVar})"
             }
             case UnknownFactorWeightBindingToConst(w) => "?"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 00be21e49..c9b444b9b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -37,7 +37,7 @@ object DeepDiveLogDeltaDeriver{
       // We don't support deriving delta rules for modifiers
       bodies foreach {
         case _: Cond | _: Atom => // supported
-        case _: QuantifiedBody => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
+        case _ => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
       }
       // Delta body
       val incDeltaBody = bodies collect {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 5ddbb60d3..8e6d3db97 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -71,7 +71,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   // print an expression
-  def printExpr(e: Expr) : String = {
+  def print(e: Expr) : String = {
     e match {
       case VarExpr(name) => name
       case ConstExpr(value) => {
@@ -80,44 +80,44 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         else value
       }
       case FuncExpr(function, args, agg) => {
-        val resolvedArgs = args map (x => printExpr(x))
+        val resolvedArgs = args map (x => print(x))
         s"${function}(${resolvedArgs.mkString(", ")})"
       }
-      case BinaryOpExpr(lhs, op, rhs) => s"(${printExpr(lhs)} ${op} ${printExpr(rhs)})"
-      case TypecastExpr(lhs, rhs) => s"(${printExpr(lhs)} :: ${rhs})"
+      case BinaryOpExpr(lhs, op, rhs) => s"(${print(lhs)} ${op} ${print(rhs)})"
+      case TypecastExpr(lhs, rhs) => s"(${print(lhs)} :: ${rhs})"
     }
   }
 
-  // print a condition
-  def printCond(cond: Cond) : String = {
-    cond match {
-      case ComparisonCond(lhs, op, rhs) => s"${printExpr(lhs)} ${op} ${printExpr(rhs)}"
-      case NegationCond(c) => s"[!${printCond(c)}]"
-      case CompoundCond(lhs, op, rhs) => {
-        op match {
-          case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]"
-          case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
-        }
-      }
+  // print a body
+  def print(b: Body) : String = {
+    def printAtom(a: Atom) = {
+      val vars = a.terms map print
+      s"${a.name}(${vars.mkString(", ")})"
     }
-  }
 
-  def printAtom(a: Atom) = {
-    val vars = a.terms map printExpr
-    s"${a.name}(${vars.mkString(", ")})"
-  }
-
-  def printQuantifiedBody(a: QuantifiedBody) : String = {
-    val modifier = a.modifier match {
-      case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
-      case OuterModifier() => "OPTIONAL"
-      case AllModifier() => "ALL"
+    def printQuantifiedBody(a: QuantifiedBody) : String = {
+      val modifier = a.modifier match {
+        case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
+        case OuterModifier() => "OPTIONAL"
+        case AllModifier() => "ALL"
+      }
+      val bodyStr = (a.bodies map print).mkString(", ")
+      s"${modifier}[${bodyStr}]"
     }
-    val bodyStr = (a.bodies map printBody).mkString(", ")
-    s"${modifier}[${bodyStr}]"
-  }
 
-  def printBody(b: Body) = {
+    // print a condition
+    def printCond(cond: Cond) : String = {
+      cond match {
+        case ComparisonCond(lhs, op, rhs) => s"${print(lhs)} ${op} ${print(rhs)}"
+        case NegationCond(c) => s"[!${printCond(c)}]"
+        case CompoundCond(lhs, op, rhs) => {
+          op match {
+            case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]"
+            case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
+          }
+        }
+      }
+    }
     b match {
       case b: Atom => printAtom(b)
       case b: Cond => printCond(b)
@@ -128,18 +128,15 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   def print(cq: ConjunctiveQuery): String = {
 
     def printBodyList(b: List[Body]) = {
-      s"${(b map printBody).mkString(",\n    ")}"
+      s"${(b map print).mkString(",\n    ")}"
     }
 
     val bodyStr = (cq.bodies map printBodyList).mkString(";\n    ")
 
     val distinctStr = if (cq.isDistinct) "*" else ""
-    val limitStr = cq.limit match {
-      case Some(s) => s" | ${s}"
-      case None => ""
-    }
+    val limitStr = cq.limit map { " | " + _ } getOrElse("")
 
-    s"""${printAtom(cq.head)} ${distinctStr}${limitStr} :-
+    s"""${print(cq.head)} ${distinctStr}${limitStr} :-
        |    ${bodyStr}""".stripMargin
   }
 
@@ -164,10 +161,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         case UnknownFactorWeightBindingToConst(vs) => "\"" + vs + "\""
       })
     ) +
-    ( stmt.function match {
-        case Some(f) => s"\n  function = ${f}"
-        case None => ""
-      }
+    ( stmt.function map { "\n  function = " + _ } getOrElse("")
     ) + ".\n"
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 69d721df6..585be2b3c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -34,13 +34,14 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkFunctionDefined(stmt)
     checkVariableRelationSchema(stmt)
     checkNumberOfColumns(stmt)
+    checkOptionalModifier(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
-  def checkBodyAtoms(bodies: List[Body], checker: Atom => Unit) : Unit = {
+  def checkBodyAtoms(checker: Atom => Unit)(bodies: List[Body]) : Unit = {
     bodies foreach {
       case a: Atom => checker(a)
-      case a: QuantifiedBody => checkBodyAtoms(a.bodies, checker)
+      case a: QuantifiedBody => checkBodyAtoms(checker)(a.bodies)
       case _ =>
     }
   }
@@ -52,9 +53,10 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       if (!(heads contains a.name))
         error(stmt, s"""relation "${a.name}" is not defined""")
     }
+    def check = checkBodyAtoms(checkRelation)(_)
     stmt match {
-      case s: ExtractionRule => checkBodyAtoms(s.q.bodies.flatten, checkRelation)
-      case s: InferenceRule => checkBodyAtoms(s.q.bodies.flatten, checkRelation)
+      case s: ExtractionRule => s.q.bodies foreach check
+      case s: InferenceRule => s.q.bodies foreach check
       case s: FunctionCallRule => checkRelation(Atom(s.input, Nil))
       case _ =>
     }
@@ -96,7 +98,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
     def checkCq(cq: ConjunctiveQuery) {
       checkAtom(cq.head)
-      checkBodyAtoms(cq.bodies.flatten, checkAtom)
+      checkBodyAtoms(checkAtom)(cq.bodies.flatten)
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
@@ -106,7 +108,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   // check if outer join body contains one atom
-  def checkOuterJoin(stmt: Statement) {
+  def checkOptionalModifier(stmt: Statement) {
     def checkOuterJoinBodies(bodies: List[Body]) {
       bodies.foreach {
         case b: QuantifiedBody => {
diff --git a/test/compile-error-test/optional_modifier/compile-error.expected b/test/compile-error-test/optional_modifier/compile-error.expected
new file mode 100644
index 000000000..354e90ff2
--- /dev/null
+++ b/test/compile-error-test/optional_modifier/compile-error.expected
@@ -0,0 +1,5 @@
+[error] One and only one atom should be supplied in OPTIONAL modifier
+Q(y, z)  :-
+    a(x),
+    OPTIONAL[x > 1].
+
diff --git a/test/compile-error-test/optional_modifier/input.ddl b/test/compile-error-test/optional_modifier/input.ddl
new file mode 100644
index 000000000..173259cb1
--- /dev/null
+++ b/test/compile-error-test/optional_modifier/input.ddl
@@ -0,0 +1,5 @@
+a(k int).
+b(k int, p text, q text, r int).
+c(s text, n int, t text).
+
+Q(y, z) :- a(x), OPTIONAL[x > 1].
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 53513d50a..38e2c3c93 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -58,7 +58,7 @@
       deepdive.extraction.extractors.extraction_rule_9 {
         sql: """ DROP VIEW IF EXISTS E;
         CREATE VIEW E AS 
-            SELECT (R0.k :: INT) AS column_0
+            SELECT (R0.k :: INT) AS "column_0" 
             FROM b R0
         
         """
@@ -118,7 +118,7 @@
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS F;
         CREATE VIEW F AS 
-            SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
+            SELECT ((R0.k :: INT) + (R0.r :: INT)) AS "column_0" 
             FROM b R0
         
         """
@@ -130,7 +130,7 @@
       deepdive.extraction.extractors.extraction_rule_5 {
         sql: """ DROP VIEW IF EXISTS A;
         CREATE VIEW A AS 
-            SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
+            SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS "column_0" 
             FROM b R0
         
         """
@@ -190,7 +190,7 @@
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS 
-            SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS "a.R0.k" , unnest(R1.q) AS column_3
+            SELECT DISTINCT ('test' :: TEXT) AS "column_0" , 123 AS "column_1" , R0.k AS "a.R0.k" , unnest(R1.q) AS "column_3" 
             FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
         """
@@ -214,7 +214,7 @@
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS B;
         CREATE VIEW B AS 
-            SELECT func((R0.k + (R0.r + R0.k))) AS column_0
+            SELECT func((R0.k + (R0.r + R0.k))) AS "column_0" 
             FROM b R0
         
         """
@@ -226,7 +226,7 @@
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ DROP VIEW IF EXISTS P;
         CREATE VIEW P AS 
-            SELECT R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS column_2
+            SELECT R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS "column_2" 
             FROM a R0, b R1
         WHERE R1.k = R0.k 
         GROUP BY R1.p, R1.q
@@ -239,7 +239,7 @@
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS C;
         CREATE VIEW C AS 
-            SELECT func(func(func(R0.k))) AS column_0
+            SELECT func(func(func(R0.k))) AS "column_0" 
             FROM b R0
         
         """
@@ -299,7 +299,7 @@
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
         CREATE VIEW D AS 
-            SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
+            SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS "column_0" 
             FROM b R0
         
         """

From c79875ceac8f16c98cb37409d275081b8da69a0d Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 21 Jul 2015 00:57:15 -0700
Subject: [PATCH 189/347] Allow expressions in weights

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 14 ++--
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  8 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  3 +-
 .../chunking_example/compile.expected         |  4 +-
 .../ocr_example/compile-incremental.expected  |  8 +-
 .../compile-materialization.expected          |  8 +-
 .../ocr_example/compile.expected              |  8 +-
 .../compile-incremental.expected              |  6 +-
 .../compile-materialization.expected          |  4 +-
 .../spouse_example/compile.expected           |  4 +-
 .../compile-incremental.expected              |  6 +-
 .../compile-incremental.expected              |  6 +-
 .../compile.expected                          |  4 +-
 .../weights/compile.expected                  | 83 +++++++++++++++++++
 test/expected-output-test/weights/input.ddl   |  9 ++
 .../weights/print.expected                    | 16 ++++
 16 files changed, 150 insertions(+), 41 deletions(-)
 create mode 100644 test/expected-output-test/weights/compile.expected
 create mode 100644 test/expected-output-test/weights/input.ddl
 create mode 100644 test/expected-output-test/weights/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 3d10d96f7..655c8c1ff 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -619,8 +619,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         // weight string
         val uwStr = stmt.weights match {
-          case UnknownFactorWeight(w) => Some(w.map(s =>
-            qc.compileExpr(VarExpr(s)) + s""" AS "${qc.compileAlias(VarExpr(s))}" """ ).mkString(", "))
+          case UnknownFactorWeight(w) => Some(w.zipWithIndex.flatMap {
+            case(s: ConstExpr, i) => None
+            case(s: Expr, i) => Some(qc.compileExpr(s) + s""" AS "dd_weight_column_${i}" """)
+          } mkString(", "))
           case _ => None
         }
 
@@ -653,10 +655,12 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           weight = stmt.weights match {
             case KnownFactorWeight(x) => s"${x}"
             case UnknownFactorWeight(w) => {
-              val weightVar = w.map(s => qc.compileAlias(VarExpr(s))).mkString(", ")
-              s"?(${weightVar})"
+              val weightStr = w.zipWithIndex.flatMap {
+                case(s: ConstExpr, i) => None
+                case(s: Expr, i) => Some(s"dd_weight_column_${i}")
+              } mkString(", ")
+              if (weightStr.isEmpty) "?" else s"?(${weightStr})"
             }
-            case UnknownFactorWeightBindingToConst(w) => "?"
           }
       }
       val blockName = ss.resolveInferenceBlockName(stmt)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 3ae63f968..ecbf407ee 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -66,8 +66,7 @@ case class MultinomialType(numCategories: Int) extends VariableType {
 sealed trait FactorWeight
 
 case class KnownFactorWeight(value: Double) extends FactorWeight
-case class UnknownFactorWeight(variables: List[String]) extends FactorWeight
-case class UnknownFactorWeightBindingToConst(value: String) extends FactorWeight
+case class UnknownFactorWeight(variables: List[Expr]) extends FactorWeight
 
 trait RelationType
 case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
@@ -277,9 +276,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def constantWeight = floatingPointNumberAsDouble ^^ {   KnownFactorWeight(_) }
-  def unknownWeight  = repsep(variableName, ",")   ^^ { UnknownFactorWeight(_) }
-  def unknownWeightBindingToConst = stringLiteralAsString ^^ { UnknownFactorWeightBindingToConst(_) }
-  def factorWeight = "weight" ~> "=" ~> (constantWeight | unknownWeightBindingToConst | unknownWeight)
+  def unknownWeight  = repsep(expr, ",")   ^^ { UnknownFactorWeight(_) }
+  def factorWeight = "weight" ~> "=" ~> (constantWeight | unknownWeight)
 
   def supervision = "label" ~> "=" ~> variableName
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 8e6d3db97..e8df2a9b9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -157,8 +157,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     ( if (stmt.weights == null) ""
       else "\n  weight = " + (stmt.weights match {
         case KnownFactorWeight(w) => w.toString
-        case UnknownFactorWeight(vs) => vs.mkString(", ")
-        case UnknownFactorWeightBindingToConst(vs) => "\"" + vs + "\""
+        case UnknownFactorWeight(vs) => vs.map(print).mkString(", ")
       })
     ) +
     ( stmt.function map { "\n  function = " + _ } getOrElse("")
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index d8c429231..8432494ed 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -115,11 +115,11 @@
 
         deepdive.inference.factors.tag_0 {
           input_query: """
-          SELECT R0.id AS "tag.R0.id" , R1.feature AS "word_features.R1.feature" 
+          SELECT R0.id AS "tag.R0.id" , R1.feature AS "dd_weight_column_0" 
           FROM tag R0, word_features R1
         WHERE R1.word_id = R0.word_id """
           function: "Multinomial(tag.R0.label)"
-          weight: "?(word_features.R1.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index c06a83f8c..e39f4f451 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -221,21 +221,21 @@ q1.label: Boolean
 
         deepdive.inference.factors.dd_new_q2_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
+          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM dd_new_q2 R0, dd_delta_features R1
         WHERE R1.word_id = R0.wid """
           function: "Imply(dd_new_q2.R0.label)"
-          weight: "?(dd_delta_features.R1.feature_id)"
+          weight: "?(dd_weight_column_0)"
         }
       
 
         deepdive.inference.factors.dd_new_q1_1 {
           input_query: """
-          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_delta_features.R1.feature_id" 
+          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM dd_new_q1 R0, dd_delta_features R1
         WHERE R1.word_id = R0.wid """
           function: "Imply(dd_new_q1.R0.label)"
-          weight: "?(dd_delta_features.R1.feature_id)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index ab23cf330..6d696e434 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -104,21 +104,21 @@ q2.label: Boolean
 
         deepdive.inference.factors.q1_0 {
           input_query: """
-          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
         WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
-          weight: "?(features.R1.feature_id)"
+          weight: "?(dd_weight_column_0)"
         }
       
 
         deepdive.inference.factors.q2_1 {
           input_query: """
-          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
         WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
-          weight: "?(features.R1.feature_id)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 76468eafa..8a684eacf 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -104,21 +104,21 @@ q2.label: Boolean
 
         deepdive.inference.factors.q1_0 {
           input_query: """
-          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
         WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
-          weight: "?(features.R1.feature_id)"
+          weight: "?(dd_weight_column_0)"
         }
       
 
         deepdive.inference.factors.q2_1 {
           input_query: """
-          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "features.R1.feature_id" 
+          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
         WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
-          weight: "?(features.R1.feature_id)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 80491a2eb..37a54b670 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -350,14 +350,14 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
-          weight: "?(has_spouse_features.R2.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 185550e95..a6639ef68 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -178,11 +178,11 @@
 
         deepdive.inference.factors.has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
-          weight: "?(has_spouse_features.R2.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 86fb5a642..043956e93 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -178,11 +178,11 @@
 
         deepdive.inference.factors.has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
-          weight: "?(has_spouse_features.R2.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 21a2237ec..1b71dab25 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -353,14 +353,14 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Linear(dd_new_has_spouse.R0.label)"
-          weight: "?(has_spouse_features.R2.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 5834ec14c..2b325dea6 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -350,14 +350,14 @@ dd_new_has_spouse.label: Boolean
 
         deepdive.inference.factors.dd_new_has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_delta_has_spouse_features.R2.feature" 
+          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
-          weight: "?(has_spouse_features.R2.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 2cde7eac4..2bfe86d43 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -178,11 +178,11 @@
 
         deepdive.inference.factors.has_spouse_0 {
           input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "has_spouse_features.R2.feature" 
+          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
-          weight: "?(has_spouse_features.R2.feature)"
+          weight: "?(dd_weight_column_0)"
         }
       
 
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
new file mode 100644
index 000000000..bc2bb8fca
--- /dev/null
+++ b/test/expected-output-test/weights/compile.expected
@@ -0,0 +1,83 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        a.label: Boolean
+c.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS b CASCADE;
+            CREATE TABLE
+            b(k int,
+ p int,
+ q text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS a CASCADE;
+            CREATE TABLE
+            a(k int,
+ id bigint,
+ label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_1 {
+            sql: """ DROP TABLE IF EXISTS c CASCADE;
+            CREATE TABLE
+            c(k int,
+ id bigint,
+ label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE b;
+          TRUNCATE a;
+          TRUNCATE c;
+          """
+          style: "sql_extractor"
+        }
+
+        deepdive.inference.factors.a_0 {
+          input_query: """
+          SELECT R0.id AS "a.R0.id" , (R0.k + R1.p) AS "dd_weight_column_0" 
+          FROM a R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(a.R0.label)"
+          weight: "?(dd_weight_column_0)"
+        }
+      
+
+        deepdive.inference.factors.c_1 {
+          input_query: """
+          SELECT R0.id AS "c.R0.id" , 
+          FROM c R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(c.R0.label)"
+          weight: "?"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_0, extraction_rule_1]
+deepdive.pipeline.pipelines.inference: [a_0, c_1]
+deepdive.pipeline.pipelines.endtoend: [a_0, c_1]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/weights/input.ddl b/test/expected-output-test/weights/input.ddl
new file mode 100644
index 000000000..623ffa279
--- /dev/null
+++ b/test/expected-output-test/weights/input.ddl
@@ -0,0 +1,9 @@
+a?(k int).
+c?(k int).
+b(k int, p int, q text).
+
+a(x) :- b(x,y,_)
+weight = x + y.
+
+c(x) :- b(x,y,_)
+weight = "string".
\ No newline at end of file
diff --git a/test/expected-output-test/weights/print.expected b/test/expected-output-test/weights/print.expected
new file mode 100644
index 000000000..96883910c
--- /dev/null
+++ b/test/expected-output-test/weights/print.expected
@@ -0,0 +1,16 @@
+a?(k int).
+
+c?(k int).
+
+b(k int,
+  p int,
+  q text).
+
+a(x)  :-
+    b(x, y, _)
+  weight = (x + y).
+
+c(x)  :-
+    b(x, y, _)
+  weight =  "string" .
+

From a24788e27ac65d4118a518f1b92f9f2d950af02f Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 21 Jul 2015 16:34:36 -0700
Subject: [PATCH 190/347] Refactoring

1. Seperate different types of expressions
2. Update floating point number and integer parsers to resolve parsing ambiguation with dot delimiter
3. Unify factor weight
4. More tests for factor weight
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 42 ++++-----
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 30 ++++---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 71 +++++++--------
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 22 +++--
 .../weight/compile-error.expected             |  5 ++
 test/compile-error-test/weight/input.ddl      |  5 ++
 .../annotations/export-schema.expected        |  2 +-
 .../annotations/print.expected                |  2 +-
 .../weights/compile.expected                  | 90 ++++++++++++++++---
 test/expected-output-test/weights/input.ddl   | 14 ++-
 .../weights/print.expected                    | 20 ++++-
 11 files changed, 210 insertions(+), 93 deletions(-)
 create mode 100644 test/compile-error-test/weight/compile-error.expected
 create mode 100644 test/compile-error-test/weight/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 655c8c1ff..8ad1dd87c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -294,7 +294,11 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   def compileExpr(e: Expr) : String = {
     e match {
       case VarExpr(name) => compileVariable(name)
-      case ConstExpr(value) => value
+      case NullConst() => "NULL"
+      case IntConst(value) => value.toString
+      case DoubleConst(value) => value.toString
+      case BooleanConst(value) => value.toString
+      case StringConst(value) => s"'${value.replaceAll("'", "''")}'"
       case FuncExpr(function, args, agg) => {
         val resolvedArgs = args map (x => compileExpr(x))
         val resolved = s"${function}(${resolvedArgs.mkString(", ")})"
@@ -416,7 +420,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
     def containsAggregation(expr: Expr) : Boolean = {
       expr match {
         case VarExpr(name) => false
-        case ConstExpr(value) => false
+        case _: ConstExpr => false
         case FuncExpr(function, args, agg) => if (agg) agg else {
           args.map(containsAggregation).foldLeft(false)(_ || _)
         }
@@ -613,20 +617,15 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             else
               None
           case _ => None
-        })
-
-        val variableIdsStr = Some(varInBody.mkString(", "))
+        }) mkString(", ")
 
         // weight string
-        val uwStr = stmt.weights match {
-          case UnknownFactorWeight(w) => Some(w.zipWithIndex.flatMap {
-            case(s: ConstExpr, i) => None
-            case(s: Expr, i) => Some(qc.compileExpr(s) + s""" AS "dd_weight_column_${i}" """)
-          } mkString(", "))
-          case _ => None
-        }
+        val uwStr = stmt.weights.variables.zipWithIndex.flatMap {
+          case(s: ConstExpr, i) => None
+          case(s: Expr, i) => Some(qc.compileExpr(s) + s""" AS "dd_weight_column_${i}" """)
+        } mkString(", ")
 
-        val selectStr = (List(variableIdsStr, uwStr) flatten).mkString(", ")
+        val selectStr = List(varInBody, uwStr).filterNot(_.isEmpty).mkString(", ")
 
         // factor input query
         inputQueries += s"""
@@ -651,17 +650,20 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           func = s"""${function}(${(funcBody.tail :+ firstFunc).mkString(", ")})"""
         }
         // weight
-        if (weight.length == 0)
-          weight = stmt.weights match {
-            case KnownFactorWeight(x) => s"${x}"
-            case UnknownFactorWeight(w) => {
-              val weightStr = w.zipWithIndex.flatMap {
-                case(s: ConstExpr, i) => None
+        if (weight.length == 0) {
+          // note error cases should be handled in semantic checker
+          weight = stmt.weights.variables(0) match {
+            case IntConst(value) => value.toString
+            case DoubleConst(value) => value.toString
+            case StringConst(value) => "?"
+            case _ => {
+              val weightVars = stmt.weights.variables.zipWithIndex.flatMap {
                 case(s: Expr, i) => Some(s"dd_weight_column_${i}")
               } mkString(", ")
-              if (weightStr.isEmpty) "?" else s"?(${weightStr})"
+              s"?(${weightVars})"
             }
           }
+        }
       }
       val blockName = ss.resolveInferenceBlockName(stmt)
       blocks ::= s"""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index ecbf407ee..669bd7790 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -14,7 +14,12 @@ case class Variable(varName : String, relName : String, index : Int )
 
 sealed trait Expr
 case class VarExpr(name: String) extends Expr
-case class ConstExpr(value: String) extends Expr
+sealed trait ConstExpr extends Expr
+case class StringConst(value: String) extends ConstExpr
+case class IntConst(value: Int) extends ConstExpr
+case class DoubleConst(value: Double) extends ConstExpr
+case class BooleanConst(value: Boolean) extends ConstExpr
+case class NullConst extends ConstExpr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
@@ -63,10 +68,7 @@ case class MultinomialType(numCategories: Int) extends VariableType {
   def cardinality = numCategories
 }
 
-sealed trait FactorWeight
-
-case class KnownFactorWeight(value: Double) extends FactorWeight
-case class UnknownFactorWeight(variables: List[Expr]) extends FactorWeight
+case class FactorWeight(variables: List[Expr])
 
 trait RelationType
 case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
@@ -92,9 +94,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // JavaTokenParsers provides several useful number parsers:
   //   wholeNumber, decimalNumber, floatingPointNumber
-  def floatingPointNumberAsDouble = floatingPointNumber ^^ { _.toDouble }
-  def wholeNumberAsInt = wholeNumber ^^ { _.toInt }
-  def wholeNumberAsLong = wholeNumber ^^ { _.toLong }
+  def double = opt("-") ~ """\d+\.\d+""".r ^^ { case (neg ~ num) => (neg.getOrElse("") + num).toDouble }
+  def integer = opt("-") ~ wholeNumber ^^ { case (neg ~ num) => (neg.getOrElse("") + num).toInt }
   def stringLiteralAsString = stringLiteral ^^ {
     s => StringEscapeUtils.unescapeJava(
       s.stripPrefix("\"").stripSuffix("\""))
@@ -102,7 +103,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def stringLiteralAsSqlString = stringLiteral ^^ { s =>
     s"""'${s.stripPrefix("\"").stripSuffix("\"")}'"""
   }
-  def constant = stringLiteralAsSqlString | wholeNumber | "TRUE" | "FALSE" | "NULL"
 
   // Single-line comments beginning with # or // are supported by treating them as whiteSpace
   // C/Java/Scala style multi-line comments cannot be easily supported with RegexParsers unless we introduce a dedicated lexer.
@@ -133,7 +133,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case name ~ _ ~ value => name -> value
     }
   def annotationArgumentValue: Parser[Any] =
-    stringLiteralAsString | floatingPointNumberAsDouble | wholeNumberAsInt
+    stringLiteralAsString | double | integer
 
   def columnDeclaration: Parser[Column] =
     rep(annotation) ~
@@ -175,7 +175,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
     ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
-    | constant ^^ { ConstExpr(_) }
+    | stringLiteralAsString ^^ { StringConst(_) }
+    | double ^^ { DoubleConst(_) }
+    | integer ^^ { IntConst(_) }
+    | ("TRUE" | "FALSE") ^^ { x => BooleanConst(x.toBoolean) }
+    | "NULL" ^^ { _ => new NullConst }
     | variableName ^^ { VarExpr(_) }
     | "(" ~> expr <~ ")"
     )
@@ -275,9 +279,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
         FunctionCallRule(in, out, fn)
     }
 
-  def constantWeight = floatingPointNumberAsDouble ^^ {   KnownFactorWeight(_) }
-  def unknownWeight  = repsep(expr, ",")   ^^ { UnknownFactorWeight(_) }
-  def factorWeight = "weight" ~> "=" ~> (constantWeight | unknownWeight)
+  def factorWeight = "weight" ~> "=" ~> rep1sep(expr, ",") ^^ { FactorWeight(_) }
 
   def supervision = "label" ~> "=" ~> variableName
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index e8df2a9b9..99d0427b4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -74,11 +74,11 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   def print(e: Expr) : String = {
     e match {
       case VarExpr(name) => name
-      case ConstExpr(value) => {
-        // TODO use distinct class for different types
-        if (value.startsWith("'")) s""" "${value.stripPrefix("'").stripSuffix("'")}" """
-        else value
-      }
+      case NullConst() => "NULL"
+      case IntConst(value) => value.toString
+      case DoubleConst(value) => value.toString
+      case BooleanConst(value) => value.toString
+      case StringConst(value) => "\"" + StringEscapeUtils.escapeJava(value) + "\""
       case FuncExpr(function, args, agg) => {
         val resolvedArgs = args map (x => print(x))
         s"${function}(${resolvedArgs.mkString(", ")})"
@@ -88,41 +88,39 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     }
   }
 
-  // print a body
-  def print(b: Body) : String = {
-    def printAtom(a: Atom) = {
-      val vars = a.terms map print
-      s"${a.name}(${vars.mkString(", ")})"
-    }
+  def print(a: Atom) : String = {
+    val vars = a.terms map print
+    s"${a.name}(${vars.mkString(", ")})"
+  }
 
-    def printQuantifiedBody(a: QuantifiedBody) : String = {
-      val modifier = a.modifier match {
-        case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
-        case OuterModifier() => "OPTIONAL"
-        case AllModifier() => "ALL"
-      }
-      val bodyStr = (a.bodies map print).mkString(", ")
-      s"${modifier}[${bodyStr}]"
+  def print(a: QuantifiedBody) : String = {
+    val modifier = a.modifier match {
+      case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
+      case OuterModifier() => "OPTIONAL"
+      case AllModifier() => "ALL"
     }
+    val bodyStr = (a.bodies map print).mkString(", ")
+    s"${modifier}[${bodyStr}]"
+  }
 
-    // print a condition
-    def printCond(cond: Cond) : String = {
-      cond match {
-        case ComparisonCond(lhs, op, rhs) => s"${print(lhs)} ${op} ${print(rhs)}"
-        case NegationCond(c) => s"[!${printCond(c)}]"
-        case CompoundCond(lhs, op, rhs) => {
-          op match {
-            case LogicOperator.AND => s"[${printCond(lhs)}, ${printCond(rhs)}]"
-            case LogicOperator.OR  => s"[${printCond(lhs)}; ${printCond(rhs)}]"
-          }
+  // print a condition
+  def print(cond: Cond) : String = {
+    cond match {
+      case ComparisonCond(lhs, op, rhs) => s"${print(lhs)} ${op} ${print(rhs)}"
+      case NegationCond(c) => s"[!${print(c)}]"
+      case CompoundCond(lhs, op, rhs) => {
+        op match {
+          case LogicOperator.AND => s"[${print(lhs)}, ${print(rhs)}]"
+          case LogicOperator.OR  => s"[${print(lhs)}; ${print(rhs)}]"
         }
       }
     }
-    b match {
-      case b: Atom => printAtom(b)
-      case b: Cond => printCond(b)
-      case b: QuantifiedBody => printQuantifiedBody(b)
-    }
+  }
+
+  def print(b: Body) : String = b match {
+    case b: Atom => print(b)
+    case b: Cond => print(b)
+    case b: QuantifiedBody => print(b)
   }
 
   def print(cq: ConjunctiveQuery): String = {
@@ -155,10 +153,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   def print(stmt: InferenceRule): String = {
     print(stmt.q) +
     ( if (stmt.weights == null) ""
-      else "\n  weight = " + (stmt.weights match {
-        case KnownFactorWeight(w) => w.toString
-        case UnknownFactorWeight(vs) => vs.map(print).mkString(", ")
-      })
+      else "\n  weight = " + (stmt.weights.variables.map(print).mkString(", "))
     ) +
     ( stmt.function map { "\n  function = " + _ } getOrElse("")
     ) + ".\n"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 585be2b3c..25e13bd0f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -35,10 +35,11 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkVariableRelationSchema(stmt)
     checkNumberOfColumns(stmt)
     checkOptionalModifier(stmt)
+    checkWeight(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
-  def checkBodyAtoms(checker: Atom => Unit)(bodies: List[Body]) : Unit = {
+  def checkBodyAtoms(checker: Atom => Unit): List[Body] => Unit = bodies => {
     bodies foreach {
       case a: Atom => checker(a)
       case a: QuantifiedBody => checkBodyAtoms(checker)(a.bodies)
@@ -53,7 +54,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       if (!(heads contains a.name))
         error(stmt, s"""relation "${a.name}" is not defined""")
     }
-    def check = checkBodyAtoms(checkRelation)(_)
+    def check = checkBodyAtoms(checkRelation)
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach check
       case s: InferenceRule => s.q.bodies foreach check
@@ -98,7 +99,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
     def checkCq(cq: ConjunctiveQuery) {
       checkAtom(cq.head)
-      checkBodyAtoms(checkAtom)(cq.bodies.flatten)
+      cq.bodies foreach checkBodyAtoms(checkAtom)
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
@@ -124,8 +125,19 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       }
     }
     stmt match {
-      case s: ExtractionRule => checkOuterJoinBodies(s.q.bodies.flatten)
-      case s: InferenceRule => checkOuterJoinBodies(s.q.bodies.flatten)
+      case s: ExtractionRule => s.q.bodies foreach checkOuterJoinBodies
+      case s: InferenceRule => s.q.bodies foreach checkOuterJoinBodies
+      case _ =>
+    }
+  }
+
+  // check if the weights makes sense
+  def checkWeight(stmt: Statement) {
+    stmt match {
+      case s: InferenceRule => {
+        if ((s.weights.variables collect { case x: ConstExpr => x }).size >= 2)
+          error(stmt, s"Weight variables can contain at most one constant")
+      }
       case _ =>
     }
   }
diff --git a/test/compile-error-test/weight/compile-error.expected b/test/compile-error-test/weight/compile-error.expected
new file mode 100644
index 000000000..8fffc16a1
--- /dev/null
+++ b/test/compile-error-test/weight/compile-error.expected
@@ -0,0 +1,5 @@
+[error] Weight variables can contain at most one constant
+a(x)  :-
+    b(x, y, _, _)
+  weight = 1, 2.
+
diff --git a/test/compile-error-test/weight/input.ddl b/test/compile-error-test/weight/input.ddl
new file mode 100644
index 000000000..376cba024
--- /dev/null
+++ b/test/compile-error-test/weight/input.ddl
@@ -0,0 +1,5 @@
+a?(k int).
+b(k int, p text, q text, r int).
+c(s text, n int, t text).
+
+a(x) :- b(x, y, _, _) weight = 1, 2.
\ No newline at end of file
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
index dde7a42cd..040510c44 100644
--- a/test/expected-output-test/annotations/export-schema.expected
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -1 +1 @@
-{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float"}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1.0}}, {"name" : "qux", "args" : {"y" : 2.345}}]}}}
+{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float"}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}]}}}
diff --git a/test/expected-output-test/annotations/print.expected b/test/expected-output-test/annotations/print.expected
index 640cece52..e7559d089 100644
--- a/test/expected-output-test/annotations/print.expected
+++ b/test/expected-output-test/annotations/print.expected
@@ -6,7 +6,7 @@ mention_candidate(doc_id text,
                   len int).
 
 @foo
-@bar(x=1.0)
+@bar(x=1)
 @qux(y=2.345)
 R(p text,
   q int,
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index bc2bb8fca..484d2e109 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -14,16 +14,29 @@
 
       deepdive.schema.variables {
         a.label: Boolean
+f.label: Boolean
+e.label: Boolean
+d.label: Boolean
 c.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_2 {
-            sql: """ DROP TABLE IF EXISTS b CASCADE;
+          deepdive.extraction.extractors.extraction_rule_3 {
+            sql: """ DROP TABLE IF EXISTS e CASCADE;
             CREATE TABLE
-            b(k int,
- p int,
- q text)
+            e(k int,
+ id bigint,
+ label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_4 {
+            sql: """ DROP TABLE IF EXISTS f CASCADE;
+            CREATE TABLE
+            f(k int,
+ id bigint,
+ label boolean)
             """
             style: "sql_extractor"
           }
@@ -38,11 +51,31 @@ c.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.extraction_rule_5 {
+            sql: """ DROP TABLE IF EXISTS b CASCADE;
+            CREATE TABLE
+            b(k int,
+ p int,
+ q text)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.extraction_rule_1 {
             sql: """ DROP TABLE IF EXISTS c CASCADE;
             CREATE TABLE
             c(k int,
  id bigint,
+ label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.extraction_rule_2 {
+            sql: """ DROP TABLE IF EXISTS d CASCADE;
+            CREATE TABLE
+            d(k int,
+ id bigint,
  label boolean)
             """
             style: "sql_extractor"
@@ -50,14 +83,37 @@ c.label: Boolean
 
         deepdive.extraction.extractors.cleanup {
           sql: """
-          TRUNCATE b;
+          TRUNCATE e;
+          TRUNCATE f;
           TRUNCATE a;
+          TRUNCATE b;
           TRUNCATE c;
+          TRUNCATE d;
           """
           style: "sql_extractor"
         }
 
-        deepdive.inference.factors.a_0 {
+        deepdive.inference.factors.e_0 {
+          input_query: """
+          SELECT R0.id AS "e.R0.id" 
+          FROM e R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(e.R0.label)"
+          weight: "-10"
+        }
+      
+
+        deepdive.inference.factors.f_1 {
+          input_query: """
+          SELECT R0.id AS "f.R0.id" 
+          FROM f R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(f.R0.label)"
+          weight: "-0.3"
+        }
+      
+
+        deepdive.inference.factors.a_2 {
           input_query: """
           SELECT R0.id AS "a.R0.id" , (R0.k + R1.p) AS "dd_weight_column_0" 
           FROM a R0, b R1
@@ -67,17 +123,27 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.c_1 {
+        deepdive.inference.factors.c_3 {
           input_query: """
-          SELECT R0.id AS "c.R0.id" , 
+          SELECT R0.id AS "c.R0.id" 
           FROM c R0, b R1
         WHERE R1.k = R0.k """
           function: "Imply(c.R0.label)"
           weight: "?"
         }
       
+
+        deepdive.inference.factors.d_4 {
+          input_query: """
+          SELECT R0.id AS "d.R0.id" , R0.k AS "dd_weight_column_0" , R1.p AS "dd_weight_column_1" 
+          FROM d R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(d.R0.label)"
+          weight: "?(dd_weight_column_0, dd_weight_column_1)"
+        }
+      
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_0, extraction_rule_1]
-deepdive.pipeline.pipelines.inference: [a_0, c_1]
-deepdive.pipeline.pipelines.endtoend: [a_0, c_1]
+deepdive.pipeline.pipelines.initdb: [extraction_rule_3, extraction_rule_4, extraction_rule_0, extraction_rule_5, extraction_rule_1, extraction_rule_2]
+deepdive.pipeline.pipelines.inference: [e_0, f_1, a_2, c_3, d_4]
+deepdive.pipeline.pipelines.endtoend: [e_0, f_1, a_2, c_3, d_4]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/weights/input.ddl b/test/expected-output-test/weights/input.ddl
index 623ffa279..0d5b1801d 100644
--- a/test/expected-output-test/weights/input.ddl
+++ b/test/expected-output-test/weights/input.ddl
@@ -1,9 +1,21 @@
 a?(k int).
 c?(k int).
+d?(k int).
+e?(k int).
+f?(k int).
 b(k int, p int, q text).
 
 a(x) :- b(x,y,_)
 weight = x + y.
 
 c(x) :- b(x,y,_)
-weight = "string".
\ No newline at end of file
+weight = "string".
+
+d(x) :- b(x,y,_)
+weight = x, y.
+
+e(x) :- b(x,y,_)
+weight = -10.
+
+f(x) :- b(x,y,_)
+weight = -0.3.
\ No newline at end of file
diff --git a/test/expected-output-test/weights/print.expected b/test/expected-output-test/weights/print.expected
index 96883910c..d1e1ca44c 100644
--- a/test/expected-output-test/weights/print.expected
+++ b/test/expected-output-test/weights/print.expected
@@ -2,6 +2,12 @@ a?(k int).
 
 c?(k int).
 
+d?(k int).
+
+e?(k int).
+
+f?(k int).
+
 b(k int,
   p int,
   q text).
@@ -12,5 +18,17 @@ a(x)  :-
 
 c(x)  :-
     b(x, y, _)
-  weight =  "string" .
+  weight = "string".
+
+d(x)  :-
+    b(x, y, _)
+  weight = x, y.
+
+e(x)  :-
+    b(x, y, _)
+  weight = -10.
+
+f(x)  :-
+    b(x, y, _)
+  weight = -0.3.
 

From 1808a4d58bc2fef9b2cf0bc1e7b709f03ec034aa Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 21 Jul 2015 22:51:23 -0700
Subject: [PATCH 191/347] Support placeholder

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala |  5 +++--
 .../org/deepdive/ddlog/DeepDiveLogParser.scala   |  9 ++++-----
 .../ddlog/DeepDiveLogPrettyPrinter.scala         |  1 +
 .../expressions/compile.expected                 | 16 ++++++++++++++--
 test/expected-output-test/expressions/input.ddl  |  4 +++-
 .../expressions/print.expected                   | 10 +++++++---
 6 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 8ad1dd87c..f7905a84e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -313,6 +313,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         val resovledLhs = compileExpr(lhs)
         s"(${resovledLhs} :: ${rhs})"
       }
+      case Placeholder() => ""
     }
   }
 
@@ -362,6 +363,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
               }
+              case Placeholder() => None
               // other expressions indicate a filter condition on the column
               case _ => {
                 val resolved = compileExpr(expr)
@@ -419,13 +421,12 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
     // check if an expression contains an aggregation function
     def containsAggregation(expr: Expr) : Boolean = {
       expr match {
-        case VarExpr(name) => false
-        case _: ConstExpr => false
         case FuncExpr(function, args, agg) => if (agg) agg else {
           args.map(containsAggregation).foldLeft(false)(_ || _)
         }
         case BinaryOpExpr(lhs, op, rhs) => containsAggregation(lhs) || containsAggregation(rhs)
         case TypecastExpr(lhs, rhs) => containsAggregation(lhs)
+        case _ => false
       }
     }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 669bd7790..6a2ef2fe5 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -23,6 +23,7 @@ case class NullConst extends ConstExpr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
+case class Placeholder extends Expr
 
 sealed trait Body
 case class Atom(name : String, terms : List[Expr]) extends Body
@@ -39,7 +40,6 @@ case class Column(name : String // name of the column
                  , t : String // type of the column
                  , annotation: List[Annotation] = List.empty // optional annotation
                  )
-case class BodyWithCondition(body: List[Atom], condition: Option[Cond])
 
 case class Annotation( name : String // name of the annotation
                      , args : Map[String, Any] = Map.empty // optional, named arguments
@@ -100,9 +100,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     s => StringEscapeUtils.unescapeJava(
       s.stripPrefix("\"").stripSuffix("\""))
   }
-  def stringLiteralAsSqlString = stringLiteral ^^ { s =>
-    s"""'${s.stripPrefix("\"").stripSuffix("\"")}'"""
-  }
 
   // Single-line comments beginning with # or // are supported by treating them as whiteSpace
   // C/Java/Scala style multi-line comments cannot be easily supported with RegexParsers unless we introduce a dedicated lexer.
@@ -184,6 +181,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "(" ~> expr <~ ")"
     )
 
+  def pattern : Parser[Expr] = "_" ^^ { case _ => Placeholder() } | expr
+
   def cqHead = relationName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
     case (r ~ "(" ~ expressions ~ ")") => Atom(r, expressions)
   }
@@ -213,7 +212,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "[" ~> cond <~ "]"
     )
 
-  def atom = relationName ~ "(" ~ repsep(expr, ",") ~ ")" ^^ {
+  def atom = relationName ~ "(" ~ repsep(pattern, ",") ~ ")" ^^ {
     case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
   }
   def modifierAtom = (opt("!") ~ "EXISTS" | "OPTIONAL" | "ALL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 99d0427b4..35c0778b6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -85,6 +85,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
       case BinaryOpExpr(lhs, op, rhs) => s"(${print(lhs)} ${op} ${print(rhs)})"
       case TypecastExpr(lhs, rhs) => s"(${print(lhs)} :: ${rhs})"
+      case Placeholder() => "_"
     }
   }
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 38e2c3c93..c6830afe5 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -67,6 +67,18 @@
       }
     
 
+      deepdive.extraction.extractors.extraction_rule_25 {
+        sql: """ DROP VIEW IF EXISTS X;
+        CREATE VIEW X AS 
+            SELECT R0.k AS "b.R0.k" 
+            FROM b R0, c R1
+        WHERE R1.n = R0.k 
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
       deepdive.extraction.extractors.extraction_rule_18 {
         sql: """ DROP VIEW IF EXISTS N;
         CREATE VIEW N AS 
@@ -321,6 +333,6 @@
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_25, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_25, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddl
index ee376dd7f..e167cab4b 100644
--- a/test/expected-output-test/expressions/input.ddl
+++ b/test/expected-output-test/expressions/input.ddl
@@ -51,4 +51,6 @@ U(x) :- OPTIONAL[b(x,y,z,w)], OPTIONAL[c(a,x,b)].
 W(x) :- a(x), ALL[c(_,y,_), y < x].
 
 # placeholder
-V(x) :- c(_,x,_), a(x).
\ No newline at end of file
+V(x) :- c(_,x,_), a(x).
+
+X(x) :- b(x,_,_,z), c(_,x,y).
\ No newline at end of file
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 89508d817..71ac2afae 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -9,10 +9,10 @@ c(s text,
   n int,
   t text).
 
-Q(( "test"  :: TEXT), 123, id, unnest(y)) * :-
+Q(("test" :: TEXT), 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c((x || y), 10,  "foo" ),
+    c((x || y), 10, "foo"),
     [z > 100; [[!z < 20], z < 50]].
 
 P(y, z, MAX(w))  :-
@@ -66,7 +66,7 @@ M(x)  :-
 
 N(x)  :-
     b(x, y, z, w),
-    EXISTS[c(a, x, b), a >  "a" ].
+    EXISTS[c(a, x, b), a > "a"].
 
 O(x)  :-
     b(x, y, z, w),
@@ -93,3 +93,7 @@ V(x)  :-
     c(_, x, _),
     a(x).
 
+X(x)  :-
+    b(x, _, _, z),
+    c(_, x, y).
+

From 98d701407a3eb695399b5846d0a636ee15fa99f7 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 21 Jul 2015 23:46:16 -0700
Subject: [PATCH 192/347] More semantic checking and tests

---
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 60 ++++++++++++++++---
 .../compile-error.expected                    |  4 ++
 .../undefined_head_variable/input.ddl         |  3 +
 3 files changed, 58 insertions(+), 9 deletions(-)
 create mode 100644 test/compile-error-test/undefined_head_variable/compile-error.expected
 create mode 100644 test/compile-error-test/undefined_head_variable/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 25e13bd0f..cc55cd658 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -34,8 +34,9 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkFunctionDefined(stmt)
     checkVariableRelationSchema(stmt)
     checkNumberOfColumns(stmt)
-    checkOptionalModifier(stmt)
+    checkQuantifiedBody(stmt)
     checkWeight(stmt)
+    checkHeadVariables(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
@@ -108,25 +109,29 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
-  // check if outer join body contains one atom
-  def checkOptionalModifier(stmt: Statement) {
-    def checkOuterJoinBodies(bodies: List[Body]) {
+  // check if quantified body contains required number of atoms
+  def checkQuantifiedBody(stmt: Statement) {
+    def checkBody(bodies: List[Body]) {
       bodies.foreach {
         case b: QuantifiedBody => {
           b.modifier match {
             case OuterModifier() =>
-              if ((b.bodies collect { case x: Atom => 1 }).size != 1) {
+              if ((b.bodies collect { case x: Atom => 1 }).size != 1)
                 error(stmt, s"One and only one atom should be supplied in OPTIONAL modifier")
-              }
-            case _ =>
+            case ExistModifier(_) =>
+              if ((b.bodies collect { case x: Atom => 1 }).size == 0)
+                error(stmt, s"At least one atom should be supplied in EXISTS modifier")
+            case AllModifier() =>
+              if ((b.bodies collect { case x: Atom => 1 }).size == 0)
+                error(stmt, s"At least one atom should be supplied in ALL modifier")
           }
         }
         case _ =>
       }
     }
     stmt match {
-      case s: ExtractionRule => s.q.bodies foreach checkOuterJoinBodies
-      case s: InferenceRule => s.q.bodies foreach checkOuterJoinBodies
+      case s: ExtractionRule => s.q.bodies foreach checkBody
+      case s: InferenceRule => s.q.bodies foreach checkBody
       case _ =>
     }
   }
@@ -142,6 +147,43 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
+  // check if head variables have bindings in the body
+  def checkHeadVariables(stmt: Statement) {
+    var variableSet = new HashSet[String]()
+    def addVariable(body: List[Body]) {
+      body foreach {
+        case a: Atom => a.terms.foreach {
+          case VarExpr(v) => variableSet += v
+          case _ =>
+        }
+        case a: QuantifiedBody => addVariable(a.bodies)
+        case _ =>
+      }
+    }
+    def checkHeadExpr(e: Expr) {
+      e match {
+        case VarExpr(v) =>
+          if (!variableSet.contains(v)) error(stmt, s"Head variable ${v} is not defined in the body")
+        case FuncExpr(_, args, _) => args foreach checkHeadExpr
+        case BinaryOpExpr(lhs, _, rhs) => {
+          checkHeadExpr(lhs)
+          checkHeadExpr(rhs)
+        }
+        case TypecastExpr(lhs, _) => checkHeadExpr(lhs)
+        case _ =>
+      }
+    }
+    def checkCq(cq: ConjunctiveQuery) {
+      cq.bodies foreach addVariable
+      cq.head.terms foreach checkHeadExpr
+    }
+    stmt match {
+      case s: ExtractionRule => checkCq(s.q)
+      case s: InferenceRule  => checkCq(s.q)
+      case _ =>
+    }
+  }
+
   // throw exception
   def error(stmt: Statement, message: String) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
diff --git a/test/compile-error-test/undefined_head_variable/compile-error.expected b/test/compile-error-test/undefined_head_variable/compile-error.expected
new file mode 100644
index 000000000..d170520dd
--- /dev/null
+++ b/test/compile-error-test/undefined_head_variable/compile-error.expected
@@ -0,0 +1,4 @@
+[error] Head variable y is not defined in the body
+Q(y)  :-
+    a(x).
+
diff --git a/test/compile-error-test/undefined_head_variable/input.ddl b/test/compile-error-test/undefined_head_variable/input.ddl
new file mode 100644
index 000000000..2723059e0
--- /dev/null
+++ b/test/compile-error-test/undefined_head_variable/input.ddl
@@ -0,0 +1,3 @@
+a(k int).
+
+Q(y) :- a(x).
\ No newline at end of file

From 683f9fa98fd713f168a3aa188332fff0009fa77c Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 22 Jul 2015 01:13:51 -0700
Subject: [PATCH 193/347] New syntax for rule annotation, first step

---
 examples/chunking.ddl                         |  6 ++-
 examples/ocr.ddl                              | 15 +++----
 examples/smoke.ddl                            | 15 ++++---
 examples/spouse_example.ddl                   |  7 ++--
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 39 +++++++++++--------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 19 ++++-----
 .../weight/compile-error.expected             |  4 +-
 test/compile-error-test/weight/input.ddl      |  3 +-
 .../comments/print.expected                   |  2 +-
 .../many_joins/print-incremental.expected     | 10 ++---
 .../ocr_example/print-incremental.expected    | 16 ++++----
 .../ocr_example/print.expected                | 16 ++++----
 test/expected-output-test/semantics/input.ddl |  6 +--
 .../smoke_example/print-incremental.expected  | 16 ++++----
 .../smoke_example/print.expected              | 16 ++++----
 .../spouse_example/print-incremental.expected |  8 ++--
 .../spouse_example/print.expected             |  8 ++--
 .../spouse_example_new_feature/input.ddl      | 13 ++++---
 .../print-incremental.expected                | 13 ++++---
 .../spouse_example_new_inference/input.ddl    | 13 ++++---
 .../print-incremental.expected                | 12 +++---
 .../print.expected                            | 12 +++---
 test/expected-output-test/weights/input.ddl   | 20 +++++-----
 .../weights/print.expected                    | 20 +++++-----
 24 files changed, 161 insertions(+), 148 deletions(-)

diff --git a/examples/chunking.ddl b/examples/chunking.ddl
index f73307681..4745d7140 100644
--- a/examples/chunking.ddl
+++ b/examples/chunking.ddl
@@ -38,6 +38,8 @@ function ext_features
 
 word_features :- !ext_features(ext_features_input).
 
-tag(word_id) :- words(word_id, a, b, c, tag) label = tag.
+@label(tag)
+tag(word_id) :- words(word_id, a, b, c, tag).
 
-tag(word_id) :- word_features(word_id, f) weight = f.
+@weight(f)
+tag(word_id) :- word_features(word_id, f).
diff --git a/examples/ocr.ddl b/examples/ocr.ddl
index 0960ecaf4..cf897d6d2 100644
--- a/examples/ocr.ddl
+++ b/examples/ocr.ddl
@@ -18,11 +18,12 @@ label2(
 q1?(wid INT).
 q2?(wid INT).
 
-q1(wid) :- label1(wid, val) label = val.
-q2(wid) :- label2(wid, val) label = val.
+@label(val)
+q1(wid) :- label1(wid, val).
+@label(val)
+q2(wid) :- label2(wid, val).
 
-q1(wid) :- features(id, wid, fid, fval)
-weight = fid.
-
-q2(wid) :- features(id, wid, fid, fval)
-weight = fid.
\ No newline at end of file
+@weight(fid)
+q1(wid) :- features(id, wid, fid, fval).
+@weight(fid)
+q2(wid) :- features(id, wid, fid, fval).
\ No newline at end of file
diff --git a/examples/smoke.ddl b/examples/smoke.ddl
index c3aa5cdd4..63a3ca777 100644
--- a/examples/smoke.ddl
+++ b/examples/smoke.ddl
@@ -29,11 +29,14 @@ cancer? (
     person_id bigint
 ).
 
-smoke(pid)  :- person_smokes(pid, l)     label = l.
-cancer(pid) :- person_has_cancer(pid, l) label = l.
+@label(l)
+smoke(pid)  :- person_smokes(pid, l).
 
-cancer(pid) :- smoke(pid), person_smokes(pid, l)
-    weight = 0.5.
+@label(l)
+cancer(pid) :- person_has_cancer(pid, l).
 
-smoke(pid)  :- smoke(pid1), friends(pid1, pid)
-    weight = 0.4.
\ No newline at end of file
+@weight(0.5)
+cancer(pid) :- smoke(pid), person_smokes(pid, l).
+
+@weight(0.4)
+smoke(pid)  :- smoke(pid1), friends(pid1, pid).
\ No newline at end of file
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 1aaa9703f..b9ef92edf 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -68,9 +68,10 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
-has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
+@label(l)
+has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
 
+@weight(f)
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
-  has_spouse_features(rid, f)
-weight = f.
+  has_spouse_features(rid, f).
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 6a2ef2fe5..7941d27d9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -44,6 +44,7 @@ case class Column(name : String // name of the column
 case class Annotation( name : String // name of the annotation
                      , args : Map[String, Any] = Map.empty // optional, named arguments
                      )
+case class RuleAnnotation(name: String, args: List[Any])
 
 // condition
 sealed trait Cond extends Body
@@ -241,8 +242,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
-  def functionMode = "mode" ~> "=" ~> functionModeType
-  def inferenceMode = "mode" ~> "=" ~> inferenceModeType
+  def ruleAnnotation(arg: Parser[Any]) = "@" ~> annotationName ~ "(" ~ rep1sep(arg, ",") <~ ")" ^^ {
+    case (name ~ _ ~ args) => RuleAnnotation(name, args)
+  }
+
+  def ruleAnnotations(arg: Parser[Any]) = rep(ruleAnnotation(arg))
+
+  def functionMode = "@mode" ~> "(" ~> functionModeType <~ ")"
+  def inferenceMode = "@mode" ~> "(" ~> inferenceModeType <~ ")"
 
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
     ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
@@ -254,41 +261,39 @@ class DeepDiveLogParser extends JavaTokenParsers {
     )
 
   def functionDeclaration : Parser[FunctionDeclaration] =
-    ( "function" ~ functionName ~ "over" ~ relationType
+    ( opt(functionMode) ~ "function" ~ functionName ~ "over" ~ relationType
                              ~ "returns" ~ relationType
-                 ~ (functionImplementation+) ~ opt(functionMode)
+                 ~ (functionImplementation+)
     ) ^^ {
-      case ("function" ~ a ~ "over" ~ inTy
+      case (mode ~ "function" ~ a ~ "over" ~ inTy
                            ~ "returns" ~ outTy
-                       ~ implementationDecls ~ mode) =>
+                       ~ implementationDecls) =>
              FunctionDeclaration(a, inTy, outTy, implementationDecls, mode.getOrElse(null))
     }
 
   def extractionRule : Parser[ExtractionRule] =
-    conjunctiveQuery ~ opt(supervision) ^^ {
-      case (q ~ supervision) =>
+    opt(supervision) ~ conjunctiveQuery ^^ {
+      case (supervision ~ q) =>
         ExtractionRule(q, supervision.getOrElse(null))
     }
 
   def functionCallRule : Parser[FunctionCallRule] =
-    ( relationName ~ ":-" ~ "!"
-    ~ functionName ~ "(" ~ relationName ~ ")"
-    ) ^^ {
-      case (out ~ ":-" ~ "!" ~ fn ~ "(" ~ in ~ ")") =>
+    ( relationName ~ ":-" ~ "!" ~ functionName ~ "(" ~ relationName ~ ")" ) ^^ {
+      case (out ~ ":-" ~ _ ~ fn ~ "(" ~ in ~ ")") =>
         FunctionCallRule(in, out, fn)
     }
 
-  def factorWeight = "weight" ~> "=" ~> rep1sep(expr, ",") ^^ { FactorWeight(_) }
+  def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
 
-  def supervision = "label" ~> "=" ~> variableName
+  def supervision = "@label" ~> "(" ~> variableName <~ ")"
 
   def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
-  def factorFunction = "function" ~> "=" ~> factorFunctionName
+  def factorFunction = "@function" ~> "(" ~> factorFunctionName <~ ")"
 
   def inferenceRule : Parser[InferenceRule] =
-    ( conjunctiveQuery ~ factorWeight ~ opt(factorFunction) ~ opt(inferenceMode)
+    ( opt(inferenceMode) ~ opt(factorFunction) ~ factorWeight ~ conjunctiveQuery
     ) ^^ {
-      case (q ~ weight ~ function ~ mode) =>
+      case (mode ~ function ~ weight ~ q) =>
         InferenceRule(q, weight, function, mode.getOrElse(null))
     }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 35c0778b6..179b1b166 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -57,11 +57,11 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" + styleStr
       }
     }
-    val modeStr = if (stmt.mode == null) "" else s" mode = ${stmt.mode}"
-    s"""function ${stmt.functionName}
+    val modeStr = if (stmt.mode == null) "" else s"@mode(${stmt.mode})\n"
+    s"""${modeStr}function ${stmt.functionName}
        |    over ${inputType}
        | returns ${outputType}
-       | ${(impls map {"implementation " + _}).mkString("\n ")}${modeStr}.
+       | ${(impls map {"implementation " + _}).mkString("\n ")}.
        |""".stripMargin
   }
 
@@ -140,10 +140,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-    print(stmt.q) +
     ( if (stmt.supervision == null) ""
-      else  "\n  label = " + stmt.supervision
-    ) + ".\n"
+      else  s"@label(${stmt.supervision})\n"
+    ) + print(stmt.q) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
@@ -152,12 +151,10 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: InferenceRule): String = {
-    print(stmt.q) +
+    ( stmt.function map { f => s"@function(${f})\n" } getOrElse("") ) +
     ( if (stmt.weights == null) ""
-      else "\n  weight = " + (stmt.weights.variables.map(print).mkString(", "))
-    ) +
-    ( stmt.function map { "\n  function = " + _ } getOrElse("")
-    ) + ".\n"
+      else s"@weight(${stmt.weights.variables.map(print).mkString(", ")})\n"
+    ) + print(stmt.q) + ".\n"
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/test/compile-error-test/weight/compile-error.expected b/test/compile-error-test/weight/compile-error.expected
index 8fffc16a1..0339cc784 100644
--- a/test/compile-error-test/weight/compile-error.expected
+++ b/test/compile-error-test/weight/compile-error.expected
@@ -1,5 +1,5 @@
 [error] Weight variables can contain at most one constant
+@weight(1, 2)
 a(x)  :-
-    b(x, y, _, _)
-  weight = 1, 2.
+    b(x, y, _, _).
 
diff --git a/test/compile-error-test/weight/input.ddl b/test/compile-error-test/weight/input.ddl
index 376cba024..b3174defc 100644
--- a/test/compile-error-test/weight/input.ddl
+++ b/test/compile-error-test/weight/input.ddl
@@ -2,4 +2,5 @@ a?(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-a(x) :- b(x, y, _, _) weight = 1, 2.
\ No newline at end of file
+@weight(1,2)
+a(x) :- b(x, y, _, _).
\ No newline at end of file
diff --git a/test/expected-output-test/comments/print.expected b/test/expected-output-test/comments/print.expected
index 8b8213f4c..a5fd9a790 100644
--- a/test/expected-output-test/comments/print.expected
+++ b/test/expected-output-test/comments/print.expected
@@ -4,6 +4,6 @@ S(a int,
   b text,
   c float).
 
-R(x) :-
+R(x)  :-
     S(x, y, z).
 
diff --git a/test/expected-output-test/many_joins/print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
index 6edb3d0f8..dd52a2b15 100644
--- a/test/expected-output-test/many_joins/print-incremental.expected
+++ b/test/expected-output-test/many_joins/print-incremental.expected
@@ -4,7 +4,7 @@ dd_delta_R?(x text).
 
 dd_new_R?(x text).
 
-dd_new_R(x) :-
+dd_new_R(x)  :-
     R(x);
     dd_delta_R(x).
 
@@ -14,7 +14,7 @@ dd_delta_S(x text).
 
 dd_new_S(x text).
 
-dd_new_S(x) :-
+dd_new_S(x)  :-
     S(x);
     dd_delta_S(x).
 
@@ -27,7 +27,7 @@ dd_delta_T(x text,
 dd_new_T(x text,
          f text).
 
-dd_new_T(x, f) :-
+dd_new_T(x, f)  :-
     T(x, f);
     dd_delta_T(x, f).
 
@@ -40,11 +40,11 @@ dd_delta_U(x text,
 dd_new_U(x text,
          l text).
 
-dd_new_U(x, l) :-
+dd_new_U(x, l)  :-
     U(x, l);
     dd_delta_U(x, l).
 
-dd_delta_R(x) :-
+dd_delta_R(x)  :-
     dd_delta_S(x),
     T(x, f),
     U(x, l);
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
index fc4e69079..a0dab2c2b 100644
--- a/test/expected-output-test/ocr_example/print-incremental.expected
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -63,19 +63,19 @@ dd_new_q2(wid)  :-
     q2(wid);
     dd_delta_q2(wid).
 
+@label(val)
 dd_delta_q1(wid)  :-
-    dd_delta_label1(wid, val)
-  label = val.
+    dd_delta_label1(wid, val).
 
+@label(val)
 dd_delta_q2(wid)  :-
-    dd_delta_label2(wid, val)
-  label = val.
+    dd_delta_label2(wid, val).
 
+@weight(fid)
 dd_new_q1(wid)  :-
-    dd_delta_features(id, wid, fid, fval)
-  weight = fid.
+    dd_delta_features(id, wid, fid, fval).
 
+@weight(fid)
 dd_new_q2(wid)  :-
-    dd_delta_features(id, wid, fid, fval)
-  weight = fid.
+    dd_delta_features(id, wid, fid, fval).
 
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
index d3ff92171..4249fde41 100644
--- a/test/expected-output-test/ocr_example/print.expected
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -13,19 +13,19 @@ q1?(wid INT).
 
 q2?(wid INT).
 
+@label(val)
 q1(wid)  :-
-    label1(wid, val)
-  label = val.
+    label1(wid, val).
 
+@label(val)
 q2(wid)  :-
-    label2(wid, val)
-  label = val.
+    label2(wid, val).
 
+@weight(fid)
 q1(wid)  :-
-    features(id, wid, fid, fval)
-  weight = fid.
+    features(id, wid, fid, fval).
 
+@weight(fid)
 q2(wid)  :-
-    features(id, wid, fid, fval)
-  weight = fid.
+    features(id, wid, fid, fval).
 
diff --git a/test/expected-output-test/semantics/input.ddl b/test/expected-output-test/semantics/input.ddl
index 6f3a9f36c..389ed0c5b 100644
--- a/test/expected-output-test/semantics/input.ddl
+++ b/test/expected-output-test/semantics/input.ddl
@@ -3,6 +3,6 @@ S(a int, b int, c int).
 T(a int, b int, c int).
 Q?(x int).
 
-Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w)
-weight = y
-function = Linear.
+@function(Linear)
+@weight(y)
+Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w).
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index 3a17e8fba..adcb8864c 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -70,25 +70,25 @@ dd_new_cancer(person_id)  :-
     cancer(person_id);
     dd_delta_cancer(person_id).
 
+@label(l)
 dd_delta_smoke(pid)  :-
-    dd_delta_person_smokes(pid, l)
-  label = l.
+    dd_delta_person_smokes(pid, l).
 
+@label(l)
 dd_delta_cancer(pid)  :-
-    dd_delta_person_has_cancer(pid, l)
-  label = l.
+    dd_delta_person_has_cancer(pid, l).
 
+@weight(0.5)
 dd_new_cancer(pid)  :-
     dd_delta_smoke(pid),
     person_smokes(pid, l);
     dd_new_smoke(pid),
-    dd_delta_person_smokes(pid, l)
-  weight = 0.5.
+    dd_delta_person_smokes(pid, l).
 
+@weight(0.4)
 dd_new_smoke(pid)  :-
     dd_delta_smoke(pid1),
     friends(pid1, pid);
     dd_new_smoke(pid1),
-    dd_delta_friends(pid1, pid)
-  weight = 0.4.
+    dd_delta_friends(pid1, pid).
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index f9e81e54d..384367f7f 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -14,21 +14,21 @@ smoke?(person_id bigint).
 
 cancer?(person_id bigint).
 
+@label(l)
 smoke(pid)  :-
-    person_smokes(pid, l)
-  label = l.
+    person_smokes(pid, l).
 
+@label(l)
 cancer(pid)  :-
-    person_has_cancer(pid, l)
-  label = l.
+    person_has_cancer(pid, l).
 
+@weight(0.5)
 cancer(pid)  :-
     smoke(pid),
-    person_smokes(pid, l)
-  weight = 0.5.
+    person_smokes(pid, l).
 
+@weight(0.4)
 smoke(pid)  :-
     smoke(pid1),
-    friends(pid1, pid)
-  weight = 0.4.
+    friends(pid1, pid).
 
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 90523ea59..911992840 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -166,14 +166,14 @@ function ext_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+@label(l)
 dd_delta_has_spouse(rid)  :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
-  label = l.
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
 
+@weight(f)
 dd_new_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
-    dd_delta_has_spouse_features(rid, f)
-  weight = f.
+    dd_delta_has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 5e07df218..0d917ad52 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -66,12 +66,12 @@ function ext_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+@label(l)
 has_spouse(rid)  :-
-    has_spouse_candidates(a, b, c, d, rid, l)
-  label = l.
+    has_spouse_candidates(a, b, c, d, rid, l).
 
+@weight(f)
 has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l),
-    has_spouse_features(rid, f)
-  weight = f.
+    has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 0b1563441..6bb6bf573 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -40,10 +40,10 @@ people_mentions :-
 ext_people_input(s, words, ner_tags) :-
   sentences(a, b, words, c, d, e, ner_tags, f, s).
 
+@mode(inc)
 function ext_people over like ext_people_input
                  returns like people_mentions
-  implementation "udf/ext_people.py" handles tsv lines
-  mode = inc.
+  implementation "udf/ext_people.py" handles tsv lines.
 
 has_spouse_candidates :-
   !ext_has_spouse(ext_has_spouse_input).
@@ -69,10 +69,11 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
-has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
+@label(l)
+has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
 
+@function(Linear)
+@weight(f)
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
-  has_spouse_features(rid, f)
-weight = f
-function = Linear.
+  has_spouse_features(rid, f).
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 7575d31f3..90edb04ff 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -121,11 +121,12 @@ dd_delta_ext_people_input(s, words, ner_tags)  :-
     sentences(a, b, words, c, d, e, ner_tags, f, s);
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
+@mode(inc)
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
  implementation "udf/ext_people.py"
-        handles tsv lines mode = inc.
+        handles tsv lines.
 
 dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
 
@@ -167,15 +168,15 @@ function ext_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+@label(l)
 dd_delta_has_spouse(rid)  :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
-  label = l.
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
 
+@function(Linear)
+@weight(f)
 dd_new_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
-    dd_delta_has_spouse_features(rid, f)
-  weight = f
-  function = Linear.
+    dd_delta_has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 08e9b910e..34861fe2e 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -68,16 +68,17 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
-has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l) label = l.
+@label(l)
+has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
 
+@weight(f)
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
-  has_spouse_features(rid, f)
-weight = f.
+  has_spouse_features(rid, f).
 
+@mode(inc)
+@weight(3.0)
 has_spouse(rid) :-
   has_spouse(rid2),
   has_spouse_candidates(a1, b1, c1, d1, rid, l1),
-  has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
-weight = 3.0
-mode = inc.
+  has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 71b4f119d..9fc97fa19 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -166,20 +166,20 @@ function ext_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+@label(l)
 dd_delta_has_spouse(rid)  :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l)
-  label = l.
+    dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
 
+@weight(f)
 dd_new_has_spouse(rid)  :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
-    dd_delta_has_spouse_features(rid, f)
-  weight = f.
+    dd_delta_has_spouse_features(rid, f).
 
+@weight(3.0)
 dd_new_has_spouse(rid)  :-
     dd_new_has_spouse(rid2),
     dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
-    dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
-  weight = 3.0.
+    dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 742839292..c60344ef2 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -66,18 +66,18 @@ function ext_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+@label(l)
 has_spouse(rid)  :-
-    has_spouse_candidates(a, b, c, d, rid, l)
-  label = l.
+    has_spouse_candidates(a, b, c, d, rid, l).
 
+@weight(f)
 has_spouse(rid)  :-
     has_spouse_candidates(a, b, c, d, rid, l),
-    has_spouse_features(rid, f)
-  weight = f.
+    has_spouse_features(rid, f).
 
+@weight(3.0)
 has_spouse(rid)  :-
     has_spouse(rid2),
     has_spouse_candidates(a1, b1, c1, d1, rid, l1),
-    has_spouse_candidates(b1, a1, c2, d2, rid2, l2)
-  weight = 3.0.
+    has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
 
diff --git a/test/expected-output-test/weights/input.ddl b/test/expected-output-test/weights/input.ddl
index 0d5b1801d..3922a6ec8 100644
--- a/test/expected-output-test/weights/input.ddl
+++ b/test/expected-output-test/weights/input.ddl
@@ -5,17 +5,17 @@ e?(k int).
 f?(k int).
 b(k int, p int, q text).
 
-a(x) :- b(x,y,_)
-weight = x + y.
+@weight(x + y)
+a(x) :- b(x,y,_).
 
-c(x) :- b(x,y,_)
-weight = "string".
+@weight("string")
+c(x) :- b(x,y,_).
 
-d(x) :- b(x,y,_)
-weight = x, y.
+@weight(x, y)
+d(x) :- b(x,y,_).
 
-e(x) :- b(x,y,_)
-weight = -10.
+@weight(-10)
+e(x) :- b(x,y,_).
 
-f(x) :- b(x,y,_)
-weight = -0.3.
\ No newline at end of file
+@weight(-0.3)
+f(x) :- b(x,y,_).
\ No newline at end of file
diff --git a/test/expected-output-test/weights/print.expected b/test/expected-output-test/weights/print.expected
index d1e1ca44c..8b79c10ff 100644
--- a/test/expected-output-test/weights/print.expected
+++ b/test/expected-output-test/weights/print.expected
@@ -12,23 +12,23 @@ b(k int,
   p int,
   q text).
 
+@weight((x + y))
 a(x)  :-
-    b(x, y, _)
-  weight = (x + y).
+    b(x, y, _).
 
+@weight("string")
 c(x)  :-
-    b(x, y, _)
-  weight = "string".
+    b(x, y, _).
 
+@weight(x, y)
 d(x)  :-
-    b(x, y, _)
-  weight = x, y.
+    b(x, y, _).
 
+@weight(-10)
 e(x)  :-
-    b(x, y, _)
-  weight = -10.
+    b(x, y, _).
 
+@weight(-0.3)
 f(x)  :-
-    b(x, y, _)
-  weight = -0.3.
+    b(x, y, _).
 

From ef6979cb65dd4ca725900fbd9618d5587d83e6a8 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 26 Jul 2015 12:06:58 -0700
Subject: [PATCH 194/347] Separate patterns and expressions

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 41 ++++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 18 ++++----
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  4 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 32 ++++++++++-----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 16 ++++++--
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 32 ++++++++-------
 6 files changed, 85 insertions(+), 58 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index f7905a84e..a16d335ea 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -208,10 +208,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case f : FunctionCallRule => dependencies += {
         f -> (( Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case e : ExtractionRule   => dependencies += {
-        e -> (((e.q.bodies.flatten collect { case x: Atom => x.name })
+        e -> (((e.q.bodies.flatten collect { case x: BodyAtom => x.name })
           flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case w : InferenceRule    => dependencies += {
-        w -> (((w.q.bodies.flatten collect { case x: Atom => x.name })
+        w -> (((w.q.bodies.flatten collect { case x: BodyAtom => x.name })
           flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case _ =>
     }
@@ -241,10 +241,10 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
   def generateCanonicalVar()  = {
-    def generateCanonicalVarFromAtom(a: Atom, index: String) {
+    def generateCanonicalVarFromAtom(a: BodyAtom, index: String) {
       a.terms.zipWithIndex.foreach { case (expr, i) =>
         expr match {
-          case VarExpr(v) =>
+          case VarPattern(v) =>
             if (! (query_schema contains v) )
               query_schema += { v -> (index, Variable(v,a.name,i) ) }
           case _ =>
@@ -254,7 +254,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
     // For quantified body, we need to recursively add variables from the atoms inside the quantified body
     def generateCanonicalVarFromBodies(bodies: List[Body], indexPrefix: String) {
       bodies.zipWithIndex.foreach {
-        case (a: Atom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
+        case (a: BodyAtom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
         // we need to recursively handle the atoms inside the modifier
         case (a: QuantifiedBody, index) => generateCanonicalVarFromBodies(a.bodies, s"${indexPrefix}${index}_")
         case _ =>
@@ -313,7 +313,6 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         val resovledLhs = compileExpr(lhs)
         s"(${resovledLhs} :: ${rhs})"
       }
-      case Placeholder() => ""
     }
   }
 
@@ -350,24 +349,24 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
     // generate where clause from unification and conditions
     def generateWhereClause(bodies: List[Body], indexPrefix: String) : String = {
       val conditions = bodies.zipWithIndex.flatMap {
-        case (Atom(relName, terms), index) => {
+        case (BodyAtom(relName, terms), index) => {
           val bodyIndex = s"${indexPrefix}${index}"
-          terms.zipWithIndex flatMap { case (expr, atomIndex) =>
-            expr match {
+          terms.zipWithIndex flatMap { case (pattern, termIndex) =>
+            pattern match {
               // a simple variable indicates a join condition with other columns having the same variable name
-              case VarExpr(varName) => {
+              case VarPattern(varName) => {
                 val canonical_body_index = getBodyIndex(varName)
                 if (canonical_body_index != bodyIndex) {
-                  val real_attr_name1 = ss.resolveName( Variable(varName, relName, atomIndex) )
+                  val real_attr_name1 = ss.resolveName( Variable(varName, relName, termIndex) )
                   val real_attr_name2 = ss.resolveName( getVar(varName))
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
               }
-              case Placeholder() => None
-              // other expressions indicate a filter condition on the column
-              case _ => {
+              case PlaceholderPattern() => None
+              // expression patterns indicate a filter condition on the column
+              case ExprPattern(expr) => {
                 val resolved = compileExpr(expr)
-                val attr = ss.schema(relName, atomIndex)
+                val attr = ss.schema(relName, termIndex)
                 Some(s"R${bodyIndex}.${attr} = ${resolved}")
               }
             }
@@ -390,7 +389,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
 
     def generateFromClause(bodies: List[Body], indexPrefix: String) : String = {
       val atoms = bodies.zipWithIndex flatMap {
-        case (x:Atom,i) => Some(s"${x.name} R${indexPrefix}${i}")
+        case (x:BodyAtom,i) => Some(s"${x.name} R${indexPrefix}${i}")
         case _ => None
       }
       val outers = bodies.zipWithIndex flatMap {
@@ -604,15 +603,19 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
         // edge query
-        val fakeBody        = stmt.q.head +: cqBody
+        val fakeHeadAsBody  = BodyAtom(stmt.q.head.name, stmt.q.head.terms map {
+          case x: VarExpr => VarPattern(x.name)
+          case x: Expr    => ExprPattern(x)
+        })
+        val fakeBody        = fakeHeadAsBody +: cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
-        val fakeBodyAtoms   = fakeBody.collect { case x: Atom => x }
+        val fakeBodyAtoms   = fakeBody.collect { case x: BodyAtom => x }
 
         val index = cqBody.length + 1
         val qc = new QueryCompiler(fakeCQ, ss)
         // TODO self-join?
         val varInBody = (fakeBody.zipWithIndex flatMap {
-          case (x: Atom, i) =>
+          case (x: BodyAtom, i) =>
             if (ss.variableTableNames contains x.name)
               Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
             else
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index c9b444b9b..964bfc0d5 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -36,23 +36,23 @@ object DeepDiveLogDeltaDeriver{
     cq.bodies foreach { bodies =>
       // We don't support deriving delta rules for modifiers
       bodies foreach {
-        case _: Cond | _: Atom => // supported
+        case _: Cond | _: BodyAtom => // supported
         case _ => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
       }
       // Delta body
       val incDeltaBody = bodies collect {
-        case a: Atom => a.copy(name = deltaPrefix + a.name)
+        case a: BodyAtom => a.copy(name = deltaPrefix + a.name)
         case a: Cond => a
       }
       // New body
       val incNewBody = bodies collect {
-        case a: Atom => a.copy(name = newPrefix + a.name)
+        case a: BodyAtom => a.copy(name = newPrefix + a.name)
         case a: Cond => a
       }
-      val bodyAtoms         = bodies       collect { case a: Atom => a }
+      val bodyAtoms         = bodies       collect { case a: BodyAtom => a }
       val bodyConds         = bodies       collect { case a: Cond => a }
-      val incDeltaBodyAtoms = incDeltaBody collect { case a: Atom => a }
-      val incNewBodyAtoms   = incNewBody   collect { case a: Atom => a }
+      val incDeltaBodyAtoms = incDeltaBody collect { case a: BodyAtom => a }
+      val incNewBodyAtoms   = incNewBody   collect { case a: BodyAtom => a }
 
       var i = 0
       var j = 0
@@ -103,9 +103,9 @@ object DeepDiveLogDeltaDeriver{
 
     // if (!stmt.isQuery) {
     incrementalStatement += ExtractionRule(ConjunctiveQuery(
-      Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
-      List(List(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) })),
-        List(Atom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarExpr(_) }))),
+      HeadAtom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
+      List(List(BodyAtom(stmt.a.name, stmt.a.terms map { VarPattern(_) })),
+        List(BodyAtom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarPattern(_) }))),
       false, None))
     // }
     incrementalStatement.toList
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index b2d2ce509..1b5203fc2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -17,8 +17,8 @@ object DeepDiveLogMergeDeriver{
       )
     )
 
-    ExtractionRule(ConjunctiveQuery(Atom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
-      List(List(Atom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) }))),
+    ExtractionRule(ConjunctiveQuery(HeadAtom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
+      List(List(BodyAtom(incNewStmt.a.name, incNewStmt.a.terms map { VarPattern(_) }))),
       false, None))
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 6a2ef2fe5..c6ff24b5b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -23,10 +23,16 @@ case class NullConst extends ConstExpr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
-case class Placeholder extends Expr
+
+sealed trait Pattern
+case class VarPattern(name: String) extends Pattern
+case class ExprPattern(expr: Expr) extends Pattern
+case class PlaceholderPattern extends Pattern
+
+case class HeadAtom(name : String, terms : List[Expr])
 
 sealed trait Body
-case class Atom(name : String, terms : List[Expr]) extends Body
+case class BodyAtom(name : String, terms : List[Pattern]) extends Body
 case class QuantifiedBody(modifier: BodyModifier, bodies: List[Body]) extends Body
 
 sealed trait BodyModifier
@@ -35,7 +41,7 @@ case class OuterModifier extends BodyModifier
 case class AllModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
-case class ConjunctiveQuery(head: Atom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
+case class ConjunctiveQuery(head: HeadAtom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
 case class Column(name : String // name of the column
                  , t : String // type of the column
                  , annotation: List[Annotation] = List.empty // optional annotation
@@ -181,10 +187,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "(" ~> expr <~ ")"
     )
 
-  def pattern : Parser[Expr] = "_" ^^ { case _ => Placeholder() } | expr
-
   def cqHead = relationName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ expressions ~ ")") => Atom(r, expressions)
+    case (r ~ _ ~ expressions ~ _) => HeadAtom(r, expressions)
   }
 
   // conditional expressions
@@ -212,10 +216,18 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "[" ~> cond <~ "]"
     )
 
-  def atom = relationName ~ "(" ~ repsep(pattern, ",") ~ ")" ^^ {
-    case (r ~ "(" ~ patterns ~ ")") => Atom(r, patterns)
+  def pattern : Parser[Pattern] =
+    ( "_"  ^^ { case _ => PlaceholderPattern() }
+    | expr ^^ {
+        case VarExpr(x) => VarPattern(x)
+        case x: Expr => ExprPattern(x)
+      }
+    )
+
+  def atom = relationName ~ "(" ~ rep1sep(pattern, ",") ~ ")" ^^ {
+    case (r ~ _ ~ patterns ~ _) => BodyAtom(r, patterns)
   }
-  def modifierAtom = (opt("!") ~ "EXISTS" | "OPTIONAL" | "ALL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
+  def quantifiedBody = (opt("!") ~ "EXISTS" | "OPTIONAL" | "ALL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
       case (not ~ "EXISTS") => new ExistModifier(not != None)
       case "OPTIONAL" => new OuterModifier
@@ -224,7 +236,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     QuantifiedBody(modifier, b)
   }
 
-  def cqBody: Parser[Body] = cond | modifierAtom | atom
+  def cqBody: Parser[Body] = cond | quantifiedBody | atom
 
   def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 35c0778b6..f152ce9f0 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -85,15 +85,25 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
       case BinaryOpExpr(lhs, op, rhs) => s"(${print(lhs)} ${op} ${print(rhs)})"
       case TypecastExpr(lhs, rhs) => s"(${print(lhs)} :: ${rhs})"
-      case Placeholder() => "_"
     }
   }
 
-  def print(a: Atom) : String = {
+  def print(a: BodyAtom) : String = {
     val vars = a.terms map print
     s"${a.name}(${vars.mkString(", ")})"
   }
 
+  def print(a: HeadAtom) : String = {
+    val vars = a.terms map print
+    s"${a.name}(${vars.mkString(", ")})"
+  }
+
+  def print(p: Pattern) : String = p match {
+    case VarPattern(x) => x
+    case PlaceholderPattern() => "_"
+    case ExprPattern(e) => print(e)
+  }
+
   def print(a: QuantifiedBody) : String = {
     val modifier = a.modifier match {
       case ExistModifier(negated) => if(negated) "NOT " else "" + "EXISTS"
@@ -119,7 +129,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(b: Body) : String = b match {
-    case b: Atom => print(b)
+    case b: BodyAtom => print(b)
     case b: Cond => print(b)
     case b: QuantifiedBody => print(b)
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index cc55cd658..566c0b10f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -40,9 +40,9 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   // iterate over all atoms contained in the body list and apply the checker
-  def checkBodyAtoms(checker: Atom => Unit): List[Body] => Unit = bodies => {
+  def checkBodyAtoms(checker: BodyAtom => Unit): List[Body] => Unit = bodies => {
     bodies foreach {
-      case a: Atom => checker(a)
+      case a: BodyAtom => checker(a)
       case a: QuantifiedBody => checkBodyAtoms(checker)(a.bodies)
       case _ =>
     }
@@ -51,7 +51,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // check if relations in the body are defined
   def checkRelationDefined(stmt: Statement) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
-    def checkRelation(a: Atom) {
+    def checkRelation(a: BodyAtom) {
       if (!(heads contains a.name))
         error(stmt, s"""relation "${a.name}" is not defined""")
     }
@@ -59,7 +59,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach check
       case s: InferenceRule => s.q.bodies foreach check
-      case s: FunctionCallRule => checkRelation(Atom(s.input, Nil))
+      case s: FunctionCallRule => checkRelation(BodyAtom(s.input, Nil))
       case _ =>
     }
   }
@@ -93,14 +93,16 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
 
   // check if the number of columns match schema declaration
   def checkNumberOfColumns(stmt: Statement) {
-    def checkAtom(a: Atom) {
-      if ((schemaDeclaration.keySet contains a.name) &&
-        (a.terms.size != schemaDeclaration(a.name).a.terms.size))
-        error(stmt, s""""${a.name}": number of columns in the query does not match number of columns in the schema""")
+    def check(name: String, size: Int) {
+      if ((schemaDeclaration.keySet contains name) &&
+        (size != schemaDeclaration(name).a.terms.size))
+        error(stmt, s""""${name}": number of columns in the query does not match number of columns in the schema""")
     }
+    def checkBodyAtom(a: BodyAtom) = check(a.name, a.terms.size)
+    def checkHeadAtom(a: HeadAtom) = check(a.name, a.terms.size)
     def checkCq(cq: ConjunctiveQuery) {
-      checkAtom(cq.head)
-      cq.bodies foreach checkBodyAtoms(checkAtom)
+      checkHeadAtom(cq.head)
+      cq.bodies foreach checkBodyAtoms(checkBodyAtom)
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
@@ -116,13 +118,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         case b: QuantifiedBody => {
           b.modifier match {
             case OuterModifier() =>
-              if ((b.bodies collect { case x: Atom => 1 }).size != 1)
+              if ((b.bodies collect { case x: BodyAtom => 1 }).size != 1)
                 error(stmt, s"One and only one atom should be supplied in OPTIONAL modifier")
             case ExistModifier(_) =>
-              if ((b.bodies collect { case x: Atom => 1 }).size == 0)
+              if ((b.bodies collect { case x: BodyAtom => 1 }).size == 0)
                 error(stmt, s"At least one atom should be supplied in EXISTS modifier")
             case AllModifier() =>
-              if ((b.bodies collect { case x: Atom => 1 }).size == 0)
+              if ((b.bodies collect { case x: BodyAtom => 1 }).size == 0)
                 error(stmt, s"At least one atom should be supplied in ALL modifier")
           }
         }
@@ -152,8 +154,8 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     var variableSet = new HashSet[String]()
     def addVariable(body: List[Body]) {
       body foreach {
-        case a: Atom => a.terms.foreach {
-          case VarExpr(v) => variableSet += v
+        case a: BodyAtom => a.terms.foreach {
+          case VarPattern(v) => variableSet += v
           case _ =>
         }
         case a: QuantifiedBody => addVariable(a.bodies)

From d6074ffd454cc04601d5bde38c84d3d6ef8330aa Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 26 Jul 2015 16:30:52 -0700
Subject: [PATCH 195/347] Add checks for unbounded variables

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |   4 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |   5 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   6 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 105 +++++++++++++-----
 .../unbound_variable_1/compile-error.expected |   4 +
 .../input.ddl                                 |   0
 .../unbound_variable_2/compile-error.expected |   5 +
 .../unbound_variable_2/input.ddl              |   3 +
 .../unbound_variable_3/compile-error.expected |   5 +
 .../unbound_variable_3/input.ddl              |   4 +
 .../compile-error.expected                    |   4 -
 11 files changed, 105 insertions(+), 40 deletions(-)
 create mode 100644 test/compile-error-test/unbound_variable_1/compile-error.expected
 rename test/compile-error-test/{undefined_head_variable => unbound_variable_1}/input.ddl (100%)
 create mode 100644 test/compile-error-test/unbound_variable_2/compile-error.expected
 create mode 100644 test/compile-error-test/unbound_variable_2/input.ddl
 create mode 100644 test/compile-error-test/unbound_variable_3/compile-error.expected
 create mode 100644 test/compile-error-test/unbound_variable_3/input.ddl
 delete mode 100644 test/compile-error-test/undefined_head_variable/compile-error.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a16d335ea..9c65605e9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -508,10 +508,10 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         // Generate the body of the query.
         val qc              = new QueryCompiler(tmpCq, ss)
 
-        if (stmt.supervision != null) {
+        if (stmt.supervision != None) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
           val headStr = qc.generateSQLHead(false)
-          val labelCol = qc.compileVariable(stmt.supervision)
+          val labelCol = qc.compileVariable(stmt.supervision.get)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index c6ff24b5b..1d5c61687 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -91,7 +91,7 @@ case class SchemaDeclaration( a : Attribute
                             , annotation : List[Annotation] = List.empty // optional annotation
                             ) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
-case class ExtractionRule(q : ConjunctiveQuery, supervision: String = null) extends Statement // Extraction rule
+case class ExtractionRule(q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
 case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: String = null) extends Statement // Weighted rule
 
@@ -278,8 +278,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def extractionRule : Parser[ExtractionRule] =
     conjunctiveQuery ~ opt(supervision) ^^ {
-      case (q ~ supervision) =>
-        ExtractionRule(q, supervision.getOrElse(null))
+      case (q ~ supervision) => ExtractionRule(q, supervision)
     }
 
   def functionCallRule : Parser[FunctionCallRule] =
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index f152ce9f0..88161311f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -151,8 +151,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(stmt: ExtractionRule): String = {
     print(stmt.q) +
-    ( if (stmt.supervision == null) ""
-      else  "\n  label = " + stmt.supervision
+    ( stmt.supervision map ("\n  label = " + _) getOrElse("")
     ) + ".\n"
   }
 
@@ -163,8 +162,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(stmt: InferenceRule): String = {
     print(stmt.q) +
-    ( if (stmt.weights == null) ""
-      else "\n  weight = " + (stmt.weights.variables.map(print).mkString(", "))
+    ( "\n  weight = " + (stmt.weights.variables.map(print).mkString(", "))
     ) +
     ( stmt.function map { "\n  function = " + _ } getOrElse("")
     ) + ".\n"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 566c0b10f..2a45e50d1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -36,7 +36,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkNumberOfColumns(stmt)
     checkQuantifiedBody(stmt)
     checkWeight(stmt)
-    checkHeadVariables(stmt)
+    checkVariableBindings(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
@@ -149,39 +149,90 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
-  // check if head variables have bindings in the body
-  def checkHeadVariables(stmt: Statement) {
-    var variableSet = new HashSet[String]()
-    def addVariable(body: List[Body]) {
-      body foreach {
-        case a: BodyAtom => a.terms.foreach {
-          case VarPattern(v) => variableSet += v
-          case _ =>
-        }
-        case a: QuantifiedBody => addVariable(a.bodies)
-        case _ =>
+  // collect variables used in the expression
+  def collectVariables(expr: Expr) : Set[String] = {
+    var set = new HashSet[String]()
+    def collectVariablesInner(e: Expr) : Unit = e match {
+      case VarExpr(name) => set += name
+      case FuncExpr(function, args, agg) => args foreach (collectVariablesInner(_))
+      case BinaryOpExpr(lhs, op, rhs) => {
+        collectVariablesInner(lhs)
+        collectVariablesInner(rhs)
       }
+      case TypecastExpr(lhs, rhs) => collectVariablesInner(lhs)
+      case _ =>
     }
-    def checkHeadExpr(e: Expr) {
-      e match {
-        case VarExpr(v) =>
-          if (!variableSet.contains(v)) error(stmt, s"Head variable ${v} is not defined in the body")
-        case FuncExpr(_, args, _) => args foreach checkHeadExpr
-        case BinaryOpExpr(lhs, _, rhs) => {
-          checkHeadExpr(lhs)
-          checkHeadExpr(rhs)
-        }
-        case TypecastExpr(lhs, _) => checkHeadExpr(lhs)
-        case _ =>
+    collectVariablesInner(expr)
+    set
+  }
+
+  def collectVariables(pattern: Pattern, definitionOnly: Boolean) : Set[String] = {
+    var set = new HashSet[String]()
+    pattern match {
+      case VarPattern(name) => set += name
+      case ExprPattern(e) => if (!definitionOnly) set ++= collectVariables(e)
+      case PlaceholderPattern() =>
+    }
+    set
+  }
+
+  def collectVariables(cond: Cond) : Set[String] = {
+    var set = new HashSet[String]()
+    cond match {
+      case ComparisonCond(lhs, op, rhs) => {
+        set ++= collectVariables(lhs)
+        set ++= collectVariables(rhs)
+      }
+      case CompoundCond(lhs, op, rhs) => {
+        set ++= collectVariables(lhs)
+        set ++= collectVariables(rhs)
       }
+      case NegationCond(c) => set ++= collectVariables(c)
     }
-    def checkCq(cq: ConjunctiveQuery) {
-      cq.bodies foreach addVariable
-      cq.head.terms foreach checkHeadExpr
+    set
+  }
+
+  // collect variable
+  def collectVariablesFromBody(body: Body, definitionOnly: Boolean) : Set[String] = {
+    var set = new HashSet[String]()
+    body match {
+      case a: BodyAtom => a.terms.foreach { x =>
+        set ++= collectVariables(x, definitionOnly)
+      }
+      case a: QuantifiedBody => a.bodies.foreach {
+        x => set ++= collectVariablesFromBody(x, definitionOnly)
+      }
+      case a: Cond => if (!definitionOnly) set ++= collectVariables(a)
+    }
+    set
+  }
+
+  // check if variables have bindings in the body
+  def checkVariableBindings(stmt: Statement) {
+    // check variable bindings in a conjunctive query
+    def checkCq(cq: ConjunctiveQuery, additionalVars: Set[String] = Set()) {
+      // collect variable definitions and usages
+      var varDefSet = new HashSet[String]()
+      var varUseSet = new HashSet[String]()
+      cq.bodies.foreach { case x =>
+        x.foreach { case a =>
+          varDefSet ++= collectVariablesFromBody(a, true)
+          varUseSet ++= collectVariablesFromBody(a, false)
+        }
+      }
+      cq.head.terms.foreach  { x => varUseSet ++= collectVariables(x) }
+      varUseSet ++= additionalVars
+      varUseSet.foreach { x =>
+        if (!varDefSet.contains(x)) error(stmt, s"Variable ${x} does not have bindings")
+      }
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
-      case s: InferenceRule  => checkCq(s.q)
+      case s: InferenceRule  => {
+        var set = new HashSet[String]()
+        s.weights.variables.foreach { set ++= collectVariables(_) }
+        checkCq(s.q, set)
+      }
       case _ =>
     }
   }
diff --git a/test/compile-error-test/unbound_variable_1/compile-error.expected b/test/compile-error-test/unbound_variable_1/compile-error.expected
new file mode 100644
index 000000000..362b5d228
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_1/compile-error.expected
@@ -0,0 +1,4 @@
+[error] Variable y does not have bindings
+Q(y)  :-
+    a(x).
+
diff --git a/test/compile-error-test/undefined_head_variable/input.ddl b/test/compile-error-test/unbound_variable_1/input.ddl
similarity index 100%
rename from test/compile-error-test/undefined_head_variable/input.ddl
rename to test/compile-error-test/unbound_variable_1/input.ddl
diff --git a/test/compile-error-test/unbound_variable_2/compile-error.expected b/test/compile-error-test/unbound_variable_2/compile-error.expected
new file mode 100644
index 000000000..fe419e14c
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_2/compile-error.expected
@@ -0,0 +1,5 @@
+[error] Variable x does not have bindings
+Q(y)  :-
+    a(y),
+    x > 100.
+
diff --git a/test/compile-error-test/unbound_variable_2/input.ddl b/test/compile-error-test/unbound_variable_2/input.ddl
new file mode 100644
index 000000000..0764eab1b
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_2/input.ddl
@@ -0,0 +1,3 @@
+a(k int).
+
+Q(y) :- a(y), x > 100.
\ No newline at end of file
diff --git a/test/compile-error-test/unbound_variable_3/compile-error.expected b/test/compile-error-test/unbound_variable_3/compile-error.expected
new file mode 100644
index 000000000..c182c4502
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_3/compile-error.expected
@@ -0,0 +1,5 @@
+[error] Variable y does not have bindings
+b(x)  :-
+    a(x)
+  weight = y.
+
diff --git a/test/compile-error-test/unbound_variable_3/input.ddl b/test/compile-error-test/unbound_variable_3/input.ddl
new file mode 100644
index 000000000..8665dd1d1
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_3/input.ddl
@@ -0,0 +1,4 @@
+a(k int).
+b?(x int).
+
+b(x) :- a(x) weight = y.
\ No newline at end of file
diff --git a/test/compile-error-test/undefined_head_variable/compile-error.expected b/test/compile-error-test/undefined_head_variable/compile-error.expected
deleted file mode 100644
index d170520dd..000000000
--- a/test/compile-error-test/undefined_head_variable/compile-error.expected
+++ /dev/null
@@ -1,4 +0,0 @@
-[error] Head variable y is not defined in the body
-Q(y)  :-
-    a(x).
-

From 68581a3df432c4c9be5c263dc1dc697a1d834418 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 26 Jul 2015 22:19:13 -0700
Subject: [PATCH 196/347] General rule annotations

---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  8 +--
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 67 ++++++++++++-------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  2 +-
 3 files changed, 49 insertions(+), 28 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 964bfc0d5..3358f61fd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -18,7 +18,7 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
-  def transform(cq: ConjunctiveQuery, isInference: Boolean, mode: String): ConjunctiveQuery = {
+  def transform(cq: ConjunctiveQuery, isInference: Boolean, mode: Option[String]): ConjunctiveQuery = {
 
     // New head
     val incCqHead = if (isInference) {
@@ -57,7 +57,7 @@ object DeepDiveLogDeltaDeriver{
       var i = 0
       var j = 0
       var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
-      if (mode == "inc") {
+      if (mode == Some("inc")) {
         incCqBodies += incNewBody
       } else {
         for (i <- index to (bodyAtoms.length - 1)) {
@@ -148,12 +148,12 @@ object DeepDiveLogDeltaDeriver{
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(stmt.copy(q = transform(stmt.q, true, stmt.mode), mode = null))
+    List(stmt.copy(q = transform(stmt.q, true, stmt.mode), mode = None))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
     program.foreach {
-      case x:FunctionDeclaration => if (x.mode == "inc") {
+      case x:FunctionDeclaration => if (x.mode == Some("inc")) {
         x.inputType match {
           case inTy: RelationTypeAlias => incrementalFunctionInput += deltaPrefix + inTy.likeRelationName
           case _ =>
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index ec609dbe2..282ff435c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -50,7 +50,10 @@ case class Column(name : String // name of the column
 case class Annotation( name : String // name of the annotation
                      , args : Map[String, Any] = Map.empty // optional, named arguments
                      )
-case class RuleAnnotation(name: String, args: List[Any])
+case class RuleAnnotation(name: String, args: List[RuleAnnotationArg])
+sealed trait RuleAnnotationArg
+case class ExprAnnoArg(expr: Expr) extends RuleAnnotationArg
+case class IdentAnnoArg(name: String) extends RuleAnnotationArg
 
 // condition
 sealed trait Cond extends Body
@@ -91,10 +94,11 @@ case class SchemaDeclaration( a : Attribute
                             , variableType : Option[VariableType]
                             , annotation : List[Annotation] = List.empty // optional annotation
                             ) extends Statement // atom and whether this is a query relation.
-case class FunctionDeclaration( functionName: String, inputType: RelationType, outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: String = null) extends Statement
+case class FunctionDeclaration( functionName: String, inputType: RelationType,
+  outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
 case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: String = null) extends Statement // Weighted rule
+case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: Option[String] = None) extends Statement // Weighted rule
 
 // Parser
 class DeepDiveLogParser extends JavaTokenParsers {
@@ -254,11 +258,27 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
-  def ruleAnnotation(arg: Parser[Any]) = "@" ~> annotationName ~ "(" ~ rep1sep(arg, ",") <~ ")" ^^ {
+  def ruleAnnoArg : Parser[RuleAnnotationArg] = expr  ^^ {
+    case VarExpr(x) => IdentAnnoArg(x)
+    case x: Expr    => ExprAnnoArg(x)
+  }
+
+  def ruleAnnotation = "@" ~> annotationName ~ "(" ~ rep1sep(ruleAnnoArg, ",") <~ ")" ^^ {
     case (name ~ _ ~ args) => RuleAnnotation(name, args)
   }
 
-  def ruleAnnotations(arg: Parser[Any]) = rep(ruleAnnotation(arg))
+  def ruleAnnotations = rep(ruleAnnotation)
+
+  def getArgs(annos: List[RuleAnnotation], name: String) = {
+    annos.find(_.name == name) map (_.args)
+  }
+
+  def getFirstIdentArg(annos: List[RuleAnnotation], name: String)  = {
+    getArgs(annos, name) map (_(0)) map {
+      case x: IdentAnnoArg => x.name
+      case _ => error("Invalid rule annotation argument(s) for " + name)
+    }
+  }
 
   def functionMode = "@mode" ~> "(" ~> functionModeType <~ ")"
   def inferenceMode = "@mode" ~> "(" ~> inferenceModeType <~ ")"
@@ -280,12 +300,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case (mode ~ "function" ~ a ~ "over" ~ inTy
                            ~ "returns" ~ outTy
                        ~ implementationDecls) =>
-             FunctionDeclaration(a, inTy, outTy, implementationDecls, mode.getOrElse(null))
-    }
-
-  def extractionRule : Parser[ExtractionRule] =
-    opt(supervision) ~ conjunctiveQuery ^^ {
-      case (supervision ~ q) => ExtractionRule(q, supervision)
+             FunctionDeclaration(a, inTy, outTy, implementationDecls, mode)
     }
 
   def functionCallRule : Parser[FunctionCallRule] =
@@ -294,24 +309,28 @@ class DeepDiveLogParser extends JavaTokenParsers {
         FunctionCallRule(in, out, fn)
     }
 
-  def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
-
-  def supervision = "@label" ~> "(" ~> variableName <~ ")"
-
   def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
-  def factorFunction = "@function" ~> "(" ~> factorFunctionName <~ ")"
 
-  def inferenceRule : Parser[InferenceRule] =
-    ( opt(inferenceMode) ~ opt(factorFunction) ~ factorWeight ~ conjunctiveQuery
-    ) ^^ {
-      case (mode ~ function ~ weight ~ q) =>
-        InferenceRule(q, weight, function, mode.getOrElse(null))
+  def extractionOrInferenceRule = ruleAnnotations ~ conjunctiveQuery ^^ { case (annos ~ cq) =>
+    val weight = getArgs(annos, "weight")
+    if (weight == None) { // extraction rule
+      val supervision = getFirstIdentArg(annos, "label")
+      ExtractionRule(cq, supervision)
+    } else { // inference rule
+      val mode          = getFirstIdentArg(annos, "mode")
+      val function      = getFirstIdentArg(annos, "function")
+      // NOTE there's an ambiguation between ident and variable expression
+      val factorWeight  = FactorWeight(weight.get.map {
+        case x: ExprAnnoArg  => x.expr
+        case x: IdentAnnoArg => VarExpr(x.name)
+      })
+      InferenceRule(cq, factorWeight, function, mode)
     }
+  }
 
   // rules or schema elements in arbitrary order
   def statement : Parser[Statement] = ( schemaDeclaration
-                                      | inferenceRule
-                                      | extractionRule
+                                      | extractionOrInferenceRule
                                       | functionDeclaration
                                       | functionCallRule
                                       )
@@ -324,6 +343,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   }
 
+  def error(meesage: String) = throw new RuntimeException(meesage)
+
   def parseProgramFile(fileName: String): List[Statement] = {
     val source = scala.io.Source.fromFile(fileName)
     try parseProgram(source.getLines mkString "\n", Some(fileName))
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 35f35aaff..b5764a64c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -57,7 +57,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" + styleStr
       }
     }
-    val modeStr = if (stmt.mode == null) "" else s"@mode(${stmt.mode})\n"
+    val modeStr = stmt.mode map (s => s"@mode(${s})\n") getOrElse ""
     s"""${modeStr}function ${stmt.functionName}
        |    over ${inputType}
        | returns ${outputType}

From 68682ce2a440c5eeb6739ea6bfdca01c39df0eb3 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 27 Jul 2015 00:54:34 -0700
Subject: [PATCH 197/347] New function call syntax

---
 examples/chunking.ddl                         |  14 +-
 examples/spouse_example.ddl                   |  20 +--
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  29 +--
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |  11 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |   7 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   3 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    |   8 +-
 .../undefined_function/compile-error.expected |   5 +-
 .../undefined_function/input.ddl              |   2 +-
 .../chunking_example/compile.expected         |  42 ++---
 .../expressions/compile.expected              | 115 +++++-------
 .../ocr_example/compile-incremental.expected  |  44 ++---
 .../ocr_example/compile-merge.expected        |  15 +-
 .../compile-incremental.expected              |  56 +++---
 .../smoke_example/compile-merge.expected      |  20 +--
 .../compile-incremental.expected              | 166 +++++++----------
 .../compile-materialization.expected          |  74 +++-----
 .../spouse_example/compile-merge.expected     |  25 ++-
 .../spouse_example/compile.expected           |  74 +++-----
 .../spouse_example/print-incremental.expected |  12 +-
 .../spouse_example/print.expected             |  12 +-
 .../compile-incremental.expected              | 169 +++++++-----------
 .../spouse_example_new_feature/input.ddl      |  20 +--
 .../print-incremental.expected                |  13 +-
 .../compile-incremental.expected              | 166 +++++++----------
 .../compile.expected                          |  74 +++-----
 .../spouse_example_new_inference/input.ddl    |  20 +--
 .../print-incremental.expected                |  12 +-
 .../print.expected                            |  12 +-
 29 files changed, 493 insertions(+), 747 deletions(-)

diff --git a/examples/chunking.ddl b/examples/chunking.ddl
index 4745d7140..e2fd8c94f 100644
--- a/examples/chunking.ddl
+++ b/examples/chunking.ddl
@@ -20,23 +20,23 @@ word_features(
 
 tag?(word_id bigint) Categorical(13).
 
-function ext_training 
+function ext_training
   over like words_raw
   returns like words
   implementation "udf/ext_training.py" handles tsv lines.
 
-words :- !ext_training(words_raw).
-
-ext_features_input(word_id1, word1, pos1, word2, pos2) :-
-  words(sent_id, word_id1, word1, pos1, tag1),
-  words(sent_id, word_id2, word2, pos2, tag2).
+words +=
+  ext_training(wid, word, pos, tag) :- words_raw(wid, word, pos, tag).
 
 function ext_features
   over like ext_features_input
   returns like word_features
   implementation "udf/ext_features.py" handles tsv lines.
 
-word_features :- !ext_features(ext_features_input).
+word_features +=
+  ext_features(word_id1, word1, pos1, word2, pos2) :-
+  words(sent_id, word_id1, word1, pos1, tag1),
+  words(sent_id, word_id2, word2, pos2, tag2).
 
 @label(tag)
 tag(word_id) :- words(word_id, a, b, c, tag).
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index b9ef92edf..50a9f7de3 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -34,20 +34,16 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-people_mentions :-
-  !ext_people(ext_people_input).
-
-ext_people_input(s, words, ner_tags) :-
+people_mentions +=
+  ext_people(s, words, ner_tags) :-
   sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates :-
-  !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+has_spouse_candidates +=
+  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, a, b, p1_text, p1_id),
   people_mentions(s, c, d, p2_text, p2_id).
 
@@ -55,15 +51,13 @@ function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
-has_spouse_features :-
-  !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+has_spouse_features +=
+  ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
   has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
-  
+
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9c65605e9..0a3aecad7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -95,7 +95,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
   var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
   var inferenceRuleGroupByHead      : Map[String, List[InferenceRule]] = new HashMap[String, List[InferenceRule]]()
-  var functionCallRuleGroupByInput  : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
   var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
   var functionCallList              : ListBuffer[FunctionCallRule] = new ListBuffer[FunctionCallRule]()
 
@@ -188,7 +187,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
     extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.q.head.name)
     inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
-    functionCallRuleGroupByInput   = functionCallRuleToCompile.toList.groupBy(_.input)
     functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
   }
 
@@ -206,7 +204,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // Look at the body of each statement to construct a dependency graph
     statements foreach {
       case f : FunctionCallRule => dependencies += {
-        f -> (( Some(f.input) flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+        f -> ((( f.input.bodies.flatten collect { case x: BodyAtom => x.name })
+          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case e : ExtractionRule   => dependencies += {
         e -> (((e.q.bodies.flatten collect { case x: BodyAtom => x.name })
           flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
@@ -446,6 +445,12 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${limitStr}"""
   }
 
+  def generateSQL(useAlias: Boolean) = {
+    val head = generateSQLHead(useAlias)
+    val body = cq.bodies map generateSQLBody mkString("\nUNION ALL\n")
+    s"SELECT ${head}\n${body}"
+  }
+
 }
 
 
@@ -527,9 +532,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             case MERGE => false
             case _     => if (tmpCq.head.name.startsWith("dd_new_")) false else true
           }
-          inputQueries += s"""
-            SELECT ${qc.generateSQLHead(useAlias)}
-            ${ qc.generateSQLBody(cqBody) }"""
+          inputQueries += qc.generateSQL(useAlias)
         }
       }
     }
@@ -552,7 +555,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" ${sqlCmdForCleanUp}
-        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString(" UNION ALL ")}
+        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString("\nUNION ALL\n")}
         \"\"\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
@@ -568,7 +571,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       SELECT * FROM ${stmt.input}
       """
 
-      val function = ss.resolveFunctionName(stmt.function)
+      val function = ss.resolveFunctionName(stmt.input.head.name)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
           s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
@@ -576,13 +579,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       })
 
       if (udfDetails.isEmpty)
-        ss.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
+        ss.error(s"Cannot find compilable implementation for function ${stmt.input.head.name} among:\n  "
           + (function.implementations mkString "\n  "))
 
       val blockName = ss.resolveExtractorBlockName(stmt)
       val extractor = s"""
         deepdive.extraction.extractors.${blockName} {
-          input: \"\"\" SELECT * FROM ${stmt.input}
+          input: \"\"\" ${new QueryCompiler(stmt.input, ss).generateSQL(true)}
           \"\"\"
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
@@ -781,9 +784,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
     val body = new ListBuffer[String]()
     body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
-    state.extractionRuleGroupByHead    foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
-    state.functionCallRuleGroupByInput foreach {keyVal => body ++= compileFunctionCallRules(keyVal._2, state)}
-    state.inferenceRuleGroupByHead     foreach {keyVal => body ++= compileInferenceRules(keyVal._2, state)}
+    state.extractionRuleGroupByHead foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
+    state.functionCallList          foreach {func   => body ++= compileFunctionCallRules(List(func), state)}
+    state.inferenceRuleGroupByHead  foreach {keyVal => body ++= compileInferenceRules(keyVal._2, state)}
 
     // compile the program into blocks of application.conf
     val blocks = (
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 3358f61fd..4df275213 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -30,7 +30,11 @@ object DeepDiveLogDeltaDeriver{
         name = deltaPrefix + cq.head.name
       )
     }
+    val incCqBodies = transformBody(cq, incCqHead.name, mode)
+    cq.copy(head = incCqHead, bodies = incCqBodies)
+  }
 
+  def transformBody(cq: ConjunctiveQuery, incCqHead: String, mode: Option[String]) : List[List[Body]] = {
     var incCqBodies = new ListBuffer[List[Body]]()
     // New incremental bodies
     cq.bodies foreach { bodies =>
@@ -56,7 +60,7 @@ object DeepDiveLogDeltaDeriver{
 
       var i = 0
       var j = 0
-      var index = if (incrementalFunctionInput contains incCqHead.name) -1 else 0
+      var index = if (incrementalFunctionInput contains incCqHead) -1 else 0
       if (mode == Some("inc")) {
         incCqBodies += incNewBody
       } else {
@@ -75,7 +79,7 @@ object DeepDiveLogDeltaDeriver{
         }
       }
     }
-    cq.copy(head = incCqHead, bodies = incCqBodies.toList)
+    incCqBodies.toList
   }
 
   // Incremental scheme declaration,
@@ -142,7 +146,8 @@ object DeepDiveLogDeltaDeriver{
   // Incremental function call rule,
   // modify function input and output
   def transform(stmt: FunctionCallRule): List[Statement] = {
-    List(FunctionCallRule(deltaPrefix + stmt.input, deltaPrefix + stmt.output, stmt.function))
+    List(FunctionCallRule(stmt.input.copy(bodies = transformBody(stmt.input, "", None)),
+      deltaPrefix + stmt.output))
   }
 
   // Incremental inference rule,
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 282ff435c..5e948d47b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -97,7 +97,7 @@ case class SchemaDeclaration( a : Attribute
 case class FunctionDeclaration( functionName: String, inputType: RelationType,
   outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
 case class ExtractionRule(q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
-case class FunctionCallRule(input : String, output : String, function : String) extends Statement // Extraction rule
+case class FunctionCallRule(input : ConjunctiveQuery, output : String) extends Statement // Extraction rule
 case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: Option[String] = None) extends Statement // Weighted rule
 
 // Parser
@@ -304,9 +304,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def functionCallRule : Parser[FunctionCallRule] =
-    ( relationName ~ ":-" ~ "!" ~ functionName ~ "(" ~ relationName ~ ")" ) ^^ {
-      case (out ~ ":-" ~ _ ~ fn ~ "(" ~ in ~ ")") =>
-        FunctionCallRule(in, out, fn)
+    relationName ~ "+=" ~ conjunctiveQuery ^^ {
+      case (out ~ _ ~ cq) => FunctionCallRule(cq, out)
     }
 
   def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index b5764a64c..7dc7f80ae 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -155,8 +155,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: FunctionCallRule): String = {
-    s"""${stmt.output} :- !${stmt.function}(${stmt.input}).
-       |""".stripMargin
+    s"${stmt.output} += ${print(stmt.input)}.\n"
   }
 
   def print(stmt: InferenceRule): String = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 2a45e50d1..864fa81eb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -22,7 +22,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       case f: FunctionDeclaration => {
         functionDeclaration += { f.functionName -> f }
       }
-      case FunctionCallRule(input, output, function) => {
+      case FunctionCallRule(input, output) => {
         heads += output
       }
     }
@@ -59,7 +59,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach check
       case s: InferenceRule => s.q.bodies foreach check
-      case s: FunctionCallRule => checkRelation(BodyAtom(s.input, Nil))
+      case s: FunctionCallRule => s.input.bodies foreach check
       case _ =>
     }
   }
@@ -68,8 +68,8 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkFunctionDefined(stmt: Statement) {
     stmt match {
       case s: FunctionCallRule => {
-        if (!(functionDeclaration.keySet contains s.function))
-          error(stmt, s"""function "${s.function}" is not defined""")
+        if (!(functionDeclaration.keySet contains s.input.head.name))
+          error(stmt, s"""function "${s.input.head.name}" is not defined""")
       }
       case _ =>
     }
diff --git a/test/compile-error-test/undefined_function/compile-error.expected b/test/compile-error-test/undefined_function/compile-error.expected
index 90ffa0742..f30362ca4 100644
--- a/test/compile-error-test/undefined_function/compile-error.expected
+++ b/test/compile-error-test/undefined_function/compile-error.expected
@@ -1,3 +1,4 @@
 [error] function "ext" is not defined
-Q :- !ext(a).
-    
+Q += ext(x)  :-
+    a(x).
+
diff --git a/test/compile-error-test/undefined_function/input.ddl b/test/compile-error-test/undefined_function/input.ddl
index 27a2a045a..0d805016f 100644
--- a/test/compile-error-test/undefined_function/input.ddl
+++ b/test/compile-error-test/undefined_function/input.ddl
@@ -2,4 +2,4 @@ a(k int).
 b(k int, p text, q text, r int).
 c(s text, n int, t text).
 
-Q :- !ext(a).
\ No newline at end of file
+Q += ext(x) :- a(x).
\ No newline at end of file
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 8432494ed..8ba11e63d 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -69,19 +69,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_6 {
-        sql: """ DROP VIEW IF EXISTS ext_features_input;
-        CREATE VIEW ext_features_input AS 
-            SELECT R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
-            FROM words R0, words R1
-        WHERE R1.sent_id = R0.sent_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_5" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_9 {
+      deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ 
         INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
           FROM words R0
@@ -93,23 +81,27 @@
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_8 {
-          input: """ SELECT * FROM ext_features_input
+        deepdive.extraction.extractors.extraction_rule_5 {
+          input: """ SELECT R0.word_id AS "words_raw.R0.word_id" , R0.word AS "words_raw.R0.word" , R0.pos AS "words_raw.R0.pos" , R0.tag AS "words_raw.R0.tag" 
+FROM words_raw R0
+        
           """
-          output_relation: "word_features"
-          udf: ${APP_HOME}"/udf/ext_features.py"
+          output_relation: "words"
+          udf: ${APP_HOME}"/udf/ext_training.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_6" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_5 {
-          input: """ SELECT * FROM words_raw
+        deepdive.extraction.extractors.extraction_rule_7 {
+          input: """ SELECT R0.word_id AS "words.R0.word_id" , R0.word AS "words.R0.word" , R0.pos AS "words.R0.pos" , R1.word AS "words.R1.word" , R1.pos AS "words.R1.pos" 
+FROM words R0, words R1
+        WHERE R1.sent_id = R0.sent_id 
           """
-          output_relation: "words"
-          udf: ${APP_HOME}"/udf/ext_training.py"
+          output_relation: "word_features"
+          udf: ${APP_HOME}"/udf/ext_features.py"
           style: "tsv_extractor" 
-          
+          dependencies: [ "extraction_rule_5" ]
         }
       
 
@@ -124,7 +116,7 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_0, extraction_rule_1, extraction_rule_3, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_6, extraction_rule_9, extraction_rule_5, extraction_rule_8]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_8, extraction_rule_5, extraction_rule_7]
 deepdive.pipeline.pipelines.inference: [tag_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_6, extraction_rule_9, extraction_rule_5, extraction_rule_8, tag_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_8, extraction_rule_5, extraction_rule_7, tag_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index c6830afe5..50766e57a 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -57,9 +57,8 @@
 
       deepdive.extraction.extractors.extraction_rule_9 {
         sql: """ DROP VIEW IF EXISTS E;
-        CREATE VIEW E AS 
-            SELECT (R0.k :: INT) AS "column_0" 
-            FROM b R0
+        CREATE VIEW E AS SELECT (R0.k :: INT) AS "column_0" 
+FROM b R0
         
         """
         style: "sql_extractor"
@@ -69,9 +68,8 @@
 
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS X;
-        CREATE VIEW X AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0, c R1
+        CREATE VIEW X AS SELECT R0.k AS "b.R0.k" 
+FROM b R0, c R1
         WHERE R1.n = R0.k 
         """
         style: "sql_extractor"
@@ -81,9 +79,8 @@
 
       deepdive.extraction.extractors.extraction_rule_18 {
         sql: """ DROP VIEW IF EXISTS N;
-        CREATE VIEW N AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW N AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
         """
         style: "sql_extractor"
@@ -93,9 +90,8 @@
 
       deepdive.extraction.extractors.extraction_rule_21 {
         sql: """ DROP VIEW IF EXISTS T;
-        CREATE VIEW T AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
+        CREATE VIEW T AS SELECT R0.k AS "b.R0.k" 
+FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         WHERE R1_0.s > R0.p
         """
         style: "sql_extractor"
@@ -105,9 +101,8 @@
 
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
-        CREATE VIEW J AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW J AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
         """
         style: "sql_extractor"
@@ -117,9 +112,8 @@
 
       deepdive.extraction.extractors.extraction_rule_22 {
         sql: """ DROP VIEW IF EXISTS U;
-        CREATE VIEW U AS 
-            SELECT R0_0.k AS "b.R0_0.k" 
-            FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
+        CREATE VIEW U AS SELECT R0_0.k AS "b.R0_0.k" 
+FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
         
         """
         style: "sql_extractor"
@@ -129,9 +123,8 @@
 
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS F;
-        CREATE VIEW F AS 
-            SELECT ((R0.k :: INT) + (R0.r :: INT)) AS "column_0" 
-            FROM b R0
+        CREATE VIEW F AS SELECT ((R0.k :: INT) + (R0.r :: INT)) AS "column_0" 
+FROM b R0
         
         """
         style: "sql_extractor"
@@ -141,9 +134,8 @@
 
       deepdive.extraction.extractors.extraction_rule_5 {
         sql: """ DROP VIEW IF EXISTS A;
-        CREATE VIEW A AS 
-            SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS "column_0" 
-            FROM b R0
+        CREATE VIEW A AS SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS "column_0" 
+FROM b R0
         
         """
         style: "sql_extractor"
@@ -153,9 +145,8 @@
 
       deepdive.extraction.extractors.extraction_rule_17 {
         sql: """ DROP VIEW IF EXISTS M;
-        CREATE VIEW M AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW M AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
         """
         style: "sql_extractor"
@@ -165,9 +156,8 @@
 
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS I;
-        CREATE VIEW I AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW I AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
         """
         style: "sql_extractor"
@@ -177,9 +167,8 @@
 
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ DROP VIEW IF EXISTS G;
-        CREATE VIEW G AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW G AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE (R0.k + R0.r) = 100
         """
         style: "sql_extractor"
@@ -189,9 +178,8 @@
 
       deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ DROP VIEW IF EXISTS V;
-        CREATE VIEW V AS 
-            SELECT R0.n AS "c.R0.n" 
-            FROM c R0, a R1
+        CREATE VIEW V AS SELECT R0.n AS "c.R0.n" 
+FROM c R0, a R1
         WHERE R1.k = R0.n 
         """
         style: "sql_extractor"
@@ -201,9 +189,8 @@
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
-        CREATE VIEW Q AS 
-            SELECT DISTINCT ('test' :: TEXT) AS "column_0" , 123 AS "column_1" , R0.k AS "a.R0.k" , unnest(R1.q) AS "column_3" 
-            FROM a R0, b R1, c R2
+        CREATE VIEW Q AS SELECT DISTINCT ('test' :: TEXT) AS "column_0" , 123 AS "column_1" , R0.k AS "a.R0.k" , unnest(R1.q) AS "column_3" 
+FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
         """
         style: "sql_extractor"
@@ -213,9 +200,8 @@
 
       deepdive.extraction.extractors.extraction_rule_16 {
         sql: """ DROP VIEW IF EXISTS L;
-        CREATE VIEW L AS 
-            SELECT DISTINCT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW L AS SELECT DISTINCT R0.k AS "b.R0.k" 
+FROM b R0
         LIMIT 100
         """
         style: "sql_extractor"
@@ -225,9 +211,8 @@
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS B;
-        CREATE VIEW B AS 
-            SELECT func((R0.k + (R0.r + R0.k))) AS "column_0" 
-            FROM b R0
+        CREATE VIEW B AS SELECT func((R0.k + (R0.r + R0.k))) AS "column_0" 
+FROM b R0
         
         """
         style: "sql_extractor"
@@ -237,9 +222,8 @@
 
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ DROP VIEW IF EXISTS P;
-        CREATE VIEW P AS 
-            SELECT R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS "column_2" 
-            FROM a R0, b R1
+        CREATE VIEW P AS SELECT R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS "column_2" 
+FROM a R0, b R1
         WHERE R1.k = R0.k 
         GROUP BY R1.p, R1.q
         """
@@ -250,9 +234,8 @@
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS C;
-        CREATE VIEW C AS 
-            SELECT func(func(func(R0.k))) AS "column_0" 
-            FROM b R0
+        CREATE VIEW C AS SELECT func(func(func(R0.k))) AS "column_0" 
+FROM b R0
         
         """
         style: "sql_extractor"
@@ -262,9 +245,8 @@
 
       deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ DROP VIEW IF EXISTS H;
-        CREATE VIEW H AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW H AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
         """
         style: "sql_extractor"
@@ -274,9 +256,8 @@
 
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ DROP VIEW IF EXISTS W;
-        CREATE VIEW W AS 
-            SELECT R0.k AS "a.R0.k" 
-            FROM a R0
+        CREATE VIEW W AS SELECT R0.k AS "a.R0.k" 
+FROM a R0
         WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
         """
         style: "sql_extractor"
@@ -286,9 +267,8 @@
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ DROP VIEW IF EXISTS K;
-        CREATE VIEW K AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW K AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
         """
         style: "sql_extractor"
@@ -298,9 +278,8 @@
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ DROP VIEW IF EXISTS O;
-        CREATE VIEW O AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0
+        CREATE VIEW O AS SELECT R0.k AS "b.R0.k" 
+FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
         """
         style: "sql_extractor"
@@ -310,9 +289,8 @@
 
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
-        CREATE VIEW D AS 
-            SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS "column_0" 
-            FROM b R0
+        CREATE VIEW D AS SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS "column_0" 
+FROM b R0
         
         """
         style: "sql_extractor"
@@ -322,9 +300,8 @@
 
       deepdive.extraction.extractors.extraction_rule_20 {
         sql: """ DROP VIEW IF EXISTS S;
-        CREATE VIEW S AS 
-            SELECT R0.k AS "b.R0.k" 
-            FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
+        CREATE VIEW S AS SELECT R0.k AS "b.R0.k" 
+FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
         
         """
         style: "sql_extractor"
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index e39f4f451..e9ea50a68 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -122,12 +122,12 @@ q1.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_label2;
-        INSERT INTO dd_new_label2 
-            SELECT R0.wid, R0.val
-            FROM label2 R0
-         UNION ALL 
-            SELECT R0.wid, R0.val
-            FROM dd_delta_label2 R0
+        INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
+FROM label2 R0
+        
+UNION ALL
+SELECT R0.wid, R0.val
+FROM dd_delta_label2 R0
         
         """
         style: "sql_extractor"
@@ -140,7 +140,9 @@ q1.label: Boolean
         CREATE VIEW dd_new_q1 AS SELECT DISTINCT R0.wid, id, label
           FROM q1 R0
         
-           UNION ALL SELECT DISTINCT R0.wid, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.wid, id, label
           FROM dd_delta_q1 R0
         
           
@@ -152,12 +154,12 @@ q1.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_label1;
-        INSERT INTO dd_new_label1 
-            SELECT R0.wid, R0.val
-            FROM label1 R0
-         UNION ALL 
-            SELECT R0.wid, R0.val
-            FROM dd_delta_label1 R0
+        INSERT INTO dd_new_label1 SELECT R0.wid, R0.val
+FROM label1 R0
+        
+UNION ALL
+SELECT R0.wid, R0.val
+FROM dd_delta_label1 R0
         
         """
         style: "sql_extractor"
@@ -179,12 +181,12 @@ q1.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_features;
-        INSERT INTO dd_new_features 
-            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
-            FROM features R0
-         UNION ALL 
-            SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
-            FROM dd_delta_features R0
+        INSERT INTO dd_new_features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+FROM features R0
+        
+UNION ALL
+SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+FROM dd_delta_features R0
         
         """
         style: "sql_extractor"
@@ -209,7 +211,9 @@ q1.label: Boolean
         CREATE VIEW dd_new_q2 AS SELECT DISTINCT R0.wid, id, label
           FROM q2 R0
         
-           UNION ALL SELECT DISTINCT R0.wid, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.wid, id, label
           FROM dd_delta_q2 R0
         
           
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
index a6ffd7d42..35e714156 100644
--- a/test/expected-output-test/ocr_example/compile-merge.expected
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -19,9 +19,8 @@
 
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE label2;
-        INSERT INTO label2 
-            SELECT  R0.wid, R0.val
-            FROM dd_new_label2 R0
+        INSERT INTO label2 SELECT R0.wid, R0.val
+FROM dd_new_label2 R0
         
         """
         style: "sql_extractor"
@@ -31,9 +30,8 @@
 
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE label1;
-        INSERT INTO label1 
-            SELECT  R0.wid, R0.val
-            FROM dd_new_label1 R0
+        INSERT INTO label1 SELECT R0.wid, R0.val
+FROM dd_new_label1 R0
         
         """
         style: "sql_extractor"
@@ -43,9 +41,8 @@
 
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE features;
-        INSERT INTO features 
-            SELECT  R0.id, R0.word_id, R0.feature_id, R0.feature_val
-            FROM dd_new_features R0
+        INSERT INTO features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+FROM dd_new_features R0
         
         """
         style: "sql_extractor"
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 31b12e7f5..ad309aa0a 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -150,12 +150,12 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_person_has_cancer;
-        INSERT INTO dd_new_person_has_cancer 
-            SELECT R0.person_id, R0.has_cancer
-            FROM person_has_cancer R0
-         UNION ALL 
-            SELECT R0.person_id, R0.has_cancer
-            FROM dd_delta_person_has_cancer R0
+        INSERT INTO dd_new_person_has_cancer SELECT R0.person_id, R0.has_cancer
+FROM person_has_cancer R0
+        
+UNION ALL
+SELECT R0.person_id, R0.has_cancer
+FROM dd_delta_person_has_cancer R0
         
         """
         style: "sql_extractor"
@@ -165,12 +165,12 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_person;
-        INSERT INTO dd_new_person 
-            SELECT R0.person_id, R0.name
-            FROM person R0
-         UNION ALL 
-            SELECT R0.person_id, R0.name
-            FROM dd_delta_person R0
+        INSERT INTO dd_new_person SELECT R0.person_id, R0.name
+FROM person R0
+        
+UNION ALL
+SELECT R0.person_id, R0.name
+FROM dd_delta_person R0
         
         """
         style: "sql_extractor"
@@ -183,7 +183,9 @@ dd_delta_smoke.label: Boolean
         CREATE VIEW dd_new_smoke AS SELECT DISTINCT R0.person_id, id, label
           FROM smoke R0
         
-           UNION ALL SELECT DISTINCT R0.person_id, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.person_id, id, label
           FROM dd_delta_smoke R0
         
           
@@ -210,7 +212,9 @@ dd_delta_smoke.label: Boolean
         CREATE VIEW dd_new_cancer AS SELECT DISTINCT R0.person_id, id, label
           FROM cancer R0
         
-           UNION ALL SELECT DISTINCT R0.person_id, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.person_id, id, label
           FROM dd_delta_cancer R0
         
           
@@ -222,12 +226,12 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_person_smokes;
-        INSERT INTO dd_new_person_smokes 
-            SELECT R0.person_id, R0.smokes
-            FROM person_smokes R0
-         UNION ALL 
-            SELECT R0.person_id, R0.smokes
-            FROM dd_delta_person_smokes R0
+        INSERT INTO dd_new_person_smokes SELECT R0.person_id, R0.smokes
+FROM person_smokes R0
+        
+UNION ALL
+SELECT R0.person_id, R0.smokes
+FROM dd_delta_person_smokes R0
         
         """
         style: "sql_extractor"
@@ -237,12 +241,12 @@ dd_delta_smoke.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_friends;
-        INSERT INTO dd_new_friends 
-            SELECT R0.person_id, R0.friend_id
-            FROM friends R0
-         UNION ALL 
-            SELECT R0.person_id, R0.friend_id
-            FROM dd_delta_friends R0
+        INSERT INTO dd_new_friends SELECT R0.person_id, R0.friend_id
+FROM friends R0
+        
+UNION ALL
+SELECT R0.person_id, R0.friend_id
+FROM dd_delta_friends R0
         
         """
         style: "sql_extractor"
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
index 12622b100..845c5337d 100644
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -19,9 +19,8 @@
 
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE person_smokes;
-        INSERT INTO person_smokes 
-            SELECT  R0.person_id, R0.smokes
-            FROM dd_new_person_smokes R0
+        INSERT INTO person_smokes SELECT R0.person_id, R0.smokes
+FROM dd_new_person_smokes R0
         
         """
         style: "sql_extractor"
@@ -31,9 +30,8 @@
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE friends;
-        INSERT INTO friends 
-            SELECT  R0.person_id, R0.friend_id
-            FROM dd_new_friends R0
+        INSERT INTO friends SELECT R0.person_id, R0.friend_id
+FROM dd_new_friends R0
         
         """
         style: "sql_extractor"
@@ -43,9 +41,8 @@
 
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE person_has_cancer;
-        INSERT INTO person_has_cancer 
-            SELECT  R0.person_id, R0.has_cancer
-            FROM dd_new_person_has_cancer R0
+        INSERT INTO person_has_cancer SELECT R0.person_id, R0.has_cancer
+FROM dd_new_person_has_cancer R0
         
         """
         style: "sql_extractor"
@@ -55,9 +52,8 @@
 
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE person;
-        INSERT INTO person 
-            SELECT  R0.person_id, R0.name
-            FROM dd_new_person R0
+        INSERT INTO person SELECT R0.person_id, R0.name
+FROM dd_new_person R0
         
         """
         style: "sql_extractor"
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 37a54b670..e7c1c20d1 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -168,35 +168,14 @@ dd_new_has_spouse.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_31 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
-        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
-        INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM people_mentions R0
-         UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM dd_delta_people_mentions R0
+        INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM people_mentions R0
+        
+UNION ALL
+SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
@@ -206,24 +185,12 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
-        INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text
-            FROM articles R0
-         UNION ALL 
-            SELECT R0.article_id, R0.text
-            FROM dd_delta_articles R0
+        INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
+FROM articles R0
         
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_25 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
-        CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
-            FROM dd_delta_sentences R0
+UNION ALL
+SELECT R0.article_id, R0.text
+FROM dd_delta_articles R0
         
         """
         style: "sql_extractor"
@@ -233,42 +200,42 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
-        INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM has_spouse_candidates R0
-         UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM dd_delta_has_spouse_candidates R0
+        INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM has_spouse_candidates R0
+        
+UNION ALL
+SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
-        INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature
-            FROM has_spouse_features R0
-         UNION ALL 
-            SELECT R0.relation_id, R0.feature
-            FROM dd_delta_has_spouse_features R0
+        INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
+FROM has_spouse_features R0
+        
+UNION ALL
+SELECT R0.relation_id, R0.feature
+FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_28" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
-        INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM sentences R0
-         UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM dd_delta_sentences R0
+        INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM sentences R0
+        
+UNION ALL
+SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -276,22 +243,7 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_28 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
-        CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-            FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
-            FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_33 {
+      deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
@@ -299,7 +251,7 @@ dd_new_has_spouse.label: Boolean
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
@@ -308,43 +260,63 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
-           UNION ALL SELECT DISTINCT R0.relation_id, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_33" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
         deepdive.extraction.extractors.extraction_rule_24 {
-          input: """ SELECT * FROM dd_delta_ext_people_input
+          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+FROM dd_delta_sentences R0
+        
           """
           output_relation: "dd_delta_people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_25" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_30 {
-          input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
+        deepdive.extraction.extractors.extraction_rule_26 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+FROM dd_delta_people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+UNION ALL
+FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
           """
-          output_relation: "dd_delta_has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          output_relation: "dd_delta_has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_31" ]
+          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_27 {
-          input: """ SELECT * FROM dd_delta_ext_has_spouse_input
+        deepdive.extraction.extractors.extraction_rule_28 {
+          input: """ SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
-          output_relation: "dd_delta_has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          output_relation: "dd_delta_has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
         }
       
 
@@ -362,8 +334,8 @@ dd_new_has_spouse.label: Boolean
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index a6639ef68..2f00faedb 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -98,7 +98,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
@@ -106,73 +106,43 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_7 {
-        sql: """ DROP VIEW IF EXISTS ext_people_input;
-        CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-            FROM sentences R0
-        
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_13 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
-        CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_10 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
-        CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-            FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_8" ]
       }
     
 
         deepdive.extraction.extractors.extraction_rule_6 {
-          input: """ SELECT * FROM ext_people_input
+          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+FROM sentences R0
+        
           """
           output_relation: "people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_7" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_12 {
-          input: """ SELECT * FROM ext_has_spouse_features_input
+        deepdive.extraction.extractors.extraction_rule_8 {
+          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+FROM people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
           """
-          output_relation: "has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          output_relation: "has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_13" ]
+          dependencies: [ "extraction_rule_6" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          input: """ SELECT * FROM ext_has_spouse_input
+        deepdive.extraction.extractors.extraction_rule_10 {
+          input: """ SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
-          output_relation: "has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          output_relation: "has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_10" ]
+          dependencies: [ "extraction_rule_8" ,  "extraction_rule_6" ]
         }
       
 
@@ -187,7 +157,7 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
 deepdive.pipeline.pipelines.inference: [has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6, has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, has_spouse_0]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index 632d934f0..44c7e62a3 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -19,9 +19,8 @@
 
       deepdive.extraction.extractors.extraction_rule_1 {
         sql: """ TRUNCATE sentences;
-        INSERT INTO sentences 
-            SELECT  R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM dd_new_sentences R0
+        INSERT INTO sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM dd_new_sentences R0
         
         """
         style: "sql_extractor"
@@ -31,9 +30,8 @@
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE has_spouse_candidates;
-        INSERT INTO has_spouse_candidates 
-            SELECT  R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM dd_new_has_spouse_candidates R0
+        INSERT INTO has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM dd_new_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
@@ -43,9 +41,8 @@
 
       deepdive.extraction.extractors.extraction_rule_0 {
         sql: """ TRUNCATE articles;
-        INSERT INTO articles 
-            SELECT  R0.article_id, R0.text
-            FROM dd_new_articles R0
+        INSERT INTO articles SELECT R0.article_id, R0.text
+FROM dd_new_articles R0
         
         """
         style: "sql_extractor"
@@ -55,9 +52,8 @@
 
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ TRUNCATE has_spouse_features;
-        INSERT INTO has_spouse_features 
-            SELECT  R0.relation_id, R0.feature
-            FROM dd_new_has_spouse_features R0
+        INSERT INTO has_spouse_features SELECT R0.relation_id, R0.feature
+FROM dd_new_has_spouse_features R0
         
         """
         style: "sql_extractor"
@@ -67,9 +63,8 @@
 
       deepdive.extraction.extractors.extraction_rule_2 {
         sql: """ TRUNCATE people_mentions;
-        INSERT INTO people_mentions 
-            SELECT  R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM dd_new_people_mentions R0
+        INSERT INTO people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM dd_new_people_mentions R0
         
         """
         style: "sql_extractor"
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 043956e93..ba5983cbc 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -98,7 +98,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
@@ -106,73 +106,43 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_7 {
-        sql: """ DROP VIEW IF EXISTS ext_people_input;
-        CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-            FROM sentences R0
-        
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_13 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
-        CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_10 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
-        CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-            FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_8" ]
       }
     
 
         deepdive.extraction.extractors.extraction_rule_6 {
-          input: """ SELECT * FROM ext_people_input
+          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+FROM sentences R0
+        
           """
           output_relation: "people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_7" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_12 {
-          input: """ SELECT * FROM ext_has_spouse_features_input
+        deepdive.extraction.extractors.extraction_rule_8 {
+          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+FROM people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
           """
-          output_relation: "has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          output_relation: "has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_13" ]
+          dependencies: [ "extraction_rule_6" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          input: """ SELECT * FROM ext_has_spouse_input
+        deepdive.extraction.extractors.extraction_rule_10 {
+          input: """ SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
-          output_relation: "has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          output_relation: "has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_10" ]
+          dependencies: [ "extraction_rule_8" ,  "extraction_rule_6" ]
         }
       
 
@@ -187,7 +157,7 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
 deepdive.pipeline.pipelines.inference: [has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6, has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 911992840..cdd9a95e4 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -115,9 +115,7 @@ dd_new_has_spouse(relation_id)  :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
-
-dd_delta_ext_people_input(s, words, ner_tags)  :-
+dd_delta_people_mentions += ext_people(s, words, ner_tags)  :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -126,9 +124,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
-
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -140,9 +136,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
+dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 0d917ad52..ed7cc5b88 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -29,9 +29,7 @@ has_spouse_features(relation_id text,
 
 has_spouse?(relation_id text).
 
-people_mentions :- !ext_people(ext_people_input).
-
-ext_people_input(s, words, ner_tags)  :-
+people_mentions += ext_people(s, words, ner_tags)  :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -40,9 +38,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
+has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
@@ -52,9 +48,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
+has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 1b71dab25..03ca349fd 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -168,35 +168,14 @@ dd_new_has_spouse.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_31 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
-        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
-        INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM people_mentions R0
-         UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM dd_delta_people_mentions R0
+        INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM people_mentions R0
+        
+UNION ALL
+SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
@@ -206,27 +185,12 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
-        INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text
-            FROM articles R0
-         UNION ALL 
-            SELECT R0.article_id, R0.text
-            FROM dd_delta_articles R0
+        INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
+FROM articles R0
         
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_25 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
-        CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-            FROM sentences R0
-         UNION ALL 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
-            FROM dd_delta_sentences R0
+UNION ALL
+SELECT R0.article_id, R0.text
+FROM dd_delta_articles R0
         
         """
         style: "sql_extractor"
@@ -236,42 +200,42 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
-        INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM has_spouse_candidates R0
-         UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM dd_delta_has_spouse_candidates R0
+        INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM has_spouse_candidates R0
+        
+UNION ALL
+SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
-        INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature
-            FROM has_spouse_features R0
-         UNION ALL 
-            SELECT R0.relation_id, R0.feature
-            FROM dd_delta_has_spouse_features R0
+        INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
+FROM has_spouse_features R0
+        
+UNION ALL
+SELECT R0.relation_id, R0.feature
+FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_28" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
-        INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM sentences R0
-         UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM dd_delta_sentences R0
+        INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM sentences R0
+        
+UNION ALL
+SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -279,22 +243,7 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_28 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
-        CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-            FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
-            FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_33 {
+      deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
@@ -302,7 +251,7 @@ dd_new_has_spouse.label: Boolean
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
@@ -311,43 +260,63 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
-           UNION ALL SELECT DISTINCT R0.relation_id, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_33" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
         deepdive.extraction.extractors.extraction_rule_24 {
-          input: """ SELECT * FROM dd_delta_ext_people_input
+          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+FROM dd_delta_sentences R0
+        
           """
           output_relation: "dd_delta_people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_25" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_30 {
-          input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
+        deepdive.extraction.extractors.extraction_rule_26 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+FROM dd_delta_people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+UNION ALL
+FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
           """
-          output_relation: "dd_delta_has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          output_relation: "dd_delta_has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_31" ]
+          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_27 {
-          input: """ SELECT * FROM dd_delta_ext_has_spouse_input
+        deepdive.extraction.extractors.extraction_rule_28 {
+          input: """ SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
-          output_relation: "dd_delta_has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          output_relation: "dd_delta_has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
         }
       
 
@@ -365,8 +334,8 @@ dd_new_has_spouse.label: Boolean
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 6bb6bf573..c924ede8d 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -34,10 +34,8 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-people_mentions :-
-  !ext_people(ext_people_input).
-
-ext_people_input(s, words, ner_tags) :-
+people_mentions +=
+  ext_people(s, words, ner_tags) :-
   sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 @mode(inc)
@@ -45,10 +43,8 @@ function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates :-
-  !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+has_spouse_candidates +=
+  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, a, b, p1_text, p1_id),
   people_mentions(s, c, d, p2_text, p2_id).
 
@@ -56,15 +52,13 @@ function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
-has_spouse_features :-
-  !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+has_spouse_features +=
+  ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
   has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
-  
+
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 90edb04ff..edb1888da 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -115,10 +115,7 @@ dd_new_has_spouse(relation_id)  :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
-
-dd_delta_ext_people_input(s, words, ner_tags)  :-
-    sentences(a, b, words, c, d, e, ner_tags, f, s);
+dd_delta_people_mentions += ext_people(s, words, ner_tags)  :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 @mode(inc)
@@ -128,9 +125,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
-
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -142,9 +137,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
+dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 2b325dea6..acd0fe36b 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -168,35 +168,14 @@ dd_new_has_spouse.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_31 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_features_input;
-        CREATE VIEW dd_delta_ext_has_spouse_features_input AS 
-            SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_delta_has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_delta_people_mentions.R2.start_position" , R2.length AS "dd_delta_people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id  UNION ALL 
-            SELECT R0.words AS "dd_new_sentences.R0.words" , R1.relation_id AS "dd_new_has_spouse_candidates.R1.relation_id" , R2.start_position AS "dd_new_people_mentions.R2.start_position" , R2.length AS "dd_new_people_mentions.R2.length" , R3.start_position AS "dd_delta_people_mentions.R3.start_position" , R3.length AS "dd_delta_people_mentions.R3.length" 
-            FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
-      }
-    
-
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ TRUNCATE dd_new_people_mentions;
-        INSERT INTO dd_new_people_mentions 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM people_mentions R0
-         UNION ALL 
-            SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-            FROM dd_delta_people_mentions R0
+        INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM people_mentions R0
+        
+UNION ALL
+SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
@@ -206,24 +185,12 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ TRUNCATE dd_new_articles;
-        INSERT INTO dd_new_articles 
-            SELECT R0.article_id, R0.text
-            FROM articles R0
-         UNION ALL 
-            SELECT R0.article_id, R0.text
-            FROM dd_delta_articles R0
+        INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
+FROM articles R0
         
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_25 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_people_input;
-        CREATE VIEW dd_delta_ext_people_input AS 
-            SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
-            FROM dd_delta_sentences R0
+UNION ALL
+SELECT R0.article_id, R0.text
+FROM dd_delta_articles R0
         
         """
         style: "sql_extractor"
@@ -233,42 +200,42 @@ dd_new_has_spouse.label: Boolean
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
-        INSERT INTO dd_new_has_spouse_candidates 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM has_spouse_candidates R0
-         UNION ALL 
-            SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-            FROM dd_delta_has_spouse_candidates R0
+        INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM has_spouse_candidates R0
+        
+UNION ALL
+SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ TRUNCATE dd_new_has_spouse_features;
-        INSERT INTO dd_new_has_spouse_features 
-            SELECT R0.relation_id, R0.feature
-            FROM has_spouse_features R0
-         UNION ALL 
-            SELECT R0.relation_id, R0.feature
-            FROM dd_delta_has_spouse_features R0
+        INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
+FROM has_spouse_features R0
+        
+UNION ALL
+SELECT R0.relation_id, R0.feature
+FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "extraction_rule_28" ]
       }
     
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ TRUNCATE dd_new_sentences;
-        INSERT INTO dd_new_sentences 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM sentences R0
-         UNION ALL 
-            SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-            FROM dd_delta_sentences R0
+        INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM sentences R0
+        
+UNION ALL
+SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+FROM dd_delta_sentences R0
         
         """
         style: "sql_extractor"
@@ -276,22 +243,7 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_28 {
-        sql: """ DROP VIEW IF EXISTS dd_delta_ext_has_spouse_input;
-        CREATE VIEW dd_delta_ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-            FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id  UNION ALL 
-            SELECT R0.sentence_id AS "dd_new_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_new_people_mentions.R0.mention_id" , R0.text AS "dd_new_people_mentions.R0.text" , R1.mention_id AS "dd_delta_people_mentions.R1.mention_id" , R1.text AS "dd_delta_people_mentions.R1.text" 
-            FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_33 {
+      deepdive.extraction.extractors.extraction_rule_30 {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
@@ -299,7 +251,7 @@ dd_new_has_spouse.label: Boolean
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "extraction_rule_26" ]
       }
     
 
@@ -308,43 +260,63 @@ dd_new_has_spouse.label: Boolean
         CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
-           UNION ALL SELECT DISTINCT R0.relation_id, id, label
+          
+UNION ALL
+SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_33" ]
+          dependencies: [ "extraction_rule_30" ]
       }
     
 
         deepdive.extraction.extractors.extraction_rule_24 {
-          input: """ SELECT * FROM dd_delta_ext_people_input
+          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+FROM dd_delta_sentences R0
+        
           """
           output_relation: "dd_delta_people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_25" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_30 {
-          input: """ SELECT * FROM dd_delta_ext_has_spouse_features_input
+        deepdive.extraction.extractors.extraction_rule_26 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+FROM dd_delta_people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
+UNION ALL
+FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
           """
-          output_relation: "dd_delta_has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          output_relation: "dd_delta_has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_31" ]
+          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_27 {
-          input: """ SELECT * FROM dd_delta_ext_has_spouse_input
+        deepdive.extraction.extractors.extraction_rule_28 {
+          input: """ SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
-          output_relation: "dd_delta_has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          output_relation: "dd_delta_has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
         }
       
 
@@ -372,8 +344,8 @@ dd_new_has_spouse.label: Boolean
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
 deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0, dd_new_has_spouse_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_25, extraction_rule_31, extraction_rule_19, extraction_rule_3, extraction_rule_33, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0, dd_new_has_spouse_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0, dd_new_has_spouse_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 2bfe86d43..362edf96c 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -98,7 +98,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
@@ -106,73 +106,43 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_7 {
-        sql: """ DROP VIEW IF EXISTS ext_people_input;
-        CREATE VIEW ext_people_input AS 
-            SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
-            FROM sentences R0
-        
-        """
-        style: "sql_extractor"
-          
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_13 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_features_input;
-        CREATE VIEW ext_has_spouse_features_input AS 
-            SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
-            FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ,  "extraction_rule_6" ]
-      }
-    
-
-      deepdive.extraction.extractors.extraction_rule_10 {
-        sql: """ DROP VIEW IF EXISTS ext_has_spouse_input;
-        CREATE VIEW ext_has_spouse_input AS 
-            SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
-            FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        """
-        style: "sql_extractor"
-          dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_8" ]
       }
     
 
         deepdive.extraction.extractors.extraction_rule_6 {
-          input: """ SELECT * FROM ext_people_input
+          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+FROM sentences R0
+        
           """
           output_relation: "people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_7" ]
+          
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_12 {
-          input: """ SELECT * FROM ext_has_spouse_features_input
+        deepdive.extraction.extractors.extraction_rule_8 {
+          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+FROM people_mentions R0, people_mentions R1
+        WHERE R1.sentence_id = R0.sentence_id 
           """
-          output_relation: "has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
+          output_relation: "has_spouse_candidates"
+          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_13" ]
+          dependencies: [ "extraction_rule_6" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_9 {
-          input: """ SELECT * FROM ext_has_spouse_input
+        deepdive.extraction.extractors.extraction_rule_10 {
+          input: """ SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
-          output_relation: "has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
+          output_relation: "has_spouse_features"
+          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_10" ]
+          dependencies: [ "extraction_rule_8" ,  "extraction_rule_6" ]
         }
       
 
@@ -197,7 +167,7 @@
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
 deepdive.pipeline.pipelines.inference: [has_spouse_0, has_spouse_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_12, extraction_rule_10, extraction_rule_13, extraction_rule_9, extraction_rule_15, extraction_rule_6, has_spouse_0, has_spouse_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, has_spouse_0, has_spouse_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 34861fe2e..953fcad60 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -34,20 +34,16 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-people_mentions :-
-  !ext_people(ext_people_input).
-
-ext_people_input(s, words, ner_tags) :-
+people_mentions +=
+  ext_people(s, words, ner_tags) :-
   sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates :-
-  !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text) :-
+has_spouse_candidates +=
+  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
   people_mentions(s, a, b, p1_text, p1_id),
   people_mentions(s, c, d, p2_text, p2_id).
 
@@ -55,15 +51,13 @@ function ext_has_spouse over like ext_has_spouse_input
                      returns like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
-has_spouse_features :-
-  !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len) :-
+has_spouse_features +=
+  ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
   sentences(a, b, words, c, d, e, f, g, s),
   has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
   people_mentions(s, p1idx, p1len, k, person1_id),
   people_mentions(s, p2idx, p2len, l, person2_id).
-  
+
 function ext_has_spouse_features over like ext_has_spouse_features_input
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 9fc97fa19..95c66b074 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -115,9 +115,7 @@ dd_new_has_spouse(relation_id)  :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions :- !ext_people(dd_delta_ext_people_input).
-
-dd_delta_ext_people_input(s, words, ner_tags)  :-
+dd_delta_people_mentions += ext_people(s, words, ner_tags)  :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -126,9 +124,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates :- !ext_has_spouse(dd_delta_ext_has_spouse_input).
-
-dd_delta_ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -140,9 +136,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features :- !ext_has_spouse_features(dd_delta_ext_has_spouse_features_input).
-
-dd_delta_ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
+dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index c60344ef2..de36f3582 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -29,9 +29,7 @@ has_spouse_features(relation_id text,
 
 has_spouse?(relation_id text).
 
-people_mentions :- !ext_people(ext_people_input).
-
-ext_people_input(s, words, ner_tags)  :-
+people_mentions += ext_people(s, words, ner_tags)  :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -40,9 +38,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates :- !ext_has_spouse(ext_has_spouse_input).
-
-ext_has_spouse_input(s, p1_id, p1_text, p2_id, p2_text)  :-
+has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
@@ -52,9 +48,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-has_spouse_features :- !ext_has_spouse_features(ext_has_spouse_features_input).
-
-ext_has_spouse_features_input(words, rid, p1idx, p1len, p2idx, p2len)  :-
+has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),

From 63b1c82214d97cf9acdc8f9ae86254fd1c224260 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 27 Jul 2015 01:25:31 -0700
Subject: [PATCH 198/347] Refactor collect variables in semantic checking

---
 .../deepdive/ddlog/DeepDiveLogParser.scala    |   4 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   2 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 105 ++++++------------
 3 files changed, 40 insertions(+), 71 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 1d5c61687..1aa34d388 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -187,8 +187,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "(" ~> expr <~ ")"
     )
 
-  def cqHead = relationName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
-    case (r ~ _ ~ expressions ~ _) => HeadAtom(r, expressions)
+  def cqHead = relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
+    case (r ~ expressions) => HeadAtom(r, expressions)
   }
 
   // conditional expressions
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 88161311f..4797b92ed 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -162,7 +162,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(stmt: InferenceRule): String = {
     print(stmt.q) +
-    ( "\n  weight = " + (stmt.weights.variables.map(print).mkString(", "))
+    ( "\n  weight = " + (stmt.weights.variables map print mkString(", "))
     ) +
     ( stmt.function map { "\n  function = " + _ } getOrElse("")
     ) + ".\n"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 2a45e50d1..f00aaad64 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -150,89 +150,58 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   // collect variables used in the expression
-  def collectVariables(expr: Expr) : Set[String] = {
-    var set = new HashSet[String]()
-    def collectVariablesInner(e: Expr) : Unit = e match {
-      case VarExpr(name) => set += name
-      case FuncExpr(function, args, agg) => args foreach (collectVariablesInner(_))
-      case BinaryOpExpr(lhs, op, rhs) => {
-        collectVariablesInner(lhs)
-        collectVariablesInner(rhs)
-      }
-      case TypecastExpr(lhs, rhs) => collectVariablesInner(lhs)
-      case _ =>
-    }
-    collectVariablesInner(expr)
-    set
+  def collectVars(expr: Expr) : Set[String] = expr match {
+    case VarExpr(name) => Set(name)
+    case FuncExpr(function, args, agg) => args flatMap collectVars toSet
+    case BinaryOpExpr(lhs, op, rhs) => collectVars(lhs) ++ collectVars(rhs)
+    case TypecastExpr(lhs, rhs) => collectVars(lhs)
+    case _ => Set()
   }
 
-  def collectVariables(pattern: Pattern, definitionOnly: Boolean) : Set[String] = {
-    var set = new HashSet[String]()
-    pattern match {
-      case VarPattern(name) => set += name
-      case ExprPattern(e) => if (!definitionOnly) set ++= collectVariables(e)
-      case PlaceholderPattern() =>
-    }
-    set
+  def collectUsedVars(pattern: Pattern) : Set[String] = pattern match {
+    case VarPattern(name) => Set(name)
+    case ExprPattern(e) => collectVars(e)
+    case PlaceholderPattern() => Set()
   }
 
-  def collectVariables(cond: Cond) : Set[String] = {
-    var set = new HashSet[String]()
-    cond match {
-      case ComparisonCond(lhs, op, rhs) => {
-        set ++= collectVariables(lhs)
-        set ++= collectVariables(rhs)
-      }
-      case CompoundCond(lhs, op, rhs) => {
-        set ++= collectVariables(lhs)
-        set ++= collectVariables(rhs)
-      }
-      case NegationCond(c) => set ++= collectVariables(c)
-    }
-    set
+  def collectDefinedVars(pattern: Pattern) : Set[String] = pattern match {
+    case VarPattern(name) => Set(name)
+    case _ => Set()
   }
 
-  // collect variable
-  def collectVariablesFromBody(body: Body, definitionOnly: Boolean) : Set[String] = {
-    var set = new HashSet[String]()
-    body match {
-      case a: BodyAtom => a.terms.foreach { x =>
-        set ++= collectVariables(x, definitionOnly)
-      }
-      case a: QuantifiedBody => a.bodies.foreach {
-        x => set ++= collectVariablesFromBody(x, definitionOnly)
-      }
-      case a: Cond => if (!definitionOnly) set ++= collectVariables(a)
-    }
-    set
+  def collectVars(cond: Cond) : Set[String] = cond match {
+    case ComparisonCond(lhs, op, rhs) => collectVars(lhs) ++ collectVars(rhs)
+    case CompoundCond(lhs, op, rhs)   => collectVars(lhs) ++ collectVars(rhs)
+    case NegationCond(c)              => collectVars(c)
+  }
+
+  def collectUsedVars(body: Body) : Set[String] = body match {
+    case a: BodyAtom => a.terms flatMap collectUsedVars toSet
+    case a: QuantifiedBody => a.bodies flatMap collectUsedVars toSet
+    case a: Cond => collectVars(a)
+  }
+
+  def collectDefinedVars(body: Body) : Set[String] = body match {
+    case a: BodyAtom => a.terms flatMap collectDefinedVars toSet
+    case a: QuantifiedBody => a.bodies flatMap collectDefinedVars toSet
+    case a: Cond => Set()
   }
 
   // check if variables have bindings in the body
   def checkVariableBindings(stmt: Statement) {
     // check variable bindings in a conjunctive query
-    def checkCq(cq: ConjunctiveQuery, additionalVars: Set[String] = Set()) {
+    def checkCq(cq: ConjunctiveQuery, additionalUsedVars: Set[String] = Set()) {
       // collect variable definitions and usages
-      var varDefSet = new HashSet[String]()
-      var varUseSet = new HashSet[String]()
-      cq.bodies.foreach { case x =>
-        x.foreach { case a =>
-          varDefSet ++= collectVariablesFromBody(a, true)
-          varUseSet ++= collectVariablesFromBody(a, false)
-        }
-      }
-      cq.head.terms.foreach  { x => varUseSet ++= collectVariables(x) }
-      varUseSet ++= additionalVars
-      varUseSet.foreach { x =>
-        if (!varDefSet.contains(x)) error(stmt, s"Variable ${x} does not have bindings")
-      }
+      var varDefs = cq.bodies flatMap (_ flatMap collectDefinedVars) toSet
+      val varUses = (cq.bodies flatMap (_ flatMap collectUsedVars) toSet) ++
+        (cq.head.terms flatMap collectVars) ++
+        (additionalUsedVars)
+      val varUndefined = varUses -- varDefs
+      varUndefined foreach { x => error(stmt, s"Variable ${x} does not have bindings") }
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
-      case s: InferenceRule  => {
-        var set = new HashSet[String]()
-        s.weights.variables.foreach { set ++= collectVariables(_) }
-        checkCq(s.q, set)
-      }
+      case s: InferenceRule  => checkCq(s.q, (s.weights.variables flatMap collectVars toSet))
       case _ =>
     }
   }

From 25055fde099b9eb41d38d581962eb4b88b2ddf4d Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 27 Jul 2015 10:38:25 -0700
Subject: [PATCH 199/347] Minor update

---
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index f00aaad64..2427b6b12 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -150,17 +150,17 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   // collect variables used in the expression
-  def collectVars(expr: Expr) : Set[String] = expr match {
+  def collectUsedVars(expr: Expr) : Set[String] = expr match {
     case VarExpr(name) => Set(name)
-    case FuncExpr(function, args, agg) => args flatMap collectVars toSet
-    case BinaryOpExpr(lhs, op, rhs) => collectVars(lhs) ++ collectVars(rhs)
-    case TypecastExpr(lhs, rhs) => collectVars(lhs)
+    case FuncExpr(function, args, agg) => args flatMap collectUsedVars toSet
+    case BinaryOpExpr(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
+    case TypecastExpr(lhs, rhs) => collectUsedVars(lhs)
     case _ => Set()
   }
 
   def collectUsedVars(pattern: Pattern) : Set[String] = pattern match {
     case VarPattern(name) => Set(name)
-    case ExprPattern(e) => collectVars(e)
+    case ExprPattern(e) => collectUsedVars(e)
     case PlaceholderPattern() => Set()
   }
 
@@ -169,16 +169,16 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     case _ => Set()
   }
 
-  def collectVars(cond: Cond) : Set[String] = cond match {
-    case ComparisonCond(lhs, op, rhs) => collectVars(lhs) ++ collectVars(rhs)
-    case CompoundCond(lhs, op, rhs)   => collectVars(lhs) ++ collectVars(rhs)
-    case NegationCond(c)              => collectVars(c)
+  def collectUsedVars(cond: Cond) : Set[String] = cond match {
+    case ComparisonCond(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
+    case CompoundCond(lhs, op, rhs)   => collectUsedVars(lhs) ++ collectUsedVars(rhs)
+    case NegationCond(c)              => collectUsedVars(c)
   }
 
   def collectUsedVars(body: Body) : Set[String] = body match {
     case a: BodyAtom => a.terms flatMap collectUsedVars toSet
     case a: QuantifiedBody => a.bodies flatMap collectUsedVars toSet
-    case a: Cond => collectVars(a)
+    case a: Cond => collectUsedVars(a)
   }
 
   def collectDefinedVars(body: Body) : Set[String] = body match {
@@ -194,14 +194,14 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       // collect variable definitions and usages
       var varDefs = cq.bodies flatMap (_ flatMap collectDefinedVars) toSet
       val varUses = (cq.bodies flatMap (_ flatMap collectUsedVars) toSet) ++
-        (cq.head.terms flatMap collectVars) ++
+        (cq.head.terms flatMap collectUsedVars) ++
         (additionalUsedVars)
       val varUndefined = varUses -- varDefs
-      varUndefined foreach { x => error(stmt, s"Variable ${x} does not have bindings") }
+      if (!varUndefined.isEmpty) error(stmt, varUndefined map { x => s"Variable ${x} does not have bindings" } mkString("\n"))
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
-      case s: InferenceRule  => checkCq(s.q, (s.weights.variables flatMap collectVars toSet))
+      case s: InferenceRule  => checkCq(s.q, (s.weights.variables flatMap collectUsedVars toSet))
       case _ =>
     }
   }

From 837e0eac506aecb948285e58ad36d91e457ca2c3 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@users.noreply.github.com>
Date: Mon, 27 Jul 2015 11:58:04 -0700
Subject: [PATCH 200/347] minor: Updates unbound variable error msg

---
 .../scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala | 4 ++--
 .../unbound_variable_1/compile-error.expected                 | 2 +-
 .../unbound_variable_2/compile-error.expected                 | 2 +-
 .../unbound_variable_3/compile-error.expected                 | 2 +-
 .../unbound_variable_4/compile-error.expected                 | 4 ++++
 test/compile-error-test/unbound_variable_4/input.ddl          | 3 +++
 6 files changed, 12 insertions(+), 5 deletions(-)
 create mode 100644 test/compile-error-test/unbound_variable_4/compile-error.expected
 create mode 100644 test/compile-error-test/unbound_variable_4/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 2427b6b12..5fa2c7cd8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -197,7 +197,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         (cq.head.terms flatMap collectUsedVars) ++
         (additionalUsedVars)
       val varUndefined = varUses -- varDefs
-      if (!varUndefined.isEmpty) error(stmt, varUndefined map { x => s"Variable ${x} does not have bindings" } mkString("\n"))
+      if (varUndefined nonEmpty) error(stmt, s"Variable ${varUndefined mkString(", ")} must have bindings")
     }
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
@@ -225,4 +225,4 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // function declaration
   var functionDeclaration : Map[String, FunctionDeclaration] = new HashMap[String, FunctionDeclaration]()
 
-}
\ No newline at end of file
+}
diff --git a/test/compile-error-test/unbound_variable_1/compile-error.expected b/test/compile-error-test/unbound_variable_1/compile-error.expected
index 362b5d228..560383a45 100644
--- a/test/compile-error-test/unbound_variable_1/compile-error.expected
+++ b/test/compile-error-test/unbound_variable_1/compile-error.expected
@@ -1,4 +1,4 @@
-[error] Variable y does not have bindings
+[error] Variable y must have bindings
 Q(y)  :-
     a(x).
 
diff --git a/test/compile-error-test/unbound_variable_2/compile-error.expected b/test/compile-error-test/unbound_variable_2/compile-error.expected
index fe419e14c..7541c2667 100644
--- a/test/compile-error-test/unbound_variable_2/compile-error.expected
+++ b/test/compile-error-test/unbound_variable_2/compile-error.expected
@@ -1,4 +1,4 @@
-[error] Variable x does not have bindings
+[error] Variable x must have bindings
 Q(y)  :-
     a(y),
     x > 100.
diff --git a/test/compile-error-test/unbound_variable_3/compile-error.expected b/test/compile-error-test/unbound_variable_3/compile-error.expected
index c182c4502..45f0086bb 100644
--- a/test/compile-error-test/unbound_variable_3/compile-error.expected
+++ b/test/compile-error-test/unbound_variable_3/compile-error.expected
@@ -1,4 +1,4 @@
-[error] Variable y does not have bindings
+[error] Variable y must have bindings
 b(x)  :-
     a(x)
   weight = y.
diff --git a/test/compile-error-test/unbound_variable_4/compile-error.expected b/test/compile-error-test/unbound_variable_4/compile-error.expected
new file mode 100644
index 000000000..76cc8e1ae
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_4/compile-error.expected
@@ -0,0 +1,4 @@
+[error] Variable y, z must have bindings
+Q(y, z)  :-
+    a(x).
+
diff --git a/test/compile-error-test/unbound_variable_4/input.ddl b/test/compile-error-test/unbound_variable_4/input.ddl
new file mode 100644
index 000000000..324d77cfc
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_4/input.ddl
@@ -0,0 +1,3 @@
+a(k int).
+
+Q(y,z) :- a(x).

From bde0b6b5cef7695e4e005382abad0febe117dc61 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 28 Jul 2015 00:37:13 -0700
Subject: [PATCH 201/347] Refactor conjunctive query and function call rule

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 76 +++++++++----------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 47 +++++-------
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  3 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 52 ++++++-------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 19 ++---
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 33 ++++----
 6 files changed, 106 insertions(+), 124 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 0a3aecad7..e2ce4d863 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -112,10 +112,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         }
         if (decl.isQuery) variableTableNames += r
       }
-      case ExtractionRule(_,_) => ()
-      case InferenceRule(_,_,_,_) => ()
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case f: FunctionCallRule => functionCallList += f
+      case _ =>
     }
     groupByHead(statements)
     analyzeVisible(statements)
@@ -134,13 +133,13 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case s: SchemaDeclaration => s"extraction_rule_${statements indexOf s}"
       case s: FunctionCallRule  => s"extraction_rule_${statements indexOf s}"
       case s: ExtractionRule    => s"extraction_rule_${statements indexOf s}"
-      case s: InferenceRule     => s"extraction_rule_${s.q.head.name}"
+      case s: InferenceRule     => s"extraction_rule_${s.headName}"
     }
   }
 
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
-    s"${s.q.head.name}_${(inferenceRuleGroupByHead map (_._2)).flatten.toList indexOf s}"
+    s"${s.headName}_${(inferenceRuleGroupByHead map (_._2)).flatten.toList indexOf s}"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
@@ -185,8 +184,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case INCREMENTAL => schemaDeclarationToCompile.toList.filter(_.a.name.startsWith("dd_")).groupBy(_.a.name)
       case _           => schemaDeclarationToCompile.toList.groupBy(_.a.name)
     }
-    extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.q.head.name)
-    inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.q.head.name)
+    extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.headName)
+    inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.headName)
     functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
   }
 
@@ -204,7 +203,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     // Look at the body of each statement to construct a dependency graph
     statements foreach {
       case f : FunctionCallRule => dependencies += {
-        f -> ((( f.input.bodies.flatten collect { case x: BodyAtom => x.name })
+        f -> ((( f.q.bodies.flatten collect { case x: BodyAtom => x.name })
           flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case e : ExtractionRule   => dependencies += {
         e -> (((e.q.bodies.flatten collect { case x: BodyAtom => x.name })
@@ -276,17 +275,15 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // compile alias
-  def compileAlias(e: Expr) = {
-    e match {
-      case VarExpr(v) => {
-        val index = getBodyIndex(v)
-        val variable = getVar(v)
-        val name  = ss.resolveName(variable)
-        val relation = variable.relName
-        s"${relation}.R${index}.${name}"
-      }
-      case _ => s"column_${cq.head.terms indexOf e}"
+  def compileAlias(e: Expr) = e match {
+    case VarExpr(v) => {
+      val index = getBodyIndex(v)
+      val variable = getVar(v)
+      val name  = ss.resolveName(variable)
+      val relation = variable.relName
+      s"${relation}.R${index}.${name}"
     }
+    case _ => s"column_${cq.headTerms indexOf e}"
   }
 
   // resolve an expression
@@ -335,9 +332,9 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
 
   // generate SQL SELECT cluase
   def generateSQLHead(useAlias: Boolean) = {
-    val head = (cq.head.terms map { expr =>
+    val head = cq.headTerms map { expr =>
       compileExpr(expr) + (if (useAlias) s""" AS "${compileAlias(expr)}" """ else "")
-    }).mkString(", ")
+    } mkString(", ")
     val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
     s"${distinctStr}${head}"
   }
@@ -430,9 +427,9 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
 
     // handle group by
     // map head terms, leaving out aggregation functions
-    val groupbyTerms = cq.head.terms.filterNot(containsAggregation) map (compileExpr(_))
+    val groupbyTerms = cq.headTerms.filterNot(containsAggregation) map (compileExpr(_))
 
-    val groupbyStr = if (groupbyTerms.size == cq.head.terms.size || groupbyTerms.isEmpty) {
+    val groupbyStr = if (groupbyTerms.size == cq.headTerms.size || groupbyTerms.isEmpty) {
       ""
     } else {
       s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
@@ -520,7 +517,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
-        } else if ((ss.schemaDeclarationGroupByHead contains stmt.q.head.name) && (ss.schemaDeclarationGroupByHead(stmt.q.head.name)(0).isQuery) && (stmt.q.head.name startsWith "dd_new_")) {
+        } else if ((ss.schemaDeclarationGroupByHead contains stmt.headName) &&
+          (ss.schemaDeclarationGroupByHead(stmt.headName)(0).isQuery) &&
+          (stmt.headName startsWith "dd_new_")) {
           val headStr = qc.generateSQLHead(false)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, id, label
           ${ qc.generateSQLBody(cqBody) }
@@ -530,32 +529,34 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
           var useAlias = ss.mode match {
             case MERGE => false
-            case _     => if (tmpCq.head.name.startsWith("dd_new_")) false else true
+            case _     => if (stmt.headName.startsWith("dd_new_")) false else true
           }
           inputQueries += qc.generateSQL(useAlias)
         }
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
-    // val createTable = if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) true else false
     val sqlCmdForCleanUp = ss.mode match {
-      case MERGE => s"TRUNCATE ${stmts(0).q.head.name};"
-      case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name) {
-        if (stmts(0).q.head.name.startsWith("dd_new_") && !(ss.inferenceRuleGroupByHead contains stmts(0).q.head.name))
-          s"TRUNCATE ${stmts(0).q.head.name};"
+      case MERGE => s"TRUNCATE ${stmts(0).headName};"
+      case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).headName) {
+        if (stmts(0).headName.startsWith("dd_new_") && !(ss.inferenceRuleGroupByHead contains stmts(0).headName))
+          s"TRUNCATE ${stmts(0).headName};"
         else ""
-      } else s"DROP VIEW IF EXISTS ${stmts(0).q.head.name};"
+      } else s"DROP VIEW IF EXISTS ${stmts(0).headName};"
     }
     val createTable = ss.mode match {
       case MERGE => true
-      case _ => if ((!(stmts(0).q.head.name startsWith "dd_new_") && (ss.schemaDeclarationGroupByHead contains stmts(0).q.head.name)) || ((stmts(0).q.head.name startsWith "dd_new_") && !(ss.inferenceRuleGroupByHead contains stmts(0).q.head.name))) true else false
+      case _ => (!(stmts(0).headName startsWith "dd_new_") &&
+        (ss.schemaDeclarationGroupByHead contains stmts(0).headName)) ||
+        ((stmts(0).headName startsWith "dd_new_") &&
+        !(ss.inferenceRuleGroupByHead contains stmts(0).headName))
     }
     val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
     val useAS            = if (createTable) "" else " AS"
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         sql: \"\"\" ${sqlCmdForCleanUp}
-        ${sqlCmdForInsert} ${stmts(0).q.head.name}${useAS} ${inputQueries.mkString("\nUNION ALL\n")}
+        ${sqlCmdForInsert} ${stmts(0).headName}${useAS} ${inputQueries.mkString("\nUNION ALL\n")}
         \"\"\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
@@ -567,11 +568,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileFunctionCallRules(stmts: List[FunctionCallRule], ss: CompilationState): CompiledBlocks = {
     var extractors = new ListBuffer[String]()
     for (stmt <- stmts) {
-      val inputQuery = s"""
-      SELECT * FROM ${stmt.input}
-      """
 
-      val function = ss.resolveFunctionName(stmt.input.head.name)
+      val function = ss.resolveFunctionName(stmt.function)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
           s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
@@ -579,13 +577,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       })
 
       if (udfDetails.isEmpty)
-        ss.error(s"Cannot find compilable implementation for function ${stmt.input.head.name} among:\n  "
+        ss.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
           + (function.implementations mkString "\n  "))
 
       val blockName = ss.resolveExtractorBlockName(stmt)
       val extractor = s"""
         deepdive.extraction.extractors.${blockName} {
-          input: \"\"\" ${new QueryCompiler(stmt.input, ss).generateSQL(true)}
+          input: \"\"\" ${new QueryCompiler(stmt.q, ss).generateSQL(true)}
           \"\"\"
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
@@ -606,7 +604,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
         // edge query
-        val fakeHeadAsBody  = BodyAtom(stmt.q.head.name, stmt.q.head.terms map {
+        val fakeHeadAsBody  = BodyAtom(stmt.headName, stmt.q.headTerms map {
           case x: VarExpr => VarPattern(x.name)
           case x: Expr    => ExprPattern(x)
         })
@@ -649,7 +647,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           // if function is not specified, use Imply for boolean, and Multinomial for multinomial variables
           val function  = stmt.function match {
             case Some(f) => f
-            case None => ss.variableType get stmt.q.head.name match {
+            case None => ss.variableType get stmt.headName match {
               case Some(BooleanType)        => "Imply"
               case Some(MultinomialType(_)) => "Multinomial"
             }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 4df275213..7f8c16c51 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -18,23 +18,11 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
-  def transform(cq: ConjunctiveQuery, isInference: Boolean, mode: Option[String]): ConjunctiveQuery = {
+  def transform(headName: String, cq: ConjunctiveQuery, isInference: Boolean, mode: Option[String]): ConjunctiveQuery = {
 
     // New head
-    val incCqHead = if (isInference) {
-      cq.head.copy(
-        name = newPrefix + cq.head.name
-      )
-    } else {
-      cq.head.copy(
-        name = deltaPrefix + cq.head.name
-      )
-    }
-    val incCqBodies = transformBody(cq, incCqHead.name, mode)
-    cq.copy(head = incCqHead, bodies = incCqBodies)
-  }
+    val incCqHead = transform(headName, isInference)
 
-  def transformBody(cq: ConjunctiveQuery, incCqHead: String, mode: Option[String]) : List[List[Body]] = {
     var incCqBodies = new ListBuffer[List[Body]]()
     // New incremental bodies
     cq.bodies foreach { bodies =>
@@ -79,7 +67,12 @@ object DeepDiveLogDeltaDeriver{
         }
       }
     }
-    incCqBodies.toList
+
+    cq.copy(bodies = incCqBodies.toList)
+  }
+
+  def transform(headName: String, isInference: Boolean) : String = {
+    (if (isInference) newPrefix else deltaPrefix) + headName
   }
 
   // Incremental scheme declaration,
@@ -105,13 +98,12 @@ object DeepDiveLogDeltaDeriver{
     )
     incrementalStatement += incNewStmt
 
-    // if (!stmt.isQuery) {
-    incrementalStatement += ExtractionRule(ConjunctiveQuery(
-      HeadAtom(incNewStmt.a.name, incNewStmt.a.terms map { VarExpr(_) } ),
+    incrementalStatement += ExtractionRule(incNewStmt.a.name,
+      ConjunctiveQuery(incNewStmt.a.terms map { VarExpr(_) },
       List(List(BodyAtom(stmt.a.name, stmt.a.terms map { VarPattern(_) })),
-        List(BodyAtom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarPattern(_) }))),
+      List(BodyAtom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarPattern(_) }))),
       false, None))
-    // }
+
     incrementalStatement.toList
   }
 
@@ -137,23 +129,24 @@ object DeepDiveLogDeltaDeriver{
   // Incremental extraction rule,
   // create delta rules based on original extraction rule
   def transform(stmt: ExtractionRule): List[Statement] = {
-    // if (stmt.supervision != null)
-      // List(ExtractionRule(transform(stmt.q, true, null), stmt.supervision))
-    // else
-      List(ExtractionRule(transform(stmt.q, false, null), stmt.supervision))
+    List(stmt.copy(
+      headName = transform(stmt.headName, false),
+      q = transform(stmt.headName, stmt.q, false, None)))
   }
 
   // Incremental function call rule,
   // modify function input and output
   def transform(stmt: FunctionCallRule): List[Statement] = {
-    List(FunctionCallRule(stmt.input.copy(bodies = transformBody(stmt.input, "", None)),
-      deltaPrefix + stmt.output))
+    List(stmt.copy(
+      output = deltaPrefix + stmt.output,
+      q = transform(stmt.output, stmt.q, false, None)))
   }
 
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(stmt.copy(q = transform(stmt.q, true, stmt.mode), mode = None))
+    List(stmt.copy(headName = transform(stmt.headName, true),
+      q = transform(stmt.headName, stmt.q, true, stmt.mode), mode = None))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
index 1b5203fc2..c2244bbd1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
@@ -17,7 +17,8 @@ object DeepDiveLogMergeDeriver{
       )
     )
 
-    ExtractionRule(ConjunctiveQuery(HeadAtom(stmt.a.name, stmt.a.terms map { VarExpr(_) }),
+    ExtractionRule(stmt.a.name,
+      ConjunctiveQuery(stmt.a.terms map { VarExpr(_) },
       List(List(BodyAtom(incNewStmt.a.name, incNewStmt.a.terms map { VarPattern(_) }))),
       false, None))
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 3f3c302e1..520453b15 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -29,8 +29,6 @@ case class VarPattern(name: String) extends Pattern
 case class ExprPattern(expr: Expr) extends Pattern
 case class PlaceholderPattern extends Pattern
 
-case class HeadAtom(name : String, terms : List[Expr])
-
 sealed trait Body
 case class BodyAtom(name : String, terms : List[Pattern]) extends Body
 case class QuantifiedBody(modifier: BodyModifier, bodies: List[Body]) extends Body
@@ -41,7 +39,7 @@ case class OuterModifier extends BodyModifier
 case class AllModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
-case class ConjunctiveQuery(head: HeadAtom, bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
+case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
 case class Column(name : String // name of the column
                  , t : String // type of the column
                  , annotation: List[Annotation] = List.empty // optional annotation
@@ -96,9 +94,9 @@ case class SchemaDeclaration( a : Attribute
                             ) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: RelationType,
   outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
-case class ExtractionRule(q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
-case class FunctionCallRule(input : ConjunctiveQuery, output : String) extends Statement // Extraction rule
-case class InferenceRule(q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: Option[String] = None) extends Statement // Weighted rule
+case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
+case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery) extends Statement // Extraction rule
+case class InferenceRule(headName: String, q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: Option[String] = None) extends Statement // Weighted rule
 
 // Parser
 class DeepDiveLogParser extends JavaTokenParsers {
@@ -192,10 +190,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "(" ~> expr <~ ")"
     )
 
-  def cqHead = relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
-    case (r ~ expressions) => HeadAtom(r, expressions)
-  }
-
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
 
@@ -241,16 +235,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     QuantifiedBody(modifier, b)
   }
 
-  def cqBody: Parser[Body] = cond | quantifiedBody | atom
-
-  def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
-
-  def conjunctiveQuery : Parser[ConjunctiveQuery] =
-    cqHead ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
-      case (headatom ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(headatom, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
-  }
-
   def relationType: Parser[RelationType] =
     ( "like" ~> relationName ^^ { RelationTypeAlias(_) }
     | rep1sep(columnDeclaration, ",") ^^ {
@@ -280,9 +264,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   }
 
-  def functionMode = "@mode" ~> "(" ~> functionModeType <~ ")"
-  def inferenceMode = "@mode" ~> "(" ~> inferenceModeType <~ ")"
-
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
     ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
         case (_ ~ command ~ _ ~ style ~ _) => RowWiseLineHandler(command=command, style=style)
@@ -292,6 +273,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
+  def functionMode = "@mode" ~> "(" ~> functionModeType <~ ")"
+
   def functionDeclaration : Parser[FunctionDeclaration] =
     ( opt(functionMode) ~ "function" ~ functionName ~ "over" ~ relationType
                              ~ "returns" ~ relationType
@@ -303,18 +286,31 @@ class DeepDiveLogParser extends JavaTokenParsers {
              FunctionDeclaration(a, inTy, outTy, implementationDecls, mode)
     }
 
+  def cqBody: Parser[Body] = cond | quantifiedBody | atom
+
+  def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
+
+  def cqHeadTerms = "(" ~> rep1sep(expr, ",") <~ ")"
+
+  def conjunctiveQuery : Parser[ConjunctiveQuery] =
+    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
+      case (head ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
+        ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
+  }
+
   def functionCallRule : Parser[FunctionCallRule] =
-    relationName ~ "+=" ~ conjunctiveQuery ^^ {
-      case (out ~ _ ~ cq) => FunctionCallRule(cq, out)
+    relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
+      case (out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq)
     }
 
   def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
 
-  def extractionOrInferenceRule = ruleAnnotations ~ conjunctiveQuery ^^ { case (annos ~ cq) =>
+  def extractionOrInferenceRule =
+    ruleAnnotations ~ relationName ~ conjunctiveQuery ^^ { case (annos ~ head ~ cq) =>
     val weight = getArgs(annos, "weight")
     if (weight == None) { // extraction rule
       val supervision = getFirstIdentArg(annos, "label")
-      ExtractionRule(cq, supervision)
+      ExtractionRule(head, cq, supervision)
     } else { // inference rule
       val mode          = getFirstIdentArg(annos, "mode")
       val function      = getFirstIdentArg(annos, "function")
@@ -323,7 +319,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
         case x: ExprAnnoArg  => x.expr
         case x: IdentAnnoArg => VarExpr(x.name)
       })
-      InferenceRule(cq, factorWeight, function, mode)
+      InferenceRule(head, cq, factorWeight, function, mode)
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 953514dd6..7a787ec8f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -93,11 +93,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     s"${a.name}(${vars.mkString(", ")})"
   }
 
-  def print(a: HeadAtom) : String = {
-    val vars = a.terms map print
-    s"${a.name}(${vars.mkString(", ")})"
-  }
-
   def print(p: Pattern) : String = p match {
     case VarPattern(x) => x
     case PlaceholderPattern() => "_"
@@ -142,26 +137,26 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
     val bodyStr = (cq.bodies map printBodyList).mkString(";\n    ")
 
-    val distinctStr = if (cq.isDistinct) "*" else ""
-    val limitStr = cq.limit map { " | " + _ } getOrElse("")
+    val distinctStr = if (cq.isDistinct) " *" else ""
+    val limitStr    = cq.limit map { " | " + _ } getOrElse("")
+    val headStr     = cq.headTerms map print mkString("(", ", ", ")")
 
-    s"""${print(cq.head)} ${distinctStr}${limitStr} :-
-       |    ${bodyStr}""".stripMargin
+    headStr + distinctStr + limitStr + " :-\n    " + bodyStr
   }
 
   def print(stmt: ExtractionRule): String = {
     ( stmt.supervision map (s => s"@label(${s})\n") getOrElse("") ) +
-    print(stmt.q) + ".\n"
+    stmt.headName + print(stmt.q) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
-    s"${stmt.output} += ${print(stmt.input)}.\n"
+    s"${stmt.output} += ${stmt.function}${print(stmt.q)}.\n"
   }
 
   def print(stmt: InferenceRule): String = {
     ( stmt.function map { f => s"@function(${f})\n" } getOrElse("") ) +
     ( s"@weight(${stmt.weights.variables map print mkString(", ")})\n"
-    ) + print(stmt.q) + ".\n"
+    ) + stmt.headName + print(stmt.q) + ".\n"
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 37b1ae603..18ef37fbe 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -13,17 +13,17 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         heads += s.a.name
         schemaDeclaration += { s.a.name -> s }
       }
-      case ExtractionRule(q, supervision) => {
-        heads += q.head.name
+      case s: ExtractionRule => {
+        heads += s.headName
       }
-      case InferenceRule(q, weight, semantic, mode) => {
-        heads += q.head.name
+      case s: InferenceRule => {
+        heads += s.headName
       }
-      case f: FunctionDeclaration => {
-        functionDeclaration += { f.functionName -> f }
+      case s: FunctionDeclaration => {
+        functionDeclaration += { s.functionName -> s }
       }
-      case FunctionCallRule(input, output) => {
-        heads += output
+      case s: FunctionCallRule => {
+        heads += s.output
       }
     }
   }
@@ -59,7 +59,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach check
       case s: InferenceRule => s.q.bodies foreach check
-      case s: FunctionCallRule => s.input.bodies foreach check
+      case s: FunctionCallRule => s.q.bodies foreach check
       case _ =>
     }
   }
@@ -68,8 +68,8 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkFunctionDefined(stmt: Statement) {
     stmt match {
       case s: FunctionCallRule => {
-        if (!(functionDeclaration.keySet contains s.input.head.name))
-          error(stmt, s"""function "${s.input.head.name}" is not defined""")
+        if (!(functionDeclaration.keySet contains s.function))
+          error(stmt, s"""function "${s.function}" is not defined""")
       }
       case _ =>
     }
@@ -99,14 +99,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         error(stmt, s""""${name}": number of columns in the query does not match number of columns in the schema""")
     }
     def checkBodyAtom(a: BodyAtom) = check(a.name, a.terms.size)
-    def checkHeadAtom(a: HeadAtom) = check(a.name, a.terms.size)
-    def checkCq(cq: ConjunctiveQuery) {
-      checkHeadAtom(cq.head)
+    def checkCq(headName: String, cq: ConjunctiveQuery) {
+      check(headName, cq.headTerms.size)
       cq.bodies foreach checkBodyAtoms(checkBodyAtom)
     }
     stmt match {
-      case s: ExtractionRule => checkCq(s.q)
-      case s: InferenceRule  => checkCq(s.q)
+      case s: ExtractionRule   => checkCq(s.headName, s.q)
+      case s: InferenceRule    => checkCq(s.headName, s.q)
       case _ =>
     }
   }
@@ -194,7 +193,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       // collect variable definitions and usages
       var varDefs = cq.bodies flatMap (_ flatMap collectDefinedVars) toSet
       val varUses = (cq.bodies flatMap (_ flatMap collectUsedVars) toSet) ++
-        (cq.head.terms flatMap collectUsedVars) ++
+        (cq.headTerms flatMap collectUsedVars) ++
         (additionalUsedVars)
       val varUndefined = varUses -- varDefs
       if (!varUndefined.isEmpty) error(stmt, varUndefined map { x => s"Variable ${x} does not have bindings" } mkString("\n"))

From cf5759fab85cfd507d6abaf6b9c25ad71a0e56cd Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 28 Jul 2015 01:11:48 -0700
Subject: [PATCH 202/347] Revert to old annotation parsing

---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 57 +++++++------------
 1 file changed, 20 insertions(+), 37 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 520453b15..d5f21f116 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -48,10 +48,7 @@ case class Column(name : String // name of the column
 case class Annotation( name : String // name of the annotation
                      , args : Map[String, Any] = Map.empty // optional, named arguments
                      )
-case class RuleAnnotation(name: String, args: List[RuleAnnotationArg])
-sealed trait RuleAnnotationArg
-case class ExprAnnoArg(expr: Expr) extends RuleAnnotationArg
-case class IdentAnnoArg(name: String) extends RuleAnnotationArg
+case class RuleAnnotation(name: String, args: List[String])
 
 // condition
 sealed trait Cond extends Body
@@ -242,26 +239,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
-  def ruleAnnoArg : Parser[RuleAnnotationArg] = expr  ^^ {
-    case VarExpr(x) => IdentAnnoArg(x)
-    case x: Expr    => ExprAnnoArg(x)
-  }
-
-  def ruleAnnotation = "@" ~> annotationName ~ "(" ~ rep1sep(ruleAnnoArg, ",") <~ ")" ^^ {
-    case (name ~ _ ~ args) => RuleAnnotation(name, args)
+  def ruleAnnotation = "@" ~> annotationName ~ ("(" ~> rep1sep(ident, ",") <~ ")") ^^ {
+    case (name ~ args) => RuleAnnotation(name, args)
   }
 
   def ruleAnnotations = rep(ruleAnnotation)
 
-  def getArgs(annos: List[RuleAnnotation], name: String) = {
-    annos.find(_.name == name) map (_.args)
-  }
-
-  def getFirstIdentArg(annos: List[RuleAnnotation], name: String)  = {
-    getArgs(annos, name) map (_(0)) map {
-      case x: IdentAnnoArg => x.name
-      case _ => error("Invalid rule annotation argument(s) for " + name)
-    }
+  def getArg(annos: List[RuleAnnotation], name: String)  = {
+    annos.find(_.name == name) map (_.args) map (_(0))
   }
 
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
@@ -305,27 +290,25 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
 
-  def extractionOrInferenceRule =
-    ruleAnnotations ~ relationName ~ conjunctiveQuery ^^ { case (annos ~ head ~ cq) =>
-    val weight = getArgs(annos, "weight")
-    if (weight == None) { // extraction rule
-      val supervision = getFirstIdentArg(annos, "label")
-      ExtractionRule(head, cq, supervision)
-    } else { // inference rule
-      val mode          = getFirstIdentArg(annos, "mode")
-      val function      = getFirstIdentArg(annos, "function")
-      // NOTE there's an ambiguation between ident and variable expression
-      val factorWeight  = FactorWeight(weight.get.map {
-        case x: ExprAnnoArg  => x.expr
-        case x: IdentAnnoArg => VarExpr(x.name)
-      })
-      InferenceRule(head, cq, factorWeight, function, mode)
-    }
+  def supervision = "@label" ~> "(" ~> variableName <~ ")"
+  def extractionRule =
+    opt(supervision) ~ relationName ~ conjunctiveQuery ^^ {
+      case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
+  }
+
+  def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
+  def factorFunction = "@function" ~> "(" ~> factorFunctionName <~ ")"
+  def inferenceMode = "@mode" ~> "(" ~> inferenceModeType <~ ")"
+  def inferenceRule =
+    opt(inferenceMode) ~ opt(factorFunction) ~ factorWeight ~ relationName ~ conjunctiveQuery ^^ {
+      case (mode ~ function ~ weight ~ head ~ cq) => InferenceRule(head, cq, weight, function, mode)
   }
 
+
   // rules or schema elements in arbitrary order
   def statement : Parser[Statement] = ( schemaDeclaration
-                                      | extractionOrInferenceRule
+                                      | inferenceRule
+                                      | extractionRule
                                       | functionDeclaration
                                       | functionCallRule
                                       )

From 7acf85bb76f70517fd5d4db7ce4c6e9642163330 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Tue, 28 Jul 2015 03:59:24 -0700
Subject: [PATCH 203/347] MLN style inference rule head

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 65 ++++++++++---------
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 22 +++----
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 53 +++++++++++++--
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 25 ++++++-
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 18 +++--
 .../chunking_example/compile.expected         |  6 +-
 .../factor_functions/input.ddl                |  6 ++
 .../ocr_example/compile-incremental.expected  | 20 +++---
 .../compile-materialization.expected          |  8 +--
 .../ocr_example/compile.expected              |  8 +--
 .../ocr_example/print-incremental.expected    | 18 ++---
 test/expected-output-test/semantics/input.ddl |  8 ---
 .../compile-incremental.expected              |  8 +--
 .../compile-materialization.expected          |  8 +--
 .../smoke_example/compile.expected            |  8 +--
 .../smoke_example/print-incremental.expected  | 20 +++---
 .../compile-incremental.expected              |  6 +-
 .../compile-materialization.expected          |  6 +-
 .../spouse_example/compile.expected           |  6 +-
 .../spouse_example/print-incremental.expected | 22 +++----
 .../compile-incremental.expected              |  8 +--
 .../spouse_example_new_feature/input.ddl      |  1 -
 .../print-incremental.expected                | 23 ++++---
 .../compile-incremental.expected              |  8 +--
 .../compile.expected                          |  8 +--
 .../print-incremental.expected                | 24 +++----
 .../weights/compile.expected                  | 50 +++++++-------
 27 files changed, 263 insertions(+), 200 deletions(-)
 create mode 100644 test/expected-output-test/factor_functions/input.ddl
 delete mode 100644 test/expected-output-test/semantics/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index e2ce4d863..fb00eb4c4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -94,9 +94,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // Mapping head names to the actual statements
   var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
   var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
-  var inferenceRuleGroupByHead      : Map[String, List[InferenceRule]] = new HashMap[String, List[InferenceRule]]()
   var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
   var functionCallList              : ListBuffer[FunctionCallRule] = new ListBuffer[FunctionCallRule]()
+  var inferenceRules : ListBuffer[InferenceRule] = new ListBuffer[InferenceRule]()
 
   def init() = {
     // generate the statements.
@@ -114,6 +114,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       }
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
       case f: FunctionCallRule => functionCallList += f
+      case f: InferenceRule => inferenceRules += f
       case _ =>
     }
     groupByHead(statements)
@@ -128,18 +129,19 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   // Given a statement, resolve its name for the compiled extractor block.
-  def resolveExtractorBlockName(s: Statement): String = {
-    s match {
-      case s: SchemaDeclaration => s"extraction_rule_${statements indexOf s}"
-      case s: FunctionCallRule  => s"extraction_rule_${statements indexOf s}"
-      case s: ExtractionRule    => s"extraction_rule_${statements indexOf s}"
-      case s: InferenceRule     => s"extraction_rule_${s.headName}"
-    }
-  }
+  def resolveExtractorBlockName(s: Statement): String = s"extraction_rule_${statements indexOf s}"
+  // {
+  //   s match {
+  //     case s: SchemaDeclaration => s"extraction_rule_${statements indexOf s}"
+  //     case s: FunctionCallRule  => s"extraction_rule_${statements indexOf s}"
+  //     case s: ExtractionRule    => s"extraction_rule_${statements indexOf s}"
+  //     case s: InferenceRule     => s"extraction_rule_${statements indexOf s}"
+  //   }
+  // }
 
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
-    s"${s.headName}_${(inferenceRuleGroupByHead map (_._2)).flatten.toList indexOf s}"
+    s"inference_rule_${inferenceRules indexOf s}"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
@@ -185,7 +187,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case _           => schemaDeclarationToCompile.toList.groupBy(_.a.name)
     }
     extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.headName)
-    inferenceRuleGroupByHead       = inferenceRuleToCompile.toList.groupBy(_.headName)
     functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
   }
 
@@ -197,7 +198,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Analyze the dependency between statements and construct a graph.
   def analyzeDependency(statements: List[Statement]) = {
-    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++ inferenceRuleGroupByHead.toSeq ++
+    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++
       functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
     // Look at the body of each statement to construct a dependency graph
@@ -208,9 +209,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case e : ExtractionRule   => dependencies += {
         e -> (((e.q.bodies.flatten collect { case x: BodyAtom => x.name })
           flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
-      case w : InferenceRule    => dependencies += {
-        w -> (((w.q.bodies.flatten collect { case x: BodyAtom => x.name })
-          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
       case _ =>
     }
   }
@@ -460,7 +458,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
     for (stmt <- stmts) {
-      if ((stmt.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains stmt.a.name)) {
+      if ((stmt.a.name startsWith "dd_new_") && (ss.isQueryTerm(stmt.a.name))) {
       } else {
         var columnDecls = stmt.a.terms.zipWithIndex map {
           case (name,i) => s"${name} ${stmt.a.types(i)}"
@@ -486,7 +484,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     }
     // Cleanup incremental table extractor
     val truncateTableList = (stmts map (x =>
-      if ((x.a.name startsWith "dd_new_") && (ss.inferenceRuleGroupByHead contains x.a.name)) ""
+      if ((x.a.name startsWith "dd_new_") && (ss.isQueryTerm(x.a.name))) ""
       else s"TRUNCATE ${x.a.name};")).filter(_ != "")
     if (truncateTableList.length > 0) {
       schemas += s"""
@@ -539,7 +537,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val sqlCmdForCleanUp = ss.mode match {
       case MERGE => s"TRUNCATE ${stmts(0).headName};"
       case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).headName) {
-        if (stmts(0).headName.startsWith("dd_new_") && !(ss.inferenceRuleGroupByHead contains stmts(0).headName))
+        if (stmts(0).headName.startsWith("dd_new_") && !(ss.isQueryTerm(stmts(0).headName)))
           s"TRUNCATE ${stmts(0).headName};"
         else ""
       } else s"DROP VIEW IF EXISTS ${stmts(0).headName};"
@@ -549,7 +547,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       case _ => (!(stmts(0).headName startsWith "dd_new_") &&
         (ss.schemaDeclarationGroupByHead contains stmts(0).headName)) ||
         ((stmts(0).headName startsWith "dd_new_") &&
-        !(ss.inferenceRuleGroupByHead contains stmts(0).headName))
+        !(ss.isQueryTerm(stmts(0).headName)))
     }
     val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
     val useAS            = if (createTable) "" else " AS"
@@ -604,11 +602,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
         // edge query
-        val fakeHeadAsBody  = BodyAtom(stmt.headName, stmt.q.headTerms map {
-          case x: VarExpr => VarPattern(x.name)
-          case x: Expr    => ExprPattern(x)
-        })
-        val fakeBody        = fakeHeadAsBody +: cqBody
+        val headAsBody = stmt.head.terms map { x =>
+          BodyAtom(x.name, x.terms map {
+            case x: VarExpr => VarPattern(x.name)
+            case x: Expr    => ExprPattern(x)
+          })
+        }
+        val fakeBody        = headAsBody ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
         val fakeBodyAtoms   = fakeBody.collect { case x: BodyAtom => x }
 
@@ -644,10 +644,15 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           else ""
           }).filter(_ != "")
           val firstFunc = funcBody(0)
-          // if function is not specified, use Imply for boolean, and Multinomial for multinomial variables
-          val function  = stmt.function match {
-            case Some(f) => f
-            case None => ss.variableType get stmt.headName match {
+
+          val function = stmt.head.function match {
+            case FactorFunction.Imply  => "Imply"
+            case FactorFunction.And    => "And"
+            case FactorFunction.Or     => "Or"
+            case FactorFunction.Equal  => "Equal"
+            case FactorFunction.Linear => "Linear"
+            case FactorFunction.Ratio  => "Ratio"
+            case FactorFunction.IsTrue => ss.variableType get stmt.head.terms(0).name match {
               case Some(BooleanType)        => "Imply"
               case Some(MultinomialType(_)) => "Multinomial"
             }
@@ -726,7 +731,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [${setup_database_pipeline}]" else ""
     val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
     val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [${extraction}]" else ""
-    val inference = ((ss.inferenceRuleGroupByHead map (_._2)).flatten map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
+    val inference = (ss.inferenceRules map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [${inference}]" else ""
     val endtoend = List(extraction, inference).filter(_ != "").mkString(", ")
     val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [${endtoend}]" else ""
@@ -784,7 +789,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
     state.extractionRuleGroupByHead foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
     state.functionCallList          foreach {func   => body ++= compileFunctionCallRules(List(func), state)}
-    state.inferenceRuleGroupByHead  foreach {keyVal => body ++= compileInferenceRules(keyVal._2, state)}
+    state.inferenceRules            foreach {inf    => body ++= compileInferenceRules(List(inf), state)}
 
     // compile the program into blocks of application.conf
     val blocks = (
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 7f8c16c51..ac4ef9739 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -18,10 +18,10 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
-  def transform(headName: String, cq: ConjunctiveQuery, isInference: Boolean, mode: Option[String]): ConjunctiveQuery = {
+  def transform(headName: String, cq: ConjunctiveQuery, mode: Option[String]): ConjunctiveQuery = {
 
     // New head
-    val incCqHead = transform(headName, isInference)
+    val incCqHead = transform(headName)
 
     var incCqBodies = new ListBuffer[List[Body]]()
     // New incremental bodies
@@ -71,9 +71,9 @@ object DeepDiveLogDeltaDeriver{
     cq.copy(bodies = incCqBodies.toList)
   }
 
-  def transform(headName: String, isInference: Boolean) : String = {
-    (if (isInference) newPrefix else deltaPrefix) + headName
-  }
+  def transform(headName: String) : String = deltaPrefix + headName
+
+  def transform(a: HeadAtom) : HeadAtom = a.copy(name = newPrefix + a.name)
 
   // Incremental scheme declaration,
   // keep the original scheme and create one delta scheme
@@ -130,23 +130,23 @@ object DeepDiveLogDeltaDeriver{
   // create delta rules based on original extraction rule
   def transform(stmt: ExtractionRule): List[Statement] = {
     List(stmt.copy(
-      headName = transform(stmt.headName, false),
-      q = transform(stmt.headName, stmt.q, false, None)))
+      headName = transform(stmt.headName),
+      q = transform(stmt.headName, stmt.q, None)))
   }
 
   // Incremental function call rule,
   // modify function input and output
   def transform(stmt: FunctionCallRule): List[Statement] = {
     List(stmt.copy(
-      output = deltaPrefix + stmt.output,
-      q = transform(stmt.output, stmt.q, false, None)))
+      output = transform(stmt.output),
+      q = transform(stmt.output, stmt.q, None)))
   }
 
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
-    List(stmt.copy(headName = transform(stmt.headName, true),
-      q = transform(stmt.headName, stmt.q, true, stmt.mode), mode = None))
+    List(stmt.copy(head = stmt.head.copy(terms = stmt.head.terms map transform),
+      q = transform("", stmt.q, stmt.mode), mode = None))
   }
 
   def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index d5f21f116..1816b0fe1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -75,6 +75,15 @@ case class MultinomialType(numCategories: Int) extends VariableType {
 
 case class FactorWeight(variables: List[Expr])
 
+// factor function
+object FactorFunction extends Enumeration {
+  type FactorFunction = Value
+  val  IsTrue, Imply, Or, And, Equal, Multinomial, Linear, Ratio = Value
+}
+case class HeadAtom(name : String, terms : List[Expr])
+case class InferenceRuleHead(function: FactorFunction.FactorFunction, terms: List[HeadAtom])
+
+
 trait RelationType
 case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
 case class RelationTypeAlias(likeRelationName: String) extends RelationType
@@ -93,7 +102,7 @@ case class FunctionDeclaration( functionName: String, inputType: RelationType,
   outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
 case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
 case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery) extends Statement // Extraction rule
-case class InferenceRule(headName: String, q : ConjunctiveQuery, weights : FactorWeight, function : Option[String], mode: Option[String] = None) extends Statement // Weighted rule
+case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
 
 // Parser
 class DeepDiveLogParser extends JavaTokenParsers {
@@ -288,8 +297,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case (out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq)
     }
 
-  def factorFunctionName = "Imply" | "And" | "Equal" | "Or" | "Multinomial" | "Linear" | "Ratio"
-
   def supervision = "@label" ~> "(" ~> variableName <~ ")"
   def extractionRule =
     opt(supervision) ~ relationName ~ conjunctiveQuery ^^ {
@@ -297,13 +304,45 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
-  def factorFunction = "@function" ~> "(" ~> factorFunctionName <~ ")"
   def inferenceMode = "@mode" ~> "(" ~> inferenceModeType <~ ")"
-  def inferenceRule =
-    opt(inferenceMode) ~ opt(factorFunction) ~ factorWeight ~ relationName ~ conjunctiveQuery ^^ {
-      case (mode ~ function ~ weight ~ head ~ cq) => InferenceRule(head, cq, weight, function, mode)
+
+  // factor functions
+  def headAtom = relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
+    case (r ~ expressions) => HeadAtom(r, expressions)
+  }
+  def implyHead = rep1sep(headAtom, ",") ~ "=>" ~ headAtom ^^ {
+    case (a ~ _ ~ b) => InferenceRuleHead(FactorFunction.Imply, a :+ b)
+  }
+  def isTrueHead = headAtom ^^ { x => InferenceRuleHead(FactorFunction.IsTrue, List(x)) }
+  def equalHead = headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
+    InferenceRuleHead(FactorFunction.Equal, a +: b)
+  }
+  def andHead   = headAtom ~ "^" ~ rep1sep(headAtom, "^") ^^ { case (a ~ _ ~ b) =>
+    InferenceRuleHead(FactorFunction.And, a +: b)
   }
+  def orHead    = headAtom ~ "v" ~ rep1sep(headAtom, "v") ^^ { case (a ~ _ ~ b) =>
+    InferenceRuleHead(FactorFunction.Or, a +: b)
+  }
+  def multinomialHead = "Multinomial" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
+    InferenceRuleHead(FactorFunction.Multinomial, _)
+  }
+  def linearHead = "Linear" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
+    InferenceRuleHead(FactorFunction.Linear, _)
+  }
+  def ratioHead = "Ratio" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
+    InferenceRuleHead(FactorFunction.Ratio, _)
+  }
+  def inferenceRuleHead = implyHead | equalHead | andHead | orHead | multinomialHead | linearHead | ratioHead | isTrueHead
 
+  def inferenceConjunctiveQuery : Parser[ConjunctiveQuery] =
+    ":-" ~> rep1sep(cqConjunctiveBody, ";") ^^ {
+      ConjunctiveQuery(List(), _, false, None)
+  }
+
+  def inferenceRule =
+    opt(inferenceMode) ~ factorWeight ~ inferenceRuleHead ~ inferenceConjunctiveQuery ^^ {
+      case (mode ~ weight ~ head ~ cq) => InferenceRule(head, cq, weight, mode)
+  }
 
   // rules or schema elements in arbitrary order
   def statement : Parser[Statement] = ( schemaDeclaration
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 7a787ec8f..983e63e83 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -139,11 +139,31 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
     val distinctStr = if (cq.isDistinct) " *" else ""
     val limitStr    = cq.limit map { " | " + _ } getOrElse("")
-    val headStr     = cq.headTerms map print mkString("(", ", ", ")")
+    val headStrTmp  = cq.headTerms map print mkString(", ")
+    val headStr     = if (headStrTmp isEmpty) "" else s"(${headStrTmp})"
 
     headStr + distinctStr + limitStr + " :-\n    " + bodyStr
   }
 
+  def print(a: HeadAtom) : String = {
+    val vars = a.terms map print
+    s"${a.name}(${vars.mkString(", ")})"
+  }
+
+  def print(head: InferenceRuleHead) : String = {
+    def printHead(a: List[HeadAtom], delim: String) : String = a map print mkString(delim)
+    head.function match {
+      case FactorFunction.Imply  =>
+        s"""${printHead(head.terms.dropRight(1), ", ")} => ${print(head.terms.last)}"""
+      case FactorFunction.And    => printHead(head.terms, " ^ ")
+      case FactorFunction.Or     => printHead(head.terms, " v ")
+      case FactorFunction.Equal  => printHead(head.terms, " = ")
+      case FactorFunction.Linear => s"Linear(${printHead(head.terms, ", ")})"
+      case FactorFunction.Ratio  => s"Ratio(${printHead(head.terms, ", ")})"
+      case FactorFunction.IsTrue => printHead(head.terms, "")
+    }
+  }
+
   def print(stmt: ExtractionRule): String = {
     ( stmt.supervision map (s => s"@label(${s})\n") getOrElse("") ) +
     stmt.headName + print(stmt.q) + ".\n"
@@ -154,9 +174,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: InferenceRule): String = {
-    ( stmt.function map { f => s"@function(${f})\n" } getOrElse("") ) +
     ( s"@weight(${stmt.weights.variables map print mkString(", ")})\n"
-    ) + stmt.headName + print(stmt.q) + ".\n"
+    ) + print(stmt.head) + print(stmt.q) + ".\n"
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 18ef37fbe..23a81b227 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -16,15 +16,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       case s: ExtractionRule => {
         heads += s.headName
       }
-      case s: InferenceRule => {
-        heads += s.headName
-      }
       case s: FunctionDeclaration => {
         functionDeclaration += { s.functionName -> s }
       }
       case s: FunctionCallRule => {
         heads += s.output
       }
+      case _ =>
     }
   }
 
@@ -99,13 +97,19 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         error(stmt, s""""${name}": number of columns in the query does not match number of columns in the schema""")
     }
     def checkBodyAtom(a: BodyAtom) = check(a.name, a.terms.size)
-    def checkCq(headName: String, cq: ConjunctiveQuery) {
-      check(headName, cq.headTerms.size)
+    def checkHeadAtom(a: HeadAtom) = check(a.name, a.terms.size)
+    def checkCq(cq: ConjunctiveQuery) {
       cq.bodies foreach checkBodyAtoms(checkBodyAtom)
     }
     stmt match {
-      case s: ExtractionRule   => checkCq(s.headName, s.q)
-      case s: InferenceRule    => checkCq(s.headName, s.q)
+      case s: ExtractionRule   => {
+        check(s.headName, s.q.headTerms.size)
+        checkCq(s.q)
+      }
+      case s: InferenceRule    => {
+        s.head.terms foreach checkHeadAtom
+        checkCq(s.q)
+      }
       case _ =>
     }
   }
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 8ba11e63d..3d2e8093e 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -105,7 +105,7 @@ FROM words R0, words R1
         }
       
 
-        deepdive.inference.factors.tag_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "tag.R0.id" , R1.feature AS "dd_weight_column_0" 
           FROM tag R0, word_features R1
@@ -117,6 +117,6 @@ FROM words R0, words R1
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_0, extraction_rule_1, extraction_rule_3, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_8, extraction_rule_5, extraction_rule_7]
-deepdive.pipeline.pipelines.inference: [tag_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_8, extraction_rule_5, extraction_rule_7, tag_0]
+deepdive.pipeline.pipelines.inference: [inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_8, extraction_rule_5, extraction_rule_7, inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/factor_functions/input.ddl b/test/expected-output-test/factor_functions/input.ddl
new file mode 100644
index 000000000..e4c31c642
--- /dev/null
+++ b/test/expected-output-test/factor_functions/input.ddl
@@ -0,0 +1,6 @@
+R(a int, b int, c int).
+S?(x int).
+Q?(x int).
+
+@weight(y)
+Q(x) => Q(y) :- R(x, y, z).
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index e9ea50a68..a84485712 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -223,29 +223,29 @@ SELECT DISTINCT R0.wid, id, label
       }
     
 
-        deepdive.inference.factors.dd_new_q2_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM dd_new_q2 R0, dd_delta_features R1
+          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
+          FROM dd_new_q1 R0, dd_delta_features R1
         WHERE R1.word_id = R0.wid """
-          function: "Imply(dd_new_q2.R0.label)"
+          function: "Imply(dd_new_q1.R0.label)"
           weight: "?(dd_weight_column_0)"
         }
       
 
-        deepdive.inference.factors.dd_new_q1_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
-          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM dd_new_q1 R0, dd_delta_features R1
+          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
+          FROM dd_new_q2 R0, dd_delta_features R1
         WHERE R1.word_id = R0.wid """
-          function: "Imply(dd_new_q1.R0.label)"
+          function: "Imply(dd_new_q2.R0.label)"
           weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_10, extraction_rule_5, extraction_rule_14, extraction_rule_6, extraction_rule_1, extraction_rule_17, extraction_rule_9, extraction_rule_2, extraction_rule_13, extraction_rule_18]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_q2_0, dd_new_q1_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15, dd_new_q2_0, dd_new_q1_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index 6d696e434..4f854bb71 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -102,7 +102,7 @@ q2.label: Boolean
       }
     
 
-        deepdive.inference.factors.q1_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
@@ -112,7 +112,7 @@ q2.label: Boolean
         }
       
 
-        deepdive.inference.factors.q2_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
@@ -124,6 +124,6 @@ q2.label: Boolean
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, q1_0, q2_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, inference_rule_0, inference_rule_1]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 8a684eacf..109a00cf7 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -102,7 +102,7 @@ q2.label: Boolean
       }
     
 
-        deepdive.inference.factors.q1_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
@@ -112,7 +112,7 @@ q2.label: Boolean
         }
       
 
-        deepdive.inference.factors.q2_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
@@ -124,6 +124,6 @@ q2.label: Boolean
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [q1_0, q2_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, q1_0, q2_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
index a0dab2c2b..f0e488c26 100644
--- a/test/expected-output-test/ocr_example/print-incremental.expected
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -13,7 +13,7 @@ dd_new_features(id BIGSERIAL,
                 feature_id INT,
                 feature_val BOOLEAN).
 
-dd_new_features(id, word_id, feature_id, feature_val)  :-
+dd_new_features(id, word_id, feature_id, feature_val) :-
     features(id, word_id, feature_id, feature_val);
     dd_delta_features(id, word_id, feature_id, feature_val).
 
@@ -26,7 +26,7 @@ dd_delta_label1(wid INT,
 dd_new_label1(wid INT,
               val BOOLEAN).
 
-dd_new_label1(wid, val)  :-
+dd_new_label1(wid, val) :-
     label1(wid, val);
     dd_delta_label1(wid, val).
 
@@ -39,7 +39,7 @@ dd_delta_label2(wid INT,
 dd_new_label2(wid INT,
               val BOOLEAN).
 
-dd_new_label2(wid, val)  :-
+dd_new_label2(wid, val) :-
     label2(wid, val);
     dd_delta_label2(wid, val).
 
@@ -49,7 +49,7 @@ dd_delta_q1?(wid INT).
 
 dd_new_q1?(wid INT).
 
-dd_new_q1(wid)  :-
+dd_new_q1(wid) :-
     q1(wid);
     dd_delta_q1(wid).
 
@@ -59,23 +59,23 @@ dd_delta_q2?(wid INT).
 
 dd_new_q2?(wid INT).
 
-dd_new_q2(wid)  :-
+dd_new_q2(wid) :-
     q2(wid);
     dd_delta_q2(wid).
 
 @label(val)
-dd_delta_q1(wid)  :-
+dd_delta_q1(wid) :-
     dd_delta_label1(wid, val).
 
 @label(val)
-dd_delta_q2(wid)  :-
+dd_delta_q2(wid) :-
     dd_delta_label2(wid, val).
 
 @weight(fid)
-dd_new_q1(wid)  :-
+dd_new_q1(wid) :-
     dd_delta_features(id, wid, fid, fval).
 
 @weight(fid)
-dd_new_q2(wid)  :-
+dd_new_q2(wid) :-
     dd_delta_features(id, wid, fid, fval).
 
diff --git a/test/expected-output-test/semantics/input.ddl b/test/expected-output-test/semantics/input.ddl
deleted file mode 100644
index 389ed0c5b..000000000
--- a/test/expected-output-test/semantics/input.ddl
+++ /dev/null
@@ -1,8 +0,0 @@
-R(a int, b int, c int).
-S(a int, b int, c int).
-T(a int, b int, c int).
-Q?(x int).
-
-@function(Linear)
-@weight(y)
-Q(x) :- R(x, y, z); R(x, y, z), S(y, z, w); S(y, x, w), T(x, z, w).
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index ad309aa0a..4c78b95d1 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -254,7 +254,7 @@ FROM dd_delta_friends R0
       }
     
 
-        deepdive.inference.factors.dd_new_cancer_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
@@ -267,7 +267,7 @@ FROM dd_delta_friends R0
         }
       
 
-        deepdive.inference.factors.dd_new_smoke_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_delta_smoke R1, friends R2
@@ -282,7 +282,7 @@ FROM dd_delta_friends R0
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_cancer_0, dd_new_smoke_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_cancer_0, dd_new_smoke_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index 0081014f5..fcdb96463 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -110,7 +110,7 @@ cancer.label: Boolean
       }
     
 
-        deepdive.inference.factors.cancer_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
@@ -120,7 +120,7 @@ cancer.label: Boolean
         }
       
 
-        deepdive.inference.factors.smoke_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
@@ -132,6 +132,6 @@ cancer.label: Boolean
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, cancer_0, smoke_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, inference_rule_0, inference_rule_1]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 109c667d8..fbe109863 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -110,7 +110,7 @@ cancer.label: Boolean
       }
     
 
-        deepdive.inference.factors.cancer_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
           FROM cancer R0, smoke R1, person_smokes R2
@@ -120,7 +120,7 @@ cancer.label: Boolean
         }
       
 
-        deepdive.inference.factors.smoke_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
@@ -132,6 +132,6 @@ cancer.label: Boolean
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [cancer_0, smoke_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, cancer_0, smoke_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index adcb8864c..b46ed6539 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_person(person_id bigint,
 dd_new_person(person_id bigint,
               name text).
 
-dd_new_person(person_id, name)  :-
+dd_new_person(person_id, name) :-
     person(person_id, name);
     dd_delta_person(person_id, name).
 
@@ -20,7 +20,7 @@ dd_delta_person_has_cancer(person_id bigint,
 dd_new_person_has_cancer(person_id bigint,
                          has_cancer boolean).
 
-dd_new_person_has_cancer(person_id, has_cancer)  :-
+dd_new_person_has_cancer(person_id, has_cancer) :-
     person_has_cancer(person_id, has_cancer);
     dd_delta_person_has_cancer(person_id, has_cancer).
 
@@ -33,7 +33,7 @@ dd_delta_person_smokes(person_id bigint,
 dd_new_person_smokes(person_id bigint,
                      smokes boolean).
 
-dd_new_person_smokes(person_id, smokes)  :-
+dd_new_person_smokes(person_id, smokes) :-
     person_smokes(person_id, smokes);
     dd_delta_person_smokes(person_id, smokes).
 
@@ -46,7 +46,7 @@ dd_delta_friends(person_id bigint,
 dd_new_friends(person_id bigint,
                friend_id bigint).
 
-dd_new_friends(person_id, friend_id)  :-
+dd_new_friends(person_id, friend_id) :-
     friends(person_id, friend_id);
     dd_delta_friends(person_id, friend_id).
 
@@ -56,7 +56,7 @@ dd_delta_smoke?(person_id bigint).
 
 dd_new_smoke?(person_id bigint).
 
-dd_new_smoke(person_id)  :-
+dd_new_smoke(person_id) :-
     smoke(person_id);
     dd_delta_smoke(person_id).
 
@@ -66,27 +66,27 @@ dd_delta_cancer?(person_id bigint).
 
 dd_new_cancer?(person_id bigint).
 
-dd_new_cancer(person_id)  :-
+dd_new_cancer(person_id) :-
     cancer(person_id);
     dd_delta_cancer(person_id).
 
 @label(l)
-dd_delta_smoke(pid)  :-
+dd_delta_smoke(pid) :-
     dd_delta_person_smokes(pid, l).
 
 @label(l)
-dd_delta_cancer(pid)  :-
+dd_delta_cancer(pid) :-
     dd_delta_person_has_cancer(pid, l).
 
 @weight(0.5)
-dd_new_cancer(pid)  :-
+dd_new_cancer(pid) :-
     dd_delta_smoke(pid),
     person_smokes(pid, l);
     dd_new_smoke(pid),
     dd_delta_person_smokes(pid, l).
 
 @weight(0.4)
-dd_new_smoke(pid)  :-
+dd_new_smoke(pid) :-
     dd_delta_smoke(pid1),
     friends(pid1, pid);
     dd_new_smoke(pid1),
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index e7c1c20d1..a973f3a01 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -320,7 +320,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 
-        deepdive.inference.factors.dd_new_has_spouse_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -335,7 +335,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
+deepdive.pipeline.pipelines.inference: [inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 2f00faedb..b417d3c24 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -146,7 +146,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
-        deepdive.inference.factors.has_spouse_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -158,6 +158,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
-deepdive.pipeline.pipelines.inference: [has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, has_spouse_0]
+deepdive.pipeline.pipelines.inference: [inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, inference_rule_0]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index ba5983cbc..12825b755 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -146,7 +146,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
-        deepdive.inference.factors.has_spouse_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -158,6 +158,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
-deepdive.pipeline.pipelines.inference: [has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, has_spouse_0]
+deepdive.pipeline.pipelines.inference: [inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index cdd9a95e4..4177762f3 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_articles(article_id text,
 dd_new_articles(article_id text,
                 text text).
 
-dd_new_articles(article_id, text)  :-
+dd_new_articles(article_id, text) :-
     articles(article_id, text);
     dd_delta_articles(article_id, text).
 
@@ -41,7 +41,7 @@ dd_new_sentences(document_id text,
                  sentence_offset int,
                  sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)  :-
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
     sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
@@ -63,7 +63,7 @@ dd_new_people_mentions(sentence_id text,
                        text text,
                        mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id)  :-
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
     people_mentions(sentence_id, start_position, length, text, mention_id);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
@@ -88,7 +88,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              relation_id text,
                              is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true)  :-
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
     has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
@@ -101,7 +101,7 @@ dd_delta_has_spouse_features(relation_id text,
 dd_new_has_spouse_features(relation_id text,
                            feature text).
 
-dd_new_has_spouse_features(relation_id, feature)  :-
+dd_new_has_spouse_features(relation_id, feature) :-
     has_spouse_features(relation_id, feature);
     dd_delta_has_spouse_features(relation_id, feature).
 
@@ -111,11 +111,11 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
-dd_new_has_spouse(relation_id)  :-
+dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions += ext_people(s, words, ner_tags)  :-
+dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -124,7 +124,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -136,7 +136,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
+dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -161,11 +161,11 @@ function ext_has_spouse_features
         handles tsv lines.
 
 @label(l)
-dd_delta_has_spouse(rid)  :-
+dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
 
 @weight(f)
-dd_new_has_spouse(rid)  :-
+dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 03ca349fd..a973f3a01 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -320,7 +320,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 
-        deepdive.inference.factors.dd_new_has_spouse_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -328,14 +328,14 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Linear(dd_new_has_spouse.R0.label)"
+          function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
         }
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0]
+deepdive.pipeline.pipelines.inference: [inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index c924ede8d..61f64c208 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -66,7 +66,6 @@ function ext_has_spouse_features over like ext_has_spouse_features_input
 @label(l)
 has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
 
-@function(Linear)
 @weight(f)
 has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index edb1888da..358552514 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_articles(article_id text,
 dd_new_articles(article_id text,
                 text text).
 
-dd_new_articles(article_id, text)  :-
+dd_new_articles(article_id, text) :-
     articles(article_id, text);
     dd_delta_articles(article_id, text).
 
@@ -41,7 +41,7 @@ dd_new_sentences(document_id text,
                  sentence_offset int,
                  sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)  :-
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
     sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
@@ -63,7 +63,7 @@ dd_new_people_mentions(sentence_id text,
                        text text,
                        mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id)  :-
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
     people_mentions(sentence_id, start_position, length, text, mention_id);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
@@ -88,7 +88,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              relation_id text,
                              is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true)  :-
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
     has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
@@ -101,7 +101,7 @@ dd_delta_has_spouse_features(relation_id text,
 dd_new_has_spouse_features(relation_id text,
                            feature text).
 
-dd_new_has_spouse_features(relation_id, feature)  :-
+dd_new_has_spouse_features(relation_id, feature) :-
     has_spouse_features(relation_id, feature);
     dd_delta_has_spouse_features(relation_id, feature).
 
@@ -111,11 +111,11 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
-dd_new_has_spouse(relation_id)  :-
+dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions += ext_people(s, words, ner_tags)  :-
+dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 @mode(inc)
@@ -125,7 +125,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -137,7 +137,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
+dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -162,12 +162,11 @@ function ext_has_spouse_features
         handles tsv lines.
 
 @label(l)
-dd_delta_has_spouse(rid)  :-
+dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
 
-@function(Linear)
 @weight(f)
-dd_new_has_spouse(rid)  :-
+dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index acd0fe36b..58088223f 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -320,7 +320,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 
-        deepdive.inference.factors.dd_new_has_spouse_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -333,7 +333,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 
-        deepdive.inference.factors.dd_new_has_spouse_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
@@ -345,7 +345,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_new_has_spouse_0, dd_new_has_spouse_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_new_has_spouse_0, dd_new_has_spouse_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 362edf96c..43684586b 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -146,7 +146,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
-        deepdive.inference.factors.has_spouse_0 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -156,7 +156,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
-        deepdive.inference.factors.has_spouse_1 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
@@ -168,6 +168,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
-deepdive.pipeline.pipelines.inference: [has_spouse_0, has_spouse_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, has_spouse_0, has_spouse_1]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 95c66b074..eb4cf60ee 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -7,7 +7,7 @@ dd_delta_articles(article_id text,
 dd_new_articles(article_id text,
                 text text).
 
-dd_new_articles(article_id, text)  :-
+dd_new_articles(article_id, text) :-
     articles(article_id, text);
     dd_delta_articles(article_id, text).
 
@@ -41,7 +41,7 @@ dd_new_sentences(document_id text,
                  sentence_offset int,
                  sentence_id text).
 
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id)  :-
+dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
     sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
     dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
 
@@ -63,7 +63,7 @@ dd_new_people_mentions(sentence_id text,
                        text text,
                        mention_id text).
 
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id)  :-
+dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
     people_mentions(sentence_id, start_position, length, text, mention_id);
     dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
 
@@ -88,7 +88,7 @@ dd_new_has_spouse_candidates(person1_id text,
                              relation_id text,
                              is_true boolean).
 
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true)  :-
+dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
     has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
     dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
 
@@ -101,7 +101,7 @@ dd_delta_has_spouse_features(relation_id text,
 dd_new_has_spouse_features(relation_id text,
                            feature text).
 
-dd_new_has_spouse_features(relation_id, feature)  :-
+dd_new_has_spouse_features(relation_id, feature) :-
     has_spouse_features(relation_id, feature);
     dd_delta_has_spouse_features(relation_id, feature).
 
@@ -111,11 +111,11 @@ dd_delta_has_spouse?(relation_id text).
 
 dd_new_has_spouse?(relation_id text).
 
-dd_new_has_spouse(relation_id)  :-
+dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions += ext_people(s, words, ner_tags)  :-
+dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -124,7 +124,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
     dd_delta_people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id);
     dd_new_people_mentions(s, a, b, p1_text, p1_id),
@@ -136,7 +136,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
+dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
     dd_delta_sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -161,18 +161,18 @@ function ext_has_spouse_features
         handles tsv lines.
 
 @label(l)
-dd_delta_has_spouse(rid)  :-
+dd_delta_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
 
 @weight(f)
-dd_new_has_spouse(rid)  :-
+dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f);
     dd_new_has_spouse_candidates(a, b, c, d, rid, l),
     dd_delta_has_spouse_features(rid, f).
 
 @weight(3.0)
-dd_new_has_spouse(rid)  :-
+dd_new_has_spouse(rid) :-
     dd_new_has_spouse(rid2),
     dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 484d2e109..fb8f623a2 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -93,27 +93,7 @@ c.label: Boolean
           style: "sql_extractor"
         }
 
-        deepdive.inference.factors.e_0 {
-          input_query: """
-          SELECT R0.id AS "e.R0.id" 
-          FROM e R0, b R1
-        WHERE R1.k = R0.k """
-          function: "Imply(e.R0.label)"
-          weight: "-10"
-        }
-      
-
-        deepdive.inference.factors.f_1 {
-          input_query: """
-          SELECT R0.id AS "f.R0.id" 
-          FROM f R0, b R1
-        WHERE R1.k = R0.k """
-          function: "Imply(f.R0.label)"
-          weight: "-0.3"
-        }
-      
-
-        deepdive.inference.factors.a_2 {
+        deepdive.inference.factors.inference_rule_0 {
           input_query: """
           SELECT R0.id AS "a.R0.id" , (R0.k + R1.p) AS "dd_weight_column_0" 
           FROM a R0, b R1
@@ -123,7 +103,7 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.c_3 {
+        deepdive.inference.factors.inference_rule_1 {
           input_query: """
           SELECT R0.id AS "c.R0.id" 
           FROM c R0, b R1
@@ -133,7 +113,7 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.d_4 {
+        deepdive.inference.factors.inference_rule_2 {
           input_query: """
           SELECT R0.id AS "d.R0.id" , R0.k AS "dd_weight_column_0" , R1.p AS "dd_weight_column_1" 
           FROM d R0, b R1
@@ -142,8 +122,28 @@ c.label: Boolean
           weight: "?(dd_weight_column_0, dd_weight_column_1)"
         }
       
+
+        deepdive.inference.factors.inference_rule_3 {
+          input_query: """
+          SELECT R0.id AS "e.R0.id" 
+          FROM e R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(e.R0.label)"
+          weight: "-10"
+        }
+      
+
+        deepdive.inference.factors.inference_rule_4 {
+          input_query: """
+          SELECT R0.id AS "f.R0.id" 
+          FROM f R0, b R1
+        WHERE R1.k = R0.k """
+          function: "Imply(f.R0.label)"
+          weight: "-0.3"
+        }
+      
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_3, extraction_rule_4, extraction_rule_0, extraction_rule_5, extraction_rule_1, extraction_rule_2]
-deepdive.pipeline.pipelines.inference: [e_0, f_1, a_2, c_3, d_4]
-deepdive.pipeline.pipelines.endtoend: [e_0, f_1, a_2, c_3, d_4]
+deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1, inference_rule_2, inference_rule_3, inference_rule_4]
+deepdive.pipeline.pipelines.endtoend: [inference_rule_0, inference_rule_1, inference_rule_2, inference_rule_3, inference_rule_4]
 deepdive.pipeline.pipelines.cleanup: [cleanup]

From bd03d7705079d555e8a8d7bf9a599d4d36809d35 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 31 Jul 2015 15:27:09 -0700
Subject: [PATCH 204/347] Bug fix and clean up

1. Fix UNION ALL bug in generating SQL queries.
2. Rewrite smoke and spouse example using new imply head
3. Code clean up
---
 examples/smoke.ddl                            |  4 +-
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 64 ++++++++++---------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 54 +++++++++-------
 .../ocr_example/print.expected                |  8 +--
 .../compile-incremental.expected              | 16 ++---
 .../compile-materialization.expected          | 10 +--
 .../smoke_example/compile.expected            | 10 +--
 .../smoke_example/print-incremental.expected  | 10 +--
 .../smoke_example/print.expected              | 10 ++-
 .../compile-incremental.expected              |  4 ++
 .../spouse_example/print.expected             | 10 +--
 .../compile-incremental.expected              |  4 ++
 .../compile-incremental.expected              |  8 ++-
 .../compile.expected                          |  4 +-
 .../spouse_example_new_inference/input.ddl    |  3 +-
 .../print-incremental.expected                |  3 +-
 .../print.expected                            | 13 ++--
 17 files changed, 120 insertions(+), 115 deletions(-)

diff --git a/examples/smoke.ddl b/examples/smoke.ddl
index 63a3ca777..fa8434d47 100644
--- a/examples/smoke.ddl
+++ b/examples/smoke.ddl
@@ -36,7 +36,7 @@ smoke(pid)  :- person_smokes(pid, l).
 cancer(pid) :- person_has_cancer(pid, l).
 
 @weight(0.5)
-cancer(pid) :- smoke(pid), person_smokes(pid, l).
+smoke(pid) => cancer(pid) :- person_smokes(pid, l).
 
 @weight(0.4)
-smoke(pid)  :- smoke(pid1), friends(pid1, pid).
\ No newline at end of file
+smoke(pid1) => smoke(pid) :- friends(pid1, pid).
\ No newline at end of file
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index fb00eb4c4..64b686c6a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -95,8 +95,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
   var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
   var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
-  var functionCallList              : ListBuffer[FunctionCallRule] = new ListBuffer[FunctionCallRule]()
-  var inferenceRules : ListBuffer[InferenceRule] = new ListBuffer[InferenceRule]()
+  var functionCallList              : List[FunctionCallRule] = Nil
+  var inferenceRules                : List[InferenceRule] = Nil
 
   def init() = {
     // generate the statements.
@@ -113,10 +113,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         if (decl.isQuery) variableTableNames += r
       }
       case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
-      case f: FunctionCallRule => functionCallList += f
-      case f: InferenceRule => inferenceRules += f
       case _ =>
     }
+    functionCallList = statements collect { case s: FunctionCallRule => s }
+    inferenceRules   = statements collect { case s: InferenceRule    => s }
     groupByHead(statements)
     analyzeVisible(statements)
     analyzeDependency(statements)
@@ -130,14 +130,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Given a statement, resolve its name for the compiled extractor block.
   def resolveExtractorBlockName(s: Statement): String = s"extraction_rule_${statements indexOf s}"
-  // {
-  //   s match {
-  //     case s: SchemaDeclaration => s"extraction_rule_${statements indexOf s}"
-  //     case s: FunctionCallRule  => s"extraction_rule_${statements indexOf s}"
-  //     case s: ExtractionRule    => s"extraction_rule_${statements indexOf s}"
-  //     case s: InferenceRule     => s"extraction_rule_${statements indexOf s}"
-  //   }
-  // }
 
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
@@ -166,6 +158,11 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     if( ground_relations contains relName ) !ground_relations(relName) else true
   }
 
+  // has schema declared
+  def hasSchemaDeclared(relName: String) : Boolean = {
+    schemaDeclarationGroupByHead contains relName
+  }
+
   // Group statements by head
   def groupByHead(statements: List[Statement]) = {
     // Compile compilation states by head name based on type
@@ -201,14 +198,17 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++
       functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
+    def collectUsedRelations(bodies: List[List[Body]]): Set[Statement] = {
+      (bodies.flatten collect { case x: BodyAtom => x.name }
+      flatMap (stmtByHeadName get _)).toSet.flatten.flatten
+    }
+
     // Look at the body of each statement to construct a dependency graph
     statements foreach {
       case f : FunctionCallRule => dependencies += {
-        f -> ((( f.q.bodies.flatten collect { case x: BodyAtom => x.name })
-          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+        f -> collectUsedRelations(f.q.bodies) }
       case e : ExtractionRule   => dependencies += {
-        e -> (((e.q.bodies.flatten collect { case x: BodyAtom => x.name })
-          flatMap (stmtByHeadName get _)).toSet.flatten.flatten) }
+        e -> collectUsedRelations(e.q.bodies) }
       case _ =>
     }
   }
@@ -442,8 +442,8 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
 
   def generateSQL(useAlias: Boolean) = {
     val head = generateSQLHead(useAlias)
-    val body = cq.bodies map generateSQLBody mkString("\nUNION ALL\n")
-    s"SELECT ${head}\n${body}"
+    val body = cq.bodies map generateSQLBody
+    body map { b => s"SELECT ${head}\n${b}" } mkString("\nUNION ALL\n")
   }
 
 }
@@ -454,11 +454,13 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
 
+  def isForIncremental(name: String) = name startsWith "dd_new_"
+
   // Generate schema and cleanup part for database
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
     for (stmt <- stmts) {
-      if ((stmt.a.name startsWith "dd_new_") && (ss.isQueryTerm(stmt.a.name))) {
+      if (isForIncremental(stmt.a.name) && (ss.isQueryTerm(stmt.a.name))) {
       } else {
         var columnDecls = stmt.a.terms.zipWithIndex map {
           case (name,i) => s"${name} ${stmt.a.types(i)}"
@@ -484,7 +486,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     }
     // Cleanup incremental table extractor
     val truncateTableList = (stmts map (x =>
-      if ((x.a.name startsWith "dd_new_") && (ss.isQueryTerm(x.a.name))) ""
+      if (isForIncremental(x.a.name) && (ss.isQueryTerm(x.a.name))) ""
       else s"TRUNCATE ${x.a.name};")).filter(_ != "")
     if (truncateTableList.length > 0) {
       schemas += s"""
@@ -515,9 +517,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
-        } else if ((ss.schemaDeclarationGroupByHead contains stmt.headName) &&
+        } else if ((ss.hasSchemaDeclared(stmt.headName)) &&
           (ss.schemaDeclarationGroupByHead(stmt.headName)(0).isQuery) &&
-          (stmt.headName startsWith "dd_new_")) {
+          isForIncremental(stmt.headName)) {
           val headStr = qc.generateSQLHead(false)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, id, label
           ${ qc.generateSQLBody(cqBody) }
@@ -527,7 +529,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
           var useAlias = ss.mode match {
             case MERGE => false
-            case _     => if (stmt.headName.startsWith("dd_new_")) false else true
+            case _     => !isForIncremental(stmt.headName)
           }
           inputQueries += qc.generateSQL(useAlias)
         }
@@ -536,17 +538,17 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val blockName = ss.resolveExtractorBlockName(stmts(0))
     val sqlCmdForCleanUp = ss.mode match {
       case MERGE => s"TRUNCATE ${stmts(0).headName};"
-      case _ => if (ss.schemaDeclarationGroupByHead contains stmts(0).headName) {
-        if (stmts(0).headName.startsWith("dd_new_") && !(ss.isQueryTerm(stmts(0).headName)))
+      case _ => if (ss.hasSchemaDeclared(stmts(0).headName)) {
+        if (isForIncremental(stmts(0).headName) && !(ss.isQueryTerm(stmts(0).headName)))
           s"TRUNCATE ${stmts(0).headName};"
         else ""
       } else s"DROP VIEW IF EXISTS ${stmts(0).headName};"
     }
     val createTable = ss.mode match {
       case MERGE => true
-      case _ => (!(stmts(0).headName startsWith "dd_new_") &&
-        (ss.schemaDeclarationGroupByHead contains stmts(0).headName)) ||
-        ((stmts(0).headName startsWith "dd_new_") &&
+      case _ => (!isForIncremental(stmts(0).headName) &&
+        (ss.hasSchemaDeclared(stmts(0).headName))) ||
+        (isForIncremental(stmts(0).headName) &&
         !(ss.isQueryTerm(stmts(0).headName)))
     }
     val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
@@ -602,6 +604,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       var weight = ""
       for (cqBody <- stmt.q.bodies) {
         // edge query
+        // Here we need to select from the bodies atoms as well as the head atoms,
+        // which are the variable relations.
+        // This is achieved by puting head atoms into the body.
         val headAsBody = stmt.head.terms map { x =>
           BodyAtom(x.name, x.terms map {
             case x: VarExpr => VarPattern(x.name)
@@ -643,7 +648,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             s"""${x.name}.R${fakeBody indexOf x}.label"""
           else ""
           }).filter(_ != "")
-          val firstFunc = funcBody(0)
 
           val function = stmt.head.function match {
             case FactorFunction.Imply  => "Imply"
@@ -657,7 +661,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
               case Some(MultinomialType(_)) => "Multinomial"
             }
           }
-          func = s"""${function}(${(funcBody.tail :+ firstFunc).mkString(", ")})"""
+          func = s"""${function}(${funcBody.mkString(", ")})"""
         }
         // weight
         if (weight.length == 0) {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 1816b0fe1..072f8e75a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -310,29 +310,37 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def headAtom = relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
     case (r ~ expressions) => HeadAtom(r, expressions)
   }
-  def implyHead = rep1sep(headAtom, ",") ~ "=>" ~ headAtom ^^ {
-    case (a ~ _ ~ b) => InferenceRuleHead(FactorFunction.Imply, a :+ b)
-  }
-  def isTrueHead = headAtom ^^ { x => InferenceRuleHead(FactorFunction.IsTrue, List(x)) }
-  def equalHead = headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
-    InferenceRuleHead(FactorFunction.Equal, a +: b)
-  }
-  def andHead   = headAtom ~ "^" ~ rep1sep(headAtom, "^") ^^ { case (a ~ _ ~ b) =>
-    InferenceRuleHead(FactorFunction.And, a +: b)
-  }
-  def orHead    = headAtom ~ "v" ~ rep1sep(headAtom, "v") ^^ { case (a ~ _ ~ b) =>
-    InferenceRuleHead(FactorFunction.Or, a +: b)
-  }
-  def multinomialHead = "Multinomial" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
-    InferenceRuleHead(FactorFunction.Multinomial, _)
-  }
-  def linearHead = "Linear" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
-    InferenceRuleHead(FactorFunction.Linear, _)
-  }
-  def ratioHead = "Ratio" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
-    InferenceRuleHead(FactorFunction.Ratio, _)
+
+  def implyHeadAtoms = rep1sep(headAtom, ",") ~ "=>" ~ headAtom ^^ {
+    case (a ~ _ ~ b) => a :+ b
   }
-  def inferenceRuleHead = implyHead | equalHead | andHead | orHead | multinomialHead | linearHead | ratioHead | isTrueHead
+
+  def inferenceRuleHead =
+  ( implyHeadAtoms ^^ {
+      InferenceRuleHead(FactorFunction.Imply, _)
+    }
+  | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
+      InferenceRuleHead(FactorFunction.Equal, a +: b)
+    }
+  | headAtom ~ "^" ~ rep1sep(headAtom, "^") ^^ { case (a ~ _ ~ b) =>
+      InferenceRuleHead(FactorFunction.And, a +: b)
+    }
+  | headAtom ~ "v" ~ rep1sep(headAtom, "v") ^^ { case (a ~ _ ~ b) =>
+      InferenceRuleHead(FactorFunction.Or, a +: b)
+    }
+  | "Multinomial" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
+      InferenceRuleHead(FactorFunction.Multinomial, _)
+    }
+  | "@semantics(linear)" ~> implyHeadAtoms ^^ {
+      InferenceRuleHead(FactorFunction.Linear, _)
+    }
+  | "@semantics(ratio)" ~> implyHeadAtoms ^^ {
+      InferenceRuleHead(FactorFunction.Ratio, _)
+    }
+  | headAtom ^^ {
+      x => InferenceRuleHead(FactorFunction.IsTrue, List(x))
+    }
+  )
 
   def inferenceConjunctiveQuery : Parser[ConjunctiveQuery] =
     ":-" ~> rep1sep(cqConjunctiveBody, ";") ^^ {
@@ -360,8 +368,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   }
 
-  def error(meesage: String) = throw new RuntimeException(meesage)
-
   def parseProgramFile(fileName: String): List[Statement] = {
     val source = scala.io.Source.fromFile(fileName)
     try parseProgram(source.getLines mkString "\n", Some(fileName))
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
index 4249fde41..2828b5e91 100644
--- a/test/expected-output-test/ocr_example/print.expected
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -14,18 +14,18 @@ q1?(wid INT).
 q2?(wid INT).
 
 @label(val)
-q1(wid)  :-
+q1(wid) :-
     label1(wid, val).
 
 @label(val)
-q2(wid)  :-
+q2(wid) :-
     label2(wid, val).
 
 @weight(fid)
-q1(wid)  :-
+q1(wid) :-
     features(id, wid, fid, fval).
 
 @weight(fid)
-q2(wid)  :-
+q2(wid) :-
     features(id, wid, fid, fval).
 
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 4c78b95d1..e0c500474 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -256,26 +256,20 @@ FROM dd_delta_friends R0
 
         deepdive.inference.factors.inference_rule_0 {
           input_query: """
-          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
-          FROM dd_new_cancer R0, dd_delta_smoke R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id  UNION ALL 
-          SELECT R0.id AS "dd_new_cancer.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
-          FROM dd_new_cancer R0, dd_new_smoke R1, dd_delta_person_smokes R2
+          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_cancer.R1.id" 
+          FROM dd_new_smoke R0, dd_new_cancer R1, dd_delta_person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(dd_delta_smoke.R1.label, dd_new_cancer.R0.label)"
+          function: "Imply(dd_new_smoke.R0.label, dd_new_cancer.R1.label)"
           weight: "0.5"
         }
       
 
         deepdive.inference.factors.inference_rule_1 {
           input_query: """
-          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_delta_smoke.R1.id" 
-          FROM dd_new_smoke R0, dd_delta_smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id  UNION ALL 
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
-          function: "Imply(dd_delta_smoke.R1.label, dd_new_smoke.R0.label)"
+        WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
+          function: "Imply(dd_new_smoke.R0.label, dd_new_smoke.R1.label)"
           weight: "0.4"
         }
       
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index fcdb96463..ef0420ddf 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -112,10 +112,10 @@ cancer.label: Boolean
 
         deepdive.inference.factors.inference_rule_0 {
           input_query: """
-          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
-          FROM cancer R0, smoke R1, person_smokes R2
+          SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
+          FROM smoke R0, cancer R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(smoke.R1.label, cancer.R0.label)"
+          function: "Imply(smoke.R0.label, cancer.R1.label)"
           weight: "0.5"
         }
       
@@ -124,8 +124,8 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
-          function: "Imply(smoke.R1.label, smoke.R0.label)"
+        WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
+          function: "Imply(smoke.R0.label, smoke.R1.label)"
           weight: "0.4"
         }
       
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index fbe109863..5ec2e5abd 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -112,10 +112,10 @@ cancer.label: Boolean
 
         deepdive.inference.factors.inference_rule_0 {
           input_query: """
-          SELECT R0.id AS "cancer.R0.id" , R1.id AS "smoke.R1.id" 
-          FROM cancer R0, smoke R1, person_smokes R2
+          SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
+          FROM smoke R0, cancer R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(smoke.R1.label, cancer.R0.label)"
+          function: "Imply(smoke.R0.label, cancer.R1.label)"
           weight: "0.5"
         }
       
@@ -124,8 +124,8 @@ cancer.label: Boolean
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R1.person_id  AND R2.friend_id = R0.person_id """
-          function: "Imply(smoke.R1.label, smoke.R0.label)"
+        WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
+          function: "Imply(smoke.R0.label, smoke.R1.label)"
           weight: "0.4"
         }
       
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index b46ed6539..c585081d0 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -79,16 +79,10 @@ dd_delta_cancer(pid) :-
     dd_delta_person_has_cancer(pid, l).
 
 @weight(0.5)
-dd_new_cancer(pid) :-
-    dd_delta_smoke(pid),
-    person_smokes(pid, l);
-    dd_new_smoke(pid),
+dd_new_smoke(pid) => dd_new_cancer(pid) :-
     dd_delta_person_smokes(pid, l).
 
 @weight(0.4)
-dd_new_smoke(pid) :-
-    dd_delta_smoke(pid1),
-    friends(pid1, pid);
-    dd_new_smoke(pid1),
+dd_new_smoke(pid1) => dd_new_smoke(pid) :-
     dd_delta_friends(pid1, pid).
 
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index 384367f7f..84176ea94 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -15,20 +15,18 @@ smoke?(person_id bigint).
 cancer?(person_id bigint).
 
 @label(l)
-smoke(pid)  :-
+smoke(pid) :-
     person_smokes(pid, l).
 
 @label(l)
-cancer(pid)  :-
+cancer(pid) :-
     person_has_cancer(pid, l).
 
 @weight(0.5)
-cancer(pid)  :-
-    smoke(pid),
+smoke(pid) => cancer(pid) :-
     person_smokes(pid, l).
 
 @weight(0.4)
-smoke(pid)  :-
-    smoke(pid1),
+smoke(pid1) => smoke(pid) :-
     friends(pid1, pid).
 
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index a973f3a01..dc17543dc 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -289,6 +289,7 @@ FROM dd_delta_sentences R0
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
 UNION ALL
+SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
 FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
@@ -304,12 +305,15 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index ed7cc5b88..13293b09a 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -29,7 +29,7 @@ has_spouse_features(relation_id text,
 
 has_spouse?(relation_id text).
 
-people_mentions += ext_people(s, words, ner_tags)  :-
+people_mentions += ext_people(s, words, ner_tags) :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -38,7 +38,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
+has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
@@ -48,7 +48,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
+has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -61,11 +61,11 @@ function ext_has_spouse_features
         handles tsv lines.
 
 @label(l)
-has_spouse(rid)  :-
+has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l).
 
 @weight(f)
-has_spouse(rid)  :-
+has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index a973f3a01..dc17543dc 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -289,6 +289,7 @@ FROM dd_delta_sentences R0
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
 UNION ALL
+SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
 FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
@@ -304,12 +305,15 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 58088223f..af799726f 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -289,6 +289,7 @@ FROM dd_delta_sentences R0
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
 UNION ALL
+SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
 FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
@@ -304,12 +305,15 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
+SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
@@ -337,8 +341,8 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
-        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
-          function: "Imply(dd_new_has_spouse.R1.label, dd_new_has_spouse.R0.label)"
+        WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
+          function: "Imply(dd_new_has_spouse.R0.label, dd_new_has_spouse.R1.label)"
           weight: "3.0"
         }
       
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 43684586b..645696441 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -160,8 +160,8 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
-        WHERE R2.relation_id = R0.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R1.relation_id """
-          function: "Imply(has_spouse.R1.label, has_spouse.R0.label)"
+        WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
+          function: "Imply(has_spouse.R0.label, has_spouse.R1.label)"
           weight: "3.0"
         }
       
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 953fcad60..1527e7b37 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -72,7 +72,6 @@ has_spouse(rid) :-
 
 @mode(inc)
 @weight(3.0)
-has_spouse(rid) :-
-  has_spouse(rid2),
+has_spouse(rid2) => has_spouse(rid) :-
   has_spouse_candidates(a1, b1, c1, d1, rid, l1),
   has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index eb4cf60ee..6eefc4324 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -172,8 +172,7 @@ dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_features(rid, f).
 
 @weight(3.0)
-dd_new_has_spouse(rid) :-
-    dd_new_has_spouse(rid2),
+dd_new_has_spouse(rid2) => dd_new_has_spouse(rid) :-
     dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index de36f3582..f2e1cdffe 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -29,7 +29,7 @@ has_spouse_features(relation_id text,
 
 has_spouse?(relation_id text).
 
-people_mentions += ext_people(s, words, ner_tags)  :-
+people_mentions += ext_people(s, words, ner_tags) :-
     sentences(a, b, words, c, d, e, ner_tags, f, s).
 
 function ext_people
@@ -38,7 +38,7 @@ function ext_people
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text)  :-
+has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
     people_mentions(s, a, b, p1_text, p1_id),
     people_mentions(s, c, d, p2_text, p2_id).
 
@@ -48,7 +48,7 @@ function ext_has_spouse
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len)  :-
+has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
     sentences(a, b, words, c, d, e, f, g, s),
     has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
     people_mentions(s, p1idx, p1len, k, person1_id),
@@ -61,17 +61,16 @@ function ext_has_spouse_features
         handles tsv lines.
 
 @label(l)
-has_spouse(rid)  :-
+has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l).
 
 @weight(f)
-has_spouse(rid)  :-
+has_spouse(rid) :-
     has_spouse_candidates(a, b, c, d, rid, l),
     has_spouse_features(rid, f).
 
 @weight(3.0)
-has_spouse(rid)  :-
-    has_spouse(rid2),
+has_spouse(rid2) => has_spouse(rid) :-
     has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
 

From 47acbd6a57b91844d6970a0545037ac70f73a6c2 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 5 Aug 2015 16:10:53 -0700
Subject: [PATCH 205/347] Update spouse example test with equal function

---
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 12 ++++++------
 .../compile-incremental.expected                     |  2 +-
 .../spouse_example_new_inference/compile.expected    |  2 +-
 .../spouse_example_new_inference/input.ddl           |  2 +-
 .../print-incremental.expected                       |  2 +-
 .../spouse_example_new_inference/print.expected      |  2 +-
 6 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 072f8e75a..250dac089 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -319,6 +319,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
   ( implyHeadAtoms ^^ {
       InferenceRuleHead(FactorFunction.Imply, _)
     }
+  | "@semantics(linear)" ~> implyHeadAtoms ^^ {
+      InferenceRuleHead(FactorFunction.Linear, _)
+    }
+  | "@semantics(ratio)" ~> implyHeadAtoms ^^ {
+      InferenceRuleHead(FactorFunction.Ratio, _)
+    }
   | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
       InferenceRuleHead(FactorFunction.Equal, a +: b)
     }
@@ -331,12 +337,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
   | "Multinomial" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
       InferenceRuleHead(FactorFunction.Multinomial, _)
     }
-  | "@semantics(linear)" ~> implyHeadAtoms ^^ {
-      InferenceRuleHead(FactorFunction.Linear, _)
-    }
-  | "@semantics(ratio)" ~> implyHeadAtoms ^^ {
-      InferenceRuleHead(FactorFunction.Ratio, _)
-    }
   | headAtom ^^ {
       x => InferenceRuleHead(FactorFunction.IsTrue, List(x))
     }
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index af799726f..64a47860d 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -342,7 +342,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
         WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
-          function: "Imply(dd_new_has_spouse.R0.label, dd_new_has_spouse.R1.label)"
+          function: "Equal(dd_new_has_spouse.R0.label, dd_new_has_spouse.R1.label)"
           weight: "3.0"
         }
       
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 645696441..7954e4e5e 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -161,7 +161,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
         WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
-          function: "Imply(has_spouse.R0.label, has_spouse.R1.label)"
+          function: "Equal(has_spouse.R0.label, has_spouse.R1.label)"
           weight: "3.0"
         }
       
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 1527e7b37..05fbac45d 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -72,6 +72,6 @@ has_spouse(rid) :-
 
 @mode(inc)
 @weight(3.0)
-has_spouse(rid2) => has_spouse(rid) :-
+has_spouse(rid2) = has_spouse(rid) :-
   has_spouse_candidates(a1, b1, c1, d1, rid, l1),
   has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 6eefc4324..477fc1e5d 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -172,7 +172,7 @@ dd_new_has_spouse(rid) :-
     dd_delta_has_spouse_features(rid, f).
 
 @weight(3.0)
-dd_new_has_spouse(rid2) => dd_new_has_spouse(rid) :-
+dd_new_has_spouse(rid2) = dd_new_has_spouse(rid) :-
     dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index f2e1cdffe..4ed66dff6 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -70,7 +70,7 @@ has_spouse(rid) :-
     has_spouse_features(rid, f).
 
 @weight(3.0)
-has_spouse(rid2) => has_spouse(rid) :-
+has_spouse(rid2) = has_spouse(rid) :-
     has_spouse_candidates(a1, b1, c1, d1, rid, l1),
     has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
 

From 15279a8196b31cd1f849bd27f77d425ed6e0af65 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 9 Aug 2015 23:41:37 -0700
Subject: [PATCH 206/347] Removes SBT_OPT that shows warning in Java 8

---
 project/sbt/sbt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/sbt/sbt b/project/sbt/sbt
index be43b76e8..07184ee7c 100755
--- a/project/sbt/sbt
+++ b/project/sbt/sbt
@@ -1,3 +1,3 @@
 #!/bin/bash
-SBT_OPTS="-Xms512M -Xmx1536M -Xss1M -XX:+CMSClassUnloadingEnabled -XX:MaxPermSize=256M"
+SBT_OPTS="-Xms512M -Xmx1536M -Xss1M -XX:+CMSClassUnloadingEnabled"
 java $SBT_OPTS -jar `dirname $0`/sbt-launch.jar "$@"

From 7c1514e77fbf1cacc3cb1c49918154b527da4633 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 10 Aug 2015 00:38:20 -0700
Subject: [PATCH 207/347] Adds support for unnamed list arguments for schema
 annotations

which map to JSON arrays instead of objects.
E.g., `@foo(1,"two", 3.45)` as well as `@bar(x=67, y="eight", z=9.0)`
---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 20 ++++++++++++++-----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  9 ++++++---
 .../ddlog/DeepDiveLogSchemaExporter.scala     |  2 +-
 .../annotations/export-schema.expected        |  2 +-
 .../annotations/input.ddl                     |  3 +++
 .../annotations/print.expected                |  3 +++
 6 files changed, 29 insertions(+), 10 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 250dac089..00ee35aaa 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -46,7 +46,7 @@ case class Column(name : String // name of the column
                  )
 
 case class Annotation( name : String // name of the annotation
-                     , args : Map[String, Any] = Map.empty // optional, named arguments
+                     , args : Option[Either[Map[String, Any],List[Any]]] = None // optional, named arguments map or unnamed list
                      )
 case class RuleAnnotation(name: String, args: List[String])
 
@@ -135,12 +135,22 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def annotationArgumentName = ident
 
   def annotation: Parser[Annotation] =
-    "@" ~ annotationName ~ opt("(" ~> repsep(annotationArgument, ",") <~ ")") ^^ {
-      case (_ ~ name ~ optArgs) =>
-        Annotation(name, optArgs getOrElse { List.empty } toMap)
+    "@" ~ annotationName ~ opt(annotationArguments) ^^ {
+      case (_ ~ name ~ optArgs) => Annotation(name, optArgs)
     }
 
-  def annotationArgument: Parser[(String, Any)] =
+  def annotationArguments: Parser[Either[Map[String, Any], List[Any]]] =
+    "(" ~> (
+      // XXX rep1sep must be above repsep to parse "()"
+      rep1sep(annotationArgumentValue, ",") ^^ {
+        case values => Right(values)
+      }
+    |
+      repsep(annotationNamedArgument, ",") ^^ {
+        case namedArgs => Left(namedArgs toMap)
+      }
+    ) <~ ")"
+  def annotationNamedArgument: Parser[(String, Any)] =
     annotationArgumentName ~ "=" ~ annotationArgumentValue ^^ {
       case name ~ _ ~ value => name -> value
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 983e63e83..519c213fd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -20,9 +20,12 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case anno =>
         s"@${anno.name}${
           if (anno.args isEmpty) ""
-          else s"(${anno.args map {
-            case (name, value) => s"${name}=${printLiteral(value)}"
-          } mkString(", ")})"
+          else s"(${anno.args.get fold (
+            // named arguments case
+            {_ map { case (name, value) => s"${name}=${printLiteral(value)}" }},
+            // unnamed argument list case
+            {_ map printLiteral}
+          ) mkString(", ") })"
         }" + ("\n" + indentation)
     } mkString
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 59fd44796..cdc4e30e2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -44,7 +44,7 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
       "name" -> anno.name
     )
     if (anno.args nonEmpty)
-      a += "args" -> JSONObject(anno.args)
+      a += "args" -> (anno.args.get fold (JSONObject, JSONArray))
     JSONObject(a)
   }
 
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
index 040510c44..2b3e2e8d3 100644
--- a/test/expected-output-test/annotations/export-schema.expected
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -1 +1 @@
-{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float"}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}]}}}
+{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float", "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}}}
diff --git a/test/expected-output-test/annotations/input.ddl b/test/expected-output-test/annotations/input.ddl
index 4124b63b5..1eedb30c9 100644
--- a/test/expected-output-test/annotations/input.ddl
+++ b/test/expected-output-test/annotations/input.ddl
@@ -11,8 +11,11 @@ mention_candidate(
 
 
 @foo @bar(x=1) @qux(y=2.345)
+@unnamed_args_list(1,"two",3.0)
+@unnamed_args_list("four",5.6,7)
 R(
     p text,
     q int,
+    @empty_args()
     r float
 ).
diff --git a/test/expected-output-test/annotations/print.expected b/test/expected-output-test/annotations/print.expected
index e7559d089..5f682a844 100644
--- a/test/expected-output-test/annotations/print.expected
+++ b/test/expected-output-test/annotations/print.expected
@@ -8,7 +8,10 @@ mention_candidate(doc_id text,
 @foo
 @bar(x=1)
 @qux(y=2.345)
+@unnamed_args_list(1, "two", 3.0)
+@unnamed_args_list("four", 5.6, 7)
 R(p text,
   q int,
+  @empty_args()
   r float).
 

From cd9ea9062c1ed17ec8d533812639f1a36a74eec4 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 10 Aug 2015 00:47:37 -0700
Subject: [PATCH 208/347] Exports whether a relation is a variable or not in
 JSON

using "variable_type" and "variable_cardinality" fields for relations
---
 .../deepdive/ddlog/DeepDiveLogSchemaExporter.scala  | 13 ++++++++++++-
 .../annotations/export-schema.expected              |  2 +-
 test/expected-output-test/annotations/input.ddl     |  7 +++++++
 .../expected-output-test/annotations/print.expected |  5 +++++
 4 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index cdc4e30e2..4eb061f80 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -32,8 +32,19 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
     // relation annotations are omitted when not present
     if (decl.annotation nonEmpty)
       schema += "annotations" -> exportAnnotations(decl.annotation)
+    // what type of random variable this relation is
+    if (decl.isQuery)
+      decl.variableType getOrElse { BooleanType } match {
+        case ty =>
+          schema += "variable_type" -> (ty match {
+            case BooleanType        => "boolean"
+            case MultinomialType(n) => "multinomial"
+          })
+          schema += "variable_cardinality" -> ty.cardinality
+      }
 
-    (decl.a.name, JSONObject(schema))
+    // finally, mapping for this relation
+    decl.a.name -> JSONObject(schema)
   }
 
   def exportAnnotations(annos: Seq[Annotation]): JSONArray =
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
index 2b3e2e8d3..47d08fd25 100644
--- a/test/expected-output-test/annotations/export-schema.expected
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -1 +1 @@
-{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float", "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}}}
+{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float", "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}, "has_spouse" : {"columns" : {"couple_id" : {"type" : "text", "annotations" : [{"name" : "key"}, {"name" : "references", "args" : {"relation" : "couples", "column" : "id"}}]}}, "annotations" : [{"name" : "fact"}], "variable_type" : "boolean", "variable_cardinality" : 2}}}
diff --git a/test/expected-output-test/annotations/input.ddl b/test/expected-output-test/annotations/input.ddl
index 1eedb30c9..8eae795d6 100644
--- a/test/expected-output-test/annotations/input.ddl
+++ b/test/expected-output-test/annotations/input.ddl
@@ -19,3 +19,10 @@ R(
     @empty_args()
     r float
 ).
+
+@fact
+has_spouse?(
+    @key
+    @references(relation="couples", column="id")
+    couple_id text
+).
diff --git a/test/expected-output-test/annotations/print.expected b/test/expected-output-test/annotations/print.expected
index 5f682a844..44883711f 100644
--- a/test/expected-output-test/annotations/print.expected
+++ b/test/expected-output-test/annotations/print.expected
@@ -15,3 +15,8 @@ R(p text,
   @empty_args()
   r float).
 
+@fact
+has_spouse?(@key
+            @references(relation="couples", column="id")
+            couple_id text).
+

From a3c4eb74207013022410972ed3ef222aa5e75198 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 13 Aug 2015 15:33:31 -0700
Subject: [PATCH 209/347] Adds a CLI wrapper (test/ddlog) for easier
 interactive tests

---
 Makefile                                      |  3 ++
 README.md                                     | 52 +++++++++++++++----
 .../org/deepdive/ddlog/DeepDiveLog.scala      |  4 +-
 test/ddlog                                    | 33 ++++++++++++
 4 files changed, 81 insertions(+), 11 deletions(-)
 create mode 100755 test/ddlog

diff --git a/Makefile b/Makefile
index 91e440c6a..cc62ab99d 100644
--- a/Makefile
+++ b/Makefile
@@ -3,6 +3,9 @@
 
 ### Build & Clean #############################################################
 
+.PHONY: build
+build: scala-build
+
 # build a standalone jar
 JAR = ddlog.jar
 .PHONY: package
diff --git a/README.md b/README.md
index 78933f57c..4542d6fcf 100644
--- a/README.md
+++ b/README.md
@@ -4,31 +4,65 @@ DeepDiveLog [![Build Status](https://travis-ci.org/HazyResearch/ddlog.svg)](http
 A Datalog-like language for writing DeepDive apps.
 
 ## Building
-The following command produces a standalone jar that contains the compiler.
+The following command builds all Scala code under src/.
 
 ```bash
-make ddlog.jar
+make
 ```
 
-## Running
-The following will generate an application.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
+
+## Testing
+
+### Interactive Tests
+To play with DDlog compiler's command-line interface interactively, use the following script after running `make`.
 
 ```bash
-mkdir -p examples/spouse_example
-java -jar ddlog.jar compile examples/spouse_example.ddl >examples/spouse_example/application.conf
+test/ddlog
 ```
 
+This provides a quick way to see the effects from the command-line after changing the source code as it directly runs the compiled classes under target/ rather than having to assemble a jar every time.
+After running `make` at least once, you can solely rely on an IDE such as [IntelliJ IDEA][] to compile individual .scala files and test it with this script.
 
-## Testing
+### Automated Tests
 The following command runs all tests under test/.
+Tests are written in [BATS][].
 
 ```bash
-make  # or make test
+make test
 ```
 
-## Coverage
+To run tests selectively, see the long make command produced by:
+
+```bash
+make test-list
+```
+
+### Test Coverage
 The following command produces a test coverage report.
 
 ```bash
 make test-coverage
 ```
+
+
+## Deploying
+
+### Assembling a standalone jar
+The following command produces a standalone jar that contains the DDlog compiler.
+
+```bash
+make ddlog.jar
+```
+
+### Running the standalone jar
+The following command generates a deepdive.conf for the [spouse example in DeepDive's tutorial](http://deepdive.stanford.edu/doc/basics/walkthrough/walkthrough.html).
+
+```bash
+mkdir -p examples/spouse_example
+java -jar ddlog.jar compile examples/spouse_example.ddl >examples/spouse_example/deepdive.conf
+```
+
+
+
+[BATS]: https://github.com/sstephenson/bats#readme "Bash Automated Testing System"
+[IntelliJ IDEA]: https://www.jetbrains.com/idea/
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index b47c5102f..7459cd9ee 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -22,8 +22,8 @@ object DeepDiveLog {
   , inputFiles: List[String] = List()
   , mode: Mode = ORIGINAL
   )
-  val parser = new scopt.OptionParser[Config]("ddlogc") {
-    head("ddlogc", "0.0.1")
+  val parser = new scopt.OptionParser[Config]("ddlog") {
+    head("DDlog Compiler", "0.0.1")
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
     cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) }
diff --git a/test/ddlog b/test/ddlog
new file mode 100755
index 000000000..1bb641006
--- /dev/null
+++ b/test/ddlog
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+# A helper script to play with DDlog command-line interface
+set -eu
+
+# find itself
+Self=$(readlink -f "$0" 2>/dev/null || {
+    # XXX readlink -f is only available in GNU coreutils
+    cd $(dirname -- "$0")
+    n=$(basename -- "$0")
+    if [ -L "$n" ]; then
+        L=$(readlink "$n")
+        if [ x"$L" != x"${L#/}" ]; then
+            echo "$L"; exit
+        else
+            cd "$(dirname -- "$L")"
+            n=$(basename -- "$L")
+        fi
+    fi
+    echo "$(pwd -P)/$n"
+})
+Here=$(dirname "$Self")
+
+# set up environment
+classpathFile="$Here"/../target/scala-2.10/classpath
+[[ -s "$classpathFile" ]] || {
+    echo "ERROR: missing $classpathFile"
+    echo 'Run `make` before using test/ddlog!'
+    false
+} >&2
+CLASSPATH=$(cat "$classpathFile")
+export CLASSPATH
+
+exec java org.deepdive.ddlog.DeepDiveLog "$@"

From a5c60f0cd81cb86104276e6e69eea38d3bb81535 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 12 Aug 2015 16:24:41 -0700
Subject: [PATCH 210/347] Export column index in export-schema

---
 .../scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala    | 1 +
 test/expected-output-test/annotations/export-schema.expected    | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 4eb061f80..591d286f6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -22,6 +22,7 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
 //              "name" -> name, // XXX redundant but potentially useful
               "type" -> decl.a.types(i)
           )
+          columnSchema += "index" -> i
           // column annotations are omitted when not present
           val annos = decl.a.annotations(i)
           if (annos nonEmpty)
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
index 47d08fd25..cb9142969 100644
--- a/test/expected-output-test/annotations/export-schema.expected
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -1 +1 @@
-{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text"}, "start_pos" : {"type" : "int", "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text"}, "q" : {"type" : "int"}, "r" : {"type" : "float", "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}, "has_spouse" : {"columns" : {"couple_id" : {"type" : "text", "annotations" : [{"name" : "key"}, {"name" : "references", "args" : {"relation" : "couples", "column" : "id"}}]}}, "annotations" : [{"name" : "fact"}], "variable_type" : "boolean", "variable_cardinality" : 2}}}
+{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text", "index" : 0}, "start_pos" : {"type" : "int", "index" : 1, "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "index" : 2, "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text", "index" : 0}, "q" : {"type" : "int", "index" : 1}, "r" : {"type" : "float", "index" : 2, "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}, "has_spouse" : {"columns" : {"couple_id" : {"type" : "text", "index" : 0, "annotations" : [{"name" : "key"}, {"name" : "references", "args" : {"relation" : "couples", "column" : "id"}}]}}, "annotations" : [{"name" : "fact"}], "variable_type" : "boolean", "variable_cardinality" : 2}}}

From faedbfa303a1c2d737c09554c27ba2576541253e Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Fri, 14 Aug 2015 17:16:42 -0700
Subject: [PATCH 211/347] Use string literals in mode and semantics, fix
 semantics printing and add tests

---
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala  |  9 ++++-----
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala | 10 +++++-----
 test/expected-output-test/semantics/input.ddl         |  7 +++++++
 test/expected-output-test/semantics/print.expected    | 11 +++++++++++
 .../spouse_example_new_feature/input.ddl              |  2 +-
 .../print-incremental.expected                        |  2 +-
 .../spouse_example_new_inference/input.ddl            |  2 +-
 7 files changed, 30 insertions(+), 13 deletions(-)
 create mode 100644 test/expected-output-test/semantics/input.ddl
 create mode 100644 test/expected-output-test/semantics/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 00ee35aaa..a8ff71655 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -128,9 +128,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
   def variableName = ident
   def functionName = ident
-  def semanticType = ident
-  def functionModeType = ident
-  def inferenceModeType = ident
+  def functionModeType = stringLiteralAsString
+  def inferenceModeType = stringLiteralAsString
   def annotationName = ident
   def annotationArgumentName = ident
 
@@ -329,10 +328,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
   ( implyHeadAtoms ^^ {
       InferenceRuleHead(FactorFunction.Imply, _)
     }
-  | "@semantics(linear)" ~> implyHeadAtoms ^^ {
+  | ("@semantics" ~ "(" ~ "\"linear\"" ~ ")") ~> implyHeadAtoms ^^ {
       InferenceRuleHead(FactorFunction.Linear, _)
     }
-  | "@semantics(ratio)" ~> implyHeadAtoms ^^ {
+  | ("@semantics" ~ "(" ~ "\"ratio\"" ~ ")") ~> implyHeadAtoms ^^ {
       InferenceRuleHead(FactorFunction.Ratio, _)
     }
   | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 519c213fd..03588dfd2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -60,7 +60,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" + styleStr
       }
     }
-    val modeStr = stmt.mode map (s => s"@mode(${s})\n") getOrElse ""
+    val modeStr = stmt.mode map (s => s"""@mode("${s}")\n""") getOrElse ""
     s"""${modeStr}function ${stmt.functionName}
        |    over ${inputType}
        | returns ${outputType}
@@ -154,15 +154,15 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(head: InferenceRuleHead) : String = {
+    def printImplyHead = s"""${printHead(head.terms.dropRight(1), ", ")} => ${print(head.terms.last)}"""
     def printHead(a: List[HeadAtom], delim: String) : String = a map print mkString(delim)
     head.function match {
-      case FactorFunction.Imply  =>
-        s"""${printHead(head.terms.dropRight(1), ", ")} => ${print(head.terms.last)}"""
+      case FactorFunction.Imply  => printImplyHead
+      case FactorFunction.Linear => s"""@semantics("linear")\n${printImplyHead}"""
+      case FactorFunction.Ratio  => s"""@semantics("ratio")\n${printImplyHead}"""
       case FactorFunction.And    => printHead(head.terms, " ^ ")
       case FactorFunction.Or     => printHead(head.terms, " v ")
       case FactorFunction.Equal  => printHead(head.terms, " = ")
-      case FactorFunction.Linear => s"Linear(${printHead(head.terms, ", ")})"
-      case FactorFunction.Ratio  => s"Ratio(${printHead(head.terms, ", ")})"
       case FactorFunction.IsTrue => printHead(head.terms, "")
     }
   }
diff --git a/test/expected-output-test/semantics/input.ddl b/test/expected-output-test/semantics/input.ddl
new file mode 100644
index 000000000..53d6f10a5
--- /dev/null
+++ b/test/expected-output-test/semantics/input.ddl
@@ -0,0 +1,7 @@
+R?(x text).
+S?(x text).
+T(x text).
+
+@weight(3)
+@semantics("linear")
+R(x) => S(x) :- T(x).
\ No newline at end of file
diff --git a/test/expected-output-test/semantics/print.expected b/test/expected-output-test/semantics/print.expected
new file mode 100644
index 000000000..f303f3978
--- /dev/null
+++ b/test/expected-output-test/semantics/print.expected
@@ -0,0 +1,11 @@
+R?(x text).
+
+S?(x text).
+
+T(x text).
+
+@weight(3)
+@semantics("linear")
+R(x) => S(x) :-
+    T(x).
+
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 61f64c208..cbd8b90cc 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -38,7 +38,7 @@ people_mentions +=
   ext_people(s, words, ner_tags) :-
   sentences(a, b, words, c, d, e, ner_tags, f, s).
 
-@mode(inc)
+@mode("inc")
 function ext_people over like ext_people_input
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 358552514..6f9d094a1 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -118,7 +118,7 @@ dd_new_has_spouse(relation_id) :-
 dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
     dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
 
-@mode(inc)
+@mode("inc")
 function ext_people
     over like dd_delta_ext_people_input
  returns like dd_delta_people_mentions
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 05fbac45d..944df4a41 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -70,7 +70,7 @@ has_spouse(rid) :-
   has_spouse_candidates(a, b, c, d, rid, l),
   has_spouse_features(rid, f).
 
-@mode(inc)
+@mode("inc")
 @weight(3.0)
 has_spouse(rid2) = has_spouse(rid) :-
   has_spouse_candidates(a1, b1, c1, d1, rid, l1),

From f7541949f3a427c7e0fd716cf1d4b53198c4caa9 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 16 Aug 2015 02:37:44 -0700
Subject: [PATCH 212/347] Add tests for mode and semantics annotation

---
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala   | 10 +++++-----
 test/parse-error-test/annotation_mode/input.ddl        |  3 +++
 .../annotation_mode/parse-error.expected               |  4 ++++
 test/parse-error-test/annotation_semantics/input.ddl   |  3 +++
 .../annotation_semantics/parse-error.expected          |  4 ++++
 5 files changed, 19 insertions(+), 5 deletions(-)
 create mode 100644 test/parse-error-test/annotation_mode/input.ddl
 create mode 100644 test/parse-error-test/annotation_mode/parse-error.expected
 create mode 100644 test/parse-error-test/annotation_semantics/input.ddl
 create mode 100644 test/parse-error-test/annotation_semantics/parse-error.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index a8ff71655..5d0fba9dc 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -328,11 +328,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
   ( implyHeadAtoms ^^ {
       InferenceRuleHead(FactorFunction.Imply, _)
     }
-  | ("@semantics" ~ "(" ~ "\"linear\"" ~ ")") ~> implyHeadAtoms ^^ {
-      InferenceRuleHead(FactorFunction.Linear, _)
-    }
-  | ("@semantics" ~ "(" ~ "\"ratio\"" ~ ")") ~> implyHeadAtoms ^^ {
-      InferenceRuleHead(FactorFunction.Ratio, _)
+  | ("@semantics" ~> "(" ~> stringLiteralAsString <~ ")" ^? ({
+      case "linear" => FactorFunction.Linear
+      case "ratio"  => FactorFunction.Ratio
+    }, { "Unrecognized semantics: " + _ })) ~ implyHeadAtoms ^^ {
+      case s ~ h => InferenceRuleHead(s, h)
     }
   | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
       InferenceRuleHead(FactorFunction.Equal, a +: b)
diff --git a/test/parse-error-test/annotation_mode/input.ddl b/test/parse-error-test/annotation_mode/input.ddl
new file mode 100644
index 000000000..4ecdf9306
--- /dev/null
+++ b/test/parse-error-test/annotation_mode/input.ddl
@@ -0,0 +1,3 @@
+@weight(3)
+@mode("unknown")
+Q(x) :- R(x).
diff --git a/test/parse-error-test/annotation_mode/parse-error.expected b/test/parse-error-test/annotation_mode/parse-error.expected
new file mode 100644
index 000000000..a2ad15abe
--- /dev/null
+++ b/test/parse-error-test/annotation_mode/parse-error.expected
@@ -0,0 +1,4 @@
+[error] test/parse-error-test/annotation_mode/input.ddl[3.4] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `)' found
+
+Q(x) :- R(x).
+   ^
diff --git a/test/parse-error-test/annotation_semantics/input.ddl b/test/parse-error-test/annotation_semantics/input.ddl
new file mode 100644
index 000000000..a4d549e44
--- /dev/null
+++ b/test/parse-error-test/annotation_semantics/input.ddl
@@ -0,0 +1,3 @@
+@weight(3)
+@semantics("unknown")
+Q(x) => P(x) :- R(x).
diff --git a/test/parse-error-test/annotation_semantics/parse-error.expected b/test/parse-error-test/annotation_semantics/parse-error.expected
new file mode 100644
index 000000000..fea53957f
--- /dev/null
+++ b/test/parse-error-test/annotation_semantics/parse-error.expected
@@ -0,0 +1,4 @@
+[error] test/parse-error-test/annotation_semantics/input.ddl[3.4] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `)' found
+
+Q(x) => P(x) :- R(x).
+   ^

From 1f686fc21f54874ddd6ac8e370324656ccf16e21 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 17 Aug 2015 21:24:39 -0700
Subject: [PATCH 213/347] Catch mode and semantics parse error

---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 20 +++++++++++--------
 .../annotation_mode/input.ddl                 |  2 +-
 .../annotation_mode/parse-error.expected      |  7 ++++---
 .../annotation_semantics/parse-error.expected |  7 ++++---
 4 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 5d0fba9dc..1e508780d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -114,7 +114,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def stringLiteralAsString = stringLiteral ^^ {
     s => StringEscapeUtils.unescapeJava(
       s.stripPrefix("\"").stripSuffix("\""))
-  }
+  } withFailureMessage "a string literal is expected"
 
   // Single-line comments beginning with # or // are supported by treating them as whiteSpace
   // C/Java/Scala style multi-line comments cannot be easily supported with RegexParsers unless we introduce a dedicated lexer.
@@ -276,7 +276,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
-  def functionMode = "@mode" ~> "(" ~> functionModeType <~ ")"
+  def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
+    case "inc" => "inc"
+  }, (s) => s"${s}: unrecognized mode"))
 
   def functionDeclaration : Parser[FunctionDeclaration] =
     ( opt(functionMode) ~ "function" ~ functionName ~ "over" ~ relationType
@@ -313,7 +315,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
-  def inferenceMode = "@mode" ~> "(" ~> inferenceModeType <~ ")"
+  def inferenceMode = "@mode" ~> commit("(" ~> inferenceModeType <~ ")" ^? ({
+    case "inc" => "inc"
+  }, (s) => s"${s}: unrecognized mode"))
 
   // factor functions
   def headAtom = relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
@@ -328,11 +332,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
   ( implyHeadAtoms ^^ {
       InferenceRuleHead(FactorFunction.Imply, _)
     }
-  | ("@semantics" ~> "(" ~> stringLiteralAsString <~ ")" ^? ({
+  | "@semantics" ~> commit("(" ~> stringLiteralAsString <~ ")" ^? ({
       case "linear" => FactorFunction.Linear
       case "ratio"  => FactorFunction.Ratio
-    }, { "Unrecognized semantics: " + _ })) ~ implyHeadAtoms ^^ {
-      case s ~ h => InferenceRuleHead(s, h)
+    }, (s) => s"${s}: unrecognized semantics")) ~ implyHeadAtoms ^^ {
+      case (s ~ h) => InferenceRuleHead(s, h)
     }
   | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
       InferenceRuleHead(FactorFunction.Equal, a +: b)
@@ -362,8 +366,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }
 
   // rules or schema elements in arbitrary order
-  def statement : Parser[Statement] = ( schemaDeclaration
-                                      | inferenceRule
+  def statement : Parser[Statement] = ( inferenceRule
+                                      | schemaDeclaration
                                       | extractionRule
                                       | functionDeclaration
                                       | functionCallRule
diff --git a/test/parse-error-test/annotation_mode/input.ddl b/test/parse-error-test/annotation_mode/input.ddl
index 4ecdf9306..4d59175af 100644
--- a/test/parse-error-test/annotation_mode/input.ddl
+++ b/test/parse-error-test/annotation_mode/input.ddl
@@ -1,3 +1,3 @@
-@weight(3)
 @mode("unknown")
+@weight(3)
 Q(x) :- R(x).
diff --git a/test/parse-error-test/annotation_mode/parse-error.expected b/test/parse-error-test/annotation_mode/parse-error.expected
index a2ad15abe..0155261a6 100644
--- a/test/parse-error-test/annotation_mode/parse-error.expected
+++ b/test/parse-error-test/annotation_mode/parse-error.expected
@@ -1,4 +1,5 @@
-[error] test/parse-error-test/annotation_mode/input.ddl[3.4] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `)' found
+[error] test/parse-error-test/annotation_mode/input.ddl[1.17] error: unknown: unrecognized mode
 
-Q(x) :- R(x).
-   ^
+@mode("unknown")
+
+                ^
diff --git a/test/parse-error-test/annotation_semantics/parse-error.expected b/test/parse-error-test/annotation_semantics/parse-error.expected
index fea53957f..f42219924 100644
--- a/test/parse-error-test/annotation_semantics/parse-error.expected
+++ b/test/parse-error-test/annotation_semantics/parse-error.expected
@@ -1,4 +1,5 @@
-[error] test/parse-error-test/annotation_semantics/input.ddl[3.4] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `)' found
+[error] test/parse-error-test/annotation_semantics/input.ddl[2.22] error: unknown: unrecognized semantics
 
-Q(x) => P(x) :- R(x).
-   ^
+@semantics("unknown")
+
+                     ^

From 5998c1814afda7a582df5a292d750606b24796d0 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 17 Aug 2015 22:31:48 -0700
Subject: [PATCH 214/347] Add support for views

Head relations not defined in the schema are defined as views.
It can be used in the bodies in other rules.
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 56 +++++++++++------
 .../expressions/compile.expected              | 46 +++++++-------
 .../views/compile.expected                    | 61 +++++++++++++++++++
 test/expected-output-test/views/input.ddl     |  4 ++
 .../expected-output-test/views/print.expected | 10 +++
 5 files changed, 134 insertions(+), 43 deletions(-)
 create mode 100644 test/expected-output-test/views/compile.expected
 create mode 100644 test/expected-output-test/views/input.ddl
 create mode 100644 test/expected-output-test/views/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 64b686c6a..8a8dc33f9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -64,6 +64,14 @@ import scala.collection.mutable.ListBuffer
 import org.deepdive.ddlog.DeepDiveLog.Mode._
 import scala.language.postfixOps
 
+object AliasStyle extends Enumeration {
+  type AliasStyle = Value
+  // TableStyle: tableName.R{tableIndex}.columnName
+  // ViewStyle: column_{columnIndex}
+  val ViewAlias, TableAlias, NoAlias = Value
+}
+import AliasStyle._
+
 // This handles the schema statements.
 // It can tell you if a predicate is a "query" predicate or a "ground prediate"
 // and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
@@ -144,7 +152,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       if(schema contains (relName,i)) {
         schema(relName,i)
       } else {
-        return v // I do not like this default, as it allows some errors. TOOD: MAKE MORE PRECISE!
+        // for views, columns names are in the form of "column_index"
+        return if (DeepDiveLogCompiler.isForIncremental(relName)) v else s"column_${i}"
       }
     }
   }
@@ -273,15 +282,19 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // compile alias
-  def compileAlias(e: Expr) = e match {
-    case VarExpr(v) => {
-      val index = getBodyIndex(v)
-      val variable = getVar(v)
-      val name  = ss.resolveName(variable)
-      val relation = variable.relName
-      s"${relation}.R${index}.${name}"
+  def compileAlias(e: Expr, aliasStyle: AliasStyle) = aliasStyle match {
+    case NoAlias => ""
+    case TableAlias => e match {
+      case VarExpr(v) => {
+        val index = getBodyIndex(v)
+        val variable = getVar(v)
+        val name  = ss.resolveName(variable)
+        val relation = variable.relName
+        s""" AS "${relation}.R${index}.${name}"""" //"
+      }
+      case _ => s" AS column_${cq.headTerms indexOf e}"
     }
-    case _ => s"column_${cq.headTerms indexOf e}"
+    case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
   }
 
   // resolve an expression
@@ -329,9 +342,9 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // generate SQL SELECT cluase
-  def generateSQLHead(useAlias: Boolean) = {
+  def generateSQLHead(aliasStyle: AliasStyle) = {
     val head = cq.headTerms map { expr =>
-      compileExpr(expr) + (if (useAlias) s""" AS "${compileAlias(expr)}" """ else "")
+      compileExpr(expr) + compileAlias(expr, aliasStyle)
     } mkString(", ")
     val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
     s"${distinctStr}${head}"
@@ -440,8 +453,8 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${limitStr}"""
   }
 
-  def generateSQL(useAlias: Boolean) = {
-    val head = generateSQLHead(useAlias)
+  def generateSQL(aliasStyle: AliasStyle) = {
+    val head = generateSQLHead(aliasStyle)
     val body = cq.bodies map generateSQLBody
     body map { b => s"SELECT ${head}\n${b}" } mkString("\nUNION ALL\n")
   }
@@ -512,7 +525,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
         if (stmt.supervision != None) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
-          val headStr = qc.generateSQLHead(false)
+          val headStr = qc.generateSQLHead(NoAlias)
           val labelCol = qc.compileVariable(stmt.supervision.get)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
@@ -520,18 +533,21 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         } else if ((ss.hasSchemaDeclared(stmt.headName)) &&
           (ss.schemaDeclarationGroupByHead(stmt.headName)(0).isQuery) &&
           isForIncremental(stmt.headName)) {
-          val headStr = qc.generateSQLHead(false)
+          val headStr = qc.generateSQLHead(NoAlias)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, id, label
           ${ qc.generateSQLBody(cqBody) }
           """
         } else {
           // variable columns
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
-          var useAlias = ss.mode match {
-            case MERGE => false
-            case _     => !isForIncremental(stmt.headName)
+          // views uses view alias
+          val aliasStyle = ss.mode match {
+            case MERGE => NoAlias
+            case _     => if (isForIncremental(stmt.headName)) NoAlias
+              else if (!ss.hasSchemaDeclared(stmt.headName)) ViewAlias
+              else TableAlias
           }
-          inputQueries += qc.generateSQL(useAlias)
+          inputQueries += qc.generateSQL(aliasStyle)
         }
       }
     }
@@ -583,7 +599,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       val blockName = ss.resolveExtractorBlockName(stmt)
       val extractor = s"""
         deepdive.extraction.extractors.${blockName} {
-          input: \"\"\" ${new QueryCompiler(stmt.q, ss).generateSQL(true)}
+          input: \"\"\" ${new QueryCompiler(stmt.q, ss).generateSQL(TableAlias)}
           \"\"\"
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 50766e57a..5a69fcae2 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -57,7 +57,7 @@
 
       deepdive.extraction.extractors.extraction_rule_9 {
         sql: """ DROP VIEW IF EXISTS E;
-        CREATE VIEW E AS SELECT (R0.k :: INT) AS "column_0" 
+        CREATE VIEW E AS SELECT (R0.k :: INT) AS column_0
 FROM b R0
         
         """
@@ -68,7 +68,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_25 {
         sql: """ DROP VIEW IF EXISTS X;
-        CREATE VIEW X AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW X AS SELECT R0.k AS column_0
 FROM b R0, c R1
         WHERE R1.n = R0.k 
         """
@@ -79,7 +79,7 @@ FROM b R0, c R1
 
       deepdive.extraction.extractors.extraction_rule_18 {
         sql: """ DROP VIEW IF EXISTS N;
-        CREATE VIEW N AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW N AS SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
         """
@@ -90,7 +90,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_21 {
         sql: """ DROP VIEW IF EXISTS T;
-        CREATE VIEW T AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW T AS SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         WHERE R1_0.s > R0.p
         """
@@ -101,7 +101,7 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
 
       deepdive.extraction.extractors.extraction_rule_14 {
         sql: """ DROP VIEW IF EXISTS J;
-        CREATE VIEW J AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW J AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
         """
@@ -112,7 +112,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_22 {
         sql: """ DROP VIEW IF EXISTS U;
-        CREATE VIEW U AS SELECT R0_0.k AS "b.R0_0.k" 
+        CREATE VIEW U AS SELECT R0_0.k AS column_0
 FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
         
         """
@@ -123,7 +123,7 @@ FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
 
       deepdive.extraction.extractors.extraction_rule_10 {
         sql: """ DROP VIEW IF EXISTS F;
-        CREATE VIEW F AS SELECT ((R0.k :: INT) + (R0.r :: INT)) AS "column_0" 
+        CREATE VIEW F AS SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
 FROM b R0
         
         """
@@ -134,7 +134,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_5 {
         sql: """ DROP VIEW IF EXISTS A;
-        CREATE VIEW A AS SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS "column_0" 
+        CREATE VIEW A AS SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
 FROM b R0
         
         """
@@ -145,7 +145,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_17 {
         sql: """ DROP VIEW IF EXISTS M;
-        CREATE VIEW M AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW M AS SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
         """
@@ -156,7 +156,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_13 {
         sql: """ DROP VIEW IF EXISTS I;
-        CREATE VIEW I AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW I AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
         """
@@ -167,7 +167,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_11 {
         sql: """ DROP VIEW IF EXISTS G;
-        CREATE VIEW G AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW G AS SELECT R0.k AS column_0
 FROM b R0
         WHERE (R0.k + R0.r) = 100
         """
@@ -178,7 +178,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_24 {
         sql: """ DROP VIEW IF EXISTS V;
-        CREATE VIEW V AS SELECT R0.n AS "c.R0.n" 
+        CREATE VIEW V AS SELECT R0.n AS column_0
 FROM c R0, a R1
         WHERE R1.k = R0.n 
         """
@@ -189,7 +189,7 @@ FROM c R0, a R1
 
       deepdive.extraction.extractors.extraction_rule_3 {
         sql: """ DROP VIEW IF EXISTS Q;
-        CREATE VIEW Q AS SELECT DISTINCT ('test' :: TEXT) AS "column_0" , 123 AS "column_1" , R0.k AS "a.R0.k" , unnest(R1.q) AS "column_3" 
+        CREATE VIEW Q AS SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
         """
@@ -200,7 +200,7 @@ FROM a R0, b R1, c R2
 
       deepdive.extraction.extractors.extraction_rule_16 {
         sql: """ DROP VIEW IF EXISTS L;
-        CREATE VIEW L AS SELECT DISTINCT R0.k AS "b.R0.k" 
+        CREATE VIEW L AS SELECT DISTINCT R0.k AS column_0
 FROM b R0
         LIMIT 100
         """
@@ -211,7 +211,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_6 {
         sql: """ DROP VIEW IF EXISTS B;
-        CREATE VIEW B AS SELECT func((R0.k + (R0.r + R0.k))) AS "column_0" 
+        CREATE VIEW B AS SELECT func((R0.k + (R0.r + R0.k))) AS column_0
 FROM b R0
         
         """
@@ -222,7 +222,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_4 {
         sql: """ DROP VIEW IF EXISTS P;
-        CREATE VIEW P AS SELECT R1.p AS "b.R1.p" , R1.q AS "b.R1.q" , MAX(R1.r) AS "column_2" 
+        CREATE VIEW P AS SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
 FROM a R0, b R1
         WHERE R1.k = R0.k 
         GROUP BY R1.p, R1.q
@@ -234,7 +234,7 @@ FROM a R0, b R1
 
       deepdive.extraction.extractors.extraction_rule_7 {
         sql: """ DROP VIEW IF EXISTS C;
-        CREATE VIEW C AS SELECT func(func(func(R0.k))) AS "column_0" 
+        CREATE VIEW C AS SELECT func(func(func(R0.k))) AS column_0
 FROM b R0
         
         """
@@ -245,7 +245,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_12 {
         sql: """ DROP VIEW IF EXISTS H;
-        CREATE VIEW H AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW H AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
         """
@@ -256,7 +256,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_23 {
         sql: """ DROP VIEW IF EXISTS W;
-        CREATE VIEW W AS SELECT R0.k AS "a.R0.k" 
+        CREATE VIEW W AS SELECT R0.k AS column_0
 FROM a R0
         WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
         """
@@ -267,7 +267,7 @@ FROM a R0
 
       deepdive.extraction.extractors.extraction_rule_15 {
         sql: """ DROP VIEW IF EXISTS K;
-        CREATE VIEW K AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW K AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
         """
@@ -278,7 +278,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_19 {
         sql: """ DROP VIEW IF EXISTS O;
-        CREATE VIEW O AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW O AS SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
         """
@@ -289,7 +289,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_8 {
         sql: """ DROP VIEW IF EXISTS D;
-        CREATE VIEW D AS SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS "column_0" 
+        CREATE VIEW D AS SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
 FROM b R0
         
         """
@@ -300,7 +300,7 @@ FROM b R0
 
       deepdive.extraction.extractors.extraction_rule_20 {
         sql: """ DROP VIEW IF EXISTS S;
-        CREATE VIEW S AS SELECT R0.k AS "b.R0.k" 
+        CREATE VIEW S AS SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
         
         """
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
new file mode 100644
index 000000000..11e1625b7
--- /dev/null
+++ b/test/expected-output-test/views/compile.expected
@@ -0,0 +1,61 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+          deepdive.extraction.extractors.extraction_rule_0 {
+            sql: """ DROP TABLE IF EXISTS R CASCADE;
+            CREATE TABLE
+            R(a int,
+ b int)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE R;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.extraction_rule_1 {
+        sql: """ DROP VIEW IF EXISTS A;
+        CREATE VIEW A AS SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
+FROM R R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.extraction_rule_2 {
+        sql: """ DROP VIEW IF EXISTS B;
+        CREATE VIEW B AS SELECT R0.column_0 AS column_0, R1.b AS column_1
+FROM A R0, R R1
+        WHERE R1.a = R0.column_1 
+        """
+        style: "sql_extractor"
+          dependencies: [ "extraction_rule_1" ]
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [extraction_rule_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_1, extraction_rule_2]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_1, extraction_rule_2]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
\ No newline at end of file
diff --git a/test/expected-output-test/views/input.ddl b/test/expected-output-test/views/input.ddl
new file mode 100644
index 000000000..dbb59db53
--- /dev/null
+++ b/test/expected-output-test/views/input.ddl
@@ -0,0 +1,4 @@
+R(a int, b int).
+
+A(x, x + y) :- R(x, y).
+B(x, z) :- A(x, y), R(y, z).
\ No newline at end of file
diff --git a/test/expected-output-test/views/print.expected b/test/expected-output-test/views/print.expected
new file mode 100644
index 000000000..734e24d5f
--- /dev/null
+++ b/test/expected-output-test/views/print.expected
@@ -0,0 +1,10 @@
+R(a int,
+  b int).
+
+A(x, (x + y)) :-
+    R(x, y).
+
+B(x, z) :-
+    A(x, y),
+    R(y, z).
+

From 5b8b2b60548b715924f776f1e420cacff699e1cc Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 19 Aug 2015 17:02:02 -0700
Subject: [PATCH 215/347] Fix semantic checking for inference rule head

---
 .../ddlog/DeepDiveLogSemanticChecker.scala       | 16 ++++++++++------
 .../undefined_relation_2/compile-error.expected  |  5 +++++
 .../undefined_relation_2/input.ddl               |  4 ++++
 3 files changed, 19 insertions(+), 6 deletions(-)
 create mode 100644 test/compile-error-test/undefined_relation_2/compile-error.expected
 create mode 100644 test/compile-error-test/undefined_relation_2/input.ddl

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 75c28e27f..a779a16e7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -14,7 +14,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
         schemaDeclaration += { s.a.name -> s }
       }
       case s: ExtractionRule => {
-        heads += s.headName
+        if (s.supervision == None) heads += s.headName
       }
       case s: FunctionDeclaration => {
         functionDeclaration += { s.functionName -> s }
@@ -49,14 +49,18 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // check if relations in the body are defined
   def checkRelationDefined(stmt: Statement) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
-    def checkRelation(a: BodyAtom) {
-      if (!(heads contains a.name))
-        error(stmt, s"""relation "${a.name}" is not defined""")
+    def checkRelation(name: String) {
+      if (!(heads contains name))
+        error(stmt, s"""relation "${name}" is not defined""")
     }
-    def check = checkBodyAtoms(checkRelation)
+    def checkAtom(a: BodyAtom) = checkRelation(a.name)
+    def check = checkBodyAtoms(checkAtom)
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach check
-      case s: InferenceRule => s.q.bodies foreach check
+      case s: InferenceRule => {
+        s.q.bodies foreach check
+        s.head.terms map(_.name) foreach checkRelation
+      }
       case s: FunctionCallRule => s.q.bodies foreach check
       case _ =>
     }
diff --git a/test/compile-error-test/undefined_relation_2/compile-error.expected b/test/compile-error-test/undefined_relation_2/compile-error.expected
new file mode 100644
index 000000000..e64739a0a
--- /dev/null
+++ b/test/compile-error-test/undefined_relation_2/compile-error.expected
@@ -0,0 +1,5 @@
+[error] relation "Q" is not defined
+@weight(1)
+Q(x) :-
+    a(x).
+
diff --git a/test/compile-error-test/undefined_relation_2/input.ddl b/test/compile-error-test/undefined_relation_2/input.ddl
new file mode 100644
index 000000000..c3e5305c4
--- /dev/null
+++ b/test/compile-error-test/undefined_relation_2/input.ddl
@@ -0,0 +1,4 @@
+a(k int).
+
+@weight(1)
+Q(x) :- a(x).
\ No newline at end of file

From ba9ac8185ec9ce85fe687042b88ae8314602925c Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 19 Aug 2015 23:55:59 -0700
Subject: [PATCH 216/347] Add parenthesis to function input type declarations

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 1e508780d..2502b934f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -252,7 +252,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def relationType: Parser[RelationType] =
     ( "like" ~> relationName ^^ { RelationTypeAlias(_) }
-    | rep1sep(columnDeclaration, ",") ^^ {
+    | "(" ~> rep1sep(columnDeclaration, ",") <~ ")" ^^ {
         attrs => RelationTypeDeclaration(attrs map { _.name }, attrs map { _.t })
       }
     )

From 32ec1cee9bd4c39ddbc21979807288bb1553fdbc Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 20 Aug 2015 17:24:42 -0700
Subject: [PATCH 217/347] Update incremental inference rule naming. Update
 examples

---
 examples/spouse_example.ddl                   | 48 +++++-----
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  5 +-
 .../ocr_example/compile-incremental.expected  |  8 +-
 .../compile-incremental.expected              |  8 +-
 .../compile-incremental.expected              | 60 ++++++------
 .../compile-materialization.expected          | 32 +++----
 .../spouse_example/compile.expected           | 32 +++----
 .../spouse_example/print-incremental.expected | 92 +++++++++---------
 .../spouse_example/print.expected             | 42 ++++----
 .../compile-incremental.expected              | 60 ++++++------
 .../spouse_example_new_feature/input.ddl      | 48 +++++-----
 .../print-incremental.expected                | 92 +++++++++---------
 .../compile-incremental.expected              | 62 ++++++------
 .../compile.expected                          | 32 +++----
 .../spouse_example_new_inference/input.ddl    | 52 +++++-----
 .../print-incremental.expected                | 96 +++++++++----------
 .../print.expected                            | 46 ++++-----
 17 files changed, 408 insertions(+), 407 deletions(-)

diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index 50a9f7de3..ac76b9909 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -5,11 +5,11 @@ articles(
 sentences(
   document_id     text,
   sentence        text,
-  words           text,
-  lemma           text,
-  pos_tags        text,
-  dependencies    text,
-  ner_tags        text,
+  words           text[],
+  lemma           text[],
+  pos_tags        text[],
+  dependencies    text[],
+  ner_tags        text[],
   sentence_offset int,
   sentence_id     text).
 
@@ -34,38 +34,38 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-people_mentions +=
-  ext_people(s, words, ner_tags) :-
-  sentences(a, b, words, c, d, e, ner_tags, f, s).
-
-function ext_people over like ext_people_input
+function ext_people over (sentence_id text, words text, ner_tags text)
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates +=
-  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, a, b, p1_text, p1_id),
-  people_mentions(s, c, d, p2_text, p2_id).
+people_mentions +=
+  ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+  sentences(_, _, words, _, _, _, ner_tags, _, s).
 
-function ext_has_spouse over like ext_has_spouse_input
+function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
                      returns like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
-has_spouse_features +=
-  ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-  people_mentions(s, p1idx, p1len, k, person1_id),
-  people_mentions(s, p2idx, p2len, l, person2_id).
+has_spouse_candidates +=
+  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, _, _, p1_text, p1_id),
+  people_mentions(s, _, _, p2_text, p2_id).
 
-function ext_has_spouse_features over like ext_has_spouse_features_input
+function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
+has_spouse_features +=
+  ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(_, _, words, _, _, _, _, _, s),
+  has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+  people_mentions(s, p1idx, p1len, _, person1_id),
+  people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
-has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
+has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_candidates(_, _, _, _, rid, _),
   has_spouse_features(rid, f).
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 8a8dc33f9..8ff81a0a6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -140,8 +140,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   def resolveExtractorBlockName(s: Statement): String = s"extraction_rule_${statements indexOf s}"
 
   // Given an inference rule, resolve its name for the compiled inference block.
-  def resolveInferenceBlockName(s: InferenceRule): String = {
-    s"inference_rule_${inferenceRules indexOf s}"
+  def resolveInferenceBlockName(s: InferenceRule): String = mode match {
+    case INCREMENTAL => s"dd_delta_inference_rule_${inferenceRules indexOf s}"
+    case _ =>           s"inference_rule_${inferenceRules indexOf s}"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index a84485712..62d8957b8 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -223,7 +223,7 @@ SELECT DISTINCT R0.wid, id, label
       }
     
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM dd_new_q1 R0, dd_delta_features R1
@@ -233,7 +233,7 @@ SELECT DISTINCT R0.wid, id, label
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.dd_delta_inference_rule_1 {
           input_query: """
           SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM dd_new_q2 R0, dd_delta_features R1
@@ -245,7 +245,7 @@ SELECT DISTINCT R0.wid, id, label
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_10, extraction_rule_5, extraction_rule_14, extraction_rule_6, extraction_rule_1, extraction_rule_17, extraction_rule_9, extraction_rule_2, extraction_rule_13, extraction_rule_18]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15, inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0, dd_delta_inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15, dd_delta_inference_rule_0, dd_delta_inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index e0c500474..145bf5f88 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -254,7 +254,7 @@ FROM dd_delta_friends R0
       }
     
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_cancer.R1.id" 
           FROM dd_new_smoke R0, dd_new_cancer R1, dd_delta_person_smokes R2
@@ -264,7 +264,7 @@ FROM dd_delta_friends R0
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.dd_delta_inference_rule_1 {
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
@@ -276,7 +276,7 @@ FROM dd_delta_friends R0
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
 deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0, dd_delta_inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_delta_inference_rule_0, dd_delta_inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index dc17543dc..bfad83044 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -89,11 +89,11 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_new_sentences(document_id text,
                 sentence text,
-                words text,
-                lemma text,
-                pos_tags text,
-                dependencies text,
-                ner_tags text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
                 sentence_offset int,
                 sentence_id text)
             """
@@ -130,11 +130,11 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_delta_sentences(document_id text,
                   sentence text,
-                  words text,
-                  lemma text,
-                  pos_tags text,
-                  dependencies text,
-                  ner_tags text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
                   sentence_offset int,
                   sentence_id text)
             """
@@ -179,7 +179,7 @@ FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "extraction_rule_25" ]
       }
     
 
@@ -209,7 +209,7 @@ FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -224,7 +224,7 @@ FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_29" ]
       }
     
 
@@ -251,7 +251,7 @@ FROM dd_delta_sentences R0
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -272,8 +272,8 @@ SELECT DISTINCT R0.relation_id, id, label
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_24 {
-          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+        deepdive.extraction.extractors.extraction_rule_25 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM dd_delta_sentences R0
         
           """
@@ -284,47 +284,47 @@ FROM dd_delta_sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_26 {
-          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        deepdive.extraction.extractors.extraction_rule_27 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
 UNION ALL
-SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_25" ,  "extraction_rule_11" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_28 {
-          input: """ SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        deepdive.extraction.extractors.extraction_rule_29 {
+          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_25" ]
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -338,8 +338,8 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15, dd_delta_inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index b417d3c24..9e5c9132f 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -22,11 +22,11 @@
             CREATE TABLE
             sentences(document_id text,
          sentence text,
-         words text,
-         lemma text,
-         pos_tags text,
-         dependencies text,
-         ner_tags text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
          sentence_offset int,
          sentence_id text)
             """
@@ -106,12 +106,12 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_8" ]
+          dependencies: [ "extraction_rule_9" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+        deepdive.extraction.extractors.extraction_rule_7 {
+          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
         
           """
@@ -122,27 +122,27 @@ FROM sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_8 {
-          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        deepdive.extraction.extractors.extraction_rule_9 {
+          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_7" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          input: """ SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        deepdive.extraction.extractors.extraction_rule_11 {
+          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_8" ,  "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_9" ,  "extraction_rule_7" ]
         }
       
 
@@ -157,7 +157,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11]
 deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11, inference_rule_0]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 12825b755..53ca958c9 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -22,11 +22,11 @@
             CREATE TABLE
             sentences(document_id text,
          sentence text,
-         words text,
-         lemma text,
-         pos_tags text,
-         dependencies text,
-         ner_tags text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
          sentence_offset int,
          sentence_id text)
             """
@@ -106,12 +106,12 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_8" ]
+          dependencies: [ "extraction_rule_9" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+        deepdive.extraction.extractors.extraction_rule_7 {
+          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
         
           """
@@ -122,27 +122,27 @@ FROM sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_8 {
-          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        deepdive.extraction.extractors.extraction_rule_9 {
+          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_7" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          input: """ SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        deepdive.extraction.extractors.extraction_rule_11 {
+          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_8" ,  "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_9" ,  "extraction_rule_7" ]
         }
       
 
@@ -157,7 +157,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11]
 deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11, inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 4177762f3..bcbcad68e 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -13,31 +13,31 @@ dd_new_articles(article_id, text) :-
 
 sentences(document_id text,
           sentence text,
-          words text,
-          lemma text,
-          pos_tags text,
-          dependencies text,
-          ner_tags text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
           sentence_offset int,
           sentence_id text).
 
 dd_delta_sentences(document_id text,
                    sentence text,
-                   words text,
-                   lemma text,
-                   pos_tags text,
-                   dependencies text,
-                   ner_tags text,
+                   words text[],
+                   lemma text[],
+                   pos_tags text[],
+                   dependencies text[],
+                   ner_tags text[],
                    sentence_offset int,
                    sentence_id text).
 
 dd_new_sentences(document_id text,
                  sentence text,
-                 words text,
-                 lemma text,
-                 pos_tags text,
-                 dependencies text,
-                 ner_tags text,
+                 words text[],
+                 lemma text[],
+                 pos_tags text[],
+                 dependencies text[],
+                 ner_tags text[],
                  sentence_offset int,
                  sentence_id text).
 
@@ -115,59 +115,59 @@ dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
-    dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
-
 function ext_people
-    over like dd_delta_ext_people_input
+    over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
  returns like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
-    people_mentions(s, c, d, p2_text, p2_id);
-    dd_new_people_mentions(s, a, b, p1_text, p1_id),
-    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+    dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over like dd_delta_ext_has_spouse_input
+    over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
  returns like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, _, _, p1_text, p1_id),
+    people_mentions(s, _, _, p2_text, p2_id);
+    dd_new_people_mentions(s, _, _, p1_text, p1_id),
+    dd_delta_people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over like dd_delta_ext_has_spouse_features_input
+    over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
  returns like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(_, _, words, _, _, _, _, _, s),
+    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    dd_delta_people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
 dd_delta_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
+    dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 dd_new_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_candidates(_, _, _, _, rid, _),
     has_spouse_features(rid, f);
-    dd_new_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_new_has_spouse_candidates(_, _, _, _, rid, _),
     dd_delta_has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 13293b09a..1c100ef3e 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -3,11 +3,11 @@ articles(article_id text,
 
 sentences(document_id text,
           sentence text,
-          words text,
-          lemma text,
-          pos_tags text,
-          dependencies text,
-          ner_tags text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
           sentence_offset int,
           sentence_id text).
 
@@ -29,43 +29,43 @@ has_spouse_features(relation_id text,
 
 has_spouse?(relation_id text).
 
-people_mentions += ext_people(s, words, ner_tags) :-
-    sentences(a, b, words, c, d, e, ner_tags, f, s).
-
 function ext_people
-    over like ext_people_input
+    over (sentence_id text, words text, ner_tags text)
  returns like people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    people_mentions(s, a, b, p1_text, p1_id),
-    people_mentions(s, c, d, p2_text, p2_id).
+people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+    sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over like ext_has_spouse_input
+    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
  returns like has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
+has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+    people_mentions(s, _, _, p1_text, p1_id),
+    people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over like ext_has_spouse_features_input
+    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
  returns like has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(_, _, words, _, _, _, _, _, s),
+    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
 has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l).
+    has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_candidates(_, _, _, _, rid, _),
     has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index dc17543dc..bfad83044 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -89,11 +89,11 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_new_sentences(document_id text,
                 sentence text,
-                words text,
-                lemma text,
-                pos_tags text,
-                dependencies text,
-                ner_tags text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
                 sentence_offset int,
                 sentence_id text)
             """
@@ -130,11 +130,11 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_delta_sentences(document_id text,
                   sentence text,
-                  words text,
-                  lemma text,
-                  pos_tags text,
-                  dependencies text,
-                  ner_tags text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
                   sentence_offset int,
                   sentence_id text)
             """
@@ -179,7 +179,7 @@ FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "extraction_rule_25" ]
       }
     
 
@@ -209,7 +209,7 @@ FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -224,7 +224,7 @@ FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_29" ]
       }
     
 
@@ -251,7 +251,7 @@ FROM dd_delta_sentences R0
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -272,8 +272,8 @@ SELECT DISTINCT R0.relation_id, id, label
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_24 {
-          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+        deepdive.extraction.extractors.extraction_rule_25 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM dd_delta_sentences R0
         
           """
@@ -284,47 +284,47 @@ FROM dd_delta_sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_26 {
-          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        deepdive.extraction.extractors.extraction_rule_27 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
 UNION ALL
-SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_25" ,  "extraction_rule_11" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_28 {
-          input: """ SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        deepdive.extraction.extractors.extraction_rule_29 {
+          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_25" ]
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -338,8 +338,8 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15, dd_delta_inference_rule_0]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index cbd8b90cc..1b7abd4d8 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -5,11 +5,11 @@ articles(
 sentences(
   document_id     text,
   sentence        text,
-  words           text,
-  lemma           text,
-  pos_tags        text,
-  dependencies    text,
-  ner_tags        text,
+  words           text[],
+  lemma           text[],
+  pos_tags        text[],
+  dependencies    text[],
+  ner_tags        text[],
   sentence_offset int,
   sentence_id     text).
 
@@ -34,39 +34,39 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-people_mentions +=
-  ext_people(s, words, ner_tags) :-
-  sentences(a, b, words, c, d, e, ner_tags, f, s).
-
 @mode("inc")
-function ext_people over like ext_people_input
+function ext_people over (sentence_id text, words text, ner_tags text)
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates +=
-  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, a, b, p1_text, p1_id),
-  people_mentions(s, c, d, p2_text, p2_id).
+people_mentions +=
+  ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+  sentences(_, _, words, _, _, _, ner_tags, _, s).
 
-function ext_has_spouse over like ext_has_spouse_input
+function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
                      returns like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
-has_spouse_features +=
-  ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-  people_mentions(s, p1idx, p1len, k, person1_id),
-  people_mentions(s, p2idx, p2len, l, person2_id).
+has_spouse_candidates +=
+  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, _, _, p1_text, p1_id),
+  people_mentions(s, _, _, p2_text, p2_id).
 
-function ext_has_spouse_features over like ext_has_spouse_features_input
+function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
+has_spouse_features +=
+  ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(_, _, words, _, _, _, _, _, s),
+  has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+  people_mentions(s, p1idx, p1len, _, person1_id),
+  people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
-has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
+has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_candidates(_, _, _, _, rid, _),
   has_spouse_features(rid, f).
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 6f9d094a1..6372db739 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -13,31 +13,31 @@ dd_new_articles(article_id, text) :-
 
 sentences(document_id text,
           sentence text,
-          words text,
-          lemma text,
-          pos_tags text,
-          dependencies text,
-          ner_tags text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
           sentence_offset int,
           sentence_id text).
 
 dd_delta_sentences(document_id text,
                    sentence text,
-                   words text,
-                   lemma text,
-                   pos_tags text,
-                   dependencies text,
-                   ner_tags text,
+                   words text[],
+                   lemma text[],
+                   pos_tags text[],
+                   dependencies text[],
+                   ner_tags text[],
                    sentence_offset int,
                    sentence_id text).
 
 dd_new_sentences(document_id text,
                  sentence text,
-                 words text,
-                 lemma text,
-                 pos_tags text,
-                 dependencies text,
-                 ner_tags text,
+                 words text[],
+                 lemma text[],
+                 pos_tags text[],
+                 dependencies text[],
+                 ner_tags text[],
                  sentence_offset int,
                  sentence_id text).
 
@@ -115,60 +115,60 @@ dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
-    dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
-
 @mode("inc")
 function ext_people
-    over like dd_delta_ext_people_input
+    over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
  returns like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
-    people_mentions(s, c, d, p2_text, p2_id);
-    dd_new_people_mentions(s, a, b, p1_text, p1_id),
-    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+    dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over like dd_delta_ext_has_spouse_input
+    over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
  returns like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, _, _, p1_text, p1_id),
+    people_mentions(s, _, _, p2_text, p2_id);
+    dd_new_people_mentions(s, _, _, p1_text, p1_id),
+    dd_delta_people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over like dd_delta_ext_has_spouse_features_input
+    over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
  returns like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(_, _, words, _, _, _, _, _, s),
+    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    dd_delta_people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
 dd_delta_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
+    dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 dd_new_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_candidates(_, _, _, _, rid, _),
     has_spouse_features(rid, f);
-    dd_new_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_new_has_spouse_candidates(_, _, _, _, rid, _),
     dd_delta_has_spouse_features(rid, f).
 
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 64a47860d..81a21801e 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -89,11 +89,11 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_new_sentences(document_id text,
                 sentence text,
-                words text,
-                lemma text,
-                pos_tags text,
-                dependencies text,
-                ner_tags text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
                 sentence_offset int,
                 sentence_id text)
             """
@@ -130,11 +130,11 @@ dd_new_has_spouse.label: Boolean
             CREATE TABLE
             dd_delta_sentences(document_id text,
                   sentence text,
-                  words text,
-                  lemma text,
-                  pos_tags text,
-                  dependencies text,
-                  ner_tags text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
                   sentence_offset int,
                   sentence_id text)
             """
@@ -179,7 +179,7 @@ FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "extraction_rule_25" ]
       }
     
 
@@ -209,7 +209,7 @@ FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -224,7 +224,7 @@ FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_28" ]
+          dependencies: [ "extraction_rule_29" ]
       }
     
 
@@ -251,7 +251,7 @@ FROM dd_delta_sentences R0
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_26" ]
+          dependencies: [ "extraction_rule_27" ]
       }
     
 
@@ -272,8 +272,8 @@ SELECT DISTINCT R0.relation_id, id, label
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_24 {
-          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id" , R0.words AS "dd_delta_sentences.R0.words" , R0.ner_tags AS "dd_delta_sentences.R0.ner_tags" 
+        deepdive.extraction.extractors.extraction_rule_25 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM dd_delta_sentences R0
         
           """
@@ -284,47 +284,47 @@ FROM dd_delta_sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_26 {
-          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        deepdive.extraction.extractors.extraction_rule_27 {
+          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
 UNION ALL
-SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id" , R0.mention_id AS "dd_delta_people_mentions.R0.mention_id" , R0.text AS "dd_delta_people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_24" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_25" ,  "extraction_rule_11" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_28 {
-          input: """ SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        deepdive.extraction.extractors.extraction_rule_29 {
+          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
-SELECT R0.words AS "dd_delta_sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_26" ,  "extraction_rule_24" ,  "extraction_rule_7" ,  "extraction_rule_11" ]
+          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_25" ]
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inference_rule_0 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -337,7 +337,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.dd_delta_inference_rule_1 {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
@@ -348,8 +348,8 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_28, extraction_rule_19, extraction_rule_3, extraction_rule_26, extraction_rule_30, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15]
+deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0, dd_delta_inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15, dd_delta_inference_rule_0, dd_delta_inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 7954e4e5e..49063eed9 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -22,11 +22,11 @@
             CREATE TABLE
             sentences(document_id text,
          sentence text,
-         words text,
-         lemma text,
-         pos_tags text,
-         dependencies text,
-         ner_tags text,
+         words text[],
+         lemma text[],
+         pos_tags text[],
+         dependencies text[],
+         ner_tags text[],
          sentence_offset int,
          sentence_id text)
             """
@@ -106,12 +106,12 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_8" ]
+          dependencies: [ "extraction_rule_9" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_6 {
-          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id" , R0.words AS "sentences.R0.words" , R0.ner_tags AS "sentences.R0.ner_tags" 
+        deepdive.extraction.extractors.extraction_rule_7 {
+          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
         
           """
@@ -122,27 +122,27 @@ FROM sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_8 {
-          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id" , R0.mention_id AS "people_mentions.R0.mention_id" , R0.text AS "people_mentions.R0.text" , R1.mention_id AS "people_mentions.R1.mention_id" , R1.text AS "people_mentions.R1.text" 
+        deepdive.extraction.extractors.extraction_rule_9 {
+          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
           """
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_7" ]
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_10 {
-          input: """ SELECT R0.words AS "sentences.R0.words" , R1.relation_id AS "has_spouse_candidates.R1.relation_id" , R2.start_position AS "people_mentions.R2.start_position" , R2.length AS "people_mentions.R2.length" , R3.start_position AS "people_mentions.R3.start_position" , R3.length AS "people_mentions.R3.length" 
+        deepdive.extraction.extractors.extraction_rule_11 {
+          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
           """
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_8" ,  "extraction_rule_6" ]
+          dependencies: [ "extraction_rule_9" ,  "extraction_rule_7" ]
         }
       
 
@@ -167,7 +167,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10]
+deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11]
 deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_6, extraction_rule_8, extraction_rule_10, inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11, inference_rule_0, inference_rule_1]
 deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 944df4a41..01ded96ac 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -5,11 +5,11 @@ articles(
 sentences(
   document_id     text,
   sentence        text,
-  words           text,
-  lemma           text,
-  pos_tags        text,
-  dependencies    text,
-  ner_tags        text,
+  words           text[],
+  lemma           text[],
+  pos_tags        text[],
+  dependencies    text[],
+  ner_tags        text[],
   sentence_offset int,
   sentence_id     text).
 
@@ -34,44 +34,44 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-people_mentions +=
-  ext_people(s, words, ner_tags) :-
-  sentences(a, b, words, c, d, e, ner_tags, f, s).
-
-function ext_people over like ext_people_input
+function ext_people over (sentence_id text, words text, ner_tags text)
                  returns like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
-has_spouse_candidates +=
-  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, a, b, p1_text, p1_id),
-  people_mentions(s, c, d, p2_text, p2_id).
+people_mentions +=
+  ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+  sentences(_, _, words, _, _, _, ner_tags, _, s).
 
-function ext_has_spouse over like ext_has_spouse_input
+function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
                      returns like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
-has_spouse_features +=
-  ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(a, b, words, c, d, e, f, g, s),
-  has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-  people_mentions(s, p1idx, p1len, k, person1_id),
-  people_mentions(s, p2idx, p2len, l, person2_id).
+has_spouse_candidates +=
+  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+  people_mentions(s, _, _, p1_text, p1_id),
+  people_mentions(s, _, _, p2_text, p2_id).
 
-function ext_has_spouse_features over like ext_has_spouse_features_input
+function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
                               returns like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
+has_spouse_features +=
+  ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+  sentences(_, _, words, _, _, _, _, _, s),
+  has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+  people_mentions(s, p1idx, p1len, _, person1_id),
+  people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
-has_spouse(rid) :- has_spouse_candidates(a, b, c, d, rid, l).
+has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
-  has_spouse_candidates(a, b, c, d, rid, l),
+  has_spouse_candidates(_, _, _, _, rid, _),
   has_spouse_features(rid, f).
 
 @mode("inc")
 @weight(3.0)
 has_spouse(rid2) = has_spouse(rid) :-
-  has_spouse_candidates(a1, b1, c1, d1, rid, l1),
-  has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
+  has_spouse_candidates(a1, b1, _, _, rid, _),
+  has_spouse_candidates(b1, a1, _, _, rid2, _).
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 477fc1e5d..fca7c6c03 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -13,31 +13,31 @@ dd_new_articles(article_id, text) :-
 
 sentences(document_id text,
           sentence text,
-          words text,
-          lemma text,
-          pos_tags text,
-          dependencies text,
-          ner_tags text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
           sentence_offset int,
           sentence_id text).
 
 dd_delta_sentences(document_id text,
                    sentence text,
-                   words text,
-                   lemma text,
-                   pos_tags text,
-                   dependencies text,
-                   ner_tags text,
+                   words text[],
+                   lemma text[],
+                   pos_tags text[],
+                   dependencies text[],
+                   ner_tags text[],
                    sentence_offset int,
                    sentence_id text).
 
 dd_new_sentences(document_id text,
                  sentence text,
-                 words text,
-                 lemma text,
-                 pos_tags text,
-                 dependencies text,
-                 ner_tags text,
+                 words text[],
+                 lemma text[],
+                 pos_tags text[],
+                 dependencies text[],
+                 ner_tags text[],
                  sentence_offset int,
                  sentence_id text).
 
@@ -115,64 +115,64 @@ dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-dd_delta_people_mentions += ext_people(s, words, ner_tags) :-
-    dd_delta_sentences(a, b, words, c, d, e, ner_tags, f, s).
-
 function ext_people
-    over like dd_delta_ext_people_input
+    over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
  returns like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, a, b, p1_text, p1_id),
-    people_mentions(s, c, d, p2_text, p2_id);
-    dd_new_people_mentions(s, a, b, p1_text, p1_id),
-    dd_delta_people_mentions(s, c, d, p2_text, p2_id).
+dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+    dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over like dd_delta_ext_has_spouse_input
+    over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
  returns like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-dd_delta_has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_delta_people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id);
-    dd_new_sentences(a, b, words, c, d, e, f, g, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    dd_new_people_mentions(s, p1idx, p1len, k, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, l, person2_id).
+dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+    dd_delta_people_mentions(s, _, _, p1_text, p1_id),
+    people_mentions(s, _, _, p2_text, p2_id);
+    dd_new_people_mentions(s, _, _, p1_text, p1_id),
+    dd_delta_people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over like dd_delta_ext_has_spouse_features_input
+    over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
  returns like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+    dd_delta_sentences(_, _, words, _, _, _, _, _, s),
+    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_delta_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    dd_delta_people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
+    dd_new_sentences(_, _, words, _, _, _, _, _, s),
+    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
+    dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
 dd_delta_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l).
+    dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 dd_new_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_delta_has_spouse_candidates(_, _, _, _, rid, _),
     has_spouse_features(rid, f);
-    dd_new_has_spouse_candidates(a, b, c, d, rid, l),
+    dd_new_has_spouse_candidates(_, _, _, _, rid, _),
     dd_delta_has_spouse_features(rid, f).
 
 @weight(3.0)
 dd_new_has_spouse(rid2) = dd_new_has_spouse(rid) :-
-    dd_new_has_spouse_candidates(a1, b1, c1, d1, rid, l1),
-    dd_new_has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
+    dd_new_has_spouse_candidates(a1, b1, _, _, rid, _),
+    dd_new_has_spouse_candidates(b1, a1, _, _, rid2, _).
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 4ed66dff6..5576bb6a2 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -3,11 +3,11 @@ articles(article_id text,
 
 sentences(document_id text,
           sentence text,
-          words text,
-          lemma text,
-          pos_tags text,
-          dependencies text,
-          ner_tags text,
+          words text[],
+          lemma text[],
+          pos_tags text[],
+          dependencies text[],
+          ner_tags text[],
           sentence_offset int,
           sentence_id text).
 
@@ -29,48 +29,48 @@ has_spouse_features(relation_id text,
 
 has_spouse?(relation_id text).
 
-people_mentions += ext_people(s, words, ner_tags) :-
-    sentences(a, b, words, c, d, e, ner_tags, f, s).
-
 function ext_people
-    over like ext_people_input
+    over (sentence_id text, words text, ner_tags text)
  returns like people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
-has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    people_mentions(s, a, b, p1_text, p1_id),
-    people_mentions(s, c, d, p2_text, p2_id).
+people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
+    sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over like ext_has_spouse_input
+    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
  returns like has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
-has_spouse_features += ext_has_spouse_features(words, rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(a, b, words, c, d, e, f, g, s),
-    has_spouse_candidates(person1_id, person2_id, s, h, rid, x),
-    people_mentions(s, p1idx, p1len, k, person1_id),
-    people_mentions(s, p2idx, p2len, l, person2_id).
+has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
+    people_mentions(s, _, _, p1_text, p1_id),
+    people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over like ext_has_spouse_features_input
+    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
  returns like has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
+has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(_, _, words, _, _, _, _, _, s),
+    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id).
+
 @label(l)
 has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l).
+    has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
-    has_spouse_candidates(a, b, c, d, rid, l),
+    has_spouse_candidates(_, _, _, _, rid, _),
     has_spouse_features(rid, f).
 
 @weight(3.0)
 has_spouse(rid2) = has_spouse(rid) :-
-    has_spouse_candidates(a1, b1, c1, d1, rid, l1),
-    has_spouse_candidates(b1, a1, c2, d2, rid2, l2).
+    has_spouse_candidates(a1, b1, _, _, rid, _),
+    has_spouse_candidates(b1, a1, _, _, rid2, _).
 

From 8aeec0eaac22729661e65d42d0a31cfb136f8646 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 20 Aug 2015 18:11:13 -0700
Subject: [PATCH 218/347] Use "rows like" instead of "like" in function
 declaration

---
 examples/chunking.ddl                          |  8 ++++----
 examples/spouse_example.ddl                    |  6 +++---
 .../org/deepdive/ddlog/DeepDiveLogParser.scala | 18 +++++++++---------
 .../ddlog/DeepDiveLogPrettyPrinter.scala       |  4 ++--
 .../spouse_example/print-incremental.expected  |  6 +++---
 .../spouse_example/print.expected              |  6 +++---
 .../spouse_example_new_feature/input.ddl       |  6 +++---
 .../print-incremental.expected                 |  6 +++---
 .../spouse_example_new_inference/input.ddl     |  6 +++---
 .../print-incremental.expected                 |  6 +++---
 .../print.expected                             |  6 +++---
 11 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/examples/chunking.ddl b/examples/chunking.ddl
index e2fd8c94f..28a172de8 100644
--- a/examples/chunking.ddl
+++ b/examples/chunking.ddl
@@ -21,16 +21,16 @@ word_features(
 tag?(word_id bigint) Categorical(13).
 
 function ext_training
-  over like words_raw
-  returns like words
+  over rows like words_raw
+  returns rows like words
   implementation "udf/ext_training.py" handles tsv lines.
 
 words +=
   ext_training(wid, word, pos, tag) :- words_raw(wid, word, pos, tag).
 
 function ext_features
-  over like ext_features_input
-  returns like word_features
+  over (word_id1 bigint, word1 text, pos1 text, word2 text, pos2 text)
+  returns rows like word_features
   implementation "udf/ext_features.py" handles tsv lines.
 
 word_features +=
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddl
index ac76b9909..079083c3d 100644
--- a/examples/spouse_example.ddl
+++ b/examples/spouse_example.ddl
@@ -35,7 +35,7 @@ has_spouse_features(
 has_spouse?(relation_id text).
 
 function ext_people over (sentence_id text, words text, ner_tags text)
-                 returns like people_mentions
+                 returns rows like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
 people_mentions +=
@@ -43,7 +43,7 @@ people_mentions +=
   sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
-                     returns like has_spouse_candidates
+                     returns rows like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_candidates +=
@@ -52,7 +52,7 @@ has_spouse_candidates +=
   people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
-                              returns like has_spouse_features
+                              returns rows like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse_features +=
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 2502b934f..f6cb61308 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -84,9 +84,9 @@ case class HeadAtom(name : String, terms : List[Expr])
 case class InferenceRuleHead(function: FactorFunction.FactorFunction, terms: List[HeadAtom])
 
 
-trait RelationType
-case class RelationTypeDeclaration(names: List[String], types: List[String]) extends RelationType
-case class RelationTypeAlias(likeRelationName: String) extends RelationType
+trait FunctionInputOutputType
+case class RelationTypeDeclaration(names: List[String], types: List[String]) extends FunctionInputOutputType
+case class RelationTypeAlias(likeRelationName: String) extends FunctionInputOutputType
 
 trait FunctionImplementationDeclaration
 case class RowWiseLineHandler(style: String, command: String) extends FunctionImplementationDeclaration
@@ -98,8 +98,8 @@ case class SchemaDeclaration( a : Attribute
                             , variableType : Option[VariableType]
                             , annotation : List[Annotation] = List.empty // optional annotation
                             ) extends Statement // atom and whether this is a query relation.
-case class FunctionDeclaration( functionName: String, inputType: RelationType,
-  outputType: RelationType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
+case class FunctionDeclaration( functionName: String, inputType: FunctionInputOutputType,
+  outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
 case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
 case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery) extends Statement // Extraction rule
 case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
@@ -250,8 +250,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
     QuantifiedBody(modifier, b)
   }
 
-  def relationType: Parser[RelationType] =
-    ( "like" ~> relationName ^^ { RelationTypeAlias(_) }
+  def functionInputOutputType: Parser[FunctionInputOutputType] =
+    ( "rows" ~> "like" ~> relationName ^^ { RelationTypeAlias(_) }
     | "(" ~> rep1sep(columnDeclaration, ",") <~ ")" ^^ {
         attrs => RelationTypeDeclaration(attrs map { _.name }, attrs map { _.t })
       }
@@ -281,8 +281,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }, (s) => s"${s}: unrecognized mode"))
 
   def functionDeclaration : Parser[FunctionDeclaration] =
-    ( opt(functionMode) ~ "function" ~ functionName ~ "over" ~ relationType
-                             ~ "returns" ~ relationType
+    ( opt(functionMode) ~ "function" ~ functionName ~ "over" ~ functionInputOutputType
+                             ~ "returns" ~ functionInputOutputType
                  ~ (functionImplementation+)
     ) ^^ {
       case (mode ~ "function" ~ a ~ "over" ~ inTy
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 03588dfd2..d6a5f475d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -43,8 +43,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
        |""".stripMargin
   }
 
-  def print(relationType: RelationType): String = relationType match {
-    case ty: RelationTypeAlias => s"like ${ty.likeRelationName}"
+  def print(functionInputOutputType: FunctionInputOutputType): String = functionInputOutputType match {
+    case ty: RelationTypeAlias => s"rows like ${ty.likeRelationName}"
     case ty: RelationTypeDeclaration =>
       val namesWithTypes = (ty.names, ty.types).zipped map {
         (colName,colType) => s"${colName} ${colType}"}
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index bcbcad68e..a8f7a2397 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -117,7 +117,7 @@ dd_new_has_spouse(relation_id) :-
 
 function ext_people
     over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
- returns like dd_delta_people_mentions
+ returns rows like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
@@ -126,7 +126,7 @@ dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_T
 
 function ext_has_spouse
     over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
- returns like dd_delta_has_spouse_candidates
+ returns rows like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -138,7 +138,7 @@ dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_te
 
 function ext_has_spouse_features
     over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
- returns like dd_delta_has_spouse_features
+ returns rows like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 1c100ef3e..401e9aed3 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -31,7 +31,7 @@ has_spouse?(relation_id text).
 
 function ext_people
     over (sentence_id text, words text, ner_tags text)
- returns like people_mentions
+ returns rows like people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
@@ -40,7 +40,7 @@ people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(
 
 function ext_has_spouse
     over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
- returns like has_spouse_candidates
+ returns rows like has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -50,7 +50,7 @@ has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse_features
     over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
- returns like has_spouse_features
+ returns rows like has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddl
index 1b7abd4d8..9ded3b9d4 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddl
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddl
@@ -36,7 +36,7 @@ has_spouse?(relation_id text).
 
 @mode("inc")
 function ext_people over (sentence_id text, words text, ner_tags text)
-                 returns like people_mentions
+                 returns rows like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
 people_mentions +=
@@ -44,7 +44,7 @@ people_mentions +=
   sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
-                     returns like has_spouse_candidates
+                     returns rows like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_candidates +=
@@ -53,7 +53,7 @@ has_spouse_candidates +=
   people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
-                              returns like has_spouse_features
+                              returns rows like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse_features +=
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 6372db739..d8831de26 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -118,7 +118,7 @@ dd_new_has_spouse(relation_id) :-
 @mode("inc")
 function ext_people
     over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
- returns like dd_delta_people_mentions
+ returns rows like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
@@ -127,7 +127,7 @@ dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_T
 
 function ext_has_spouse
     over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
- returns like dd_delta_has_spouse_candidates
+ returns rows like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -139,7 +139,7 @@ dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_te
 
 function ext_has_spouse_features
     over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
- returns like dd_delta_has_spouse_features
+ returns rows like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddl
index 01ded96ac..36c64c8e4 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddl
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddl
@@ -35,7 +35,7 @@ has_spouse_features(
 has_spouse?(relation_id text).
 
 function ext_people over (sentence_id text, words text, ner_tags text)
-                 returns like people_mentions
+                 returns rows like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
 
 people_mentions +=
@@ -43,7 +43,7 @@ people_mentions +=
   sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
-                     returns like has_spouse_candidates
+                     returns rows like has_spouse_candidates
   implementation "udf/ext_has_spouse.py" handles tsv lines.
 
 has_spouse_candidates +=
@@ -52,7 +52,7 @@ has_spouse_candidates +=
   people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
-                              returns like has_spouse_features
+                              returns rows like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
 has_spouse_features +=
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index fca7c6c03..095cdab0f 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -117,7 +117,7 @@ dd_new_has_spouse(relation_id) :-
 
 function ext_people
     over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
- returns like dd_delta_people_mentions
+ returns rows like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
@@ -126,7 +126,7 @@ dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_T
 
 function ext_has_spouse
     over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
- returns like dd_delta_has_spouse_candidates
+ returns rows like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -138,7 +138,7 @@ dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_te
 
 function ext_has_spouse_features
     over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
- returns like dd_delta_has_spouse_features
+ returns rows like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 5576bb6a2..4068d8de9 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -31,7 +31,7 @@ has_spouse?(relation_id text).
 
 function ext_people
     over (sentence_id text, words text, ner_tags text)
- returns like people_mentions
+ returns rows like people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
 
@@ -40,7 +40,7 @@ people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(
 
 function ext_has_spouse
     over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
- returns like has_spouse_candidates
+ returns rows like has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
 
@@ -50,7 +50,7 @@ has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
 
 function ext_has_spouse_features
     over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
- returns like has_spouse_features
+ returns rows like has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 

From 048fc6f18d6bd99688a6766285351a5f1b3c0883 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 20 Aug 2015 21:49:20 -0700
Subject: [PATCH 219/347] Change file extension from .ddl to .ddlog

---
 examples/{chunking.ddl => chunking.ddlog}     |  0
 examples/{ocr.ddl => ocr.ddlog}               |  0
 examples/{smoke.ddl => smoke.ddlog}           |  0
 ...pouse_example.ddl => spouse_example.ddlog} |  0
 test/compile-error-test.bats.template         |  2 +-
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../weight/{input.ddl => input.ddlog}         |  0
 test/expected-output-test.bats.template       | 20 +++++++++----------
 test/expected-output-test/README.md           |  2 +-
 .../annotations/{input.ddl => input.ddlog}    |  0
 .../chunking_example/input.ddl                |  1 -
 .../chunking_example/input.ddlog              |  1 +
 .../comments/{input.ddl => input.ddlog}       |  0
 .../expressions/{input.ddl => input.ddlog}    |  0
 .../{input.ddl => input.ddlog}                |  0
 .../many_joins/{input.ddl => input.ddlog}     |  0
 .../multibody/{input.ddl => input.ddlog}      |  0
 .../ocr_example/input.ddl                     |  1 -
 .../ocr_example/input.ddlog                   |  1 +
 .../semantics/{input.ddl => input.ddlog}      |  0
 .../smoke_example/input.ddl                   |  1 -
 .../smoke_example/input.ddlog                 |  1 +
 .../spouse_example/input.ddl                  |  1 -
 .../spouse_example/input.ddlog                |  1 +
 .../{input.ddl => input.ddlog}                |  0
 .../{input.ddl => input.ddlog}                |  0
 .../views/{input.ddl => input.ddlog}          |  0
 .../weights/{input.ddl => input.ddlog}        |  0
 test/parse-error-test.bats.template           |  2 +-
 .../{input.ddl => input.ddlog}                |  0
 .../annotation_mode/parse-error.expected      |  2 +-
 .../{input.ddl => input.ddlog}                |  0
 .../annotation_semantics/parse-error.expected |  2 +-
 .../{input.ddl => input.ddlog}                |  0
 .../parse-error.expected                      |  2 +-
 44 files changed, 20 insertions(+), 20 deletions(-)
 rename examples/{chunking.ddl => chunking.ddlog} (100%)
 rename examples/{ocr.ddl => ocr.ddlog} (100%)
 rename examples/{smoke.ddl => smoke.ddlog} (100%)
 rename examples/{spouse_example.ddl => spouse_example.ddlog} (100%)
 rename test/compile-error-test/column_dismatch/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/invalid_variable_schema/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/optional_modifier/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/unbound_variable_1/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/unbound_variable_2/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/unbound_variable_3/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/unbound_variable_4/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/undefined_function/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/undefined_relation/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/undefined_relation_2/{input.ddl => input.ddlog} (100%)
 rename test/compile-error-test/weight/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/annotations/{input.ddl => input.ddlog} (100%)
 delete mode 120000 test/expected-output-test/chunking_example/input.ddl
 create mode 120000 test/expected-output-test/chunking_example/input.ddlog
 rename test/expected-output-test/comments/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/expressions/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/factor_functions/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/many_joins/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/multibody/{input.ddl => input.ddlog} (100%)
 delete mode 120000 test/expected-output-test/ocr_example/input.ddl
 create mode 120000 test/expected-output-test/ocr_example/input.ddlog
 rename test/expected-output-test/semantics/{input.ddl => input.ddlog} (100%)
 delete mode 120000 test/expected-output-test/smoke_example/input.ddl
 create mode 120000 test/expected-output-test/smoke_example/input.ddlog
 delete mode 120000 test/expected-output-test/spouse_example/input.ddl
 create mode 120000 test/expected-output-test/spouse_example/input.ddlog
 rename test/expected-output-test/spouse_example_new_feature/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/spouse_example_new_inference/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/views/{input.ddl => input.ddlog} (100%)
 rename test/expected-output-test/weights/{input.ddl => input.ddlog} (100%)
 rename test/parse-error-test/annotation_mode/{input.ddl => input.ddlog} (100%)
 rename test/parse-error-test/annotation_semantics/{input.ddl => input.ddlog} (100%)
 rename test/parse-error-test/nested_multiline_comments/{input.ddl => input.ddlog} (100%)

diff --git a/examples/chunking.ddl b/examples/chunking.ddlog
similarity index 100%
rename from examples/chunking.ddl
rename to examples/chunking.ddlog
diff --git a/examples/ocr.ddl b/examples/ocr.ddlog
similarity index 100%
rename from examples/ocr.ddl
rename to examples/ocr.ddlog
diff --git a/examples/smoke.ddl b/examples/smoke.ddlog
similarity index 100%
rename from examples/smoke.ddl
rename to examples/smoke.ddlog
diff --git a/examples/spouse_example.ddl b/examples/spouse_example.ddlog
similarity index 100%
rename from examples/spouse_example.ddl
rename to examples/spouse_example.ddlog
diff --git a/test/compile-error-test.bats.template b/test/compile-error-test.bats.template
index 2488fa915..42c937cde 100644
--- a/test/compile-error-test.bats.template
+++ b/test/compile-error-test.bats.template
@@ -15,7 +15,7 @@ setup() {
 
 # check if input produces a compile error
 @test "$it compiles input" {
-    ! ddlog check "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+    ! ddlog check "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError"
     diff "$expectedError" "$actualError"
 }
 
diff --git a/test/compile-error-test/column_dismatch/input.ddl b/test/compile-error-test/column_dismatch/input.ddlog
similarity index 100%
rename from test/compile-error-test/column_dismatch/input.ddl
rename to test/compile-error-test/column_dismatch/input.ddlog
diff --git a/test/compile-error-test/invalid_variable_schema/input.ddl b/test/compile-error-test/invalid_variable_schema/input.ddlog
similarity index 100%
rename from test/compile-error-test/invalid_variable_schema/input.ddl
rename to test/compile-error-test/invalid_variable_schema/input.ddlog
diff --git a/test/compile-error-test/optional_modifier/input.ddl b/test/compile-error-test/optional_modifier/input.ddlog
similarity index 100%
rename from test/compile-error-test/optional_modifier/input.ddl
rename to test/compile-error-test/optional_modifier/input.ddlog
diff --git a/test/compile-error-test/unbound_variable_1/input.ddl b/test/compile-error-test/unbound_variable_1/input.ddlog
similarity index 100%
rename from test/compile-error-test/unbound_variable_1/input.ddl
rename to test/compile-error-test/unbound_variable_1/input.ddlog
diff --git a/test/compile-error-test/unbound_variable_2/input.ddl b/test/compile-error-test/unbound_variable_2/input.ddlog
similarity index 100%
rename from test/compile-error-test/unbound_variable_2/input.ddl
rename to test/compile-error-test/unbound_variable_2/input.ddlog
diff --git a/test/compile-error-test/unbound_variable_3/input.ddl b/test/compile-error-test/unbound_variable_3/input.ddlog
similarity index 100%
rename from test/compile-error-test/unbound_variable_3/input.ddl
rename to test/compile-error-test/unbound_variable_3/input.ddlog
diff --git a/test/compile-error-test/unbound_variable_4/input.ddl b/test/compile-error-test/unbound_variable_4/input.ddlog
similarity index 100%
rename from test/compile-error-test/unbound_variable_4/input.ddl
rename to test/compile-error-test/unbound_variable_4/input.ddlog
diff --git a/test/compile-error-test/undefined_function/input.ddl b/test/compile-error-test/undefined_function/input.ddlog
similarity index 100%
rename from test/compile-error-test/undefined_function/input.ddl
rename to test/compile-error-test/undefined_function/input.ddlog
diff --git a/test/compile-error-test/undefined_relation/input.ddl b/test/compile-error-test/undefined_relation/input.ddlog
similarity index 100%
rename from test/compile-error-test/undefined_relation/input.ddl
rename to test/compile-error-test/undefined_relation/input.ddlog
diff --git a/test/compile-error-test/undefined_relation_2/input.ddl b/test/compile-error-test/undefined_relation_2/input.ddlog
similarity index 100%
rename from test/compile-error-test/undefined_relation_2/input.ddl
rename to test/compile-error-test/undefined_relation_2/input.ddlog
diff --git a/test/compile-error-test/weight/input.ddl b/test/compile-error-test/weight/input.ddlog
similarity index 100%
rename from test/compile-error-test/weight/input.ddl
rename to test/compile-error-test/weight/input.ddlog
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index ba628fd47..a6ac9954e 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -19,18 +19,18 @@ setup() {
     if [ -e "$expectedError" ]; then
         # input is expected to have parse errors
         actualError=${expectedError%.expected}.actual
-        ! ddlog print "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+        ! ddlog print "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError"
         diff "$expectedError" "$actualError"
     else
         # input is supposed to parse without errors
-        ddlog print "$TESTDIR"/input.ddl >/dev/null
+        ddlog print "$TESTDIR"/input.ddlog >/dev/null
     fi
 }
 
 # check if print is idempotent
 @test "$it parses and prints what it prints (idempotent)" {
     printed=$TESTDIR/printed.actual
-    ddlog print "$TESTDIR"/input.ddl >"$printed" || skip
+    ddlog print "$TESTDIR"/input.ddlog >"$printed" || skip
     ddlog print "$printed" >"$TESTDIR"/printed-printed.actual
     diff "$printed" "$TESTDIR"/printed-printed.actual
 }
@@ -41,7 +41,7 @@ setup() {
     expectedOutput=$TESTDIR/compile.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog compile "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog compile "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
@@ -50,7 +50,7 @@ setup() {
     expectedOutput=$TESTDIR/print.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog print "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog print "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
@@ -59,7 +59,7 @@ setup() {
     expectedOutput=$TESTDIR/export-schema.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog export-schema "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog export-schema "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
@@ -71,7 +71,7 @@ setup() {
     expectedOutput=$TESTDIR/compile-incremental.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog compile --incremental "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog compile --incremental "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
@@ -80,7 +80,7 @@ setup() {
     expectedOutput=$TESTDIR/print-incremental.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog print --incremental "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog print --incremental "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
@@ -91,7 +91,7 @@ setup() {
     expectedOutput=$TESTDIR/compile-merge.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog compile --merge "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog compile --merge "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
@@ -102,6 +102,6 @@ setup() {
     expectedOutput=$TESTDIR/compile-materialization.expected
     actualOutput=${expectedOutput%.expected}.actual
     [ -e "$expectedOutput" ] || skip
-    ddlog compile --materialization "$TESTDIR"/input.ddl >"$actualOutput"
+    ddlog compile --materialization "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
diff --git a/test/expected-output-test/README.md b/test/expected-output-test/README.md
index 2e9915962..3dc325523 100644
--- a/test/expected-output-test/README.md
+++ b/test/expected-output-test/README.md
@@ -2,7 +2,7 @@ Here are test cases for running the "expected-output-test".
 
 Each test case is a directory that contains the following files:
 
-* `input.ddl` is the input DDLog program.
+* `input.ddlog` is the input DDLog program.
     * Parser is tested against every input program.
     * If the input is supposed to cause a parse error, `parse.error.expected` containing an expected error message should be there.
 * `print.expected` is the expected output of running the `print` command.  Test is skipped if not available.
diff --git a/test/expected-output-test/annotations/input.ddl b/test/expected-output-test/annotations/input.ddlog
similarity index 100%
rename from test/expected-output-test/annotations/input.ddl
rename to test/expected-output-test/annotations/input.ddlog
diff --git a/test/expected-output-test/chunking_example/input.ddl b/test/expected-output-test/chunking_example/input.ddl
deleted file mode 120000
index 64139b0ef..000000000
--- a/test/expected-output-test/chunking_example/input.ddl
+++ /dev/null
@@ -1 +0,0 @@
-../../../examples/chunking.ddl
\ No newline at end of file
diff --git a/test/expected-output-test/chunking_example/input.ddlog b/test/expected-output-test/chunking_example/input.ddlog
new file mode 120000
index 000000000..fbb0cefdd
--- /dev/null
+++ b/test/expected-output-test/chunking_example/input.ddlog
@@ -0,0 +1 @@
+../../../examples/chunking.ddlog
\ No newline at end of file
diff --git a/test/expected-output-test/comments/input.ddl b/test/expected-output-test/comments/input.ddlog
similarity index 100%
rename from test/expected-output-test/comments/input.ddl
rename to test/expected-output-test/comments/input.ddlog
diff --git a/test/expected-output-test/expressions/input.ddl b/test/expected-output-test/expressions/input.ddlog
similarity index 100%
rename from test/expected-output-test/expressions/input.ddl
rename to test/expected-output-test/expressions/input.ddlog
diff --git a/test/expected-output-test/factor_functions/input.ddl b/test/expected-output-test/factor_functions/input.ddlog
similarity index 100%
rename from test/expected-output-test/factor_functions/input.ddl
rename to test/expected-output-test/factor_functions/input.ddlog
diff --git a/test/expected-output-test/many_joins/input.ddl b/test/expected-output-test/many_joins/input.ddlog
similarity index 100%
rename from test/expected-output-test/many_joins/input.ddl
rename to test/expected-output-test/many_joins/input.ddlog
diff --git a/test/expected-output-test/multibody/input.ddl b/test/expected-output-test/multibody/input.ddlog
similarity index 100%
rename from test/expected-output-test/multibody/input.ddl
rename to test/expected-output-test/multibody/input.ddlog
diff --git a/test/expected-output-test/ocr_example/input.ddl b/test/expected-output-test/ocr_example/input.ddl
deleted file mode 120000
index 69125ec70..000000000
--- a/test/expected-output-test/ocr_example/input.ddl
+++ /dev/null
@@ -1 +0,0 @@
-../../../examples/ocr.ddl
\ No newline at end of file
diff --git a/test/expected-output-test/ocr_example/input.ddlog b/test/expected-output-test/ocr_example/input.ddlog
new file mode 120000
index 000000000..d922c1526
--- /dev/null
+++ b/test/expected-output-test/ocr_example/input.ddlog
@@ -0,0 +1 @@
+../../../examples/ocr.ddlog
\ No newline at end of file
diff --git a/test/expected-output-test/semantics/input.ddl b/test/expected-output-test/semantics/input.ddlog
similarity index 100%
rename from test/expected-output-test/semantics/input.ddl
rename to test/expected-output-test/semantics/input.ddlog
diff --git a/test/expected-output-test/smoke_example/input.ddl b/test/expected-output-test/smoke_example/input.ddl
deleted file mode 120000
index 5c2cf2d32..000000000
--- a/test/expected-output-test/smoke_example/input.ddl
+++ /dev/null
@@ -1 +0,0 @@
-../../../examples/smoke.ddl
\ No newline at end of file
diff --git a/test/expected-output-test/smoke_example/input.ddlog b/test/expected-output-test/smoke_example/input.ddlog
new file mode 120000
index 000000000..31478af72
--- /dev/null
+++ b/test/expected-output-test/smoke_example/input.ddlog
@@ -0,0 +1 @@
+../../../examples/smoke.ddlog
\ No newline at end of file
diff --git a/test/expected-output-test/spouse_example/input.ddl b/test/expected-output-test/spouse_example/input.ddl
deleted file mode 120000
index 63c01729c..000000000
--- a/test/expected-output-test/spouse_example/input.ddl
+++ /dev/null
@@ -1 +0,0 @@
-../../../examples/spouse_example.ddl
\ No newline at end of file
diff --git a/test/expected-output-test/spouse_example/input.ddlog b/test/expected-output-test/spouse_example/input.ddlog
new file mode 120000
index 000000000..2b803e7b5
--- /dev/null
+++ b/test/expected-output-test/spouse_example/input.ddlog
@@ -0,0 +1 @@
+../../../examples/spouse_example.ddlog
\ No newline at end of file
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddl b/test/expected-output-test/spouse_example_new_feature/input.ddlog
similarity index 100%
rename from test/expected-output-test/spouse_example_new_feature/input.ddl
rename to test/expected-output-test/spouse_example_new_feature/input.ddlog
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddl b/test/expected-output-test/spouse_example_new_inference/input.ddlog
similarity index 100%
rename from test/expected-output-test/spouse_example_new_inference/input.ddl
rename to test/expected-output-test/spouse_example_new_inference/input.ddlog
diff --git a/test/expected-output-test/views/input.ddl b/test/expected-output-test/views/input.ddlog
similarity index 100%
rename from test/expected-output-test/views/input.ddl
rename to test/expected-output-test/views/input.ddlog
diff --git a/test/expected-output-test/weights/input.ddl b/test/expected-output-test/weights/input.ddlog
similarity index 100%
rename from test/expected-output-test/weights/input.ddl
rename to test/expected-output-test/weights/input.ddlog
diff --git a/test/parse-error-test.bats.template b/test/parse-error-test.bats.template
index 35b9020b8..258c303a9 100644
--- a/test/parse-error-test.bats.template
+++ b/test/parse-error-test.bats.template
@@ -15,7 +15,7 @@ setup() {
 
 # check if input produces a parse error
 @test "$it parses input" {
-    ! ddlog print "$TESTDIR"/input.ddl >/dev/null 2>"$actualError"
+    ! ddlog print "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError"
     diff "$expectedError" "$actualError"
 }
 
diff --git a/test/parse-error-test/annotation_mode/input.ddl b/test/parse-error-test/annotation_mode/input.ddlog
similarity index 100%
rename from test/parse-error-test/annotation_mode/input.ddl
rename to test/parse-error-test/annotation_mode/input.ddlog
diff --git a/test/parse-error-test/annotation_mode/parse-error.expected b/test/parse-error-test/annotation_mode/parse-error.expected
index 0155261a6..56d929dca 100644
--- a/test/parse-error-test/annotation_mode/parse-error.expected
+++ b/test/parse-error-test/annotation_mode/parse-error.expected
@@ -1,4 +1,4 @@
-[error] test/parse-error-test/annotation_mode/input.ddl[1.17] error: unknown: unrecognized mode
+[error] test/parse-error-test/annotation_mode/input.ddlog[1.17] error: unknown: unrecognized mode
 
 @mode("unknown")
 
diff --git a/test/parse-error-test/annotation_semantics/input.ddl b/test/parse-error-test/annotation_semantics/input.ddlog
similarity index 100%
rename from test/parse-error-test/annotation_semantics/input.ddl
rename to test/parse-error-test/annotation_semantics/input.ddlog
diff --git a/test/parse-error-test/annotation_semantics/parse-error.expected b/test/parse-error-test/annotation_semantics/parse-error.expected
index f42219924..8679133fb 100644
--- a/test/parse-error-test/annotation_semantics/parse-error.expected
+++ b/test/parse-error-test/annotation_semantics/parse-error.expected
@@ -1,4 +1,4 @@
-[error] test/parse-error-test/annotation_semantics/input.ddl[2.22] error: unknown: unrecognized semantics
+[error] test/parse-error-test/annotation_semantics/input.ddlog[2.22] error: unknown: unrecognized semantics
 
 @semantics("unknown")
 
diff --git a/test/parse-error-test/nested_multiline_comments/input.ddl b/test/parse-error-test/nested_multiline_comments/input.ddlog
similarity index 100%
rename from test/parse-error-test/nested_multiline_comments/input.ddl
rename to test/parse-error-test/nested_multiline_comments/input.ddlog
diff --git a/test/parse-error-test/nested_multiline_comments/parse-error.expected b/test/parse-error-test/nested_multiline_comments/parse-error.expected
index 39ddabdaf..24c0769df 100644
--- a/test/parse-error-test/nested_multiline_comments/parse-error.expected
+++ b/test/parse-error-test/nested_multiline_comments/parse-error.expected
@@ -1,4 +1,4 @@
-[error] test/parse-error-test/nested_multiline_comments/input.ddl[1.1] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `/' found
+[error] test/parse-error-test/nested_multiline_comments/input.ddlog[1.1] failure: string matching regex `\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*' expected but `/' found
 
 /* Multi-line comments are not supported */
 ^

From 1d87e247fb023b477f26ff005bdffeb540c2abb2 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 30 Aug 2015 18:30:18 -0400
Subject: [PATCH 220/347] A temp solution for parallelism

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala     | 3 ++-
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala  | 7 ++++---
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala      | 1 +
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 8ff81a0a6..dd7931569 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -598,13 +598,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           + (function.implementations mkString "\n  "))
 
       val blockName = ss.resolveExtractorBlockName(stmt)
+      val parallelism = stmt.parallelism map (s => s"\nparallelism: $s") getOrElse("")
       val extractor = s"""
         deepdive.extraction.extractors.${blockName} {
           input: \"\"\" ${new QueryCompiler(stmt.q, ss).generateSQL(TableAlias)}
           \"\"\"
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
-          ${ss.generateDependenciesOfCompiledBlockFor(List(stmt))}
+          ${ss.generateDependenciesOfCompiledBlockFor(List(stmt))}${parallelism}
         }
       """
       extractors += extractor
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index f6cb61308..58165c0a2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -101,7 +101,7 @@ case class SchemaDeclaration( a : Attribute
 case class FunctionDeclaration( functionName: String, inputType: FunctionInputOutputType,
   outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
 case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
-case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery) extends Statement // Extraction rule
+case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery, parallelism: Option[Int]) extends Statement // Extraction rule
 case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
 
 // Parser
@@ -303,9 +303,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
         ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
   }
 
+  def parallelism = "@parallelism" ~> "(" ~> integer <~ ")"
   def functionCallRule : Parser[FunctionCallRule] =
-    relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
-      case (out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq)
+    opt(parallelism) ~ relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
+      case (parallelism ~ out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq, parallelism)
     }
 
   def supervision = "@label" ~> "(" ~> variableName <~ ")"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index d6a5f475d..0edf040bc 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -173,6 +173,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: FunctionCallRule): String = {
+    stmt.parallelism map (s => s"@parallelism($s)\n") getOrElse("") +
     s"${stmt.output} += ${stmt.function}${print(stmt.q)}.\n"
   }
 

From e9a60ebe2fb65b6ebd5d7bb42678bd78729354d6 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 31 Aug 2015 20:20:08 -0400
Subject: [PATCH 221/347] New way to indicate incremental function call. Fix
 delta deriver for such usage.

Incremental function call is annotated at function call rule instead of function declaration.
---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 51 +++++++++----------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 24 +++++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  5 +-
 .../spouse_example/print-incremental.expected |  6 +--
 .../compile-incremental.expected              |  4 ++
 .../spouse_example_new_feature/input.ddlog    |  2 +-
 .../print-incremental.expected                | 11 ++--
 .../print-incremental.expected                |  6 +--
 .../print.expected                            |  1 +
 9 files changed, 58 insertions(+), 52 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index ac4ef9739..4ee3f63c7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -2,14 +2,22 @@ package org.deepdive.ddlog
 
 import scala.collection.mutable.ListBuffer
 
+
+object Mode extends Enumeration {
+  type Mode = Value
+  // NewInference: a new inference rule
+  // NewFunction: a new function call
+  // Normal: existing rules
+  val NewInference, NewFunction, Normal = Value
+}
+import Mode._
+
 object DeepDiveLogDeltaDeriver{
 
   // Default prefix for incremental tables
   val deltaPrefix = "dd_delta_"
   val newPrefix = "dd_new_"
 
-  var incrementalFunctionInput = new ListBuffer[String]()
-
   def transform(stmt: Statement): List[Statement] = stmt match {
     case s: SchemaDeclaration   => transform(s)
     case s: FunctionDeclaration => transform(s)
@@ -18,7 +26,7 @@ object DeepDiveLogDeltaDeriver{
     case s: InferenceRule       => transform(s)
   }
 
-  def transform(headName: String, cq: ConjunctiveQuery, mode: Option[String]): ConjunctiveQuery = {
+  def transform(headName: String, cq: ConjunctiveQuery, mode: Mode): ConjunctiveQuery = {
 
     // New head
     val incCqHead = transform(headName)
@@ -46,12 +54,12 @@ object DeepDiveLogDeltaDeriver{
       val incDeltaBodyAtoms = incDeltaBody collect { case a: BodyAtom => a }
       val incNewBodyAtoms   = incNewBody   collect { case a: BodyAtom => a }
 
-      var i = 0
-      var j = 0
-      var index = if (incrementalFunctionInput contains incCqHead) -1 else 0
-      if (mode == Some("inc")) {
+      if (mode == NewInference) {
         incCqBodies += incNewBody
       } else {
+        var i = 0
+        var j = 0
+        val index = if (mode == NewFunction) -1 else 0
         for (i <- index to (bodyAtoms.length - 1)) {
           var newBody = new ListBuffer[Body]()
           for (j <- 0 to (bodyAtoms.length - 1)) {
@@ -112,14 +120,12 @@ object DeepDiveLogDeltaDeriver{
   def transform(stmt: FunctionDeclaration): List[Statement] = {
     List(stmt.copy(
       inputType = stmt.inputType match {
-        case inTy: RelationTypeDeclaration =>
-          inTy.copy(names = inTy.names map {name => deltaPrefix + name})
+        case inTy: RelationTypeDeclaration => inTy
         case inTy: RelationTypeAlias =>
           inTy.copy(likeRelationName = deltaPrefix + inTy.likeRelationName)
       },
       outputType = stmt.outputType match {
-        case outTy: RelationTypeDeclaration =>
-          outTy.copy(names = outTy.names map {name => deltaPrefix + name})
+        case outTy: RelationTypeDeclaration => outTy
         case outTy: RelationTypeAlias =>
           outTy.copy(likeRelationName = deltaPrefix + outTy.likeRelationName)
       }
@@ -131,41 +137,30 @@ object DeepDiveLogDeltaDeriver{
   def transform(stmt: ExtractionRule): List[Statement] = {
     List(stmt.copy(
       headName = transform(stmt.headName),
-      q = transform(stmt.headName, stmt.q, None)))
+      q = transform(stmt.headName, stmt.q, Normal)))
   }
 
   // Incremental function call rule,
   // modify function input and output
   def transform(stmt: FunctionCallRule): List[Statement] = {
+    val mode = if (stmt.mode == Some("inc")) NewFunction else Normal
     List(stmt.copy(
       output = transform(stmt.output),
-      q = transform(stmt.output, stmt.q, None)))
+      q = transform(stmt.output, stmt.q, mode),
+      mode = None))
   }
 
   // Incremental inference rule,
   // create delta rules based on original extraction rule
   def transform(stmt: InferenceRule): List[Statement] = {
+    val mode = if (stmt.mode == Some("inc")) NewInference else Normal
     List(stmt.copy(head = stmt.head.copy(terms = stmt.head.terms map transform),
-      q = transform("", stmt.q, stmt.mode), mode = None))
-  }
-
-  def generateIncrementalFunctionInputList(program: DeepDiveLog.Program) {
-    program.foreach {
-      case x:FunctionDeclaration => if (x.mode == Some("inc")) {
-        x.inputType match {
-          case inTy: RelationTypeAlias => incrementalFunctionInput += deltaPrefix + inTy.likeRelationName
-          case _ =>
-        }
-      }
-      case _ =>
-    }
+      q = transform("", stmt.q, mode), mode = None))
   }
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
     var incrementalProgram = new ListBuffer[Statement]()
 
-    generateIncrementalFunctionInputList(program)
-
     for (x <- program) {
       incrementalProgram = incrementalProgram ++ transform(x)
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index f6cb61308..ad2997bb1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -99,9 +99,9 @@ case class SchemaDeclaration( a : Attribute
                             , annotation : List[Annotation] = List.empty // optional annotation
                             ) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: FunctionInputOutputType,
-  outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration], mode: Option[String] = None) extends Statement
+  outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration]) extends Statement
 case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
-case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery) extends Statement // Extraction rule
+case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery, mode: Option[String]) extends Statement // Extraction rule
 case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
 
 // Parser
@@ -276,19 +276,15 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     )
 
-  def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
-    case "inc" => "inc"
-  }, (s) => s"${s}: unrecognized mode"))
-
   def functionDeclaration : Parser[FunctionDeclaration] =
-    ( opt(functionMode) ~ "function" ~ functionName ~ "over" ~ functionInputOutputType
+    ( "function" ~ functionName ~ "over" ~ functionInputOutputType
                              ~ "returns" ~ functionInputOutputType
                  ~ (functionImplementation+)
     ) ^^ {
-      case (mode ~ "function" ~ a ~ "over" ~ inTy
+      case ("function" ~ a ~ "over" ~ inTy
                            ~ "returns" ~ outTy
                        ~ implementationDecls) =>
-             FunctionDeclaration(a, inTy, outTy, implementationDecls, mode)
+             FunctionDeclaration(a, inTy, outTy, implementationDecls)
     }
 
   def cqBody: Parser[Body] = cond | quantifiedBody | atom
@@ -303,9 +299,15 @@ class DeepDiveLogParser extends JavaTokenParsers {
         ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
   }
 
+  def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
+    case "inc" => "inc"
+  }, (s) => s"${s}: unrecognized mode"))
+
   def functionCallRule : Parser[FunctionCallRule] =
-    relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
-      case (out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq)
+    opt(functionMode) ~ relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
+      case (mode ~ out ~ _ ~ func ~ cq) => {
+        FunctionCallRule(out, func, cq, mode)
+      }
     }
 
   def supervision = "@label" ~> "(" ~> variableName <~ ")"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index d6a5f475d..4e9619024 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -60,8 +60,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" + styleStr
       }
     }
-    val modeStr = stmt.mode map (s => s"""@mode("${s}")\n""") getOrElse ""
-    s"""${modeStr}function ${stmt.functionName}
+    s"""function ${stmt.functionName}
        |    over ${inputType}
        | returns ${outputType}
        | ${(impls map {"implementation " + _}).mkString("\n ")}.
@@ -173,10 +172,12 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: FunctionCallRule): String = {
+    ( stmt.mode map (s => s"""@mode("${s}")\n""") getOrElse "" ) +
     s"${stmt.output} += ${stmt.function}${print(stmt.q)}.\n"
   }
 
   def print(stmt: InferenceRule): String = {
+    ( stmt.mode map (s => s"""@mode("${s}")\n""") getOrElse "" ) +
     ( s"@weight(${stmt.weights.variables map print mkString(", ")})\n"
     ) + print(stmt.head) + print(stmt.q) + ".\n"
   }
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index a8f7a2397..1effb249a 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -116,7 +116,7 @@ dd_new_has_spouse(relation_id) :-
     dd_delta_has_spouse(relation_id).
 
 function ext_people
-    over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
+    over (sentence_id text, words text, ner_tags text)
  returns rows like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
@@ -125,7 +125,7 @@ dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_T
     dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
+    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
  returns rows like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
@@ -137,7 +137,7 @@ dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_te
     dd_delta_people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
+    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
  returns rows like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index bfad83044..2ab9a7445 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -302,6 +302,10 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
 
         deepdive.extraction.extractors.extraction_rule_29 {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
+FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
+UNION ALL
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
 UNION ALL
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddlog b/test/expected-output-test/spouse_example_new_feature/input.ddlog
index 9ded3b9d4..cc0b4234c 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddlog
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddlog
@@ -34,7 +34,6 @@ has_spouse_features(
 
 has_spouse?(relation_id text).
 
-@mode("inc")
 function ext_people over (sentence_id text, words text, ner_tags text)
                  returns rows like people_mentions
   implementation "udf/ext_people.py" handles tsv lines.
@@ -56,6 +55,7 @@ function ext_has_spouse_features over (words text, rid text, position1 int, leng
                               returns rows like has_spouse_features
   implementation "udf/ext_has_spouse_features.py" handles tsv lines.
 
+@mode("inc")
 has_spouse_features +=
   ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
   sentences(_, _, words, _, _, _, _, _, s),
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index d8831de26..3e96b851c 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -115,9 +115,8 @@ dd_new_has_spouse(relation_id) :-
     has_spouse(relation_id);
     dd_delta_has_spouse(relation_id).
 
-@mode("inc")
 function ext_people
-    over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
+    over (sentence_id text, words text, ner_tags text)
  returns rows like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
@@ -126,7 +125,7 @@ dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_T
     dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
+    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
  returns rows like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
@@ -138,12 +137,16 @@ dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_te
     dd_delta_people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
+    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
  returns rows like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
 
 dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
+    sentences(_, _, words, _, _, _, _, _, s),
+    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
+    people_mentions(s, p1idx, p1len, _, person1_id),
+    people_mentions(s, p2idx, p2len, _, person2_id);
     dd_delta_sentences(_, _, words, _, _, _, _, _, s),
     has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
     people_mentions(s, p1idx, p1len, _, person1_id),
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 095cdab0f..ee866f032 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -116,7 +116,7 @@ dd_new_has_spouse(relation_id) :-
     dd_delta_has_spouse(relation_id).
 
 function ext_people
-    over (dd_delta_sentence_id text, dd_delta_words text, dd_delta_ner_tags text)
+    over (sentence_id text, words text, ner_tags text)
  returns rows like dd_delta_people_mentions
  implementation "udf/ext_people.py"
         handles tsv lines.
@@ -125,7 +125,7 @@ dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_T
     dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
 
 function ext_has_spouse
-    over (dd_delta_sentence_id text, dd_delta_mid1 text, dd_delta_text1 text, dd_delta_mid2 text, dd_delta_text2 text)
+    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
  returns rows like dd_delta_has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
         handles tsv lines.
@@ -137,7 +137,7 @@ dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_te
     dd_delta_people_mentions(s, _, _, p2_text, p2_id).
 
 function ext_has_spouse_features
-    over (dd_delta_words text, dd_delta_rid text, dd_delta_position1 int, dd_delta_length1 int, dd_delta_position2 int, dd_delta_length2 int)
+    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
  returns rows like dd_delta_has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
         handles tsv lines.
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 4068d8de9..6d9ff118a 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -69,6 +69,7 @@ has_spouse(rid) :-
     has_spouse_candidates(_, _, _, _, rid, _),
     has_spouse_features(rid, f).
 
+@mode("inc")
 @weight(3.0)
 has_spouse(rid2) = has_spouse(rid) :-
     has_spouse_candidates(a1, b1, _, _, rid, _),

From 5efe1776bb16877cad7aed42a8787cfd7543479d Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Mon, 31 Aug 2015 22:53:17 -0700
Subject: [PATCH 222/347] Implemented new syntax for supervision rules

---
 examples/chunking.ddlog                             |  3 +--
 examples/ocr.ddlog                                  |  8 +++-----
 examples/smoke.ddlog                                |  8 +++-----
 examples/spouse_example.ddlog                       |  3 +--
 .../org/deepdive/ddlog/DeepDiveLogParser.scala      | 13 ++++++++++---
 .../deepdive/ddlog/DeepDiveLogPrettyPrinter.scala   |  8 ++++----
 .../ocr_example/print-incremental.expected          |  6 ++----
 .../expected-output-test/ocr_example/print.expected |  6 ++----
 .../smoke_example/print-incremental.expected        |  6 ++----
 .../smoke_example/print.expected                    |  6 ++----
 .../spouse_example/print-incremental.expected       |  3 +--
 .../spouse_example/print.expected                   |  3 +--
 .../spouse_example_new_feature/input.ddlog          |  3 +--
 .../print-incremental.expected                      |  3 +--
 .../spouse_example_new_inference/input.ddlog        |  3 +--
 .../print-incremental.expected                      |  3 +--
 .../spouse_example_new_inference/print.expected     |  3 +--
 17 files changed, 37 insertions(+), 51 deletions(-)

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index 28a172de8..a020048a2 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -38,8 +38,7 @@ word_features +=
   words(sent_id, word_id1, word1, pos1, tag1),
   words(sent_id, word_id2, word2, pos2, tag2).
 
-@label(tag)
-tag(word_id) :- words(word_id, a, b, c, tag).
+tag(word_id) = tag :- words(word_id, a, b, c, tag).
 
 @weight(f)
 tag(word_id) :- word_features(word_id, f).
diff --git a/examples/ocr.ddlog b/examples/ocr.ddlog
index cf897d6d2..5f9e367b9 100644
--- a/examples/ocr.ddlog
+++ b/examples/ocr.ddlog
@@ -18,12 +18,10 @@ label2(
 q1?(wid INT).
 q2?(wid INT).
 
-@label(val)
-q1(wid) :- label1(wid, val).
-@label(val)
-q2(wid) :- label2(wid, val).
+q1(wid) = val :- label1(wid, val).
+q2(wid) = val :- label2(wid, val).
 
 @weight(fid)
 q1(wid) :- features(id, wid, fid, fval).
 @weight(fid)
-q2(wid) :- features(id, wid, fid, fval).
\ No newline at end of file
+q2(wid) :- features(id, wid, fid, fval).
diff --git a/examples/smoke.ddlog b/examples/smoke.ddlog
index fa8434d47..a7fbb4ff0 100644
--- a/examples/smoke.ddlog
+++ b/examples/smoke.ddlog
@@ -29,14 +29,12 @@ cancer? (
     person_id bigint
 ).
 
-@label(l)
-smoke(pid)  :- person_smokes(pid, l).
+smoke(pid) = l :- person_smokes(pid, l).
 
-@label(l)
-cancer(pid) :- person_has_cancer(pid, l).
+cancer(pid) = l :- person_has_cancer(pid, l).
 
 @weight(0.5)
 smoke(pid) => cancer(pid) :- person_smokes(pid, l).
 
 @weight(0.4)
-smoke(pid1) => smoke(pid) :- friends(pid1, pid).
\ No newline at end of file
+smoke(pid1) => smoke(pid) :- friends(pid1, pid).
diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index 079083c3d..a1884f4b8 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -62,8 +62,7 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index f6cb61308..3345806a5 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -303,15 +303,22 @@ class DeepDiveLogParser extends JavaTokenParsers {
         ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
   }
 
+  def supervision = "=" ~> (variableName | "TRUE" | "FALSE")
+
+  def conjunctiveQueryWithSupervision  = // returns Parser[String], Parser[ConjunctiveQuery]
+    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ opt(supervision) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
+      case (head ~ isDistinct ~ limit ~ sup ~ ":-" ~ disjunctiveBodies) =>
+        (sup, ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt)))
+  }
+
   def functionCallRule : Parser[FunctionCallRule] =
     relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
       case (out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq)
     }
 
-  def supervision = "@label" ~> "(" ~> variableName <~ ")"
   def extractionRule =
-    opt(supervision) ~ relationName ~ conjunctiveQuery ^^ {
-      case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
+    relationName ~ conjunctiveQueryWithSupervision ^^ {
+      case (head ~ cq) => ExtractionRule(head, cq._2, cq._1)
   }
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index d6a5f475d..8f71957ec 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -132,7 +132,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     case b: QuantifiedBody => print(b)
   }
 
-  def print(cq: ConjunctiveQuery): String = {
+  def print(cq: ConjunctiveQuery, supervision: String = ""): String = {
 
     def printBodyList(b: List[Body]) = {
       s"${(b map print).mkString(",\n    ")}"
@@ -145,7 +145,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val headStrTmp  = cq.headTerms map print mkString(", ")
     val headStr     = if (headStrTmp isEmpty) "" else s"(${headStrTmp})"
 
-    headStr + distinctStr + limitStr + " :-\n    " + bodyStr
+    headStr + distinctStr + limitStr + supervision + " :-\n    " + bodyStr
   }
 
   def print(a: HeadAtom) : String = {
@@ -168,8 +168,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-    ( stmt.supervision map (s => s"@label(${s})\n") getOrElse("") ) +
-    stmt.headName + print(stmt.q) + ".\n"
+      var supervision = stmt.supervision map (s => s" = ${s}") getOrElse("");
+      stmt.headName + print(stmt.q, supervision) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
index f0e488c26..a7fb4bca8 100644
--- a/test/expected-output-test/ocr_example/print-incremental.expected
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -63,12 +63,10 @@ dd_new_q2(wid) :-
     q2(wid);
     dd_delta_q2(wid).
 
-@label(val)
-dd_delta_q1(wid) :-
+dd_delta_q1(wid) = val :-
     dd_delta_label1(wid, val).
 
-@label(val)
-dd_delta_q2(wid) :-
+dd_delta_q2(wid) = val :-
     dd_delta_label2(wid, val).
 
 @weight(fid)
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
index 2828b5e91..34d0e14f5 100644
--- a/test/expected-output-test/ocr_example/print.expected
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -13,12 +13,10 @@ q1?(wid INT).
 
 q2?(wid INT).
 
-@label(val)
-q1(wid) :-
+q1(wid) = val :-
     label1(wid, val).
 
-@label(val)
-q2(wid) :-
+q2(wid) = val :-
     label2(wid, val).
 
 @weight(fid)
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index c585081d0..a1d712c12 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -70,12 +70,10 @@ dd_new_cancer(person_id) :-
     cancer(person_id);
     dd_delta_cancer(person_id).
 
-@label(l)
-dd_delta_smoke(pid) :-
+dd_delta_smoke(pid) = l :-
     dd_delta_person_smokes(pid, l).
 
-@label(l)
-dd_delta_cancer(pid) :-
+dd_delta_cancer(pid) = l:-
     dd_delta_person_has_cancer(pid, l).
 
 @weight(0.5)
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index 84176ea94..0dfc3c69a 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -14,12 +14,10 @@ smoke?(person_id bigint).
 
 cancer?(person_id bigint).
 
-@label(l)
-smoke(pid) :-
+smoke(pid) = l :-
     person_smokes(pid, l).
 
-@label(l)
-cancer(pid) :-
+cancer(pid) = l :-
     person_has_cancer(pid, l).
 
 @weight(0.5)
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index a8f7a2397..eccf80e65 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -160,8 +160,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid) = l :-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 401e9aed3..917067752 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -60,8 +60,7 @@ has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), ri
     people_mentions(s, p1idx, p1len, _, person1_id),
     people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :-
+has_spouse(rid) = l :-
     has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddlog b/test/expected-output-test/spouse_example_new_feature/input.ddlog
index 9ded3b9d4..4b6e46eb7 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddlog
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddlog
@@ -63,8 +63,7 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index d8831de26..3ad162db1 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -161,8 +161,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid) = l:-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddlog b/test/expected-output-test/spouse_example_new_inference/input.ddlog
index 36c64c8e4..15cfd39c6 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddlog
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddlog
@@ -62,8 +62,7 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index 095cdab0f..656f4d572 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -160,8 +160,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid) = l :-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 4068d8de9..541aa26ad 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -60,8 +60,7 @@ has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), ri
     people_mentions(s, p1idx, p1len, _, person1_id),
     people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :-
+has_spouse(rid) = l :-
     has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)

From cc55ac984b2f4378d73496664a3c0a12f6c7ea60 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Mon, 31 Aug 2015 22:53:17 -0700
Subject: [PATCH 223/347] Implemented new syntax for supervision rules

---
 examples/chunking.ddlog                            |  3 +--
 examples/ocr.ddlog                                 |  8 +++-----
 examples/smoke.ddlog                               |  8 +++-----
 examples/spouse_example.ddlog                      |  3 +--
 .../org/deepdive/ddlog/DeepDiveLogParser.scala     | 14 +++++++++++---
 .../deepdive/ddlog/DeepDiveLogPrettyPrinter.scala  |  8 ++++----
 .../ocr_example/print-incremental.expected         |  6 ++----
 .../ocr_example/print.expected                     |  6 ++----
 .../smoke_example/print-incremental.expected       |  6 ++----
 .../smoke_example/print.expected                   |  6 ++----
 .../spouse_example/print-incremental.expected      |  3 +--
 .../spouse_example/print.expected                  |  3 +--
 .../spouse_example_new_feature/input.ddlog         |  3 +--
 .../print-incremental.expected                     |  3 +--
 .../spouse_example_new_inference/input.ddlog       |  3 +--
 .../print-incremental.expected                     |  3 +--
 .../spouse_example_new_inference/print.expected    |  3 +--
 17 files changed, 38 insertions(+), 51 deletions(-)

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index 28a172de8..a020048a2 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -38,8 +38,7 @@ word_features +=
   words(sent_id, word_id1, word1, pos1, tag1),
   words(sent_id, word_id2, word2, pos2, tag2).
 
-@label(tag)
-tag(word_id) :- words(word_id, a, b, c, tag).
+tag(word_id) = tag :- words(word_id, a, b, c, tag).
 
 @weight(f)
 tag(word_id) :- word_features(word_id, f).
diff --git a/examples/ocr.ddlog b/examples/ocr.ddlog
index cf897d6d2..5f9e367b9 100644
--- a/examples/ocr.ddlog
+++ b/examples/ocr.ddlog
@@ -18,12 +18,10 @@ label2(
 q1?(wid INT).
 q2?(wid INT).
 
-@label(val)
-q1(wid) :- label1(wid, val).
-@label(val)
-q2(wid) :- label2(wid, val).
+q1(wid) = val :- label1(wid, val).
+q2(wid) = val :- label2(wid, val).
 
 @weight(fid)
 q1(wid) :- features(id, wid, fid, fval).
 @weight(fid)
-q2(wid) :- features(id, wid, fid, fval).
\ No newline at end of file
+q2(wid) :- features(id, wid, fid, fval).
diff --git a/examples/smoke.ddlog b/examples/smoke.ddlog
index fa8434d47..a7fbb4ff0 100644
--- a/examples/smoke.ddlog
+++ b/examples/smoke.ddlog
@@ -29,14 +29,12 @@ cancer? (
     person_id bigint
 ).
 
-@label(l)
-smoke(pid)  :- person_smokes(pid, l).
+smoke(pid) = l :- person_smokes(pid, l).
 
-@label(l)
-cancer(pid) :- person_has_cancer(pid, l).
+cancer(pid) = l :- person_has_cancer(pid, l).
 
 @weight(0.5)
 smoke(pid) => cancer(pid) :- person_smokes(pid, l).
 
 @weight(0.4)
-smoke(pid1) => smoke(pid) :- friends(pid1, pid).
\ No newline at end of file
+smoke(pid1) => smoke(pid) :- friends(pid1, pid).
diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index 079083c3d..a1884f4b8 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -62,8 +62,7 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 97799298b..fc50bd013 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -304,15 +304,23 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }, (s) => s"${s}: unrecognized mode"))
 
   def parallelism = "@parallelism" ~> "(" ~> integer <~ ")"
+
+  def supervision = "=" ~> (variableName | "TRUE" | "FALSE")
+
+  def conjunctiveQueryWithSupervision  = // returns Parser[String], Parser[ConjunctiveQuery]
+    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ opt(supervision) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
+      case (head ~ isDistinct ~ limit ~ sup ~ ":-" ~ disjunctiveBodies) =>
+        (sup, ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt)))
+  }
+
   def functionCallRule : Parser[FunctionCallRule] =
     opt(functionMode) ~ opt(parallelism) ~ relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
       case (mode ~ parallelism ~ out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq, mode, parallelism)
     }
 
-  def supervision = "@label" ~> "(" ~> variableName <~ ")"
   def extractionRule =
-    opt(supervision) ~ relationName ~ conjunctiveQuery ^^ {
-      case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
+    relationName ~ conjunctiveQueryWithSupervision ^^ {
+      case (head ~ cq) => ExtractionRule(head, cq._2, cq._1)
   }
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index d88868890..49e5d20e2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -131,7 +131,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     case b: QuantifiedBody => print(b)
   }
 
-  def print(cq: ConjunctiveQuery): String = {
+  def print(cq: ConjunctiveQuery, supervision: String = ""): String = {
 
     def printBodyList(b: List[Body]) = {
       s"${(b map print).mkString(",\n    ")}"
@@ -144,7 +144,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val headStrTmp  = cq.headTerms map print mkString(", ")
     val headStr     = if (headStrTmp isEmpty) "" else s"(${headStrTmp})"
 
-    headStr + distinctStr + limitStr + " :-\n    " + bodyStr
+    headStr + distinctStr + limitStr + supervision + " :-\n    " + bodyStr
   }
 
   def print(a: HeadAtom) : String = {
@@ -167,8 +167,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-    ( stmt.supervision map (s => s"@label(${s})\n") getOrElse("") ) +
-    stmt.headName + print(stmt.q) + ".\n"
+      var supervision = stmt.supervision map (s => s" = ${s}") getOrElse("");
+      stmt.headName + print(stmt.q, supervision) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
index f0e488c26..a7fb4bca8 100644
--- a/test/expected-output-test/ocr_example/print-incremental.expected
+++ b/test/expected-output-test/ocr_example/print-incremental.expected
@@ -63,12 +63,10 @@ dd_new_q2(wid) :-
     q2(wid);
     dd_delta_q2(wid).
 
-@label(val)
-dd_delta_q1(wid) :-
+dd_delta_q1(wid) = val :-
     dd_delta_label1(wid, val).
 
-@label(val)
-dd_delta_q2(wid) :-
+dd_delta_q2(wid) = val :-
     dd_delta_label2(wid, val).
 
 @weight(fid)
diff --git a/test/expected-output-test/ocr_example/print.expected b/test/expected-output-test/ocr_example/print.expected
index 2828b5e91..34d0e14f5 100644
--- a/test/expected-output-test/ocr_example/print.expected
+++ b/test/expected-output-test/ocr_example/print.expected
@@ -13,12 +13,10 @@ q1?(wid INT).
 
 q2?(wid INT).
 
-@label(val)
-q1(wid) :-
+q1(wid) = val :-
     label1(wid, val).
 
-@label(val)
-q2(wid) :-
+q2(wid) = val :-
     label2(wid, val).
 
 @weight(fid)
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index c585081d0..a1d712c12 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -70,12 +70,10 @@ dd_new_cancer(person_id) :-
     cancer(person_id);
     dd_delta_cancer(person_id).
 
-@label(l)
-dd_delta_smoke(pid) :-
+dd_delta_smoke(pid) = l :-
     dd_delta_person_smokes(pid, l).
 
-@label(l)
-dd_delta_cancer(pid) :-
+dd_delta_cancer(pid) = l:-
     dd_delta_person_has_cancer(pid, l).
 
 @weight(0.5)
diff --git a/test/expected-output-test/smoke_example/print.expected b/test/expected-output-test/smoke_example/print.expected
index 84176ea94..0dfc3c69a 100644
--- a/test/expected-output-test/smoke_example/print.expected
+++ b/test/expected-output-test/smoke_example/print.expected
@@ -14,12 +14,10 @@ smoke?(person_id bigint).
 
 cancer?(person_id bigint).
 
-@label(l)
-smoke(pid) :-
+smoke(pid) = l :-
     person_smokes(pid, l).
 
-@label(l)
-cancer(pid) :-
+cancer(pid) = l :-
     person_has_cancer(pid, l).
 
 @weight(0.5)
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
index 1effb249a..0faf7c26e 100644
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ b/test/expected-output-test/spouse_example/print-incremental.expected
@@ -160,8 +160,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid) = l :-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 401e9aed3..917067752 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -60,8 +60,7 @@ has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), ri
     people_mentions(s, p1idx, p1len, _, person1_id),
     people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :-
+has_spouse(rid) = l :-
     has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddlog b/test/expected-output-test/spouse_example_new_feature/input.ddlog
index cc0b4234c..30fcae415 100644
--- a/test/expected-output-test/spouse_example_new_feature/input.ddlog
+++ b/test/expected-output-test/spouse_example_new_feature/input.ddlog
@@ -63,8 +63,7 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 3e96b851c..0e6082a82 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -164,8 +164,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid) = l:-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddlog b/test/expected-output-test/spouse_example_new_inference/input.ddlog
index 36c64c8e4..15cfd39c6 100644
--- a/test/expected-output-test/spouse_example_new_inference/input.ddlog
+++ b/test/expected-output-test/spouse_example_new_inference/input.ddlog
@@ -62,8 +62,7 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
index ee866f032..c924799cb 100644
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
@@ -160,8 +160,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-dd_delta_has_spouse(rid) :-
+dd_delta_has_spouse(rid) = l :-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
index 6d9ff118a..20d6f1ecb 100644
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ b/test/expected-output-test/spouse_example_new_inference/print.expected
@@ -60,8 +60,7 @@ has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), ri
     people_mentions(s, p1idx, p1len, _, person1_id),
     people_mentions(s, p2idx, p2len, _, person2_id).
 
-@label(l)
-has_spouse(rid) :-
+has_spouse(rid) = l :-
     has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)

From a395a0bef23b32deaec197af456359f217b15b88 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Sat, 19 Sep 2015 00:12:41 -0700
Subject: [PATCH 224/347] Keeping old syntax (@label) for supervision

---
 examples/spouse_example.ddlog                          |  6 +++++-
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala   | 10 ++++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index a1884f4b8..e2328c240 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -62,7 +62,11 @@ has_spouse_features +=
   people_mentions(s, p1idx, p1len, _, person1_id),
   people_mentions(s, p2idx, p2len, _, person2_id).
 
-has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
+// testing old syntax for supervision
+@label(l)
+has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+
+// new syntax for above is:  has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
 has_spouse(rid) :-
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index fc50bd013..7d934f29b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -318,10 +318,16 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case (mode ~ parallelism ~ out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq, mode, parallelism)
     }
 
+  def oldstyleSupervision = "@label" ~> "(" ~> (variableName | "TRUE" | "FALSE") <~ ")"
+
   def extractionRule =
-    relationName ~ conjunctiveQueryWithSupervision ^^ {
+  ( relationName ~ conjunctiveQueryWithSupervision ^^ {
       case (head ~ cq) => ExtractionRule(head, cq._2, cq._1)
-  }
+    }
+  | oldstyleSupervision ~ relationName ~ conjunctiveQuery ^^ {
+      case (sup ~ head ~ cq) => ExtractionRule(head, cq, Some(sup))
+    }
+  )
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
   def inferenceMode = "@mode" ~> commit("(" ~> inferenceModeType <~ ")" ^? ({

From ce365aab8f907c1da50bc2db87aabb165eedfce9 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Mon, 31 Aug 2015 22:53:17 -0700
Subject: [PATCH 225/347] Implemented new syntax for supervision rules

---
 examples/spouse_example.ddlog                             | 1 +
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 1 +
 2 files changed, 2 insertions(+)

diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index e2328c240..f984e3cbb 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -65,6 +65,7 @@ has_spouse_features +=
 // testing old syntax for supervision
 @label(l)
 has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
+>>>>>>> Implemented new syntax for supervision rules
 
 // new syntax for above is:  has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 7d934f29b..1ec0cd247 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -299,6 +299,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
         ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
   }
 
+<<<<<<< HEAD
   def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
     case "inc" => "inc"
   }, (s) => s"${s}: unrecognized mode"))

From d5d1c76bbb6210b5fdc5b5be72a29627ac7f1745 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Mon, 31 Aug 2015 22:53:17 -0700
Subject: [PATCH 226/347] Implemented new syntax for supervision rules

---
 examples/spouse_example.ddlog | 1 -
 1 file changed, 1 deletion(-)

diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index f984e3cbb..fd0844496 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -66,7 +66,6 @@ has_spouse_features +=
 @label(l)
 has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
 >>>>>>> Implemented new syntax for supervision rules
-
 // new syntax for above is:  has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)

From f145804c1632b888625e8b4aa9073bf954d93839 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Mon, 21 Sep 2015 23:58:00 -0700
Subject: [PATCH 227/347] Adding type checker for supervision variable

---
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index a779a16e7..785018c60 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -35,6 +35,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkQuantifiedBody(stmt)
     checkWeight(stmt)
     checkVariableBindings(stmt)
+    checkSupervisionLabelType(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
@@ -156,6 +157,46 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
+  def checkSupervisionLableType(s: ExtractionRule, expType: VariableType, SupVariable: VarPattern, b: BodyAtom) {
+    b.terms.zipWithIndex.foreach {
+      case (SupVariable, index) => {
+        val expColumnType = if (expType.isInstanceOf[BooleanType.type]) "boolean" else "int"
+        if (schemaDeclaration(b.name).a.types(index) != expColumnType) {
+          error(s, s"Unexpected supervision type")
+        }
+      }
+      case _ =>
+    }
+  }
+
+  def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, body: Body) {
+    body match {
+      case qb: QuantifiedBody => qb.bodies.foreach { b => checkSupervisionLabelType(s, expType, supVariable, b)}
+      case b: BodyAtom =>  checkSupervisionLableType(s, expType, supVariable, b)
+      case _: Cond =>
+    }
+  }
+
+  def checkSupervisionLabelType(stmt: Statement) {
+    stmt match {
+      case s: ExtractionRule => {
+        val expectedVarType = schemaDeclaration(s.headName).variableType.get
+        s.supervision match {
+          case Some("TRUE") | Some("FALSE") => {
+            if (expectedVarType != BooleanType)
+              error(s, s"Unexpected supervision type")
+          }
+          case Some(varname) =>
+            s.q.bodies.foreach { bodies: List[Body] =>
+              bodies.foreach { b => checkSupervisionLabelType(s, expectedVarType, VarPattern(varname), b) }
+            }
+          case None =>
+        }
+      }
+      case _ =>
+    }
+  }
+
   // collect variables used in the expression
   def collectUsedVars(expr: Expr) : Set[String] = expr match {
     case VarExpr(name) => Set(name)

From 13560a10cc33a5271a8061a383116efbae97d6b1 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Tue, 22 Sep 2015 13:50:52 -0700
Subject: [PATCH 228/347] Bugfix for semantic checker

---
 examples/spouse_example.ddlog                          |  1 -
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala   |  1 -
 .../deepdive/ddlog/DeepDiveLogSemanticChecker.scala    | 10 +++++-----
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index fd0844496..014352b9d 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -65,7 +65,6 @@ has_spouse_features +=
 // testing old syntax for supervision
 @label(l)
 has_spouse(rid) :- has_spouse_candidates(_, _, _, _, rid, l).
->>>>>>> Implemented new syntax for supervision rules
 // new syntax for above is:  has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 1ec0cd247..7d934f29b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -299,7 +299,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
         ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
   }
 
-<<<<<<< HEAD
   def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
     case "inc" => "inc"
   }, (s) => s"${s}: unrecognized mode"))
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 785018c60..145ae06cb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -160,8 +160,8 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkSupervisionLableType(s: ExtractionRule, expType: VariableType, SupVariable: VarPattern, b: BodyAtom) {
     b.terms.zipWithIndex.foreach {
       case (SupVariable, index) => {
-        val expColumnType = if (expType.isInstanceOf[BooleanType.type]) "boolean" else "int"
-        if (schemaDeclaration(b.name).a.types(index) != expColumnType) {
+        val expColumnType = if (expType.isInstanceOf[BooleanType.type]) "boolean" else "text"
+        if (schemaDeclaration(b.name).a.types(index).toLowerCase != expColumnType) {
           error(s, s"Unexpected supervision type")
         }
       }
@@ -180,15 +180,15 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkSupervisionLabelType(stmt: Statement) {
     stmt match {
       case s: ExtractionRule => {
-        val expectedVarType = schemaDeclaration(s.headName).variableType.get
         s.supervision match {
           case Some("TRUE") | Some("FALSE") => {
-            if (expectedVarType != BooleanType)
+            if (schemaDeclaration(s.headName).variableType.get != BooleanType)
               error(s, s"Unexpected supervision type")
           }
           case Some(varname) =>
             s.q.bodies.foreach { bodies: List[Body] =>
-              bodies.foreach { b => checkSupervisionLabelType(s, expectedVarType, VarPattern(varname), b) }
+              bodies.foreach { b =>
+                checkSupervisionLabelType(s, schemaDeclaration(s.headName).variableType.get, VarPattern(varname), b) }
             }
           case None =>
         }

From 5ed205175d3e1b572010b6894c9cb87d10e87010 Mon Sep 17 00:00:00 2001
From: Jiwon Seo <seojiwon@gmail.com>
Date: Fri, 25 Sep 2015 01:29:52 -0700
Subject: [PATCH 229/347] Fixed error messages. Some minor refactoring

---
 .../ddlog/DeepDiveLogSemanticChecker.scala      | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 145ae06cb..ddbebd263 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -157,12 +157,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
-  def checkSupervisionLableType(s: ExtractionRule, expType: VariableType, SupVariable: VarPattern, b: BodyAtom) {
+  def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, b: BodyAtom) {
     b.terms.zipWithIndex.foreach {
-      case (SupVariable, index) => {
+      case (`supVariable`, index) => {
         val expColumnType = if (expType.isInstanceOf[BooleanType.type]) "boolean" else "text"
         if (schemaDeclaration(b.name).a.types(index).toLowerCase != expColumnType) {
-          error(s, s"Unexpected supervision type")
+          val actualColumnType = schemaDeclaration(b.name).a.types(index).toLowerCase
+          error(s, s"Supervision column ${supVariable.name} should be ${expColumnType} type, but is ${actualColumnType} type")
         }
       }
       case _ =>
@@ -172,8 +173,8 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, body: Body) {
     body match {
       case qb: QuantifiedBody => qb.bodies.foreach { b => checkSupervisionLabelType(s, expType, supVariable, b)}
-      case b: BodyAtom =>  checkSupervisionLableType(s, expType, supVariable, b)
-      case _: Cond =>
+      case b: BodyAtom =>  checkSupervisionLabelType(s, expType, supVariable, b)
+      case _ =>
     }
   }
 
@@ -182,8 +183,10 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       case s: ExtractionRule => {
         s.supervision match {
           case Some("TRUE") | Some("FALSE") => {
-            if (schemaDeclaration(s.headName).variableType.get != BooleanType)
-              error(s, s"Unexpected supervision type")
+            if (schemaDeclaration(s.headName).variableType.get != BooleanType) {
+              val actualColumnType = schemaDeclaration(s.headName).variableType.get
+              error(s, s"Supervision column ${s.supervision} should be boolean type but is ${actualColumnType} type")
+            }
           }
           case Some(varname) =>
             s.q.bodies.foreach { bodies: List[Body] =>

From e7d2a1ffa0b683982c5f8becaa1d422455f23f0d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 27 Sep 2015 01:06:22 +0900
Subject: [PATCH 230/347] Fixes checker to expect int for multinomial variable
 relations

---
 examples/chunking.ddlog                                   | 2 +-
 .../org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala   | 8 +++++++-
 .../chunking_example/compile.expected                     | 2 +-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index a020048a2..2b07f7eba 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -12,7 +12,7 @@ words(
   word_id bigint,
   word text,
   pos text,
-  true_tag text).
+  true_tag int).
 
 word_features(
   word_id bigint,
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index ddbebd263..55dca8de4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -160,7 +160,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, b: BodyAtom) {
     b.terms.zipWithIndex.foreach {
       case (`supVariable`, index) => {
-        val expColumnType = if (expType.isInstanceOf[BooleanType.type]) "boolean" else "text"
+        val expColumnType =
+          if (expType.isInstanceOf[BooleanType.type])
+            // binary
+            "boolean"
+          else
+            // multinomial
+            "int"
         if (schemaDeclaration(b.name).a.types(index).toLowerCase != expColumnType) {
           val actualColumnType = schemaDeclaration(b.name).a.types(index).toLowerCase
           error(s, s"Supervision column ${supVariable.name} should be ${expColumnType} type, but is ${actualColumnType} type")
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 90961832b..dcfcf8287 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -35,7 +35,7 @@
      word_id bigint,
      word text,
      pos text,
-     true_tag text)
+     true_tag int)
             """
             style: "sql_extractor"
           }

From 61861fa6c0a3f92f511adf91116996ecf81c4b3e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 27 Sep 2015 01:06:46 +0900
Subject: [PATCH 231/347] Fixes whitespace changes in test

---
 .../smoke_example/print-incremental.expected                    | 2 +-
 .../spouse_example_new_feature/print-incremental.expected       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
index a1d712c12..594b54980 100644
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ b/test/expected-output-test/smoke_example/print-incremental.expected
@@ -73,7 +73,7 @@ dd_new_cancer(person_id) :-
 dd_delta_smoke(pid) = l :-
     dd_delta_person_smokes(pid, l).
 
-dd_delta_cancer(pid) = l:-
+dd_delta_cancer(pid) = l :-
     dd_delta_person_has_cancer(pid, l).
 
 @weight(0.5)
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
index 0e6082a82..2a57231de 100644
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
@@ -164,7 +164,7 @@ dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "
     dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
     dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
 
-dd_delta_has_spouse(rid) = l:-
+dd_delta_has_spouse(rid) = l :-
     dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
 
 @weight(f)

From a210b081ed7905114f8ebd95ea924131f538195d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 30 Sep 2015 22:08:00 -0700
Subject: [PATCH 232/347] Fixes supervision column type checker to accept rules
 using columns of undeclared relations

fixes HazyResearch/deepdive#423
---
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 11 +++++----
 test/checker-test.bats.template               | 23 +++++++++++++++++++
 .../supervision_binary_variable/input.ddlog   |  4 ++++
 .../supervision_multinomial/input.ddlog       |  4 ++++
 .../input.ddlog                               | 10 ++++++++
 test/compile-error-test.bats.template         |  9 ++++----
 .../compile-error.expected                    |  4 ++++
 .../input.ddlog                               |  4 ++++
 8 files changed, 59 insertions(+), 10 deletions(-)
 create mode 100644 test/checker-test.bats.template
 create mode 100644 test/checker-test/supervision_binary_variable/input.ddlog
 create mode 100644 test/checker-test/supervision_multinomial/input.ddlog
 create mode 100644 test/checker-test/supervision_with_undeclared_relation/input.ddlog
 create mode 100644 test/compile-error-test/supervision_label_type_mismatch/compile-error.expected
 create mode 100644 test/compile-error-test/supervision_label_type_mismatch/input.ddlog

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 55dca8de4..aff0f7c7f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -158,6 +158,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, b: BodyAtom) {
+    if (schemaDeclaration contains b.name)
     b.terms.zipWithIndex.foreach {
       case (`supVariable`, index) => {
         val expColumnType =
@@ -186,18 +187,18 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
 
   def checkSupervisionLabelType(stmt: Statement) {
     stmt match {
-      case s: ExtractionRule => {
+      case s: ExtractionRule if schemaDeclaration contains s.headName => {
+        val headType = schemaDeclaration(s.headName).variableType.get
         s.supervision match {
           case Some("TRUE") | Some("FALSE") => {
-            if (schemaDeclaration(s.headName).variableType.get != BooleanType) {
-              val actualColumnType = schemaDeclaration(s.headName).variableType.get
-              error(s, s"Supervision column ${s.supervision} should be boolean type but is ${actualColumnType} type")
+            if (headType != BooleanType) {
+              error(s, s"Supervision column ${s.supervision} should be boolean type but is ${headType} type")
             }
           }
           case Some(varname) =>
             s.q.bodies.foreach { bodies: List[Body] =>
               bodies.foreach { b =>
-                checkSupervisionLabelType(s, schemaDeclaration(s.headName).variableType.get, VarPattern(varname), b) }
+                checkSupervisionLabelType(s, headType, VarPattern(varname), b) }
             }
           case None =>
         }
diff --git a/test/checker-test.bats.template b/test/checker-test.bats.template
new file mode 100644
index 000000000..6436d9be6
--- /dev/null
+++ b/test/checker-test.bats.template
@@ -0,0 +1,23 @@
+#!/usr/bin/env bats
+# Tests that should pass the semantic checker
+#
+# The test case here feeds a correct .ddlog into ddlog's check command.
+
+source "$BATS_TEST_DIRNAME"/../bats-template.bash  # for $TESTDIR, $it, etc.
+
+# some preconditions
+setup() {
+    [ -e "$TESTDIR" ]
+}
+
+# test if input passes the checker
+@test "$it should pass semantic checker" {
+    expectedError="$TESTDIR"/check.expected
+    if [ -e "$expectedError" ]; then
+        actualError=${expectedError%.expected}.actual
+        ddlog check "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError"
+        diff "$expectedError" "$actualError"
+    else
+        ddlog check "$TESTDIR"/input.ddlog
+    fi
+}
diff --git a/test/checker-test/supervision_binary_variable/input.ddlog b/test/checker-test/supervision_binary_variable/input.ddlog
new file mode 100644
index 000000000..3e68150ad
--- /dev/null
+++ b/test/checker-test/supervision_binary_variable/input.ddlog
@@ -0,0 +1,4 @@
+Q?(x int).
+R(x int, label boolean).
+
+Q(x) = label :- R(x, label).
diff --git a/test/checker-test/supervision_multinomial/input.ddlog b/test/checker-test/supervision_multinomial/input.ddlog
new file mode 100644
index 000000000..3b8a4ab70
--- /dev/null
+++ b/test/checker-test/supervision_multinomial/input.ddlog
@@ -0,0 +1,4 @@
+Q?(x int) Categorical(10).
+R(x int, label int).
+
+Q(x) = label :- R(x, label).
diff --git a/test/checker-test/supervision_with_undeclared_relation/input.ddlog b/test/checker-test/supervision_with_undeclared_relation/input.ddlog
new file mode 100644
index 000000000..6f8ee0bcd
--- /dev/null
+++ b/test/checker-test/supervision_with_undeclared_relation/input.ddlog
@@ -0,0 +1,10 @@
+Q?(x int).
+S(y text, l boolean).
+T(x int, y text).
+
+# XXX R is not declared but implicitly defined
+# R(x int, label boolean).
+R(x, l) :- T(x,y), S(y,l).
+
+# ideally, checker should infer the type of undeclared relation to check S.l's type is boolean
+Q(x) = label :- R(x, label).
diff --git a/test/compile-error-test.bats.template b/test/compile-error-test.bats.template
index 42c937cde..6d289b7e2 100644
--- a/test/compile-error-test.bats.template
+++ b/test/compile-error-test.bats.template
@@ -8,14 +8,13 @@ source "$BATS_TEST_DIRNAME"/../bats-template.bash  # for $TESTDIR, $it, etc.
 # some preconditions
 setup() {
     [ -e "$TESTDIR" ]
-    expectedError="$TESTDIR"/compile-error.expected
-    [ -e "$expectedError" ]
-    actualError=${expectedError%.expected}.actual
 }
 
 # check if input produces a compile error
-@test "$it compiles input" {
+@test "$it should produce an expected compilation error" {
+    expectedError="$TESTDIR"/compile-error.expected
+    [ -e "$expectedError" ] || skip
+    actualError=${expectedError%.expected}.actual
     ! ddlog check "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError"
     diff "$expectedError" "$actualError"
 }
-
diff --git a/test/compile-error-test/supervision_label_type_mismatch/compile-error.expected b/test/compile-error-test/supervision_label_type_mismatch/compile-error.expected
new file mode 100644
index 000000000..a93055da1
--- /dev/null
+++ b/test/compile-error-test/supervision_label_type_mismatch/compile-error.expected
@@ -0,0 +1,4 @@
+[error] Supervision column label should be boolean type, but is text type
+Q(x) = label :-
+    R(x, label).
+
diff --git a/test/compile-error-test/supervision_label_type_mismatch/input.ddlog b/test/compile-error-test/supervision_label_type_mismatch/input.ddlog
new file mode 100644
index 000000000..24750149f
--- /dev/null
+++ b/test/compile-error-test/supervision_label_type_mismatch/input.ddlog
@@ -0,0 +1,4 @@
+Q?(x int).
+R(x int, label text).
+
+Q(x) = label :- R(x, label).

From 36ab5b15c043a37a846b7dbb2c88d92741034096 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 11 Oct 2015 22:19:47 -0700
Subject: [PATCH 233/347] Add '%' operator

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 7d934f29b..020ea1945 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -181,7 +181,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
-  def operator = "||" | "+" | "-" | "*" | "/" | "&"
+  def operator = "||" | "+" | "-" | "*" | "/" | "&" | "%"
   def typeOperator = "::"
   val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG", "COUNT")
 

From fedcac848197f8e2bf88aee8631a18d369542fcb Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 12 Oct 2015 02:19:33 -0700
Subject: [PATCH 234/347] Changes compiled extractor/factor names to be
 readable

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  43 ++-
 .../compile-incremental.expected              | 340 ++++++++++++++++++
 .../compile.expected                          | 219 +++++++++++
 .../multiple_rules_for_same_head/input.ddlog  |  36 ++
 4 files changed, 634 insertions(+), 4 deletions(-)
 create mode 100644 test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
 create mode 100644 test/expected-output-test/multiple_rules_for_same_head/compile.expected
 create mode 100644 test/expected-output-test/multiple_rules_for_same_head/input.ddlog

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9155728a5..acf79d7ae 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -136,13 +136,48 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     throw new RuntimeException(message)
   }
 
+  def optionalIndex(idx: Int) =
+    if (idx < 1) "" else s"${idx}"
+
   // Given a statement, resolve its name for the compiled extractor block.
-  def resolveExtractorBlockName(s: Statement): String = s"extraction_rule_${statements indexOf s}"
+  def resolveExtractorBlockName(s: Statement): String = s match {
+    case d: SchemaDeclaration => s"init_${d.a.name}"
+    case e: ExtractionRule => s"ext_${e.headName}"
+    case f: FunctionCallRule => s"ext${
+      // Extra numbering is necessary because there can be many function calls to the same head relation
+      // XXX This comes right after the prefix to prevent potential collision with user's name
+      val functionCallsForSameOutputAndFunction =
+        (functionCallRuleGroupByOutput getOrElse(f.output, Set.empty) toList).filter (_.function == f.function)
+      val idx = functionCallsForSameOutputAndFunction indexOf f
+      optionalIndex(idx)
+    }_${f.output}_by_${f.function}"
+    case _ => sys.error(s"${s}: Cannot determine extractor block name for rule")
+  }
 
   // Given an inference rule, resolve its name for the compiled inference block.
-  def resolveInferenceBlockName(s: InferenceRule): String = mode match {
-    case INCREMENTAL => s"dd_delta_inference_rule_${inferenceRules indexOf s}"
-    case _ =>           s"inference_rule_${inferenceRules indexOf s}"
+  def resolveInferenceBlockName(s: InferenceRule): String = {
+    val factorFuncName: String = s.head.function.toString.toLowerCase
+    val idxInInferenceRulesSharingHead = inferenceRules filter(_.head equals s.head) indexOf(s)
+    mode match {
+      case INCREMENTAL => s"dd_delta_inf${
+        // XXX This comes right after the prefix to prevent potential collision with user's name
+        optionalIndex(idxInInferenceRulesSharingHead)
+      }_${
+        factorFuncName
+      }_${
+        s.head.terms map {_.name stripPrefix("dd_new_")} mkString("_")
+      }"
+      case _ =>           s"inf${
+        // XXX This comes right after the prefix to prevent potential collision with user's name
+        optionalIndex(idxInInferenceRulesSharingHead)
+      }_${
+        // function name
+        factorFuncName
+      }_${
+        // followed by variable names
+        s.head.terms map {_.name} mkString("_")
+      }"
+    }
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
new file mode 100644
index 000000000..0ba2f1653
--- /dev/null
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -0,0 +1,340 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: INCREMENTAL
+    }
+    
+
+      deepdive.schema.keys {
+        dd_new_Q : [x]
+        dd_delta_Q : [x]
+      }
+
+      deepdive.schema.variables {
+        Q.label: Boolean
+dd_delta_Q.label: Boolean
+dd_new_Q.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.init_dd_new_S {
+            sql: """ DROP TABLE IF EXISTS dd_new_S CASCADE;
+            CREATE TABLE
+            dd_new_S(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_T {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T CASCADE;
+            CREATE TABLE
+            dd_delta_T(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_T {
+            sql: """ DROP TABLE IF EXISTS dd_new_T CASCADE;
+            CREATE TABLE
+            dd_new_T(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_S {
+            sql: """ DROP TABLE IF EXISTS dd_delta_S CASCADE;
+            CREATE TABLE
+            dd_delta_S(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_R {
+            sql: """ DROP TABLE IF EXISTS dd_new_R CASCADE;
+            CREATE TABLE
+            dd_new_R(a int,
+        b int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_R {
+            sql: """ DROP TABLE IF EXISTS dd_delta_R CASCADE;
+            CREATE TABLE
+            dd_delta_R(a int,
+          b int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_Q {
+            sql: """ DROP TABLE IF EXISTS dd_delta_Q CASCADE;
+            CREATE TABLE
+            dd_delta_Q(x int,
+          id bigint,
+          label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_new_S;
+          TRUNCATE dd_delta_T;
+          TRUNCATE dd_new_T;
+          TRUNCATE dd_delta_S;
+          TRUNCATE dd_new_R;
+          TRUNCATE dd_delta_R;
+          TRUNCATE dd_delta_Q;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.ext_dd_new_S {
+        sql: """ TRUNCATE dd_new_S;
+        INSERT INTO dd_new_S SELECT R0.a
+FROM S R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_S R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_dd_new_T {
+        sql: """ TRUNCATE dd_new_T;
+        INSERT INTO dd_new_T SELECT R0.a
+FROM T R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_T R0
+        
+        """
+        style: "sql_extractor"
+          dependencies: [ "ext_dd_delta_T_by_f" ,  "ext1_dd_delta_T_by_f" ,  "ext2_dd_delta_T_by_f" ,  "ext_dd_delta_T_by_f_1" ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_dd_delta_S {
+        sql: """ 
+        INSERT INTO dd_delta_S SELECT R0.a AS "dd_delta_R.R0.a"
+FROM dd_delta_R R0, R R1
+        WHERE R1.a = R0.b  AND R0.a > 100
+UNION ALL
+SELECT R0.a AS "dd_new_R.R0.a"
+FROM dd_new_R R0, dd_delta_R R1
+        WHERE R1.a = R0.b  AND R0.a > 100
+UNION ALL
+SELECT R0.a AS "dd_delta_R.R0.a"
+FROM dd_delta_R R0, R R1
+        WHERE R1.a = R0.b  AND R0.a < -100
+UNION ALL
+SELECT R0.a AS "dd_new_R.R0.a"
+FROM dd_new_R R0, dd_delta_R R1
+        WHERE R1.a = R0.b  AND R0.a < -100
+UNION ALL
+SELECT R0.a AS "dd_delta_R.R0.a"
+FROM dd_delta_R R0, R R1
+        WHERE R1.a = R0.b  AND R0.a = 0
+UNION ALL
+SELECT R0.a AS "dd_new_R.R0.a"
+FROM dd_new_R R0, dd_delta_R R1
+        WHERE R1.a = R0.b  AND R0.a = 0
+        """
+        style: "sql_extractor"
+          dependencies: [ "ext_dd_new_R" ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_dd_new_R {
+        sql: """ TRUNCATE dd_new_R;
+        INSERT INTO dd_new_R SELECT R0.a, R0.b
+FROM R R0
+        
+UNION ALL
+SELECT R0.a, R0.b
+FROM dd_delta_R R0
+        
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+      deepdive.extraction.extractors.ext_dd_new_Q {
+        sql: """ 
+        CREATE VIEW dd_new_Q AS SELECT DISTINCT R0.x, id, label
+          FROM Q R0
+        
+          
+UNION ALL
+SELECT DISTINCT R0.x, id, label
+          FROM dd_delta_Q R0
+        
+          
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.extraction.extractors.ext_dd_delta_T_by_f {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        WHERE R0.a > 1000
+          """
+          output_relation: "dd_delta_T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext1_dd_delta_T_by_f {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        WHERE (10 < R0.a AND R0.a < 20)
+          """
+          output_relation: "dd_delta_T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext2_dd_delta_T_by_f {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        WHERE (100 < R0.a AND R0.a < 200)
+          """
+          output_relation: "dd_delta_T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext_dd_delta_S_by_f {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        WHERE R0.a < 0
+          """
+          output_relation: "dd_delta_S"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext1_dd_delta_S_by_f {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        WHERE R0.a > 0
+          """
+          output_relation: "dd_delta_S"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext_dd_delta_T_by_f_1 {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        
+          """
+          output_relation: "dd_delta_T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext_dd_delta_S_by_f_1 {
+          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
+FROM dd_delta_R R0
+        WHERE R0.a > 0
+          """
+          output_relation: "dd_delta_S"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.inference.factors.dd_delta_inf_istrue_Q {
+          input_query: """
+          SELECT R0.id AS "dd_new_Q.R0.id" , R0.x AS "dd_weight_column_0" 
+          FROM dd_new_Q R0, dd_delta_S R1
+        WHERE R1.a = R0.x  AND R0.x > 1000"""
+          function: "Imply(dd_new_Q.R0.label)"
+          weight: "?(dd_weight_column_0)"
+        }
+      
+
+        deepdive.inference.factors.dd_delta_inf1_istrue_Q {
+          input_query: """
+          SELECT R0.id AS "dd_new_Q.R0.id" 
+          FROM dd_new_Q R0, dd_delta_S R1
+        WHERE R1.a = R0.x  AND R0.x = 0"""
+          function: "Imply(dd_new_Q.R0.label)"
+          weight: "1.0"
+        }
+      
+
+        deepdive.inference.factors.dd_delta_inf_imply_Q_Q {
+          input_query: """
+          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" , R0.x AS "dd_weight_column_0" 
+          FROM dd_new_Q R0, dd_new_Q R1, dd_delta_S R2, R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  UNION ALL 
+          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" , R0.x AS "dd_weight_column_0" 
+          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_delta_R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  UNION ALL 
+          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" , R0.x AS "dd_weight_column_0" 
+          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_new_R R3, dd_delta_S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
+          function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
+          weight: "?(dd_weight_column_0)"
+        }
+      
+
+        deepdive.inference.factors.dd_delta_inf1_imply_Q_Q {
+          input_query: """
+          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
+          FROM dd_new_Q R0, dd_new_Q R1, dd_delta_S R2, R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
+          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
+          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_delta_R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
+          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
+          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_new_R R3, dd_delta_S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
+          function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
+          weight: "-10.0"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [init_dd_new_S, init_dd_delta_T, init_dd_new_T, init_dd_delta_S, init_dd_new_R, init_dd_delta_R, init_dd_new_Q, init_dd_delta_Q]
+deepdive.pipeline.pipelines.extraction: [ext_dd_new_R, ext_dd_delta_T_by_f, ext1_dd_delta_T_by_f, ext2_dd_delta_T_by_f, ext_dd_delta_S, ext_dd_new_T, ext_dd_new_S, ext_dd_delta_S_by_f, ext_dd_new_Q, ext_dd_delta_S_by_f_1, ext_dd_delta_T_by_f_1, ext1_dd_delta_S_by_f]
+deepdive.pipeline.pipelines.inference: [dd_delta_inf_istrue_Q, dd_delta_inf1_istrue_Q, dd_delta_inf_imply_Q_Q, dd_delta_inf1_imply_Q_Q]
+deepdive.pipeline.pipelines.endtoend: [ext_dd_new_R, ext_dd_delta_T_by_f, ext1_dd_delta_T_by_f, ext2_dd_delta_T_by_f, ext_dd_delta_S, ext_dd_new_T, ext_dd_new_S, ext_dd_delta_S_by_f, ext_dd_new_Q, ext_dd_delta_S_by_f_1, ext_dd_delta_T_by_f_1, ext1_dd_delta_S_by_f, dd_delta_inf_istrue_Q, dd_delta_inf1_istrue_Q, dd_delta_inf_imply_Q_Q, dd_delta_inf1_imply_Q_Q]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
new file mode 100644
index 000000000..7bbd3b7cc
--- /dev/null
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -0,0 +1,219 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        Q.label: Boolean
+      }
+    
+
+          deepdive.extraction.extractors.init_S {
+            sql: """ DROP TABLE IF EXISTS S CASCADE;
+            CREATE TABLE
+            S(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_R {
+            sql: """ DROP TABLE IF EXISTS R CASCADE;
+            CREATE TABLE
+            R(a int,
+ b int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_Q {
+            sql: """ DROP TABLE IF EXISTS Q CASCADE;
+            CREATE TABLE
+            Q(x int,
+ id bigint,
+ label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_T {
+            sql: """ DROP TABLE IF EXISTS T CASCADE;
+            CREATE TABLE
+            T(a int)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE S;
+          TRUNCATE R;
+          TRUNCATE Q;
+          TRUNCATE T;
+          """
+          style: "sql_extractor"
+        }
+
+      deepdive.extraction.extractors.ext_S {
+        sql: """ 
+        INSERT INTO S SELECT R0.a AS "R.R0.a"
+FROM R R0, R R1
+        WHERE R1.a = R0.b  AND R0.a > 100
+UNION ALL
+SELECT R0.a AS "R.R0.a"
+FROM R R0, R R1
+        WHERE R1.a = R0.b  AND R0.a < -100
+UNION ALL
+SELECT R0.a AS "R.R0.a"
+FROM R R0, R R1
+        WHERE R1.a = R0.b  AND R0.a = 0
+        """
+        style: "sql_extractor"
+          
+      }
+    
+
+        deepdive.extraction.extractors.ext_T_by_f {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE R0.a > 1000
+          """
+          output_relation: "T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext1_T_by_f {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE (10 < R0.a AND R0.a < 20)
+          """
+          output_relation: "T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext2_T_by_f {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE (100 < R0.a AND R0.a < 200)
+          """
+          output_relation: "T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext_S_by_f {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE R0.a < 0
+          """
+          output_relation: "S"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext1_S_by_f {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE R0.a > 0
+          """
+          output_relation: "S"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext_T_by_f_1 {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        
+          """
+          output_relation: "T"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.extraction.extractors.ext_S_by_f_1 {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE R0.a > 0
+          """
+          output_relation: "S"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
+          parallelism: ${PARALLELISM}
+        }
+      
+
+        deepdive.inference.factors.inf_istrue_Q {
+          input_query: """
+          SELECT R0.id AS "Q.R0.id" , R0.x AS "dd_weight_column_0" 
+          FROM Q R0, S R1
+        WHERE R1.a = R0.x  AND R0.x > 1000"""
+          function: "Imply(Q.R0.label)"
+          weight: "?(dd_weight_column_0)"
+        }
+      
+
+        deepdive.inference.factors.inf1_istrue_Q {
+          input_query: """
+          SELECT R0.id AS "Q.R0.id" 
+          FROM Q R0, S R1
+        WHERE R1.a = R0.x  AND R0.x = 0"""
+          function: "Imply(Q.R0.label)"
+          weight: "1.0"
+        }
+      
+
+        deepdive.inference.factors.inf_imply_Q_Q {
+          input_query: """
+          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R0.x AS "dd_weight_column_0" 
+          FROM Q R0, Q R1, S R2, R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
+          function: "Imply(Q.R0.label, Q.R1.label)"
+          weight: "?(dd_weight_column_0)"
+        }
+      
+
+        deepdive.inference.factors.inf1_imply_Q_Q {
+          input_query: """
+          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
+          FROM Q R0, Q R1, S R2, R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
+          function: "Imply(Q.R0.label, Q.R1.label)"
+          weight: "-10.0"
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.initdb: [init_S, init_R, init_Q, init_T]
+deepdive.pipeline.pipelines.extraction: [ext2_T_by_f, ext_S_by_f_1, ext_S_by_f, ext1_S_by_f, ext_T_by_f_1, ext1_T_by_f, ext_S, ext_T_by_f]
+deepdive.pipeline.pipelines.inference: [inf_istrue_Q, inf1_istrue_Q, inf_imply_Q_Q, inf1_imply_Q_Q]
+deepdive.pipeline.pipelines.endtoend: [ext2_T_by_f, ext_S_by_f_1, ext_S_by_f, ext1_S_by_f, ext_T_by_f_1, ext1_T_by_f, ext_S, ext_T_by_f, inf_istrue_Q, inf1_istrue_Q, inf_imply_Q_Q, inf1_imply_Q_Q]
+deepdive.pipeline.pipelines.cleanup: [cleanup]
diff --git a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
new file mode 100644
index 000000000..690e53204
--- /dev/null
+++ b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
@@ -0,0 +1,36 @@
+R(a int, b int).
+S(a int).
+T(a int).
+Q?(x int).
+
+# multiple rules for normal extraction rules
+S(a) :- R(a, b), R(b, _), a > 100.
+S(a) :- R(a, b), R(b, _), a < -100.
+S(a) :- R(a, b), R(b, _), a = 0.
+
+# multiple calls to the same function for the same head
+function f over (a int, b int) returns (a int)
+    implementation "/bin/false" handles tsv lines.
+T += f(a, b) :- R(a, b), a > 1000.
+T += f(a, b) :- R(a, b), 10 < a, a < 20.
+T += f(a, b) :- R(a, b), 100 < a, a < 200.
+# different head
+S += f(a, b) :- R(a, b), a < 0.
+S += f(a, b) :- R(a, b), a > 0.
+
+# test to check name clash with functions
+function f_1 over (a int, b int) returns (a int)
+    implementation "/bin/false" handles tsv lines.
+T += f_1(a, b) :- R(a, b).
+S += f_1(a, b) :- R(a, b), a > 0.
+
+# multiple inference rules for the same head
+@weight(a)
+Q(a) :- S(a), a > 1000.
+@weight(1.0)
+Q(a) :- S(a), a = 0.
+
+@weight(a)
+Q(a) => Q(b) :- S(a), R(a, b), S(b).
+@weight(-10.0)
+Q(a) => Q(b) :- S(a), R(a, b), S(b), a + b < 1000.

From e2ebe1e59b8324567e720534ba8ede56ac02bf64 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 12 Oct 2015 02:43:34 -0700
Subject: [PATCH 235/347] Fixes a None.get bug in supervision column type
 checker

Also adds support for DDLOG_STACK_TRACE environment to show full stack
trace for RuntimeExceptions.
---
 src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala           | 4 +++-
 .../scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 7459cd9ee..7123056ce 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -58,7 +58,9 @@ trait DeepDiveLogHandler {
     // run handler with the parsed program
     run(parsedProgram, config)
   } catch {
-    case e: RuntimeException => die(e.getMessage)
+    case e: RuntimeException =>
+      if (sys.env contains "DDLOG_STACK_TRACE") throw e
+      else die(e.getMessage)
   }
 
   def parseFiles(fileNames: List[String]): DeepDiveLog.Program = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index aff0f7c7f..b644269de 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -187,7 +187,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
 
   def checkSupervisionLabelType(stmt: Statement) {
     stmt match {
-      case s: ExtractionRule if schemaDeclaration contains s.headName => {
+      case s: ExtractionRule if (schemaDeclaration contains s.headName) && (schemaDeclaration(s.headName).variableType nonEmpty) => {
         val headType = schemaDeclaration(s.headName).variableType.get
         s.supervision match {
           case Some("TRUE") | Some("FALSE") => {

From 4172e796da75ac101d7e777801ad823b5c9f8a85 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 12 Oct 2015 15:54:00 -0700
Subject: [PATCH 236/347] Fixes tests' expected output according to new
 compilation naming scheme

also makes the list of extractors and factors in pipeline more readable
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  18 +--
 .../column_dismatch/compile-error.expected    |   2 +-
 .../compile-error.expected                    |   6 +-
 .../optional_modifier/compile-error.expected  |   2 +-
 .../unbound_variable_1/compile-error.expected |   2 +-
 .../unbound_variable_2/compile-error.expected |   2 +-
 .../unbound_variable_4/compile-error.expected |   2 +-
 .../undefined_function/compile-error.expected |   2 +-
 .../undefined_relation/compile-error.expected |   2 +-
 .../weight/compile-error.expected             |   2 +-
 .../annotations/printed.expected              |   7 --
 .../chunking_example/compile.expected         |  48 +++++---
 .../comments/print.expected                   |   2 +-
 .../expressions/compile.expected              | 114 +++++++++++++-----
 .../expressions/print.expected                |  42 +++----
 .../many_joins/print-incremental.expected     |  10 +-
 .../compile-incremental.expected              |  56 ++++++++-
 .../compile.expected                          |  44 ++++++-
 .../ocr_example/compile-incremental.expected  |  82 +++++++++----
 .../compile-materialization.expected          |  43 +++++--
 .../ocr_example/compile-merge.expected        |  18 ++-
 .../ocr_example/compile.expected              |  47 +++++---
 .../compile-incremental.expected              |  92 +++++++++-----
 .../compile-materialization.expected          |  46 ++++---
 .../smoke_example/compile-merge.expected      |  22 +++-
 .../smoke_example/compile.expected            |  50 +++++---
 .../compile-incremental.expected              | 108 +++++++++++------
 .../compile-materialization.expected          |  56 ++++++---
 .../spouse_example/compile-merge.expected     |  26 ++--
 .../spouse_example/compile.expected           |  60 ++++++---
 .../compile-incremental.expected              | 108 +++++++++++------
 .../compile-incremental.expected              | 112 +++++++++++------
 .../compile.expected                          |  64 +++++++---
 .../views/compile.expected                    |  26 ++--
 .../weights/compile.expected                  |  51 +++++---
 .../weights/print.expected                    |  10 +-
 36 files changed, 962 insertions(+), 422 deletions(-)
 delete mode 100644 test/expected-output-test/annotations/printed.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index acf79d7ae..2477ae92c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -785,16 +785,16 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   // generate application.conf pipelines
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
-    val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
-    val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [${setup_database_pipeline}]" else ""
-    val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString(", ")
-    val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [${extraction}]" else ""
-    val inference = (ss.inferenceRules map {s => ss.resolveInferenceBlockName(s)}).mkString(", ")
-    val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [${inference}]" else ""
-    val endtoend = List(extraction, inference).filter(_ != "").mkString(", ")
-    val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [${endtoend}]" else ""
+    val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
+    val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [\n  ${setup_database_pipeline}\n]" else ""
+    val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
+    val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [\n  ${extraction}\n]" else ""
+    val inference = (ss.inferenceRules map {s => ss.resolveInferenceBlockName(s)}).mkString("\n  ")
+    val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [\n  ${inference}\n]" else ""
+    val endtoend = List(extraction, inference).filter(_ != "").mkString("\n  ")
+    val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [\n  ${endtoend}\n]" else ""
     val cleanup_pipeline = ss.mode match {
-      case INCREMENTAL | ORIGINAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [cleanup]" else ""
+      case INCREMENTAL | ORIGINAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [\n  cleanup\n]" else ""
       case _ => ""
     }
     val base_dir = ss.mode match {
diff --git a/test/compile-error-test/column_dismatch/compile-error.expected b/test/compile-error-test/column_dismatch/compile-error.expected
index 06dd1101f..6004d4ce5 100644
--- a/test/compile-error-test/column_dismatch/compile-error.expected
+++ b/test/compile-error-test/column_dismatch/compile-error.expected
@@ -1,5 +1,5 @@
 [error] "c": number of columns in the query does not match number of columns in the schema
-Q(y, z)  :-
+Q(y, z) :-
     a(x),
     c(x, y, z, w).
 
diff --git a/test/compile-error-test/invalid_variable_schema/compile-error.expected b/test/compile-error-test/invalid_variable_schema/compile-error.expected
index 6086a2b35..c74cc14ed 100644
--- a/test/compile-error-test/invalid_variable_schema/compile-error.expected
+++ b/test/compile-error-test/invalid_variable_schema/compile-error.expected
@@ -1,6 +1,6 @@
 [error] variable relation contains reserved column "id" 
 c?(id int,
-  s text,
-  n int,
-  t text).
+   s text,
+   n int,
+   t text).
 
diff --git a/test/compile-error-test/optional_modifier/compile-error.expected b/test/compile-error-test/optional_modifier/compile-error.expected
index 354e90ff2..890a0c796 100644
--- a/test/compile-error-test/optional_modifier/compile-error.expected
+++ b/test/compile-error-test/optional_modifier/compile-error.expected
@@ -1,5 +1,5 @@
 [error] One and only one atom should be supplied in OPTIONAL modifier
-Q(y, z)  :-
+Q(y, z) :-
     a(x),
     OPTIONAL[x > 1].
 
diff --git a/test/compile-error-test/unbound_variable_1/compile-error.expected b/test/compile-error-test/unbound_variable_1/compile-error.expected
index 560383a45..3803d6672 100644
--- a/test/compile-error-test/unbound_variable_1/compile-error.expected
+++ b/test/compile-error-test/unbound_variable_1/compile-error.expected
@@ -1,4 +1,4 @@
 [error] Variable y must have bindings
-Q(y)  :-
+Q(y) :-
     a(x).
 
diff --git a/test/compile-error-test/unbound_variable_2/compile-error.expected b/test/compile-error-test/unbound_variable_2/compile-error.expected
index 7541c2667..d8df62269 100644
--- a/test/compile-error-test/unbound_variable_2/compile-error.expected
+++ b/test/compile-error-test/unbound_variable_2/compile-error.expected
@@ -1,5 +1,5 @@
 [error] Variable x must have bindings
-Q(y)  :-
+Q(y) :-
     a(y),
     x > 100.
 
diff --git a/test/compile-error-test/unbound_variable_4/compile-error.expected b/test/compile-error-test/unbound_variable_4/compile-error.expected
index 76cc8e1ae..369de188e 100644
--- a/test/compile-error-test/unbound_variable_4/compile-error.expected
+++ b/test/compile-error-test/unbound_variable_4/compile-error.expected
@@ -1,4 +1,4 @@
 [error] Variable y, z must have bindings
-Q(y, z)  :-
+Q(y, z) :-
     a(x).
 
diff --git a/test/compile-error-test/undefined_function/compile-error.expected b/test/compile-error-test/undefined_function/compile-error.expected
index f30362ca4..7f52706b8 100644
--- a/test/compile-error-test/undefined_function/compile-error.expected
+++ b/test/compile-error-test/undefined_function/compile-error.expected
@@ -1,4 +1,4 @@
 [error] function "ext" is not defined
-Q += ext(x)  :-
+Q += ext(x) :-
     a(x).
 
diff --git a/test/compile-error-test/undefined_relation/compile-error.expected b/test/compile-error-test/undefined_relation/compile-error.expected
index b8e721de4..b697625a5 100644
--- a/test/compile-error-test/undefined_relation/compile-error.expected
+++ b/test/compile-error-test/undefined_relation/compile-error.expected
@@ -1,5 +1,5 @@
 [error] relation "d" is not defined
-Q(y, z)  :-
+Q(y, z) :-
     a(x),
     d(x, y, z, w).
 
diff --git a/test/compile-error-test/weight/compile-error.expected b/test/compile-error-test/weight/compile-error.expected
index 0339cc784..ee90b1266 100644
--- a/test/compile-error-test/weight/compile-error.expected
+++ b/test/compile-error-test/weight/compile-error.expected
@@ -1,5 +1,5 @@
 [error] Weight variables can contain at most one constant
 @weight(1, 2)
-a(x)  :-
+a(x) :-
     b(x, y, _, _).
 
diff --git a/test/expected-output-test/annotations/printed.expected b/test/expected-output-test/annotations/printed.expected
deleted file mode 100644
index 8a34c9821..000000000
--- a/test/expected-output-test/annotations/printed.expected
+++ /dev/null
@@ -1,7 +0,0 @@
-@textspan(from="start_pos", length="len")
-mention_candidate(doc_id text,
-                  @textspan_start
-                  start_pos int,
-                  @textspan_length
-                  len int).
-
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index dcfcf8287..8b4298920 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -17,7 +17,7 @@
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_words_raw {
             sql: """ DROP TABLE IF EXISTS words_raw CASCADE;
             CREATE TABLE
             words_raw(word_id bigserial,
@@ -28,7 +28,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_words {
             sql: """ DROP TABLE IF EXISTS words CASCADE;
             CREATE TABLE
             words(sent_id bigint,
@@ -40,7 +40,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_tag {
             sql: """ DROP TABLE IF EXISTS tag CASCADE;
             CREATE TABLE
             tag(word_id bigint,
@@ -50,7 +50,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_word_features {
             sql: """ DROP TABLE IF EXISTS word_features CASCADE;
             CREATE TABLE
             word_features(word_id bigint,
@@ -69,7 +69,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_8 {
+      deepdive.extraction.extractors.ext_tag {
         sql: """ 
         INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
           FROM words R0
@@ -77,11 +77,11 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_5" ]
+          dependencies: [ "ext_words_by_ext_training" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_5 {
+        deepdive.extraction.extractors.ext_words_by_ext_training {
           input: """ SELECT R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.tag AS "words_raw.R0.tag"
 FROM words_raw R0
         
@@ -94,7 +94,7 @@ FROM words_raw R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_7 {
+        deepdive.extraction.extractors.ext_word_features_by_ext_features {
           input: """ SELECT R0.word_id AS "words.R0.word_id", R0.word AS "words.R0.word", R0.pos AS "words.R0.pos", R1.word AS "words.R1.word", R1.pos AS "words.R1.pos"
 FROM words R0, words R1
         WHERE R1.sent_id = R0.sent_id 
@@ -102,12 +102,12 @@ FROM words R0, words R1
           output_relation: "word_features"
           udf: ${APP_HOME}"/udf/ext_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_5" ]
+          dependencies: [ "ext_words_by_ext_training" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_tag {
           input_query: """
           SELECT R0.id AS "tag.R0.id" , R1.feature AS "dd_weight_column_0" 
           FROM tag R0, word_features R1
@@ -117,8 +117,26 @@ FROM words R0, words R1
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_0, extraction_rule_1, extraction_rule_3, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_8, extraction_rule_5, extraction_rule_7]
-deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_8, extraction_rule_5, extraction_rule_7, inference_rule_0]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_words_raw
+  init_words
+  init_tag
+  init_word_features
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_tag
+  ext_words_by_ext_training
+  ext_word_features_by_ext_features
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_tag
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_tag
+  ext_words_by_ext_training
+  ext_word_features_by_ext_features
+  inf_istrue_tag
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/comments/print.expected b/test/expected-output-test/comments/print.expected
index a5fd9a790..8b8213f4c 100644
--- a/test/expected-output-test/comments/print.expected
+++ b/test/expected-output-test/comments/print.expected
@@ -4,6 +4,6 @@ S(a int,
   b text,
   c float).
 
-R(x)  :-
+R(x) :-
     S(x, y, z).
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 5a69fcae2..27a13ba61 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -17,7 +17,7 @@
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_b {
             sql: """ DROP TABLE IF EXISTS b CASCADE;
             CREATE TABLE
             b(k int,
@@ -28,7 +28,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_a {
             sql: """ DROP TABLE IF EXISTS a CASCADE;
             CREATE TABLE
             a(k int)
@@ -36,7 +36,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_c {
             sql: """ DROP TABLE IF EXISTS c CASCADE;
             CREATE TABLE
             c(s text,
@@ -55,7 +55,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_9 {
+      deepdive.extraction.extractors.ext_E {
         sql: """ DROP VIEW IF EXISTS E;
         CREATE VIEW E AS SELECT (R0.k :: INT) AS column_0
 FROM b R0
@@ -66,7 +66,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_25 {
+      deepdive.extraction.extractors.ext_X {
         sql: """ DROP VIEW IF EXISTS X;
         CREATE VIEW X AS SELECT R0.k AS column_0
 FROM b R0, c R1
@@ -77,7 +77,7 @@ FROM b R0, c R1
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_18 {
+      deepdive.extraction.extractors.ext_N {
         sql: """ DROP VIEW IF EXISTS N;
         CREATE VIEW N AS SELECT R0.k AS column_0
 FROM b R0
@@ -88,7 +88,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_21 {
+      deepdive.extraction.extractors.ext_T {
         sql: """ DROP VIEW IF EXISTS T;
         CREATE VIEW T AS SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
@@ -99,7 +99,7 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_14 {
+      deepdive.extraction.extractors.ext_J {
         sql: """ DROP VIEW IF EXISTS J;
         CREATE VIEW J AS SELECT R0.k AS column_0
 FROM b R0
@@ -110,7 +110,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_22 {
+      deepdive.extraction.extractors.ext_U {
         sql: """ DROP VIEW IF EXISTS U;
         CREATE VIEW U AS SELECT R0_0.k AS column_0
 FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
@@ -121,7 +121,7 @@ FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_10 {
+      deepdive.extraction.extractors.ext_F {
         sql: """ DROP VIEW IF EXISTS F;
         CREATE VIEW F AS SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
 FROM b R0
@@ -132,7 +132,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_5 {
+      deepdive.extraction.extractors.ext_A {
         sql: """ DROP VIEW IF EXISTS A;
         CREATE VIEW A AS SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
 FROM b R0
@@ -143,7 +143,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_17 {
+      deepdive.extraction.extractors.ext_M {
         sql: """ DROP VIEW IF EXISTS M;
         CREATE VIEW M AS SELECT R0.k AS column_0
 FROM b R0
@@ -154,7 +154,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_13 {
+      deepdive.extraction.extractors.ext_I {
         sql: """ DROP VIEW IF EXISTS I;
         CREATE VIEW I AS SELECT R0.k AS column_0
 FROM b R0
@@ -165,7 +165,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_11 {
+      deepdive.extraction.extractors.ext_G {
         sql: """ DROP VIEW IF EXISTS G;
         CREATE VIEW G AS SELECT R0.k AS column_0
 FROM b R0
@@ -176,7 +176,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_24 {
+      deepdive.extraction.extractors.ext_V {
         sql: """ DROP VIEW IF EXISTS V;
         CREATE VIEW V AS SELECT R0.n AS column_0
 FROM c R0, a R1
@@ -187,7 +187,7 @@ FROM c R0, a R1
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_Q {
         sql: """ DROP VIEW IF EXISTS Q;
         CREATE VIEW Q AS SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
@@ -198,7 +198,7 @@ FROM a R0, b R1, c R2
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_16 {
+      deepdive.extraction.extractors.ext_L {
         sql: """ DROP VIEW IF EXISTS L;
         CREATE VIEW L AS SELECT DISTINCT R0.k AS column_0
 FROM b R0
@@ -209,7 +209,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_6 {
+      deepdive.extraction.extractors.ext_B {
         sql: """ DROP VIEW IF EXISTS B;
         CREATE VIEW B AS SELECT func((R0.k + (R0.r + R0.k))) AS column_0
 FROM b R0
@@ -220,7 +220,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_4 {
+      deepdive.extraction.extractors.ext_P {
         sql: """ DROP VIEW IF EXISTS P;
         CREATE VIEW P AS SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
 FROM a R0, b R1
@@ -232,7 +232,7 @@ FROM a R0, b R1
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_C {
         sql: """ DROP VIEW IF EXISTS C;
         CREATE VIEW C AS SELECT func(func(func(R0.k))) AS column_0
 FROM b R0
@@ -243,7 +243,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_12 {
+      deepdive.extraction.extractors.ext_H {
         sql: """ DROP VIEW IF EXISTS H;
         CREATE VIEW H AS SELECT R0.k AS column_0
 FROM b R0
@@ -254,7 +254,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.ext_W {
         sql: """ DROP VIEW IF EXISTS W;
         CREATE VIEW W AS SELECT R0.k AS column_0
 FROM a R0
@@ -265,7 +265,7 @@ FROM a R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.ext_K {
         sql: """ DROP VIEW IF EXISTS K;
         CREATE VIEW K AS SELECT R0.k AS column_0
 FROM b R0
@@ -276,7 +276,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
+      deepdive.extraction.extractors.ext_O {
         sql: """ DROP VIEW IF EXISTS O;
         CREATE VIEW O AS SELECT R0.k AS column_0
 FROM b R0
@@ -287,7 +287,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_8 {
+      deepdive.extraction.extractors.ext_D {
         sql: """ DROP VIEW IF EXISTS D;
         CREATE VIEW D AS SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
 FROM b R0
@@ -298,7 +298,7 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_20 {
+      deepdive.extraction.extractors.ext_S {
         sql: """ DROP VIEW IF EXISTS S;
         CREATE VIEW S AS SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
@@ -309,7 +309,61 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_25, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_12, extraction_rule_20, extraction_rule_16, extraction_rule_25, extraction_rule_19, extraction_rule_22, extraction_rule_3, extraction_rule_4, extraction_rule_18, extraction_rule_8, extraction_rule_10, extraction_rule_13, extraction_rule_23, extraction_rule_5, extraction_rule_9, extraction_rule_14, extraction_rule_17, extraction_rule_11, extraction_rule_24, extraction_rule_15, extraction_rule_6]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_b
+  init_a
+  init_c
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_M
+  ext_Q
+  ext_B
+  ext_U
+  ext_F
+  ext_I
+  ext_N
+  ext_T
+  ext_A
+  ext_P
+  ext_K
+  ext_E
+  ext_W
+  ext_J
+  ext_D
+  ext_O
+  ext_L
+  ext_G
+  ext_X
+  ext_S
+  ext_C
+  ext_V
+  ext_H
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_M
+  ext_Q
+  ext_B
+  ext_U
+  ext_F
+  ext_I
+  ext_N
+  ext_T
+  ext_A
+  ext_P
+  ext_K
+  ext_E
+  ext_W
+  ext_J
+  ext_D
+  ext_O
+  ext_L
+  ext_G
+  ext_X
+  ext_S
+  ext_C
+  ext_V
+  ext_H
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 71ac2afae..b5f266959 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -15,85 +15,85 @@ Q(("test" :: TEXT), 123, id, unnest(y)) * :-
     c((x || y), 10, "foo"),
     [z > 100; [[!z < 20], z < 50]].
 
-P(y, z, MAX(w))  :-
+P(y, z, MAX(w)) :-
     a(x),
     b(x, y, z, w).
 
-A((x + (w * (x + w))))  :-
+A((x + (w * (x + w)))) :-
     b(x, y, z, w).
 
-B(func((x + (w + x))))  :-
+B(func((x + (w + x)))) :-
     b(x, y, z, w).
 
-C(func(func(func(x))))  :-
+C(func(func(func(x)))) :-
     b(x, y, z, w).
 
-D((func((x * func2((w + x)))) + x))  :-
+D((func((x * func2((w + x)))) + x)) :-
     b(x, y, z, w).
 
-E((x :: INT))  :-
+E((x :: INT)) :-
     b(x, y, z, w).
 
-F(((x :: INT) + (w :: INT)))  :-
+F(((x :: INT) + (w :: INT))) :-
     b(x, y, z, w).
 
-G(x)  :-
+G(x) :-
     b(x, y, z, w),
     (x + w) = 100.
 
-H(x)  :-
+H(x) :-
     b(x, y, z, w),
     [(x + w) = 100, x > 50].
 
-I(x)  :-
+I(x) :-
     b(x, y, z, w),
     [(x + w) = 100; [x > 50, w < 10]].
 
-J(x)  :-
+J(x) :-
     b(x, y, z, w),
     [(x + w) = 100; [!x > 50]].
 
-K(x)  :-
+K(x) :-
     b(x, y, z, w),
     [(x + w) = 100, [[!x > 50]; x = 40]].
 
 L(x) * | 100 :-
     b(x, y, z, w).
 
-M(x)  :-
+M(x) :-
     b(x, y, z, w),
     EXISTS[c(a, x, b)].
 
-N(x)  :-
+N(x) :-
     b(x, y, z, w),
     EXISTS[c(a, x, b), a > "a"].
 
-O(x)  :-
+O(x) :-
     b(x, y, z, w),
     EXISTS[c(a, x, b), a(x)].
 
-S(x)  :-
+S(x) :-
     b(x, y, z, w),
     OPTIONAL[c(a, x, b)].
 
-T(x)  :-
+T(x) :-
     b(x, y, z, w),
     OPTIONAL[c(a, x, b), a > y],
     a > y.
 
-U(x)  :-
+U(x) :-
     OPTIONAL[b(x, y, z, w)],
     OPTIONAL[c(a, x, b)].
 
-W(x)  :-
+W(x) :-
     a(x),
     ALL[c(_, y, _), y < x].
 
-V(x)  :-
+V(x) :-
     c(_, x, _),
     a(x).
 
-X(x)  :-
+X(x) :-
     b(x, _, _, z),
     c(_, x, y).
 
diff --git a/test/expected-output-test/many_joins/print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
index dd52a2b15..6edb3d0f8 100644
--- a/test/expected-output-test/many_joins/print-incremental.expected
+++ b/test/expected-output-test/many_joins/print-incremental.expected
@@ -4,7 +4,7 @@ dd_delta_R?(x text).
 
 dd_new_R?(x text).
 
-dd_new_R(x)  :-
+dd_new_R(x) :-
     R(x);
     dd_delta_R(x).
 
@@ -14,7 +14,7 @@ dd_delta_S(x text).
 
 dd_new_S(x text).
 
-dd_new_S(x)  :-
+dd_new_S(x) :-
     S(x);
     dd_delta_S(x).
 
@@ -27,7 +27,7 @@ dd_delta_T(x text,
 dd_new_T(x text,
          f text).
 
-dd_new_T(x, f)  :-
+dd_new_T(x, f) :-
     T(x, f);
     dd_delta_T(x, f).
 
@@ -40,11 +40,11 @@ dd_delta_U(x text,
 dd_new_U(x text,
          l text).
 
-dd_new_U(x, l)  :-
+dd_new_U(x, l) :-
     U(x, l);
     dd_delta_U(x, l).
 
-dd_delta_R(x)  :-
+dd_delta_R(x) :-
     dd_delta_S(x),
     T(x, f),
     U(x, l);
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index 0ba2f1653..5aee66846 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -332,9 +332,55 @@ FROM dd_delta_R R0
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [init_dd_new_S, init_dd_delta_T, init_dd_new_T, init_dd_delta_S, init_dd_new_R, init_dd_delta_R, init_dd_new_Q, init_dd_delta_Q]
-deepdive.pipeline.pipelines.extraction: [ext_dd_new_R, ext_dd_delta_T_by_f, ext1_dd_delta_T_by_f, ext2_dd_delta_T_by_f, ext_dd_delta_S, ext_dd_new_T, ext_dd_new_S, ext_dd_delta_S_by_f, ext_dd_new_Q, ext_dd_delta_S_by_f_1, ext_dd_delta_T_by_f_1, ext1_dd_delta_S_by_f]
-deepdive.pipeline.pipelines.inference: [dd_delta_inf_istrue_Q, dd_delta_inf1_istrue_Q, dd_delta_inf_imply_Q_Q, dd_delta_inf1_imply_Q_Q]
-deepdive.pipeline.pipelines.endtoend: [ext_dd_new_R, ext_dd_delta_T_by_f, ext1_dd_delta_T_by_f, ext2_dd_delta_T_by_f, ext_dd_delta_S, ext_dd_new_T, ext_dd_new_S, ext_dd_delta_S_by_f, ext_dd_new_Q, ext_dd_delta_S_by_f_1, ext_dd_delta_T_by_f_1, ext1_dd_delta_S_by_f, dd_delta_inf_istrue_Q, dd_delta_inf1_istrue_Q, dd_delta_inf_imply_Q_Q, dd_delta_inf1_imply_Q_Q]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_new_S
+  init_dd_delta_T
+  init_dd_new_T
+  init_dd_delta_S
+  init_dd_new_R
+  init_dd_delta_R
+  init_dd_new_Q
+  init_dd_delta_Q
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_dd_new_R
+  ext_dd_delta_T_by_f
+  ext1_dd_delta_T_by_f
+  ext2_dd_delta_T_by_f
+  ext_dd_delta_S
+  ext_dd_new_T
+  ext_dd_new_S
+  ext_dd_delta_S_by_f
+  ext_dd_new_Q
+  ext_dd_delta_S_by_f_1
+  ext_dd_delta_T_by_f_1
+  ext1_dd_delta_S_by_f
+]
+deepdive.pipeline.pipelines.inference: [
+  dd_delta_inf_istrue_Q
+  dd_delta_inf1_istrue_Q
+  dd_delta_inf_imply_Q_Q
+  dd_delta_inf1_imply_Q_Q
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_new_R
+  ext_dd_delta_T_by_f
+  ext1_dd_delta_T_by_f
+  ext2_dd_delta_T_by_f
+  ext_dd_delta_S
+  ext_dd_new_T
+  ext_dd_new_S
+  ext_dd_delta_S_by_f
+  ext_dd_new_Q
+  ext_dd_delta_S_by_f_1
+  ext_dd_delta_T_by_f_1
+  ext1_dd_delta_S_by_f
+  dd_delta_inf_istrue_Q
+  dd_delta_inf1_istrue_Q
+  dd_delta_inf_imply_Q_Q
+  dd_delta_inf1_imply_Q_Q
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 7bbd3b7cc..8e889f377 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -212,8 +212,42 @@ FROM R R0
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [init_S, init_R, init_Q, init_T]
-deepdive.pipeline.pipelines.extraction: [ext2_T_by_f, ext_S_by_f_1, ext_S_by_f, ext1_S_by_f, ext_T_by_f_1, ext1_T_by_f, ext_S, ext_T_by_f]
-deepdive.pipeline.pipelines.inference: [inf_istrue_Q, inf1_istrue_Q, inf_imply_Q_Q, inf1_imply_Q_Q]
-deepdive.pipeline.pipelines.endtoend: [ext2_T_by_f, ext_S_by_f_1, ext_S_by_f, ext1_S_by_f, ext_T_by_f_1, ext1_T_by_f, ext_S, ext_T_by_f, inf_istrue_Q, inf1_istrue_Q, inf_imply_Q_Q, inf1_imply_Q_Q]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_S
+  init_R
+  init_Q
+  init_T
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext2_T_by_f
+  ext_S_by_f_1
+  ext_S_by_f
+  ext1_S_by_f
+  ext_T_by_f_1
+  ext1_T_by_f
+  ext_S
+  ext_T_by_f
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_Q
+  inf1_istrue_Q
+  inf_imply_Q_Q
+  inf1_imply_Q_Q
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext2_T_by_f
+  ext_S_by_f_1
+  ext_S_by_f
+  ext1_S_by_f
+  ext_T_by_f_1
+  ext1_T_by_f
+  ext_S
+  ext_T_by_f
+  inf_istrue_Q
+  inf1_istrue_Q
+  inf_imply_Q_Q
+  inf1_imply_Q_Q
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index 62d8957b8..1614219c9 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -28,7 +28,7 @@ q1.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_10 {
+          deepdive.extraction.extractors.init_dd_new_label2 {
             sql: """ DROP TABLE IF EXISTS dd_new_label2 CASCADE;
             CREATE TABLE
             dd_new_label2(wid INT,
@@ -37,7 +37,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_dd_delta_label1 {
             sql: """ DROP TABLE IF EXISTS dd_delta_label1 CASCADE;
             CREATE TABLE
             dd_delta_label1(wid INT,
@@ -46,7 +46,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_6 {
+          deepdive.extraction.extractors.init_dd_new_label1 {
             sql: """ DROP TABLE IF EXISTS dd_new_label1 CASCADE;
             CREATE TABLE
             dd_new_label1(wid INT,
@@ -55,7 +55,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_dd_delta_features {
             sql: """ DROP TABLE IF EXISTS dd_delta_features CASCADE;
             CREATE TABLE
             dd_delta_features(id BIGSERIAL,
@@ -66,7 +66,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_17 {
+          deepdive.extraction.extractors.init_dd_delta_q2 {
             sql: """ DROP TABLE IF EXISTS dd_delta_q2 CASCADE;
             CREATE TABLE
             dd_delta_q2(wid INT,
@@ -76,7 +76,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_9 {
+          deepdive.extraction.extractors.init_dd_delta_label2 {
             sql: """ DROP TABLE IF EXISTS dd_delta_label2 CASCADE;
             CREATE TABLE
             dd_delta_label2(wid INT,
@@ -85,7 +85,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_dd_new_features {
             sql: """ DROP TABLE IF EXISTS dd_new_features CASCADE;
             CREATE TABLE
             dd_new_features(id BIGSERIAL,
@@ -96,7 +96,7 @@ q1.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_13 {
+          deepdive.extraction.extractors.init_dd_delta_q1 {
             sql: """ DROP TABLE IF EXISTS dd_delta_q1 CASCADE;
             CREATE TABLE
             dd_delta_q1(wid INT,
@@ -120,7 +120,7 @@ q1.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_11 {
+      deepdive.extraction.extractors.ext_dd_new_label2 {
         sql: """ TRUNCATE dd_new_label2;
         INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
 FROM label2 R0
@@ -135,7 +135,7 @@ FROM dd_delta_label2 R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.ext_dd_new_q1 {
         sql: """ 
         CREATE VIEW dd_new_q1 AS SELECT DISTINCT R0.wid, id, label
           FROM q1 R0
@@ -148,11 +148,11 @@ SELECT DISTINCT R0.wid, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_20" ]
+          dependencies: [ "ext_dd_delta_q1" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_dd_new_label1 {
         sql: """ TRUNCATE dd_new_label1;
         INSERT INTO dd_new_label1 SELECT R0.wid, R0.val
 FROM label1 R0
@@ -167,7 +167,7 @@ FROM dd_delta_label1 R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_21 {
+      deepdive.extraction.extractors.ext_dd_delta_q2 {
         sql: """ 
         INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM dd_delta_label2 R0
@@ -179,7 +179,7 @@ FROM dd_delta_label1 R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_dd_new_features {
         sql: """ TRUNCATE dd_new_features;
         INSERT INTO dd_new_features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
 FROM features R0
@@ -194,7 +194,7 @@ FROM dd_delta_features R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_20 {
+      deepdive.extraction.extractors.ext_dd_delta_q1 {
         sql: """ 
         INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM dd_delta_label1 R0
@@ -206,7 +206,7 @@ FROM dd_delta_features R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
+      deepdive.extraction.extractors.ext_dd_new_q2 {
         sql: """ 
         CREATE VIEW dd_new_q2 AS SELECT DISTINCT R0.wid, id, label
           FROM q2 R0
@@ -219,11 +219,11 @@ SELECT DISTINCT R0.wid, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_21" ]
+          dependencies: [ "ext_dd_delta_q2" ]
       }
     
 
-        deepdive.inference.factors.dd_delta_inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inf_istrue_q1 {
           input_query: """
           SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM dd_new_q1 R0, dd_delta_features R1
@@ -233,7 +233,7 @@ SELECT DISTINCT R0.wid, id, label
         }
       
 
-        deepdive.inference.factors.dd_delta_inference_rule_1 {
+        deepdive.inference.factors.dd_delta_inf_istrue_q2 {
           input_query: """
           SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM dd_new_q2 R0, dd_delta_features R1
@@ -243,9 +243,43 @@ SELECT DISTINCT R0.wid, id, label
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_10, extraction_rule_5, extraction_rule_14, extraction_rule_6, extraction_rule_1, extraction_rule_17, extraction_rule_9, extraction_rule_2, extraction_rule_13, extraction_rule_18]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0, dd_delta_inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_21, extraction_rule_7, extraction_rule_20, extraction_rule_19, extraction_rule_3, extraction_rule_11, extraction_rule_15, dd_delta_inference_rule_0, dd_delta_inference_rule_1]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_new_label2
+  init_dd_delta_label1
+  init_dd_new_q1
+  init_dd_new_label1
+  init_dd_delta_features
+  init_dd_delta_q2
+  init_dd_delta_label2
+  init_dd_new_features
+  init_dd_delta_q1
+  init_dd_new_q2
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_dd_delta_q1
+  ext_dd_new_q1
+  ext_dd_new_label1
+  ext_dd_new_features
+  ext_dd_delta_q2
+  ext_dd_new_label2
+  ext_dd_new_q2
+]
+deepdive.pipeline.pipelines.inference: [
+  dd_delta_inf_istrue_q1
+  dd_delta_inf_istrue_q2
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_delta_q1
+  ext_dd_new_q1
+  ext_dd_new_label1
+  ext_dd_new_features
+  ext_dd_delta_q2
+  ext_dd_new_label2
+  ext_dd_new_q2
+  dd_delta_inf_istrue_q1
+  dd_delta_inf_istrue_q2
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index 4f854bb71..fc85eb005 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -18,7 +18,7 @@ q2.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_label1 {
             sql: """ DROP TABLE IF EXISTS label1 CASCADE;
             CREATE TABLE
             label1(wid INT,
@@ -27,7 +27,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_features {
             sql: """ DROP TABLE IF EXISTS features CASCADE;
             CREATE TABLE
             features(id BIGSERIAL,
@@ -38,7 +38,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_label2 {
             sql: """ DROP TABLE IF EXISTS label2 CASCADE;
             CREATE TABLE
             label2(wid INT,
@@ -47,7 +47,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_q1 {
             sql: """ DROP TABLE IF EXISTS q1 CASCADE;
             CREATE TABLE
             q1(wid INT,
@@ -57,7 +57,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_q2 {
             sql: """ DROP TABLE IF EXISTS q2 CASCADE;
             CREATE TABLE
             q2(wid INT,
@@ -78,7 +78,7 @@ q2.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_5 {
+      deepdive.extraction.extractors.ext_q1 {
         sql: """ 
         INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label1 R0
@@ -90,7 +90,7 @@ q2.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_6 {
+      deepdive.extraction.extractors.ext_q2 {
         sql: """ 
         INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label2 R0
@@ -102,7 +102,7 @@ q2.label: Boolean
       }
     
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_q1 {
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
@@ -112,7 +112,7 @@ q2.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.inf_istrue_q2 {
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
@@ -122,8 +122,25 @@ q2.label: Boolean
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.initdb: [
+  init_label1
+  init_features
+  init_label2
+  init_q1
+  init_q2
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_q1
+  ext_q2
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_q1
+  inf_istrue_q2
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_q1
+  ext_q2
+  inf_istrue_q1
+  inf_istrue_q2
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
index 35e714156..eb3431649 100644
--- a/test/expected-output-test/ocr_example/compile-merge.expected
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -17,7 +17,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_2 {
+      deepdive.extraction.extractors.ext_label2 {
         sql: """ TRUNCATE label2;
         INSERT INTO label2 SELECT R0.wid, R0.val
 FROM dd_new_label2 R0
@@ -28,7 +28,7 @@ FROM dd_new_label2 R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_1 {
+      deepdive.extraction.extractors.ext_label1 {
         sql: """ TRUNCATE label1;
         INSERT INTO label1 SELECT R0.wid, R0.val
 FROM dd_new_label1 R0
@@ -39,7 +39,7 @@ FROM dd_new_label1 R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_0 {
+      deepdive.extraction.extractors.ext_features {
         sql: """ TRUNCATE features;
         INSERT INTO features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
 FROM dd_new_features R0
@@ -50,5 +50,13 @@ FROM dd_new_features R0
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_1, extraction_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_2, extraction_rule_1, extraction_rule_0]
+deepdive.pipeline.pipelines.extraction: [
+  ext_label2
+  ext_label1
+  ext_features
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_label2
+  ext_label1
+  ext_features
+]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 109a00cf7..c3b48771a 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -18,7 +18,7 @@ q2.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_label1 {
             sql: """ DROP TABLE IF EXISTS label1 CASCADE;
             CREATE TABLE
             label1(wid INT,
@@ -27,7 +27,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_features {
             sql: """ DROP TABLE IF EXISTS features CASCADE;
             CREATE TABLE
             features(id BIGSERIAL,
@@ -38,7 +38,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_label2 {
             sql: """ DROP TABLE IF EXISTS label2 CASCADE;
             CREATE TABLE
             label2(wid INT,
@@ -47,7 +47,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_q1 {
             sql: """ DROP TABLE IF EXISTS q1 CASCADE;
             CREATE TABLE
             q1(wid INT,
@@ -57,7 +57,7 @@ q2.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_q2 {
             sql: """ DROP TABLE IF EXISTS q2 CASCADE;
             CREATE TABLE
             q2(wid INT,
@@ -78,7 +78,7 @@ q2.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_5 {
+      deepdive.extraction.extractors.ext_q1 {
         sql: """ 
         INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label1 R0
@@ -90,7 +90,7 @@ q2.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_6 {
+      deepdive.extraction.extractors.ext_q2 {
         sql: """ 
         INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label2 R0
@@ -102,7 +102,7 @@ q2.label: Boolean
       }
     
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_q1 {
           input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
@@ -112,7 +112,7 @@ q2.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.inf_istrue_q2 {
           input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
@@ -122,8 +122,27 @@ q2.label: Boolean
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_0, extraction_rule_2, extraction_rule_3, extraction_rule_4]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_5, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_5, extraction_rule_6, inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_label1
+  init_features
+  init_label2
+  init_q1
+  init_q2
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_q1
+  ext_q2
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_q1
+  inf_istrue_q2
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_q1
+  ext_q2
+  inf_istrue_q1
+  inf_istrue_q2
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 145bf5f88..d5879b72d 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -28,7 +28,7 @@ dd_delta_smoke.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_13 {
+          deepdive.extraction.extractors.init_dd_delta_friends {
             sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
             CREATE TABLE
             dd_delta_friends(person_id bigint,
@@ -37,7 +37,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_17 {
+          deepdive.extraction.extractors.init_dd_delta_smoke {
             sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
             CREATE TABLE
             dd_delta_smoke(person_id bigint,
@@ -47,7 +47,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_6 {
+          deepdive.extraction.extractors.init_dd_new_person_has_cancer {
             sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
             CREATE TABLE
             dd_new_person_has_cancer(person_id bigint,
@@ -56,7 +56,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_dd_delta_person {
             sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
             CREATE TABLE
             dd_delta_person(person_id bigint,
@@ -65,7 +65,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_dd_new_person {
             sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
             CREATE TABLE
             dd_new_person(person_id bigint,
@@ -74,7 +74,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_dd_delta_person_has_cancer {
             sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
             CREATE TABLE
             dd_delta_person_has_cancer(person_id bigint,
@@ -83,7 +83,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_21 {
+          deepdive.extraction.extractors.init_dd_delta_cancer {
             sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
             CREATE TABLE
             dd_delta_cancer(person_id bigint,
@@ -93,7 +93,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_9 {
+          deepdive.extraction.extractors.init_dd_delta_person_smokes {
             sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
             CREATE TABLE
             dd_delta_person_smokes(person_id bigint,
@@ -102,7 +102,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_10 {
+          deepdive.extraction.extractors.init_dd_new_person_smokes {
             sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
             CREATE TABLE
             dd_new_person_smokes(person_id bigint,
@@ -111,7 +111,7 @@ dd_delta_smoke.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_14 {
+          deepdive.extraction.extractors.init_dd_new_friends {
             sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
             CREATE TABLE
             dd_new_friends(person_id bigint,
@@ -136,7 +136,7 @@ dd_delta_smoke.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_24 {
+      deepdive.extraction.extractors.ext_dd_delta_smoke {
         sql: """ 
         INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM dd_delta_person_smokes R0
@@ -148,7 +148,7 @@ dd_delta_smoke.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_dd_new_person_has_cancer {
         sql: """ TRUNCATE dd_new_person_has_cancer;
         INSERT INTO dd_new_person_has_cancer SELECT R0.person_id, R0.has_cancer
 FROM person_has_cancer R0
@@ -163,7 +163,7 @@ FROM dd_delta_person_has_cancer R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_dd_new_person {
         sql: """ TRUNCATE dd_new_person;
         INSERT INTO dd_new_person SELECT R0.person_id, R0.name
 FROM person R0
@@ -178,7 +178,7 @@ FROM dd_delta_person R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
+      deepdive.extraction.extractors.ext_dd_new_smoke {
         sql: """ 
         CREATE VIEW dd_new_smoke AS SELECT DISTINCT R0.person_id, id, label
           FROM smoke R0
@@ -191,11 +191,11 @@ SELECT DISTINCT R0.person_id, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_24" ]
+          dependencies: [ "ext_dd_delta_smoke" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_25 {
+      deepdive.extraction.extractors.ext_dd_delta_cancer {
         sql: """ 
         INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM dd_delta_person_has_cancer R0
@@ -207,7 +207,7 @@ SELECT DISTINCT R0.person_id, id, label
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.ext_dd_new_cancer {
         sql: """ 
         CREATE VIEW dd_new_cancer AS SELECT DISTINCT R0.person_id, id, label
           FROM cancer R0
@@ -220,11 +220,11 @@ SELECT DISTINCT R0.person_id, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_cancer" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_11 {
+      deepdive.extraction.extractors.ext_dd_new_person_smokes {
         sql: """ TRUNCATE dd_new_person_smokes;
         INSERT INTO dd_new_person_smokes SELECT R0.person_id, R0.smokes
 FROM person_smokes R0
@@ -239,7 +239,7 @@ FROM dd_delta_person_smokes R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.ext_dd_new_friends {
         sql: """ TRUNCATE dd_new_friends;
         INSERT INTO dd_new_friends SELECT R0.person_id, R0.friend_id
 FROM friends R0
@@ -254,7 +254,7 @@ FROM dd_delta_friends R0
       }
     
 
-        deepdive.inference.factors.dd_delta_inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inf_imply_smoke_cancer {
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_cancer.R1.id" 
           FROM dd_new_smoke R0, dd_new_cancer R1, dd_delta_person_smokes R2
@@ -264,7 +264,7 @@ FROM dd_delta_friends R0
         }
       
 
-        deepdive.inference.factors.dd_delta_inference_rule_1 {
+        deepdive.inference.factors.dd_delta_inf_imply_smoke_smoke {
           input_query: """
           SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
           FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
@@ -274,9 +274,47 @@ FROM dd_delta_friends R0
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_13, extraction_rule_17, extraction_rule_6, extraction_rule_1, extraction_rule_2, extraction_rule_5, extraction_rule_18, extraction_rule_21, extraction_rule_22, extraction_rule_9, extraction_rule_10, extraction_rule_14]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0, dd_delta_inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_23, extraction_rule_11, extraction_rule_24, extraction_rule_15, dd_delta_inference_rule_0, dd_delta_inference_rule_1]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_friends
+  init_dd_delta_smoke
+  init_dd_new_person_has_cancer
+  init_dd_delta_person
+  init_dd_new_person
+  init_dd_delta_person_has_cancer
+  init_dd_new_smoke
+  init_dd_delta_cancer
+  init_dd_new_cancer
+  init_dd_delta_person_smokes
+  init_dd_new_person_smokes
+  init_dd_new_friends
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_dd_delta_cancer
+  ext_dd_delta_smoke
+  ext_dd_new_person_smokes
+  ext_dd_new_person_has_cancer
+  ext_dd_new_cancer
+  ext_dd_new_person
+  ext_dd_new_friends
+  ext_dd_new_smoke
+]
+deepdive.pipeline.pipelines.inference: [
+  dd_delta_inf_imply_smoke_cancer
+  dd_delta_inf_imply_smoke_smoke
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_delta_cancer
+  ext_dd_delta_smoke
+  ext_dd_new_person_smokes
+  ext_dd_new_person_has_cancer
+  ext_dd_new_cancer
+  ext_dd_new_person
+  ext_dd_new_friends
+  ext_dd_new_smoke
+  dd_delta_inf_imply_smoke_cancer
+  dd_delta_inf_imply_smoke_smoke
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index ef0420ddf..b7c32d00e 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -18,7 +18,7 @@ cancer.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_person_smokes {
             sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
             CREATE TABLE
             person_smokes(person_id bigint,
@@ -27,7 +27,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_smoke {
             sql: """ DROP TABLE IF EXISTS smoke CASCADE;
             CREATE TABLE
             smoke(person_id bigint,
@@ -37,7 +37,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_cancer {
             sql: """ DROP TABLE IF EXISTS cancer CASCADE;
             CREATE TABLE
             cancer(person_id bigint,
@@ -47,7 +47,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_friends {
             sql: """ DROP TABLE IF EXISTS friends CASCADE;
             CREATE TABLE
             friends(person_id bigint,
@@ -56,7 +56,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_person_has_cancer {
             sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
             CREATE TABLE
             person_has_cancer(person_id bigint,
@@ -65,7 +65,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_person {
             sql: """ DROP TABLE IF EXISTS person CASCADE;
             CREATE TABLE
             person(person_id bigint,
@@ -86,7 +86,7 @@ cancer.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_cancer {
         sql: """ 
         INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM person_has_cancer R0
@@ -98,7 +98,7 @@ cancer.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_6 {
+      deepdive.extraction.extractors.ext_smoke {
         sql: """ 
         INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM person_smokes R0
@@ -110,7 +110,7 @@ cancer.label: Boolean
       }
     
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_imply_smoke_cancer {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
           FROM smoke R0, cancer R1, person_smokes R2
@@ -120,7 +120,7 @@ cancer.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.inf_imply_smoke_smoke {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
@@ -130,8 +130,26 @@ cancer.label: Boolean
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, inference_rule_0, inference_rule_1]
+deepdive.pipeline.pipelines.initdb: [
+  init_person_smokes
+  init_smoke
+  init_cancer
+  init_friends
+  init_person_has_cancer
+  init_person
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_cancer
+  ext_smoke
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_imply_smoke_cancer
+  inf_imply_smoke_smoke
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_cancer
+  ext_smoke
+  inf_imply_smoke_cancer
+  inf_imply_smoke_smoke
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
index 845c5337d..0a64e447e 100644
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -17,7 +17,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_2 {
+      deepdive.extraction.extractors.ext_person_smokes {
         sql: """ TRUNCATE person_smokes;
         INSERT INTO person_smokes SELECT R0.person_id, R0.smokes
 FROM dd_new_person_smokes R0
@@ -28,7 +28,7 @@ FROM dd_new_person_smokes R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_friends {
         sql: """ TRUNCATE friends;
         INSERT INTO friends SELECT R0.person_id, R0.friend_id
 FROM dd_new_friends R0
@@ -39,7 +39,7 @@ FROM dd_new_friends R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_1 {
+      deepdive.extraction.extractors.ext_person_has_cancer {
         sql: """ TRUNCATE person_has_cancer;
         INSERT INTO person_has_cancer SELECT R0.person_id, R0.has_cancer
 FROM dd_new_person_has_cancer R0
@@ -50,7 +50,7 @@ FROM dd_new_person_has_cancer R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_0 {
+      deepdive.extraction.extractors.ext_person {
         sql: """ TRUNCATE person;
         INSERT INTO person SELECT R0.person_id, R0.name
 FROM dd_new_person R0
@@ -61,5 +61,15 @@ FROM dd_new_person R0
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [extraction_rule_2, extraction_rule_3, extraction_rule_1, extraction_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_2, extraction_rule_3, extraction_rule_1, extraction_rule_0]
+deepdive.pipeline.pipelines.extraction: [
+  ext_person_smokes
+  ext_friends
+  ext_person_has_cancer
+  ext_person
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_person_smokes
+  ext_friends
+  ext_person_has_cancer
+  ext_person
+]
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 5ec2e5abd..ece741288 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -18,7 +18,7 @@ cancer.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_person_smokes {
             sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
             CREATE TABLE
             person_smokes(person_id bigint,
@@ -27,7 +27,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_smoke {
             sql: """ DROP TABLE IF EXISTS smoke CASCADE;
             CREATE TABLE
             smoke(person_id bigint,
@@ -37,7 +37,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_cancer {
             sql: """ DROP TABLE IF EXISTS cancer CASCADE;
             CREATE TABLE
             cancer(person_id bigint,
@@ -47,7 +47,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_friends {
             sql: """ DROP TABLE IF EXISTS friends CASCADE;
             CREATE TABLE
             friends(person_id bigint,
@@ -56,7 +56,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_person_has_cancer {
             sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
             CREATE TABLE
             person_has_cancer(person_id bigint,
@@ -65,7 +65,7 @@ cancer.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_person {
             sql: """ DROP TABLE IF EXISTS person CASCADE;
             CREATE TABLE
             person(person_id bigint,
@@ -86,7 +86,7 @@ cancer.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_cancer {
         sql: """ 
         INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM person_has_cancer R0
@@ -98,7 +98,7 @@ cancer.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_6 {
+      deepdive.extraction.extractors.ext_smoke {
         sql: """ 
         INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM person_smokes R0
@@ -110,7 +110,7 @@ cancer.label: Boolean
       }
     
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_imply_smoke_cancer {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
           FROM smoke R0, cancer R1, person_smokes R2
@@ -120,7 +120,7 @@ cancer.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.inf_imply_smoke_smoke {
           input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
@@ -130,8 +130,28 @@ cancer.label: Boolean
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_2, extraction_rule_4, extraction_rule_5, extraction_rule_3, extraction_rule_1, extraction_rule_0]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_6]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_6, inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_person_smokes
+  init_smoke
+  init_cancer
+  init_friends
+  init_person_has_cancer
+  init_person
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_cancer
+  ext_smoke
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_imply_smoke_cancer
+  inf_imply_smoke_smoke
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_cancer
+  ext_smoke
+  inf_imply_smoke_cancer
+  inf_imply_smoke_smoke
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index aacb14325..dcd168a3d 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -23,7 +23,7 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_dd_delta_articles {
             sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
             CREATE TABLE
             dd_delta_articles(article_id text,
@@ -32,7 +32,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_10 {
+          deepdive.extraction.extractors.init_dd_new_people_mentions {
             sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
             CREATE TABLE
             dd_new_people_mentions(sentence_id text,
@@ -44,7 +44,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_17 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_features(relation_id text,
@@ -53,7 +53,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_dd_new_articles {
             sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
             CREATE TABLE
             dd_new_articles(article_id text,
@@ -62,7 +62,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_14 {
+          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
             CREATE TABLE
             dd_new_has_spouse_candidates(person1_id text,
@@ -75,7 +75,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_18 {
+          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
             CREATE TABLE
             dd_new_has_spouse_features(relation_id text,
@@ -84,7 +84,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_6 {
+          deepdive.extraction.extractors.init_dd_new_sentences {
             sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
             CREATE TABLE
             dd_new_sentences(document_id text,
@@ -100,7 +100,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_9 {
+          deepdive.extraction.extractors.init_dd_delta_people_mentions {
             sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
             CREATE TABLE
             dd_delta_people_mentions(sentence_id text,
@@ -112,7 +112,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_13 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_candidates(person1_id text,
@@ -125,7 +125,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_dd_delta_sentences {
             sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
             CREATE TABLE
             dd_delta_sentences(document_id text,
@@ -141,7 +141,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_21 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
             CREATE TABLE
             dd_delta_has_spouse(relation_id text,
@@ -168,7 +168,7 @@ dd_new_has_spouse.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_11 {
+      deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM people_mentions R0
@@ -179,11 +179,11 @@ FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_dd_new_articles {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
 FROM articles R0
@@ -198,7 +198,7 @@ FROM dd_delta_articles R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM has_spouse_candidates R0
@@ -209,11 +209,11 @@ FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
 FROM has_spouse_features R0
@@ -224,11 +224,11 @@ FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_29" ]
+          dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_dd_new_sentences {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM sentences R0
@@ -243,7 +243,7 @@ FROM dd_delta_sentences R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_30 {
+      deepdive.extraction.extractors.ext_dd_delta_has_spouse {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
@@ -251,11 +251,11 @@ FROM dd_delta_sentences R0
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse {
         sql: """ 
         CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
@@ -268,11 +268,11 @@ SELECT DISTINCT R0.relation_id, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "ext_dd_delta_has_spouse" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_25 {
+        deepdive.extraction.extractors.ext_dd_delta_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM dd_delta_sentences R0
         
@@ -285,7 +285,7 @@ FROM dd_delta_sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_27 {
+        deepdive.extraction.extractors.ext_dd_delta_has_spouse_candidates_by_ext_has_spouse {
           input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -297,12 +297,12 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_25" ,  "extraction_rule_11" ]
+          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_29 {
+        deepdive.extraction.extractors.ext_dd_delta_has_spouse_features_by_ext_has_spouse_features {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -322,12 +322,12 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.dd_delta_inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -340,9 +340,49 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15, dd_delta_inference_rule_0]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_articles
+  init_dd_new_people_mentions
+  init_dd_delta_has_spouse_features
+  init_dd_new_articles
+  init_dd_new_has_spouse_candidates
+  init_dd_new_has_spouse_features
+  init_dd_new_sentences
+  init_dd_delta_people_mentions
+  init_dd_delta_has_spouse_candidates
+  init_dd_delta_sentences
+  init_dd_delta_has_spouse
+  init_dd_new_has_spouse
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_dd_new_has_spouse_candidates
+  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
+  ext_dd_new_has_spouse
+  ext_dd_delta_has_spouse
+  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
+  ext_dd_new_has_spouse_features
+  ext_dd_delta_people_mentions_by_ext_people
+  ext_dd_new_people_mentions
+  ext_dd_new_sentences
+  ext_dd_new_articles
+]
+deepdive.pipeline.pipelines.inference: [
+  dd_delta_inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_new_has_spouse_candidates
+  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
+  ext_dd_new_has_spouse
+  ext_dd_delta_has_spouse
+  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
+  ext_dd_new_has_spouse_features
+  ext_dd_delta_people_mentions_by_ext_people
+  ext_dd_new_people_mentions
+  ext_dd_new_sentences
+  ext_dd_new_articles
+  dd_delta_inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index f8dbfa5d4..ac5dd299d 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -17,7 +17,7 @@
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_sentences {
             sql: """ DROP TABLE IF EXISTS sentences CASCADE;
             CREATE TABLE
             sentences(document_id text,
@@ -33,7 +33,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
             CREATE TABLE
             has_spouse_candidates(person1_id text,
@@ -46,7 +46,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_has_spouse {
             sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
             CREATE TABLE
             has_spouse(relation_id text,
@@ -56,7 +56,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_articles {
             sql: """ DROP TABLE IF EXISTS articles CASCADE;
             CREATE TABLE
             articles(article_id text,
@@ -65,7 +65,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
             CREATE TABLE
             has_spouse_features(relation_id text,
@@ -74,7 +74,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_people_mentions {
             sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
             CREATE TABLE
             people_mentions(sentence_id text,
@@ -98,7 +98,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_12 {
+      deepdive.extraction.extractors.ext_has_spouse {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
@@ -106,11 +106,11 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ]
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_7 {
+        deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
         
@@ -123,7 +123,7 @@ FROM sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_9 {
+        deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
           input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -131,12 +131,12 @@ FROM people_mentions R0, people_mentions R1
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_7" ]
+          dependencies: [ "ext_people_mentions_by_ext_people" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_11 {
+        deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -144,12 +144,12 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_9" ,  "extraction_rule_7" ]
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -159,8 +159,28 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11]
-deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11, inference_rule_0]
+deepdive.pipeline.pipelines.initdb: [
+  init_sentences
+  init_has_spouse_candidates
+  init_has_spouse
+  init_articles
+  init_has_spouse_features
+  init_people_mentions
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_has_spouse
+  ext_people_mentions_by_ext_people
+  ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_has_spouse
+  ext_people_mentions_by_ext_people
+  ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  inf_istrue_has_spouse
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index 44c7e62a3..45b0833e5 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -17,7 +17,7 @@
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_1 {
+      deepdive.extraction.extractors.ext_sentences {
         sql: """ TRUNCATE sentences;
         INSERT INTO sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM dd_new_sentences R0
@@ -28,7 +28,7 @@ FROM dd_new_sentences R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_has_spouse_candidates {
         sql: """ TRUNCATE has_spouse_candidates;
         INSERT INTO has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM dd_new_has_spouse_candidates R0
@@ -39,7 +39,7 @@ FROM dd_new_has_spouse_candidates R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_0 {
+      deepdive.extraction.extractors.ext_articles {
         sql: """ TRUNCATE articles;
         INSERT INTO articles SELECT R0.article_id, R0.text
 FROM dd_new_articles R0
@@ -50,7 +50,7 @@ FROM dd_new_articles R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_4 {
+      deepdive.extraction.extractors.ext_has_spouse_features {
         sql: """ TRUNCATE has_spouse_features;
         INSERT INTO has_spouse_features SELECT R0.relation_id, R0.feature
 FROM dd_new_has_spouse_features R0
@@ -61,7 +61,7 @@ FROM dd_new_has_spouse_features R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_2 {
+      deepdive.extraction.extractors.ext_people_mentions {
         sql: """ TRUNCATE people_mentions;
         INSERT INTO people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_new_people_mentions R0
@@ -72,5 +72,17 @@ FROM dd_new_people_mentions R0
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [extraction_rule_0, extraction_rule_3, extraction_rule_4, extraction_rule_2, extraction_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_0, extraction_rule_3, extraction_rule_4, extraction_rule_2, extraction_rule_1]
+deepdive.pipeline.pipelines.extraction: [
+  ext_sentences
+  ext_people_mentions
+  ext_has_spouse_candidates
+  ext_has_spouse_features
+  ext_articles
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_sentences
+  ext_people_mentions
+  ext_has_spouse_candidates
+  ext_has_spouse_features
+  ext_articles
+]
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index a25bf1449..75a430560 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -17,7 +17,7 @@
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_sentences {
             sql: """ DROP TABLE IF EXISTS sentences CASCADE;
             CREATE TABLE
             sentences(document_id text,
@@ -33,7 +33,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
             CREATE TABLE
             has_spouse_candidates(person1_id text,
@@ -46,7 +46,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_has_spouse {
             sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
             CREATE TABLE
             has_spouse(relation_id text,
@@ -56,7 +56,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_articles {
             sql: """ DROP TABLE IF EXISTS articles CASCADE;
             CREATE TABLE
             articles(article_id text,
@@ -65,7 +65,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
             CREATE TABLE
             has_spouse_features(relation_id text,
@@ -74,7 +74,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_people_mentions {
             sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
             CREATE TABLE
             people_mentions(sentence_id text,
@@ -98,7 +98,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_12 {
+      deepdive.extraction.extractors.ext_has_spouse {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
@@ -106,11 +106,11 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ]
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_7 {
+        deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
         
@@ -123,7 +123,7 @@ FROM sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_9 {
+        deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
           input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -131,12 +131,12 @@ FROM people_mentions R0, people_mentions R1
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_7" ]
+          dependencies: [ "ext_people_mentions_by_ext_people" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_11 {
+        deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -144,12 +144,12 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_9" ,  "extraction_rule_7" ]
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -159,8 +159,30 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11]
-deepdive.pipeline.pipelines.inference: [inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11, inference_rule_0]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_sentences
+  init_has_spouse_candidates
+  init_has_spouse
+  init_articles
+  init_has_spouse_features
+  init_people_mentions
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_has_spouse
+  ext_people_mentions_by_ext_people
+  ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_has_spouse
+  ext_people_mentions_by_ext_people
+  ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index f59284397..9078fa5b0 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -23,7 +23,7 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_dd_delta_articles {
             sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
             CREATE TABLE
             dd_delta_articles(article_id text,
@@ -32,7 +32,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_10 {
+          deepdive.extraction.extractors.init_dd_new_people_mentions {
             sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
             CREATE TABLE
             dd_new_people_mentions(sentence_id text,
@@ -44,7 +44,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_17 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_features(relation_id text,
@@ -53,7 +53,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_dd_new_articles {
             sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
             CREATE TABLE
             dd_new_articles(article_id text,
@@ -62,7 +62,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_14 {
+          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
             CREATE TABLE
             dd_new_has_spouse_candidates(person1_id text,
@@ -75,7 +75,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_18 {
+          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
             CREATE TABLE
             dd_new_has_spouse_features(relation_id text,
@@ -84,7 +84,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_6 {
+          deepdive.extraction.extractors.init_dd_new_sentences {
             sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
             CREATE TABLE
             dd_new_sentences(document_id text,
@@ -100,7 +100,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_9 {
+          deepdive.extraction.extractors.init_dd_delta_people_mentions {
             sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
             CREATE TABLE
             dd_delta_people_mentions(sentence_id text,
@@ -112,7 +112,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_13 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_candidates(person1_id text,
@@ -125,7 +125,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_dd_delta_sentences {
             sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
             CREATE TABLE
             dd_delta_sentences(document_id text,
@@ -141,7 +141,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_21 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
             CREATE TABLE
             dd_delta_has_spouse(relation_id text,
@@ -168,7 +168,7 @@ dd_new_has_spouse.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_11 {
+      deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM people_mentions R0
@@ -179,11 +179,11 @@ FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_dd_new_articles {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
 FROM articles R0
@@ -198,7 +198,7 @@ FROM dd_delta_articles R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM has_spouse_candidates R0
@@ -209,11 +209,11 @@ FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
 FROM has_spouse_features R0
@@ -224,11 +224,11 @@ FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_29" ]
+          dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_dd_new_sentences {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM sentences R0
@@ -243,7 +243,7 @@ FROM dd_delta_sentences R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_30 {
+      deepdive.extraction.extractors.ext_dd_delta_has_spouse {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
@@ -251,11 +251,11 @@ FROM dd_delta_sentences R0
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse {
         sql: """ 
         CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
@@ -268,11 +268,11 @@ SELECT DISTINCT R0.relation_id, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "ext_dd_delta_has_spouse" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_25 {
+        deepdive.extraction.extractors.ext_dd_delta_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM dd_delta_sentences R0
         
@@ -285,7 +285,7 @@ FROM dd_delta_sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_27 {
+        deepdive.extraction.extractors.ext_dd_delta_has_spouse_candidates_by_ext_has_spouse {
           input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -297,12 +297,12 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_25" ,  "extraction_rule_11" ]
+          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_29 {
+        deepdive.extraction.extractors.ext_dd_delta_has_spouse_features_by_ext_has_spouse_features {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -326,12 +326,12 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.dd_delta_inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -344,9 +344,49 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15, dd_delta_inference_rule_0]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_articles
+  init_dd_new_people_mentions
+  init_dd_delta_has_spouse_features
+  init_dd_new_articles
+  init_dd_new_has_spouse_candidates
+  init_dd_new_has_spouse_features
+  init_dd_new_sentences
+  init_dd_delta_people_mentions
+  init_dd_delta_has_spouse_candidates
+  init_dd_delta_sentences
+  init_dd_delta_has_spouse
+  init_dd_new_has_spouse
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_dd_new_has_spouse_candidates
+  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
+  ext_dd_new_has_spouse
+  ext_dd_delta_has_spouse
+  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
+  ext_dd_new_has_spouse_features
+  ext_dd_delta_people_mentions_by_ext_people
+  ext_dd_new_people_mentions
+  ext_dd_new_sentences
+  ext_dd_new_articles
+]
+deepdive.pipeline.pipelines.inference: [
+  dd_delta_inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_new_has_spouse_candidates
+  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
+  ext_dd_new_has_spouse
+  ext_dd_delta_has_spouse
+  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
+  ext_dd_new_has_spouse_features
+  ext_dd_delta_people_mentions_by_ext_people
+  ext_dd_new_people_mentions
+  ext_dd_new_sentences
+  ext_dd_new_articles
+  dd_delta_inf_istrue_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 48f85f880..0ab525f43 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -23,7 +23,7 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_dd_delta_articles {
             sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
             CREATE TABLE
             dd_delta_articles(article_id text,
@@ -32,7 +32,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_10 {
+          deepdive.extraction.extractors.init_dd_new_people_mentions {
             sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
             CREATE TABLE
             dd_new_people_mentions(sentence_id text,
@@ -44,7 +44,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_17 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_features(relation_id text,
@@ -53,7 +53,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_dd_new_articles {
             sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
             CREATE TABLE
             dd_new_articles(article_id text,
@@ -62,7 +62,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_14 {
+          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
             CREATE TABLE
             dd_new_has_spouse_candidates(person1_id text,
@@ -75,7 +75,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_18 {
+          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
             CREATE TABLE
             dd_new_has_spouse_features(relation_id text,
@@ -84,7 +84,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_6 {
+          deepdive.extraction.extractors.init_dd_new_sentences {
             sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
             CREATE TABLE
             dd_new_sentences(document_id text,
@@ -100,7 +100,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_9 {
+          deepdive.extraction.extractors.init_dd_delta_people_mentions {
             sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
             CREATE TABLE
             dd_delta_people_mentions(sentence_id text,
@@ -112,7 +112,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_13 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
             CREATE TABLE
             dd_delta_has_spouse_candidates(person1_id text,
@@ -125,7 +125,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_dd_delta_sentences {
             sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
             CREATE TABLE
             dd_delta_sentences(document_id text,
@@ -141,7 +141,7 @@ dd_new_has_spouse.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_21 {
+          deepdive.extraction.extractors.init_dd_delta_has_spouse {
             sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
             CREATE TABLE
             dd_delta_has_spouse(relation_id text,
@@ -168,7 +168,7 @@ dd_new_has_spouse.label: Boolean
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_11 {
+      deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM people_mentions R0
@@ -179,11 +179,11 @@ FROM dd_delta_people_mentions R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_3 {
+      deepdive.extraction.extractors.ext_dd_new_articles {
         sql: """ TRUNCATE dd_new_articles;
         INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
 FROM articles R0
@@ -198,7 +198,7 @@ FROM dd_delta_articles R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_15 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
         sql: """ TRUNCATE dd_new_has_spouse_candidates;
         INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM has_spouse_candidates R0
@@ -209,11 +209,11 @@ FROM dd_delta_has_spouse_candidates R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_19 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
         sql: """ TRUNCATE dd_new_has_spouse_features;
         INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
 FROM has_spouse_features R0
@@ -224,11 +224,11 @@ FROM dd_delta_has_spouse_features R0
         
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_29" ]
+          dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_7 {
+      deepdive.extraction.extractors.ext_dd_new_sentences {
         sql: """ TRUNCATE dd_new_sentences;
         INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM sentences R0
@@ -243,7 +243,7 @@ FROM dd_delta_sentences R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_30 {
+      deepdive.extraction.extractors.ext_dd_delta_has_spouse {
         sql: """ 
         INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
@@ -251,11 +251,11 @@ FROM dd_delta_sentences R0
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_27" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_23 {
+      deepdive.extraction.extractors.ext_dd_new_has_spouse {
         sql: """ 
         CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
@@ -268,11 +268,11 @@ SELECT DISTINCT R0.relation_id, id, label
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_30" ]
+          dependencies: [ "ext_dd_delta_has_spouse" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_25 {
+        deepdive.extraction.extractors.ext_dd_delta_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM dd_delta_sentences R0
         
@@ -285,7 +285,7 @@ FROM dd_delta_sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_27 {
+        deepdive.extraction.extractors.ext_dd_delta_has_spouse_candidates_by_ext_has_spouse {
           input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM dd_delta_people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -297,12 +297,12 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           output_relation: "dd_delta_has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_25" ,  "extraction_rule_11" ]
+          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_29 {
+        deepdive.extraction.extractors.ext_dd_delta_has_spouse_features_by_ext_has_spouse_features {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -322,12 +322,12 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           output_relation: "dd_delta_has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_15" ,  "extraction_rule_27" ,  "extraction_rule_7" ,  "extraction_rule_11" ,  "extraction_rule_25" ]
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.dd_delta_inference_rule_0 {
+        deepdive.inference.factors.dd_delta_inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
@@ -340,7 +340,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 
-        deepdive.inference.factors.dd_delta_inference_rule_1 {
+        deepdive.inference.factors.dd_delta_inf_equal_has_spouse_has_spouse {
           input_query: """
           SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
           FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
@@ -350,9 +350,51 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_10, extraction_rule_17, extraction_rule_2, extraction_rule_14, extraction_rule_18, extraction_rule_6, extraction_rule_9, extraction_rule_13, extraction_rule_5, extraction_rule_21, extraction_rule_22]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15]
-deepdive.pipeline.pipelines.inference: [dd_delta_inference_rule_0, dd_delta_inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_7, extraction_rule_25, extraction_rule_19, extraction_rule_3, extraction_rule_30, extraction_rule_23, extraction_rule_27, extraction_rule_11, extraction_rule_29, extraction_rule_15, dd_delta_inference_rule_0, dd_delta_inference_rule_1]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_articles
+  init_dd_new_people_mentions
+  init_dd_delta_has_spouse_features
+  init_dd_new_articles
+  init_dd_new_has_spouse_candidates
+  init_dd_new_has_spouse_features
+  init_dd_new_sentences
+  init_dd_delta_people_mentions
+  init_dd_delta_has_spouse_candidates
+  init_dd_delta_sentences
+  init_dd_delta_has_spouse
+  init_dd_new_has_spouse
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_dd_new_has_spouse_candidates
+  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
+  ext_dd_new_has_spouse
+  ext_dd_delta_has_spouse
+  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
+  ext_dd_new_has_spouse_features
+  ext_dd_delta_people_mentions_by_ext_people
+  ext_dd_new_people_mentions
+  ext_dd_new_sentences
+  ext_dd_new_articles
+]
+deepdive.pipeline.pipelines.inference: [
+  dd_delta_inf_istrue_has_spouse
+  dd_delta_inf_equal_has_spouse_has_spouse
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_new_has_spouse_candidates
+  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
+  ext_dd_new_has_spouse
+  ext_dd_delta_has_spouse
+  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
+  ext_dd_new_has_spouse_features
+  ext_dd_delta_people_mentions_by_ext_people
+  ext_dd_new_people_mentions
+  ext_dd_new_sentences
+  ext_dd_new_articles
+  dd_delta_inf_istrue_has_spouse
+  dd_delta_inf_equal_has_spouse_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 3c02726fc..d35b165b4 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -17,7 +17,7 @@
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_sentences {
             sql: """ DROP TABLE IF EXISTS sentences CASCADE;
             CREATE TABLE
             sentences(document_id text,
@@ -33,7 +33,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_has_spouse_candidates {
             sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
             CREATE TABLE
             has_spouse_candidates(person1_id text,
@@ -46,7 +46,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_has_spouse {
             sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
             CREATE TABLE
             has_spouse(relation_id text,
@@ -56,7 +56,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_articles {
             sql: """ DROP TABLE IF EXISTS articles CASCADE;
             CREATE TABLE
             articles(article_id text,
@@ -65,7 +65,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_has_spouse_features {
             sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
             CREATE TABLE
             has_spouse_features(relation_id text,
@@ -74,7 +74,7 @@
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_people_mentions {
             sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
             CREATE TABLE
             people_mentions(sentence_id text,
@@ -98,7 +98,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_12 {
+      deepdive.extraction.extractors.ext_has_spouse {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
@@ -106,11 +106,11 @@
           
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_9" ]
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
       }
     
 
-        deepdive.extraction.extractors.extraction_rule_7 {
+        deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
         
@@ -123,7 +123,7 @@ FROM sentences R0
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_9 {
+        deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
           input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
         WHERE R1.sentence_id = R0.sentence_id 
@@ -131,12 +131,12 @@ FROM people_mentions R0, people_mentions R1
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_7" ]
+          dependencies: [ "ext_people_mentions_by_ext_people" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.extraction.extractors.extraction_rule_11 {
+        deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
           input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
         WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
@@ -144,12 +144,12 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "extraction_rule_9" ,  "extraction_rule_7" ]
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
           parallelism: ${PARALLELISM}
         }
       
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
@@ -159,7 +159,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.inf_equal_has_spouse_has_spouse {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
@@ -169,8 +169,32 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_1, extraction_rule_3, extraction_rule_5, extraction_rule_0, extraction_rule_4, extraction_rule_2]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_12, extraction_rule_7, extraction_rule_9, extraction_rule_11, inference_rule_0, inference_rule_1]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_sentences
+  init_has_spouse_candidates
+  init_has_spouse
+  init_articles
+  init_has_spouse_features
+  init_people_mentions
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_has_spouse
+  ext_people_mentions_by_ext_people
+  ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_has_spouse
+  inf_equal_has_spouse_has_spouse
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_has_spouse
+  ext_people_mentions_by_ext_people
+  ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  inf_istrue_has_spouse
+  inf_equal_has_spouse_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 11e1625b7..816504966 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -17,7 +17,7 @@
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_R {
             sql: """ DROP TABLE IF EXISTS R CASCADE;
             CREATE TABLE
             R(a int,
@@ -33,7 +33,7 @@
           style: "sql_extractor"
         }
 
-      deepdive.extraction.extractors.extraction_rule_1 {
+      deepdive.extraction.extractors.ext_A {
         sql: """ DROP VIEW IF EXISTS A;
         CREATE VIEW A AS SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
 FROM R R0
@@ -44,18 +44,28 @@ FROM R R0
       }
     
 
-      deepdive.extraction.extractors.extraction_rule_2 {
+      deepdive.extraction.extractors.ext_B {
         sql: """ DROP VIEW IF EXISTS B;
         CREATE VIEW B AS SELECT R0.column_0 AS column_0, R1.b AS column_1
 FROM A R0, R R1
         WHERE R1.a = R0.column_1 
         """
         style: "sql_extractor"
-          dependencies: [ "extraction_rule_1" ]
+          dependencies: [ "ext_A" ]
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_0]
-deepdive.pipeline.pipelines.extraction: [extraction_rule_1, extraction_rule_2]
-deepdive.pipeline.pipelines.endtoend: [extraction_rule_1, extraction_rule_2]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
\ No newline at end of file
+deepdive.pipeline.pipelines.initdb: [
+  init_R
+]
+deepdive.pipeline.pipelines.extraction: [
+  ext_A
+  ext_B
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_A
+  ext_B
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index fb8f623a2..db8336991 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -21,7 +21,7 @@ c.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.extraction_rule_3 {
+          deepdive.extraction.extractors.init_e {
             sql: """ DROP TABLE IF EXISTS e CASCADE;
             CREATE TABLE
             e(k int,
@@ -31,7 +31,7 @@ c.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_4 {
+          deepdive.extraction.extractors.init_f {
             sql: """ DROP TABLE IF EXISTS f CASCADE;
             CREATE TABLE
             f(k int,
@@ -41,7 +41,7 @@ c.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_0 {
+          deepdive.extraction.extractors.init_a {
             sql: """ DROP TABLE IF EXISTS a CASCADE;
             CREATE TABLE
             a(k int,
@@ -51,7 +51,7 @@ c.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_5 {
+          deepdive.extraction.extractors.init_b {
             sql: """ DROP TABLE IF EXISTS b CASCADE;
             CREATE TABLE
             b(k int,
@@ -61,7 +61,7 @@ c.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_1 {
+          deepdive.extraction.extractors.init_c {
             sql: """ DROP TABLE IF EXISTS c CASCADE;
             CREATE TABLE
             c(k int,
@@ -71,7 +71,7 @@ c.label: Boolean
             style: "sql_extractor"
           }
 
-          deepdive.extraction.extractors.extraction_rule_2 {
+          deepdive.extraction.extractors.init_d {
             sql: """ DROP TABLE IF EXISTS d CASCADE;
             CREATE TABLE
             d(k int,
@@ -93,7 +93,7 @@ c.label: Boolean
           style: "sql_extractor"
         }
 
-        deepdive.inference.factors.inference_rule_0 {
+        deepdive.inference.factors.inf_istrue_a {
           input_query: """
           SELECT R0.id AS "a.R0.id" , (R0.k + R1.p) AS "dd_weight_column_0" 
           FROM a R0, b R1
@@ -103,7 +103,7 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_1 {
+        deepdive.inference.factors.inf_istrue_c {
           input_query: """
           SELECT R0.id AS "c.R0.id" 
           FROM c R0, b R1
@@ -113,7 +113,7 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_2 {
+        deepdive.inference.factors.inf_istrue_d {
           input_query: """
           SELECT R0.id AS "d.R0.id" , R0.k AS "dd_weight_column_0" , R1.p AS "dd_weight_column_1" 
           FROM d R0, b R1
@@ -123,7 +123,7 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_3 {
+        deepdive.inference.factors.inf_istrue_e {
           input_query: """
           SELECT R0.id AS "e.R0.id" 
           FROM e R0, b R1
@@ -133,7 +133,7 @@ c.label: Boolean
         }
       
 
-        deepdive.inference.factors.inference_rule_4 {
+        deepdive.inference.factors.inf_istrue_f {
           input_query: """
           SELECT R0.id AS "f.R0.id" 
           FROM f R0, b R1
@@ -143,7 +143,28 @@ c.label: Boolean
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [extraction_rule_3, extraction_rule_4, extraction_rule_0, extraction_rule_5, extraction_rule_1, extraction_rule_2]
-deepdive.pipeline.pipelines.inference: [inference_rule_0, inference_rule_1, inference_rule_2, inference_rule_3, inference_rule_4]
-deepdive.pipeline.pipelines.endtoend: [inference_rule_0, inference_rule_1, inference_rule_2, inference_rule_3, inference_rule_4]
-deepdive.pipeline.pipelines.cleanup: [cleanup]
+deepdive.pipeline.pipelines.initdb: [
+  init_e
+  init_f
+  init_a
+  init_b
+  init_c
+  init_d
+]
+deepdive.pipeline.pipelines.inference: [
+  inf_istrue_a
+  inf_istrue_c
+  inf_istrue_d
+  inf_istrue_e
+  inf_istrue_f
+]
+deepdive.pipeline.pipelines.endtoend: [
+  inf_istrue_a
+  inf_istrue_c
+  inf_istrue_d
+  inf_istrue_e
+  inf_istrue_f
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/weights/print.expected b/test/expected-output-test/weights/print.expected
index 8b79c10ff..cb35dea74 100644
--- a/test/expected-output-test/weights/print.expected
+++ b/test/expected-output-test/weights/print.expected
@@ -13,22 +13,22 @@ b(k int,
   q text).
 
 @weight((x + y))
-a(x)  :-
+a(x) :-
     b(x, y, _).
 
 @weight("string")
-c(x)  :-
+c(x) :-
     b(x, y, _).
 
 @weight(x, y)
-d(x)  :-
+d(x) :-
     b(x, y, _).
 
 @weight(-10)
-e(x)  :-
+e(x) :-
     b(x, y, _).
 
 @weight(-0.3)
-f(x)  :-
+f(x) :-
     b(x, y, _).
 

From 384488ceb6a5c3ac8bd5a9a96c8c5861be366ffa Mon Sep 17 00:00:00 2001
From: Xiao Ling <bardminz@gmail.com>
Date: Mon, 26 Oct 2015 18:10:22 +0000
Subject: [PATCH 237/347] adds the input_batch_size parameter

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 2477ae92c..86be9f981 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -641,6 +641,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
           ${ss.generateDependenciesOfCompiledBlockFor(List(stmt))}
+          input_batch_size: $${INPUT_BATCH_SIZE}
           parallelism: ${parallelism}
         }
       """

From 9df3e2666ccbd0b5c9b3ab7d9cf1bffe85caa319 Mon Sep 17 00:00:00 2001
From: Xiao Ling <bardminz@gmail.com>
Date: Mon, 26 Oct 2015 18:17:27 +0000
Subject: [PATCH 238/347] bug fix: changed the order of comparator keywords so
 that IS NOT can be correctly recognized.

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 020ea1945..5efcc73ac 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -206,7 +206,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     )
 
   // conditional expressions
-  def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" | "IS NOT"
+  def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS NOT" | "IS"
 
   def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>

From 117670ab6908a012619daa02f4228e4dd008e50c Mon Sep 17 00:00:00 2001
From: Xiao Ling <bardminz@gmail.com>
Date: Mon, 26 Oct 2015 21:45:16 +0000
Subject: [PATCH 239/347] adds input_batch_size to the expected test outputs

---
 .../expected-output-test/chunking_example/compile.expected | 4 +++-
 .../compile-incremental.expected                           | 7 +++++++
 .../multiple_rules_for_same_head/compile.expected          | 7 +++++++
 .../spouse_example/compile-incremental.expected            | 3 +++
 .../spouse_example/compile-materialization.expected        | 3 +++
 test/expected-output-test/spouse_example/compile.expected  | 3 +++
 .../compile-incremental.expected                           | 3 +++
 .../compile-incremental.expected                           | 3 +++
 .../spouse_example_new_inference/compile.expected          | 3 +++
 9 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 8b4298920..061606227 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -89,7 +89,8 @@ FROM words_raw R0
           output_relation: "words"
           udf: ${APP_HOME}"/udf/ext_training.py"
           style: "tsv_extractor" 
-          
+         
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -103,6 +104,7 @@ FROM words R0, words R1
           udf: ${APP_HOME}"/udf/ext_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_words_by_ext_training" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index 5aee66846..60bc1c1fc 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -198,6 +198,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -211,6 +212,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -224,6 +226,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -237,6 +240,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -250,6 +254,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -263,6 +268,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -276,6 +282,7 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 8e889f377..cbc508528 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -90,6 +90,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -103,6 +104,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -116,6 +118,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -129,6 +132,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -142,6 +146,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -155,6 +160,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -168,6 +174,7 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index dcd168a3d..a7a89dbd9 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -281,6 +281,7 @@ FROM dd_delta_sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -298,6 +299,7 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -323,6 +325,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index ac5dd299d..6c85b1ee2 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -119,6 +119,7 @@ FROM sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -132,6 +133,7 @@ FROM people_mentions R0, people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_people_mentions_by_ext_people" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -145,6 +147,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 75a430560..19a359c2a 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -119,6 +119,7 @@ FROM sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -132,6 +133,7 @@ FROM people_mentions R0, people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_people_mentions_by_ext_people" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -145,6 +147,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 9078fa5b0..f56797ecd 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -281,6 +281,7 @@ FROM dd_delta_sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -298,6 +299,7 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
@@ -327,6 +329,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
+          input_batch_size: ${INPUT_BATCH_SIZE} 
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 0ab525f43..bf5a4ccab 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -281,6 +281,7 @@ FROM dd_delta_sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -298,6 +299,7 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -323,6 +325,7 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index d35b165b4..53fe8218a 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -119,6 +119,7 @@ FROM sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -132,6 +133,7 @@ FROM people_mentions R0, people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_people_mentions_by_ext_people" ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -145,6 +147,7 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       

From fb2f3377eacbbf74d2f3b62884e3c663f6dd7da5 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 10 Nov 2015 04:59:10 -0800
Subject: [PATCH 240/347] Adds dependencies to inference.factors and
 output_relation for sql_extractors

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 86be9f981..42218c407 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -254,6 +254,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         f -> collectUsedRelations(f.q.bodies) }
       case e : ExtractionRule   => dependencies += {
         e -> collectUsedRelations(e.q.bodies) }
+      case e : InferenceRule    => dependencies += {
+        e -> collectUsedRelations(e.q.bodies) }
       case _ =>
     }
   }
@@ -610,6 +612,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         sql: \"\"\" ${sqlCmdForCleanUp}
         ${sqlCmdForInsert} ${stmts(0).headName}${useAS} ${inputQueries.mkString("\nUNION ALL\n")}
         \"\"\"
+          output_relation: \"${stmts(0).headName}\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
       }
@@ -740,6 +743,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           input_query: \"\"\"${inputQueries.mkString(" UNION ALL ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
+          ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
         }
       """
     }

From f98757369546b9cab15ca0de8300ff3286fc5c66 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 10 Nov 2015 04:59:24 -0800
Subject: [PATCH 241/347] Adds input_relations field to extractors and factors

while removing the init_* extractors and initdb,cleanup pipelines
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  33 ++-
 .../chunking_example/compile.expected         |  82 ++-----
 .../expressions/compile.expected              | 151 ++++++++----
 .../compile-incremental.expected              | 177 +++++++-------
 .../compile.expected                          | 115 +++++----
 .../ocr_example/compile-incremental.expected  | 150 ++++--------
 .../compile-materialization.expected          |  85 ++-----
 .../ocr_example/compile-merge.expected        |  12 +
 .../ocr_example/compile.expected              |  88 ++-----
 .../compile-incremental.expected              | 174 ++++---------
 .../compile-materialization.expected          |  95 ++------
 .../smoke_example/compile-merge.expected      |  16 ++
 .../smoke_example/compile.expected            |  98 ++------
 .../compile-incremental.expected              | 228 +++++------------
 .../compile-materialization.expected          | 116 ++-------
 .../spouse_example/compile-merge.expected     |  20 ++
 .../spouse_example/compile.expected           | 119 ++-------
 .../compile-incremental.expected              | 229 +++++-------------
 .../compile-incremental.expected              | 227 +++++------------
 .../compile.expected                          | 118 ++-------
 .../views/compile.expected                    |  31 +--
 .../weights/compile.expected                  | 108 ++-------
 22 files changed, 800 insertions(+), 1672 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 42218c407..0107e9378 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -244,6 +244,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
     def collectUsedRelations(bodies: List[List[Body]]): Set[Statement] = {
+      // FIXME need to be recursively defined on QuantifiedBody
       (bodies.flatten collect { case x: BodyAtom => x.name }
       flatMap (stmtByHeadName get _)).toSet.flatten.flatten
     }
@@ -270,6 +271,18 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       s"dependencies: [${depStr}]"
     }
   }
+
+  def collectUsedRelations1(body: Body): List[String] = body match {
+    case a: BodyAtom => List(a.name)
+    case q: QuantifiedBody => collectUsedRelations(q.bodies)
+    case _ => List.empty
+  }
+  def collectUsedRelations(bodies: List[Body]): List[String] = bodies flatMap collectUsedRelations1
+  val relationNamesUsedByStatement = statements collect {
+      case f : FunctionCallRule => f -> (f.q.bodies flatMap collectUsedRelations distinct)
+      case e : ExtractionRule   => e -> (e.q.bodies flatMap collectUsedRelations distinct)
+      case e : InferenceRule    => e -> (e.q.bodies flatMap collectUsedRelations distinct)
+    } toMap
 }
 
 // This is responsible for compiling a single conjunctive query
@@ -615,6 +628,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           output_relation: \"${stmts(0).headName}\"
         style: "sql_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
+          input_relations: [${
+            (stmts flatMap ss.relationNamesUsedByStatement distinct
+            ) mkString("\n            ", "\n            ", "\n          ")}]
       }
     """
     List(extractor)
@@ -644,6 +660,9 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
           ${ss.generateDependenciesOfCompiledBlockFor(List(stmt))}
+          input_relations: [${
+            (List(stmt) flatMap ss.relationNamesUsedByStatement distinct
+            ) mkString("\n            ", "\n            ", "\n          ")}]
           input_batch_size: $${INPUT_BATCH_SIZE}
           parallelism: ${parallelism}
         }
@@ -744,6 +763,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           function: "${func}"
           weight: "${weight}"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
+          input_relations: [${
+            val relationsInHead = stmts flatMap (_.head.terms map (_.name))
+            val relationsInBody = stmts flatMap ss.relationNamesUsedByStatement
+            ((relationsInHead ++ relationsInBody) distinct
+            ) mkString("\n            ", "\n            ", "\n          ")}]
         }
       """
     }
@@ -790,23 +814,17 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   // generate application.conf pipelines
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
-    val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
-    val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [\n  ${setup_database_pipeline}\n]" else ""
     val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
     val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [\n  ${extraction}\n]" else ""
     val inference = (ss.inferenceRules map {s => ss.resolveInferenceBlockName(s)}).mkString("\n  ")
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [\n  ${inference}\n]" else ""
     val endtoend = List(extraction, inference).filter(_ != "").mkString("\n  ")
     val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [\n  ${endtoend}\n]" else ""
-    val cleanup_pipeline = ss.mode match {
-      case INCREMENTAL | ORIGINAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [\n  cleanup\n]" else ""
-      case _ => ""
-    }
     val base_dir = ss.mode match {
       case MATERIALIZATION | INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
       case _ => ""
     }
-    List(run, initdb, extraction_pipeline, inference_pipeline, endtoend_pipeline, cleanup_pipeline, base_dir).filter(_ != "")
+    List(run, extraction_pipeline, inference_pipeline, endtoend_pipeline, base_dir).filter(_ != "")
   }
 
   // generate variable schema statements
@@ -849,7 +867,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val state = new CompilationState( programToCompile, config )
 
     val body = new ListBuffer[String]()
-    body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
     state.extractionRuleGroupByHead foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
     state.functionCallList          foreach {func   => body ++= compileFunctionCallRules(List(func), state)}
     state.inferenceRules            foreach {inf    => body ++= compileInferenceRules(List(inf), state)}
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 061606227..3d885b7a2 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -17,58 +17,6 @@
       }
     
 
-          deepdive.extraction.extractors.init_words_raw {
-            sql: """ DROP TABLE IF EXISTS words_raw CASCADE;
-            CREATE TABLE
-            words_raw(word_id bigserial,
-         word text,
-         pos text,
-         tag text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_words {
-            sql: """ DROP TABLE IF EXISTS words CASCADE;
-            CREATE TABLE
-            words(sent_id bigint,
-     word_id bigint,
-     word text,
-     pos text,
-     true_tag int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_tag {
-            sql: """ DROP TABLE IF EXISTS tag CASCADE;
-            CREATE TABLE
-            tag(word_id bigint,
-   id bigint,
-   label int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_word_features {
-            sql: """ DROP TABLE IF EXISTS word_features CASCADE;
-            CREATE TABLE
-            word_features(word_id bigint,
-             feature text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE words_raw;
-          TRUNCATE words;
-          TRUNCATE tag;
-          TRUNCATE word_features;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_tag {
         sql: """ 
         INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
@@ -76,8 +24,12 @@
         
           
         """
+          output_relation: "tag"
         style: "sql_extractor"
           dependencies: [ "ext_words_by_ext_training" ]
+          input_relations: [
+            words
+          ]
       }
     
 
@@ -89,8 +41,11 @@ FROM words_raw R0
           output_relation: "words"
           udf: ${APP_HOME}"/udf/ext_training.py"
           style: "tsv_extractor" 
-         
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          
+          input_relations: [
+            words_raw
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -104,7 +59,10 @@ FROM words R0, words R1
           udf: ${APP_HOME}"/udf/ext_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_words_by_ext_training" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            words
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -116,15 +74,14 @@ FROM words R0, words R1
         WHERE R1.word_id = R0.word_id """
           function: "Multinomial(tag.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_word_features_by_ext_features" ]
+          input_relations: [
+            tag
+            word_features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_words_raw
-  init_words
-  init_tag
-  init_word_features
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_tag
   ext_words_by_ext_training
@@ -139,6 +96,3 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_word_features_by_ext_features
   inf_istrue_tag
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 27a13ba61..4df543ab1 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -17,52 +17,18 @@
       }
     
 
-          deepdive.extraction.extractors.init_b {
-            sql: """ DROP TABLE IF EXISTS b CASCADE;
-            CREATE TABLE
-            b(k int,
- p text,
- q text,
- r int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_a {
-            sql: """ DROP TABLE IF EXISTS a CASCADE;
-            CREATE TABLE
-            a(k int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_c {
-            sql: """ DROP TABLE IF EXISTS c CASCADE;
-            CREATE TABLE
-            c(s text,
- n int,
- t text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE b;
-          TRUNCATE a;
-          TRUNCATE c;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_E {
         sql: """ DROP VIEW IF EXISTS E;
         CREATE VIEW E AS SELECT (R0.k :: INT) AS column_0
 FROM b R0
         
         """
+          output_relation: "E"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -72,8 +38,13 @@ FROM b R0
 FROM b R0, c R1
         WHERE R1.n = R0.k 
         """
+          output_relation: "X"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+          ]
       }
     
 
@@ -83,8 +54,13 @@ FROM b R0, c R1
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
         """
+          output_relation: "N"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+          ]
       }
     
 
@@ -94,8 +70,13 @@ FROM b R0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         WHERE R1_0.s > R0.p
         """
+          output_relation: "T"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+          ]
       }
     
 
@@ -105,8 +86,12 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
         """
+          output_relation: "J"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -116,8 +101,13 @@ FROM b R0
 FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
         
         """
+          output_relation: "U"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+          ]
       }
     
 
@@ -127,8 +117,12 @@ FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
 FROM b R0
         
         """
+          output_relation: "F"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -138,8 +132,12 @@ FROM b R0
 FROM b R0
         
         """
+          output_relation: "A"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -149,8 +147,13 @@ FROM b R0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
         """
+          output_relation: "M"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+          ]
       }
     
 
@@ -160,8 +163,12 @@ FROM b R0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
         """
+          output_relation: "I"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -171,8 +178,12 @@ FROM b R0
 FROM b R0
         WHERE (R0.k + R0.r) = 100
         """
+          output_relation: "G"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -182,8 +193,13 @@ FROM b R0
 FROM c R0, a R1
         WHERE R1.k = R0.n 
         """
+          output_relation: "V"
         style: "sql_extractor"
           
+          input_relations: [
+            c
+            a
+          ]
       }
     
 
@@ -193,8 +209,14 @@ FROM c R0, a R1
 FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
         """
+          output_relation: "Q"
         style: "sql_extractor"
           
+          input_relations: [
+            a
+            b
+            c
+          ]
       }
     
 
@@ -204,8 +226,12 @@ FROM a R0, b R1, c R2
 FROM b R0
         LIMIT 100
         """
+          output_relation: "L"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -215,8 +241,12 @@ FROM b R0
 FROM b R0
         
         """
+          output_relation: "B"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -227,8 +257,13 @@ FROM a R0, b R1
         WHERE R1.k = R0.k 
         GROUP BY R1.p, R1.q
         """
+          output_relation: "P"
         style: "sql_extractor"
           
+          input_relations: [
+            a
+            b
+          ]
       }
     
 
@@ -238,8 +273,12 @@ FROM a R0, b R1
 FROM b R0
         
         """
+          output_relation: "C"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -249,8 +288,12 @@ FROM b R0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
         """
+          output_relation: "H"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -260,8 +303,13 @@ FROM b R0
 FROM a R0
         WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
         """
+          output_relation: "W"
         style: "sql_extractor"
           
+          input_relations: [
+            a
+            c
+          ]
       }
     
 
@@ -271,8 +319,12 @@ FROM a R0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
         """
+          output_relation: "K"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -282,8 +334,14 @@ FROM b R0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
         """
+          output_relation: "O"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+            a
+          ]
       }
     
 
@@ -293,8 +351,12 @@ FROM b R0
 FROM b R0
         
         """
+          output_relation: "D"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+          ]
       }
     
 
@@ -304,16 +366,16 @@ FROM b R0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
         
         """
+          output_relation: "S"
         style: "sql_extractor"
           
+          input_relations: [
+            b
+            c
+          ]
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_b
-  init_a
-  init_c
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_M
   ext_Q
@@ -364,6 +426,3 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_V
   ext_H
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index 60bc1c1fc..33873bab3 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -23,79 +23,6 @@ dd_new_Q.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_dd_new_S {
-            sql: """ DROP TABLE IF EXISTS dd_new_S CASCADE;
-            CREATE TABLE
-            dd_new_S(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T CASCADE;
-            CREATE TABLE
-            dd_delta_T(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T {
-            sql: """ DROP TABLE IF EXISTS dd_new_T CASCADE;
-            CREATE TABLE
-            dd_new_T(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_S {
-            sql: """ DROP TABLE IF EXISTS dd_delta_S CASCADE;
-            CREATE TABLE
-            dd_delta_S(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_R {
-            sql: """ DROP TABLE IF EXISTS dd_new_R CASCADE;
-            CREATE TABLE
-            dd_new_R(a int,
-        b int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_R {
-            sql: """ DROP TABLE IF EXISTS dd_delta_R CASCADE;
-            CREATE TABLE
-            dd_delta_R(a int,
-          b int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_Q {
-            sql: """ DROP TABLE IF EXISTS dd_delta_Q CASCADE;
-            CREATE TABLE
-            dd_delta_Q(x int,
-          id bigint,
-          label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_new_S;
-          TRUNCATE dd_delta_T;
-          TRUNCATE dd_new_T;
-          TRUNCATE dd_delta_S;
-          TRUNCATE dd_new_R;
-          TRUNCATE dd_delta_R;
-          TRUNCATE dd_delta_Q;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_dd_new_S {
         sql: """ TRUNCATE dd_new_S;
         INSERT INTO dd_new_S SELECT R0.a
@@ -106,8 +33,13 @@ SELECT R0.a
 FROM dd_delta_S R0
         
         """
+          output_relation: "dd_new_S"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          input_relations: [
+            S
+            dd_delta_S
+          ]
       }
     
 
@@ -121,8 +53,13 @@ SELECT R0.a
 FROM dd_delta_T R0
         
         """
+          output_relation: "dd_new_T"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_T_by_f" ,  "ext1_dd_delta_T_by_f" ,  "ext2_dd_delta_T_by_f" ,  "ext_dd_delta_T_by_f_1" ]
+          input_relations: [
+            T
+            dd_delta_T
+          ]
       }
     
 
@@ -152,8 +89,14 @@ SELECT R0.a AS "dd_new_R.R0.a"
 FROM dd_new_R R0, dd_delta_R R1
         WHERE R1.a = R0.b  AND R0.a = 0
         """
+          output_relation: "dd_delta_S"
         style: "sql_extractor"
           dependencies: [ "ext_dd_new_R" ]
+          input_relations: [
+            dd_delta_R
+            R
+            dd_new_R
+          ]
       }
     
 
@@ -167,8 +110,13 @@ SELECT R0.a, R0.b
 FROM dd_delta_R R0
         
         """
+          output_relation: "dd_new_R"
         style: "sql_extractor"
           
+          input_relations: [
+            R
+            dd_delta_R
+          ]
       }
     
 
@@ -184,8 +132,13 @@ SELECT DISTINCT R0.x, id, label
         
           
         """
+          output_relation: "dd_new_Q"
         style: "sql_extractor"
           
+          input_relations: [
+            Q
+            dd_delta_Q
+          ]
       }
     
 
@@ -198,7 +151,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -212,7 +168,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -226,7 +185,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -240,7 +202,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -254,7 +219,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -268,7 +236,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -282,7 +253,10 @@ FROM dd_delta_R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -294,6 +268,11 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          input_relations: [
+            dd_new_Q
+            dd_delta_S
+          ]
         }
       
 
@@ -304,6 +283,11 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "1.0"
+          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          input_relations: [
+            dd_new_Q
+            dd_delta_S
+          ]
         }
       
 
@@ -320,6 +304,16 @@ FROM dd_delta_R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_new_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S" ]
+          input_relations: [
+            dd_new_Q
+            dd_delta_S
+            R
+            S
+            dd_new_S
+            dd_delta_R
+            dd_new_R
+          ]
         }
       
 
@@ -336,19 +330,19 @@ FROM dd_delta_R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
           weight: "-10.0"
+          dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_new_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S" ]
+          input_relations: [
+            dd_new_Q
+            dd_delta_S
+            R
+            S
+            dd_new_S
+            dd_delta_R
+            dd_new_R
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_new_S
-  init_dd_delta_T
-  init_dd_new_T
-  init_dd_delta_S
-  init_dd_new_R
-  init_dd_delta_R
-  init_dd_new_Q
-  init_dd_delta_Q
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_new_R
   ext_dd_delta_T_by_f
@@ -387,7 +381,4 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_imply_Q_Q
   dd_delta_inf1_imply_Q_Q
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index cbc508528..690bdc867 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -17,51 +17,6 @@
       }
     
 
-          deepdive.extraction.extractors.init_S {
-            sql: """ DROP TABLE IF EXISTS S CASCADE;
-            CREATE TABLE
-            S(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_R {
-            sql: """ DROP TABLE IF EXISTS R CASCADE;
-            CREATE TABLE
-            R(a int,
- b int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_Q {
-            sql: """ DROP TABLE IF EXISTS Q CASCADE;
-            CREATE TABLE
-            Q(x int,
- id bigint,
- label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_T {
-            sql: """ DROP TABLE IF EXISTS T CASCADE;
-            CREATE TABLE
-            T(a int)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE S;
-          TRUNCATE R;
-          TRUNCATE Q;
-          TRUNCATE T;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_S {
         sql: """ 
         INSERT INTO S SELECT R0.a AS "R.R0.a"
@@ -76,8 +31,12 @@ SELECT R0.a AS "R.R0.a"
 FROM R R0, R R1
         WHERE R1.a = R0.b  AND R0.a = 0
         """
+          output_relation: "S"
         style: "sql_extractor"
           
+          input_relations: [
+            R
+          ]
       }
     
 
@@ -90,7 +49,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -104,7 +66,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -118,7 +83,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -132,7 +100,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -146,7 +117,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -160,7 +134,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -174,7 +151,10 @@ FROM R R0
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            R
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -186,6 +166,11 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(Q.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          input_relations: [
+            Q
+            S
+          ]
         }
       
 
@@ -196,6 +181,11 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(Q.R0.label)"
           weight: "1.0"
+          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          input_relations: [
+            Q
+            S
+          ]
         }
       
 
@@ -206,6 +196,12 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          input_relations: [
+            Q
+            S
+            R
+          ]
         }
       
 
@@ -216,15 +212,15 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "-10.0"
+          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          input_relations: [
+            Q
+            S
+            R
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_S
-  init_R
-  init_Q
-  init_T
-]
 deepdive.pipeline.pipelines.extraction: [
   ext2_T_by_f
   ext_S_by_f_1
@@ -255,6 +251,3 @@ deepdive.pipeline.pipelines.endtoend: [
   inf_imply_Q_Q
   inf1_imply_Q_Q
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index 1614219c9..b36a8f25e 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -28,98 +28,6 @@ q1.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_dd_new_label2 {
-            sql: """ DROP TABLE IF EXISTS dd_new_label2 CASCADE;
-            CREATE TABLE
-            dd_new_label2(wid INT,
-             val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_label1 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_label1 CASCADE;
-            CREATE TABLE
-            dd_delta_label1(wid INT,
-               val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_label1 {
-            sql: """ DROP TABLE IF EXISTS dd_new_label1 CASCADE;
-            CREATE TABLE
-            dd_new_label1(wid INT,
-             val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_features CASCADE;
-            CREATE TABLE
-            dd_delta_features(id BIGSERIAL,
-                 word_id INT,
-                 feature_id INT,
-                 feature_val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_q2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_q2 CASCADE;
-            CREATE TABLE
-            dd_delta_q2(wid INT,
-           id bigint,
-           label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_label2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_label2 CASCADE;
-            CREATE TABLE
-            dd_delta_label2(wid INT,
-               val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_features CASCADE;
-            CREATE TABLE
-            dd_new_features(id BIGSERIAL,
-               word_id INT,
-               feature_id INT,
-               feature_val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_q1 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_q1 CASCADE;
-            CREATE TABLE
-            dd_delta_q1(wid INT,
-           id bigint,
-           label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_new_label2;
-          TRUNCATE dd_delta_label1;
-          TRUNCATE dd_new_label1;
-          TRUNCATE dd_delta_features;
-          TRUNCATE dd_delta_q2;
-          TRUNCATE dd_delta_label2;
-          TRUNCATE dd_new_features;
-          TRUNCATE dd_delta_q1;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_dd_new_label2 {
         sql: """ TRUNCATE dd_new_label2;
         INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
@@ -130,8 +38,13 @@ SELECT R0.wid, R0.val
 FROM dd_delta_label2 R0
         
         """
+          output_relation: "dd_new_label2"
         style: "sql_extractor"
           
+          input_relations: [
+            label2
+            dd_delta_label2
+          ]
       }
     
 
@@ -147,8 +60,13 @@ SELECT DISTINCT R0.wid, id, label
         
           
         """
+          output_relation: "dd_new_q1"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_q1" ]
+          input_relations: [
+            q1
+            dd_delta_q1
+          ]
       }
     
 
@@ -162,8 +80,13 @@ SELECT R0.wid, R0.val
 FROM dd_delta_label1 R0
         
         """
+          output_relation: "dd_new_label1"
         style: "sql_extractor"
           
+          input_relations: [
+            label1
+            dd_delta_label1
+          ]
       }
     
 
@@ -174,8 +97,12 @@ FROM dd_delta_label1 R0
         
           
         """
+          output_relation: "dd_delta_q2"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_delta_label2
+          ]
       }
     
 
@@ -189,8 +116,13 @@ SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
 FROM dd_delta_features R0
         
         """
+          output_relation: "dd_new_features"
         style: "sql_extractor"
           
+          input_relations: [
+            features
+            dd_delta_features
+          ]
       }
     
 
@@ -201,8 +133,12 @@ FROM dd_delta_features R0
         
           
         """
+          output_relation: "dd_delta_q1"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_delta_label1
+          ]
       }
     
 
@@ -218,8 +154,13 @@ SELECT DISTINCT R0.wid, id, label
         
           
         """
+          output_relation: "dd_new_q2"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_q2" ]
+          input_relations: [
+            q2
+            dd_delta_q2
+          ]
       }
     
 
@@ -230,6 +171,11 @@ SELECT DISTINCT R0.wid, id, label
         WHERE R1.word_id = R0.wid """
           function: "Imply(dd_new_q1.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            dd_new_q1
+            dd_delta_features
+          ]
         }
       
 
@@ -240,21 +186,14 @@ SELECT DISTINCT R0.wid, id, label
         WHERE R1.word_id = R0.wid """
           function: "Imply(dd_new_q2.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            dd_new_q2
+            dd_delta_features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_new_label2
-  init_dd_delta_label1
-  init_dd_new_q1
-  init_dd_new_label1
-  init_dd_delta_features
-  init_dd_delta_q2
-  init_dd_delta_label2
-  init_dd_new_features
-  init_dd_delta_q1
-  init_dd_new_q2
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_delta_q1
   ext_dd_new_q1
@@ -279,7 +218,4 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_istrue_q1
   dd_delta_inf_istrue_q2
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index fc85eb005..c6ad59e23 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -18,66 +18,6 @@ q2.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_label1 {
-            sql: """ DROP TABLE IF EXISTS label1 CASCADE;
-            CREATE TABLE
-            label1(wid INT,
-      val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_features {
-            sql: """ DROP TABLE IF EXISTS features CASCADE;
-            CREATE TABLE
-            features(id BIGSERIAL,
-        word_id INT,
-        feature_id INT,
-        feature_val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_label2 {
-            sql: """ DROP TABLE IF EXISTS label2 CASCADE;
-            CREATE TABLE
-            label2(wid INT,
-      val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_q1 {
-            sql: """ DROP TABLE IF EXISTS q1 CASCADE;
-            CREATE TABLE
-            q1(wid INT,
-  id bigint,
-  label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_q2 {
-            sql: """ DROP TABLE IF EXISTS q2 CASCADE;
-            CREATE TABLE
-            q2(wid INT,
-  id bigint,
-  label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE label1;
-          TRUNCATE features;
-          TRUNCATE label2;
-          TRUNCATE q1;
-          TRUNCATE q2;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_q1 {
         sql: """ 
         INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
@@ -85,8 +25,12 @@ q2.label: Boolean
         
           
         """
+          output_relation: "q1"
         style: "sql_extractor"
           
+          input_relations: [
+            label1
+          ]
       }
     
 
@@ -97,8 +41,12 @@ q2.label: Boolean
         
           
         """
+          output_relation: "q2"
         style: "sql_extractor"
           
+          input_relations: [
+            label2
+          ]
       }
     
 
@@ -109,6 +57,11 @@ q2.label: Boolean
         WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            q1
+            features
+          ]
         }
       
 
@@ -119,16 +72,14 @@ q2.label: Boolean
         WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            q2
+            features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_label1
-  init_features
-  init_label2
-  init_q1
-  init_q2
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_q1
   ext_q2
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
index eb3431649..01e56b7bf 100644
--- a/test/expected-output-test/ocr_example/compile-merge.expected
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -23,8 +23,12 @@
 FROM dd_new_label2 R0
         
         """
+          output_relation: "label2"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_label2
+          ]
       }
     
 
@@ -34,8 +38,12 @@ FROM dd_new_label2 R0
 FROM dd_new_label1 R0
         
         """
+          output_relation: "label1"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_label1
+          ]
       }
     
 
@@ -45,8 +53,12 @@ FROM dd_new_label1 R0
 FROM dd_new_features R0
         
         """
+          output_relation: "features"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_features
+          ]
       }
     
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index c3b48771a..9490160f0 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -18,66 +18,6 @@ q2.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_label1 {
-            sql: """ DROP TABLE IF EXISTS label1 CASCADE;
-            CREATE TABLE
-            label1(wid INT,
-      val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_features {
-            sql: """ DROP TABLE IF EXISTS features CASCADE;
-            CREATE TABLE
-            features(id BIGSERIAL,
-        word_id INT,
-        feature_id INT,
-        feature_val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_label2 {
-            sql: """ DROP TABLE IF EXISTS label2 CASCADE;
-            CREATE TABLE
-            label2(wid INT,
-      val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_q1 {
-            sql: """ DROP TABLE IF EXISTS q1 CASCADE;
-            CREATE TABLE
-            q1(wid INT,
-  id bigint,
-  label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_q2 {
-            sql: """ DROP TABLE IF EXISTS q2 CASCADE;
-            CREATE TABLE
-            q2(wid INT,
-  id bigint,
-  label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE label1;
-          TRUNCATE features;
-          TRUNCATE label2;
-          TRUNCATE q1;
-          TRUNCATE q2;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_q1 {
         sql: """ 
         INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
@@ -85,8 +25,12 @@ q2.label: Boolean
         
           
         """
+          output_relation: "q1"
         style: "sql_extractor"
           
+          input_relations: [
+            label1
+          ]
       }
     
 
@@ -97,8 +41,12 @@ q2.label: Boolean
         
           
         """
+          output_relation: "q2"
         style: "sql_extractor"
           
+          input_relations: [
+            label2
+          ]
       }
     
 
@@ -109,6 +57,11 @@ q2.label: Boolean
         WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            q1
+            features
+          ]
         }
       
 
@@ -119,16 +72,14 @@ q2.label: Boolean
         WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            q2
+            features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_label1
-  init_features
-  init_label2
-  init_q1
-  init_q2
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_q1
   ext_q2
@@ -143,6 +94,3 @@ deepdive.pipeline.pipelines.endtoend: [
   inf_istrue_q1
   inf_istrue_q2
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index d5879b72d..94624454e 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -28,114 +28,6 @@ dd_delta_smoke.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_dd_delta_friends {
-            sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
-            CREATE TABLE
-            dd_delta_friends(person_id bigint,
-                friend_id bigint)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_smoke {
-            sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
-            CREATE TABLE
-            dd_delta_smoke(person_id bigint,
-              id bigint,
-              label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_person_has_cancer {
-            sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
-            CREATE TABLE
-            dd_new_person_has_cancer(person_id bigint,
-                        has_cancer boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_person {
-            sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
-            CREATE TABLE
-            dd_delta_person(person_id bigint,
-               name text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_person {
-            sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
-            CREATE TABLE
-            dd_new_person(person_id bigint,
-             name text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_person_has_cancer {
-            sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
-            CREATE TABLE
-            dd_delta_person_has_cancer(person_id bigint,
-                          has_cancer boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_cancer {
-            sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
-            CREATE TABLE
-            dd_delta_cancer(person_id bigint,
-               id bigint,
-               label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_person_smokes {
-            sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
-            CREATE TABLE
-            dd_delta_person_smokes(person_id bigint,
-                      smokes boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_person_smokes {
-            sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
-            CREATE TABLE
-            dd_new_person_smokes(person_id bigint,
-                    smokes boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_friends {
-            sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
-            CREATE TABLE
-            dd_new_friends(person_id bigint,
-              friend_id bigint)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_friends;
-          TRUNCATE dd_delta_smoke;
-          TRUNCATE dd_new_person_has_cancer;
-          TRUNCATE dd_delta_person;
-          TRUNCATE dd_new_person;
-          TRUNCATE dd_delta_person_has_cancer;
-          TRUNCATE dd_delta_cancer;
-          TRUNCATE dd_delta_person_smokes;
-          TRUNCATE dd_new_person_smokes;
-          TRUNCATE dd_new_friends;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_dd_delta_smoke {
         sql: """ 
         INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
@@ -143,8 +35,12 @@ dd_delta_smoke.label: Boolean
         
           
         """
+          output_relation: "dd_delta_smoke"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_delta_person_smokes
+          ]
       }
     
 
@@ -158,8 +54,13 @@ SELECT R0.person_id, R0.has_cancer
 FROM dd_delta_person_has_cancer R0
         
         """
+          output_relation: "dd_new_person_has_cancer"
         style: "sql_extractor"
           
+          input_relations: [
+            person_has_cancer
+            dd_delta_person_has_cancer
+          ]
       }
     
 
@@ -173,8 +74,13 @@ SELECT R0.person_id, R0.name
 FROM dd_delta_person R0
         
         """
+          output_relation: "dd_new_person"
         style: "sql_extractor"
           
+          input_relations: [
+            person
+            dd_delta_person
+          ]
       }
     
 
@@ -190,8 +96,13 @@ SELECT DISTINCT R0.person_id, id, label
         
           
         """
+          output_relation: "dd_new_smoke"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_smoke" ]
+          input_relations: [
+            smoke
+            dd_delta_smoke
+          ]
       }
     
 
@@ -202,8 +113,12 @@ SELECT DISTINCT R0.person_id, id, label
         
           
         """
+          output_relation: "dd_delta_cancer"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_delta_person_has_cancer
+          ]
       }
     
 
@@ -219,8 +134,13 @@ SELECT DISTINCT R0.person_id, id, label
         
           
         """
+          output_relation: "dd_new_cancer"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_cancer" ]
+          input_relations: [
+            cancer
+            dd_delta_cancer
+          ]
       }
     
 
@@ -234,8 +154,13 @@ SELECT R0.person_id, R0.smokes
 FROM dd_delta_person_smokes R0
         
         """
+          output_relation: "dd_new_person_smokes"
         style: "sql_extractor"
           
+          input_relations: [
+            person_smokes
+            dd_delta_person_smokes
+          ]
       }
     
 
@@ -249,8 +174,13 @@ SELECT R0.person_id, R0.friend_id
 FROM dd_delta_friends R0
         
         """
+          output_relation: "dd_new_friends"
         style: "sql_extractor"
           
+          input_relations: [
+            friends
+            dd_delta_friends
+          ]
       }
     
 
@@ -261,6 +191,12 @@ FROM dd_delta_friends R0
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(dd_new_smoke.R0.label, dd_new_cancer.R1.label)"
           weight: "0.5"
+          
+          input_relations: [
+            dd_new_smoke
+            dd_new_cancer
+            dd_delta_person_smokes
+          ]
         }
       
 
@@ -271,23 +207,14 @@ FROM dd_delta_friends R0
         WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
           function: "Imply(dd_new_smoke.R0.label, dd_new_smoke.R1.label)"
           weight: "0.4"
+          
+          input_relations: [
+            dd_new_smoke
+            dd_delta_friends
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_friends
-  init_dd_delta_smoke
-  init_dd_new_person_has_cancer
-  init_dd_delta_person
-  init_dd_new_person
-  init_dd_delta_person_has_cancer
-  init_dd_new_smoke
-  init_dd_delta_cancer
-  init_dd_new_cancer
-  init_dd_delta_person_smokes
-  init_dd_new_person_smokes
-  init_dd_new_friends
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_delta_cancer
   ext_dd_delta_smoke
@@ -314,7 +241,4 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_imply_smoke_cancer
   dd_delta_inf_imply_smoke_smoke
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index b7c32d00e..d5296e70a 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -18,74 +18,6 @@ cancer.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_person_smokes {
-            sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
-            CREATE TABLE
-            person_smokes(person_id bigint,
-             smokes boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_smoke {
-            sql: """ DROP TABLE IF EXISTS smoke CASCADE;
-            CREATE TABLE
-            smoke(person_id bigint,
-     id bigint,
-     label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_cancer {
-            sql: """ DROP TABLE IF EXISTS cancer CASCADE;
-            CREATE TABLE
-            cancer(person_id bigint,
-      id bigint,
-      label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_friends {
-            sql: """ DROP TABLE IF EXISTS friends CASCADE;
-            CREATE TABLE
-            friends(person_id bigint,
-       friend_id bigint)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_person_has_cancer {
-            sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
-            CREATE TABLE
-            person_has_cancer(person_id bigint,
-                 has_cancer boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_person {
-            sql: """ DROP TABLE IF EXISTS person CASCADE;
-            CREATE TABLE
-            person(person_id bigint,
-      name text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE person_smokes;
-          TRUNCATE smoke;
-          TRUNCATE cancer;
-          TRUNCATE friends;
-          TRUNCATE person_has_cancer;
-          TRUNCATE person;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_cancer {
         sql: """ 
         INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
@@ -93,8 +25,12 @@ cancer.label: Boolean
         
           
         """
+          output_relation: "cancer"
         style: "sql_extractor"
           
+          input_relations: [
+            person_has_cancer
+          ]
       }
     
 
@@ -105,8 +41,12 @@ cancer.label: Boolean
         
           
         """
+          output_relation: "smoke"
         style: "sql_extractor"
           
+          input_relations: [
+            person_smokes
+          ]
       }
     
 
@@ -117,6 +57,12 @@ cancer.label: Boolean
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R0.label, cancer.R1.label)"
           weight: "0.5"
+          
+          input_relations: [
+            smoke
+            cancer
+            person_smokes
+          ]
         }
       
 
@@ -127,17 +73,14 @@ cancer.label: Boolean
         WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
           function: "Imply(smoke.R0.label, smoke.R1.label)"
           weight: "0.4"
+          
+          input_relations: [
+            smoke
+            friends
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_person_smokes
-  init_smoke
-  init_cancer
-  init_friends
-  init_person_has_cancer
-  init_person
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_cancer
   ext_smoke
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
index 0a64e447e..09d176f4b 100644
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -23,8 +23,12 @@
 FROM dd_new_person_smokes R0
         
         """
+          output_relation: "person_smokes"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_person_smokes
+          ]
       }
     
 
@@ -34,8 +38,12 @@ FROM dd_new_person_smokes R0
 FROM dd_new_friends R0
         
         """
+          output_relation: "friends"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_friends
+          ]
       }
     
 
@@ -45,8 +53,12 @@ FROM dd_new_friends R0
 FROM dd_new_person_has_cancer R0
         
         """
+          output_relation: "person_has_cancer"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_person_has_cancer
+          ]
       }
     
 
@@ -56,8 +68,12 @@ FROM dd_new_person_has_cancer R0
 FROM dd_new_person R0
         
         """
+          output_relation: "person"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_person
+          ]
       }
     
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index ece741288..752971856 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -18,74 +18,6 @@ cancer.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_person_smokes {
-            sql: """ DROP TABLE IF EXISTS person_smokes CASCADE;
-            CREATE TABLE
-            person_smokes(person_id bigint,
-             smokes boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_smoke {
-            sql: """ DROP TABLE IF EXISTS smoke CASCADE;
-            CREATE TABLE
-            smoke(person_id bigint,
-     id bigint,
-     label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_cancer {
-            sql: """ DROP TABLE IF EXISTS cancer CASCADE;
-            CREATE TABLE
-            cancer(person_id bigint,
-      id bigint,
-      label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_friends {
-            sql: """ DROP TABLE IF EXISTS friends CASCADE;
-            CREATE TABLE
-            friends(person_id bigint,
-       friend_id bigint)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_person_has_cancer {
-            sql: """ DROP TABLE IF EXISTS person_has_cancer CASCADE;
-            CREATE TABLE
-            person_has_cancer(person_id bigint,
-                 has_cancer boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_person {
-            sql: """ DROP TABLE IF EXISTS person CASCADE;
-            CREATE TABLE
-            person(person_id bigint,
-      name text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE person_smokes;
-          TRUNCATE smoke;
-          TRUNCATE cancer;
-          TRUNCATE friends;
-          TRUNCATE person_has_cancer;
-          TRUNCATE person;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_cancer {
         sql: """ 
         INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
@@ -93,8 +25,12 @@ cancer.label: Boolean
         
           
         """
+          output_relation: "cancer"
         style: "sql_extractor"
           
+          input_relations: [
+            person_has_cancer
+          ]
       }
     
 
@@ -105,8 +41,12 @@ cancer.label: Boolean
         
           
         """
+          output_relation: "smoke"
         style: "sql_extractor"
           
+          input_relations: [
+            person_smokes
+          ]
       }
     
 
@@ -117,6 +57,12 @@ cancer.label: Boolean
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R0.label, cancer.R1.label)"
           weight: "0.5"
+          
+          input_relations: [
+            smoke
+            cancer
+            person_smokes
+          ]
         }
       
 
@@ -127,17 +73,14 @@ cancer.label: Boolean
         WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
           function: "Imply(smoke.R0.label, smoke.R1.label)"
           weight: "0.4"
+          
+          input_relations: [
+            smoke
+            friends
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_person_smokes
-  init_smoke
-  init_cancer
-  init_friends
-  init_person_has_cancer
-  init_person
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_cancer
   ext_smoke
@@ -152,6 +95,3 @@ deepdive.pipeline.pipelines.endtoend: [
   inf_imply_smoke_cancer
   inf_imply_smoke_smoke
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index a7a89dbd9..4dc00ba3b 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -23,151 +23,6 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_dd_delta_articles {
-            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-            CREATE TABLE
-            dd_delta_articles(article_id text,
-                 text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-            CREATE TABLE
-            dd_new_people_mentions(sentence_id text,
-                      start_position int,
-                      length int,
-                      text text,
-                      mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_features(relation_id text,
-                            feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_articles {
-            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-            CREATE TABLE
-            dd_new_articles(article_id text,
-               text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_candidates(person1_id text,
-                            person2_id text,
-                            sentence_id text,
-                            description text,
-                            relation_id text,
-                            is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_features(relation_id text,
-                          feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-            CREATE TABLE
-            dd_new_sentences(document_id text,
-                sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
-                sentence_offset int,
-                sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-            CREATE TABLE
-            dd_delta_people_mentions(sentence_id text,
-                        start_position int,
-                        length int,
-                        text text,
-                        mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_candidates(person1_id text,
-                              person2_id text,
-                              sentence_id text,
-                              description text,
-                              relation_id text,
-                              is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-            CREATE TABLE
-            dd_delta_sentences(document_id text,
-                  sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
-                  sentence_offset int,
-                  sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse(relation_id text,
-                   id bigint,
-                   label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_articles;
-          TRUNCATE dd_new_people_mentions;
-          TRUNCATE dd_delta_has_spouse_features;
-          TRUNCATE dd_new_articles;
-          TRUNCATE dd_new_has_spouse_candidates;
-          TRUNCATE dd_new_has_spouse_features;
-          TRUNCATE dd_new_sentences;
-          TRUNCATE dd_delta_people_mentions;
-          TRUNCATE dd_delta_has_spouse_candidates;
-          TRUNCATE dd_delta_sentences;
-          TRUNCATE dd_delta_has_spouse;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
@@ -178,8 +33,13 @@ SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_delta_people_mentions R0
         
         """
+          output_relation: "dd_new_people_mentions"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
+          input_relations: [
+            people_mentions
+            dd_delta_people_mentions
+          ]
       }
     
 
@@ -193,8 +53,13 @@ SELECT R0.article_id, R0.text
 FROM dd_delta_articles R0
         
         """
+          output_relation: "dd_new_articles"
         style: "sql_extractor"
           
+          input_relations: [
+            articles
+            dd_delta_articles
+          ]
       }
     
 
@@ -208,8 +73,13 @@ SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation
 FROM dd_delta_has_spouse_candidates R0
         
         """
+          output_relation: "dd_new_has_spouse_candidates"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+            dd_delta_has_spouse_candidates
+          ]
       }
     
 
@@ -223,8 +93,13 @@ SELECT R0.relation_id, R0.feature
 FROM dd_delta_has_spouse_features R0
         
         """
+          output_relation: "dd_new_has_spouse_features"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            has_spouse_features
+            dd_delta_has_spouse_features
+          ]
       }
     
 
@@ -238,8 +113,13 @@ SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependen
 FROM dd_delta_sentences R0
         
         """
+          output_relation: "dd_new_sentences"
         style: "sql_extractor"
           
+          input_relations: [
+            sentences
+            dd_delta_sentences
+          ]
       }
     
 
@@ -250,8 +130,12 @@ FROM dd_delta_sentences R0
         
           
         """
+          output_relation: "dd_delta_has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            dd_delta_has_spouse_candidates
+          ]
       }
     
 
@@ -267,8 +151,13 @@ SELECT DISTINCT R0.relation_id, id, label
         
           
         """
+          output_relation: "dd_new_has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse" ]
+          input_relations: [
+            has_spouse
+            dd_delta_has_spouse
+          ]
       }
     
 
@@ -281,7 +170,10 @@ FROM dd_delta_sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_sentences
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -299,7 +191,12 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_people_mentions
+            people_mentions
+            dd_new_people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -325,7 +222,17 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_sentences
+            has_spouse_candidates
+            people_mentions
+            dd_new_sentences
+            dd_delta_has_spouse_candidates
+            dd_new_has_spouse_candidates
+            dd_delta_people_mentions
+            dd_new_people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -340,23 +247,17 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_has_spouse_candidates" ,  "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            dd_new_has_spouse
+            dd_delta_has_spouse_candidates
+            has_spouse_features
+            dd_new_has_spouse_candidates
+            dd_delta_has_spouse_features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_articles
-  init_dd_new_people_mentions
-  init_dd_delta_has_spouse_features
-  init_dd_new_articles
-  init_dd_new_has_spouse_candidates
-  init_dd_new_has_spouse_features
-  init_dd_new_sentences
-  init_dd_delta_people_mentions
-  init_dd_delta_has_spouse_candidates
-  init_dd_delta_sentences
-  init_dd_delta_has_spouse
-  init_dd_new_has_spouse
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_new_has_spouse_candidates
   ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
@@ -385,7 +286,4 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_dd_new_articles
   dd_delta_inf_istrue_has_spouse
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index 6c85b1ee2..eb428a6a8 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -17,87 +17,6 @@
       }
     
 
-          deepdive.extraction.extractors.init_sentences {
-            sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-            CREATE TABLE
-            sentences(document_id text,
-         sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
-         sentence_offset int,
-         sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-            CREATE TABLE
-            has_spouse_candidates(person1_id text,
-                     person2_id text,
-                     sentence_id text,
-                     description text,
-                     relation_id text,
-                     is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse {
-            sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-            CREATE TABLE
-            has_spouse(relation_id text,
-          id bigint,
-          label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_articles {
-            sql: """ DROP TABLE IF EXISTS articles CASCADE;
-            CREATE TABLE
-            articles(article_id text,
-        text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-            CREATE TABLE
-            has_spouse_features(relation_id text,
-                   feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_people_mentions {
-            sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-            CREATE TABLE
-            people_mentions(sentence_id text,
-               start_position int,
-               length int,
-               text text,
-               mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE sentences;
-          TRUNCATE has_spouse_candidates;
-          TRUNCATE has_spouse;
-          TRUNCATE articles;
-          TRUNCATE has_spouse_features;
-          TRUNCATE people_mentions;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_has_spouse {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
@@ -105,8 +24,12 @@
         
           
         """
+          output_relation: "has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+          ]
       }
     
 
@@ -119,7 +42,10 @@ FROM sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            sentences
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -133,7 +59,10 @@ FROM people_mentions R0, people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_people_mentions_by_ext_people" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -147,7 +76,12 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            sentences
+            has_spouse_candidates
+            people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -159,17 +93,15 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            has_spouse
+            has_spouse_candidates
+            has_spouse_features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_sentences
-  init_has_spouse_candidates
-  init_has_spouse
-  init_articles
-  init_has_spouse_features
-  init_people_mentions
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index 45b0833e5..266e4f579 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -23,8 +23,12 @@
 FROM dd_new_sentences R0
         
         """
+          output_relation: "sentences"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_sentences
+          ]
       }
     
 
@@ -34,8 +38,12 @@ FROM dd_new_sentences R0
 FROM dd_new_has_spouse_candidates R0
         
         """
+          output_relation: "has_spouse_candidates"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_has_spouse_candidates
+          ]
       }
     
 
@@ -45,8 +53,12 @@ FROM dd_new_has_spouse_candidates R0
 FROM dd_new_articles R0
         
         """
+          output_relation: "articles"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_articles
+          ]
       }
     
 
@@ -56,8 +68,12 @@ FROM dd_new_articles R0
 FROM dd_new_has_spouse_features R0
         
         """
+          output_relation: "has_spouse_features"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_has_spouse_features
+          ]
       }
     
 
@@ -67,8 +83,12 @@ FROM dd_new_has_spouse_features R0
 FROM dd_new_people_mentions R0
         
         """
+          output_relation: "people_mentions"
         style: "sql_extractor"
           
+          input_relations: [
+            dd_new_people_mentions
+          ]
       }
     
 deepdive.pipeline.run: ${PIPELINE}
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 19a359c2a..0fe3bfbb2 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -17,87 +17,6 @@
       }
     
 
-          deepdive.extraction.extractors.init_sentences {
-            sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-            CREATE TABLE
-            sentences(document_id text,
-         sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
-         sentence_offset int,
-         sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-            CREATE TABLE
-            has_spouse_candidates(person1_id text,
-                     person2_id text,
-                     sentence_id text,
-                     description text,
-                     relation_id text,
-                     is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse {
-            sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-            CREATE TABLE
-            has_spouse(relation_id text,
-          id bigint,
-          label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_articles {
-            sql: """ DROP TABLE IF EXISTS articles CASCADE;
-            CREATE TABLE
-            articles(article_id text,
-        text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-            CREATE TABLE
-            has_spouse_features(relation_id text,
-                   feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_people_mentions {
-            sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-            CREATE TABLE
-            people_mentions(sentence_id text,
-               start_position int,
-               length int,
-               text text,
-               mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE sentences;
-          TRUNCATE has_spouse_candidates;
-          TRUNCATE has_spouse;
-          TRUNCATE articles;
-          TRUNCATE has_spouse_features;
-          TRUNCATE people_mentions;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_has_spouse {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
@@ -105,8 +24,12 @@
         
           
         """
+          output_relation: "has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+          ]
       }
     
 
@@ -119,7 +42,10 @@ FROM sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            sentences
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -133,7 +59,10 @@ FROM people_mentions R0, people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_people_mentions_by_ext_people" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -147,7 +76,12 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            sentences
+            has_spouse_candidates
+            people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -159,17 +93,15 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            has_spouse
+            has_spouse_candidates
+            has_spouse_features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_sentences
-  init_has_spouse_candidates
-  init_has_spouse
-  init_articles
-  init_has_spouse_features
-  init_people_mentions
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
@@ -186,6 +118,3 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_has_spouse_features_by_ext_has_spouse_features
   inf_istrue_has_spouse
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index f56797ecd..350f08550 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -23,151 +23,6 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_dd_delta_articles {
-            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-            CREATE TABLE
-            dd_delta_articles(article_id text,
-                 text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-            CREATE TABLE
-            dd_new_people_mentions(sentence_id text,
-                      start_position int,
-                      length int,
-                      text text,
-                      mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_features(relation_id text,
-                            feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_articles {
-            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-            CREATE TABLE
-            dd_new_articles(article_id text,
-               text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_candidates(person1_id text,
-                            person2_id text,
-                            sentence_id text,
-                            description text,
-                            relation_id text,
-                            is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_features(relation_id text,
-                          feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-            CREATE TABLE
-            dd_new_sentences(document_id text,
-                sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
-                sentence_offset int,
-                sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-            CREATE TABLE
-            dd_delta_people_mentions(sentence_id text,
-                        start_position int,
-                        length int,
-                        text text,
-                        mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_candidates(person1_id text,
-                              person2_id text,
-                              sentence_id text,
-                              description text,
-                              relation_id text,
-                              is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-            CREATE TABLE
-            dd_delta_sentences(document_id text,
-                  sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
-                  sentence_offset int,
-                  sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse(relation_id text,
-                   id bigint,
-                   label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_articles;
-          TRUNCATE dd_new_people_mentions;
-          TRUNCATE dd_delta_has_spouse_features;
-          TRUNCATE dd_new_articles;
-          TRUNCATE dd_new_has_spouse_candidates;
-          TRUNCATE dd_new_has_spouse_features;
-          TRUNCATE dd_new_sentences;
-          TRUNCATE dd_delta_people_mentions;
-          TRUNCATE dd_delta_has_spouse_candidates;
-          TRUNCATE dd_delta_sentences;
-          TRUNCATE dd_delta_has_spouse;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
@@ -178,8 +33,13 @@ SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_delta_people_mentions R0
         
         """
+          output_relation: "dd_new_people_mentions"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
+          input_relations: [
+            people_mentions
+            dd_delta_people_mentions
+          ]
       }
     
 
@@ -193,8 +53,13 @@ SELECT R0.article_id, R0.text
 FROM dd_delta_articles R0
         
         """
+          output_relation: "dd_new_articles"
         style: "sql_extractor"
           
+          input_relations: [
+            articles
+            dd_delta_articles
+          ]
       }
     
 
@@ -208,8 +73,13 @@ SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation
 FROM dd_delta_has_spouse_candidates R0
         
         """
+          output_relation: "dd_new_has_spouse_candidates"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+            dd_delta_has_spouse_candidates
+          ]
       }
     
 
@@ -223,8 +93,13 @@ SELECT R0.relation_id, R0.feature
 FROM dd_delta_has_spouse_features R0
         
         """
+          output_relation: "dd_new_has_spouse_features"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            has_spouse_features
+            dd_delta_has_spouse_features
+          ]
       }
     
 
@@ -238,8 +113,13 @@ SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependen
 FROM dd_delta_sentences R0
         
         """
+          output_relation: "dd_new_sentences"
         style: "sql_extractor"
           
+          input_relations: [
+            sentences
+            dd_delta_sentences
+          ]
       }
     
 
@@ -250,8 +130,12 @@ FROM dd_delta_sentences R0
         
           
         """
+          output_relation: "dd_delta_has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            dd_delta_has_spouse_candidates
+          ]
       }
     
 
@@ -267,8 +151,13 @@ SELECT DISTINCT R0.relation_id, id, label
         
           
         """
+          output_relation: "dd_new_has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse" ]
+          input_relations: [
+            has_spouse
+            dd_delta_has_spouse
+          ]
       }
     
 
@@ -281,7 +170,10 @@ FROM dd_delta_sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_sentences
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -299,7 +191,12 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            dd_delta_people_mentions
+            people_mentions
+            dd_new_people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -329,7 +226,18 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
-          input_batch_size: ${INPUT_BATCH_SIZE} 
+          input_relations: [
+            sentences
+            has_spouse_candidates
+            people_mentions
+            dd_delta_sentences
+            dd_new_sentences
+            dd_delta_has_spouse_candidates
+            dd_new_has_spouse_candidates
+            dd_delta_people_mentions
+            dd_new_people_mentions
+          ]
+          input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
       
@@ -344,23 +252,17 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_has_spouse_candidates" ,  "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            dd_new_has_spouse
+            dd_delta_has_spouse_candidates
+            has_spouse_features
+            dd_new_has_spouse_candidates
+            dd_delta_has_spouse_features
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_articles
-  init_dd_new_people_mentions
-  init_dd_delta_has_spouse_features
-  init_dd_new_articles
-  init_dd_new_has_spouse_candidates
-  init_dd_new_has_spouse_features
-  init_dd_new_sentences
-  init_dd_delta_people_mentions
-  init_dd_delta_has_spouse_candidates
-  init_dd_delta_sentences
-  init_dd_delta_has_spouse
-  init_dd_new_has_spouse
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_new_has_spouse_candidates
   ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
@@ -389,7 +291,4 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_dd_new_articles
   dd_delta_inf_istrue_has_spouse
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index bf5a4ccab..3ba3754c5 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -23,151 +23,6 @@ dd_new_has_spouse.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_dd_delta_articles {
-            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-            CREATE TABLE
-            dd_delta_articles(article_id text,
-                 text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-            CREATE TABLE
-            dd_new_people_mentions(sentence_id text,
-                      start_position int,
-                      length int,
-                      text text,
-                      mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_features(relation_id text,
-                            feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_articles {
-            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-            CREATE TABLE
-            dd_new_articles(article_id text,
-               text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_candidates(person1_id text,
-                            person2_id text,
-                            sentence_id text,
-                            description text,
-                            relation_id text,
-                            is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_features(relation_id text,
-                          feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-            CREATE TABLE
-            dd_new_sentences(document_id text,
-                sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
-                sentence_offset int,
-                sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-            CREATE TABLE
-            dd_delta_people_mentions(sentence_id text,
-                        start_position int,
-                        length int,
-                        text text,
-                        mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_candidates(person1_id text,
-                              person2_id text,
-                              sentence_id text,
-                              description text,
-                              relation_id text,
-                              is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-            CREATE TABLE
-            dd_delta_sentences(document_id text,
-                  sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
-                  sentence_offset int,
-                  sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse(relation_id text,
-                   id bigint,
-                   label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_articles;
-          TRUNCATE dd_new_people_mentions;
-          TRUNCATE dd_delta_has_spouse_features;
-          TRUNCATE dd_new_articles;
-          TRUNCATE dd_new_has_spouse_candidates;
-          TRUNCATE dd_new_has_spouse_features;
-          TRUNCATE dd_new_sentences;
-          TRUNCATE dd_delta_people_mentions;
-          TRUNCATE dd_delta_has_spouse_candidates;
-          TRUNCATE dd_delta_sentences;
-          TRUNCATE dd_delta_has_spouse;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
@@ -178,8 +33,13 @@ SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_delta_people_mentions R0
         
         """
+          output_relation: "dd_new_people_mentions"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
+          input_relations: [
+            people_mentions
+            dd_delta_people_mentions
+          ]
       }
     
 
@@ -193,8 +53,13 @@ SELECT R0.article_id, R0.text
 FROM dd_delta_articles R0
         
         """
+          output_relation: "dd_new_articles"
         style: "sql_extractor"
           
+          input_relations: [
+            articles
+            dd_delta_articles
+          ]
       }
     
 
@@ -208,8 +73,13 @@ SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation
 FROM dd_delta_has_spouse_candidates R0
         
         """
+          output_relation: "dd_new_has_spouse_candidates"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+            dd_delta_has_spouse_candidates
+          ]
       }
     
 
@@ -223,8 +93,13 @@ SELECT R0.relation_id, R0.feature
 FROM dd_delta_has_spouse_features R0
         
         """
+          output_relation: "dd_new_has_spouse_features"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            has_spouse_features
+            dd_delta_has_spouse_features
+          ]
       }
     
 
@@ -238,8 +113,13 @@ SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependen
 FROM dd_delta_sentences R0
         
         """
+          output_relation: "dd_new_sentences"
         style: "sql_extractor"
           
+          input_relations: [
+            sentences
+            dd_delta_sentences
+          ]
       }
     
 
@@ -250,8 +130,12 @@ FROM dd_delta_sentences R0
         
           
         """
+          output_relation: "dd_delta_has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            dd_delta_has_spouse_candidates
+          ]
       }
     
 
@@ -267,8 +151,13 @@ SELECT DISTINCT R0.relation_id, id, label
         
           
         """
+          output_relation: "dd_new_has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_dd_delta_has_spouse" ]
+          input_relations: [
+            has_spouse
+            dd_delta_has_spouse
+          ]
       }
     
 
@@ -281,6 +170,9 @@ FROM dd_delta_sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_relations: [
+            dd_delta_sentences
+          ]
           input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
@@ -299,6 +191,11 @@ FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
+          input_relations: [
+            dd_delta_people_mentions
+            people_mentions
+            dd_new_people_mentions
+          ]
           input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
@@ -325,6 +222,16 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
+          input_relations: [
+            dd_delta_sentences
+            has_spouse_candidates
+            people_mentions
+            dd_new_sentences
+            dd_delta_has_spouse_candidates
+            dd_new_has_spouse_candidates
+            dd_delta_people_mentions
+            dd_new_people_mentions
+          ]
           input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
@@ -340,6 +247,14 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(dd_new_has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_has_spouse_candidates" ,  "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            dd_new_has_spouse
+            dd_delta_has_spouse_candidates
+            has_spouse_features
+            dd_new_has_spouse_candidates
+            dd_delta_has_spouse_features
+          ]
         }
       
 
@@ -350,23 +265,14 @@ FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mention
         WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
           function: "Equal(dd_new_has_spouse.R0.label, dd_new_has_spouse.R1.label)"
           weight: "3.0"
+          dependencies: [ "ext_dd_new_has_spouse_candidates" ]
+          input_relations: [
+            dd_new_has_spouse
+            dd_new_has_spouse_candidates
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_articles
-  init_dd_new_people_mentions
-  init_dd_delta_has_spouse_features
-  init_dd_new_articles
-  init_dd_new_has_spouse_candidates
-  init_dd_new_has_spouse_features
-  init_dd_new_sentences
-  init_dd_delta_people_mentions
-  init_dd_delta_has_spouse_candidates
-  init_dd_delta_sentences
-  init_dd_delta_has_spouse
-  init_dd_new_has_spouse
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_new_has_spouse_candidates
   ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
@@ -397,7 +303,4 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_istrue_has_spouse
   dd_delta_inf_equal_has_spouse_has_spouse
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
 deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 53fe8218a..818351f39 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -17,87 +17,6 @@
       }
     
 
-          deepdive.extraction.extractors.init_sentences {
-            sql: """ DROP TABLE IF EXISTS sentences CASCADE;
-            CREATE TABLE
-            sentences(document_id text,
-         sentence text,
-         words text[],
-         lemma text[],
-         pos_tags text[],
-         dependencies text[],
-         ner_tags text[],
-         sentence_offset int,
-         sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS has_spouse_candidates CASCADE;
-            CREATE TABLE
-            has_spouse_candidates(person1_id text,
-                     person2_id text,
-                     sentence_id text,
-                     description text,
-                     relation_id text,
-                     is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse {
-            sql: """ DROP TABLE IF EXISTS has_spouse CASCADE;
-            CREATE TABLE
-            has_spouse(relation_id text,
-          id bigint,
-          label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_articles {
-            sql: """ DROP TABLE IF EXISTS articles CASCADE;
-            CREATE TABLE
-            articles(article_id text,
-        text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS has_spouse_features CASCADE;
-            CREATE TABLE
-            has_spouse_features(relation_id text,
-                   feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_people_mentions {
-            sql: """ DROP TABLE IF EXISTS people_mentions CASCADE;
-            CREATE TABLE
-            people_mentions(sentence_id text,
-               start_position int,
-               length int,
-               text text,
-               mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE sentences;
-          TRUNCATE has_spouse_candidates;
-          TRUNCATE has_spouse;
-          TRUNCATE articles;
-          TRUNCATE has_spouse_features;
-          TRUNCATE people_mentions;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_has_spouse {
         sql: """ 
         INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
@@ -105,8 +24,12 @@
         
           
         """
+          output_relation: "has_spouse"
         style: "sql_extractor"
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+          ]
       }
     
 
@@ -119,6 +42,9 @@ FROM sentences R0
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
           
+          input_relations: [
+            sentences
+          ]
           input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
@@ -133,6 +59,9 @@ FROM people_mentions R0, people_mentions R1
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_people_mentions_by_ext_people" ]
+          input_relations: [
+            people_mentions
+          ]
           input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
@@ -147,6 +76,11 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
+          input_relations: [
+            sentences
+            has_spouse_candidates
+            people_mentions
+          ]
           input_batch_size: ${INPUT_BATCH_SIZE}
           parallelism: ${PARALLELISM}
         }
@@ -159,6 +93,12 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_has_spouse_features_by_ext_has_spouse_features" ]
+          input_relations: [
+            has_spouse
+            has_spouse_candidates
+            has_spouse_features
+          ]
         }
       
 
@@ -169,17 +109,14 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
           function: "Equal(has_spouse.R0.label, has_spouse.R1.label)"
           weight: "3.0"
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse
+            has_spouse_candidates
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_sentences
-  init_has_spouse_candidates
-  init_has_spouse
-  init_articles
-  init_has_spouse_features
-  init_people_mentions
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
@@ -198,6 +135,3 @@ deepdive.pipeline.pipelines.endtoend: [
   inf_istrue_has_spouse
   inf_equal_has_spouse_has_spouse
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 816504966..2b11ebded 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -17,30 +17,18 @@
       }
     
 
-          deepdive.extraction.extractors.init_R {
-            sql: """ DROP TABLE IF EXISTS R CASCADE;
-            CREATE TABLE
-            R(a int,
- b int)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE R;
-          """
-          style: "sql_extractor"
-        }
-
       deepdive.extraction.extractors.ext_A {
         sql: """ DROP VIEW IF EXISTS A;
         CREATE VIEW A AS SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
 FROM R R0
         
         """
+          output_relation: "A"
         style: "sql_extractor"
           
+          input_relations: [
+            R
+          ]
       }
     
 
@@ -50,14 +38,16 @@ FROM R R0
 FROM A R0, R R1
         WHERE R1.a = R0.column_1 
         """
+          output_relation: "B"
         style: "sql_extractor"
           dependencies: [ "ext_A" ]
+          input_relations: [
+            A
+            R
+          ]
       }
     
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_R
-]
 deepdive.pipeline.pipelines.extraction: [
   ext_A
   ext_B
@@ -66,6 +56,3 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_A
   ext_B
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index db8336991..b6595ae6b 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -21,78 +21,6 @@ c.label: Boolean
       }
     
 
-          deepdive.extraction.extractors.init_e {
-            sql: """ DROP TABLE IF EXISTS e CASCADE;
-            CREATE TABLE
-            e(k int,
- id bigint,
- label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_f {
-            sql: """ DROP TABLE IF EXISTS f CASCADE;
-            CREATE TABLE
-            f(k int,
- id bigint,
- label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_a {
-            sql: """ DROP TABLE IF EXISTS a CASCADE;
-            CREATE TABLE
-            a(k int,
- id bigint,
- label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_b {
-            sql: """ DROP TABLE IF EXISTS b CASCADE;
-            CREATE TABLE
-            b(k int,
- p int,
- q text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_c {
-            sql: """ DROP TABLE IF EXISTS c CASCADE;
-            CREATE TABLE
-            c(k int,
- id bigint,
- label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_d {
-            sql: """ DROP TABLE IF EXISTS d CASCADE;
-            CREATE TABLE
-            d(k int,
- id bigint,
- label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE e;
-          TRUNCATE f;
-          TRUNCATE a;
-          TRUNCATE b;
-          TRUNCATE c;
-          TRUNCATE d;
-          """
-          style: "sql_extractor"
-        }
-
         deepdive.inference.factors.inf_istrue_a {
           input_query: """
           SELECT R0.id AS "a.R0.id" , (R0.k + R1.p) AS "dd_weight_column_0" 
@@ -100,6 +28,11 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(a.R0.label)"
           weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            a
+            b
+          ]
         }
       
 
@@ -110,6 +43,11 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(c.R0.label)"
           weight: "?"
+          
+          input_relations: [
+            c
+            b
+          ]
         }
       
 
@@ -120,6 +58,11 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(d.R0.label)"
           weight: "?(dd_weight_column_0, dd_weight_column_1)"
+          
+          input_relations: [
+            d
+            b
+          ]
         }
       
 
@@ -130,6 +73,11 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(e.R0.label)"
           weight: "-10"
+          
+          input_relations: [
+            e
+            b
+          ]
         }
       
 
@@ -140,17 +88,14 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(f.R0.label)"
           weight: "-0.3"
+          
+          input_relations: [
+            f
+            b
+          ]
         }
       
 deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.initdb: [
-  init_e
-  init_f
-  init_a
-  init_b
-  init_c
-  init_d
-]
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_a
   inf_istrue_c
@@ -165,6 +110,3 @@ deepdive.pipeline.pipelines.endtoend: [
   inf_istrue_e
   inf_istrue_f
 ]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]

From 7dba5001e00ecf58b4dd1da69d8c6233826ec3fc Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 10 Nov 2015 04:59:33 -0800
Subject: [PATCH 242/347] Ignore IntelliJ IDEA files

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 61245514c..ee7085932 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,5 @@ target
 
 /test/*-test/**/*.bats
 /test/*-test/**/*.actual
+
+/.idea

From 049168a994da5f870f1fe25c0d3cb50fa6e45921 Mon Sep 17 00:00:00 2001
From: Juhana Kangaspunta <juhana.kangaspunta@gmail.com>
Date: Wed, 28 Oct 2015 08:47:01 -0700
Subject: [PATCH 243/347] Added CASCADE when dropping view.

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 86be9f981..3fc6488df 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -594,7 +594,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         if (isForIncremental(stmts(0).headName) && !(ss.isQueryTerm(stmts(0).headName)))
           s"TRUNCATE ${stmts(0).headName};"
         else ""
-      } else s"DROP VIEW IF EXISTS ${stmts(0).headName};"
+      } else s"DROP VIEW IF EXISTS ${stmts(0).headName} CASCADE;"
     }
     val createTable = ss.mode match {
       case MERGE => true

From 9ccc9f383ef888a387bb0286bb6d6dcedf0f9f3d Mon Sep 17 00:00:00 2001
From: Juhana Kangaspunta <juhana.kangaspunta@gmail.com>
Date: Wed, 4 Nov 2015 09:56:57 -0800
Subject: [PATCH 244/347] Fixed tests.

---
 .../expressions/compile.expected              | 170 +++++++++---------
 .../views/compile.expected                    |  20 +--
 2 files changed, 95 insertions(+), 95 deletions(-)

diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 27a13ba61..dc3f90dfb 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -9,13 +9,13 @@
     port: ${PGPORT}
     incremental_mode: ORIGINAL
     }
-    
+
 
 
       deepdive.schema.variables {
-        
+
       }
-    
+
 
           deepdive.extraction.extractors.init_b {
             sql: """ DROP TABLE IF EXISTS b CASCADE;
@@ -56,258 +56,258 @@
         }
 
       deepdive.extraction.extractors.ext_E {
-        sql: """ DROP VIEW IF EXISTS E;
+        sql: """ DROP VIEW IF EXISTS E CASCADE;
         CREATE VIEW E AS SELECT (R0.k :: INT) AS column_0
 FROM b R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_X {
-        sql: """ DROP VIEW IF EXISTS X;
+        sql: """ DROP VIEW IF EXISTS X CASCADE;
         CREATE VIEW X AS SELECT R0.k AS column_0
 FROM b R0, c R1
-        WHERE R1.n = R0.k 
+        WHERE R1.n = R0.k
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_N {
-        sql: """ DROP VIEW IF EXISTS N;
+        sql: """ DROP VIEW IF EXISTS N CASCADE;
         CREATE VIEW N AS SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_T {
-        sql: """ DROP VIEW IF EXISTS T;
+        sql: """ DROP VIEW IF EXISTS T CASCADE;
         CREATE VIEW T AS SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         WHERE R1_0.s > R0.p
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_J {
-        sql: """ DROP VIEW IF EXISTS J;
+        sql: """ DROP VIEW IF EXISTS J CASCADE;
         CREATE VIEW J AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_U {
-        sql: """ DROP VIEW IF EXISTS U;
+        sql: """ DROP VIEW IF EXISTS U CASCADE;
         CREATE VIEW U AS SELECT R0_0.k AS column_0
-FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
-        
+FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_F {
-        sql: """ DROP VIEW IF EXISTS F;
+        sql: """ DROP VIEW IF EXISTS F CASCADE;
         CREATE VIEW F AS SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
 FROM b R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_A {
-        sql: """ DROP VIEW IF EXISTS A;
+        sql: """ DROP VIEW IF EXISTS A CASCADE;
         CREATE VIEW A AS SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
 FROM b R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_M {
-        sql: """ DROP VIEW IF EXISTS M;
+        sql: """ DROP VIEW IF EXISTS M CASCADE;
         CREATE VIEW M AS SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_I {
-        sql: """ DROP VIEW IF EXISTS I;
+        sql: """ DROP VIEW IF EXISTS I CASCADE;
         CREATE VIEW I AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_G {
-        sql: """ DROP VIEW IF EXISTS G;
+        sql: """ DROP VIEW IF EXISTS G CASCADE;
         CREATE VIEW G AS SELECT R0.k AS column_0
 FROM b R0
         WHERE (R0.k + R0.r) = 100
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_V {
-        sql: """ DROP VIEW IF EXISTS V;
+        sql: """ DROP VIEW IF EXISTS V CASCADE;
         CREATE VIEW V AS SELECT R0.n AS column_0
 FROM c R0, a R1
-        WHERE R1.k = R0.n 
+        WHERE R1.k = R0.n
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_Q {
-        sql: """ DROP VIEW IF EXISTS Q;
+        sql: """ DROP VIEW IF EXISTS Q CASCADE;
         CREATE VIEW Q AS SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_L {
-        sql: """ DROP VIEW IF EXISTS L;
+        sql: """ DROP VIEW IF EXISTS L CASCADE;
         CREATE VIEW L AS SELECT DISTINCT R0.k AS column_0
 FROM b R0
         LIMIT 100
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_B {
-        sql: """ DROP VIEW IF EXISTS B;
+        sql: """ DROP VIEW IF EXISTS B CASCADE;
         CREATE VIEW B AS SELECT func((R0.k + (R0.r + R0.k))) AS column_0
 FROM b R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_P {
-        sql: """ DROP VIEW IF EXISTS P;
+        sql: """ DROP VIEW IF EXISTS P CASCADE;
         CREATE VIEW P AS SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
 FROM a R0, b R1
-        WHERE R1.k = R0.k 
+        WHERE R1.k = R0.k
         GROUP BY R1.p, R1.q
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_C {
-        sql: """ DROP VIEW IF EXISTS C;
+        sql: """ DROP VIEW IF EXISTS C CASCADE;
         CREATE VIEW C AS SELECT func(func(func(R0.k))) AS column_0
 FROM b R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_H {
-        sql: """ DROP VIEW IF EXISTS H;
+        sql: """ DROP VIEW IF EXISTS H CASCADE;
         CREATE VIEW H AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_W {
-        sql: """ DROP VIEW IF EXISTS W;
+        sql: """ DROP VIEW IF EXISTS W CASCADE;
         CREATE VIEW W AS SELECT R0.k AS column_0
 FROM a R0
         WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_K {
-        sql: """ DROP VIEW IF EXISTS K;
+        sql: """ DROP VIEW IF EXISTS K CASCADE;
         CREATE VIEW K AS SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_O {
-        sql: """ DROP VIEW IF EXISTS O;
+        sql: """ DROP VIEW IF EXISTS O CASCADE;
         CREATE VIEW O AS SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_D {
-        sql: """ DROP VIEW IF EXISTS D;
+        sql: """ DROP VIEW IF EXISTS D CASCADE;
         CREATE VIEW D AS SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
 FROM b R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_S {
-        sql: """ DROP VIEW IF EXISTS S;
+        sql: """ DROP VIEW IF EXISTS S CASCADE;
         CREATE VIEW S AS SELECT R0.k AS column_0
-FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
-        
+FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [
   init_b
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 816504966..934c0c933 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -9,13 +9,13 @@
     port: ${PGPORT}
     incremental_mode: ORIGINAL
     }
-    
+
 
 
       deepdive.schema.variables {
-        
+
       }
-    
+
 
           deepdive.extraction.extractors.init_R {
             sql: """ DROP TABLE IF EXISTS R CASCADE;
@@ -34,26 +34,26 @@
         }
 
       deepdive.extraction.extractors.ext_A {
-        sql: """ DROP VIEW IF EXISTS A;
+        sql: """ DROP VIEW IF EXISTS A CASCADE;
         CREATE VIEW A AS SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
 FROM R R0
-        
+
         """
         style: "sql_extractor"
-          
+
       }
-    
+
 
       deepdive.extraction.extractors.ext_B {
-        sql: """ DROP VIEW IF EXISTS B;
+        sql: """ DROP VIEW IF EXISTS B CASCADE;
         CREATE VIEW B AS SELECT R0.column_0 AS column_0, R1.b AS column_1
 FROM A R0, R R1
-        WHERE R1.a = R0.column_1 
+        WHERE R1.a = R0.column_1
         """
         style: "sql_extractor"
           dependencies: [ "ext_A" ]
       }
-    
+
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.initdb: [
   init_R

From 288ee0ecc39844d98f18644c1053907392c50ba8 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 17 Nov 2015 01:34:08 -0800
Subject: [PATCH 245/347] Adds back initdb and cleanup for incremental modes

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  20 ++-
 .../compile-incremental.expected              |  86 ++++++++++
 .../ocr_example/compile-incremental.expected  | 107 ++++++++++++
 .../compile-incremental.expected              | 125 ++++++++++++++
 .../compile-incremental.expected              | 162 ++++++++++++++++++
 .../compile-incremental.expected              | 162 ++++++++++++++++++
 .../compile-incremental.expected              | 162 ++++++++++++++++++
 7 files changed, 823 insertions(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 0107e9378..cca0a6c29 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -824,7 +824,20 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
       case MATERIALIZATION | INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
       case _ => ""
     }
-    List(run, extraction_pipeline, inference_pipeline, endtoend_pipeline, base_dir).filter(_ != "")
+    List(run, extraction_pipeline, inference_pipeline, endtoend_pipeline, base_dir).filter(_ != "") ++ (
+    // FIXME remove the following after fully supporting incremental uops
+    // XXX initdb pipeline and CREATE TABLE extractors has been moved to deepdive
+    ss.mode match {
+      case INCREMENTAL =>
+        val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
+        val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [\n  ${setup_database_pipeline}\n]" else ""
+        val cleanup_pipeline = ss.mode match {
+          case INCREMENTAL | ORIGINAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [\n  cleanup\n]" else ""
+          case _ => ""
+        }
+        List(initdb, cleanup_pipeline)
+      case _ => List.empty
+    }) // FIXME remove above after fully supporting incremental uops
   }
 
   // generate variable schema statements
@@ -867,6 +880,11 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val state = new CompilationState( programToCompile, config )
 
     val body = new ListBuffer[String]()
+    config.mode match {
+      case INCREMENTAL =>
+        body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
+      case _ =>
+    }
     state.extractionRuleGroupByHead foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
     state.functionCallList          foreach {func   => body ++= compileFunctionCallRules(List(func), state)}
     state.inferenceRules            foreach {inf    => body ++= compileInferenceRules(List(inf), state)}
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index 33873bab3..e5cce9abf 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -23,6 +23,79 @@ dd_new_Q.label: Boolean
       }
     
 
+          deepdive.extraction.extractors.init_dd_new_S {
+            sql: """ DROP TABLE IF EXISTS dd_new_S CASCADE;
+            CREATE TABLE
+            dd_new_S(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_T {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T CASCADE;
+            CREATE TABLE
+            dd_delta_T(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_T {
+            sql: """ DROP TABLE IF EXISTS dd_new_T CASCADE;
+            CREATE TABLE
+            dd_new_T(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_S {
+            sql: """ DROP TABLE IF EXISTS dd_delta_S CASCADE;
+            CREATE TABLE
+            dd_delta_S(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_R {
+            sql: """ DROP TABLE IF EXISTS dd_new_R CASCADE;
+            CREATE TABLE
+            dd_new_R(a int,
+        b int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_R {
+            sql: """ DROP TABLE IF EXISTS dd_delta_R CASCADE;
+            CREATE TABLE
+            dd_delta_R(a int,
+          b int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_Q {
+            sql: """ DROP TABLE IF EXISTS dd_delta_Q CASCADE;
+            CREATE TABLE
+            dd_delta_Q(x int,
+          id bigint,
+          label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_new_S;
+          TRUNCATE dd_delta_T;
+          TRUNCATE dd_new_T;
+          TRUNCATE dd_delta_S;
+          TRUNCATE dd_new_R;
+          TRUNCATE dd_delta_R;
+          TRUNCATE dd_delta_Q;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.ext_dd_new_S {
         sql: """ TRUNCATE dd_new_S;
         INSERT INTO dd_new_S SELECT R0.a
@@ -382,3 +455,16 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf1_imply_Q_Q
 ]
 deepdive.pipeline.base_dir: ${BASEDIR}
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_new_S
+  init_dd_delta_T
+  init_dd_new_T
+  init_dd_delta_S
+  init_dd_new_R
+  init_dd_delta_R
+  init_dd_new_Q
+  init_dd_delta_Q
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index b36a8f25e..66fafaca1 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -28,6 +28,98 @@ q1.label: Boolean
       }
     
 
+          deepdive.extraction.extractors.init_dd_new_label2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_label2 CASCADE;
+            CREATE TABLE
+            dd_new_label2(wid INT,
+             val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_label1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_label1 CASCADE;
+            CREATE TABLE
+            dd_delta_label1(wid INT,
+               val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_label1 {
+            sql: """ DROP TABLE IF EXISTS dd_new_label1 CASCADE;
+            CREATE TABLE
+            dd_new_label1(wid INT,
+             val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_features {
+            sql: """ DROP TABLE IF EXISTS dd_delta_features CASCADE;
+            CREATE TABLE
+            dd_delta_features(id BIGSERIAL,
+                 word_id INT,
+                 feature_id INT,
+                 feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_q2 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_q2 CASCADE;
+            CREATE TABLE
+            dd_delta_q2(wid INT,
+           id bigint,
+           label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_label2 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_label2 CASCADE;
+            CREATE TABLE
+            dd_delta_label2(wid INT,
+               val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_features {
+            sql: """ DROP TABLE IF EXISTS dd_new_features CASCADE;
+            CREATE TABLE
+            dd_new_features(id BIGSERIAL,
+               word_id INT,
+               feature_id INT,
+               feature_val BOOLEAN)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_q1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_q1 CASCADE;
+            CREATE TABLE
+            dd_delta_q1(wid INT,
+           id bigint,
+           label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_new_label2;
+          TRUNCATE dd_delta_label1;
+          TRUNCATE dd_new_label1;
+          TRUNCATE dd_delta_features;
+          TRUNCATE dd_delta_q2;
+          TRUNCATE dd_delta_label2;
+          TRUNCATE dd_new_features;
+          TRUNCATE dd_delta_q1;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.ext_dd_new_label2 {
         sql: """ TRUNCATE dd_new_label2;
         INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
@@ -219,3 +311,18 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_istrue_q2
 ]
 deepdive.pipeline.base_dir: ${BASEDIR}
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_new_label2
+  init_dd_delta_label1
+  init_dd_new_q1
+  init_dd_new_label1
+  init_dd_delta_features
+  init_dd_delta_q2
+  init_dd_delta_label2
+  init_dd_new_features
+  init_dd_delta_q1
+  init_dd_new_q2
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 94624454e..9f153630c 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -28,6 +28,114 @@ dd_delta_smoke.label: Boolean
       }
     
 
+          deepdive.extraction.extractors.init_dd_delta_friends {
+            sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
+            CREATE TABLE
+            dd_delta_friends(person_id bigint,
+                friend_id bigint)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_smoke {
+            sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
+            CREATE TABLE
+            dd_delta_smoke(person_id bigint,
+              id bigint,
+              label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_person_has_cancer {
+            sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
+            CREATE TABLE
+            dd_new_person_has_cancer(person_id bigint,
+                        has_cancer boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_person {
+            sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
+            CREATE TABLE
+            dd_delta_person(person_id bigint,
+               name text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_person {
+            sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
+            CREATE TABLE
+            dd_new_person(person_id bigint,
+             name text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_person_has_cancer {
+            sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
+            CREATE TABLE
+            dd_delta_person_has_cancer(person_id bigint,
+                          has_cancer boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_cancer {
+            sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
+            CREATE TABLE
+            dd_delta_cancer(person_id bigint,
+               id bigint,
+               label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_person_smokes {
+            sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
+            CREATE TABLE
+            dd_delta_person_smokes(person_id bigint,
+                      smokes boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_person_smokes {
+            sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
+            CREATE TABLE
+            dd_new_person_smokes(person_id bigint,
+                    smokes boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_friends {
+            sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
+            CREATE TABLE
+            dd_new_friends(person_id bigint,
+              friend_id bigint)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_friends;
+          TRUNCATE dd_delta_smoke;
+          TRUNCATE dd_new_person_has_cancer;
+          TRUNCATE dd_delta_person;
+          TRUNCATE dd_new_person;
+          TRUNCATE dd_delta_person_has_cancer;
+          TRUNCATE dd_delta_cancer;
+          TRUNCATE dd_delta_person_smokes;
+          TRUNCATE dd_new_person_smokes;
+          TRUNCATE dd_new_friends;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.ext_dd_delta_smoke {
         sql: """ 
         INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
@@ -242,3 +350,20 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_imply_smoke_smoke
 ]
 deepdive.pipeline.base_dir: ${BASEDIR}
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_friends
+  init_dd_delta_smoke
+  init_dd_new_person_has_cancer
+  init_dd_delta_person
+  init_dd_new_person
+  init_dd_delta_person_has_cancer
+  init_dd_new_smoke
+  init_dd_delta_cancer
+  init_dd_new_cancer
+  init_dd_delta_person_smokes
+  init_dd_new_person_smokes
+  init_dd_new_friends
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 4dc00ba3b..6f4b117d3 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -23,6 +23,151 @@ dd_new_has_spouse.label: Boolean
       }
     
 
+          deepdive.extraction.extractors.init_dd_delta_articles {
+            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+            CREATE TABLE
+            dd_delta_articles(article_id text,
+                 text text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_people_mentions {
+            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+            CREATE TABLE
+            dd_new_people_mentions(sentence_id text,
+                      start_position int,
+                      length int,
+                      text text,
+                      mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_features(relation_id text,
+                            feature text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_articles {
+            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+            CREATE TABLE
+            dd_new_articles(article_id text,
+               text text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_candidates(person1_id text,
+                            person2_id text,
+                            sentence_id text,
+                            description text,
+                            relation_id text,
+                            is_true boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_features(relation_id text,
+                          feature text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_sentences {
+            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+            CREATE TABLE
+            dd_new_sentences(document_id text,
+                sentence text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
+                sentence_offset int,
+                sentence_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_people_mentions {
+            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+            CREATE TABLE
+            dd_delta_people_mentions(sentence_id text,
+                        start_position int,
+                        length int,
+                        text text,
+                        mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_candidates(person1_id text,
+                              person2_id text,
+                              sentence_id text,
+                              description text,
+                              relation_id text,
+                              is_true boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_sentences {
+            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+            CREATE TABLE
+            dd_delta_sentences(document_id text,
+                  sentence text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
+                  sentence_offset int,
+                  sentence_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse(relation_id text,
+                   id bigint,
+                   label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_articles;
+          TRUNCATE dd_new_people_mentions;
+          TRUNCATE dd_delta_has_spouse_features;
+          TRUNCATE dd_new_articles;
+          TRUNCATE dd_new_has_spouse_candidates;
+          TRUNCATE dd_new_has_spouse_features;
+          TRUNCATE dd_new_sentences;
+          TRUNCATE dd_delta_people_mentions;
+          TRUNCATE dd_delta_has_spouse_candidates;
+          TRUNCATE dd_delta_sentences;
+          TRUNCATE dd_delta_has_spouse;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
@@ -287,3 +432,20 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_istrue_has_spouse
 ]
 deepdive.pipeline.base_dir: ${BASEDIR}
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_articles
+  init_dd_new_people_mentions
+  init_dd_delta_has_spouse_features
+  init_dd_new_articles
+  init_dd_new_has_spouse_candidates
+  init_dd_new_has_spouse_features
+  init_dd_new_sentences
+  init_dd_delta_people_mentions
+  init_dd_delta_has_spouse_candidates
+  init_dd_delta_sentences
+  init_dd_delta_has_spouse
+  init_dd_new_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 350f08550..60644e1bd 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -23,6 +23,151 @@ dd_new_has_spouse.label: Boolean
       }
     
 
+          deepdive.extraction.extractors.init_dd_delta_articles {
+            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+            CREATE TABLE
+            dd_delta_articles(article_id text,
+                 text text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_people_mentions {
+            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+            CREATE TABLE
+            dd_new_people_mentions(sentence_id text,
+                      start_position int,
+                      length int,
+                      text text,
+                      mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_features(relation_id text,
+                            feature text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_articles {
+            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+            CREATE TABLE
+            dd_new_articles(article_id text,
+               text text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_candidates(person1_id text,
+                            person2_id text,
+                            sentence_id text,
+                            description text,
+                            relation_id text,
+                            is_true boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_features(relation_id text,
+                          feature text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_sentences {
+            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+            CREATE TABLE
+            dd_new_sentences(document_id text,
+                sentence text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
+                sentence_offset int,
+                sentence_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_people_mentions {
+            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+            CREATE TABLE
+            dd_delta_people_mentions(sentence_id text,
+                        start_position int,
+                        length int,
+                        text text,
+                        mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_candidates(person1_id text,
+                              person2_id text,
+                              sentence_id text,
+                              description text,
+                              relation_id text,
+                              is_true boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_sentences {
+            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+            CREATE TABLE
+            dd_delta_sentences(document_id text,
+                  sentence text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
+                  sentence_offset int,
+                  sentence_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse(relation_id text,
+                   id bigint,
+                   label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_articles;
+          TRUNCATE dd_new_people_mentions;
+          TRUNCATE dd_delta_has_spouse_features;
+          TRUNCATE dd_new_articles;
+          TRUNCATE dd_new_has_spouse_candidates;
+          TRUNCATE dd_new_has_spouse_features;
+          TRUNCATE dd_new_sentences;
+          TRUNCATE dd_delta_people_mentions;
+          TRUNCATE dd_delta_has_spouse_candidates;
+          TRUNCATE dd_delta_sentences;
+          TRUNCATE dd_delta_has_spouse;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
@@ -292,3 +437,20 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_istrue_has_spouse
 ]
 deepdive.pipeline.base_dir: ${BASEDIR}
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_articles
+  init_dd_new_people_mentions
+  init_dd_delta_has_spouse_features
+  init_dd_new_articles
+  init_dd_new_has_spouse_candidates
+  init_dd_new_has_spouse_features
+  init_dd_new_sentences
+  init_dd_delta_people_mentions
+  init_dd_delta_has_spouse_candidates
+  init_dd_delta_sentences
+  init_dd_delta_has_spouse
+  init_dd_new_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 3ba3754c5..1c49f8eaa 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -23,6 +23,151 @@ dd_new_has_spouse.label: Boolean
       }
     
 
+          deepdive.extraction.extractors.init_dd_delta_articles {
+            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
+            CREATE TABLE
+            dd_delta_articles(article_id text,
+                 text text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_people_mentions {
+            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
+            CREATE TABLE
+            dd_new_people_mentions(sentence_id text,
+                      start_position int,
+                      length int,
+                      text text,
+                      mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_features(relation_id text,
+                            feature text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_articles {
+            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
+            CREATE TABLE
+            dd_new_articles(article_id text,
+               text text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_candidates(person1_id text,
+                            person2_id text,
+                            sentence_id text,
+                            description text,
+                            relation_id text,
+                            is_true boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
+            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
+            CREATE TABLE
+            dd_new_has_spouse_features(relation_id text,
+                          feature text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_new_sentences {
+            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
+            CREATE TABLE
+            dd_new_sentences(document_id text,
+                sentence text,
+                words text[],
+                lemma text[],
+                pos_tags text[],
+                dependencies text[],
+                ner_tags text[],
+                sentence_offset int,
+                sentence_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_people_mentions {
+            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
+            CREATE TABLE
+            dd_delta_people_mentions(sentence_id text,
+                        start_position int,
+                        length int,
+                        text text,
+                        mention_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse_candidates(person1_id text,
+                              person2_id text,
+                              sentence_id text,
+                              description text,
+                              relation_id text,
+                              is_true boolean)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_sentences {
+            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
+            CREATE TABLE
+            dd_delta_sentences(document_id text,
+                  sentence text,
+                  words text[],
+                  lemma text[],
+                  pos_tags text[],
+                  dependencies text[],
+                  ner_tags text[],
+                  sentence_offset int,
+                  sentence_id text)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_has_spouse {
+            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
+            CREATE TABLE
+            dd_delta_has_spouse(relation_id text,
+                   id bigint,
+                   label boolean)
+            """
+            style: "sql_extractor"
+          }
+
+        deepdive.extraction.extractors.cleanup {
+          sql: """
+          TRUNCATE dd_delta_articles;
+          TRUNCATE dd_new_people_mentions;
+          TRUNCATE dd_delta_has_spouse_features;
+          TRUNCATE dd_new_articles;
+          TRUNCATE dd_new_has_spouse_candidates;
+          TRUNCATE dd_new_has_spouse_features;
+          TRUNCATE dd_new_sentences;
+          TRUNCATE dd_delta_people_mentions;
+          TRUNCATE dd_delta_has_spouse_candidates;
+          TRUNCATE dd_delta_sentences;
+          TRUNCATE dd_delta_has_spouse;
+          """
+          style: "sql_extractor"
+        }
+
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
         sql: """ TRUNCATE dd_new_people_mentions;
         INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
@@ -304,3 +449,20 @@ deepdive.pipeline.pipelines.endtoend: [
   dd_delta_inf_equal_has_spouse_has_spouse
 ]
 deepdive.pipeline.base_dir: ${BASEDIR}
+deepdive.pipeline.pipelines.initdb: [
+  init_dd_delta_articles
+  init_dd_new_people_mentions
+  init_dd_delta_has_spouse_features
+  init_dd_new_articles
+  init_dd_new_has_spouse_candidates
+  init_dd_new_has_spouse_features
+  init_dd_new_sentences
+  init_dd_delta_people_mentions
+  init_dd_delta_has_spouse_candidates
+  init_dd_delta_sentences
+  init_dd_delta_has_spouse
+  init_dd_new_has_spouse
+]
+deepdive.pipeline.pipelines.cleanup: [
+  cleanup
+]

From ce2a8c9d98abc5ca84c13ab6455bd7ea229044c0 Mon Sep 17 00:00:00 2001
From: ThomasPalomares <thopalomares@gmail.com>
Date: Thu, 14 Jan 2016 13:37:26 -0800
Subject: [PATCH 246/347] creation table commands directly in ddlog compiled

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 22 ++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d327823d2..bffb49193 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -520,6 +520,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
   def isForIncremental(name: String) = name startsWith "dd_new_"
 
+  def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\''")}'"
+
   // Generate schema and cleanup part for database
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
@@ -618,15 +620,25 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         (isForIncremental(stmts(0).headName) &&
         !(ss.isQueryTerm(stmts(0).headName)))
     }
-    val sqlCmdForInsert  = if (createTable) "INSERT INTO" else "CREATE VIEW"
-    val useAS            = if (createTable) "" else " AS"
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
-        sql: \"\"\" ${sqlCmdForCleanUp}
-        ${sqlCmdForInsert} ${stmts(0).headName}${useAS} ${inputQueries.mkString("\nUNION ALL\n")}
+        cmd: \"\"\"
+${if (createTable) {
+	s"""
+	# TODO use temporary table
+	# TODO proper escaping for inputQueries argument
+	deepdive create table "${stmts(0).headName}"
+	deepdive sql ${escape4sh(s"INSERT INTO ${stmts(0).headName} ${inputQueries.mkString("\nUNION ALL\n")}")}
+	# TODO rename temporary table to replace output_relation
+	"""
+} else {
+	s"""
+	deepdive create view ${stmts(0).headName} as ${escape4sh(inputQueries.mkString("\nUNION ALL\n"))}
+	"""
+}}
         \"\"\"
           output_relation: \"${stmts(0).headName}\"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
           input_relations: [${
             (stmts flatMap ss.relationNamesUsedByStatement distinct

From 0b5997686812310068e01d650490a947fa6896f6 Mon Sep 17 00:00:00 2001
From: ThomasPalomares <thopalomares@gmail.com>
Date: Thu, 14 Jan 2016 17:19:07 -0800
Subject: [PATCH 247/347] escape corrected

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index bffb49193..980387fcf 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -520,7 +520,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
   def isForIncremental(name: String) = name startsWith "dd_new_"
 
-  def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\''")}'"
+  def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\\''")}'"
 
   // Generate schema and cleanup part for database
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {

From 38518476a9f01a777cfdf3116fc913deeda497ae Mon Sep 17 00:00:00 2001
From: ThomasPalomares <thopalomares@gmail.com>
Date: Thu, 14 Jan 2016 18:59:31 -0800
Subject: [PATCH 248/347] escape really corrected

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 980387fcf..297959212 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -520,7 +520,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
   def isForIncremental(name: String) = name startsWith "dd_new_"
 
-  def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\\''")}'"
+  def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\\\''")}'"
 
   // Generate schema and cleanup part for database
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {

From 4cb738f955c29e7da65c9a29da98ba48a56a565a Mon Sep 17 00:00:00 2001
From: ThomasPalomares <thopalomares@gmail.com>
Date: Thu, 14 Jan 2016 19:04:43 -0800
Subject: [PATCH 249/347] comment removed

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 297959212..bae9e0a94 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -626,7 +626,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 ${if (createTable) {
 	s"""
 	# TODO use temporary table
-	# TODO proper escaping for inputQueries argument
 	deepdive create table "${stmts(0).headName}"
 	deepdive sql ${escape4sh(s"INSERT INTO ${stmts(0).headName} ${inputQueries.mkString("\nUNION ALL\n")}")}
 	# TODO rename temporary table to replace output_relation

From 7d05bf03fd58ff6f13866cda140231cc8c86492b Mon Sep 17 00:00:00 2001
From: ThomasPalomares <thopalomares@gmail.com>
Date: Thu, 14 Jan 2016 19:42:18 -0800
Subject: [PATCH 250/347] expected outputs updated

---
 .../chunking_example/compile.expected         |  13 +-
 .../expressions/compile.expected              | 230 +++++++++++-------
 .../compile-incremental.expected              |  62 +++--
 .../compile.expected                          |  13 +-
 .../ocr_example/compile-incremental.expected  |  85 ++++---
 .../compile-materialization.expected          |  26 +-
 .../ocr_example/compile-merge.expected        |  39 ++-
 .../ocr_example/compile.expected              |  26 +-
 .../compile-incremental.expected              |  98 +++++---
 .../compile-materialization.expected          |  26 +-
 .../smoke_example/compile-merge.expected      |  52 ++--
 .../smoke_example/compile.expected            |  26 +-
 .../compile-incremental.expected              |  88 ++++---
 .../compile-materialization.expected          |  13 +-
 .../spouse_example/compile-merge.expected     |  65 +++--
 .../spouse_example/compile.expected           |  13 +-
 .../compile-incremental.expected              |  88 ++++---
 .../compile-incremental.expected              |  88 ++++---
 .../compile.expected                          |  13 +-
 .../views/compile.expected                    |  20 +-
 20 files changed, 720 insertions(+), 364 deletions(-)

diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 3d885b7a2..6a869ec16 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -18,14 +18,19 @@
     
 
       deepdive.extraction.extractors.ext_tag {
-        sql: """ 
-        INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "tag"
+	deepdive sql 'INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
           FROM words R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "tag"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_words_by_ext_training" ]
           input_relations: [
             words
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 921c520cc..d90b2472f 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -18,13 +18,15 @@
     
 
       deepdive.extraction.extractors.ext_E {
-        sql: """ DROP VIEW IF EXISTS E CASCADE;
-        CREATE VIEW E AS SELECT (R0.k :: INT) AS column_0
+        cmd: """
+
+	deepdive create view E as 'SELECT (R0.k :: INT) AS column_0
 FROM b R0
-        
+        '
+	
         """
           output_relation: "E"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -33,13 +35,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_X {
-        sql: """ DROP VIEW IF EXISTS X CASCADE;
-        CREATE VIEW X AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view X as 'SELECT R0.k AS column_0
 FROM b R0, c R1
-        WHERE R1.n = R0.k 
+        WHERE R1.n = R0.k '
+	
         """
           output_relation: "X"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -49,13 +53,15 @@ FROM b R0, c R1
     
 
       deepdive.extraction.extractors.ext_N {
-        sql: """ DROP VIEW IF EXISTS N CASCADE;
-        CREATE VIEW N AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view N as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > 'a')
+        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > '\''a'\'')'
+	
         """
           output_relation: "N"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -65,13 +71,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_T {
-        sql: """ DROP VIEW IF EXISTS T CASCADE;
-        CREATE VIEW T AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view T as 'SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
-        WHERE R1_0.s > R0.p
+        WHERE R1_0.s > R0.p'
+	
         """
           output_relation: "T"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -81,13 +89,15 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
     
 
       deepdive.extraction.extractors.ext_J {
-        sql: """ DROP VIEW IF EXISTS J CASCADE;
-        CREATE VIEW J AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view J as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))
+        WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))'
+	
         """
           output_relation: "J"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -96,13 +106,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_U {
-        sql: """ DROP VIEW IF EXISTS U CASCADE;
-        CREATE VIEW U AS SELECT R0_0.k AS column_0
+        cmd: """
+
+	deepdive create view U as 'SELECT R0_0.k AS column_0
 FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
-        
+        '
+	
         """
           output_relation: "U"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -112,13 +124,15 @@ FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
     
 
       deepdive.extraction.extractors.ext_F {
-        sql: """ DROP VIEW IF EXISTS F CASCADE;
-        CREATE VIEW F AS SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
+        cmd: """
+
+	deepdive create view F as 'SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
 FROM b R0
-        
+        '
+	
         """
           output_relation: "F"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -127,13 +141,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_A {
-        sql: """ DROP VIEW IF EXISTS A CASCADE;
-        CREATE VIEW A AS SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
+        cmd: """
+
+	deepdive create view A as 'SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
 FROM b R0
-        
+        '
+	
         """
           output_relation: "A"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -142,13 +158,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_M {
-        sql: """ DROP VIEW IF EXISTS M CASCADE;
-        CREATE VIEW M AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view M as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )
+        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )'
+	
         """
           output_relation: "M"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -158,13 +176,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_I {
-        sql: """ DROP VIEW IF EXISTS I CASCADE;
-        CREATE VIEW I AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view I as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
+        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
+	
         """
           output_relation: "I"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -173,13 +193,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_G {
-        sql: """ DROP VIEW IF EXISTS G CASCADE;
-        CREATE VIEW G AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view G as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100
+        WHERE (R0.k + R0.r) = 100'
+	
         """
           output_relation: "G"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -188,13 +210,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_V {
-        sql: """ DROP VIEW IF EXISTS V CASCADE;
-        CREATE VIEW V AS SELECT R0.n AS column_0
+        cmd: """
+
+	deepdive create view V as 'SELECT R0.n AS column_0
 FROM c R0, a R1
-        WHERE R1.k = R0.n 
+        WHERE R1.k = R0.n '
+	
         """
           output_relation: "V"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             c
@@ -204,13 +228,15 @@ FROM c R0, a R1
     
 
       deepdive.extraction.extractors.ext_Q {
-        sql: """ DROP VIEW IF EXISTS Q CASCADE;
-        CREATE VIEW Q AS SELECT DISTINCT ('test' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
+        cmd: """
+
+	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = 'foo' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))
+        WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))'
+	
         """
           output_relation: "Q"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             a
@@ -221,13 +247,15 @@ FROM a R0, b R1, c R2
     
 
       deepdive.extraction.extractors.ext_L {
-        sql: """ DROP VIEW IF EXISTS L CASCADE;
-        CREATE VIEW L AS SELECT DISTINCT R0.k AS column_0
+        cmd: """
+
+	deepdive create view L as 'SELECT DISTINCT R0.k AS column_0
 FROM b R0
-        LIMIT 100
+        LIMIT 100'
+	
         """
           output_relation: "L"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -236,13 +264,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_B {
-        sql: """ DROP VIEW IF EXISTS B CASCADE;
-        CREATE VIEW B AS SELECT func((R0.k + (R0.r + R0.k))) AS column_0
+        cmd: """
+
+	deepdive create view B as 'SELECT func((R0.k + (R0.r + R0.k))) AS column_0
 FROM b R0
-        
+        '
+	
         """
           output_relation: "B"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -251,14 +281,16 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_P {
-        sql: """ DROP VIEW IF EXISTS P CASCADE;
-        CREATE VIEW P AS SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
+        cmd: """
+
+	deepdive create view P as 'SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
 FROM a R0, b R1
         WHERE R1.k = R0.k 
-        GROUP BY R1.p, R1.q
+        GROUP BY R1.p, R1.q'
+	
         """
           output_relation: "P"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             a
@@ -268,13 +300,15 @@ FROM a R0, b R1
     
 
       deepdive.extraction.extractors.ext_C {
-        sql: """ DROP VIEW IF EXISTS C CASCADE;
-        CREATE VIEW C AS SELECT func(func(func(R0.k))) AS column_0
+        cmd: """
+
+	deepdive create view C as 'SELECT func(func(func(R0.k))) AS column_0
 FROM b R0
-        
+        '
+	
         """
           output_relation: "C"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -283,13 +317,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_H {
-        sql: """ DROP VIEW IF EXISTS H CASCADE;
-        CREATE VIEW H AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view H as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)
+        WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)'
+	
         """
           output_relation: "H"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -298,13 +334,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_W {
-        sql: """ DROP VIEW IF EXISTS W CASCADE;
-        CREATE VIEW W AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view W as 'SELECT R0.k AS column_0
 FROM a R0
-        WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
+        WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))'
+	
         """
           output_relation: "W"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             a
@@ -314,13 +352,15 @@ FROM a R0
     
 
       deepdive.extraction.extractors.ext_K {
-        sql: """ DROP VIEW IF EXISTS K CASCADE;
-        CREATE VIEW K AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view K as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))
+        WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))'
+	
         """
           output_relation: "K"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -329,13 +369,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_O {
-        sql: """ DROP VIEW IF EXISTS O CASCADE;
-        CREATE VIEW O AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view O as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )
+        WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )'
+	
         """
           output_relation: "O"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -346,13 +388,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_D {
-        sql: """ DROP VIEW IF EXISTS D CASCADE;
-        CREATE VIEW D AS SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
+        cmd: """
+
+	deepdive create view D as 'SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
 FROM b R0
-        
+        '
+	
         """
           output_relation: "D"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
@@ -361,13 +405,15 @@ FROM b R0
     
 
       deepdive.extraction.extractors.ext_S {
-        sql: """ DROP VIEW IF EXISTS S CASCADE;
-        CREATE VIEW S AS SELECT R0.k AS column_0
+        cmd: """
+
+	deepdive create view S as 'SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
-        
+        '
+	
         """
           output_relation: "S"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             b
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index e5cce9abf..24e1a8336 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -97,17 +97,22 @@ dd_new_Q.label: Boolean
         }
 
       deepdive.extraction.extractors.ext_dd_new_S {
-        sql: """ TRUNCATE dd_new_S;
-        INSERT INTO dd_new_S SELECT R0.a
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_S"
+	deepdive sql 'INSERT INTO dd_new_S SELECT R0.a
 FROM S R0
         
 UNION ALL
 SELECT R0.a
 FROM dd_delta_S R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_S"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
           input_relations: [
             S
@@ -117,17 +122,22 @@ FROM dd_delta_S R0
     
 
       deepdive.extraction.extractors.ext_dd_new_T {
-        sql: """ TRUNCATE dd_new_T;
-        INSERT INTO dd_new_T SELECT R0.a
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_T"
+	deepdive sql 'INSERT INTO dd_new_T SELECT R0.a
 FROM T R0
         
 UNION ALL
 SELECT R0.a
 FROM dd_delta_T R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_T"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_T_by_f" ,  "ext1_dd_delta_T_by_f" ,  "ext2_dd_delta_T_by_f" ,  "ext_dd_delta_T_by_f_1" ]
           input_relations: [
             T
@@ -137,8 +147,11 @@ FROM dd_delta_T R0
     
 
       deepdive.extraction.extractors.ext_dd_delta_S {
-        sql: """ 
-        INSERT INTO dd_delta_S SELECT R0.a AS "dd_delta_R.R0.a"
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_S"
+	deepdive sql 'INSERT INTO dd_delta_S SELECT R0.a AS "dd_delta_R.R0.a"
 FROM dd_delta_R R0, R R1
         WHERE R1.a = R0.b  AND R0.a > 100
 UNION ALL
@@ -160,10 +173,12 @@ FROM dd_delta_R R0, R R1
 UNION ALL
 SELECT R0.a AS "dd_new_R.R0.a"
 FROM dd_new_R R0, dd_delta_R R1
-        WHERE R1.a = R0.b  AND R0.a = 0
+        WHERE R1.a = R0.b  AND R0.a = 0'
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_S"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_new_R" ]
           input_relations: [
             dd_delta_R
@@ -174,17 +189,22 @@ FROM dd_new_R R0, dd_delta_R R1
     
 
       deepdive.extraction.extractors.ext_dd_new_R {
-        sql: """ TRUNCATE dd_new_R;
-        INSERT INTO dd_new_R SELECT R0.a, R0.b
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_R"
+	deepdive sql 'INSERT INTO dd_new_R SELECT R0.a, R0.b
 FROM R R0
         
 UNION ALL
 SELECT R0.a, R0.b
 FROM dd_delta_R R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_R"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             R
@@ -194,8 +214,9 @@ FROM dd_delta_R R0
     
 
       deepdive.extraction.extractors.ext_dd_new_Q {
-        sql: """ 
-        CREATE VIEW dd_new_Q AS SELECT DISTINCT R0.x, id, label
+        cmd: """
+
+	deepdive create view dd_new_Q as 'SELECT DISTINCT R0.x, id, label
           FROM Q R0
         
           
@@ -203,10 +224,11 @@ UNION ALL
 SELECT DISTINCT R0.x, id, label
           FROM dd_delta_Q R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_Q"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             Q
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 690bdc867..2e72c82a1 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -18,8 +18,11 @@
     
 
       deepdive.extraction.extractors.ext_S {
-        sql: """ 
-        INSERT INTO S SELECT R0.a AS "R.R0.a"
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "S"
+	deepdive sql 'INSERT INTO S SELECT R0.a AS "R.R0.a"
 FROM R R0, R R1
         WHERE R1.a = R0.b  AND R0.a > 100
 UNION ALL
@@ -29,10 +32,12 @@ FROM R R0, R R1
 UNION ALL
 SELECT R0.a AS "R.R0.a"
 FROM R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a = 0
+        WHERE R1.a = R0.b  AND R0.a = 0'
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "S"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             R
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
index 66fafaca1..d4b8bd895 100644
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ b/test/expected-output-test/ocr_example/compile-incremental.expected
@@ -121,17 +121,22 @@ q1.label: Boolean
         }
 
       deepdive.extraction.extractors.ext_dd_new_label2 {
-        sql: """ TRUNCATE dd_new_label2;
-        INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_label2"
+	deepdive sql 'INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
 FROM label2 R0
         
 UNION ALL
 SELECT R0.wid, R0.val
 FROM dd_delta_label2 R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_label2"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             label2
@@ -141,8 +146,9 @@ FROM dd_delta_label2 R0
     
 
       deepdive.extraction.extractors.ext_dd_new_q1 {
-        sql: """ 
-        CREATE VIEW dd_new_q1 AS SELECT DISTINCT R0.wid, id, label
+        cmd: """
+
+	deepdive create view dd_new_q1 as 'SELECT DISTINCT R0.wid, id, label
           FROM q1 R0
         
           
@@ -150,10 +156,11 @@ UNION ALL
 SELECT DISTINCT R0.wid, id, label
           FROM dd_delta_q1 R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_q1"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_q1" ]
           input_relations: [
             q1
@@ -163,17 +170,22 @@ SELECT DISTINCT R0.wid, id, label
     
 
       deepdive.extraction.extractors.ext_dd_new_label1 {
-        sql: """ TRUNCATE dd_new_label1;
-        INSERT INTO dd_new_label1 SELECT R0.wid, R0.val
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_label1"
+	deepdive sql 'INSERT INTO dd_new_label1 SELECT R0.wid, R0.val
 FROM label1 R0
         
 UNION ALL
 SELECT R0.wid, R0.val
 FROM dd_delta_label1 R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_label1"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             label1
@@ -183,14 +195,19 @@ FROM dd_delta_label1 R0
     
 
       deepdive.extraction.extractors.ext_dd_delta_q2 {
-        sql: """ 
-        INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_q2"
+	deepdive sql 'INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM dd_delta_label2 R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_q2"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_delta_label2
@@ -199,17 +216,22 @@ FROM dd_delta_label1 R0
     
 
       deepdive.extraction.extractors.ext_dd_new_features {
-        sql: """ TRUNCATE dd_new_features;
-        INSERT INTO dd_new_features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_features"
+	deepdive sql 'INSERT INTO dd_new_features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
 FROM features R0
         
 UNION ALL
 SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
 FROM dd_delta_features R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_features"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             features
@@ -219,14 +241,19 @@ FROM dd_delta_features R0
     
 
       deepdive.extraction.extractors.ext_dd_delta_q1 {
-        sql: """ 
-        INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_q1"
+	deepdive sql 'INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM dd_delta_label1 R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_q1"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_delta_label1
@@ -235,8 +262,9 @@ FROM dd_delta_features R0
     
 
       deepdive.extraction.extractors.ext_dd_new_q2 {
-        sql: """ 
-        CREATE VIEW dd_new_q2 AS SELECT DISTINCT R0.wid, id, label
+        cmd: """
+
+	deepdive create view dd_new_q2 as 'SELECT DISTINCT R0.wid, id, label
           FROM q2 R0
         
           
@@ -244,10 +272,11 @@ UNION ALL
 SELECT DISTINCT R0.wid, id, label
           FROM dd_delta_q2 R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_q2"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_q2" ]
           input_relations: [
             q2
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
index c6ad59e23..a96559353 100644
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ b/test/expected-output-test/ocr_example/compile-materialization.expected
@@ -19,14 +19,19 @@ q2.label: Boolean
     
 
       deepdive.extraction.extractors.ext_q1 {
-        sql: """ 
-        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "q1"
+	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label1 R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "q1"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             label1
@@ -35,14 +40,19 @@ q2.label: Boolean
     
 
       deepdive.extraction.extractors.ext_q2 {
-        sql: """ 
-        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "q2"
+	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label2 R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "q2"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             label2
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
index 01e56b7bf..e7becd7a6 100644
--- a/test/expected-output-test/ocr_example/compile-merge.expected
+++ b/test/expected-output-test/ocr_example/compile-merge.expected
@@ -18,13 +18,18 @@
     
 
       deepdive.extraction.extractors.ext_label2 {
-        sql: """ TRUNCATE label2;
-        INSERT INTO label2 SELECT R0.wid, R0.val
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "label2"
+	deepdive sql 'INSERT INTO label2 SELECT R0.wid, R0.val
 FROM dd_new_label2 R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "label2"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_label2
@@ -33,13 +38,18 @@ FROM dd_new_label2 R0
     
 
       deepdive.extraction.extractors.ext_label1 {
-        sql: """ TRUNCATE label1;
-        INSERT INTO label1 SELECT R0.wid, R0.val
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "label1"
+	deepdive sql 'INSERT INTO label1 SELECT R0.wid, R0.val
 FROM dd_new_label1 R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "label1"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_label1
@@ -48,13 +58,18 @@ FROM dd_new_label1 R0
     
 
       deepdive.extraction.extractors.ext_features {
-        sql: """ TRUNCATE features;
-        INSERT INTO features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "features"
+	deepdive sql 'INSERT INTO features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
 FROM dd_new_features R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "features"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_features
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 9490160f0..eaeb81d34 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -19,14 +19,19 @@ q2.label: Boolean
     
 
       deepdive.extraction.extractors.ext_q1 {
-        sql: """ 
-        INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "q1"
+	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label1 R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "q1"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             label1
@@ -35,14 +40,19 @@ q2.label: Boolean
     
 
       deepdive.extraction.extractors.ext_q2 {
-        sql: """ 
-        INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "q2"
+	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
           FROM label2 R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "q2"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             label2
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
index 9f153630c..731011bfa 100644
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ b/test/expected-output-test/smoke_example/compile-incremental.expected
@@ -137,14 +137,19 @@ dd_delta_smoke.label: Boolean
         }
 
       deepdive.extraction.extractors.ext_dd_delta_smoke {
-        sql: """ 
-        INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_smoke"
+	deepdive sql 'INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM dd_delta_person_smokes R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_smoke"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_delta_person_smokes
@@ -153,17 +158,22 @@ dd_delta_smoke.label: Boolean
     
 
       deepdive.extraction.extractors.ext_dd_new_person_has_cancer {
-        sql: """ TRUNCATE dd_new_person_has_cancer;
-        INSERT INTO dd_new_person_has_cancer SELECT R0.person_id, R0.has_cancer
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_person_has_cancer"
+	deepdive sql 'INSERT INTO dd_new_person_has_cancer SELECT R0.person_id, R0.has_cancer
 FROM person_has_cancer R0
         
 UNION ALL
 SELECT R0.person_id, R0.has_cancer
 FROM dd_delta_person_has_cancer R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_person_has_cancer"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person_has_cancer
@@ -173,17 +183,22 @@ FROM dd_delta_person_has_cancer R0
     
 
       deepdive.extraction.extractors.ext_dd_new_person {
-        sql: """ TRUNCATE dd_new_person;
-        INSERT INTO dd_new_person SELECT R0.person_id, R0.name
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_person"
+	deepdive sql 'INSERT INTO dd_new_person SELECT R0.person_id, R0.name
 FROM person R0
         
 UNION ALL
 SELECT R0.person_id, R0.name
 FROM dd_delta_person R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_person"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person
@@ -193,8 +208,9 @@ FROM dd_delta_person R0
     
 
       deepdive.extraction.extractors.ext_dd_new_smoke {
-        sql: """ 
-        CREATE VIEW dd_new_smoke AS SELECT DISTINCT R0.person_id, id, label
+        cmd: """
+
+	deepdive create view dd_new_smoke as 'SELECT DISTINCT R0.person_id, id, label
           FROM smoke R0
         
           
@@ -202,10 +218,11 @@ UNION ALL
 SELECT DISTINCT R0.person_id, id, label
           FROM dd_delta_smoke R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_smoke"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_smoke" ]
           input_relations: [
             smoke
@@ -215,14 +232,19 @@ SELECT DISTINCT R0.person_id, id, label
     
 
       deepdive.extraction.extractors.ext_dd_delta_cancer {
-        sql: """ 
-        INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_cancer"
+	deepdive sql 'INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM dd_delta_person_has_cancer R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_cancer"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_delta_person_has_cancer
@@ -231,8 +253,9 @@ SELECT DISTINCT R0.person_id, id, label
     
 
       deepdive.extraction.extractors.ext_dd_new_cancer {
-        sql: """ 
-        CREATE VIEW dd_new_cancer AS SELECT DISTINCT R0.person_id, id, label
+        cmd: """
+
+	deepdive create view dd_new_cancer as 'SELECT DISTINCT R0.person_id, id, label
           FROM cancer R0
         
           
@@ -240,10 +263,11 @@ UNION ALL
 SELECT DISTINCT R0.person_id, id, label
           FROM dd_delta_cancer R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_cancer"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_cancer" ]
           input_relations: [
             cancer
@@ -253,17 +277,22 @@ SELECT DISTINCT R0.person_id, id, label
     
 
       deepdive.extraction.extractors.ext_dd_new_person_smokes {
-        sql: """ TRUNCATE dd_new_person_smokes;
-        INSERT INTO dd_new_person_smokes SELECT R0.person_id, R0.smokes
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_person_smokes"
+	deepdive sql 'INSERT INTO dd_new_person_smokes SELECT R0.person_id, R0.smokes
 FROM person_smokes R0
         
 UNION ALL
 SELECT R0.person_id, R0.smokes
 FROM dd_delta_person_smokes R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_person_smokes"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person_smokes
@@ -273,17 +302,22 @@ FROM dd_delta_person_smokes R0
     
 
       deepdive.extraction.extractors.ext_dd_new_friends {
-        sql: """ TRUNCATE dd_new_friends;
-        INSERT INTO dd_new_friends SELECT R0.person_id, R0.friend_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_friends"
+	deepdive sql 'INSERT INTO dd_new_friends SELECT R0.person_id, R0.friend_id
 FROM friends R0
         
 UNION ALL
 SELECT R0.person_id, R0.friend_id
 FROM dd_delta_friends R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_friends"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             friends
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
index d5296e70a..0857a07e3 100644
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ b/test/expected-output-test/smoke_example/compile-materialization.expected
@@ -19,14 +19,19 @@ cancer.label: Boolean
     
 
       deepdive.extraction.extractors.ext_cancer {
-        sql: """ 
-        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "cancer"
+	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "cancer"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person_has_cancer
@@ -35,14 +40,19 @@ cancer.label: Boolean
     
 
       deepdive.extraction.extractors.ext_smoke {
-        sql: """ 
-        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "smoke"
+	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM person_smokes R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "smoke"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person_smokes
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
index 09d176f4b..ab4760cce 100644
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ b/test/expected-output-test/smoke_example/compile-merge.expected
@@ -18,13 +18,18 @@
     
 
       deepdive.extraction.extractors.ext_person_smokes {
-        sql: """ TRUNCATE person_smokes;
-        INSERT INTO person_smokes SELECT R0.person_id, R0.smokes
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "person_smokes"
+	deepdive sql 'INSERT INTO person_smokes SELECT R0.person_id, R0.smokes
 FROM dd_new_person_smokes R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "person_smokes"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_person_smokes
@@ -33,13 +38,18 @@ FROM dd_new_person_smokes R0
     
 
       deepdive.extraction.extractors.ext_friends {
-        sql: """ TRUNCATE friends;
-        INSERT INTO friends SELECT R0.person_id, R0.friend_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "friends"
+	deepdive sql 'INSERT INTO friends SELECT R0.person_id, R0.friend_id
 FROM dd_new_friends R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "friends"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_friends
@@ -48,13 +58,18 @@ FROM dd_new_friends R0
     
 
       deepdive.extraction.extractors.ext_person_has_cancer {
-        sql: """ TRUNCATE person_has_cancer;
-        INSERT INTO person_has_cancer SELECT R0.person_id, R0.has_cancer
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "person_has_cancer"
+	deepdive sql 'INSERT INTO person_has_cancer SELECT R0.person_id, R0.has_cancer
 FROM dd_new_person_has_cancer R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "person_has_cancer"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_person_has_cancer
@@ -63,13 +78,18 @@ FROM dd_new_person_has_cancer R0
     
 
       deepdive.extraction.extractors.ext_person {
-        sql: """ TRUNCATE person;
-        INSERT INTO person SELECT R0.person_id, R0.name
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "person"
+	deepdive sql 'INSERT INTO person SELECT R0.person_id, R0.name
 FROM dd_new_person R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "person"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_person
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 752971856..217f46d5b 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -19,14 +19,19 @@ cancer.label: Boolean
     
 
       deepdive.extraction.extractors.ext_cancer {
-        sql: """ 
-        INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "cancer"
+	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "cancer"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person_has_cancer
@@ -35,14 +40,19 @@ cancer.label: Boolean
     
 
       deepdive.extraction.extractors.ext_smoke {
-        sql: """ 
-        INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "smoke"
+	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
           FROM person_smokes R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "smoke"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             person_smokes
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
index 6f4b117d3..aedc3566e 100644
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example/compile-incremental.expected
@@ -169,17 +169,22 @@ dd_new_has_spouse.label: Boolean
         }
 
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
-        sql: """ TRUNCATE dd_new_people_mentions;
-        INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_people_mentions"
+	deepdive sql 'INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM people_mentions R0
         
 UNION ALL
 SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_delta_people_mentions R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_people_mentions"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
           input_relations: [
             people_mentions
@@ -189,17 +194,22 @@ FROM dd_delta_people_mentions R0
     
 
       deepdive.extraction.extractors.ext_dd_new_articles {
-        sql: """ TRUNCATE dd_new_articles;
-        INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_articles"
+	deepdive sql 'INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
 FROM articles R0
         
 UNION ALL
 SELECT R0.article_id, R0.text
 FROM dd_delta_articles R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_articles"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             articles
@@ -209,17 +219,22 @@ FROM dd_delta_articles R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
-        sql: """ TRUNCATE dd_new_has_spouse_candidates;
-        INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_has_spouse_candidates"
+	deepdive sql 'INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM has_spouse_candidates R0
         
 UNION ALL
 SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM dd_delta_has_spouse_candidates R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_has_spouse_candidates"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
@@ -229,17 +244,22 @@ FROM dd_delta_has_spouse_candidates R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
-        sql: """ TRUNCATE dd_new_has_spouse_features;
-        INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_has_spouse_features"
+	deepdive sql 'INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
 FROM has_spouse_features R0
         
 UNION ALL
 SELECT R0.relation_id, R0.feature
 FROM dd_delta_has_spouse_features R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_has_spouse_features"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
           input_relations: [
             has_spouse_features
@@ -249,17 +269,22 @@ FROM dd_delta_has_spouse_features R0
     
 
       deepdive.extraction.extractors.ext_dd_new_sentences {
-        sql: """ TRUNCATE dd_new_sentences;
-        INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_sentences"
+	deepdive sql 'INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM sentences R0
         
 UNION ALL
 SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM dd_delta_sentences R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_sentences"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             sentences
@@ -269,14 +294,19 @@ FROM dd_delta_sentences R0
     
 
       deepdive.extraction.extractors.ext_dd_delta_has_spouse {
-        sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_has_spouse"
+	deepdive sql 'INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             dd_delta_has_spouse_candidates
@@ -285,8 +315,9 @@ FROM dd_delta_sentences R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse {
-        sql: """ 
-        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
+        cmd: """
+
+	deepdive create view dd_new_has_spouse as 'SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
           
@@ -294,10 +325,11 @@ UNION ALL
 SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse" ]
           input_relations: [
             has_spouse
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
index eb428a6a8..3a3db96a4 100644
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ b/test/expected-output-test/spouse_example/compile-materialization.expected
@@ -18,14 +18,19 @@
     
 
       deepdive.extraction.extractors.ext_has_spouse {
-        sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse"
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
index 266e4f579..dfd4a38b4 100644
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ b/test/expected-output-test/spouse_example/compile-merge.expected
@@ -18,13 +18,18 @@
     
 
       deepdive.extraction.extractors.ext_sentences {
-        sql: """ TRUNCATE sentences;
-        INSERT INTO sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "sentences"
+	deepdive sql 'INSERT INTO sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM dd_new_sentences R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "sentences"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_sentences
@@ -33,13 +38,18 @@ FROM dd_new_sentences R0
     
 
       deepdive.extraction.extractors.ext_has_spouse_candidates {
-        sql: """ TRUNCATE has_spouse_candidates;
-        INSERT INTO has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse_candidates"
+	deepdive sql 'INSERT INTO has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM dd_new_has_spouse_candidates R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "has_spouse_candidates"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_has_spouse_candidates
@@ -48,13 +58,18 @@ FROM dd_new_has_spouse_candidates R0
     
 
       deepdive.extraction.extractors.ext_articles {
-        sql: """ TRUNCATE articles;
-        INSERT INTO articles SELECT R0.article_id, R0.text
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "articles"
+	deepdive sql 'INSERT INTO articles SELECT R0.article_id, R0.text
 FROM dd_new_articles R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "articles"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_articles
@@ -63,13 +78,18 @@ FROM dd_new_articles R0
     
 
       deepdive.extraction.extractors.ext_has_spouse_features {
-        sql: """ TRUNCATE has_spouse_features;
-        INSERT INTO has_spouse_features SELECT R0.relation_id, R0.feature
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse_features"
+	deepdive sql 'INSERT INTO has_spouse_features SELECT R0.relation_id, R0.feature
 FROM dd_new_has_spouse_features R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "has_spouse_features"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_has_spouse_features
@@ -78,13 +98,18 @@ FROM dd_new_has_spouse_features R0
     
 
       deepdive.extraction.extractors.ext_people_mentions {
-        sql: """ TRUNCATE people_mentions;
-        INSERT INTO people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "people_mentions"
+	deepdive sql 'INSERT INTO people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_new_people_mentions R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "people_mentions"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             dd_new_people_mentions
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 0fe3bfbb2..5d4b5dbeb 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -18,14 +18,19 @@
     
 
       deepdive.extraction.extractors.ext_has_spouse {
-        sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse"
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
index 60644e1bd..4a7ba4173 100644
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
@@ -169,17 +169,22 @@ dd_new_has_spouse.label: Boolean
         }
 
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
-        sql: """ TRUNCATE dd_new_people_mentions;
-        INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_people_mentions"
+	deepdive sql 'INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM people_mentions R0
         
 UNION ALL
 SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_delta_people_mentions R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_people_mentions"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
           input_relations: [
             people_mentions
@@ -189,17 +194,22 @@ FROM dd_delta_people_mentions R0
     
 
       deepdive.extraction.extractors.ext_dd_new_articles {
-        sql: """ TRUNCATE dd_new_articles;
-        INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_articles"
+	deepdive sql 'INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
 FROM articles R0
         
 UNION ALL
 SELECT R0.article_id, R0.text
 FROM dd_delta_articles R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_articles"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             articles
@@ -209,17 +219,22 @@ FROM dd_delta_articles R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
-        sql: """ TRUNCATE dd_new_has_spouse_candidates;
-        INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_has_spouse_candidates"
+	deepdive sql 'INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM has_spouse_candidates R0
         
 UNION ALL
 SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM dd_delta_has_spouse_candidates R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_has_spouse_candidates"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
@@ -229,17 +244,22 @@ FROM dd_delta_has_spouse_candidates R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
-        sql: """ TRUNCATE dd_new_has_spouse_features;
-        INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_has_spouse_features"
+	deepdive sql 'INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
 FROM has_spouse_features R0
         
 UNION ALL
 SELECT R0.relation_id, R0.feature
 FROM dd_delta_has_spouse_features R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_has_spouse_features"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
           input_relations: [
             has_spouse_features
@@ -249,17 +269,22 @@ FROM dd_delta_has_spouse_features R0
     
 
       deepdive.extraction.extractors.ext_dd_new_sentences {
-        sql: """ TRUNCATE dd_new_sentences;
-        INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_sentences"
+	deepdive sql 'INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM sentences R0
         
 UNION ALL
 SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM dd_delta_sentences R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_sentences"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             sentences
@@ -269,14 +294,19 @@ FROM dd_delta_sentences R0
     
 
       deepdive.extraction.extractors.ext_dd_delta_has_spouse {
-        sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_has_spouse"
+	deepdive sql 'INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             dd_delta_has_spouse_candidates
@@ -285,8 +315,9 @@ FROM dd_delta_sentences R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse {
-        sql: """ 
-        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
+        cmd: """
+
+	deepdive create view dd_new_has_spouse as 'SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
           
@@ -294,10 +325,11 @@ UNION ALL
 SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse" ]
           input_relations: [
             has_spouse
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
index 1c49f8eaa..dd9e085bd 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
@@ -169,17 +169,22 @@ dd_new_has_spouse.label: Boolean
         }
 
       deepdive.extraction.extractors.ext_dd_new_people_mentions {
-        sql: """ TRUNCATE dd_new_people_mentions;
-        INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_people_mentions"
+	deepdive sql 'INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM people_mentions R0
         
 UNION ALL
 SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
 FROM dd_delta_people_mentions R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_people_mentions"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
           input_relations: [
             people_mentions
@@ -189,17 +194,22 @@ FROM dd_delta_people_mentions R0
     
 
       deepdive.extraction.extractors.ext_dd_new_articles {
-        sql: """ TRUNCATE dd_new_articles;
-        INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_articles"
+	deepdive sql 'INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
 FROM articles R0
         
 UNION ALL
 SELECT R0.article_id, R0.text
 FROM dd_delta_articles R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_articles"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             articles
@@ -209,17 +219,22 @@ FROM dd_delta_articles R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
-        sql: """ TRUNCATE dd_new_has_spouse_candidates;
-        INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_has_spouse_candidates"
+	deepdive sql 'INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM has_spouse_candidates R0
         
 UNION ALL
 SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
 FROM dd_delta_has_spouse_candidates R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_has_spouse_candidates"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
@@ -229,17 +244,22 @@ FROM dd_delta_has_spouse_candidates R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
-        sql: """ TRUNCATE dd_new_has_spouse_features;
-        INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_has_spouse_features"
+	deepdive sql 'INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
 FROM has_spouse_features R0
         
 UNION ALL
 SELECT R0.relation_id, R0.feature
 FROM dd_delta_has_spouse_features R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_has_spouse_features"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
           input_relations: [
             has_spouse_features
@@ -249,17 +269,22 @@ FROM dd_delta_has_spouse_features R0
     
 
       deepdive.extraction.extractors.ext_dd_new_sentences {
-        sql: """ TRUNCATE dd_new_sentences;
-        INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_sentences"
+	deepdive sql 'INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM sentences R0
         
 UNION ALL
 SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
 FROM dd_delta_sentences R0
-        
+        '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_new_sentences"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             sentences
@@ -269,14 +294,19 @@ FROM dd_delta_sentences R0
     
 
       deepdive.extraction.extractors.ext_dd_delta_has_spouse {
-        sql: """ 
-        INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_has_spouse"
+	deepdive sql 'INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM dd_delta_has_spouse_candidates R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "dd_delta_has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             dd_delta_has_spouse_candidates
@@ -285,8 +315,9 @@ FROM dd_delta_sentences R0
     
 
       deepdive.extraction.extractors.ext_dd_new_has_spouse {
-        sql: """ 
-        CREATE VIEW dd_new_has_spouse AS SELECT DISTINCT R0.relation_id, id, label
+        cmd: """
+
+	deepdive create view dd_new_has_spouse as 'SELECT DISTINCT R0.relation_id, id, label
           FROM has_spouse R0
         
           
@@ -294,10 +325,11 @@ UNION ALL
 SELECT DISTINCT R0.relation_id, id, label
           FROM dd_delta_has_spouse R0
         
-          
+          '
+	
         """
           output_relation: "dd_new_has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_dd_delta_has_spouse" ]
           input_relations: [
             has_spouse
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 818351f39..38beb2384 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -18,14 +18,19 @@
     
 
       deepdive.extraction.extractors.ext_has_spouse {
-        sql: """ 
-        INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse"
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
-          
+          '
+	# TODO rename temporary table to replace output_relation
+	
         """
           output_relation: "has_spouse"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 2ee3ba6fa..985dbaabd 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -18,13 +18,15 @@
     
 
       deepdive.extraction.extractors.ext_A {
-        sql: """ DROP VIEW IF EXISTS A CASCADE;
-        CREATE VIEW A AS SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
+        cmd: """
+
+	deepdive create view A as 'SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
 FROM R R0
-        
+        '
+	
         """
           output_relation: "A"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           
           input_relations: [
             R
@@ -33,13 +35,15 @@ FROM R R0
     
 
       deepdive.extraction.extractors.ext_B {
-        sql: """ DROP VIEW IF EXISTS B CASCADE;
-        CREATE VIEW B AS SELECT R0.column_0 AS column_0, R1.b AS column_1
+        cmd: """
+
+	deepdive create view B as 'SELECT R0.column_0 AS column_0, R1.b AS column_1
 FROM A R0, R R1
-        WHERE R1.a = R0.column_1 
+        WHERE R1.a = R0.column_1 '
+	
         """
           output_relation: "B"
-        style: "sql_extractor"
+        style: "cmd_extractor"
           dependencies: [ "ext_A" ]
           input_relations: [
             A

From 6d2dca5befba402b7d96bdee69d9287b43b85225 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 25 Jan 2016 06:56:19 -0800
Subject: [PATCH 251/347] Makes sure schema entries are exported for rules that
 compile into views

with `type: view` relation and UNKNOWN type columns whose names are
`column_i` for i = 0 to N-1.

Fixes #69
---
 .../ddlog/DeepDiveLogSchemaExporter.scala     | 28 +++++++++++++++----
 .../views/export-schema.expected              |  1 +
 2 files changed, 24 insertions(+), 5 deletions(-)
 create mode 100644 test/expected-output-test/views/export-schema.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 591d286f6..173f41d2c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -10,16 +10,13 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
 
   def jsonMap(kvs: (String, Any)*): Map[String, Any] = kvs toMap
 
-  def export(decl: SchemaDeclaration): (String, JSONObject) = {
-    var schema = jsonMap(
-//      "name" -> decl.a.name // XXX redundant but potentially useful
-    )
+  def export(decl: SchemaDeclaration, extra: (String, Any)*): (String, JSONObject) = {
+    var schema = jsonMap(extra:_*)
     // column names with types and annotations
     schema += "columns" -> JSONObject(
       decl.a.terms.zipWithIndex map {
         case (name, i) =>
           var columnSchema = jsonMap(
-//              "name" -> name, // XXX redundant but potentially useful
               "type" -> decl.a.types(i)
           )
           columnSchema += "index" -> i
@@ -63,9 +60,30 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     val program = parsedProgram  // TODO derive the program based on config.mode?
 
+    // first find out names of the relations that have SchemaDeclaration
+    val declaredNames = program collect {
+      case decl: SchemaDeclaration => decl.a.name
+    }
+
+    // then print schema in JSON
     println(JSONObject(Map(
       "relations" -> JSONObject(program collect {
           case decl: SchemaDeclaration => export(decl)
+          case rule: ExtractionRule if ! (declaredNames contains rule.headName) =>
+            // for extraction rules whose head is not declared already,
+            // make sure a schema entry is added
+            export(SchemaDeclaration(
+                a = Attribute(
+                  name = rule.headName,
+                  terms = rule.q.headTerms.indices map { i => s"column_${i}" } toList,
+                  types = rule.q.headTerms map { _ => "UNKNOWN" },
+                  annotations = rule.q.headTerms map { _ => List.empty }
+                ),
+                isQuery = false,
+                variableType = None
+              ),
+              "type" -> "view"
+            )
         } toMap)
     )))
   }
diff --git a/test/expected-output-test/views/export-schema.expected b/test/expected-output-test/views/export-schema.expected
new file mode 100644
index 000000000..123864b86
--- /dev/null
+++ b/test/expected-output-test/views/export-schema.expected
@@ -0,0 +1 @@
+{"relations" : {"R" : {"columns" : {"a" : {"type" : "int", "index" : 0}, "b" : {"type" : "int", "index" : 1}}}, "A" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}, "B" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}}}

From d6a4514d603e1ef1c63a9580a63881f0b0d7114c Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 25 Jan 2016 19:23:33 -0800
Subject: [PATCH 252/347] Adds IfThenElseExpr

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala    |  5 +++++
 .../org/deepdive/ddlog/DeepDiveLogParser.scala      | 13 ++++++++++++-
 .../deepdive/ddlog/DeepDiveLogPrettyPrinter.scala   |  5 +++++
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index bae9e0a94..a44a49525 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -371,6 +371,11 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         val resovledLhs = compileExpr(lhs)
         s"(${resovledLhs} :: ${rhs})"
       }
+      case IfThenElseExpr(ifCondThenExprPairs, optElseExpr) => {
+        (ifCondThenExprPairs map {
+          case (ifCond, thenExpr) => s"WHEN ${compileCond(ifCond)} THEN ${compileExpr(thenExpr)}"
+        }) ++ List(optElseExpr map compileExpr mkString("ELSE ", "", ""))
+      } mkString("CASE ", "\n     ", "\nEND")
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 5efcc73ac..ef505d7ec 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -23,6 +23,7 @@ case class NullConst extends ConstExpr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
+case class IfThenElseExpr(ifCondThenExprPairs: List[(Cond, Expr)], elseExpr: Option[Expr]) extends Expr
 
 sealed trait Pattern
 case class VarPattern(name: String) extends Pattern
@@ -181,7 +182,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     }
 
-  def operator = "||" | "+" | "-" | "*" | "/" | "&" | "%"
+  def operator =
+    ( "||" | "+" | "-" | "*" | "/" | "&" | "%" )
   def typeOperator = "::"
   val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG", "COUNT")
 
@@ -196,6 +198,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
     ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
+    | "if" ~> (cond ~ ("then" ~> expr) ~ rep(elseIfExprs) ~ opt("else" ~> expr)) <~ "end" ^^ {
+        case (ifCond ~ thenExpr ~ elseIfs ~ optElseExpr) =>
+          IfThenElseExpr((ifCond, thenExpr) :: elseIfs, optElseExpr)
+      }
     | stringLiteralAsString ^^ { StringConst(_) }
     | double ^^ { DoubleConst(_) }
     | integer ^^ { IntConst(_) }
@@ -205,6 +211,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | "(" ~> expr <~ ")"
     )
 
+  def elseIfExprs =
+    ("else" ~> "if" ~> cond) ~ ("then" ~> expr) ^^ {
+      case (ifCond ~ thenExpr) => (ifCond, thenExpr)
+    }
+
   // conditional expressions
   def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS NOT" | "IS"
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 49e5d20e2..7cd9d9c63 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -87,6 +87,11 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       }
       case BinaryOpExpr(lhs, op, rhs) => s"(${print(lhs)} ${op} ${print(rhs)})"
       case TypecastExpr(lhs, rhs) => s"(${print(lhs)} :: ${rhs})"
+      case IfThenElseExpr(ifCondExprPairs, optElseExpr) => (
+        (ifCondExprPairs map {
+          case (ifCond, thenExpr) => s"if ${print(ifCond)} then ${print(thenExpr)}"
+        }) ++ List(optElseExpr map print mkString(""))
+      ) mkString(" else ")
     }
   }
 

From e51a5b8ae8bd0d2a65b4c36207bc7cbc8b6e0100 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 25 Jan 2016 19:30:33 -0800
Subject: [PATCH 253/347] Allows expression in @label(...) for supervision
 rules

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  4 ++--
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 20 ++++------------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  8 +++----
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 23 -------------------
 4 files changed, 10 insertions(+), 45 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a44a49525..ed8f6415b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -375,7 +375,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         (ifCondThenExprPairs map {
           case (ifCond, thenExpr) => s"WHEN ${compileCond(ifCond)} THEN ${compileExpr(thenExpr)}"
         }) ++ List(optElseExpr map compileExpr mkString("ELSE ", "", ""))
-      } mkString("CASE ", "\n     ", "\nEND")
+      } mkString("\nCASE ", "\n     ", "\nEND")
     }
   }
 
@@ -584,7 +584,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         if (stmt.supervision != None) {
           if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
           val headStr = qc.generateSQLHead(NoAlias)
-          val labelCol = qc.compileVariable(stmt.supervision.get)
+          val labelCol = qc.compileExpr(stmt.supervision.get)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index ef505d7ec..997e70c28 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -101,7 +101,7 @@ case class SchemaDeclaration( a : Attribute
                             ) extends Statement // atom and whether this is a query relation.
 case class FunctionDeclaration( functionName: String, inputType: FunctionInputOutputType,
   outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration]) extends Statement
-case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[String] = None) extends Statement // Extraction rule
+case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[Expr] = None) extends Statement // Extraction rule
 case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery, mode: Option[String], parallelism: Option[Int]) extends Statement // Extraction rule
 case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
 
@@ -316,29 +316,17 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def parallelism = "@parallelism" ~> "(" ~> integer <~ ")"
 
-  def supervision = "=" ~> (variableName | "TRUE" | "FALSE")
-
-  def conjunctiveQueryWithSupervision  = // returns Parser[String], Parser[ConjunctiveQuery]
-    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ opt(supervision) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
-      case (head ~ isDistinct ~ limit ~ sup ~ ":-" ~ disjunctiveBodies) =>
-        (sup, ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt)))
-  }
-
   def functionCallRule : Parser[FunctionCallRule] =
     opt(functionMode) ~ opt(parallelism) ~ relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
       case (mode ~ parallelism ~ out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq, mode, parallelism)
     }
 
-  def oldstyleSupervision = "@label" ~> "(" ~> (variableName | "TRUE" | "FALSE") <~ ")"
+  def supervisionAnnotation = ("@label" | "@supervise") ~> "(" ~> expr <~ ")"
 
   def extractionRule =
-  ( relationName ~ conjunctiveQueryWithSupervision ^^ {
-      case (head ~ cq) => ExtractionRule(head, cq._2, cq._1)
+    opt(supervisionAnnotation) ~ relationName ~ conjunctiveQuery ^^ {
+      case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
     }
-  | oldstyleSupervision ~ relationName ~ conjunctiveQuery ^^ {
-      case (sup ~ head ~ cq) => ExtractionRule(head, cq, Some(sup))
-    }
-  )
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
   def inferenceMode = "@mode" ~> commit("(" ~> inferenceModeType <~ ")" ^? ({
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 7cd9d9c63..a644341c7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -136,7 +136,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     case b: QuantifiedBody => print(b)
   }
 
-  def print(cq: ConjunctiveQuery, supervision: String = ""): String = {
+  def print(cq: ConjunctiveQuery): String = {
 
     def printBodyList(b: List[Body]) = {
       s"${(b map print).mkString(",\n    ")}"
@@ -149,7 +149,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val headStrTmp  = cq.headTerms map print mkString(", ")
     val headStr     = if (headStrTmp isEmpty) "" else s"(${headStrTmp})"
 
-    headStr + distinctStr + limitStr + supervision + " :-\n    " + bodyStr
+    headStr + distinctStr + limitStr + " :-\n    " + bodyStr
   }
 
   def print(a: HeadAtom) : String = {
@@ -172,8 +172,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-      var supervision = stmt.supervision map (s => s" = ${s}") getOrElse("");
-      stmt.headName + print(stmt.q, supervision) + ".\n"
+    (stmt.supervision map (s => s"@label(${print(s)})\n") getOrElse("")) +
+      stmt.headName + print(stmt.q) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index b644269de..bfcfef70b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -35,7 +35,6 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkQuantifiedBody(stmt)
     checkWeight(stmt)
     checkVariableBindings(stmt)
-    checkSupervisionLabelType(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
@@ -185,28 +184,6 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
-  def checkSupervisionLabelType(stmt: Statement) {
-    stmt match {
-      case s: ExtractionRule if (schemaDeclaration contains s.headName) && (schemaDeclaration(s.headName).variableType nonEmpty) => {
-        val headType = schemaDeclaration(s.headName).variableType.get
-        s.supervision match {
-          case Some("TRUE") | Some("FALSE") => {
-            if (headType != BooleanType) {
-              error(s, s"Supervision column ${s.supervision} should be boolean type but is ${headType} type")
-            }
-          }
-          case Some(varname) =>
-            s.q.bodies.foreach { bodies: List[Body] =>
-              bodies.foreach { b =>
-                checkSupervisionLabelType(s, headType, VarPattern(varname), b) }
-            }
-          case None =>
-        }
-      }
-      case _ =>
-    }
-  }
-
   // collect variables used in the expression
   def collectUsedVars(expr: Expr) : Set[String] = expr match {
     case VarExpr(name) => Set(name)

From 4ce8b35d3240ea6ca9bdccdc3142440b980c4001 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 25 Jan 2016 19:52:04 -0800
Subject: [PATCH 254/347] Fixes IS NOT to be separable tokens

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 997e70c28..9ab26c381 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -217,7 +217,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   // conditional expressions
-  def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS NOT" | "IS"
+  def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" ~ "NOT" ^^ { _ => "IS NOT" } | "IS"
 
   def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>

From f25a2e62bb2e58d9e2fe3f4cbd78bbea2a5ca393 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 06:24:38 -0800
Subject: [PATCH 255/347] Brings back Q(x) = TRUE style supervision syntax

as it seems fine to keep as default
---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 32 ++++++++++++++-----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 11 ++++---
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 9ab26c381..ff7c99758 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -304,11 +304,16 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def cqHeadTerms = "(" ~> rep1sep(expr, ",") <~ ")"
 
+  def conjunctiveQueryBody : Parser[ConjunctiveQuery] =
+    opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
+      case (isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
+        ConjunctiveQuery(List.empty, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
+    }
+
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
-    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
-      case (head ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
-  }
+    cqHeadTerms ~ conjunctiveQueryBody ^^ {
+      case (head ~ cq) => cq.copy(headTerms = head)
+    }
 
   def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
     case "inc" => "inc"
@@ -321,12 +326,23 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case (mode ~ parallelism ~ out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq, mode, parallelism)
     }
 
-  def supervisionAnnotation = ("@label" | "@supervise") ~> "(" ~> expr <~ ")"
+  def supervisionAnnotation = "@label" ~> "(" ~> expr <~ ")"
+
+  def conjunctiveQueryWithSupervision : Parser[ConjunctiveQuery] =
+    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
+      case (head ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
+        ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
+  }
 
   def extractionRule =
-    opt(supervisionAnnotation) ~ relationName ~ conjunctiveQuery ^^ {
-      case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
-    }
+    ( opt(supervisionAnnotation) ~ relationName ~ conjunctiveQuery ^^ {
+        case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
+      }
+    | relationName ~ cqHeadTerms ~ ("=" ~> expr) ~ conjunctiveQueryBody ^^ {
+        case (head ~ headTerms ~ sup ~ cq) =>
+          ExtractionRule(head, cq.copy(headTerms = headTerms), Some(sup))
+      }
+    )
 
   def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
   def inferenceMode = "@mode" ~> commit("(" ~> inferenceModeType <~ ")" ^? ({
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index a644341c7..c3dc0c243 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -91,7 +91,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         (ifCondExprPairs map {
           case (ifCond, thenExpr) => s"if ${print(ifCond)} then ${print(thenExpr)}"
         }) ++ List(optElseExpr map print mkString(""))
-      ) mkString(" else ")
+      ) mkString("", "\n\telse ", "\n\tend")
     }
   }
 
@@ -136,7 +136,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     case b: QuantifiedBody => print(b)
   }
 
-  def print(cq: ConjunctiveQuery): String = {
+  def print(cq: ConjunctiveQuery, optSupervision: Option[Expr] = None): String = {
 
     def printBodyList(b: List[Body]) = {
       s"${(b map print).mkString(",\n    ")}"
@@ -149,7 +149,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val headStrTmp  = cq.headTerms map print mkString(", ")
     val headStr     = if (headStrTmp isEmpty) "" else s"(${headStrTmp})"
 
-    headStr + distinctStr + limitStr + " :-\n    " + bodyStr
+    headStr + (
+      optSupervision map { sv => s" = ${print(sv)}" } getOrElse("")
+    ) + distinctStr + limitStr + " :-\n    " + bodyStr
   }
 
   def print(a: HeadAtom) : String = {
@@ -172,8 +174,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-    (stmt.supervision map (s => s"@label(${print(s)})\n") getOrElse("")) +
-      stmt.headName + print(stmt.q) + ".\n"
+    stmt.headName + print(stmt.q, stmt.supervision) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {

From 225a74c84bcc985fc2753f53c090968a07f5b187 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 06:36:20 -0800
Subject: [PATCH 256/347] Brings back checker for supervision rules as well

although it only works for narrow cases of boolean and variable expressions
---
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index bfcfef70b..7dec4330a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -35,6 +35,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     checkQuantifiedBody(stmt)
     checkWeight(stmt)
     checkVariableBindings(stmt)
+    checkSupervisionLabelType(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
@@ -184,6 +185,29 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     }
   }
 
+  def checkSupervisionLabelType(stmt: Statement) {
+    stmt match {
+      case s: ExtractionRule if (schemaDeclaration contains s.headName) && (schemaDeclaration(s.headName).variableType nonEmpty) => {
+        val headType = schemaDeclaration(s.headName).variableType.get
+        s.supervision foreach {
+          case b: BooleanConst => {
+            if (headType != BooleanType) {
+              error(s, s"Supervision column ${s.supervision} should be boolean type but is ${headType} type")
+            }
+          }
+          case VarExpr(varname) =>
+            s.q.bodies.foreach { bodies: List[Body] =>
+              bodies.foreach { b =>
+                checkSupervisionLabelType(s, headType, VarPattern(varname), b) }
+            }
+          case _ =>
+            // XXX assume the rest of the expressions are correct
+        }
+      }
+      case _ =>
+    }
+  }
+
   // collect variables used in the expression
   def collectUsedVars(expr: Expr) : Set[String] = expr match {
     case VarExpr(name) => Set(name)

From b1f8d940d39022ce84f05f4caf1474255a636747 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 08:03:15 -0800
Subject: [PATCH 257/347] Unifies comparison condition with binary operator
 expressions

and reduces unnecessary parentheses when compiling or printing
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 29 ++++++++++---------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 11 ++++---
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 12 +++++---
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  8 +++--
 .../expressions/compile.expected              | 20 ++++++-------
 .../expressions/print.expected                | 20 ++++++-------
 .../compile-incremental.expected              | 16 +++++-----
 .../compile.expected                          | 14 ++++-----
 .../views/compile.expected                    |  2 +-
 .../expected-output-test/views/print.expected |  2 +-
 .../weights/compile.expected                  |  2 +-
 .../weights/print.expected                    |  2 +-
 12 files changed, 74 insertions(+), 64 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index ed8f6415b..489c54138 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -349,7 +349,8 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // resolve an expression
-  def compileExpr(e: Expr) : String = {
+  def compileExpr(e: Expr) : String = compileExpr(e, 0)
+  def compileExpr(e: Expr, level: Int) : String = {
     e match {
       case VarExpr(name) => compileVariable(name)
       case NullConst() => "NULL"
@@ -363,9 +364,10 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         resolved
       }
       case BinaryOpExpr(lhs, op, rhs) => {
-        val resovledLhs = compileExpr(lhs)
-        val resovledRhs = compileExpr(rhs)
-        s"(${resovledLhs} ${op} ${resovledRhs})"
+        val resovledLhs = compileExpr(lhs, level + 1)
+        val resovledRhs = compileExpr(rhs, level + 1)
+        val sql = s"${resovledLhs} ${op} ${resovledRhs}"
+        if (level == 0) sql else s"(${sql})"
       }
       case TypecastExpr(lhs, rhs) => {
         val resovledLhs = compileExpr(lhs)
@@ -380,18 +382,19 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   }
 
   // resolve a condition
-  def compileCond(cond: Cond) : String = {
+  def compileCond(cond: Cond) : String = compileCond(cond, 0)
+  def compileCond(cond: Cond, level: Int) : String = {
     cond match {
-      case ComparisonCond(lhs, op, rhs) =>
-        s"${compileExpr(lhs)} ${op} ${compileExpr(rhs)}"
-      case NegationCond(c) => s"(NOT ${compileCond(c)})"
+      case ExprCond(e) => compileExpr(e)
+      case NegationCond(c) => s"NOT ${compileCond(c, level + 1)}"
       case CompoundCond(lhs, op, rhs) => {
-        val resolvedLhs = s"${compileCond(lhs)}"
-        val resolvedRhs = s"${compileCond(rhs)}"
-        op match {
-          case LogicOperator.AND => s"(${resolvedLhs} AND ${resolvedRhs})"
-          case LogicOperator.OR  => s"(${resolvedLhs} OR ${resolvedRhs})"
+        val resolvedLhs = s"${compileCond(lhs, level + 1)}"
+        val resolvedRhs = s"${compileCond(rhs, level + 1)}"
+        val sql = op match {
+          case LogicOperator.AND => s"${resolvedLhs} AND ${resolvedRhs}"
+          case LogicOperator.OR  => s"${resolvedLhs} OR ${resolvedRhs}"
         }
+        if (level == 0) sql else s"(${sql})"
       }
       case _ => ""
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index ff7c99758..a302a934f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -53,7 +53,7 @@ case class RuleAnnotation(name: String, args: List[String])
 
 // condition
 sealed trait Cond extends Body
-case class ComparisonCond(lhs: Expr, op: String, rhs: Expr) extends Cond
+case class ExprCond(expr: Expr) extends Cond
 case class NegationCond(cond: Cond) extends Cond
 case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
 
@@ -190,11 +190,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
   // expression
   def expr : Parser[Expr] =
     ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    | lexpr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
     )
 
-  def lexpr : Parser[Expr] =
+  def lexpr =
     ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
@@ -235,9 +236,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | bcond
     )
   def bcond : Parser[Cond] =
-    ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) =>
-        ComparisonCond(lhs, op, rhs)
-      }
+    ( expr ^^ ExprCond
     | "[" ~> cond <~ "]"
     )
 
@@ -298,7 +297,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
              FunctionDeclaration(a, inTy, outTy, implementationDecls)
     }
 
-  def cqBody: Parser[Body] = cond | quantifiedBody | atom
+  def cqBody: Parser[Body] = quantifiedBody | atom | cond
 
   def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index c3dc0c243..6089fd9ed 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -73,7 +73,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   // print an expression
-  def print(e: Expr) : String = {
+  def print(e: Expr) : String = print(e, 0)
+  def print(e: Expr, level: Int) : String = {
     e match {
       case VarExpr(name) => name
       case NullConst() => "NULL"
@@ -85,12 +86,15 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         val resolvedArgs = args map (x => print(x))
         s"${function}(${resolvedArgs.mkString(", ")})"
       }
-      case BinaryOpExpr(lhs, op, rhs) => s"(${print(lhs)} ${op} ${print(rhs)})"
+      case BinaryOpExpr(lhs, op, rhs) => {
+        val p = s"${print(lhs, level + 1)} ${op} ${print(rhs, level + 1)}"
+        if (level == 0) p else s"(${p})"
+      }
       case TypecastExpr(lhs, rhs) => s"(${print(lhs)} :: ${rhs})"
       case IfThenElseExpr(ifCondExprPairs, optElseExpr) => (
         (ifCondExprPairs map {
           case (ifCond, thenExpr) => s"if ${print(ifCond)} then ${print(thenExpr)}"
-        }) ++ List(optElseExpr map print mkString(""))
+        }) ++ (optElseExpr map print toList)
       ) mkString("", "\n\telse ", "\n\tend")
     }
   }
@@ -119,7 +123,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   // print a condition
   def print(cond: Cond) : String = {
     cond match {
-      case ComparisonCond(lhs, op, rhs) => s"${print(lhs)} ${op} ${print(rhs)}"
+      case ExprCond(e) => print(e)
       case NegationCond(c) => s"[!${print(c)}]"
       case CompoundCond(lhs, op, rhs) => {
         op match {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 7dec4330a..65a3e44ab 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -214,6 +214,10 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     case FuncExpr(function, args, agg) => args flatMap collectUsedVars toSet
     case BinaryOpExpr(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
     case TypecastExpr(lhs, rhs) => collectUsedVars(lhs)
+    case IfThenElseExpr(ifCondThenExprs, optElseExpr) =>
+      (ifCondThenExprs flatMap { case (ifCond, thenExpr) =>
+        collectUsedVars(ifCond) ++ collectUsedVars(thenExpr)
+      } toSet) ++ (optElseExpr.toSet flatMap { e:Expr => collectUsedVars(e) })
     case _ => Set()
   }
 
@@ -229,7 +233,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   def collectUsedVars(cond: Cond) : Set[String] = cond match {
-    case ComparisonCond(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
+    case ExprCond(e)                  => collectUsedVars(e)
     case CompoundCond(lhs, op, rhs)   => collectUsedVars(lhs) ++ collectUsedVars(rhs)
     case NegationCond(c)              => collectUsedVars(c)
   }
@@ -259,7 +263,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       if (varUndefined nonEmpty) error(stmt, s"Variable ${varUndefined mkString(", ")} must have bindings")
     }
     stmt match {
-      case s: ExtractionRule => checkCq(s.q)
+      case s: ExtractionRule => checkCq(s.q, (s.supervision.toSet flatMap { e:Expr => collectUsedVars(e) }))
       case s: InferenceRule  => checkCq(s.q, (s.weights.variables flatMap collectUsedVars toSet))
       case _ =>
     }
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index d90b2472f..530175de3 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -93,7 +93,7 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
 
 	deepdive create view J as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR (NOT R0.k > 50))'
+        WHERE R0.k + (R0.r = 100) OR NOT R0.k > 50'
 	
         """
           output_relation: "J"
@@ -126,7 +126,7 @@ FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
       deepdive.extraction.extractors.ext_F {
         cmd: """
 
-	deepdive create view F as 'SELECT ((R0.k :: INT) + (R0.r :: INT)) AS column_0
+	deepdive create view F as 'SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
 FROM b R0
         '
 	
@@ -143,7 +143,7 @@ FROM b R0
       deepdive.extraction.extractors.ext_A {
         cmd: """
 
-	deepdive create view A as 'SELECT (R0.k + (R0.r * (R0.k + R0.r))) AS column_0
+	deepdive create view A as 'SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
 FROM b R0
         '
 	
@@ -180,7 +180,7 @@ FROM b R0
 
 	deepdive create view I as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
+        WHERE R0.k + (R0.r = 100) OR (R0.k > 50 AND R0.r < 10)'
 	
         """
           output_relation: "I"
@@ -197,7 +197,7 @@ FROM b R0
 
 	deepdive create view G as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100'
+        WHERE R0.k + (R0.r = 100)'
 	
         """
           output_relation: "G"
@@ -232,7 +232,7 @@ FROM c R0, a R1
 
 	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = (R1.p || R1.q) AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR ((NOT R1.r < 20) AND R1.r < 50))'
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50)'
 	
         """
           output_relation: "Q"
@@ -266,7 +266,7 @@ FROM b R0
       deepdive.extraction.extractors.ext_B {
         cmd: """
 
-	deepdive create view B as 'SELECT func((R0.k + (R0.r + R0.k))) AS column_0
+	deepdive create view B as 'SELECT func(R0.k + (R0.r + R0.k)) AS column_0
 FROM b R0
         '
 	
@@ -321,7 +321,7 @@ FROM b R0
 
 	deepdive create view H as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND R0.k > 50)'
+        WHERE R0.k + (R0.r = 100) AND R0.k > 50'
 	
         """
           output_relation: "H"
@@ -356,7 +356,7 @@ FROM a R0
 
 	deepdive create view K as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND ((NOT R0.k > 50) OR R0.k = 40))'
+        WHERE R0.k + (R0.r = 100) AND (NOT R0.k > 50 OR R0.k = 40)'
 	
         """
           output_relation: "K"
@@ -390,7 +390,7 @@ FROM b R0
       deepdive.extraction.extractors.ext_D {
         cmd: """
 
-	deepdive create view D as 'SELECT (func((R0.k * func2((R0.r + R0.k)))) + R0.k) AS column_0
+	deepdive create view D as 'SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
 FROM b R0
         '
 	
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index b5f266959..264dee3cf 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -12,50 +12,50 @@ c(s text,
 Q(("test" :: TEXT), 123, id, unnest(y)) * :-
     a(id),
     b(id, x, y, z),
-    c((x || y), 10, "foo"),
+    c(x || y, 10, "foo"),
     [z > 100; [[!z < 20], z < 50]].
 
 P(y, z, MAX(w)) :-
     a(x),
     b(x, y, z, w).
 
-A((x + (w * (x + w)))) :-
+A(x + (w * (x + w))) :-
     b(x, y, z, w).
 
-B(func((x + (w + x)))) :-
+B(func(x + (w + x))) :-
     b(x, y, z, w).
 
 C(func(func(func(x)))) :-
     b(x, y, z, w).
 
-D((func((x * func2((w + x)))) + x)) :-
+D(func(x * func2(w + x)) + x) :-
     b(x, y, z, w).
 
 E((x :: INT)) :-
     b(x, y, z, w).
 
-F(((x :: INT) + (w :: INT))) :-
+F((x :: INT) + (w :: INT)) :-
     b(x, y, z, w).
 
 G(x) :-
     b(x, y, z, w),
-    (x + w) = 100.
+    x + (w = 100).
 
 H(x) :-
     b(x, y, z, w),
-    [(x + w) = 100, x > 50].
+    [x + (w = 100), x > 50].
 
 I(x) :-
     b(x, y, z, w),
-    [(x + w) = 100; [x > 50, w < 10]].
+    [x + (w = 100); [x > 50, w < 10]].
 
 J(x) :-
     b(x, y, z, w),
-    [(x + w) = 100; [!x > 50]].
+    [x + (w = 100); [!x > 50]].
 
 K(x) :-
     b(x, y, z, w),
-    [(x + w) = 100, [[!x > 50]; x = 40]].
+    [x + (w = 100), [[!x > 50]; x = 40]].
 
 L(x) * | 100 :-
     b(x, y, z, w).
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index 24e1a8336..a2bb0e410 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -113,7 +113,7 @@ FROM dd_delta_S R0
         """
           output_relation: "dd_new_S"
         style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
           input_relations: [
             S
             dd_delta_S
@@ -257,7 +257,7 @@ FROM dd_delta_R R0
         deepdive.extraction.extractors.ext1_dd_delta_T_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
-        WHERE (10 < R0.a AND R0.a < 20)
+        WHERE 10 < R0.a AND R0.a < 20
           """
           output_relation: "dd_delta_T"
           udf: ${APP_HOME}"//bin/false"
@@ -274,7 +274,7 @@ FROM dd_delta_R R0
         deepdive.extraction.extractors.ext2_dd_delta_T_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
-        WHERE (100 < R0.a AND R0.a < 200)
+        WHERE 100 < R0.a AND R0.a < 200
           """
           output_relation: "dd_delta_T"
           udf: ${APP_HOME}"//bin/false"
@@ -363,7 +363,7 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -378,7 +378,7 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -416,13 +416,13 @@ FROM dd_delta_R R0
           input_query: """
           SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
           FROM dd_new_Q R0, dd_new_Q R1, dd_delta_S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000) UNION ALL 
           SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
           FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_delta_R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000) UNION ALL 
           SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
           FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_new_R R3, dd_delta_S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000)"""
           function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
           weight: "-10.0"
           dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_new_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S" ]
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 2e72c82a1..ff2354e85 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -65,7 +65,7 @@ FROM R R0
         deepdive.extraction.extractors.ext1_T_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE (10 < R0.a AND R0.a < 20)
+        WHERE 10 < R0.a AND R0.a < 20
           """
           output_relation: "T"
           udf: ${APP_HOME}"//bin/false"
@@ -82,7 +82,7 @@ FROM R R0
         deepdive.extraction.extractors.ext2_T_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE (100 < R0.a AND R0.a < 200)
+        WHERE 100 < R0.a AND R0.a < 200
           """
           output_relation: "T"
           udf: ${APP_HOME}"//bin/false"
@@ -171,7 +171,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
@@ -186,7 +186,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
@@ -201,7 +201,7 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
@@ -214,10 +214,10 @@ FROM R R0
           input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
           FROM Q R0, Q R1, S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000)"""
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "-10.0"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 985dbaabd..f738ff7f6 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -20,7 +20,7 @@
       deepdive.extraction.extractors.ext_A {
         cmd: """
 
-	deepdive create view A as 'SELECT R0.a AS column_0, (R0.a + R0.b) AS column_1
+	deepdive create view A as 'SELECT R0.a AS column_0, R0.a + R0.b AS column_1
 FROM R R0
         '
 	
diff --git a/test/expected-output-test/views/print.expected b/test/expected-output-test/views/print.expected
index 734e24d5f..7e6ceff75 100644
--- a/test/expected-output-test/views/print.expected
+++ b/test/expected-output-test/views/print.expected
@@ -1,7 +1,7 @@
 R(a int,
   b int).
 
-A(x, (x + y)) :-
+A(x, x + y) :-
     R(x, y).
 
 B(x, z) :-
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index b6595ae6b..cd650b0fc 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -23,7 +23,7 @@ c.label: Boolean
 
         deepdive.inference.factors.inf_istrue_a {
           input_query: """
-          SELECT R0.id AS "a.R0.id" , (R0.k + R1.p) AS "dd_weight_column_0" 
+          SELECT R0.id AS "a.R0.id" , R0.k + R1.p AS "dd_weight_column_0" 
           FROM a R0, b R1
         WHERE R1.k = R0.k """
           function: "Imply(a.R0.label)"
diff --git a/test/expected-output-test/weights/print.expected b/test/expected-output-test/weights/print.expected
index cb35dea74..b9f7bbe29 100644
--- a/test/expected-output-test/weights/print.expected
+++ b/test/expected-output-test/weights/print.expected
@@ -12,7 +12,7 @@ b(k int,
   p int,
   q text).
 
-@weight((x + y))
+@weight(x + y)
 a(x) :-
     b(x, y, _).
 

From 673b3ed5f1da2db12dfee2b47b1e67fd56275375 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 08:13:50 -0800
Subject: [PATCH 258/347] Fixes expression precedence (comparison vs. normal
 binary ops)

to make use of if-then-else more intuitive.
---
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  16 ++-
 .../expressions/compile.expected              |  10 +-
 .../expressions/print.expected                |  10 +-
 .../if-then-else/compile.expected             | 106 ++++++++++++++++++
 .../if-then-else/input.ddlog                  |  14 +++
 .../if-then-else/print.expected               |  29 +++++
 .../compile-incremental.expected              |   6 +-
 7 files changed, 172 insertions(+), 19 deletions(-)
 create mode 100644 test/expected-output-test/if-then-else/compile.expected
 create mode 100644 test/expected-output-test/if-then-else/input.ddlog
 create mode 100644 test/expected-output-test/if-then-else/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index a302a934f..377a85eb9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -190,16 +190,17 @@ class DeepDiveLogParser extends JavaTokenParsers {
   // expression
   def expr : Parser[Expr] =
     ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
-    | lexpr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
     )
 
+  def cexpr =
+    ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    | expr
+    )
+
   def lexpr =
-    ( functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
-        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
-      }
-    | "if" ~> (cond ~ ("then" ~> expr) ~ rep(elseIfExprs) ~ opt("else" ~> expr)) <~ "end" ^^ {
+    ( "if" ~> (cond ~ ("then" ~> expr) ~ rep(elseIfExprs) ~ opt("else" ~> expr)) <~ "end" ^^ {
         case (ifCond ~ thenExpr ~ elseIfs ~ optElseExpr) =>
           IfThenElseExpr((ifCond, thenExpr) :: elseIfs, optElseExpr)
       }
@@ -208,6 +209,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | integer ^^ { IntConst(_) }
     | ("TRUE" | "FALSE") ^^ { x => BooleanConst(x.toBoolean) }
     | "NULL" ^^ { _ => new NullConst }
+    | functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
+        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
+      }
     | variableName ^^ { VarExpr(_) }
     | "(" ~> expr <~ ")"
     )
@@ -236,7 +240,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | bcond
     )
   def bcond : Parser[Cond] =
-    ( expr ^^ ExprCond
+    ( cexpr ^^ ExprCond
     | "[" ~> cond <~ "]"
     )
 
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 530175de3..4b8019069 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -93,7 +93,7 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
 
 	deepdive create view J as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE R0.k + (R0.r = 100) OR NOT R0.k > 50'
+        WHERE (R0.k + R0.r) = 100 OR NOT R0.k > 50'
 	
         """
           output_relation: "J"
@@ -180,7 +180,7 @@ FROM b R0
 
 	deepdive create view I as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE R0.k + (R0.r = 100) OR (R0.k > 50 AND R0.r < 10)'
+        WHERE (R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10)'
 	
         """
           output_relation: "I"
@@ -197,7 +197,7 @@ FROM b R0
 
 	deepdive create view G as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE R0.k + (R0.r = 100)'
+        WHERE (R0.k + R0.r) = 100'
 	
         """
           output_relation: "G"
@@ -321,7 +321,7 @@ FROM b R0
 
 	deepdive create view H as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE R0.k + (R0.r = 100) AND R0.k > 50'
+        WHERE (R0.k + R0.r) = 100 AND R0.k > 50'
 	
         """
           output_relation: "H"
@@ -356,7 +356,7 @@ FROM a R0
 
 	deepdive create view K as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE R0.k + (R0.r = 100) AND (NOT R0.k > 50 OR R0.k = 40)'
+        WHERE (R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40)'
 	
         """
           output_relation: "K"
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 264dee3cf..798da8600 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -39,23 +39,23 @@ F((x :: INT) + (w :: INT)) :-
 
 G(x) :-
     b(x, y, z, w),
-    x + (w = 100).
+    (x + w) = 100.
 
 H(x) :-
     b(x, y, z, w),
-    [x + (w = 100), x > 50].
+    [(x + w) = 100, x > 50].
 
 I(x) :-
     b(x, y, z, w),
-    [x + (w = 100); [x > 50, w < 10]].
+    [(x + w) = 100; [x > 50, w < 10]].
 
 J(x) :-
     b(x, y, z, w),
-    [x + (w = 100); [!x > 50]].
+    [(x + w) = 100; [!x > 50]].
 
 K(x) :-
     b(x, y, z, w),
-    [x + (w = 100), [[!x > 50]; x = 40]].
+    [(x + w) = 100, [[!x > 50]; x = 40]].
 
 L(x) * | 100 :-
     b(x, y, z, w).
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
new file mode 100644
index 000000000..33fa69f3f
--- /dev/null
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -0,0 +1,106 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        q.label: Boolean
+      }
+    
+
+      deepdive.extraction.extractors.ext_labels_resolved {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "labels_resolved"
+	deepdive sql 'INSERT INTO labels_resolved SELECT R0.x AS "labels.R0.x", SUM(
+CASE WHEN R0.l IS NULL THEN 0
+     WHEN R0.l = true THEN 1
+     ELSE -1
+END) AS column_1
+FROM labels R0
+        
+        GROUP BY R0.x'
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "labels_resolved"
+        style: "cmd_extractor"
+          
+          input_relations: [
+            labels
+          ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_q {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "q"
+	deepdive sql 'INSERT INTO q SELECT DISTINCT R0.x, 0 AS id, 
+CASE WHEN R0.l > 0 THEN true
+     WHEN R0.l < 0 THEN false
+     ELSE NULL
+END AS label
+          FROM labels_resolved R0
+        
+          '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "q"
+        style: "cmd_extractor"
+          dependencies: [ "ext_labels_resolved" ]
+          input_relations: [
+            labels_resolved
+          ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_p {
+        cmd: """
+
+	deepdive create view p as 'SELECT R0.x AS column_0, 
+CASE WHEN abs(R0.l) > 10 THEN true
+     ELSE false
+END AS column_1
+FROM labels R0
+        
+UNION ALL
+SELECT R0.x AS column_0, 
+CASE WHEN (R0.x % 10) = 0 THEN false
+     ELSE 
+END AS column_1
+FROM labels R0
+        '
+	
+        """
+          output_relation: "p"
+        style: "cmd_extractor"
+          
+          input_relations: [
+            labels
+          ]
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.extraction: [
+  ext_labels_resolved
+  ext_q
+  ext_p
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_labels_resolved
+  ext_q
+  ext_p
+]
diff --git a/test/expected-output-test/if-then-else/input.ddlog b/test/expected-output-test/if-then-else/input.ddlog
new file mode 100644
index 000000000..93974595b
--- /dev/null
+++ b/test/expected-output-test/if-then-else/input.ddlog
@@ -0,0 +1,14 @@
+labels_resolved(x INT, l INT).
+q?(x INT).
+
+q(x) = if l > 0 then TRUE
+       else if l < 0 then FALSE
+       else NULL
+       end :- labels_resolved(x, l).
+
+labels(x INT, l BOOLEAN).
+p(x, if abs(l) > 10 then TRUE else FALSE end) :- labels(x, l).
+p(x, if x % 10 = 0 then FALSE end) :- labels(x, l).
+
+labels_resolved(x, SUM(if label IS NULL then 0 else if label = TRUE then 1 else -1 end)) :-
+    labels(x, label).
diff --git a/test/expected-output-test/if-then-else/print.expected b/test/expected-output-test/if-then-else/print.expected
new file mode 100644
index 000000000..35717235c
--- /dev/null
+++ b/test/expected-output-test/if-then-else/print.expected
@@ -0,0 +1,29 @@
+labels_resolved(x INT,
+                l INT).
+
+q?(x INT).
+
+q(x) = if l > 0 then true
+	else if l < 0 then false
+	else NULL
+	end :-
+    labels_resolved(x, l).
+
+labels(x INT,
+       l BOOLEAN).
+
+p(x, if abs(l) > 10 then true
+	else false
+	end) :-
+    labels(x, l).
+
+p(x, if (x % 10) = 0 then false
+	end) :-
+    labels(x, l).
+
+labels_resolved(x, SUM(if label IS NULL then 0
+	else if label = true then 1
+	else -1
+	end)) :-
+    labels(x, label).
+
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index a2bb0e410..f1da78bb4 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -416,13 +416,13 @@ FROM dd_delta_R R0
           input_query: """
           SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
           FROM dd_new_Q R0, dd_new_Q R1, dd_delta_S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000) UNION ALL 
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
           SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
           FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_delta_R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000) UNION ALL 
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
           SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
           FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_new_R R3, dd_delta_S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000)"""
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
           weight: "-10.0"
           dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_new_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S" ]

From 393881369065f4e5737a5b399596831ad2ef62ba Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 12:14:52 -0800
Subject: [PATCH 259/347] Simplifies bats template for expected output tests to
 add desugar tests

---
 test/expected-output-test.bats.template | 43 ++++++++++++-------------
 1 file changed, 21 insertions(+), 22 deletions(-)

diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index a6ac9954e..036d56ded 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -11,6 +11,12 @@ setup() {
     [ -e "$TESTDIR" ]
 }
 
+expectedOutputExistsFor() {
+    expectedOutput="$TESTDIR"/"$1".expected
+    actualOutput="${expectedOutput%.expected}".actual
+    [ -e "$expectedOutput" ]
+}
+
 ## tests for basic compilation and pretty-printing
 
 # check if example can be parsed
@@ -29,7 +35,7 @@ setup() {
 
 # check if print is idempotent
 @test "$it parses and prints what it prints (idempotent)" {
-    printed=$TESTDIR/printed.actual
+    printed="$TESTDIR"/printed.actual
     ddlog print "$TESTDIR"/input.ddlog >"$printed" || skip
     ddlog print "$printed" >"$TESTDIR"/printed-printed.actual
     diff "$printed" "$TESTDIR"/printed-printed.actual
@@ -38,27 +44,28 @@ setup() {
 
 # compare the compiled output with what's expected
 @test "$it compiles input as expected" {
-    expectedOutput=$TESTDIR/compile.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "compile" || skip
     ddlog compile "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
 # compare the pretty-printed output with what's expected
 @test "$it prints input as expected" {
-    expectedOutput=$TESTDIR/print.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "print" || skip
     ddlog print "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
+# compare the desugared output with what's expected
+@test "$it desugars as expected" {
+    expectedOutputExistsFor "desugar" || skip
+    ddlog print --desugar "$TESTDIR"/input.ddlog >"$actualOutput"
+    diff "$expectedOutput" "$actualOutput"
+}
+
 # compare the export-schema output with what's expected
 @test "$it exports schema and annotations as expected" {
-    expectedOutput=$TESTDIR/export-schema.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "export-schema" || skip
     ddlog export-schema "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
@@ -68,18 +75,14 @@ setup() {
 
 # compare the compiled output of the incremental version with what's expected
 @test "$it compiles --incremental input as expected" {
-    expectedOutput=$TESTDIR/compile-incremental.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "compile-incremental" || skip
     ddlog compile --incremental "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
 # compare the pretty-printed output of the incremental version with what's expected
 @test "$it prints --incremental input as expected" {
-    expectedOutput=$TESTDIR/print-incremental.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "print-incremental" || skip
     ddlog print --incremental "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
@@ -88,9 +91,7 @@ setup() {
 
 # compare the compiled output of the merge version with what's expected
 @test "$it compiles --merge input as expected" {
-    expectedOutput=$TESTDIR/compile-merge.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "compile-merge" || skip
     ddlog compile --merge "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
@@ -99,9 +100,7 @@ setup() {
 
 # compare the compiled output of the merge version with what's expected
 @test "$it compiles --materialization input as expected" {
-    expectedOutput=$TESTDIR/compile-materialization.expected
-    actualOutput=${expectedOutput%.expected}.actual
-    [ -e "$expectedOutput" ] || skip
+    expectedOutputExistsFor "compile-materialization" || skip
     ddlog compile --materialization "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }

From 4d3503fb603f393f04a665d67305f9fedcf49452 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 12:15:48 -0800
Subject: [PATCH 260/347] Adds skeleton for rewriting sugar constructs

---
 .../scala/org/deepdive/ddlog/DeepDiveLog.scala |  2 ++
 .../deepdive/ddlog/DeepDiveLogCompiler.scala   |  6 ++++--
 .../ddlog/DeepDiveLogDesugarRewriter.scala     | 18 ++++++++++++++++++
 .../ddlog/DeepDiveLogPrettyPrinter.scala       |  5 ++++-
 4 files changed, 28 insertions(+), 3 deletions(-)
 create mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 7123056ce..04214f5cb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -21,6 +21,7 @@ object DeepDiveLog {
   ( handler: DeepDiveLogHandler = null
   , inputFiles: List[String] = List()
   , mode: Mode = ORIGINAL
+  , printDesugared: Boolean = false
   )
   val parser = new scopt.OptionParser[Config]("ddlog") {
     head("DDlog Compiler", "0.0.1")
@@ -31,6 +32,7 @@ object DeepDiveLog {
     opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
     opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
     opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
+    opt[Unit]("desugar")               optional() action { (_, c) => c.copy(printDesugared = true)                } text("Whether to print desugared or not")
     arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
     checkConfig { c =>
       if (c.handler == null) failure("No command specified")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 489c54138..146ac6f07 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -895,8 +895,10 @@ ${if (createTable) {
         case MATERIALIZATION => parsedProgram
         case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
       }
+    // desugar
+    val programToCompileDesugared = DeepDiveLogDesugarRewriter.derive(programToCompile)
     // take an initial pass to analyze the parsed program
-    val state = new CompilationState( programToCompile, config )
+    val state = new CompilationState( programToCompileDesugared, config )
 
     val body = new ListBuffer[String]()
     config.mode match {
@@ -914,7 +916,7 @@ ${if (createTable) {
       :::
       compileVariableKey(state)
       :::
-      compileVariableSchema(programToCompile, state)
+      compileVariableSchema(programToCompileDesugared, state)
       :::
       body.toList
       :::
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
new file mode 100644
index 000000000..a8fb9d14e
--- /dev/null
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
@@ -0,0 +1,18 @@
+package org.deepdive.ddlog
+
+object DeepDiveLogDesugarRewriter {
+
+  // Rewrite multiple types of rules with same heads as explicit union rules.
+  def desugarImplicitUnions(program: DeepDiveLog.Program) = {
+    // TODO
+    program
+  }
+
+
+  def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
+    (List(
+        desugarImplicitUnions(_)
+      ) reduce (_.compose(_))
+    )(program)
+  }
+}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 6089fd9ed..3e03a1c9f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -194,7 +194,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    val programToPrint =
+    var programToPrint =
       // derive the program based on mode information
       config.mode match {
         case ORIGINAL => parsedProgram
@@ -202,6 +202,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         case MATERIALIZATION => parsedProgram
         case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
       }
+    // desugar if requested
+    if (config.printDesugared)
+      programToPrint = DeepDiveLogDesugarRewriter.derive(programToPrint)
     // pretty print in original syntax
     programToPrint foreach {stmt => println(print(stmt))}
   }

From 826669e6cca403a588bc80f250bcb86e5609e66d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 18:08:42 -0800
Subject: [PATCH 261/347] Adds desugaring for unions implied by function calls
 mixed with normal rules

---
 .../ddlog/DeepDiveLogDesugarRewriter.scala    |  78 +++++-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |   2 +-
 .../compile-incremental.expected              | 260 +++++++++++++++---
 .../compile.expected                          | 141 +++++++---
 .../desugar.expected                          | 126 +++++++++
 .../multiple_rules_for_same_head/input.ddlog  |   4 +
 6 files changed, 534 insertions(+), 77 deletions(-)
 create mode 100644 test/expected-output-test/multiple_rules_for_same_head/desugar.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
index a8fb9d14e..b06f5b1d6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
@@ -2,16 +2,84 @@ package org.deepdive.ddlog
 
 object DeepDiveLogDesugarRewriter {
 
-  // Rewrite multiple types of rules with same heads as explicit union rules.
-  def desugarImplicitUnions(program: DeepDiveLog.Program) = {
-    // TODO
-    program
+  // Rewrite function call rules whose output coincides with normal rules.
+  def desugarUnionsImpliedByFunctionCallRules(program: DeepDiveLog.Program) = {
+    def indexByFirst[a,b](pairs: Seq[(a,b)]): Map[a,List[b]] =
+      pairs groupBy { _._1 } mapValues { _ map (_._2) toList }
+
+    val schemaByName = indexByFirst(program collect {
+      case decl: SchemaDeclaration => decl.a.name -> decl
+    }) mapValues (_ head)
+    val rulesWithIndexByName = indexByFirst(program.zipWithIndex collect {
+      case (fncall: FunctionCallRule, i) => fncall.output -> (fncall, i)
+      case (rule  : ExtractionRule  , i) => rule.headName -> (rule  , i)
+    })
+    val relationNamesUsedInProgram = program collect {
+      case decl: SchemaDeclaration  => decl.a.name
+      case fncall: FunctionCallRule => fncall.output
+      case rule: ExtractionRule     => rule.headName
+    } toSet
+
+    // find names that have multiple function calls or mixed type rules
+    val relationsToDesugar = rulesWithIndexByName flatMap {
+      case (name, allRules) =>
+        val (fncalls, rules) = allRules map {_._1} partition {_.isInstanceOf[FunctionCallRule]}
+        if ((fncalls size) > 1 || ((fncalls size) > 0 && (rules size) > 0)) {
+          Some(name)
+        } else None
+    }
+    val rulesToRewrite = relationsToDesugar flatMap rulesWithIndexByName map {
+      _._1} filter {_.isInstanceOf[FunctionCallRule]} toList
+
+    // determine a separator that does not create name clashes with existing heads for each relation to rewrite
+    val prefixForRelation: Map[String, String] = relationsToDesugar map { name =>
+      name -> (
+        Stream.from(1) map { n => s"${name}${"_" * n}"
+        } dropWhile { prefix =>
+          relationNamesUsedInProgram exists {_ startsWith prefix}
+        } head
+      )
+    } toMap
+
+    // how to make names unique
+    def makeUnique(name: String, ordLocal: Int, ordGlobal: Int): String = {
+      s"${prefixForRelation(name)}${ordLocal}"
+    }
+
+    // plan the rewrite
+    val rewritePlan : Map[Statement, List[Statement]] =
+      program collect {
+        // only function call rule needs to be rewritten
+        case fncall: FunctionCallRule if rulesToRewrite contains fncall =>
+          val relationName: String = fncall.output
+          val rulesForTheRelationToRewriteOrdered = rulesWithIndexByName(relationName
+            ) sortBy {_._2} filter {_._1.isInstanceOf[FunctionCallRule]}
+          val orderAmongRulesToRewrite = rulesForTheRelationToRewriteOrdered map {_._1} indexOf(fncall)
+          val orderInProgram = rulesForTheRelationToRewriteOrdered(orderAmongRulesToRewrite)._2
+          val nameUnique: String = makeUnique(relationName, orderAmongRulesToRewrite, orderInProgram)
+          val schema = schemaByName(relationName)
+          fncall -> List(
+            schema.copy(a = schema.a.copy(name = nameUnique)),
+            fncall.copy(output = nameUnique),
+            ExtractionRule(
+              headName = relationName,
+              q = ConjunctiveQuery(
+                headTerms = schema.a.terms map VarExpr,
+                bodies = List(List(BodyAtom(name = nameUnique, terms = schema.a.terms map VarPattern)))
+              )
+            )
+          )
+          // TODO add union after the last or first or somewhere
+      } toMap
+
+    // apply rewrite plan
+    program flatMap { case rule => rewritePlan getOrElse(rule, List(rule)) }
   }
 
 
   def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
     (List(
-        desugarImplicitUnions(_)
+        desugarUnionsImpliedByFunctionCallRules(_)
       ) reduce (_.compose(_))
     )(program)
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 377a85eb9..6c39e27a1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -40,7 +40,7 @@ case class OuterModifier extends BodyModifier
 case class AllModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
-case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
+case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean = false, limit: Option[Int] = None)
 case class Column(name : String // name of the column
                  , t : String // type of the column
                  , annotation: List[Annotation] = List.empty // optional annotation
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index f1da78bb4..de55dac5f 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -31,6 +31,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_delta_S_0 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_S_0 CASCADE;
+            CREATE TABLE
+            dd_delta_S_0(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_T {
             sql: """ DROP TABLE IF EXISTS dd_delta_T CASCADE;
             CREATE TABLE
@@ -39,6 +47,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_delta_T_2 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T_2 CASCADE;
+            CREATE TABLE
+            dd_delta_T_2(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_new_T {
             sql: """ DROP TABLE IF EXISTS dd_new_T CASCADE;
             CREATE TABLE
@@ -55,6 +71,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_delta_T___0 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T___0 CASCADE;
+            CREATE TABLE
+            dd_delta_T___0(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_new_R {
             sql: """ DROP TABLE IF EXISTS dd_new_R CASCADE;
             CREATE TABLE
@@ -64,6 +88,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_delta_S_2 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_S_2 CASCADE;
+            CREATE TABLE
+            dd_delta_S_2(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_R {
             sql: """ DROP TABLE IF EXISTS dd_delta_R CASCADE;
             CREATE TABLE
@@ -73,6 +105,30 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_delta_T___3 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T___3 CASCADE;
+            CREATE TABLE
+            dd_delta_T___3(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_S_1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_S_1 CASCADE;
+            CREATE TABLE
+            dd_delta_S_1(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_T___1 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T___1 CASCADE;
+            CREATE TABLE
+            dd_delta_T___1(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_Q {
             sql: """ DROP TABLE IF EXISTS dd_delta_Q CASCADE;
             CREATE TABLE
@@ -83,15 +139,40 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_T_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_T_2 CASCADE;
+            CREATE TABLE
+            dd_new_T_2(a int)
+            """
+            style: "sql_extractor"
+          }
+
+          deepdive.extraction.extractors.init_dd_delta_T___2 {
+            sql: """ DROP TABLE IF EXISTS dd_delta_T___2 CASCADE;
+            CREATE TABLE
+            dd_delta_T___2(a int)
+            """
+            style: "sql_extractor"
+          }
+
         deepdive.extraction.extractors.cleanup {
           sql: """
           TRUNCATE dd_new_S;
+          TRUNCATE dd_delta_S_0;
           TRUNCATE dd_delta_T;
+          TRUNCATE dd_delta_T_2;
           TRUNCATE dd_new_T;
           TRUNCATE dd_delta_S;
+          TRUNCATE dd_delta_T___0;
           TRUNCATE dd_new_R;
+          TRUNCATE dd_delta_S_2;
           TRUNCATE dd_delta_R;
+          TRUNCATE dd_delta_T___3;
+          TRUNCATE dd_delta_S_1;
+          TRUNCATE dd_delta_T___1;
           TRUNCATE dd_delta_Q;
+          TRUNCATE dd_new_T_2;
+          TRUNCATE dd_delta_T___2;
           """
           style: "sql_extractor"
         }
@@ -113,7 +194,7 @@ FROM dd_delta_S R0
         """
           output_relation: "dd_new_S"
         style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ]
           input_relations: [
             S
             dd_delta_S
@@ -121,6 +202,41 @@ FROM dd_delta_S R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_delta_T {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_delta_T"
+	deepdive sql 'INSERT INTO dd_delta_T SELECT R0.a AS "dd_delta_T___0.R0.a"
+FROM dd_delta_T___0 R0
+        
+UNION ALL
+SELECT R0.a AS "dd_delta_T___1.R0.a"
+FROM dd_delta_T___1 R0
+        
+UNION ALL
+SELECT R0.a AS "dd_delta_T___2.R0.a"
+FROM dd_delta_T___2 R0
+        
+UNION ALL
+SELECT R0.a AS "dd_delta_T___3.R0.a"
+FROM dd_delta_T___3 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_delta_T"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_T___0_by_f" ,  "ext_dd_delta_T___1_by_f" ,  "ext_dd_delta_T___2_by_f" ,  "ext_dd_delta_T___3_by_f_1" ]
+          input_relations: [
+            dd_delta_T___0
+            dd_delta_T___1
+            dd_delta_T___2
+            dd_delta_T___3
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_dd_new_T {
         cmd: """
 
@@ -138,7 +254,7 @@ FROM dd_delta_T R0
         """
           output_relation: "dd_new_T"
         style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T_by_f" ,  "ext1_dd_delta_T_by_f" ,  "ext2_dd_delta_T_by_f" ,  "ext_dd_delta_T_by_f_1" ]
+          dependencies: [ "ext_dd_delta_T" ]
           input_relations: [
             T
             dd_delta_T
@@ -173,17 +289,32 @@ FROM dd_delta_R R0, R R1
 UNION ALL
 SELECT R0.a AS "dd_new_R.R0.a"
 FROM dd_new_R R0, dd_delta_R R1
-        WHERE R1.a = R0.b  AND R0.a = 0'
+        WHERE R1.a = R0.b  AND R0.a = 0
+UNION ALL
+SELECT R0.a AS "dd_delta_S_0.R0.a"
+FROM dd_delta_S_0 R0
+        
+UNION ALL
+SELECT R0.a AS "dd_delta_S_1.R0.a"
+FROM dd_delta_S_1 R0
+        
+UNION ALL
+SELECT R0.a AS "dd_delta_S_2.R0.a"
+FROM dd_delta_S_2 R0
+        '
 	# TODO rename temporary table to replace output_relation
 	
         """
           output_relation: "dd_delta_S"
         style: "cmd_extractor"
-          dependencies: [ "ext_dd_new_R" ]
+          dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_0_by_f" ,  "ext_dd_delta_S_1_by_f" ,  "ext_dd_delta_S_2_by_f_1" ]
           input_relations: [
             dd_delta_R
             R
             dd_new_R
+            dd_delta_S_0
+            dd_delta_S_1
+            dd_delta_S_2
           ]
       }
     
@@ -213,6 +344,23 @@ FROM dd_delta_R R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_delta_T__3 {
+        cmd: """
+
+	deepdive create view dd_delta_T__3 as 'SELECT R0.a AS column_0
+FROM dd_delta_T R0
+        '
+	
+        """
+          output_relation: "dd_delta_T__3"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_T" ]
+          input_relations: [
+            dd_delta_T
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_dd_new_Q {
         cmd: """
 
@@ -237,12 +385,37 @@ SELECT DISTINCT R0.x, id, label
       }
     
 
-        deepdive.extraction.extractors.ext_dd_delta_T_by_f {
+      deepdive.extraction.extractors.ext_dd_new_T_2 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_T_2"
+	deepdive sql 'INSERT INTO dd_new_T_2 SELECT R0.a
+FROM T_2 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_T_2 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_T_2"
+        style: "cmd_extractor"
+          
+          input_relations: [
+            T_2
+            dd_delta_T_2
+          ]
+      }
+    
+
+        deepdive.extraction.extractors.ext_dd_delta_T___0_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         WHERE R0.a > 1000
           """
-          output_relation: "dd_delta_T"
+          output_relation: "dd_delta_T___0"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -254,12 +427,12 @@ FROM dd_delta_R R0
         }
       
 
-        deepdive.extraction.extractors.ext1_dd_delta_T_by_f {
+        deepdive.extraction.extractors.ext_dd_delta_T___1_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         WHERE 10 < R0.a AND R0.a < 20
           """
-          output_relation: "dd_delta_T"
+          output_relation: "dd_delta_T___1"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -271,12 +444,12 @@ FROM dd_delta_R R0
         }
       
 
-        deepdive.extraction.extractors.ext2_dd_delta_T_by_f {
+        deepdive.extraction.extractors.ext_dd_delta_T___2_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         WHERE 100 < R0.a AND R0.a < 200
           """
-          output_relation: "dd_delta_T"
+          output_relation: "dd_delta_T___2"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -288,12 +461,12 @@ FROM dd_delta_R R0
         }
       
 
-        deepdive.extraction.extractors.ext_dd_delta_S_by_f {
+        deepdive.extraction.extractors.ext_dd_delta_S_0_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         WHERE R0.a < 0
           """
-          output_relation: "dd_delta_S"
+          output_relation: "dd_delta_S_0"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -305,12 +478,12 @@ FROM dd_delta_R R0
         }
       
 
-        deepdive.extraction.extractors.ext1_dd_delta_S_by_f {
+        deepdive.extraction.extractors.ext_dd_delta_S_1_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         WHERE R0.a > 0
           """
-          output_relation: "dd_delta_S"
+          output_relation: "dd_delta_S_1"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -322,12 +495,12 @@ FROM dd_delta_R R0
         }
       
 
-        deepdive.extraction.extractors.ext_dd_delta_T_by_f_1 {
+        deepdive.extraction.extractors.ext_dd_delta_T___3_by_f_1 {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         
           """
-          output_relation: "dd_delta_T"
+          output_relation: "dd_delta_T___3"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -339,12 +512,12 @@ FROM dd_delta_R R0
         }
       
 
-        deepdive.extraction.extractors.ext_dd_delta_S_by_f_1 {
+        deepdive.extraction.extractors.ext_dd_delta_S_2_by_f_1 {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
         WHERE R0.a > 0
           """
-          output_relation: "dd_delta_S"
+          output_relation: "dd_delta_S_2"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -363,7 +536,7 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -378,7 +551,7 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -399,7 +572,7 @@ FROM dd_delta_R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_new_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S" ]
+          dependencies: [ "ext_dd_new_S" ,  "ext_dd_delta_S" ,  "ext_dd_new_R" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -425,7 +598,7 @@ FROM dd_delta_R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
           weight: "-10.0"
-          dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_new_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S" ]
+          dependencies: [ "ext_dd_new_S" ,  "ext_dd_delta_S" ,  "ext_dd_new_R" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -439,18 +612,21 @@ FROM dd_delta_R R0
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
+  ext_dd_delta_T___1_by_f
   ext_dd_new_R
-  ext_dd_delta_T_by_f
-  ext1_dd_delta_T_by_f
-  ext2_dd_delta_T_by_f
+  ext_dd_new_T_2
+  ext_dd_delta_S_0_by_f
+  ext_dd_delta_T__3
+  ext_dd_delta_S_2_by_f_1
+  ext_dd_delta_S_1_by_f
+  ext_dd_delta_T
   ext_dd_delta_S
   ext_dd_new_T
+  ext_dd_delta_T___3_by_f_1
   ext_dd_new_S
-  ext_dd_delta_S_by_f
   ext_dd_new_Q
-  ext_dd_delta_S_by_f_1
-  ext_dd_delta_T_by_f_1
-  ext1_dd_delta_S_by_f
+  ext_dd_delta_T___0_by_f
+  ext_dd_delta_T___2_by_f
 ]
 deepdive.pipeline.pipelines.inference: [
   dd_delta_inf_istrue_Q
@@ -459,18 +635,21 @@ deepdive.pipeline.pipelines.inference: [
   dd_delta_inf1_imply_Q_Q
 ]
 deepdive.pipeline.pipelines.endtoend: [
+  ext_dd_delta_T___1_by_f
   ext_dd_new_R
-  ext_dd_delta_T_by_f
-  ext1_dd_delta_T_by_f
-  ext2_dd_delta_T_by_f
+  ext_dd_new_T_2
+  ext_dd_delta_S_0_by_f
+  ext_dd_delta_T__3
+  ext_dd_delta_S_2_by_f_1
+  ext_dd_delta_S_1_by_f
+  ext_dd_delta_T
   ext_dd_delta_S
   ext_dd_new_T
+  ext_dd_delta_T___3_by_f_1
   ext_dd_new_S
-  ext_dd_delta_S_by_f
   ext_dd_new_Q
-  ext_dd_delta_S_by_f_1
-  ext_dd_delta_T_by_f_1
-  ext1_dd_delta_S_by_f
+  ext_dd_delta_T___0_by_f
+  ext_dd_delta_T___2_by_f
   dd_delta_inf_istrue_Q
   dd_delta_inf1_istrue_Q
   dd_delta_inf_imply_Q_Q
@@ -479,13 +658,22 @@ deepdive.pipeline.pipelines.endtoend: [
 deepdive.pipeline.base_dir: ${BASEDIR}
 deepdive.pipeline.pipelines.initdb: [
   init_dd_new_S
+  init_dd_delta_S_0
   init_dd_delta_T
+  init_dd_delta_T_2
   init_dd_new_T
   init_dd_delta_S
+  init_dd_delta_T___0
   init_dd_new_R
+  init_dd_delta_S_2
   init_dd_delta_R
+  init_dd_delta_T___3
+  init_dd_delta_S_1
   init_dd_new_Q
+  init_dd_delta_T___1
   init_dd_delta_Q
+  init_dd_new_T_2
+  init_dd_delta_T___2
 ]
 deepdive.pipeline.pipelines.cleanup: [
   cleanup
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index ff2354e85..ad8122631 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -32,25 +32,92 @@ FROM R R0, R R1
 UNION ALL
 SELECT R0.a AS "R.R0.a"
 FROM R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a = 0'
+        WHERE R1.a = R0.b  AND R0.a = 0
+UNION ALL
+SELECT R0.a AS "S_0.R0.a"
+FROM S_0 R0
+        
+UNION ALL
+SELECT R0.a AS "S_1.R0.a"
+FROM S_1 R0
+        
+UNION ALL
+SELECT R0.a AS "S_2.R0.a"
+FROM S_2 R0
+        '
 	# TODO rename temporary table to replace output_relation
 	
         """
           output_relation: "S"
         style: "cmd_extractor"
-          
+          dependencies: [ "ext_S_0_by_f" ,  "ext_S_1_by_f" ,  "ext_S_2_by_f_1" ]
           input_relations: [
             R
+            S_0
+            S_1
+            S_2
+          ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_T__3 {
+        cmd: """
+
+	deepdive create view T__3 as 'SELECT R0.a AS column_0
+FROM T R0
+        '
+	
+        """
+          output_relation: "T__3"
+        style: "cmd_extractor"
+          dependencies: [ "ext_T" ]
+          input_relations: [
+            T
+          ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_T {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "T"
+	deepdive sql 'INSERT INTO T SELECT R0.a AS "T___0.R0.a"
+FROM T___0 R0
+        
+UNION ALL
+SELECT R0.a AS "T___1.R0.a"
+FROM T___1 R0
+        
+UNION ALL
+SELECT R0.a AS "T___2.R0.a"
+FROM T___2 R0
+        
+UNION ALL
+SELECT R0.a AS "T___3.R0.a"
+FROM T___3 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "T"
+        style: "cmd_extractor"
+          dependencies: [ "ext_T___0_by_f" ,  "ext_T___1_by_f" ,  "ext_T___2_by_f" ,  "ext_T___3_by_f_1" ]
+          input_relations: [
+            T___0
+            T___1
+            T___2
+            T___3
           ]
       }
     
 
-        deepdive.extraction.extractors.ext_T_by_f {
+        deepdive.extraction.extractors.ext_T___0_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         WHERE R0.a > 1000
           """
-          output_relation: "T"
+          output_relation: "T___0"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -62,12 +129,12 @@ FROM R R0
         }
       
 
-        deepdive.extraction.extractors.ext1_T_by_f {
+        deepdive.extraction.extractors.ext_T___1_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         WHERE 10 < R0.a AND R0.a < 20
           """
-          output_relation: "T"
+          output_relation: "T___1"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -79,12 +146,12 @@ FROM R R0
         }
       
 
-        deepdive.extraction.extractors.ext2_T_by_f {
+        deepdive.extraction.extractors.ext_T___2_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         WHERE 100 < R0.a AND R0.a < 200
           """
-          output_relation: "T"
+          output_relation: "T___2"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -96,12 +163,12 @@ FROM R R0
         }
       
 
-        deepdive.extraction.extractors.ext_S_by_f {
+        deepdive.extraction.extractors.ext_S_0_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         WHERE R0.a < 0
           """
-          output_relation: "S"
+          output_relation: "S_0"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -113,12 +180,12 @@ FROM R R0
         }
       
 
-        deepdive.extraction.extractors.ext1_S_by_f {
+        deepdive.extraction.extractors.ext_S_1_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         WHERE R0.a > 0
           """
-          output_relation: "S"
+          output_relation: "S_1"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -130,12 +197,12 @@ FROM R R0
         }
       
 
-        deepdive.extraction.extractors.ext_T_by_f_1 {
+        deepdive.extraction.extractors.ext_T___3_by_f_1 {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         
           """
-          output_relation: "T"
+          output_relation: "T___3"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -147,12 +214,12 @@ FROM R R0
         }
       
 
-        deepdive.extraction.extractors.ext_S_by_f_1 {
+        deepdive.extraction.extractors.ext_S_2_by_f_1 {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
         WHERE R0.a > 0
           """
-          output_relation: "S"
+          output_relation: "S_2"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
           
@@ -171,7 +238,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -186,7 +253,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -201,7 +268,7 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -214,10 +281,10 @@ FROM R R0
           input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
           FROM Q R0, Q R1, S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND R0.x + (R1.x < 1000)"""
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "-10.0"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S_by_f_1" ,  "ext_S" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -227,14 +294,16 @@ FROM R R0
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
-  ext2_T_by_f
-  ext_S_by_f_1
-  ext_S_by_f
-  ext1_S_by_f
-  ext_T_by_f_1
-  ext1_T_by_f
+  ext_S_1_by_f
+  ext_T
+  ext_S_2_by_f_1
+  ext_S_0_by_f
+  ext_T___3_by_f_1
+  ext_T__3
+  ext_T___2_by_f
+  ext_T___0_by_f
   ext_S
-  ext_T_by_f
+  ext_T___1_by_f
 ]
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_Q
@@ -243,14 +312,16 @@ deepdive.pipeline.pipelines.inference: [
   inf1_imply_Q_Q
 ]
 deepdive.pipeline.pipelines.endtoend: [
-  ext2_T_by_f
-  ext_S_by_f_1
-  ext_S_by_f
-  ext1_S_by_f
-  ext_T_by_f_1
-  ext1_T_by_f
+  ext_S_1_by_f
+  ext_T
+  ext_S_2_by_f_1
+  ext_S_0_by_f
+  ext_T___3_by_f_1
+  ext_T__3
+  ext_T___2_by_f
+  ext_T___0_by_f
   ext_S
-  ext_T_by_f
+  ext_T___1_by_f
   inf_istrue_Q
   inf1_istrue_Q
   inf_imply_Q_Q
diff --git a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
new file mode 100644
index 000000000..a1767b4f4
--- /dev/null
+++ b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
@@ -0,0 +1,126 @@
+R(a int,
+  b int).
+
+S(a int).
+
+T(a int).
+
+Q?(x int).
+
+S(a) :-
+    R(a, b),
+    R(b, _),
+    a > 100.
+
+S(a) :-
+    R(a, b),
+    R(b, _),
+    a < -100.
+
+S(a) :-
+    R(a, b),
+    R(b, _),
+    a = 0.
+
+function f
+    over (a int, b int)
+ returns (a int)
+ implementation "/bin/false"
+        handles tsv lines.
+
+T___0(a int).
+
+T___0 += f(a, b) :-
+    R(a, b),
+    a > 1000.
+
+T(a) :-
+    T___0(a).
+
+T___1(a int).
+
+T___1 += f(a, b) :-
+    R(a, b),
+    [10 < a, a < 20].
+
+T(a) :-
+    T___1(a).
+
+T___2(a int).
+
+T___2 += f(a, b) :-
+    R(a, b),
+    [100 < a, a < 200].
+
+T(a) :-
+    T___2(a).
+
+S_0(a int).
+
+S_0 += f(a, b) :-
+    R(a, b),
+    a < 0.
+
+S(a) :-
+    S_0(a).
+
+S_1(a int).
+
+S_1 += f(a, b) :-
+    R(a, b),
+    a > 0.
+
+S(a) :-
+    S_1(a).
+
+function f_1
+    over (a int, b int)
+ returns (a int)
+ implementation "/bin/false"
+        handles tsv lines.
+
+T___3(a int).
+
+T___3 += f_1(a, b) :-
+    R(a, b).
+
+T(a) :-
+    T___3(a).
+
+S_2(a int).
+
+S_2 += f_1(a, b) :-
+    R(a, b),
+    a > 0.
+
+S(a) :-
+    S_2(a).
+
+@weight(a)
+Q(a) :-
+    S(a),
+    a > 1000.
+
+@weight(1.0)
+Q(a) :-
+    S(a),
+    a = 0.
+
+@weight(a)
+Q(a) => Q(b) :-
+    S(a),
+    R(a, b),
+    S(b).
+
+@weight(-10.0)
+Q(a) => Q(b) :-
+    S(a),
+    R(a, b),
+    S(b),
+    (a + b) < 1000.
+
+T_2(a int).
+
+T__3(x) :-
+    T(x).
+
diff --git a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
index 690e53204..c0dfdfca4 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
+++ b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
@@ -34,3 +34,7 @@ Q(a) :- S(a), a = 0.
 Q(a) => Q(b) :- S(a), R(a, b), S(b).
 @weight(-10.0)
 Q(a) => Q(b) :- S(a), R(a, b), S(b), a + b < 1000.
+
+# make sure desugars without name clashes
+T_2(a int).
+T__3(x) :- T(x).

From 68616a0b34ba34714aa0dc4d5eec572d1861024e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 18:18:21 -0800
Subject: [PATCH 262/347] Makes export-schema also aware of --desugar

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala    | 10 +++++-----
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala  |  2 +-
 .../org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala | 10 +++++++---
 3 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 04214f5cb..cb8c1b4e1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -18,10 +18,10 @@ object DeepDiveLog {
   type Program = List[Statement]
 
   case class Config
-  ( handler: DeepDiveLogHandler = null
-  , inputFiles: List[String] = List()
-  , mode: Mode = ORIGINAL
-  , printDesugared: Boolean = false
+  (handler: DeepDiveLogHandler = null
+   , inputFiles: List[String] = List()
+   , mode: Mode = ORIGINAL
+   , useDesugared: Boolean = false
   )
   val parser = new scopt.OptionParser[Config]("ddlog") {
     head("DDlog Compiler", "0.0.1")
@@ -32,7 +32,7 @@ object DeepDiveLog {
     opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
     opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
     opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
-    opt[Unit]("desugar")               optional() action { (_, c) => c.copy(printDesugared = true)                } text("Whether to print desugared or not")
+    opt[Unit]("desugar")               optional() action { (_, c) => c.copy(useDesugared = true)                } text("Whether to print desugared or not")
     arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
     checkConfig { c =>
       if (c.handler == null) failure("No command specified")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 3e03a1c9f..db9646fcf 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -203,7 +203,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
       }
     // desugar if requested
-    if (config.printDesugared)
+    if (config.useDesugared)
       programToPrint = DeepDiveLogDesugarRewriter.derive(programToPrint)
     // pretty print in original syntax
     programToPrint foreach {stmt => println(print(stmt))}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 173f41d2c..4280cdc85 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -58,16 +58,20 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    val program = parsedProgram  // TODO derive the program based on config.mode?
+    var programToExport = parsedProgram  // TODO derive the program based on config.mode?
+
+    if (config.useDesugared) {
+      programToExport = DeepDiveLogDesugarRewriter.derive(programToExport)
+    }
 
     // first find out names of the relations that have SchemaDeclaration
-    val declaredNames = program collect {
+    val declaredNames = programToExport collect {
       case decl: SchemaDeclaration => decl.a.name
     }
 
     // then print schema in JSON
     println(JSONObject(Map(
-      "relations" -> JSONObject(program collect {
+      "relations" -> JSONObject(programToExport collect {
           case decl: SchemaDeclaration => export(decl)
           case rule: ExtractionRule if ! (declaredNames contains rule.headName) =>
             // for extraction rules whose head is not declared already,

From 5fe3907b515237499d5c7f88d22ad068c10bfaf4 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 26 Jan 2016 18:22:57 -0800
Subject: [PATCH 263/347] Centralizes --desugar handling so all Handlers are
 uniformly affected

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala      | 9 ++++++++-
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala   | 6 ++----
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala    | 5 +----
 .../org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala   | 4 ----
 4 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index cb8c1b4e1..847f5fd5c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -57,8 +57,15 @@ trait DeepDiveLogHandler {
   def run(config: DeepDiveLog.Config): Unit = try {
     // parse each file into a single program
     val parsedProgram = parseFiles(config.inputFiles)
+
+    // desugar if needed
+    val programToRun =
+      if (config.useDesugared)
+        DeepDiveLogDesugarRewriter.derive(parsedProgram)
+      else parsedProgram
+
     // run handler with the parsed program
-    run(parsedProgram, config)
+    run(programToRun, config)
   } catch {
     case e: RuntimeException =>
       if (sys.env contains "DDLOG_STACK_TRACE") throw e
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 146ac6f07..489c54138 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -895,10 +895,8 @@ ${if (createTable) {
         case MATERIALIZATION => parsedProgram
         case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
       }
-    // desugar
-    val programToCompileDesugared = DeepDiveLogDesugarRewriter.derive(programToCompile)
     // take an initial pass to analyze the parsed program
-    val state = new CompilationState( programToCompileDesugared, config )
+    val state = new CompilationState( programToCompile, config )
 
     val body = new ListBuffer[String]()
     config.mode match {
@@ -916,7 +914,7 @@ ${if (createTable) {
       :::
       compileVariableKey(state)
       :::
-      compileVariableSchema(programToCompileDesugared, state)
+      compileVariableSchema(programToCompile, state)
       :::
       body.toList
       :::
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index db9646fcf..6089fd9ed 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -194,7 +194,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    var programToPrint =
+    val programToPrint =
       // derive the program based on mode information
       config.mode match {
         case ORIGINAL => parsedProgram
@@ -202,9 +202,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         case MATERIALIZATION => parsedProgram
         case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
       }
-    // desugar if requested
-    if (config.useDesugared)
-      programToPrint = DeepDiveLogDesugarRewriter.derive(programToPrint)
     // pretty print in original syntax
     programToPrint foreach {stmt => println(print(stmt))}
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 4280cdc85..639c9c77a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -60,10 +60,6 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     var programToExport = parsedProgram  // TODO derive the program based on config.mode?
 
-    if (config.useDesugared) {
-      programToExport = DeepDiveLogDesugarRewriter.derive(programToExport)
-    }
-
     // first find out names of the relations that have SchemaDeclaration
     val declaredNames = programToExport collect {
       case decl: SchemaDeclaration => decl.a.name

From 375567bc7937abe22852d876fdd1f01331247598 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 29 Jan 2016 16:53:42 -0800
Subject: [PATCH 264/347] Defaults to enable desugar rewriting

and flips the CLI flag to `--skip-desugar`
---
 src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala | 11 +++++------
 test/expected-output-test.bats.template             |  4 ++--
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 847f5fd5c..cf08d51e3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -21,7 +21,7 @@ object DeepDiveLog {
   (handler: DeepDiveLogHandler = null
    , inputFiles: List[String] = List()
    , mode: Mode = ORIGINAL
-   , useDesugared: Boolean = false
+   , skipDesugar: Boolean = false
   )
   val parser = new scopt.OptionParser[Config]("ddlog") {
     head("DDlog Compiler", "0.0.1")
@@ -32,7 +32,7 @@ object DeepDiveLog {
     opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
     opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
     opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
-    opt[Unit]("desugar")               optional() action { (_, c) => c.copy(useDesugared = true)                } text("Whether to print desugared or not")
+    opt[Unit]("skip-desugar")          optional() action { (_, c) => c.copy(skipDesugar = true)                   } text("Whether to skip desugaring and assume no sugar")
     arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
     checkConfig { c =>
       if (c.handler == null) failure("No command specified")
@@ -58,11 +58,10 @@ trait DeepDiveLogHandler {
     // parse each file into a single program
     val parsedProgram = parseFiles(config.inputFiles)
 
-    // desugar if needed
+    // desugar unless explicitly said to skip so
     val programToRun =
-      if (config.useDesugared)
-        DeepDiveLogDesugarRewriter.derive(parsedProgram)
-      else parsedProgram
+      if (config.skipDesugar) parsedProgram
+      else DeepDiveLogDesugarRewriter.derive(parsedProgram)
 
     // run handler with the parsed program
     run(programToRun, config)
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index 036d56ded..325b63456 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -52,14 +52,14 @@ expectedOutputExistsFor() {
 # compare the pretty-printed output with what's expected
 @test "$it prints input as expected" {
     expectedOutputExistsFor "print" || skip
-    ddlog print "$TESTDIR"/input.ddlog >"$actualOutput"
+    ddlog print --skip-desugar "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 
 # compare the desugared output with what's expected
 @test "$it desugars as expected" {
     expectedOutputExistsFor "desugar" || skip
-    ddlog print --desugar "$TESTDIR"/input.ddlog >"$actualOutput"
+    ddlog print "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
 

From b0f4f8a07dd8c80138265aeb26ead195b2855f12 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 29 Jan 2016 16:58:49 -0800
Subject: [PATCH 265/347] Updates the test to expect compiling desugared one

---
 .../compile-incremental.expected              | 259 ++++++++++++++++++
 1 file changed, 259 insertions(+)

diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index de55dac5f..85926e063 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -39,6 +39,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_T___0 {
+            sql: """ DROP TABLE IF EXISTS dd_new_T___0 CASCADE;
+            CREATE TABLE
+            dd_new_T___0(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_T {
             sql: """ DROP TABLE IF EXISTS dd_delta_T CASCADE;
             CREATE TABLE
@@ -47,6 +55,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_T___1 {
+            sql: """ DROP TABLE IF EXISTS dd_new_T___1 CASCADE;
+            CREATE TABLE
+            dd_new_T___1(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_T_2 {
             sql: """ DROP TABLE IF EXISTS dd_delta_T_2 CASCADE;
             CREATE TABLE
@@ -55,6 +71,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_S_2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_S_2 CASCADE;
+            CREATE TABLE
+            dd_new_S_2(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_new_T {
             sql: """ DROP TABLE IF EXISTS dd_new_T CASCADE;
             CREATE TABLE
@@ -71,6 +95,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_T___3 {
+            sql: """ DROP TABLE IF EXISTS dd_new_T___3 CASCADE;
+            CREATE TABLE
+            dd_new_T___3(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_T___0 {
             sql: """ DROP TABLE IF EXISTS dd_delta_T___0 CASCADE;
             CREATE TABLE
@@ -96,6 +128,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_S_1 {
+            sql: """ DROP TABLE IF EXISTS dd_new_S_1 CASCADE;
+            CREATE TABLE
+            dd_new_S_1(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_R {
             sql: """ DROP TABLE IF EXISTS dd_delta_R CASCADE;
             CREATE TABLE
@@ -105,6 +145,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_T___2 {
+            sql: """ DROP TABLE IF EXISTS dd_new_T___2 CASCADE;
+            CREATE TABLE
+            dd_new_T___2(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_T___3 {
             sql: """ DROP TABLE IF EXISTS dd_delta_T___3 CASCADE;
             CREATE TABLE
@@ -147,6 +195,14 @@ dd_new_Q.label: Boolean
             style: "sql_extractor"
           }
 
+          deepdive.extraction.extractors.init_dd_new_S_0 {
+            sql: """ DROP TABLE IF EXISTS dd_new_S_0 CASCADE;
+            CREATE TABLE
+            dd_new_S_0(a int)
+            """
+            style: "sql_extractor"
+          }
+
           deepdive.extraction.extractors.init_dd_delta_T___2 {
             sql: """ DROP TABLE IF EXISTS dd_delta_T___2 CASCADE;
             CREATE TABLE
@@ -159,19 +215,26 @@ dd_new_Q.label: Boolean
           sql: """
           TRUNCATE dd_new_S;
           TRUNCATE dd_delta_S_0;
+          TRUNCATE dd_new_T___0;
           TRUNCATE dd_delta_T;
+          TRUNCATE dd_new_T___1;
           TRUNCATE dd_delta_T_2;
+          TRUNCATE dd_new_S_2;
           TRUNCATE dd_new_T;
           TRUNCATE dd_delta_S;
+          TRUNCATE dd_new_T___3;
           TRUNCATE dd_delta_T___0;
           TRUNCATE dd_new_R;
           TRUNCATE dd_delta_S_2;
+          TRUNCATE dd_new_S_1;
           TRUNCATE dd_delta_R;
+          TRUNCATE dd_new_T___2;
           TRUNCATE dd_delta_T___3;
           TRUNCATE dd_delta_S_1;
           TRUNCATE dd_delta_T___1;
           TRUNCATE dd_delta_Q;
           TRUNCATE dd_new_T_2;
+          TRUNCATE dd_new_S_0;
           TRUNCATE dd_delta_T___2;
           """
           style: "sql_extractor"
@@ -202,6 +265,31 @@ FROM dd_delta_S R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_new_T___0 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_T___0"
+	deepdive sql 'INSERT INTO dd_new_T___0 SELECT R0.a
+FROM T___0 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_T___0 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_T___0"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_T___0_by_f" ]
+          input_relations: [
+            T___0
+            dd_delta_T___0
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_dd_delta_T {
         cmd: """
 
@@ -237,6 +325,56 @@ FROM dd_delta_T___3 R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_new_T___1 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_T___1"
+	deepdive sql 'INSERT INTO dd_new_T___1 SELECT R0.a
+FROM T___1 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_T___1 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_T___1"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_T___1_by_f" ]
+          input_relations: [
+            T___1
+            dd_delta_T___1
+          ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_dd_new_S_2 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_S_2"
+	deepdive sql 'INSERT INTO dd_new_S_2 SELECT R0.a
+FROM S_2 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_S_2 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_S_2"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_S_2_by_f_1" ]
+          input_relations: [
+            S_2
+            dd_delta_S_2
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_dd_new_T {
         cmd: """
 
@@ -319,6 +457,31 @@ FROM dd_delta_S_2 R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_new_T___3 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_T___3"
+	deepdive sql 'INSERT INTO dd_new_T___3 SELECT R0.a
+FROM T___3 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_T___3 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_T___3"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_T___3_by_f_1" ]
+          input_relations: [
+            T___3
+            dd_delta_T___3
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_dd_new_R {
         cmd: """
 
@@ -344,6 +507,56 @@ FROM dd_delta_R R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_new_S_1 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_S_1"
+	deepdive sql 'INSERT INTO dd_new_S_1 SELECT R0.a
+FROM S_1 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_S_1 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_S_1"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_S_1_by_f" ]
+          input_relations: [
+            S_1
+            dd_delta_S_1
+          ]
+      }
+    
+
+      deepdive.extraction.extractors.ext_dd_new_T___2 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_T___2"
+	deepdive sql 'INSERT INTO dd_new_T___2 SELECT R0.a
+FROM T___2 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_T___2 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_T___2"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_T___2_by_f" ]
+          input_relations: [
+            T___2
+            dd_delta_T___2
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_dd_delta_T__3 {
         cmd: """
 
@@ -410,6 +623,31 @@ FROM dd_delta_T_2 R0
       }
     
 
+      deepdive.extraction.extractors.ext_dd_new_S_0 {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "dd_new_S_0"
+	deepdive sql 'INSERT INTO dd_new_S_0 SELECT R0.a
+FROM S_0 R0
+        
+UNION ALL
+SELECT R0.a
+FROM dd_delta_S_0 R0
+        '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "dd_new_S_0"
+        style: "cmd_extractor"
+          dependencies: [ "ext_dd_delta_S_0_by_f" ]
+          input_relations: [
+            S_0
+            dd_delta_S_0
+          ]
+      }
+    
+
         deepdive.extraction.extractors.ext_dd_delta_T___0_by_f {
           input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
 FROM dd_delta_R R0
@@ -613,19 +851,26 @@ FROM dd_delta_R R0
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
   ext_dd_delta_T___1_by_f
+  ext_dd_new_T___3
   ext_dd_new_R
   ext_dd_new_T_2
   ext_dd_delta_S_0_by_f
+  ext_dd_new_T___0
   ext_dd_delta_T__3
+  ext_dd_new_S_2
   ext_dd_delta_S_2_by_f_1
   ext_dd_delta_S_1_by_f
   ext_dd_delta_T
   ext_dd_delta_S
   ext_dd_new_T
+  ext_dd_new_S_0
+  ext_dd_new_T___2
   ext_dd_delta_T___3_by_f_1
   ext_dd_new_S
   ext_dd_new_Q
   ext_dd_delta_T___0_by_f
+  ext_dd_new_S_1
+  ext_dd_new_T___1
   ext_dd_delta_T___2_by_f
 ]
 deepdive.pipeline.pipelines.inference: [
@@ -636,19 +881,26 @@ deepdive.pipeline.pipelines.inference: [
 ]
 deepdive.pipeline.pipelines.endtoend: [
   ext_dd_delta_T___1_by_f
+  ext_dd_new_T___3
   ext_dd_new_R
   ext_dd_new_T_2
   ext_dd_delta_S_0_by_f
+  ext_dd_new_T___0
   ext_dd_delta_T__3
+  ext_dd_new_S_2
   ext_dd_delta_S_2_by_f_1
   ext_dd_delta_S_1_by_f
   ext_dd_delta_T
   ext_dd_delta_S
   ext_dd_new_T
+  ext_dd_new_S_0
+  ext_dd_new_T___2
   ext_dd_delta_T___3_by_f_1
   ext_dd_new_S
   ext_dd_new_Q
   ext_dd_delta_T___0_by_f
+  ext_dd_new_S_1
+  ext_dd_new_T___1
   ext_dd_delta_T___2_by_f
   dd_delta_inf_istrue_Q
   dd_delta_inf1_istrue_Q
@@ -659,20 +911,27 @@ deepdive.pipeline.base_dir: ${BASEDIR}
 deepdive.pipeline.pipelines.initdb: [
   init_dd_new_S
   init_dd_delta_S_0
+  init_dd_new_T___0
   init_dd_delta_T
+  init_dd_new_T___1
   init_dd_delta_T_2
+  init_dd_new_S_2
   init_dd_new_T
   init_dd_delta_S
+  init_dd_new_T___3
   init_dd_delta_T___0
   init_dd_new_R
   init_dd_delta_S_2
+  init_dd_new_S_1
   init_dd_delta_R
+  init_dd_new_T___2
   init_dd_delta_T___3
   init_dd_delta_S_1
   init_dd_new_Q
   init_dd_delta_T___1
   init_dd_delta_Q
   init_dd_new_T_2
+  init_dd_new_S_0
   init_dd_delta_T___2
 ]
 deepdive.pipeline.pipelines.cleanup: [

From 7016fc4bdac4f053124d5aa847ab2a4e34cc6b6d Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 10:07:39 -0800
Subject: [PATCH 266/347] Adds sql command to generate SQL from queries in `?-
 foo(x,y,...).` like syntax

---
 .../org/deepdive/ddlog/DeepDiveLog.scala      | 29 +++++++++-----
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 39 +++++++++++++++++--
 .../ddlog/DeepDiveLogQueryCompiler.scala      | 31 +++++++++++++++
 4 files changed, 86 insertions(+), 15 deletions(-)
 create mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 7123056ce..01f0dd5cf 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -16,22 +16,29 @@ object DeepDiveLog {
   import Mode._
 
   type Program = List[Statement]
+  type Query = (ConjunctiveQuery, List[Statement])
 
   case class Config
-  ( handler: DeepDiveLogHandler = null
-  , inputFiles: List[String] = List()
-  , mode: Mode = ORIGINAL
+  (handler: DeepDiveLogHandler = null
+   , inputFiles: List[String] = List()
+   , query: String = null
+   , mode: Mode = ORIGINAL
   )
-  val parser = new scopt.OptionParser[Config]("ddlog") {
+  val commandLine = new scopt.OptionParser[Config]("ddlog") {
+    val commonProgramOpts = List(
+    )
     head("DDlog Compiler", "0.0.1")
-    cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        }
-    cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   }
-    cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) }
-    cmd("export-schema")               required() action { (_, c) => c.copy(handler = DeepDiveLogSchemaExporter)  }
+    cmd("sql")                         required() action { (_, c) => c.copy(handler = DeepDiveLogQueryCompiler)   } text("Compiles a SQL query to run against the program") children(
+      arg[String]("QUERY")             required() action { (q, c) => c.copy(query = q) }                            text("DDLog query to compile against the program")
+      )
+    cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        } text("Compiles a deepdive.conf")
+    cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   } text("Prints given program after parsing")
+    cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) } text("Checks if given program is valid")
+    cmd("export-schema")               required() action { (_, c) => c.copy(handler = DeepDiveLogSchemaExporter)  } text("Exports given program in JSON")
     opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
     opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
     opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
-    arg[String]("FILE...") unbounded() required() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Input DDLog programs files")
+    arg[String]("FILE...") minOccurs(0) unbounded() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Path to DDLog program files")
     checkConfig { c =>
       if (c.handler == null) failure("No command specified")
       else success
@@ -39,17 +46,19 @@ object DeepDiveLog {
   }
 
   def main(args: Array[String]) = {
-    parser.parse(args, Config()) match {
+    commandLine.parse(args, Config()) match {
       case Some(config) =>
         config.handler.run(config)
       case None =>
         System.err.println("[error] ")
     }
   }
+
 }
 
 // An abstraction of DeepDiveLog handlers
 trait DeepDiveLogHandler {
+
   def run(program: DeepDiveLog.Program, config: DeepDiveLog.Config): Unit
 
   def run(config: DeepDiveLog.Config): Unit = try {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index bae9e0a94..de5e66b2d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -504,7 +504,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${limitStr}"""
   }
 
-  def generateSQL(aliasStyle: AliasStyle) = {
+  def generateSQL(aliasStyle: AliasStyle = ViewAlias) = {
     val head = generateSQLHead(aliasStyle)
     val body = cq.bodies map generateSQLBody
     body map { b => s"SELECT ${head}\n${b}" } mkString("\nUNION ALL\n")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 5efcc73ac..21f9f813e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -390,10 +390,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def program : Parser[DeepDiveLog.Program] = phrase(rep1(statement <~ "."))
 
   def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
-    parse(program, inputProgram) match {
-      case result: Success[_] => result.get
-      case error:  NoSuccess  => throw new RuntimeException(fileName.getOrElse("") + error.toString())
-    }
+    val result = parse(program, inputProgram)
+    if (result successful) result.get
+    else sys.error(fileName.getOrElse("") + result.toString)
   }
 
   def parseProgramFile(fileName: String): List[Statement] = {
@@ -401,4 +400,36 @@ class DeepDiveLogParser extends JavaTokenParsers {
     try parseProgram(source.getLines mkString "\n", Some(fileName))
     finally source.close()
   }
+
+  // query is a conjunctive query with optional projection and extraction rules
+  def query : Parser[DeepDiveLog.Query] =
+    rep(normalRule <~ ".") ~ (queryWithOptionalHeadTerms <~ ".") ^^ { case rules ~ q => (q, rules) }
+
+  def normalRule: Parser[ExtractionRule] =
+    relationName ~ conjunctiveQuery ^^ {
+      case headName ~ cq =>
+        ExtractionRule(headName = headName, q = cq)
+    }
+
+  def queryWithOptionalHeadTerms =
+    (repsep(expr, ",") ~ opt("*") ~ opt("|" ~> decimalNumber)) ~ ("?-" ~> rep1sep(cqConjunctiveBody, ";")) ^^ {
+      // optional head terms without parentheses
+      case (headTerms ~ isDistinct ~ limit) ~ disjunctiveBodies =>
+        val headTermsToUse =
+          if (headTerms nonEmpty) headTerms else {
+            val definedVars = disjunctiveBodies flatMap {
+                _ flatMap DeepDiveLogSemanticChecker.collectDefinedVars
+              }
+            definedVars map VarExpr
+            // TODO get common variables from bodies for the headTerms
+          }
+        ConjunctiveQuery(headTermsToUse, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
+    }
+
+  def parseQuery(inputQuery: String): DeepDiveLog.Query = {
+    val result = parse(phrase(query), inputQuery)
+    if (result successful) result.get
+    else sys.error(result.toString)
+  }
+
 }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
new file mode 100644
index 000000000..ed06d11ee
--- /dev/null
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -0,0 +1,31 @@
+package org.deepdive.ddlog
+
+import org.deepdive.ddlog.DeepDiveLog.{Config, Program}
+
+object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
+
+  override def run(program: Program, config: Config): Unit = {
+    val (query, extraRules) = (new DeepDiveLogParser).parseQuery(config.query)
+
+    // TODO make sure extraRules don't have name clashes with program
+    // TODO run SemanticChecker
+
+    // use schema declarations, etc. in given program
+    val compilationState = new CompilationState(
+      config = config,
+      statements = program ++ extraRules
+    )
+    val sql = (extraRules collect {
+      // compile supporting rules as CREATE TEMP TABLE queries
+      case rule: ExtractionRule =>
+        val qc = new QueryCompiler(rule.q, compilationState)
+        s"""CREATE TEMPORARY TABLE ${rule.headName} AS\n${
+          qc.generateSQL(AliasStyle.ViewAlias)}"""
+    }) ++ List({
+      // compile the query
+      s"""${new QueryCompiler(query, compilationState).generateSQL()}"""
+    }) mkString(";\n\n")
+    println(sql)
+  }
+
+}

From 8084ddf02b7dfb090dee928db0ddf2d07c016e37 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 11:49:19 -0800
Subject: [PATCH 267/347] Renames to ddlog query, supports only a single
 conjunctive query body

no disjunctions separated with ";" for the query.
---
 src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala |  2 +-
 .../org/deepdive/ddlog/DeepDiveLogParser.scala      | 13 +++++--------
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 01f0dd5cf..a6d5fcccf 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -28,7 +28,7 @@ object DeepDiveLog {
     val commonProgramOpts = List(
     )
     head("DDlog Compiler", "0.0.1")
-    cmd("sql")                         required() action { (_, c) => c.copy(handler = DeepDiveLogQueryCompiler)   } text("Compiles a SQL query to run against the program") children(
+    cmd("query")                       required() action { (_, c) => c.copy(handler = DeepDiveLogQueryCompiler)   } text("Compiles a SQL query to run against the program") children(
       arg[String]("QUERY")             required() action { (q, c) => c.copy(query = q) }                            text("DDLog query to compile against the program")
       )
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        } text("Compiles a deepdive.conf")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 21f9f813e..e22393e71 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -412,18 +412,15 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def queryWithOptionalHeadTerms =
-    (repsep(expr, ",") ~ opt("*") ~ opt("|" ~> decimalNumber)) ~ ("?-" ~> rep1sep(cqConjunctiveBody, ";")) ^^ {
-      // optional head terms without parentheses
-      case (headTerms ~ isDistinct ~ limit) ~ disjunctiveBodies =>
+    ((("(" ~> rep1sep(expr, ",") <~ ")") | repsep(expr, ",")) // head terms with parentheses or optionally without
+      ~ opt("*") ~ opt("|" ~> decimalNumber)) ~ ("?-" ~> cqConjunctiveBody) ^^ {
+      case (headTerms ~ isDistinct ~ limit) ~ body =>
         val headTermsToUse =
           if (headTerms nonEmpty) headTerms else {
-            val definedVars = disjunctiveBodies flatMap {
-                _ flatMap DeepDiveLogSemanticChecker.collectDefinedVars
-              }
+            val definedVars = body flatMap DeepDiveLogSemanticChecker.collectDefinedVars
             definedVars map VarExpr
-            // TODO get common variables from bodies for the headTerms
           }
-        ConjunctiveQuery(headTermsToUse, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
+        ConjunctiveQuery(headTermsToUse, List(body), isDistinct != None, limit map (_.toInt))
     }
 
   def parseQuery(inputQuery: String): DeepDiveLog.Query = {

From 12d70dda11f705efea67c79363547495b595f3ba Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 11:51:09 -0800
Subject: [PATCH 268/347] Runs SemanticChecker on queries as well with pretty
 printing `?-`

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala  | 6 ++++--
 .../org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala      | 3 ++-
 .../org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala      | 7 +++++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index e22393e71..2be615f4a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -39,7 +39,9 @@ case class OuterModifier extends BodyModifier
 case class AllModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
-case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int])
+case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int],
+                            isForQuery: Boolean = false // XXX This flag is not ideal, but minimizes the impact of query treatment when compared to creating another case class
+                           )
 case class Column(name : String // name of the column
                  , t : String // type of the column
                  , annotation: List[Annotation] = List.empty // optional annotation
@@ -420,7 +422,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             val definedVars = body flatMap DeepDiveLogSemanticChecker.collectDefinedVars
             definedVars map VarExpr
           }
-        ConjunctiveQuery(headTermsToUse, List(body), isDistinct != None, limit map (_.toInt))
+        ConjunctiveQuery(headTermsToUse, List(body), isDistinct != None, limit map (_.toInt), isForQuery = true)
     }
 
   def parseQuery(inputQuery: String): DeepDiveLog.Query = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 49e5d20e2..ad134b3da 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -144,7 +144,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     val headStrTmp  = cq.headTerms map print mkString(", ")
     val headStr     = if (headStrTmp isEmpty) "" else s"(${headStrTmp})"
 
-    headStr + distinctStr + limitStr + supervision + " :-\n    " + bodyStr
+    val headBodySeparator = if (cq.isForQuery) "?-" else ":-"
+    headStr + distinctStr + limitStr + supervision + s" ${headBodySeparator}\n    " + bodyStr
   }
 
   def print(a: HeadAtom) : String = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index ed06d11ee..b46a61ffe 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -8,12 +8,15 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
     val (query, extraRules) = (new DeepDiveLogParser).parseQuery(config.query)
 
     // TODO make sure extraRules don't have name clashes with program
-    // TODO run SemanticChecker
+
+    // run typical checks for correct semantics
+    val programToCheck = ExtractionRule(q = query, headName = "") :: extraRules ++ program
+    DeepDiveLogSemanticChecker.run(programToCheck, config)
 
     // use schema declarations, etc. in given program
     val compilationState = new CompilationState(
       config = config,
-      statements = program ++ extraRules
+      statements = extraRules ++ program
     )
     val sql = (extraRules collect {
       // compile supporting rules as CREATE TEMP TABLE queries

From 513f5898e3172056145d33eea7ae5bf4d755e894 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 12:14:41 -0800
Subject: [PATCH 269/347] Adds a check to prevent extra rules in queries
 redefining existing relation in the program

---
 .../ddlog/DeepDiveLogQueryCompiler.scala      |  3 ++-
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index b46a61ffe..6acdcb015 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -7,7 +7,8 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
   override def run(program: Program, config: Config): Unit = {
     val (query, extraRules) = (new DeepDiveLogParser).parseQuery(config.query)
 
-    // TODO make sure extraRules don't have name clashes with program
+    // make sure extraRules don't have name clashes with the program
+    DeepDiveLogSemanticChecker.checkNoRedefinition(program, extraRules)
 
     // run typical checks for correct semantics
     val programToCheck = ExtractionRule(q = query, headName = "") :: extraRules ++ program
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index b644269de..65bb47b1e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -283,4 +283,23 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // function declaration
   var functionDeclaration : Map[String, FunctionDeclaration] = new HashMap[String, FunctionDeclaration]()
 
+  // partial function that returns relation name defined by the rule
+  def definedRelationName(rule: Statement): Option[String] = rule match {
+    case decl: SchemaDeclaration  => Some(decl.a.name)
+    case rule: ExtractionRule     => Some(rule.headName)
+    case fncall: FunctionCallRule => Some(fncall.output)
+    case _                        => None
+  }
+
+  // shorthand for checking if a set of more rules redefine anything in existing rules
+  // (useful for checking queries against a program)
+  def checkNoRedefinition(existingRules: List[Statement], moreRules: List[Statement]) = {
+    val relationsDefinedByProgram = existingRules flatMap definedRelationName
+    val relationsDefinedByExtraRules =  moreRules flatMap definedRelationName
+    val relationsRedefinedByExtraRules = relationsDefinedByExtraRules intersect relationsDefinedByProgram
+    if (relationsRedefinedByExtraRules nonEmpty)
+      sys.error(s"Following relations must not be redefined: ${
+        relationsRedefinedByExtraRules map {"'"+_+"'"} mkString(", ")}")
+  }
+
 }

From 0e1d839cd825f4fbc5fa47a6c6ed376466954eeb Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 13:16:11 -0800
Subject: [PATCH 270/347] Adds a test for ddlog query

---
 test/query-test.bats.template                 | 34 +++++++++++++++++++
 test/query-test/spouse_example/app.ddlog      |  1 +
 .../spouse_example/count-has_spouse.ddlogq    |  1 +
 .../count-has_spouse.ddlogq.expected          |  3 ++
 4 files changed, 39 insertions(+)
 create mode 100644 test/query-test.bats.template
 create mode 120000 test/query-test/spouse_example/app.ddlog
 create mode 100644 test/query-test/spouse_example/count-has_spouse.ddlogq
 create mode 100644 test/query-test/spouse_example/count-has_spouse.ddlogq.expected

diff --git a/test/query-test.bats.template b/test/query-test.bats.template
new file mode 100644
index 000000000..741b853fd
--- /dev/null
+++ b/test/query-test.bats.template
@@ -0,0 +1,34 @@
+#!/usr/bin/env bats
+# Expected output tests for queries with optional base programs
+
+source "$BATS_TEST_DIRNAME"/../bats-template.bash  # for $TESTDIR, $it, etc.
+
+# some preconditions
+setup() {
+    [ -e "$TESTDIR" ]
+}
+
+# check if example can be parsed
+@test "$it compiles all queries as expected" {
+    # all ddlog files for this test should be parsed as a precondition
+    ddlog print "$TESTDIR"/*.ddlog >/dev/null
+
+    # for each query
+    for q in "$TESTDIR"/*.ddlogq; do
+        expectedOutput="$q".expected
+        expectedError="$q".error-expected
+        [ -e "$expectedOutput" ] || [ -e "$expectedError" ] || continue
+        echo "Compiling $q"
+        actualOutput="$q".actual
+        if [ -e "$expectedError" ]; then
+            expectedOutput=$expectedError
+            # query is expected to have parse errors
+            ! ddlog query "$(cat $q)" "$TESTDIR"/*.ddlog >/dev/null 2>"$actualOutput"
+        else
+            # query is supposed to parse without errors
+            ddlog query "$(cat $q)" "$TESTDIR"/*.ddlog  >"$actualOutput"
+        fi
+        # see if there's any difference
+        diff "$expectedOutput" "$actualOutput"
+    done
+}
diff --git a/test/query-test/spouse_example/app.ddlog b/test/query-test/spouse_example/app.ddlog
new file mode 120000
index 000000000..2b803e7b5
--- /dev/null
+++ b/test/query-test/spouse_example/app.ddlog
@@ -0,0 +1 @@
+../../../examples/spouse_example.ddlog
\ No newline at end of file
diff --git a/test/query-test/spouse_example/count-has_spouse.ddlogq b/test/query-test/spouse_example/count-has_spouse.ddlogq
new file mode 100644
index 000000000..d8ef23e81
--- /dev/null
+++ b/test/query-test/spouse_example/count-has_spouse.ddlogq
@@ -0,0 +1 @@
+COUNT(r) ?- has_spouse(r).
diff --git a/test/query-test/spouse_example/count-has_spouse.ddlogq.expected b/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
new file mode 100644
index 000000000..1105cdb39
--- /dev/null
+++ b/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
@@ -0,0 +1,3 @@
+SELECT COUNT(R0.relation_id) AS column_0
+FROM has_spouse R0
+        

From 97d660370e302bf218a077a3212c33fa5bbdd139 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 22:32:09 -0800
Subject: [PATCH 271/347] Makes the generated SQL for a query use a sensible
 column name

than just column_0 and _1, etc.
---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 3 ++-
 .../scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala    | 2 +-
 .../query-test/spouse_example/count-has_spouse.ddlogq.expected | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index de5e66b2d..b59313e38 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -68,7 +68,7 @@ object AliasStyle extends Enumeration {
   type AliasStyle = Value
   // TableStyle: tableName.R{tableIndex}.columnName
   // ViewStyle: column_{columnIndex}
-  val ViewAlias, TableAlias, NoAlias = Value
+  val ViewAlias, TableAlias, NoAlias, UseVariableAsAlias = Value
 }
 import AliasStyle._
 
@@ -346,6 +346,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
       case _ => s" AS column_${cq.headTerms indexOf e}"
     }
     case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
+    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}""""
   }
 
   // resolve an expression
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index 6acdcb015..41b583db7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -27,7 +27,7 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
           qc.generateSQL(AliasStyle.ViewAlias)}"""
     }) ++ List({
       // compile the query
-      s"""${new QueryCompiler(query, compilationState).generateSQL()}"""
+      s"""${new QueryCompiler(query, compilationState).generateSQL(AliasStyle.UseVariableAsAlias)}"""
     }) mkString(";\n\n")
     println(sql)
   }
diff --git a/test/query-test/spouse_example/count-has_spouse.ddlogq.expected b/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
index 1105cdb39..66a016932 100644
--- a/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
+++ b/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
@@ -1,3 +1,3 @@
-SELECT COUNT(R0.relation_id) AS column_0
+SELECT COUNT(R0.relation_id) AS "COUNT(r)"
 FROM has_spouse R0
         

From 4997d1d36f19aa3bc4c3ed28aefe5491ff3af7f7 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sat, 30 Jan 2016 22:58:56 -0800
Subject: [PATCH 272/347] Fixes failing test's actual equivalent output as
 expected

---
 Makefile                                                  | 8 ++++++++
 .../multiple_rules_for_same_head/compile.expected         | 8 ++++----
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index cc62ab99d..da9977079 100644
--- a/Makefile
+++ b/Makefile
@@ -46,6 +46,14 @@ test: export CLASSPATH = $(realpath $(JAR))
 
 endif # TEST_JAR
 
+actual-expected:
+	for expected in test/*/*/*.expected; do \
+	    actual=${expected%.expected}.actual; \
+	    [[ "$actual" -nt "$expected" ]] && \
+	    ! diff -q "$actual" "$expected" || continue; \
+	    cp -vf "$actual" "$expected"; \
+	done
+
 # test coverage report
 .PHONY: test-coverage coveralls
 test-coverage:
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 2e72c82a1..f4b27bf05 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -171,7 +171,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
           input_relations: [
             Q
             S
@@ -186,7 +186,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
           input_relations: [
             Q
             S
@@ -201,7 +201,7 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
           input_relations: [
             Q
             S
@@ -217,7 +217,7 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "-10.0"
-          dependencies: [ "ext1_S_by_f" ,  "ext_S" ,  "ext_S_by_f_1" ,  "ext_S_by_f" ]
+          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
           input_relations: [
             Q
             S

From 5e4ad3b9170c445ea46c9bae3fea34a69c2789a8 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 31 Jan 2016 12:00:36 -0800
Subject: [PATCH 273/347] Fixes `make actual-expected` for accepting actual
 outputs as expected

which can be handy to see the difference with `git diff` afterwards.
---
 Makefile                      | 11 +++++++----
 test/query-test.bats.template |  2 +-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index da9977079..e20401e5b 100644
--- a/Makefile
+++ b/Makefile
@@ -48,10 +48,13 @@ endif # TEST_JAR
 
 actual-expected:
 	for expected in test/*/*/*.expected; do \
-	    actual=${expected%.expected}.actual; \
-	    [[ "$actual" -nt "$expected" ]] && \
-	    ! diff -q "$actual" "$expected" || continue; \
-	    cp -vf "$actual" "$expected"; \
+	    case $$expected in \
+	        *-error.expected) actual=$${expected%-error.expected}.actual;; \
+	        *)                actual=$${expected%.expected}.actual      ;; \
+	    esac; \
+	    [[ "$$actual" -nt "$$expected" ]] && \
+	    ! diff -q "$$actual" "$$expected" || continue; \
+	    cp -vf "$$actual" "$$expected"; \
 	done
 
 # test coverage report
diff --git a/test/query-test.bats.template b/test/query-test.bats.template
index 741b853fd..f047b9720 100644
--- a/test/query-test.bats.template
+++ b/test/query-test.bats.template
@@ -16,7 +16,7 @@ setup() {
     # for each query
     for q in "$TESTDIR"/*.ddlogq; do
         expectedOutput="$q".expected
-        expectedError="$q".error-expected
+        expectedError="$q"-error.expected
         [ -e "$expectedOutput" ] || [ -e "$expectedError" ] || continue
         echo "Compiling $q"
         actualOutput="$q".actual

From e1a877f8f79cdab870eab89d837cc6d0e58004e8 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 31 Jan 2016 12:00:52 -0800
Subject: [PATCH 274/347] Adds more tests for ddlog query

---
 test/query-test.bats.template                          |  9 ++++++---
 test/query-test/spouse_example/article_ids.ddlogq      |  1 +
 .../spouse_example/article_ids.ddlogq.expected         |  3 +++
 .../histogram-num_candidates-per-article.ddlogq        |  5 +++++
 ...istogram-num_candidates-per-article.ddlogq.expected | 10 ++++++++++
 .../spouse_example/histogram-supervision.ddlogq        |  1 +
 .../histogram-supervision.ddlogq.expected              |  4 ++++
 test/query-test/spouse_example/redefinition.ddlogq     |  5 +++++
 .../spouse_example/redefinition.ddlogq-error.expected  |  1 +
 test/query-test/spouse_example/schema-check.ddlogq     |  1 +
 .../spouse_example/schema-check.ddlogq-error.expected  |  4 ++++
 test/query-test/spouse_example/undefined.ddlogq        |  1 +
 .../spouse_example/undefined.ddlogq-error.expected     |  4 ++++
 13 files changed, 46 insertions(+), 3 deletions(-)
 create mode 100644 test/query-test/spouse_example/article_ids.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq
 create mode 100644 test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/histogram-supervision.ddlogq
 create mode 100644 test/query-test/spouse_example/histogram-supervision.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/redefinition.ddlogq
 create mode 100644 test/query-test/spouse_example/redefinition.ddlogq-error.expected
 create mode 100644 test/query-test/spouse_example/schema-check.ddlogq
 create mode 100644 test/query-test/spouse_example/schema-check.ddlogq-error.expected
 create mode 100644 test/query-test/spouse_example/undefined.ddlogq
 create mode 100644 test/query-test/spouse_example/undefined.ddlogq-error.expected

diff --git a/test/query-test.bats.template b/test/query-test.bats.template
index f047b9720..cb50fd71c 100644
--- a/test/query-test.bats.template
+++ b/test/query-test.bats.template
@@ -14,6 +14,7 @@ setup() {
     ddlog print "$TESTDIR"/*.ddlog >/dev/null
 
     # for each query
+    hasFailedAny=false
     for q in "$TESTDIR"/*.ddlogq; do
         expectedOutput="$q".expected
         expectedError="$q"-error.expected
@@ -23,12 +24,14 @@ setup() {
         if [ -e "$expectedError" ]; then
             expectedOutput=$expectedError
             # query is expected to have parse errors
-            ! ddlog query "$(cat $q)" "$TESTDIR"/*.ddlog >/dev/null 2>"$actualOutput"
+            ! ddlog query "$(cat $q)" "$TESTDIR"/*.ddlog >/dev/null 2>"$actualOutput" || hasFailedAny=true
         else
             # query is supposed to parse without errors
-            ddlog query "$(cat $q)" "$TESTDIR"/*.ddlog  >"$actualOutput"
+            ddlog query "$(cat $q)" "$TESTDIR"/*.ddlog  >"$actualOutput" || hasFailedAny=true
         fi
         # see if there's any difference
-        diff "$expectedOutput" "$actualOutput"
+        diff "$expectedOutput" "$actualOutput" || hasFailedAny=true
+        echo; echo; echo
     done
+    ! $hasFailedAny || false
 }
diff --git a/test/query-test/spouse_example/article_ids.ddlogq b/test/query-test/spouse_example/article_ids.ddlogq
new file mode 100644
index 000000000..a2cb8a8d7
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids.ddlogq
@@ -0,0 +1 @@
+?- articles(id, _).
diff --git a/test/query-test/spouse_example/article_ids.ddlogq.expected b/test/query-test/spouse_example/article_ids.ddlogq.expected
new file mode 100644
index 000000000..54b58a592
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids.ddlogq.expected
@@ -0,0 +1,3 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq b/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq
new file mode 100644
index 000000000..029bc7878
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq
@@ -0,0 +1,5 @@
+num_candidates_by_doc(doc, COUNT(candidate)) :-
+    has_spouse_candidates(_,_,sentence,_,candidate,_),
+    sentences(doc, _,_,_,_,_,_,_, sentence).
+
+num_candidates, COUNT(doc) ?- num_candidates_by_doc(doc, num_candidates).
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected b/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected
new file mode 100644
index 000000000..9c3604bdf
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected
@@ -0,0 +1,10 @@
+CREATE TEMPORARY TABLE num_candidates_by_doc AS
+SELECT R1.document_id AS column_0, COUNT(R0.relation_id) AS column_1
+FROM has_spouse_candidates R0, sentences R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        GROUP BY R1.document_id;
+
+SELECT R0.column_1 AS "num_candidates", COUNT(R0.column_0) AS "COUNT(doc)"
+FROM num_candidates_by_doc R0
+        
+        GROUP BY R0.column_1
diff --git a/test/query-test/spouse_example/histogram-supervision.ddlogq b/test/query-test/spouse_example/histogram-supervision.ddlogq
new file mode 100644
index 000000000..df4520c45
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-supervision.ddlogq
@@ -0,0 +1 @@
+label, COUNT(candidate) ?- has_spouse_candidates(candidate,_,_,_,_,label).
diff --git a/test/query-test/spouse_example/histogram-supervision.ddlogq.expected b/test/query-test/spouse_example/histogram-supervision.ddlogq.expected
new file mode 100644
index 000000000..a36539961
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-supervision.ddlogq.expected
@@ -0,0 +1,4 @@
+SELECT R0.is_true AS "label", COUNT(R0.person1_id) AS "COUNT(candidate)"
+FROM has_spouse_candidates R0
+        
+        GROUP BY R0.is_true
diff --git a/test/query-test/spouse_example/redefinition.ddlogq b/test/query-test/spouse_example/redefinition.ddlogq
new file mode 100644
index 000000000..3c582e419
--- /dev/null
+++ b/test/query-test/spouse_example/redefinition.ddlogq
@@ -0,0 +1,5 @@
+has_spouse(doc, COUNT(candidate)) :-
+    has_spouse_candidates(_,_,sentence,_,candidate,_),
+    sentences(doc, _,_,_,_,_,_,_, sentence).
+
+num_candidates, COUNT(doc) ?- has_spouse(doc, num_candidates).
diff --git a/test/query-test/spouse_example/redefinition.ddlogq-error.expected b/test/query-test/spouse_example/redefinition.ddlogq-error.expected
new file mode 100644
index 000000000..4f581c39b
--- /dev/null
+++ b/test/query-test/spouse_example/redefinition.ddlogq-error.expected
@@ -0,0 +1 @@
+[error] Following relations must not be redefined: 'has_spouse'
diff --git a/test/query-test/spouse_example/schema-check.ddlogq b/test/query-test/spouse_example/schema-check.ddlogq
new file mode 100644
index 000000000..884847a31
--- /dev/null
+++ b/test/query-test/spouse_example/schema-check.ddlogq
@@ -0,0 +1 @@
+?- articles(id).
diff --git a/test/query-test/spouse_example/schema-check.ddlogq-error.expected b/test/query-test/spouse_example/schema-check.ddlogq-error.expected
new file mode 100644
index 000000000..53f00e095
--- /dev/null
+++ b/test/query-test/spouse_example/schema-check.ddlogq-error.expected
@@ -0,0 +1,4 @@
+[error] "articles": number of columns in the query does not match number of columns in the schema
+(id) ?-
+    articles(id).
+
diff --git a/test/query-test/spouse_example/undefined.ddlogq b/test/query-test/spouse_example/undefined.ddlogq
new file mode 100644
index 000000000..29269bb35
--- /dev/null
+++ b/test/query-test/spouse_example/undefined.ddlogq
@@ -0,0 +1 @@
+?- nonexistent(foo,_,bar,_,_).
diff --git a/test/query-test/spouse_example/undefined.ddlogq-error.expected b/test/query-test/spouse_example/undefined.ddlogq-error.expected
new file mode 100644
index 000000000..e92755b65
--- /dev/null
+++ b/test/query-test/spouse_example/undefined.ddlogq-error.expected
@@ -0,0 +1,4 @@
+[error] relation "nonexistent" is not defined
+(foo, bar) ?-
+    nonexistent(foo, _, bar, _, _).
+

From a39cb0d376f5a7070216e58cd04ed5d0b1544ff2 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 31 Jan 2016 13:10:17 -0800
Subject: [PATCH 275/347] Supports @order_by on head terms for ddlog query

`@order_by`, `@order_by("ASC")`, `@order_by(dir="ASC")` all work.
`@order_by(priority=0)` or `@order_by("ASC", 0)` work to specify the key
index/priority when more than one head terms are used for ordering.

TODO make normal rules also support @order_by
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 35 +++++++++++++++++--
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 22 +++++++++---
 .../article_ids-ordered-revsered.ddlogq       |  1 +
 ...ticle_ids-ordered-revsered.ddlogq.expected |  4 +++
 .../article_ids-ordered-revsered2.ddlogq      |  1 +
 ...icle_ids-ordered-revsered2.ddlogq.expected |  4 +++
 .../spouse_example/article_ids-ordered.ddlogq |  1 +
 .../article_ids-ordered.ddlogq.expected       |  4 +++
 ...-num_candidates-per-article-ordered.ddlogq |  5 +++
 ...idates-per-article-ordered.ddlogq.expected | 11 ++++++
 ...idates-per-article-ordered_multikey.ddlogq |  5 +++
 ...r-article-ordered_multikey.ddlogq.expected | 11 ++++++
 12 files changed, 98 insertions(+), 6 deletions(-)
 create mode 100644 test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/article_ids-ordered.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids-ordered.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq
 create mode 100644 test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq
 create mode 100644 test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index b59313e38..411dba3df 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -499,10 +499,41 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
     }
 
     // limit clause
-    val limitStr = optionalClause("LIMIT", cq.limit.getOrElse("").toString)
+    val limitStr = optionalClause("\nLIMIT", cq.limit.getOrElse("").toString)
+
+    // order by clause by handling any @order_by annotations
+    val orderbyStr =
+      if (cq.headTermAnnotations.size != cq.headTerms.size) "" // invalid annotations
+      else {
+        val ORDER_BY_ANNOTATION_NAMES = Set("order_by")
+        val orderByAnnos = cq.headTermAnnotations map {
+          case annos => annos collectFirst {
+            case anno if ORDER_BY_ANNOTATION_NAMES contains anno.name => anno
+          }
+        }
+        val orderByExprs = cq.headTerms.zip(orderByAnnos).zipWithIndex collect {
+          case ((e, Some(orderByAnno)), i) =>
+            // TODO factor out annotation argument handling
+            val isAscending = // the "dir" or first argument of the annotation decides the sort order, defaulting to ASCending
+              orderByAnno.args collect {
+                case Left(argsMap) => (argsMap getOrElse("dir", "ASC")).toString == "ASC"
+                case Right(dir :: _) => dir.toString == "ASC"
+              } getOrElse(true)
+            val priority = // the priority or second argument decides the key index
+              orderByAnno.args collect {
+                case Left(argsMap) => (argsMap getOrElse("priority", i+1)).toString.toInt
+                case Right(_ :: priority :: _) => priority.toString.toInt
+              } getOrElse(i+1)
+            (e, isAscending, priority)
+        } sortBy { _._3 }
+        optionalClause("\nORDER BY", orderByExprs map {
+            case (e, isAscending, _) => s"${compileExpr(e)} ${if (isAscending) "ASC" else "DESC"}"
+          } mkString(", ")
+        )
+      }
 
     s"""FROM ${ generateFromClause(body, "") }
-        ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${limitStr}"""
+        ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${orderbyStr}${limitStr}"""
   }
 
   def generateSQL(aliasStyle: AliasStyle = ViewAlias) = {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 2be615f4a..bced9a0d4 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -40,7 +40,10 @@ case class AllModifier extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
 case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean, limit: Option[Int],
-                            isForQuery: Boolean = false // XXX This flag is not ideal, but minimizes the impact of query treatment when compared to creating another case class
+                            // optional annotations for head terms
+                            headTermAnnotations: List[List[Annotation]] = List.empty,
+                            // XXX This flag is not ideal, but minimizes the impact of query treatment when compared to creating another case class
+                            isForQuery: Boolean = false
                            )
 case class Column(name : String // name of the column
                  , t : String // type of the column
@@ -296,6 +299,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
   def cqHeadTerms = "(" ~> rep1sep(expr, ",") <~ ")"
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
+    // TODO fill headTermAnnotations as done in queryWithOptionalHeadTerms to support @order_by
     cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
       case (head ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
         ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
@@ -414,17 +418,27 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def queryWithOptionalHeadTerms =
-    ((("(" ~> rep1sep(expr, ",") <~ ")") | repsep(expr, ",")) // head terms with parentheses or optionally without
+    ((("(" ~> rep1sep(annotatedHeadTerm, ",") <~ ")") | repsep(annotatedHeadTerm, ",")) // head terms with parentheses or optionally without
       ~ opt("*") ~ opt("|" ~> decimalNumber)) ~ ("?-" ~> cqConjunctiveBody) ^^ {
-      case (headTerms ~ isDistinct ~ limit) ~ body =>
+      case (headTermsZippedWithAnnotations ~ isDistinct ~ limit) ~ body =>
+        val (headTerms, headTermAnnos) = headTermsZippedWithAnnotations unzip
         val headTermsToUse =
           if (headTerms nonEmpty) headTerms else {
             val definedVars = body flatMap DeepDiveLogSemanticChecker.collectDefinedVars
             definedVars map VarExpr
           }
-        ConjunctiveQuery(headTermsToUse, List(body), isDistinct != None, limit map (_.toInt), isForQuery = true)
+        ConjunctiveQuery(
+          headTerms = headTermsToUse,
+          headTermAnnotations = headTermAnnos,
+          bodies = List(body),
+          isDistinct = isDistinct != None,
+          limit = limit map (_.toInt),
+          isForQuery = true
+        )
     }
 
+  def annotatedHeadTerm = rep(annotation) ~ expr ^^ { case anno ~ e => (e, anno) }
+
   def parseQuery(inputQuery: String): DeepDiveLog.Query = {
     val result = parse(phrase(query), inputQuery)
     if (result successful) result.get
diff --git a/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq b/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq
new file mode 100644
index 000000000..b7702bcab
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq
@@ -0,0 +1 @@
+@order_by(dir="DESC") id ?- articles(id, _).
diff --git a/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected b/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected
new file mode 100644
index 000000000..71294268d
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected
@@ -0,0 +1,4 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        
+ORDER BY R0.article_id DESC
diff --git a/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq b/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq
new file mode 100644
index 000000000..7199c305c
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq
@@ -0,0 +1 @@
+@order_by("DESC") id ?- articles(id, _).
diff --git a/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected b/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected
new file mode 100644
index 000000000..71294268d
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected
@@ -0,0 +1,4 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        
+ORDER BY R0.article_id DESC
diff --git a/test/query-test/spouse_example/article_ids-ordered.ddlogq b/test/query-test/spouse_example/article_ids-ordered.ddlogq
new file mode 100644
index 000000000..99494641a
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-ordered.ddlogq
@@ -0,0 +1 @@
+@order_by id ?- articles(id, _).
diff --git a/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected b/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected
new file mode 100644
index 000000000..d52f31ca1
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected
@@ -0,0 +1,4 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        
+ORDER BY R0.article_id ASC
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq
new file mode 100644
index 000000000..a2a854632
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq
@@ -0,0 +1,5 @@
+num_candidates_by_doc(doc, COUNT(candidate)) :-
+    has_spouse_candidates(_,_,sentence,_,candidate,_),
+    sentences(doc, _,_,_,_,_,_,_, sentence).
+
+@order_by num_candidates, COUNT(doc) ?- num_candidates_by_doc(doc, num_candidates).
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected
new file mode 100644
index 000000000..a819951cf
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected
@@ -0,0 +1,11 @@
+CREATE TEMPORARY TABLE num_candidates_by_doc AS
+SELECT R1.document_id AS column_0, COUNT(R0.relation_id) AS column_1
+FROM has_spouse_candidates R0, sentences R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        GROUP BY R1.document_id;
+
+SELECT R0.column_1 AS "num_candidates", COUNT(R0.column_0) AS "COUNT(doc)"
+FROM num_candidates_by_doc R0
+        
+        GROUP BY R0.column_1
+ORDER BY R0.column_1 ASC
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq
new file mode 100644
index 000000000..d024c9d94
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq
@@ -0,0 +1,5 @@
+num_candidates_by_doc(doc, COUNT(candidate)) :-
+    has_spouse_candidates(_,_,sentence,_,candidate,_),
+    sentences(doc, _,_,_,_,_,_,_, sentence).
+
+@order_by num_candidates, @order_by(priority=-1, dir="DESC") COUNT(doc) ?- num_candidates_by_doc(doc, num_candidates).
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected
new file mode 100644
index 000000000..2783ab53c
--- /dev/null
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected
@@ -0,0 +1,11 @@
+CREATE TEMPORARY TABLE num_candidates_by_doc AS
+SELECT R1.document_id AS column_0, COUNT(R0.relation_id) AS column_1
+FROM has_spouse_candidates R0, sentences R1
+        WHERE R1.sentence_id = R0.sentence_id 
+        GROUP BY R1.document_id;
+
+SELECT R0.column_1 AS "num_candidates", COUNT(R0.column_0) AS "COUNT(doc)"
+FROM num_candidates_by_doc R0
+        
+        GROUP BY R0.column_1
+ORDER BY COUNT(R0.column_0) DESC, R0.column_1 ASC

From fd509a7762486bd078d61ec4c5690e5f5717ced2 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 31 Jan 2016 13:19:01 -0800
Subject: [PATCH 276/347] Fixes some whitespace/ordering changes in tests'
 expected outputs

No idea why some Scala Lists change order (maybe they're Sets), maybe we
should sort them to ensure a normal order.
---
 test/expected-output-test/expressions/compile.expected    | 3 ++-
 .../compile-incremental.expected                          | 6 +++---
 .../multiple_rules_for_same_head/compile.expected         | 8 ++++----
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index d90b2472f..861115e84 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -251,7 +251,8 @@ FROM a R0, b R1, c R2
 
 	deepdive create view L as 'SELECT DISTINCT R0.k AS column_0
 FROM b R0
-        LIMIT 100'
+        
+LIMIT 100'
 	
         """
           output_relation: "L"
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
index 24e1a8336..9330135a6 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
@@ -113,7 +113,7 @@ FROM dd_delta_S R0
         """
           output_relation: "dd_new_S"
         style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ]
           input_relations: [
             S
             dd_delta_S
@@ -363,7 +363,7 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
@@ -378,7 +378,7 @@ FROM dd_delta_R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(dd_new_Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext_dd_delta_S" ,  "ext1_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f" ,  "ext_dd_delta_S_by_f_1" ]
+          dependencies: [ "ext_dd_delta_S" ,  "ext_dd_delta_S_by_f_1" ,  "ext_dd_delta_S_by_f" ,  "ext1_dd_delta_S_by_f" ]
           input_relations: [
             dd_new_Q
             dd_delta_S
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index f4b27bf05..b3536433c 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -171,7 +171,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
+          dependencies: [ "ext_S_by_f_1" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
@@ -186,7 +186,7 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
+          dependencies: [ "ext_S_by_f_1" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
@@ -201,7 +201,7 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
+          dependencies: [ "ext_S_by_f_1" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S
@@ -217,7 +217,7 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "-10.0"
-          dependencies: [ "ext_S_by_f" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f_1" ]
+          dependencies: [ "ext_S_by_f_1" ,  "ext_S" ,  "ext1_S_by_f" ,  "ext_S_by_f" ]
           input_relations: [
             Q
             S

From f79eb60210bd0333c0ac4cc7d22588c71a481d12 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 1 Feb 2016 02:51:04 -0800
Subject: [PATCH 277/347] Eliminates some premature merge that left dead code

And supports multiple disjunctive bodies in query, taking the common
variables among all bodies to project, or all columns with `*`.
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 27 +++++++------------
 2 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9f8d7a8e1..a72f9ef3c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -403,7 +403,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
 
   // generate SQL SELECT cluase
   def generateSQLHead(aliasStyle: AliasStyle) = {
-    val head = cq.headTerms map { expr =>
+    val head = if (cq.headTerms isEmpty) "*" else cq.headTerms map { expr =>
       compileExpr(expr) + compileAlias(expr, aliasStyle)
     } mkString(", ")
     val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 45248313f..71bc522a5 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -312,15 +312,15 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def cqHeadTerms = "(" ~> rep1sep(expr, ",") <~ ")"
 
-  def conjunctiveQueryBody : Parser[ConjunctiveQuery] =
-    opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
-      case (isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
+  def conjunctiveQueryBody(separator: Parser[_] = ":-") : Parser[ConjunctiveQuery] =
+    opt("*") ~ opt("|" ~> decimalNumber) ~ separator ~ rep1sep(cqConjunctiveBody, ";") ^^ {
+      case (isDistinct ~ limit ~ _ ~ disjunctiveBodies) =>
         ConjunctiveQuery(List.empty, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
     }
 
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
     // TODO fill headTermAnnotations as done in queryWithOptionalHeadTerms to support @order_by
-    cqHeadTerms ~ conjunctiveQueryBody ^^ {
+    cqHeadTerms ~ conjunctiveQueryBody() ^^ {
       case (head ~ cq) => cq.copy(headTerms = head)
     }
 
@@ -337,17 +337,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def supervisionAnnotation = "@label" ~> "(" ~> expr <~ ")"
 
-  def conjunctiveQueryWithSupervision : Parser[ConjunctiveQuery] =
-    cqHeadTerms ~ opt("*") ~ opt("|" ~> decimalNumber) ~ ":-" ~ rep1sep(cqConjunctiveBody, ";") ^^ {
-      case (head ~ isDistinct ~ limit ~ ":-" ~ disjunctiveBodies) =>
-        ConjunctiveQuery(head, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
-  }
-
   def extractionRule =
     ( opt(supervisionAnnotation) ~ relationName ~ conjunctiveQuery ^^ {
         case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
       }
-    | relationName ~ cqHeadTerms ~ ("=" ~> expr) ~ conjunctiveQueryBody ^^ {
+    | relationName ~ cqHeadTerms ~ ("=" ~> expr) ~ conjunctiveQueryBody() ^^ {
         case (head ~ headTerms ~ sup ~ cq) =>
           ExtractionRule(head, cq.copy(headTerms = headTerms), Some(sup))
       }
@@ -437,20 +431,17 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def queryWithOptionalHeadTerms =
     ((("(" ~> rep1sep(annotatedHeadTerm, ",") <~ ")") | repsep(annotatedHeadTerm, ",")) // head terms with parentheses or optionally without
-      ~ opt("*") ~ opt("|" ~> decimalNumber)) ~ ("?-" ~> cqConjunctiveBody) ^^ {
-      case (headTermsZippedWithAnnotations ~ isDistinct ~ limit) ~ body =>
+      ~ conjunctiveQueryBody("?-")) ^^ {
+      case headTermsZippedWithAnnotations ~ cq =>
         val (headTerms, headTermAnnos) = headTermsZippedWithAnnotations unzip
         val headTermsToUse =
           if (headTerms nonEmpty) headTerms else {
-            val definedVars = body flatMap DeepDiveLogSemanticChecker.collectDefinedVars
+            val definedVars = cq.bodies map {_ flatMap DeepDiveLogSemanticChecker.collectDefinedVars} reduce {_ intersect _}
             definedVars map VarExpr
           }
-        ConjunctiveQuery(
+        cq.copy(
           headTerms = headTermsToUse,
           headTermAnnotations = headTermAnnos,
-          bodies = List(body),
-          isDistinct = isDistinct != None,
-          limit = limit map (_.toInt),
           isForQuery = true
         )
     }

From 08a3f3ba6b1964c01a08696d629841b77854429c Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 1 Feb 2016 03:20:34 -0800
Subject: [PATCH 278/347] Adds tests for multiple bodies in query and fixes a
 parser bug

that tried to parse conjunctive query atom as function call expression :S
---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala     | 2 +-
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala  | 2 +-
 test/query-test/spouse_example/article_ids-filtered.ddlogq | 1 +
 .../spouse_example/article_ids-filtered.ddlogq.expected    | 3 +++
 test/query-test/spouse_example/incomplete.ddlogq           | 1 +
 .../spouse_example/incomplete.ddlogq-error.expected        | 4 ++++
 test/query-test/spouse_example/union-no-common-vars.ddlogq | 1 +
 .../spouse_example/union-no-common-vars.ddlogq.expected    | 7 +++++++
 test/query-test/spouse_example/union.ddlogq                | 1 +
 test/query-test/spouse_example/union.ddlogq.expected       | 7 +++++++
 10 files changed, 27 insertions(+), 2 deletions(-)
 create mode 100644 test/query-test/spouse_example/article_ids-filtered.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids-filtered.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/incomplete.ddlogq
 create mode 100644 test/query-test/spouse_example/incomplete.ddlogq-error.expected
 create mode 100644 test/query-test/spouse_example/union-no-common-vars.ddlogq
 create mode 100644 test/query-test/spouse_example/union-no-common-vars.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/union.ddlogq
 create mode 100644 test/query-test/spouse_example/union.ddlogq.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a72f9ef3c..b94c447bd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -317,7 +317,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
       }
     }
 
-    generateCanonicalVarFromBodies(cq.bodies(0), "")
+    cq.bodies foreach { generateCanonicalVarFromBodies(_, "") }
   }
   generateCanonicalVar() // initialize
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 71bc522a5..4b187400a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -306,7 +306,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
              FunctionDeclaration(a, inTy, outTy, implementationDecls)
     }
 
-  def cqBody: Parser[Body] = quantifiedBody | atom | cond
+  def cqBody: Parser[Body] = quantifiedBody | atom | lcond
 
   def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
diff --git a/test/query-test/spouse_example/article_ids-filtered.ddlogq b/test/query-test/spouse_example/article_ids-filtered.ddlogq
new file mode 100644
index 000000000..37323da14
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-filtered.ddlogq
@@ -0,0 +1 @@
+?- articles(id, content), content LIKE "% wife %".
diff --git a/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected b/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected
new file mode 100644
index 000000000..41eb2b81c
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected
@@ -0,0 +1,3 @@
+SELECT R0.article_id AS "id", R0.text AS "content"
+FROM articles R0
+        WHERE R0.text LIKE '% wife %'
diff --git a/test/query-test/spouse_example/incomplete.ddlogq b/test/query-test/spouse_example/incomplete.ddlogq
new file mode 100644
index 000000000..773304413
--- /dev/null
+++ b/test/query-test/spouse_example/incomplete.ddlogq
@@ -0,0 +1 @@
+?- foo
diff --git a/test/query-test/spouse_example/incomplete.ddlogq-error.expected b/test/query-test/spouse_example/incomplete.ddlogq-error.expected
new file mode 100644
index 000000000..6732818dc
--- /dev/null
+++ b/test/query-test/spouse_example/incomplete.ddlogq-error.expected
@@ -0,0 +1,4 @@
+[error] [1.7] failure: `.' expected but end of source found
+
+?- foo
+      ^
diff --git a/test/query-test/spouse_example/union-no-common-vars.ddlogq b/test/query-test/spouse_example/union-no-common-vars.ddlogq
new file mode 100644
index 000000000..7d9668752
--- /dev/null
+++ b/test/query-test/spouse_example/union-no-common-vars.ddlogq
@@ -0,0 +1 @@
+?- articles(id, _); articles(_, content).
diff --git a/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected b/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected
new file mode 100644
index 000000000..79d695ca2
--- /dev/null
+++ b/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected
@@ -0,0 +1,7 @@
+SELECT *
+FROM articles R0
+        
+UNION ALL
+SELECT *
+FROM articles R0
+        
diff --git a/test/query-test/spouse_example/union.ddlogq b/test/query-test/spouse_example/union.ddlogq
new file mode 100644
index 000000000..2e243ef2a
--- /dev/null
+++ b/test/query-test/spouse_example/union.ddlogq
@@ -0,0 +1 @@
+?- articles(id, _), id < 100; articles(id, _), id > 100000.
diff --git a/test/query-test/spouse_example/union.ddlogq.expected b/test/query-test/spouse_example/union.ddlogq.expected
new file mode 100644
index 000000000..36c73977c
--- /dev/null
+++ b/test/query-test/spouse_example/union.ddlogq.expected
@@ -0,0 +1,7 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        WHERE R0.article_id < 100
+UNION ALL
+SELECT R0.article_id AS "id"
+FROM articles R0
+        WHERE R0.article_id > 100000

From 045136b77087e61b48977811eacf11c7de11ec54 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 1 Feb 2016 03:25:08 -0800
Subject: [PATCH 279/347] Fixes changed expected outputs, adds a few more test

---
 test/expected-output-test/expressions/print.expected        | 3 ++-
 .../multiple_rules_for_same_head/desugar.expected           | 6 ++++--
 test/query-test/spouse_example/article_ids-parens.ddlogq    | 1 +
 .../spouse_example/article_ids-parens.ddlogq.expected       | 3 +++
 .../spouse_example/article_ids-without_parens.ddlogq        | 1 +
 .../article_ids-without_parens.ddlogq.expected              | 3 +++
 6 files changed, 14 insertions(+), 3 deletions(-)
 create mode 100644 test/query-test/spouse_example/article_ids-parens.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids-parens.ddlogq.expected
 create mode 100644 test/query-test/spouse_example/article_ids-without_parens.ddlogq
 create mode 100644 test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected

diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 798da8600..0dfaccc0a 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -43,7 +43,8 @@ G(x) :-
 
 H(x) :-
     b(x, y, z, w),
-    [(x + w) = 100, x > 50].
+    (x + w) = 100,
+    x > 50.
 
 I(x) :-
     b(x, y, z, w),
diff --git a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
index a1767b4f4..873dc7f03 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
@@ -41,7 +41,8 @@ T___1(a int).
 
 T___1 += f(a, b) :-
     R(a, b),
-    [10 < a, a < 20].
+    10 < a,
+    a < 20.
 
 T(a) :-
     T___1(a).
@@ -50,7 +51,8 @@ T___2(a int).
 
 T___2 += f(a, b) :-
     R(a, b),
-    [100 < a, a < 200].
+    100 < a,
+    a < 200.
 
 T(a) :-
     T___2(a).
diff --git a/test/query-test/spouse_example/article_ids-parens.ddlogq b/test/query-test/spouse_example/article_ids-parens.ddlogq
new file mode 100644
index 000000000..2a3371a40
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-parens.ddlogq
@@ -0,0 +1 @@
+(id) ?- articles(id, _).
diff --git a/test/query-test/spouse_example/article_ids-parens.ddlogq.expected b/test/query-test/spouse_example/article_ids-parens.ddlogq.expected
new file mode 100644
index 000000000..54b58a592
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-parens.ddlogq.expected
@@ -0,0 +1,3 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        
diff --git a/test/query-test/spouse_example/article_ids-without_parens.ddlogq b/test/query-test/spouse_example/article_ids-without_parens.ddlogq
new file mode 100644
index 000000000..44da04ce0
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-without_parens.ddlogq
@@ -0,0 +1 @@
+id ?- articles(id, _).
diff --git a/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected b/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected
new file mode 100644
index 000000000..54b58a592
--- /dev/null
+++ b/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected
@@ -0,0 +1,3 @@
+SELECT R0.article_id AS "id"
+FROM articles R0
+        

From f5febdd06f5b0072e83a99f16fefe536b9774820 Mon Sep 17 00:00:00 2001
From: Boyoung Yoo <byoo1@stanford.edu>
Date: Mon, 1 Feb 2016 15:30:59 -0800
Subject: [PATCH 280/347] Fixes sbt issue

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index e20401e5b..1546ecabe 100644
--- a/Makefile
+++ b/Makefile
@@ -20,7 +20,7 @@ clean: scala-clean
 	rm -f $(JAR) $(wildcard test/*/*/*.actual)
 	find test/ -name '*.bats' -type l -exec rm -f {} +
 
-PATH += :$(shell pwd)/project/sbt
+PATH := $(shell pwd)/project/sbt:$(PATH)
 export PATH
 ifeq ($(shell uname),Darwin)
 SHELL := /bin/bash  # Mac requires SHELL to be forced to bash

From 34cdedcf9438702a7f5c74879a54f3104474b461 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Mon, 1 Feb 2016 21:20:07 -0800
Subject: [PATCH 281/347] Fix multinomial factor function printing and
 compiling

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala      | 1 +
 src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index b94c447bd..8e3b5a3d1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -788,6 +788,7 @@ ${if (createTable) {
               case Some(BooleanType)        => "Imply"
               case Some(MultinomialType(_)) => "Multinomial"
             }
+            case FactorFunction.Multinomial => "Multinomial"
           }
           func = s"""${function}(${funcBody.mkString(", ")})"""
         }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index f1d602ce8..12eb9738c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -175,6 +175,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case FactorFunction.Or     => printHead(head.terms, " v ")
       case FactorFunction.Equal  => printHead(head.terms, " = ")
       case FactorFunction.IsTrue => printHead(head.terms, "")
+      case FactorFunction.Multinomial => s"""Multinomial(${printHead(head.terms, ", ")})"""
     }
   }
 

From 54cb675827aa5aaf66a6a9181cb0f26dba5b8e98 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 2 Feb 2016 00:21:05 -0800
Subject: [PATCH 282/347] Fixes redundant columns compiled for join variables
 in queries

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala    | 5 +++--
 test/query-test/spouse_example/repeated-vars.ddlogq          | 1 +
 test/query-test/spouse_example/repeated-vars.ddlogq.expected | 3 +++
 3 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100644 test/query-test/spouse_example/repeated-vars.ddlogq
 create mode 100644 test/query-test/spouse_example/repeated-vars.ddlogq.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 4b187400a..cf77b3d2f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -436,8 +436,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
         val (headTerms, headTermAnnos) = headTermsZippedWithAnnotations unzip
         val headTermsToUse =
           if (headTerms nonEmpty) headTerms else {
-            val definedVars = cq.bodies map {_ flatMap DeepDiveLogSemanticChecker.collectDefinedVars} reduce {_ intersect _}
-            definedVars map VarExpr
+            val definedVarsByBodies = cq.bodies map { _ flatMap DeepDiveLogSemanticChecker.collectDefinedVars }
+            val definedVarsCommon = definedVarsByBodies reduce {_ intersect _}
+            definedVarsCommon.toSet.toList map VarExpr
           }
         cq.copy(
           headTerms = headTermsToUse,
diff --git a/test/query-test/spouse_example/repeated-vars.ddlogq b/test/query-test/spouse_example/repeated-vars.ddlogq
new file mode 100644
index 000000000..513a02ce8
--- /dev/null
+++ b/test/query-test/spouse_example/repeated-vars.ddlogq
@@ -0,0 +1 @@
+?- articles(id1, content), articles(id2, content).
diff --git a/test/query-test/spouse_example/repeated-vars.ddlogq.expected b/test/query-test/spouse_example/repeated-vars.ddlogq.expected
new file mode 100644
index 000000000..bebfd043d
--- /dev/null
+++ b/test/query-test/spouse_example/repeated-vars.ddlogq.expected
@@ -0,0 +1,3 @@
+SELECT R0.article_id AS "id1", R0.text AS "content", R1.article_id AS "id2"
+FROM articles R0, articles R1
+        WHERE R1.text = R0.text 

From b19ba0e461a20f0c3af485b29b00be1e1e4fe35e Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Wed, 10 Feb 2016 19:29:09 -0800
Subject: [PATCH 283/347] Add support for negation in inference rule head

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  8 +--
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  6 +-
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  2 +-
 .../factor_functions/compile.expected         | 58 +++++++++++++++++++
 .../factor_functions/input.ddlog              |  3 +
 .../factor_functions/print.expected           | 16 +++++
 6 files changed, 84 insertions(+), 9 deletions(-)
 create mode 100644 test/expected-output-test/factor_functions/compile.expected
 create mode 100644 test/expected-output-test/factor_functions/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 8e3b5a3d1..6ee8a1da3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -771,11 +771,9 @@ ${if (createTable) {
           ${ qc.generateSQLBody(fakeBody) }"""
         // factor function
         if (func.length == 0) {
-          val funcBody = (fakeBodyAtoms map {x =>
-          if (ss.variableTableNames contains x.name)
-            s"""${x.name}.R${fakeBody indexOf x}.label"""
-          else ""
-          }).filter(_ != "")
+          val funcBody = (headAsBody zip stmt.head.terms map { case(x, y) =>
+            s"""${if (y.isNegated) "!" else ""}${x.name}.R${fakeBody indexOf x}.label"""
+          })
 
           val function = stmt.head.function match {
             case FactorFunction.Imply  => "Imply"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index cf77b3d2f..56df976d3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -86,7 +86,7 @@ object FactorFunction extends Enumeration {
   type FactorFunction = Value
   val  IsTrue, Imply, Or, And, Equal, Multinomial, Linear, Ratio = Value
 }
-case class HeadAtom(name : String, terms : List[Expr])
+case class HeadAtom(name : String, terms : List[Expr], isNegated: Boolean = false)
 case class InferenceRuleHead(function: FactorFunction.FactorFunction, terms: List[HeadAtom])
 
 
@@ -353,8 +353,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }, (s) => s"${s}: unrecognized mode"))
 
   // factor functions
-  def headAtom = relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
-    case (r ~ expressions) => HeadAtom(r, expressions)
+  def headAtom = opt("!") ~ relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
+    case (isNegated ~ r ~ expressions) => HeadAtom(r, expressions, isNegated != None)
   }
 
   def implyHeadAtoms = rep1sep(headAtom, ",") ~ "=>" ~ headAtom ^^ {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 12eb9738c..fdfbe28a2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -161,7 +161,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
 
   def print(a: HeadAtom) : String = {
     val vars = a.terms map print
-    s"${a.name}(${vars.mkString(", ")})"
+    s"${if (a.isNegated) "!" else ""}${a.name}(${vars.mkString(", ")})"
   }
 
   def print(head: InferenceRuleHead) : String = {
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
new file mode 100644
index 000000000..059d89651
--- /dev/null
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -0,0 +1,58 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        S.label: Boolean
+Q.label: Boolean
+      }
+    
+
+        deepdive.inference.factors.inf_imply_Q_Q {
+          input_query: """
+          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
+          FROM Q R0, Q R1, R R2
+        WHERE R2.a = R0.x  AND R2.b = R1.x """
+          function: "Imply(Q.R0.label, Q.R1.label)"
+          weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            Q
+            R
+          ]
+        }
+      
+
+        deepdive.inference.factors.inf_equal_Q_Q {
+          input_query: """
+          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
+          FROM Q R0, Q R1, R R2
+        WHERE R2.a = R0.x  AND R2.b = R1.x """
+          function: "Equal(Q.R0.label, !Q.R1.label)"
+          weight: "?(dd_weight_column_0)"
+          
+          input_relations: [
+            Q
+            R
+          ]
+        }
+      
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.inference: [
+  inf_imply_Q_Q
+  inf_equal_Q_Q
+]
+deepdive.pipeline.pipelines.endtoend: [
+  inf_imply_Q_Q
+  inf_equal_Q_Q
+]
diff --git a/test/expected-output-test/factor_functions/input.ddlog b/test/expected-output-test/factor_functions/input.ddlog
index e4c31c642..2e07c87ab 100644
--- a/test/expected-output-test/factor_functions/input.ddlog
+++ b/test/expected-output-test/factor_functions/input.ddlog
@@ -4,3 +4,6 @@ Q?(x int).
 
 @weight(y)
 Q(x) => Q(y) :- R(x, y, z).
+
+@weight(y)
+Q(x) = !Q(y) :- R(x, y, z).
diff --git a/test/expected-output-test/factor_functions/print.expected b/test/expected-output-test/factor_functions/print.expected
new file mode 100644
index 000000000..d56f60a90
--- /dev/null
+++ b/test/expected-output-test/factor_functions/print.expected
@@ -0,0 +1,16 @@
+R(a int,
+  b int,
+  c int).
+
+S?(x int).
+
+Q?(x int).
+
+@weight(y)
+Q(x) => Q(y) :-
+    R(x, y, z).
+
+@weight(y)
+Q(x) = !Q(y) :-
+    R(x, y, z).
+

From 34023d83e66ff33c03db4dbed20b273469e8276a Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Thu, 11 Feb 2016 13:58:41 -0800
Subject: [PATCH 284/347] Add support for array indexing

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  3 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  4 ++
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  1 +
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  1 +
 .../arrays/compile.expected                   | 43 +++++++++++++++++++
 test/expected-output-test/arrays/input.ddlog  |  7 +++
 .../arrays/print.expected                     | 11 +++++
 7 files changed, 69 insertions(+), 1 deletion(-)
 create mode 100644 test/expected-output-test/arrays/compile.expected
 create mode 100644 test/expected-output-test/arrays/input.ddlog
 create mode 100644 test/expected-output-test/arrays/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 6ee8a1da3..a8e0ea0bc 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -346,7 +346,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
       case _ => s" AS column_${cq.headTerms indexOf e}"
     }
     case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
-    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}""""
+    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}"""" //"
   }
 
   // resolve an expression
@@ -354,6 +354,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   def compileExpr(e: Expr, level: Int) : String = {
     e match {
       case VarExpr(name) => compileVariable(name)
+      case ArrayExpr(name, index) => s"${compileVariable(name)}[${index}]"
       case NullConst() => "NULL"
       case IntConst(value) => value.toString
       case DoubleConst(value) => value.toString
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 56df976d3..f0e119cfd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -14,6 +14,7 @@ case class Variable(varName : String, relName : String, index : Int )
 
 sealed trait Expr
 case class VarExpr(name: String) extends Expr
+case class ArrayExpr(name: String, index: Int) extends Expr
 sealed trait ConstExpr extends Expr
 case class StringConst(value: String) extends ConstExpr
 case class IntConst(value: Int) extends ConstExpr
@@ -217,6 +218,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
+    | variableName ~ ("[" ~> """\d+""".r <~ "]") ^^ {
+        case (name ~ index) => ArrayExpr(name, index.toInt)
+      }
     | variableName ^^ { VarExpr(_) }
     | "(" ~> expr <~ ")"
     )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index fdfbe28a2..2baf7b4ae 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -77,6 +77,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   def print(e: Expr, level: Int) : String = {
     e match {
       case VarExpr(name) => name
+      case ArrayExpr(name, index) => s"${name}[${index}]"
       case NullConst() => "NULL"
       case IntConst(value) => value.toString
       case DoubleConst(value) => value.toString
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index e8058a4e8..dd7e4d73d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -211,6 +211,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // collect variables used in the expression
   def collectUsedVars(expr: Expr) : Set[String] = expr match {
     case VarExpr(name) => Set(name)
+    case ArrayExpr(name, _) => Set(name)
     case FuncExpr(function, args, agg) => args flatMap collectUsedVars toSet
     case BinaryOpExpr(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
     case TypecastExpr(lhs, rhs) => collectUsedVars(lhs)
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
new file mode 100644
index 000000000..3907096f2
--- /dev/null
+++ b/test/expected-output-test/arrays/compile.expected
@@ -0,0 +1,43 @@
+
+  deepdive.db.default {
+    driver: "org.postgresql.Driver"
+    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
+    user: ${PGUSER}
+    password: ${PGPASSWORD}
+    dbname: ${DBNAME}
+    host: ${PGHOST}
+    port: ${PGPORT}
+    incremental_mode: ORIGINAL
+    }
+    
+
+
+      deepdive.schema.variables {
+        
+      }
+    
+
+      deepdive.extraction.extractors.ext_T {
+        cmd: """
+
+  deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
+FROM R R0, S R1
+        WHERE R0.x[1] = R1.y[1] AND R0.x[2] = R1.y[2]'
+  
+        """
+          output_relation: "T"
+        style: "cmd_extractor"
+          
+          input_relations: [
+            R
+            S
+          ]
+      }
+    
+deepdive.pipeline.run: ${PIPELINE}
+deepdive.pipeline.pipelines.extraction: [
+  ext_T
+]
+deepdive.pipeline.pipelines.endtoend: [
+  ext_T
+]
diff --git a/test/expected-output-test/arrays/input.ddlog b/test/expected-output-test/arrays/input.ddlog
new file mode 100644
index 000000000..ab59448c6
--- /dev/null
+++ b/test/expected-output-test/arrays/input.ddlog
@@ -0,0 +1,7 @@
+R(x text[]).
+
+S(x text,
+  y text[]).
+
+T(x[3], z) :- R(x), S(z, y), x[1] = y[1], x[2] = y[2].
+
diff --git a/test/expected-output-test/arrays/print.expected b/test/expected-output-test/arrays/print.expected
new file mode 100644
index 000000000..b31afe940
--- /dev/null
+++ b/test/expected-output-test/arrays/print.expected
@@ -0,0 +1,11 @@
+R(x text[]).
+
+S(x text,
+  y text[]).
+
+T(x[3], z) :-
+    R(x),
+    S(z, y),
+    x[1] = y[1],
+    x[2] = y[2].
+

From 37e1ece5e1ca1525dd3eb285e4b6908fe2eccace Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 11 Feb 2016 18:18:44 -0800
Subject: [PATCH 285/347] Fixes incorrect WHERE clause compilation for
 disjunctive conditions

See HazyResearch/deepdive#488
---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 2 +-
 test/expected-output-test/expressions/compile.expected    | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 6ee8a1da3..b55c8538e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -439,7 +439,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
             }
           }
         }
-        case (x: Cond, _) => Some(compileCond(x))
+        case (x: Cond, _) => Some(compileCond(x, 1))
         case (x: QuantifiedBody, index) => {
           val newIndexPrefix = s"${indexPrefix}${index}_"
           val subqueryWhereStr = generateWhereClause(x.bodies, newIndexPrefix)
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 19f082a99..db1ea14c6 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -93,7 +93,7 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
 
 	deepdive create view J as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100 OR NOT R0.k > 50'
+        WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)'
 	
         """
           output_relation: "J"
@@ -180,7 +180,7 @@ FROM b R0
 
 	deepdive create view I as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10)'
+        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
 	
         """
           output_relation: "I"
@@ -232,7 +232,7 @@ FROM c R0, a R1
 
 	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50)'
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))'
 	
         """
           output_relation: "Q"
@@ -357,7 +357,7 @@ FROM a R0
 
 	deepdive create view K as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40)'
+        WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))'
 	
         """
           output_relation: "K"

From 39285b49d186b1ad8c9198d9f824464429984b7a Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 14 Feb 2016 01:43:16 -0800
Subject: [PATCH 286/347] Allow expressions in array access

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  8 +++-----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  2 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  2 +-
 .../arrays/compile.expected                   | 20 +++++++++++++++++++
 test/expected-output-test/arrays/input.ddlog  |  7 ++++---
 .../arrays/print.expected                     | 11 +++++++---
 7 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a8e0ea0bc..eec49e3c8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -354,7 +354,6 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   def compileExpr(e: Expr, level: Int) : String = {
     e match {
       case VarExpr(name) => compileVariable(name)
-      case ArrayExpr(name, index) => s"${compileVariable(name)}[${index}]"
       case NullConst() => "NULL"
       case IntConst(value) => value.toString
       case DoubleConst(value) => value.toString
@@ -380,6 +379,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
           case (ifCond, thenExpr) => s"WHEN ${compileCond(ifCond)} THEN ${compileExpr(thenExpr)}"
         }) ++ List(optElseExpr map compileExpr mkString("ELSE ", "", ""))
       } mkString("\nCASE ", "\n     ", "\nEND")
+      case ArrayElementExpr(name, index) => s"${compileExpr(name, level + 1)}[${compileExpr(index, level + 1)}]"
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index f0e119cfd..4c45a1129 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -14,7 +14,7 @@ case class Variable(varName : String, relName : String, index : Int )
 
 sealed trait Expr
 case class VarExpr(name: String) extends Expr
-case class ArrayExpr(name: String, index: Int) extends Expr
+case class ArrayElementExpr(array: Expr, index: Expr) extends Expr
 sealed trait ConstExpr extends Expr
 case class StringConst(value: String) extends ConstExpr
 case class IntConst(value: Int) extends ConstExpr
@@ -195,7 +195,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   // expression
   def expr : Parser[Expr] =
-    ( lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
+    ( lexpr ~ ("[" ~> expr <~ "]") ^^ { case (a ~ i) => ArrayElementExpr(a, i) }
+    | lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
     )
@@ -218,9 +219,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
-    | variableName ~ ("[" ~> """\d+""".r <~ "]") ^^ {
-        case (name ~ index) => ArrayExpr(name, index.toInt)
-      }
     | variableName ^^ { VarExpr(_) }
     | "(" ~> expr <~ ")"
     )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 2baf7b4ae..e193b50b7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -77,7 +77,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   def print(e: Expr, level: Int) : String = {
     e match {
       case VarExpr(name) => name
-      case ArrayExpr(name, index) => s"${name}[${index}]"
       case NullConst() => "NULL"
       case IntConst(value) => value.toString
       case DoubleConst(value) => value.toString
@@ -97,6 +96,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
           case (ifCond, thenExpr) => s"if ${print(ifCond)} then ${print(thenExpr)}"
         }) ++ (optElseExpr map print toList)
       ) mkString("", "\n\telse ", "\n\tend")
+      case ArrayElementExpr(array, index) => s"${print(array, level + 1)}[${print(index, level + 1)}]"
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index dd7e4d73d..10d74a1ad 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -211,7 +211,6 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // collect variables used in the expression
   def collectUsedVars(expr: Expr) : Set[String] = expr match {
     case VarExpr(name) => Set(name)
-    case ArrayExpr(name, _) => Set(name)
     case FuncExpr(function, args, agg) => args flatMap collectUsedVars toSet
     case BinaryOpExpr(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
     case TypecastExpr(lhs, rhs) => collectUsedVars(lhs)
@@ -219,6 +218,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       (ifCondThenExprs flatMap { case (ifCond, thenExpr) =>
         collectUsedVars(ifCond) ++ collectUsedVars(thenExpr)
       } toSet) ++ (optElseExpr.toSet flatMap { e:Expr => collectUsedVars(e) })
+    case ArrayElementExpr(array, index) => collectUsedVars(array) ++ collectUsedVars(index)
     case _ => Set()
   }
 
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index 3907096f2..61ca3f9ea 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -17,6 +17,24 @@
       }
     
 
+      deepdive.extraction.extractors.ext_U {
+        cmd: """
+
+  deepdive create view U as 'SELECT R1.x AS column_0
+FROM R R0, S R1
+        WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]'
+  
+        """
+          output_relation: "U"
+        style: "cmd_extractor"
+          
+          input_relations: [
+            R
+            S
+          ]
+      }
+    
+
       deepdive.extraction.extractors.ext_T {
         cmd: """
 
@@ -36,8 +54,10 @@ FROM R R0, S R1
     
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
+  ext_U
   ext_T
 ]
 deepdive.pipeline.pipelines.endtoend: [
+  ext_U
   ext_T
 ]
diff --git a/test/expected-output-test/arrays/input.ddlog b/test/expected-output-test/arrays/input.ddlog
index ab59448c6..9267d14f0 100644
--- a/test/expected-output-test/arrays/input.ddlog
+++ b/test/expected-output-test/arrays/input.ddlog
@@ -1,7 +1,8 @@
-R(x text[]).
+R(x int[]).
 
-S(x text,
-  y text[]).
+S(x int,
+  y int[]).
 
 T(x[3], z) :- R(x), S(z, y), x[1] = y[1], x[2] = y[2].
 
+U(z) :- R(x), S(z, y), z + f(z+1)[z + x[1]] = y[z].
diff --git a/test/expected-output-test/arrays/print.expected b/test/expected-output-test/arrays/print.expected
index b31afe940..67951f23b 100644
--- a/test/expected-output-test/arrays/print.expected
+++ b/test/expected-output-test/arrays/print.expected
@@ -1,7 +1,7 @@
-R(x text[]).
+R(x int[]).
 
-S(x text,
-  y text[]).
+S(x int,
+  y int[]).
 
 T(x[3], z) :-
     R(x),
@@ -9,3 +9,8 @@ T(x[3], z) :-
     x[1] = y[1],
     x[2] = y[2].
 
+U(z) :-
+    R(x),
+    S(z, y),
+    (z + f(z + 1)[(z + x[1])]) = y[z].
+

From 03e99194c6dc341b160aeca799cae2f292fcd961 Mon Sep 17 00:00:00 2001
From: Feiran Wang <feiran.wang1@gmail.com>
Date: Sun, 14 Feb 2016 17:23:22 -0800
Subject: [PATCH 287/347] Add comment

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index eec49e3c8..37fa10670 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -346,7 +346,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
       case _ => s" AS column_${cq.headTerms indexOf e}"
     }
     case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
-    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}"""" //"
+    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}"""" //" fix sublime highlighting
   }
 
   // resolve an expression

From 23ed428554ba6be6f6f60150814b6c763dc924ec Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 28 Feb 2016 21:15:12 -0800
Subject: [PATCH 288/347] Changes all enums to case classes with empty args

which could possibly interfere with pickling libraries
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 28 +++----
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 75 ++++++++++++-------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 20 ++---
 .../ddlog/DeepDiveLogSchemaExporter.scala     |  4 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 11 +--
 5 files changed, 78 insertions(+), 60 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d2b4e2f30..ea0d5d9e0 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -156,7 +156,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
-    val factorFuncName: String = s.head.function.toString.toLowerCase
+    val factorFuncName: String = s.head.function.getClass.getSimpleName.toLowerCase
     val idxInInferenceRulesSharingHead = inferenceRules filter(_.head equals s.head) indexOf(s)
     mode match {
       case INCREMENTAL => s"dd_delta_inf${
@@ -393,8 +393,8 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
         val resolvedLhs = s"${compileCond(lhs, level + 1)}"
         val resolvedRhs = s"${compileCond(rhs, level + 1)}"
         val sql = op match {
-          case LogicOperator.AND => s"${resolvedLhs} AND ${resolvedRhs}"
-          case LogicOperator.OR  => s"${resolvedLhs} OR ${resolvedRhs}"
+          case LogicOperator.AND() => s"${resolvedLhs} AND ${resolvedRhs}"
+          case LogicOperator.OR()  => s"${resolvedLhs} OR ${resolvedRhs}"
         }
         if (level == 0) sql else s"(${sql})"
       }
@@ -574,7 +574,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         }
         if (stmt.isQuery) {
           val labelColumn = stmt.variableType match {
-            case Some(BooleanType)        => "label boolean"
+            case Some(BooleanType())        => "label boolean"
             case Some(MultinomialType(_)) => "label int"
           }
           columnDecls = columnDecls :+ "id bigint" :+ labelColumn
@@ -777,17 +777,17 @@ ${if (createTable) {
           })
 
           val function = stmt.head.function match {
-            case FactorFunction.Imply  => "Imply"
-            case FactorFunction.And    => "And"
-            case FactorFunction.Or     => "Or"
-            case FactorFunction.Equal  => "Equal"
-            case FactorFunction.Linear => "Linear"
-            case FactorFunction.Ratio  => "Ratio"
-            case FactorFunction.IsTrue => ss.variableType get stmt.head.terms(0).name match {
-              case Some(BooleanType)        => "Imply"
+            case FactorFunction.Imply()  => "Imply"
+            case FactorFunction.And()    => "And"
+            case FactorFunction.Or()     => "Or"
+            case FactorFunction.Equal()  => "Equal"
+            case FactorFunction.Linear() => "Linear"
+            case FactorFunction.Ratio()  => "Ratio"
+            case FactorFunction.IsTrue() => ss.variableType get stmt.head.terms(0).name match {
+              case Some(BooleanType())        => "Imply"
               case Some(MultinomialType(_)) => "Multinomial"
             }
-            case FactorFunction.Multinomial => "Multinomial"
+            case FactorFunction.Multinomial() => "Multinomial"
           }
           func = s"""${function}(${funcBody.mkString(", ")})"""
         }
@@ -899,7 +899,7 @@ ${if (createTable) {
       case decl: SchemaDeclaration =>
         if (decl.isQuery) {
           val variableTypeDecl = decl.variableType match {
-            case Some(BooleanType)        => "Boolean"
+            case Some(BooleanType())        => "Boolean"
             case Some(MultinomialType(x)) => s"Categorical(${x})"
           }
           schema += s"${decl.a.name}.label: ${variableTypeDecl}"
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 4c45a1129..aaccae70e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -20,7 +20,7 @@ case class StringConst(value: String) extends ConstExpr
 case class IntConst(value: Int) extends ConstExpr
 case class DoubleConst(value: Double) extends ConstExpr
 case class BooleanConst(value: Boolean) extends ConstExpr
-case class NullConst extends ConstExpr
+case class NullConst() extends ConstExpr
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
@@ -29,7 +29,7 @@ case class IfThenElseExpr(ifCondThenExprPairs: List[(Cond, Expr)], elseExpr: Opt
 sealed trait Pattern
 case class VarPattern(name: String) extends Pattern
 case class ExprPattern(expr: Expr) extends Pattern
-case class PlaceholderPattern extends Pattern
+case class PlaceholderPattern() extends Pattern
 
 sealed trait Body
 case class BodyAtom(name : String, terms : List[Pattern]) extends Body
@@ -37,8 +37,8 @@ case class QuantifiedBody(modifier: BodyModifier, bodies: List[Body]) extends Bo
 
 sealed trait BodyModifier
 case class ExistModifier(negated: Boolean) extends BodyModifier
-case class OuterModifier extends BodyModifier
-case class AllModifier extends BodyModifier
+case class OuterModifier() extends BodyModifier
+case class AllModifier() extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
 case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean = false, limit: Option[Int] = None,
@@ -64,16 +64,17 @@ case class NegationCond(cond: Cond) extends Cond
 case class CompoundCond(lhs: Cond, op: LogicOperator.LogicOperator, rhs: Cond) extends Cond
 
 // logic operators
-object LogicOperator extends Enumeration {
-  type LogicOperator = Value
-  val  AND, OR = Value
+object LogicOperator {
+  sealed trait LogicOperator
+  case class AND() extends LogicOperator
+  case class OR() extends LogicOperator
 }
 
 // variable type
 sealed trait VariableType {
   def cardinality: Long
 }
-case object BooleanType extends VariableType {
+case class BooleanType() extends VariableType {
   def cardinality = 2
 }
 case class MultinomialType(numCategories: Int) extends VariableType {
@@ -83,9 +84,16 @@ case class MultinomialType(numCategories: Int) extends VariableType {
 case class FactorWeight(variables: List[Expr])
 
 // factor function
-object FactorFunction extends Enumeration {
-  type FactorFunction = Value
-  val  IsTrue, Imply, Or, And, Equal, Multinomial, Linear, Ratio = Value
+object FactorFunction {
+  sealed trait FactorFunction
+  case class IsTrue()      extends FactorFunction
+  case class Imply()       extends FactorFunction
+  case class Or()          extends FactorFunction
+  case class And()         extends FactorFunction
+  case class Equal()       extends FactorFunction
+  case class Multinomial() extends FactorFunction
+  case class Linear()      extends FactorFunction
+  case class Ratio()       extends FactorFunction
 }
 case class HeadAtom(name : String, terms : List[Expr], isNegated: Boolean = false)
 case class InferenceRuleHead(function: FactorFunction.FactorFunction, terms: List[HeadAtom])
@@ -111,6 +119,19 @@ case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: O
 case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery, mode: Option[String], parallelism: Option[Int]) extends Statement // Extraction rule
 case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
 
+
+
+
+
+
+
+
+
+
+
+
+
+
 // Parser
 class DeepDiveLogParser extends JavaTokenParsers {
 
@@ -170,7 +191,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   def CategoricalParser = "Categorical" ~> "(" ~> """\d+""".r <~ ")" ^^ { n => MultinomialType(n.toInt) }
-  def BooleanParser = "Boolean" ^^ { s => BooleanType }
+  def BooleanParser = "Boolean" ^^ { s => BooleanType() }
   def dataType = CategoricalParser | BooleanParser
 
   def schemaDeclaration: Parser[SchemaDeclaration] =
@@ -181,7 +202,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
         var types = attrs map (_.t)
         val annos = attrs map (_.annotation)
         val variableType = vType match {
-          case None => if (isQuery != None) Some(BooleanType) else None
+          case None => if (isQuery != None) Some(BooleanType()) else None
           case Some(s) => Some(s)
         }
         SchemaDeclaration(Attribute(r, vars, types, annos), (isQuery != None), variableType, anno)
@@ -215,7 +236,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | double ^^ { DoubleConst(_) }
     | integer ^^ { IntConst(_) }
     | ("TRUE" | "FALSE") ^^ { x => BooleanConst(x.toBoolean) }
-    | "NULL" ^^ { _ => new NullConst }
+    | "NULL" ^^ { _ => NullConst() }
     | functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
         case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
       }
@@ -233,12 +254,12 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def cond : Parser[Cond] =
     ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
-        CompoundCond(lhs, LogicOperator.OR, rhs)
+        CompoundCond(lhs, LogicOperator.OR(), rhs)
       }
     | acond
     )
   def acond : Parser[Cond] =
-    ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND, rhs) }
+    ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND(), rhs) }
     | lcond
     )
   // ! has higher priority...
@@ -264,9 +285,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
   }
   def quantifiedBody = (opt("!") ~ "EXISTS" | "OPTIONAL" | "ALL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
-      case (not ~ "EXISTS") => new ExistModifier(not != None)
-      case "OPTIONAL" => new OuterModifier
-      case "ALL" => new AllModifier
+      case (not ~ "EXISTS") => ExistModifier(not != None)
+      case "OPTIONAL" => OuterModifier()
+      case "ALL" => AllModifier()
     }
     QuantifiedBody(modifier, b)
   }
@@ -365,28 +386,28 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def inferenceRuleHead =
   ( implyHeadAtoms ^^ {
-      InferenceRuleHead(FactorFunction.Imply, _)
+      InferenceRuleHead(FactorFunction.Imply(), _)
     }
   | "@semantics" ~> commit("(" ~> stringLiteralAsString <~ ")" ^? ({
-      case "linear" => FactorFunction.Linear
-      case "ratio"  => FactorFunction.Ratio
+      case "linear" => FactorFunction.Linear()
+      case "ratio"  => FactorFunction.Ratio()
     }, (s) => s"${s}: unrecognized semantics")) ~ implyHeadAtoms ^^ {
       case (s ~ h) => InferenceRuleHead(s, h)
     }
   | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
-      InferenceRuleHead(FactorFunction.Equal, a +: b)
+      InferenceRuleHead(FactorFunction.Equal(), a +: b)
     }
   | headAtom ~ "^" ~ rep1sep(headAtom, "^") ^^ { case (a ~ _ ~ b) =>
-      InferenceRuleHead(FactorFunction.And, a +: b)
+      InferenceRuleHead(FactorFunction.And(), a +: b)
     }
   | headAtom ~ "v" ~ rep1sep(headAtom, "v") ^^ { case (a ~ _ ~ b) =>
-      InferenceRuleHead(FactorFunction.Or, a +: b)
+      InferenceRuleHead(FactorFunction.Or(), a +: b)
     }
   | "Multinomial" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
-      InferenceRuleHead(FactorFunction.Multinomial, _)
+      InferenceRuleHead(FactorFunction.Multinomial(), _)
     }
   | headAtom ^^ {
-      x => InferenceRuleHead(FactorFunction.IsTrue, List(x))
+      x => InferenceRuleHead(FactorFunction.IsTrue(), List(x))
     }
   )
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index e193b50b7..4a0b31342 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -128,8 +128,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case NegationCond(c) => s"[!${print(c)}]"
       case CompoundCond(lhs, op, rhs) => {
         op match {
-          case LogicOperator.AND => s"[${print(lhs)}, ${print(rhs)}]"
-          case LogicOperator.OR  => s"[${print(lhs)}; ${print(rhs)}]"
+          case LogicOperator.AND() => s"[${print(lhs)}, ${print(rhs)}]"
+          case LogicOperator.OR()  => s"[${print(lhs)}; ${print(rhs)}]"
         }
       }
     }
@@ -169,14 +169,14 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     def printImplyHead = s"""${printHead(head.terms.dropRight(1), ", ")} => ${print(head.terms.last)}"""
     def printHead(a: List[HeadAtom], delim: String) : String = a map print mkString(delim)
     head.function match {
-      case FactorFunction.Imply  => printImplyHead
-      case FactorFunction.Linear => s"""@semantics("linear")\n${printImplyHead}"""
-      case FactorFunction.Ratio  => s"""@semantics("ratio")\n${printImplyHead}"""
-      case FactorFunction.And    => printHead(head.terms, " ^ ")
-      case FactorFunction.Or     => printHead(head.terms, " v ")
-      case FactorFunction.Equal  => printHead(head.terms, " = ")
-      case FactorFunction.IsTrue => printHead(head.terms, "")
-      case FactorFunction.Multinomial => s"""Multinomial(${printHead(head.terms, ", ")})"""
+      case FactorFunction.Imply()  => printImplyHead
+      case FactorFunction.Linear() => s"""@semantics("linear")\n${printImplyHead}"""
+      case FactorFunction.Ratio()  => s"""@semantics("ratio")\n${printImplyHead}"""
+      case FactorFunction.And()    => printHead(head.terms, " ^ ")
+      case FactorFunction.Or()     => printHead(head.terms, " v ")
+      case FactorFunction.Equal()  => printHead(head.terms, " = ")
+      case FactorFunction.IsTrue() => printHead(head.terms, "")
+      case FactorFunction.Multinomial() => s"""Multinomial(${printHead(head.terms, ", ")})"""
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 639c9c77a..c31e8516b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -32,10 +32,10 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
       schema += "annotations" -> exportAnnotations(decl.annotation)
     // what type of random variable this relation is
     if (decl.isQuery)
-      decl.variableType getOrElse { BooleanType } match {
+      decl.variableType getOrElse { BooleanType() } match {
         case ty =>
           schema += "variable_type" -> (ty match {
-            case BooleanType        => "boolean"
+            case BooleanType()      => "boolean"
             case MultinomialType(n) => "multinomial"
           })
           schema += "variable_cardinality" -> ty.cardinality
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 10d74a1ad..e7c0fbccd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -161,13 +161,10 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     if (schemaDeclaration contains b.name)
     b.terms.zipWithIndex.foreach {
       case (`supVariable`, index) => {
-        val expColumnType =
-          if (expType.isInstanceOf[BooleanType.type])
-            // binary
-            "boolean"
-          else
-            // multinomial
-            "int"
+        val expColumnType = expType match {
+          case BooleanType() => "boolean"
+          case MultinomialType(_) => "int"
+        }
         if (schemaDeclaration(b.name).a.types(index).toLowerCase != expColumnType) {
           val actualColumnType = schemaDeclaration(b.name).a.types(index).toLowerCase
           error(s, s"Supervision column ${supVariable.name} should be ${expColumnType} type, but is ${actualColumnType} type")

From 75caba4d77c1caee7d750ed710475e03490c8104 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 28 Feb 2016 23:25:31 -0800
Subject: [PATCH 289/347] Fixes Makefile and test script to support Scala 2.11

---
 scala.mk   | 13 +++++++------
 test/ddlog |  3 ++-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/scala.mk b/scala.mk
index f9737debd..978fd9603 100644
--- a/scala.mk
+++ b/scala.mk
@@ -17,15 +17,16 @@
 #   be measured.
 
 # Some path names for Scala
+SCALA_VERSION                 = 2.11
 SCALA_BUILD_FILES             = build.sbt $(wildcard project/*.*)
 SCALA_MAIN_SOURCES            = $(shell find src/main/scala -name '*.scala' 2>/dev/null)
-SCALA_MAIN_CLASSES_DIR        = target/scala-2.10/classes
-SCALA_MAIN_CLASSPATH_EXPORTED = target/scala-2.10/classpath
+SCALA_MAIN_CLASSES_DIR        = target/scala-$(SCALA_VERSION)/classes
+SCALA_MAIN_CLASSPATH_EXPORTED = target/scala-$(SCALA_VERSION)/classpath
 SCALA_TEST_SOURCES            = $(shell find src/test/scala -name '*.scala' 2>/dev/null)
-SCALA_TEST_CLASSES_DIR        = target/scala-2.10/test-classes
-SCALA_TEST_CLASSPATH_EXPORTED = target/scala-2.10/test-classpath
-SCALA_COVERAGE_DIR            = target/scala-2.10/scoverage-data
-SCALA_ASSEMBLY_JAR            = target/scala-2.10/*-assembly-*.jar
+SCALA_TEST_CLASSES_DIR        = target/scala-$(SCALA_VERSION)/test-classes
+SCALA_TEST_CLASSPATH_EXPORTED = target/scala-$(SCALA_VERSION)/test-classpath
+SCALA_COVERAGE_DIR            = target/scala-$(SCALA_VERSION)/scoverage-data
+SCALA_ASSEMBLY_JAR            = target/scala-$(SCALA_VERSION)/*-assembly-*.jar
 
 # SBT settings
 PATH := $(PATH):$(shell pwd)/sbt
diff --git a/test/ddlog b/test/ddlog
index 1bb641006..c6de04d30 100755
--- a/test/ddlog
+++ b/test/ddlog
@@ -21,7 +21,8 @@ Self=$(readlink -f "$0" 2>/dev/null || {
 Here=$(dirname "$Self")
 
 # set up environment
-classpathFile="$Here"/../target/scala-2.10/classpath
+classpathFile=("$Here"/../target/scala-*/classpath)
+classpathFile=${classpathFile[0]}
 [[ -s "$classpathFile" ]] || {
     echo "ERROR: missing $classpathFile"
     echo 'Run `make` before using test/ddlog!'

From b0db594db1e75b060f249afa3c80991bd34ddbcc Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 28 Feb 2016 23:54:26 -0800
Subject: [PATCH 290/347] Changes to Scala 2.11.7

---
 build.sbt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/build.sbt b/build.sbt
index 198955f7d..265de9a01 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,3 +1,7 @@
+scalaVersion := "2.11.7"
+
+libraryDependencies += "org.scala-lang.modules" %% "scala-parser-combinators" % "1.0.4"
+
 libraryDependencies += "org.apache.commons" % "commons-lang3" % "3.4"
 
 libraryDependencies += "com.github.scopt" %% "scopt" % "3.3.0"

From 418d1ace6728ec9d2f15e2ccfaf52bdea901ca03 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 01:14:02 -0800
Subject: [PATCH 291/347] Drops messy incremental support to focus on core
 compilation

---
 .../org/deepdive/ddlog/DeepDiveLog.scala      |   5 +-
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 143 +--
 .../ddlog/DeepDiveLogDeltaDeriver.scala       |   9 +-
 .../ddlog/DeepDiveLogMergeDeriver.scala       |  36 -
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   9 +-
 test/expected-output-test.bats.template       |  31 +-
 .../arrays/compile.expected                   |  21 +-
 .../chunking_example/compile.expected         |  13 -
 .../expressions/compile.expected              |  13 -
 .../factor_functions/compile.expected         |  13 -
 .../if-then-else/compile.expected             |  13 -
 .../compile-incremental.expected              | 939 ------------------
 .../compile.expected                          |  13 -
 .../ocr_example/compile-incremental.expected  | 357 -------
 .../compile-materialization.expected          | 107 --
 .../ocr_example/compile-merge.expected        |  89 --
 .../ocr_example/compile.expected              |  13 -
 .../compile-incremental.expected              | 403 --------
 .../compile-materialization.expected          | 108 --
 .../smoke_example/compile-merge.expected      | 111 ---
 .../smoke_example/compile.expected            |  13 -
 .../compile-incremental.expected              | 483 ---------
 .../compile-materialization.expected          | 126 ---
 .../spouse_example/compile-merge.expected     | 133 ---
 .../spouse_example/compile.expected           |  13 -
 .../compile-incremental.expected              | 488 ---------
 .../compile-incremental.expected              | 500 ----------
 .../compile.expected                          |  13 -
 .../views/compile.expected                    |  13 -
 .../weights/compile.expected                  |  13 -
 30 files changed, 24 insertions(+), 4217 deletions(-)
 delete mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
 delete mode 100644 test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
 delete mode 100644 test/expected-output-test/ocr_example/compile-incremental.expected
 delete mode 100644 test/expected-output-test/ocr_example/compile-materialization.expected
 delete mode 100644 test/expected-output-test/ocr_example/compile-merge.expected
 delete mode 100644 test/expected-output-test/smoke_example/compile-incremental.expected
 delete mode 100644 test/expected-output-test/smoke_example/compile-materialization.expected
 delete mode 100644 test/expected-output-test/smoke_example/compile-merge.expected
 delete mode 100644 test/expected-output-test/spouse_example/compile-incremental.expected
 delete mode 100644 test/expected-output-test/spouse_example/compile-materialization.expected
 delete mode 100644 test/expected-output-test/spouse_example/compile-merge.expected
 delete mode 100644 test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
 delete mode 100644 test/expected-output-test/spouse_example_new_inference/compile-incremental.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 2ad8f75e8..9ee4b8543 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -22,7 +22,6 @@ object DeepDiveLog {
   (handler: DeepDiveLogHandler = null
    , inputFiles: List[String] = List()
    , query: String = null
-   , mode: Mode = ORIGINAL
    , skipDesugar: Boolean = false
   )
   val commandLine = new scopt.OptionParser[Config]("ddlog") {
@@ -34,11 +33,9 @@ object DeepDiveLog {
       )
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        } text("Compiles a deepdive.conf")
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   } text("Prints given program after parsing")
+    cmd("print-incremental")           required() action { (_, c) => c.copy(handler = DeepDiveLogDeltaDeriver)    } text("Prints delta rules after parsing given program")
     cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) } text("Checks if given program is valid")
     cmd("export-schema")               required() action { (_, c) => c.copy(handler = DeepDiveLogSchemaExporter)  } text("Exports given program in JSON")
-    opt[Unit]('i', "incremental")      optional() action { (_, c) => c.copy(mode    = INCREMENTAL)                } text("Whether to derive delta rules")
-    opt[Unit]("materialization")       optional() action { (_, c) => c.copy(mode    = MATERIALIZATION)            } text("Whether to materialize origin data")
-    opt[Unit]("merge")                 optional() action { (_, c) => c.copy(mode    = MERGE)                      } text("Whether to merge delta data")
     opt[Unit]("skip-desugar")          optional() action { (_, c) => c.copy(skipDesugar = true)                   } text("Whether to skip desugaring and assume no sugar")
     arg[String]("FILE...") minOccurs(0) unbounded() action { (f, c) => c.copy(inputFiles = c.inputFiles ++ List(f)) } text("Path to DDLog program files")
     checkConfig { c =>
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index ea0d5d9e0..d855b4d32 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -97,8 +97,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   var variableTableNames : Set[String] = Set()
 
-  var mode : Mode = ORIGINAL
-
   // Mapping head names to the actual statements
   var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
   var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
@@ -108,7 +106,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   def init() = {
     // generate the statements.
-    mode = config.mode
     statements.foreach {
       case decl: SchemaDeclaration => {
         val r = decl.a.name
@@ -158,16 +155,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   def resolveInferenceBlockName(s: InferenceRule): String = {
     val factorFuncName: String = s.head.function.getClass.getSimpleName.toLowerCase
     val idxInInferenceRulesSharingHead = inferenceRules filter(_.head equals s.head) indexOf(s)
-    mode match {
-      case INCREMENTAL => s"dd_delta_inf${
-        // XXX This comes right after the prefix to prevent potential collision with user's name
-        optionalIndex(idxInInferenceRulesSharingHead)
-      }_${
-        factorFuncName
-      }_${
-        s.head.terms map {_.name stripPrefix("dd_new_")} mkString("_")
-      }"
-      case _ =>           s"inf${
+    s"inf${
         // XXX This comes right after the prefix to prevent potential collision with user's name
         optionalIndex(idxInInferenceRulesSharingHead)
       }_${
@@ -177,7 +165,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         // followed by variable names
         s.head.terms map {_.name} mkString("_")
       }"
-    }
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
@@ -189,7 +176,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
         schema(relName,i)
       } else {
         // for views, columns names are in the form of "column_index"
-        return if (DeepDiveLogCompiler.isForIncremental(relName)) v else s"column_${i}"
+        return s"column_${i}"
       }
     }
   }
@@ -224,10 +211,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case _                       =>
     })
 
-    schemaDeclarationGroupByHead = mode match {
-      case INCREMENTAL => schemaDeclarationToCompile.toList.filter(_.a.name.startsWith("dd_")).groupBy(_.a.name)
-      case _           => schemaDeclarationToCompile.toList.groupBy(_.a.name)
-    }
+    schemaDeclarationGroupByHead = schemaDeclarationToCompile.toList.groupBy(_.a.name)
     extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.headName)
     functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
   }
@@ -559,16 +543,12 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   type CompiledBlock = String
   type CompiledBlocks = List[CompiledBlock]
 
-  def isForIncremental(name: String) = name startsWith "dd_new_"
-
   def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\\\''")}'"
 
   // Generate schema and cleanup part for database
   def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
     var schemas = new ListBuffer[String]()
     for (stmt <- stmts) {
-      if (isForIncremental(stmt.a.name) && (ss.isQueryTerm(stmt.a.name))) {
-      } else {
         var columnDecls = stmt.a.terms.zipWithIndex map {
           case (name,i) => s"${name} ${stmt.a.types(i)}"
         }
@@ -589,20 +569,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
             \"\"\"
             style: "sql_extractor"
           }"""
-      }
-    }
-    // Cleanup incremental table extractor
-    val truncateTableList = (stmts map (x =>
-      if (isForIncremental(x.a.name) && (ss.isQueryTerm(x.a.name))) ""
-      else s"TRUNCATE ${x.a.name};")).filter(_ != "")
-    if (truncateTableList.length > 0) {
-      schemas += s"""
-        deepdive.extraction.extractors.cleanup {
-          sql: \"\"\"
-          ${truncateTableList.mkString("\n          ")}
-          \"\"\"
-          style: "sql_extractor"
-        }"""
     }
     schemas.toList
   }
@@ -624,43 +590,18 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
-        } else if ((ss.hasSchemaDeclared(stmt.headName)) &&
-          (ss.schemaDeclarationGroupByHead(stmt.headName)(0).isQuery) &&
-          isForIncremental(stmt.headName)) {
-          val headStr = qc.generateSQLHead(NoAlias)
-          inputQueries += s"""SELECT DISTINCT ${ headStr }, id, label
-          ${ qc.generateSQLBody(cqBody) }
-          """
         } else {
           // variable columns
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
           // views uses view alias
-          val aliasStyle = ss.mode match {
-            case MERGE => NoAlias
-            case _     => if (isForIncremental(stmt.headName)) NoAlias
-              else if (!ss.hasSchemaDeclared(stmt.headName)) ViewAlias
+          val aliasStyle = if (!ss.hasSchemaDeclared(stmt.headName)) ViewAlias
               else TableAlias
-          }
           inputQueries += qc.generateSQL(aliasStyle)
         }
       }
     }
     val blockName = ss.resolveExtractorBlockName(stmts(0))
-    val sqlCmdForCleanUp = ss.mode match {
-      case MERGE => s"TRUNCATE ${stmts(0).headName};"
-      case _ => if (ss.hasSchemaDeclared(stmts(0).headName)) {
-        if (isForIncremental(stmts(0).headName) && !(ss.isQueryTerm(stmts(0).headName)))
-          s"TRUNCATE ${stmts(0).headName};"
-        else ""
-      } else s"DROP VIEW IF EXISTS ${stmts(0).headName} CASCADE;"
-    }
-    val createTable = ss.mode match {
-      case MERGE => true
-      case _ => (!isForIncremental(stmts(0).headName) &&
-        (ss.hasSchemaDeclared(stmts(0).headName))) ||
-        (isForIncremental(stmts(0).headName) &&
-        !(ss.isQueryTerm(stmts(0).headName)))
-    }
+    val createTable = ss.hasSchemaDeclared(stmts(0).headName)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         cmd: \"\"\"
@@ -826,42 +767,6 @@ ${if (createTable) {
   }
 
 
-  def compileUserSettings(ss: CompilationState): CompiledBlocks = {
-    // TODO read user's proto-application.conf and augment it
-    val mode = ss.mode match {
-      case ORIGINAL        => "ORIGINAL"
-      case INCREMENTAL     => "INCREMENTAL"
-      case MATERIALIZATION => "MATERIALIZATION"
-      case MERGE           => "MERGE"
-    }
-    List("""
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: """ + s"""${mode}
-    }
-    """)
-  }
-
-  def compileVariableKey(ss: CompilationState): CompiledBlocks = {
-    var keys = new ListBuffer[String]()
-    for (stmt <- (ss.schemaDeclarationGroupByHead map (_._2)).flatten) {
-      if (stmt.isQuery) keys += s"""${stmt.a.name} : [${stmt.a.terms.mkString(", ")}]"""
-    }
-    ss.mode match {
-      case INCREMENTAL => List(s"""
-      deepdive.schema.keys {
-        ${keys.mkString("\n        ")}
-      }""")
-      case _ => List("")
-    }
-  }
-
   // generate application.conf pipelines
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
@@ -871,24 +776,7 @@ ${if (createTable) {
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [\n  ${inference}\n]" else ""
     val endtoend = List(extraction, inference).filter(_ != "").mkString("\n  ")
     val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [\n  ${endtoend}\n]" else ""
-    val base_dir = ss.mode match {
-      case MATERIALIZATION | INCREMENTAL => "deepdive.pipeline.base_dir: ${BASEDIR}"
-      case _ => ""
-    }
-    List(run, extraction_pipeline, inference_pipeline, endtoend_pipeline, base_dir).filter(_ != "") ++ (
-    // FIXME remove the following after fully supporting incremental uops
-    // XXX initdb pipeline and CREATE TABLE extractors has been moved to deepdive
-    ss.mode match {
-      case INCREMENTAL =>
-        val setup_database_pipeline = ((ss.schemaDeclarationGroupByHead map (_._2)).flatten map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
-        val initdb = if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.initdb: [\n  ${setup_database_pipeline}\n]" else ""
-        val cleanup_pipeline = ss.mode match {
-          case INCREMENTAL | ORIGINAL => if (setup_database_pipeline.length > 0) s"deepdive.pipeline.pipelines.cleanup: [\n  cleanup\n]" else ""
-          case _ => ""
-        }
-        List(initdb, cleanup_pipeline)
-      case _ => List.empty
-    }) // FIXME remove above after fully supporting incremental uops
+    List(run, extraction_pipeline, inference_pipeline, endtoend_pipeline).filter(_ != "")
   }
 
   // generate variable schema statements
@@ -918,34 +806,17 @@ ${if (createTable) {
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     // semantic checking
     DeepDiveLogSemanticChecker.run(parsedProgram, config)
-    // determine the program to compile
-    val programToCompile =
-      // derive and compile the program based on mode information
-      config.mode match {
-        case ORIGINAL => parsedProgram
-        case INCREMENTAL => DeepDiveLogDeltaDeriver.derive(parsedProgram)
-        case MATERIALIZATION => parsedProgram
-        case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
-      }
+    val programToCompile = parsedProgram
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile, config )
 
     val body = new ListBuffer[String]()
-    config.mode match {
-      case INCREMENTAL =>
-        body ++= compileSchemaDeclarations((state.schemaDeclarationGroupByHead map (_._2)).flatten.toList, state)
-      case _ =>
-    }
     state.extractionRuleGroupByHead foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
     state.functionCallList          foreach {func   => body ++= compileFunctionCallRules(List(func), state)}
     state.inferenceRules            foreach {inf    => body ++= compileInferenceRules(List(inf), state)}
 
     // compile the program into blocks of application.conf
     val blocks = (
-      compileUserSettings(state)
-      :::
-      compileVariableKey(state)
-      :::
       compileVariableSchema(programToCompile, state)
       :::
       body.toList
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 4ee3f63c7..87b80bc25 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -1,5 +1,7 @@
 package org.deepdive.ddlog
 
+import org.deepdive.ddlog.DeepDiveLog.{Config, Program}
+
 import scala.collection.mutable.ListBuffer
 
 
@@ -12,7 +14,7 @@ object Mode extends Enumeration {
 }
 import Mode._
 
-object DeepDiveLogDeltaDeriver{
+object DeepDiveLogDeltaDeriver extends DeepDiveLogHandler {
 
   // Default prefix for incremental tables
   val deltaPrefix = "dd_delta_"
@@ -166,4 +168,9 @@ object DeepDiveLogDeltaDeriver{
     }
     incrementalProgram.toList
   }
+
+  override def run(program: Program, config: Config): Unit = {
+    DeepDiveLogPrettyPrinter.run(derive(program), config)
+  }
+
 }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
deleted file mode 100644
index c2244bbd1..000000000
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogMergeDeriver.scala
+++ /dev/null
@@ -1,36 +0,0 @@
-package org.deepdive.ddlog
-
-import scala.collection.mutable.ListBuffer
-
-object DeepDiveLogMergeDeriver{
-
-  // Default prefix for incremental tables
-  val newPrefix = "dd_new_"
-
-  // Incremental scheme declaration,
-  // keep the original scheme and create one delta scheme
-  def transform(stmt: SchemaDeclaration): Statement = {
-    // New table
-    var incNewStmt = stmt.copy(
-      a = stmt.a.copy(
-        name = newPrefix + stmt.a.name
-      )
-    )
-
-    ExtractionRule(stmt.a.name,
-      ConjunctiveQuery(stmt.a.terms map { VarExpr(_) },
-      List(List(BodyAtom(incNewStmt.a.name, incNewStmt.a.terms map { VarPattern(_) }))),
-      false, None))
-  }
-
-  def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
-    var mergeProgram = new ListBuffer[Statement]()
-    program foreach { x =>
-      x match {
-        case x: SchemaDeclaration => if (!x.isQuery) mergeProgram += transform(x)
-        case _ =>
-      }
-    }
-    mergeProgram.toList
-  }
-}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 4a0b31342..96ee0f2a6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -197,14 +197,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    val programToPrint =
-      // derive the program based on mode information
-      config.mode match {
-        case ORIGINAL => parsedProgram
-        case INCREMENTAL => DeepDiveLogDeltaDeriver.derive(parsedProgram)
-        case MATERIALIZATION => parsedProgram
-        case MERGE => DeepDiveLogMergeDeriver.derive(parsedProgram)
-      }
+    val programToPrint = parsedProgram
     // pretty print in original syntax
     programToPrint foreach {stmt => println(print(stmt))}
   }
diff --git a/test/expected-output-test.bats.template b/test/expected-output-test.bats.template
index 325b63456..ccc1cf53d 100644
--- a/test/expected-output-test.bats.template
+++ b/test/expected-output-test.bats.template
@@ -71,36 +71,11 @@ expectedOutputExistsFor() {
 }
 
 
-## tests for --incremental support
-
-# compare the compiled output of the incremental version with what's expected
-@test "$it compiles --incremental input as expected" {
-    expectedOutputExistsFor "compile-incremental" || skip
-    ddlog compile --incremental "$TESTDIR"/input.ddlog >"$actualOutput"
-    diff "$expectedOutput" "$actualOutput"
-}
+## tests for incremental support
 
 # compare the pretty-printed output of the incremental version with what's expected
-@test "$it prints --incremental input as expected" {
+@test "$it prints incremental input as expected" {
     expectedOutputExistsFor "print-incremental" || skip
-    ddlog print --incremental "$TESTDIR"/input.ddlog >"$actualOutput"
-    diff "$expectedOutput" "$actualOutput"
-}
-
-## tests for --merge support
-
-# compare the compiled output of the merge version with what's expected
-@test "$it compiles --merge input as expected" {
-    expectedOutputExistsFor "compile-merge" || skip
-    ddlog compile --merge "$TESTDIR"/input.ddlog >"$actualOutput"
-    diff "$expectedOutput" "$actualOutput"
-}
-
-## tests for --materialization support
-
-# compare the compiled output of the merge version with what's expected
-@test "$it compiles --materialization input as expected" {
-    expectedOutputExistsFor "compile-materialization" || skip
-    ddlog compile --materialization "$TESTDIR"/input.ddlog >"$actualOutput"
+    ddlog print-incremental "$TESTDIR"/input.ddlog >"$actualOutput"
     diff "$expectedOutput" "$actualOutput"
 }
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index 61ca3f9ea..4118c4e5f 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         
       }
@@ -20,10 +7,10 @@
       deepdive.extraction.extractors.ext_U {
         cmd: """
 
-  deepdive create view U as 'SELECT R1.x AS column_0
+	deepdive create view U as 'SELECT R1.x AS column_0
 FROM R R0, S R1
         WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]'
-  
+	
         """
           output_relation: "U"
         style: "cmd_extractor"
@@ -38,10 +25,10 @@ FROM R R0, S R1
       deepdive.extraction.extractors.ext_T {
         cmd: """
 
-  deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
+	deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
 FROM R R0, S R1
         WHERE R0.x[1] = R1.y[1] AND R0.x[2] = R1.y[2]'
-  
+	
         """
           output_relation: "T"
         style: "cmd_extractor"
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 6a869ec16..7f8f93a39 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         tag.label: Categorical(13)
       }
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index db1ea14c6..db8433a65 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         
       }
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 059d89651..c6fff079a 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         S.label: Boolean
 Q.label: Boolean
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 33fa69f3f..8b3de1708 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         q.label: Boolean
       }
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected b/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
deleted file mode 100644
index 854fe186e..000000000
--- a/test/expected-output-test/multiple_rules_for_same_head/compile-incremental.expected
+++ /dev/null
@@ -1,939 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: INCREMENTAL
-    }
-    
-
-      deepdive.schema.keys {
-        dd_new_Q : [x]
-        dd_delta_Q : [x]
-      }
-
-      deepdive.schema.variables {
-        Q.label: Boolean
-dd_delta_Q.label: Boolean
-dd_new_Q.label: Boolean
-      }
-    
-
-          deepdive.extraction.extractors.init_dd_new_S {
-            sql: """ DROP TABLE IF EXISTS dd_new_S CASCADE;
-            CREATE TABLE
-            dd_new_S(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_S_0 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_S_0 CASCADE;
-            CREATE TABLE
-            dd_delta_S_0(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T___0 {
-            sql: """ DROP TABLE IF EXISTS dd_new_T___0 CASCADE;
-            CREATE TABLE
-            dd_new_T___0(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T CASCADE;
-            CREATE TABLE
-            dd_delta_T(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T___1 {
-            sql: """ DROP TABLE IF EXISTS dd_new_T___1 CASCADE;
-            CREATE TABLE
-            dd_new_T___1(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T_2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T_2 CASCADE;
-            CREATE TABLE
-            dd_delta_T_2(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_S_2 {
-            sql: """ DROP TABLE IF EXISTS dd_new_S_2 CASCADE;
-            CREATE TABLE
-            dd_new_S_2(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T {
-            sql: """ DROP TABLE IF EXISTS dd_new_T CASCADE;
-            CREATE TABLE
-            dd_new_T(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_S {
-            sql: """ DROP TABLE IF EXISTS dd_delta_S CASCADE;
-            CREATE TABLE
-            dd_delta_S(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T___3 {
-            sql: """ DROP TABLE IF EXISTS dd_new_T___3 CASCADE;
-            CREATE TABLE
-            dd_new_T___3(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T___0 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T___0 CASCADE;
-            CREATE TABLE
-            dd_delta_T___0(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_R {
-            sql: """ DROP TABLE IF EXISTS dd_new_R CASCADE;
-            CREATE TABLE
-            dd_new_R(a int,
-        b int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_S_2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_S_2 CASCADE;
-            CREATE TABLE
-            dd_delta_S_2(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_S_1 {
-            sql: """ DROP TABLE IF EXISTS dd_new_S_1 CASCADE;
-            CREATE TABLE
-            dd_new_S_1(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_R {
-            sql: """ DROP TABLE IF EXISTS dd_delta_R CASCADE;
-            CREATE TABLE
-            dd_delta_R(a int,
-          b int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T___2 {
-            sql: """ DROP TABLE IF EXISTS dd_new_T___2 CASCADE;
-            CREATE TABLE
-            dd_new_T___2(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T___3 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T___3 CASCADE;
-            CREATE TABLE
-            dd_delta_T___3(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_S_1 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_S_1 CASCADE;
-            CREATE TABLE
-            dd_delta_S_1(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T___1 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T___1 CASCADE;
-            CREATE TABLE
-            dd_delta_T___1(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_Q {
-            sql: """ DROP TABLE IF EXISTS dd_delta_Q CASCADE;
-            CREATE TABLE
-            dd_delta_Q(x int,
-          id bigint,
-          label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_T_2 {
-            sql: """ DROP TABLE IF EXISTS dd_new_T_2 CASCADE;
-            CREATE TABLE
-            dd_new_T_2(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_S_0 {
-            sql: """ DROP TABLE IF EXISTS dd_new_S_0 CASCADE;
-            CREATE TABLE
-            dd_new_S_0(a int)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_T___2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_T___2 CASCADE;
-            CREATE TABLE
-            dd_delta_T___2(a int)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_new_S;
-          TRUNCATE dd_delta_S_0;
-          TRUNCATE dd_new_T___0;
-          TRUNCATE dd_delta_T;
-          TRUNCATE dd_new_T___1;
-          TRUNCATE dd_delta_T_2;
-          TRUNCATE dd_new_S_2;
-          TRUNCATE dd_new_T;
-          TRUNCATE dd_delta_S;
-          TRUNCATE dd_new_T___3;
-          TRUNCATE dd_delta_T___0;
-          TRUNCATE dd_new_R;
-          TRUNCATE dd_delta_S_2;
-          TRUNCATE dd_new_S_1;
-          TRUNCATE dd_delta_R;
-          TRUNCATE dd_new_T___2;
-          TRUNCATE dd_delta_T___3;
-          TRUNCATE dd_delta_S_1;
-          TRUNCATE dd_delta_T___1;
-          TRUNCATE dd_delta_Q;
-          TRUNCATE dd_new_T_2;
-          TRUNCATE dd_new_S_0;
-          TRUNCATE dd_delta_T___2;
-          """
-          style: "sql_extractor"
-        }
-
-      deepdive.extraction.extractors.ext_dd_new_S {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_S"
-	deepdive sql 'INSERT INTO dd_new_S SELECT R0.a
-FROM S R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_S R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_S"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S" ]
-          input_relations: [
-            S
-            dd_delta_S
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_T___0 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_T___0"
-	deepdive sql 'INSERT INTO dd_new_T___0 SELECT R0.a
-FROM T___0 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_T___0 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_T___0"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T___0_by_f" ]
-          input_relations: [
-            T___0
-            dd_delta_T___0
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_T {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_T"
-	deepdive sql 'INSERT INTO dd_delta_T SELECT R0.a AS "dd_delta_T___0.R0.a"
-FROM dd_delta_T___0 R0
-        
-UNION ALL
-SELECT R0.a AS "dd_delta_T___1.R0.a"
-FROM dd_delta_T___1 R0
-        
-UNION ALL
-SELECT R0.a AS "dd_delta_T___2.R0.a"
-FROM dd_delta_T___2 R0
-        
-UNION ALL
-SELECT R0.a AS "dd_delta_T___3.R0.a"
-FROM dd_delta_T___3 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_T"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T___0_by_f" ,  "ext_dd_delta_T___1_by_f" ,  "ext_dd_delta_T___2_by_f" ,  "ext_dd_delta_T___3_by_f_1" ]
-          input_relations: [
-            dd_delta_T___0
-            dd_delta_T___1
-            dd_delta_T___2
-            dd_delta_T___3
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_T___1 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_T___1"
-	deepdive sql 'INSERT INTO dd_new_T___1 SELECT R0.a
-FROM T___1 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_T___1 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_T___1"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T___1_by_f" ]
-          input_relations: [
-            T___1
-            dd_delta_T___1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_S_2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_S_2"
-	deepdive sql 'INSERT INTO dd_new_S_2 SELECT R0.a
-FROM S_2 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_S_2 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_S_2"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S_2_by_f_1" ]
-          input_relations: [
-            S_2
-            dd_delta_S_2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_T {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_T"
-	deepdive sql 'INSERT INTO dd_new_T SELECT R0.a
-FROM T R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_T R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_T"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T" ]
-          input_relations: [
-            T
-            dd_delta_T
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_S {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_S"
-	deepdive sql 'INSERT INTO dd_delta_S SELECT R0.a AS "dd_delta_R.R0.a"
-FROM dd_delta_R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a > 100
-UNION ALL
-SELECT R0.a AS "dd_new_R.R0.a"
-FROM dd_new_R R0, dd_delta_R R1
-        WHERE R1.a = R0.b  AND R0.a > 100
-UNION ALL
-SELECT R0.a AS "dd_delta_R.R0.a"
-FROM dd_delta_R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a < -100
-UNION ALL
-SELECT R0.a AS "dd_new_R.R0.a"
-FROM dd_new_R R0, dd_delta_R R1
-        WHERE R1.a = R0.b  AND R0.a < -100
-UNION ALL
-SELECT R0.a AS "dd_delta_R.R0.a"
-FROM dd_delta_R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a = 0
-UNION ALL
-SELECT R0.a AS "dd_new_R.R0.a"
-FROM dd_new_R R0, dd_delta_R R1
-        WHERE R1.a = R0.b  AND R0.a = 0
-UNION ALL
-SELECT R0.a AS "dd_delta_S_0.R0.a"
-FROM dd_delta_S_0 R0
-        
-UNION ALL
-SELECT R0.a AS "dd_delta_S_1.R0.a"
-FROM dd_delta_S_1 R0
-        
-UNION ALL
-SELECT R0.a AS "dd_delta_S_2.R0.a"
-FROM dd_delta_S_2 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_S"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_new_R" ,  "ext_dd_delta_S_0_by_f" ,  "ext_dd_delta_S_1_by_f" ,  "ext_dd_delta_S_2_by_f_1" ]
-          input_relations: [
-            dd_delta_R
-            R
-            dd_new_R
-            dd_delta_S_0
-            dd_delta_S_1
-            dd_delta_S_2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_T___3 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_T___3"
-	deepdive sql 'INSERT INTO dd_new_T___3 SELECT R0.a
-FROM T___3 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_T___3 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_T___3"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T___3_by_f_1" ]
-          input_relations: [
-            T___3
-            dd_delta_T___3
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_R {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_R"
-	deepdive sql 'INSERT INTO dd_new_R SELECT R0.a, R0.b
-FROM R R0
-        
-UNION ALL
-SELECT R0.a, R0.b
-FROM dd_delta_R R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_R"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            R
-            dd_delta_R
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_S_1 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_S_1"
-	deepdive sql 'INSERT INTO dd_new_S_1 SELECT R0.a
-FROM S_1 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_S_1 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_S_1"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S_1_by_f" ]
-          input_relations: [
-            S_1
-            dd_delta_S_1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_T___2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_T___2"
-	deepdive sql 'INSERT INTO dd_new_T___2 SELECT R0.a
-FROM T___2 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_T___2 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_T___2"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T___2_by_f" ]
-          input_relations: [
-            T___2
-            dd_delta_T___2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_T__3 {
-        cmd: """
-
-	deepdive create view dd_delta_T__3 as 'SELECT R0.a AS column_0
-FROM dd_delta_T R0
-        '
-	
-        """
-          output_relation: "dd_delta_T__3"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_T" ]
-          input_relations: [
-            dd_delta_T
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_Q {
-        cmd: """
-
-	deepdive create view dd_new_Q as 'SELECT DISTINCT R0.x, id, label
-          FROM Q R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.x, id, label
-          FROM dd_delta_Q R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_Q"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            Q
-            dd_delta_Q
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_T_2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_T_2"
-	deepdive sql 'INSERT INTO dd_new_T_2 SELECT R0.a
-FROM T_2 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_T_2 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_T_2"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            T_2
-            dd_delta_T_2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_S_0 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_S_0"
-	deepdive sql 'INSERT INTO dd_new_S_0 SELECT R0.a
-FROM S_0 R0
-        
-UNION ALL
-SELECT R0.a
-FROM dd_delta_S_0 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_S_0"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_S_0_by_f" ]
-          input_relations: [
-            S_0
-            dd_delta_S_0
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_dd_delta_T___0_by_f {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        WHERE R0.a > 1000
-          """
-          output_relation: "dd_delta_T___0"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_T___1_by_f {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        WHERE 10 < R0.a AND R0.a < 20
-          """
-          output_relation: "dd_delta_T___1"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_T___2_by_f {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        WHERE 100 < R0.a AND R0.a < 200
-          """
-          output_relation: "dd_delta_T___2"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_S_0_by_f {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        WHERE R0.a < 0
-          """
-          output_relation: "dd_delta_S_0"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_S_1_by_f {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        WHERE R0.a > 0
-          """
-          output_relation: "dd_delta_S_1"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_T___3_by_f_1 {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        
-          """
-          output_relation: "dd_delta_T___3"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_S_2_by_f_1 {
-          input: """ SELECT R0.a AS "dd_delta_R.R0.a", R0.b AS "dd_delta_R.R0.b"
-FROM dd_delta_R R0
-        WHERE R0.a > 0
-          """
-          output_relation: "dd_delta_S_2"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_istrue_Q {
-          input_query: """
-          SELECT R0.id AS "dd_new_Q.R0.id" , R0.x AS "dd_weight_column_0" 
-          FROM dd_new_Q R0, dd_delta_S R1
-        WHERE R1.a = R0.x  AND R0.x > 1000"""
-          function: "Imply(dd_new_Q.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_S" ]
-          input_relations: [
-            dd_new_Q
-            dd_delta_S
-          ]
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf1_istrue_Q {
-          input_query: """
-          SELECT R0.id AS "dd_new_Q.R0.id" 
-          FROM dd_new_Q R0, dd_delta_S R1
-        WHERE R1.a = R0.x  AND R0.x = 0"""
-          function: "Imply(dd_new_Q.R0.label)"
-          weight: "1.0"
-          dependencies: [ "ext_dd_delta_S" ]
-          input_relations: [
-            dd_new_Q
-            dd_delta_S
-          ]
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_imply_Q_Q {
-          input_query: """
-          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" , R0.x AS "dd_weight_column_0" 
-          FROM dd_new_Q R0, dd_new_Q R1, dd_delta_S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  UNION ALL 
-          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" , R0.x AS "dd_weight_column_0" 
-          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_delta_R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  UNION ALL 
-          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" , R0.x AS "dd_weight_column_0" 
-          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_new_R R3, dd_delta_S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
-          function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
-          weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_new_R" ,  "ext_dd_new_S" ,  "ext_dd_delta_S" ]
-          input_relations: [
-            dd_new_Q
-            dd_delta_S
-            R
-            S
-            dd_new_S
-            dd_delta_R
-            dd_new_R
-          ]
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf1_imply_Q_Q {
-          input_query: """
-          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
-          FROM dd_new_Q R0, dd_new_Q R1, dd_delta_S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
-          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
-          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_delta_R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000 UNION ALL 
-          SELECT R0.id AS "dd_new_Q.R0.id" , R1.id AS "dd_new_Q.R1.id" 
-          FROM dd_new_Q R0, dd_new_Q R1, dd_new_S R2, dd_new_R R3, dd_delta_S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
-          function: "Imply(dd_new_Q.R0.label, dd_new_Q.R1.label)"
-          weight: "-10.0"
-          dependencies: [ "ext_dd_new_R" ,  "ext_dd_new_S" ,  "ext_dd_delta_S" ]
-          input_relations: [
-            dd_new_Q
-            dd_delta_S
-            R
-            S
-            dd_new_S
-            dd_delta_R
-            dd_new_R
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_dd_delta_T___1_by_f
-  ext_dd_new_T___3
-  ext_dd_new_R
-  ext_dd_new_T_2
-  ext_dd_delta_S_0_by_f
-  ext_dd_new_T___0
-  ext_dd_delta_T__3
-  ext_dd_new_S_2
-  ext_dd_delta_S_2_by_f_1
-  ext_dd_delta_S_1_by_f
-  ext_dd_delta_T
-  ext_dd_delta_S
-  ext_dd_new_T
-  ext_dd_new_S_0
-  ext_dd_new_T___2
-  ext_dd_delta_T___3_by_f_1
-  ext_dd_new_S
-  ext_dd_new_Q
-  ext_dd_delta_T___0_by_f
-  ext_dd_new_S_1
-  ext_dd_new_T___1
-  ext_dd_delta_T___2_by_f
-]
-deepdive.pipeline.pipelines.inference: [
-  dd_delta_inf_istrue_Q
-  dd_delta_inf1_istrue_Q
-  dd_delta_inf_imply_Q_Q
-  dd_delta_inf1_imply_Q_Q
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_dd_delta_T___1_by_f
-  ext_dd_new_T___3
-  ext_dd_new_R
-  ext_dd_new_T_2
-  ext_dd_delta_S_0_by_f
-  ext_dd_new_T___0
-  ext_dd_delta_T__3
-  ext_dd_new_S_2
-  ext_dd_delta_S_2_by_f_1
-  ext_dd_delta_S_1_by_f
-  ext_dd_delta_T
-  ext_dd_delta_S
-  ext_dd_new_T
-  ext_dd_new_S_0
-  ext_dd_new_T___2
-  ext_dd_delta_T___3_by_f_1
-  ext_dd_new_S
-  ext_dd_new_Q
-  ext_dd_delta_T___0_by_f
-  ext_dd_new_S_1
-  ext_dd_new_T___1
-  ext_dd_delta_T___2_by_f
-  dd_delta_inf_istrue_Q
-  dd_delta_inf1_istrue_Q
-  dd_delta_inf_imply_Q_Q
-  dd_delta_inf1_imply_Q_Q
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_new_S
-  init_dd_delta_S_0
-  init_dd_new_T___0
-  init_dd_delta_T
-  init_dd_new_T___1
-  init_dd_delta_T_2
-  init_dd_new_S_2
-  init_dd_new_T
-  init_dd_delta_S
-  init_dd_new_T___3
-  init_dd_delta_T___0
-  init_dd_new_R
-  init_dd_delta_S_2
-  init_dd_new_S_1
-  init_dd_delta_R
-  init_dd_new_T___2
-  init_dd_delta_T___3
-  init_dd_delta_S_1
-  init_dd_new_Q
-  init_dd_delta_T___1
-  init_dd_delta_Q
-  init_dd_new_T_2
-  init_dd_new_S_0
-  init_dd_delta_T___2
-]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index ad8122631..e49a3062a 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         Q.label: Boolean
       }
diff --git a/test/expected-output-test/ocr_example/compile-incremental.expected b/test/expected-output-test/ocr_example/compile-incremental.expected
deleted file mode 100644
index d4b8bd895..000000000
--- a/test/expected-output-test/ocr_example/compile-incremental.expected
+++ /dev/null
@@ -1,357 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: INCREMENTAL
-    }
-    
-
-      deepdive.schema.keys {
-        dd_new_q1 : [wid]
-        dd_delta_q2 : [wid]
-        dd_delta_q1 : [wid]
-        dd_new_q2 : [wid]
-      }
-
-      deepdive.schema.variables {
-        dd_delta_q1.label: Boolean
-dd_new_q2.label: Boolean
-dd_new_q1.label: Boolean
-q2.label: Boolean
-dd_delta_q2.label: Boolean
-q1.label: Boolean
-      }
-    
-
-          deepdive.extraction.extractors.init_dd_new_label2 {
-            sql: """ DROP TABLE IF EXISTS dd_new_label2 CASCADE;
-            CREATE TABLE
-            dd_new_label2(wid INT,
-             val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_label1 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_label1 CASCADE;
-            CREATE TABLE
-            dd_delta_label1(wid INT,
-               val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_label1 {
-            sql: """ DROP TABLE IF EXISTS dd_new_label1 CASCADE;
-            CREATE TABLE
-            dd_new_label1(wid INT,
-             val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_features CASCADE;
-            CREATE TABLE
-            dd_delta_features(id BIGSERIAL,
-                 word_id INT,
-                 feature_id INT,
-                 feature_val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_q2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_q2 CASCADE;
-            CREATE TABLE
-            dd_delta_q2(wid INT,
-           id bigint,
-           label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_label2 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_label2 CASCADE;
-            CREATE TABLE
-            dd_delta_label2(wid INT,
-               val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_features CASCADE;
-            CREATE TABLE
-            dd_new_features(id BIGSERIAL,
-               word_id INT,
-               feature_id INT,
-               feature_val BOOLEAN)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_q1 {
-            sql: """ DROP TABLE IF EXISTS dd_delta_q1 CASCADE;
-            CREATE TABLE
-            dd_delta_q1(wid INT,
-           id bigint,
-           label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_new_label2;
-          TRUNCATE dd_delta_label1;
-          TRUNCATE dd_new_label1;
-          TRUNCATE dd_delta_features;
-          TRUNCATE dd_delta_q2;
-          TRUNCATE dd_delta_label2;
-          TRUNCATE dd_new_features;
-          TRUNCATE dd_delta_q1;
-          """
-          style: "sql_extractor"
-        }
-
-      deepdive.extraction.extractors.ext_dd_new_label2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_label2"
-	deepdive sql 'INSERT INTO dd_new_label2 SELECT R0.wid, R0.val
-FROM label2 R0
-        
-UNION ALL
-SELECT R0.wid, R0.val
-FROM dd_delta_label2 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_label2"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            label2
-            dd_delta_label2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_q1 {
-        cmd: """
-
-	deepdive create view dd_new_q1 as 'SELECT DISTINCT R0.wid, id, label
-          FROM q1 R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.wid, id, label
-          FROM dd_delta_q1 R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_q1"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_q1" ]
-          input_relations: [
-            q1
-            dd_delta_q1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_label1 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_label1"
-	deepdive sql 'INSERT INTO dd_new_label1 SELECT R0.wid, R0.val
-FROM label1 R0
-        
-UNION ALL
-SELECT R0.wid, R0.val
-FROM dd_delta_label1 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_label1"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            label1
-            dd_delta_label1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_q2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_q2"
-	deepdive sql 'INSERT INTO dd_delta_q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
-          FROM dd_delta_label2 R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_q2"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_delta_label2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_features {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_features"
-	deepdive sql 'INSERT INTO dd_new_features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
-FROM features R0
-        
-UNION ALL
-SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
-FROM dd_delta_features R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_features"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            features
-            dd_delta_features
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_q1 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_q1"
-	deepdive sql 'INSERT INTO dd_delta_q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
-          FROM dd_delta_label1 R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_q1"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_delta_label1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_q2 {
-        cmd: """
-
-	deepdive create view dd_new_q2 as 'SELECT DISTINCT R0.wid, id, label
-          FROM q2 R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.wid, id, label
-          FROM dd_delta_q2 R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_q2"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_q2" ]
-          input_relations: [
-            q2
-            dd_delta_q2
-          ]
-      }
-    
-
-        deepdive.inference.factors.dd_delta_inf_istrue_q1 {
-          input_query: """
-          SELECT R0.id AS "dd_new_q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM dd_new_q1 R0, dd_delta_features R1
-        WHERE R1.word_id = R0.wid """
-          function: "Imply(dd_new_q1.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          
-          input_relations: [
-            dd_new_q1
-            dd_delta_features
-          ]
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_istrue_q2 {
-          input_query: """
-          SELECT R0.id AS "dd_new_q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM dd_new_q2 R0, dd_delta_features R1
-        WHERE R1.word_id = R0.wid """
-          function: "Imply(dd_new_q2.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          
-          input_relations: [
-            dd_new_q2
-            dd_delta_features
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_dd_delta_q1
-  ext_dd_new_q1
-  ext_dd_new_label1
-  ext_dd_new_features
-  ext_dd_delta_q2
-  ext_dd_new_label2
-  ext_dd_new_q2
-]
-deepdive.pipeline.pipelines.inference: [
-  dd_delta_inf_istrue_q1
-  dd_delta_inf_istrue_q2
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_dd_delta_q1
-  ext_dd_new_q1
-  ext_dd_new_label1
-  ext_dd_new_features
-  ext_dd_delta_q2
-  ext_dd_new_label2
-  ext_dd_new_q2
-  dd_delta_inf_istrue_q1
-  dd_delta_inf_istrue_q2
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_new_label2
-  init_dd_delta_label1
-  init_dd_new_q1
-  init_dd_new_label1
-  init_dd_delta_features
-  init_dd_delta_q2
-  init_dd_delta_label2
-  init_dd_new_features
-  init_dd_delta_q1
-  init_dd_new_q2
-]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/ocr_example/compile-materialization.expected b/test/expected-output-test/ocr_example/compile-materialization.expected
deleted file mode 100644
index a96559353..000000000
--- a/test/expected-output-test/ocr_example/compile-materialization.expected
+++ /dev/null
@@ -1,107 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: MATERIALIZATION
-    }
-    
-
-
-      deepdive.schema.variables {
-        q1.label: Boolean
-q2.label: Boolean
-      }
-    
-
-      deepdive.extraction.extractors.ext_q1 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "q1"
-	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
-          FROM label1 R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "q1"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            label1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_q2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "q2"
-	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
-          FROM label2 R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "q2"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            label2
-          ]
-      }
-    
-
-        deepdive.inference.factors.inf_istrue_q1 {
-          input_query: """
-          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM q1 R0, features R1
-        WHERE R1.word_id = R0.wid """
-          function: "Imply(q1.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          
-          input_relations: [
-            q1
-            features
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf_istrue_q2 {
-          input_query: """
-          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM q2 R0, features R1
-        WHERE R1.word_id = R0.wid """
-          function: "Imply(q2.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          
-          input_relations: [
-            q2
-            features
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_q1
-  ext_q2
-]
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_q1
-  inf_istrue_q2
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_q1
-  ext_q2
-  inf_istrue_q1
-  inf_istrue_q2
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/ocr_example/compile-merge.expected b/test/expected-output-test/ocr_example/compile-merge.expected
deleted file mode 100644
index e7becd7a6..000000000
--- a/test/expected-output-test/ocr_example/compile-merge.expected
+++ /dev/null
@@ -1,89 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: MERGE
-    }
-    
-
-
-      deepdive.schema.variables {
-        
-      }
-    
-
-      deepdive.extraction.extractors.ext_label2 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "label2"
-	deepdive sql 'INSERT INTO label2 SELECT R0.wid, R0.val
-FROM dd_new_label2 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "label2"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_label2
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_label1 {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "label1"
-	deepdive sql 'INSERT INTO label1 SELECT R0.wid, R0.val
-FROM dd_new_label1 R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "label1"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_label1
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_features {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "features"
-	deepdive sql 'INSERT INTO features SELECT R0.id, R0.word_id, R0.feature_id, R0.feature_val
-FROM dd_new_features R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "features"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_features
-          ]
-      }
-    
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_label2
-  ext_label1
-  ext_features
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_label2
-  ext_label1
-  ext_features
-]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index eaeb81d34..dcd4c5cfb 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         q1.label: Boolean
 q2.label: Boolean
diff --git a/test/expected-output-test/smoke_example/compile-incremental.expected b/test/expected-output-test/smoke_example/compile-incremental.expected
deleted file mode 100644
index 731011bfa..000000000
--- a/test/expected-output-test/smoke_example/compile-incremental.expected
+++ /dev/null
@@ -1,403 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: INCREMENTAL
-    }
-    
-
-      deepdive.schema.keys {
-        dd_delta_smoke : [person_id]
-        dd_new_smoke : [person_id]
-        dd_delta_cancer : [person_id]
-        dd_new_cancer : [person_id]
-      }
-
-      deepdive.schema.variables {
-        dd_new_smoke.label: Boolean
-smoke.label: Boolean
-cancer.label: Boolean
-dd_delta_cancer.label: Boolean
-dd_new_cancer.label: Boolean
-dd_delta_smoke.label: Boolean
-      }
-    
-
-          deepdive.extraction.extractors.init_dd_delta_friends {
-            sql: """ DROP TABLE IF EXISTS dd_delta_friends CASCADE;
-            CREATE TABLE
-            dd_delta_friends(person_id bigint,
-                friend_id bigint)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_smoke {
-            sql: """ DROP TABLE IF EXISTS dd_delta_smoke CASCADE;
-            CREATE TABLE
-            dd_delta_smoke(person_id bigint,
-              id bigint,
-              label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_person_has_cancer {
-            sql: """ DROP TABLE IF EXISTS dd_new_person_has_cancer CASCADE;
-            CREATE TABLE
-            dd_new_person_has_cancer(person_id bigint,
-                        has_cancer boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_person {
-            sql: """ DROP TABLE IF EXISTS dd_delta_person CASCADE;
-            CREATE TABLE
-            dd_delta_person(person_id bigint,
-               name text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_person {
-            sql: """ DROP TABLE IF EXISTS dd_new_person CASCADE;
-            CREATE TABLE
-            dd_new_person(person_id bigint,
-             name text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_person_has_cancer {
-            sql: """ DROP TABLE IF EXISTS dd_delta_person_has_cancer CASCADE;
-            CREATE TABLE
-            dd_delta_person_has_cancer(person_id bigint,
-                          has_cancer boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_cancer {
-            sql: """ DROP TABLE IF EXISTS dd_delta_cancer CASCADE;
-            CREATE TABLE
-            dd_delta_cancer(person_id bigint,
-               id bigint,
-               label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_person_smokes {
-            sql: """ DROP TABLE IF EXISTS dd_delta_person_smokes CASCADE;
-            CREATE TABLE
-            dd_delta_person_smokes(person_id bigint,
-                      smokes boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_person_smokes {
-            sql: """ DROP TABLE IF EXISTS dd_new_person_smokes CASCADE;
-            CREATE TABLE
-            dd_new_person_smokes(person_id bigint,
-                    smokes boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_friends {
-            sql: """ DROP TABLE IF EXISTS dd_new_friends CASCADE;
-            CREATE TABLE
-            dd_new_friends(person_id bigint,
-              friend_id bigint)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_friends;
-          TRUNCATE dd_delta_smoke;
-          TRUNCATE dd_new_person_has_cancer;
-          TRUNCATE dd_delta_person;
-          TRUNCATE dd_new_person;
-          TRUNCATE dd_delta_person_has_cancer;
-          TRUNCATE dd_delta_cancer;
-          TRUNCATE dd_delta_person_smokes;
-          TRUNCATE dd_new_person_smokes;
-          TRUNCATE dd_new_friends;
-          """
-          style: "sql_extractor"
-        }
-
-      deepdive.extraction.extractors.ext_dd_delta_smoke {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_smoke"
-	deepdive sql 'INSERT INTO dd_delta_smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
-          FROM dd_delta_person_smokes R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_smoke"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_delta_person_smokes
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_person_has_cancer {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_person_has_cancer"
-	deepdive sql 'INSERT INTO dd_new_person_has_cancer SELECT R0.person_id, R0.has_cancer
-FROM person_has_cancer R0
-        
-UNION ALL
-SELECT R0.person_id, R0.has_cancer
-FROM dd_delta_person_has_cancer R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_person_has_cancer"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            person_has_cancer
-            dd_delta_person_has_cancer
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_person {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_person"
-	deepdive sql 'INSERT INTO dd_new_person SELECT R0.person_id, R0.name
-FROM person R0
-        
-UNION ALL
-SELECT R0.person_id, R0.name
-FROM dd_delta_person R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_person"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            person
-            dd_delta_person
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_smoke {
-        cmd: """
-
-	deepdive create view dd_new_smoke as 'SELECT DISTINCT R0.person_id, id, label
-          FROM smoke R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.person_id, id, label
-          FROM dd_delta_smoke R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_smoke"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_smoke" ]
-          input_relations: [
-            smoke
-            dd_delta_smoke
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_cancer {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_cancer"
-	deepdive sql 'INSERT INTO dd_delta_cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
-          FROM dd_delta_person_has_cancer R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_cancer"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_delta_person_has_cancer
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_cancer {
-        cmd: """
-
-	deepdive create view dd_new_cancer as 'SELECT DISTINCT R0.person_id, id, label
-          FROM cancer R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.person_id, id, label
-          FROM dd_delta_cancer R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_cancer"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_cancer" ]
-          input_relations: [
-            cancer
-            dd_delta_cancer
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_person_smokes {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_person_smokes"
-	deepdive sql 'INSERT INTO dd_new_person_smokes SELECT R0.person_id, R0.smokes
-FROM person_smokes R0
-        
-UNION ALL
-SELECT R0.person_id, R0.smokes
-FROM dd_delta_person_smokes R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_person_smokes"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            person_smokes
-            dd_delta_person_smokes
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_friends {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_friends"
-	deepdive sql 'INSERT INTO dd_new_friends SELECT R0.person_id, R0.friend_id
-FROM friends R0
-        
-UNION ALL
-SELECT R0.person_id, R0.friend_id
-FROM dd_delta_friends R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_friends"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            friends
-            dd_delta_friends
-          ]
-      }
-    
-
-        deepdive.inference.factors.dd_delta_inf_imply_smoke_cancer {
-          input_query: """
-          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_cancer.R1.id" 
-          FROM dd_new_smoke R0, dd_new_cancer R1, dd_delta_person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(dd_new_smoke.R0.label, dd_new_cancer.R1.label)"
-          weight: "0.5"
-          
-          input_relations: [
-            dd_new_smoke
-            dd_new_cancer
-            dd_delta_person_smokes
-          ]
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_imply_smoke_smoke {
-          input_query: """
-          SELECT R0.id AS "dd_new_smoke.R0.id" , R1.id AS "dd_new_smoke.R1.id" 
-          FROM dd_new_smoke R0, dd_new_smoke R1, dd_delta_friends R2
-        WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
-          function: "Imply(dd_new_smoke.R0.label, dd_new_smoke.R1.label)"
-          weight: "0.4"
-          
-          input_relations: [
-            dd_new_smoke
-            dd_delta_friends
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_dd_delta_cancer
-  ext_dd_delta_smoke
-  ext_dd_new_person_smokes
-  ext_dd_new_person_has_cancer
-  ext_dd_new_cancer
-  ext_dd_new_person
-  ext_dd_new_friends
-  ext_dd_new_smoke
-]
-deepdive.pipeline.pipelines.inference: [
-  dd_delta_inf_imply_smoke_cancer
-  dd_delta_inf_imply_smoke_smoke
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_dd_delta_cancer
-  ext_dd_delta_smoke
-  ext_dd_new_person_smokes
-  ext_dd_new_person_has_cancer
-  ext_dd_new_cancer
-  ext_dd_new_person
-  ext_dd_new_friends
-  ext_dd_new_smoke
-  dd_delta_inf_imply_smoke_cancer
-  dd_delta_inf_imply_smoke_smoke
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_friends
-  init_dd_delta_smoke
-  init_dd_new_person_has_cancer
-  init_dd_delta_person
-  init_dd_new_person
-  init_dd_delta_person_has_cancer
-  init_dd_new_smoke
-  init_dd_delta_cancer
-  init_dd_new_cancer
-  init_dd_delta_person_smokes
-  init_dd_new_person_smokes
-  init_dd_new_friends
-]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/smoke_example/compile-materialization.expected b/test/expected-output-test/smoke_example/compile-materialization.expected
deleted file mode 100644
index 0857a07e3..000000000
--- a/test/expected-output-test/smoke_example/compile-materialization.expected
+++ /dev/null
@@ -1,108 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: MATERIALIZATION
-    }
-    
-
-
-      deepdive.schema.variables {
-        smoke.label: Boolean
-cancer.label: Boolean
-      }
-    
-
-      deepdive.extraction.extractors.ext_cancer {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "cancer"
-	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
-          FROM person_has_cancer R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "cancer"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            person_has_cancer
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_smoke {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "smoke"
-	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
-          FROM person_smokes R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "smoke"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            person_smokes
-          ]
-      }
-    
-
-        deepdive.inference.factors.inf_imply_smoke_cancer {
-          input_query: """
-          SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
-          FROM smoke R0, cancer R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(smoke.R0.label, cancer.R1.label)"
-          weight: "0.5"
-          
-          input_relations: [
-            smoke
-            cancer
-            person_smokes
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf_imply_smoke_smoke {
-          input_query: """
-          SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
-          FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
-          function: "Imply(smoke.R0.label, smoke.R1.label)"
-          weight: "0.4"
-          
-          input_relations: [
-            smoke
-            friends
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_cancer
-  ext_smoke
-]
-deepdive.pipeline.pipelines.inference: [
-  inf_imply_smoke_cancer
-  inf_imply_smoke_smoke
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_cancer
-  ext_smoke
-  inf_imply_smoke_cancer
-  inf_imply_smoke_smoke
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/smoke_example/compile-merge.expected b/test/expected-output-test/smoke_example/compile-merge.expected
deleted file mode 100644
index ab4760cce..000000000
--- a/test/expected-output-test/smoke_example/compile-merge.expected
+++ /dev/null
@@ -1,111 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: MERGE
-    }
-    
-
-
-      deepdive.schema.variables {
-        
-      }
-    
-
-      deepdive.extraction.extractors.ext_person_smokes {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "person_smokes"
-	deepdive sql 'INSERT INTO person_smokes SELECT R0.person_id, R0.smokes
-FROM dd_new_person_smokes R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "person_smokes"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_person_smokes
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_friends {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "friends"
-	deepdive sql 'INSERT INTO friends SELECT R0.person_id, R0.friend_id
-FROM dd_new_friends R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "friends"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_friends
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_person_has_cancer {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "person_has_cancer"
-	deepdive sql 'INSERT INTO person_has_cancer SELECT R0.person_id, R0.has_cancer
-FROM dd_new_person_has_cancer R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "person_has_cancer"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_person_has_cancer
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_person {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "person"
-	deepdive sql 'INSERT INTO person SELECT R0.person_id, R0.name
-FROM dd_new_person R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "person"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_person
-          ]
-      }
-    
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_person_smokes
-  ext_friends
-  ext_person_has_cancer
-  ext_person
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_person_smokes
-  ext_friends
-  ext_person_has_cancer
-  ext_person
-]
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 217f46d5b..765f6234c 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         smoke.label: Boolean
 cancer.label: Boolean
diff --git a/test/expected-output-test/spouse_example/compile-incremental.expected b/test/expected-output-test/spouse_example/compile-incremental.expected
deleted file mode 100644
index aedc3566e..000000000
--- a/test/expected-output-test/spouse_example/compile-incremental.expected
+++ /dev/null
@@ -1,483 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: INCREMENTAL
-    }
-    
-
-      deepdive.schema.keys {
-        dd_delta_has_spouse : [relation_id]
-        dd_new_has_spouse : [relation_id]
-      }
-
-      deepdive.schema.variables {
-        has_spouse.label: Boolean
-dd_delta_has_spouse.label: Boolean
-dd_new_has_spouse.label: Boolean
-      }
-    
-
-          deepdive.extraction.extractors.init_dd_delta_articles {
-            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-            CREATE TABLE
-            dd_delta_articles(article_id text,
-                 text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-            CREATE TABLE
-            dd_new_people_mentions(sentence_id text,
-                      start_position int,
-                      length int,
-                      text text,
-                      mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_features(relation_id text,
-                            feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_articles {
-            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-            CREATE TABLE
-            dd_new_articles(article_id text,
-               text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_candidates(person1_id text,
-                            person2_id text,
-                            sentence_id text,
-                            description text,
-                            relation_id text,
-                            is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_features(relation_id text,
-                          feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-            CREATE TABLE
-            dd_new_sentences(document_id text,
-                sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
-                sentence_offset int,
-                sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-            CREATE TABLE
-            dd_delta_people_mentions(sentence_id text,
-                        start_position int,
-                        length int,
-                        text text,
-                        mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_candidates(person1_id text,
-                              person2_id text,
-                              sentence_id text,
-                              description text,
-                              relation_id text,
-                              is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-            CREATE TABLE
-            dd_delta_sentences(document_id text,
-                  sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
-                  sentence_offset int,
-                  sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse(relation_id text,
-                   id bigint,
-                   label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_articles;
-          TRUNCATE dd_new_people_mentions;
-          TRUNCATE dd_delta_has_spouse_features;
-          TRUNCATE dd_new_articles;
-          TRUNCATE dd_new_has_spouse_candidates;
-          TRUNCATE dd_new_has_spouse_features;
-          TRUNCATE dd_new_sentences;
-          TRUNCATE dd_delta_people_mentions;
-          TRUNCATE dd_delta_has_spouse_candidates;
-          TRUNCATE dd_delta_sentences;
-          TRUNCATE dd_delta_has_spouse;
-          """
-          style: "sql_extractor"
-        }
-
-      deepdive.extraction.extractors.ext_dd_new_people_mentions {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_people_mentions"
-	deepdive sql 'INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM people_mentions R0
-        
-UNION ALL
-SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM dd_delta_people_mentions R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_people_mentions"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
-          input_relations: [
-            people_mentions
-            dd_delta_people_mentions
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_articles {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_articles"
-	deepdive sql 'INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
-FROM articles R0
-        
-UNION ALL
-SELECT R0.article_id, R0.text
-FROM dd_delta_articles R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_articles"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            articles
-            dd_delta_articles
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_has_spouse_candidates"
-	deepdive sql 'INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM has_spouse_candidates R0
-        
-UNION ALL
-SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM dd_delta_has_spouse_candidates R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_has_spouse_candidates"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            has_spouse_candidates
-            dd_delta_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_has_spouse_features"
-	deepdive sql 'INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
-FROM has_spouse_features R0
-        
-UNION ALL
-SELECT R0.relation_id, R0.feature
-FROM dd_delta_has_spouse_features R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_has_spouse_features"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            has_spouse_features
-            dd_delta_has_spouse_features
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_sentences {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_sentences"
-	deepdive sql 'INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM sentences R0
-        
-UNION ALL
-SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM dd_delta_sentences R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_sentences"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            sentences
-            dd_delta_sentences
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_has_spouse {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_has_spouse"
-	deepdive sql 'INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
-          FROM dd_delta_has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            dd_delta_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse {
-        cmd: """
-
-	deepdive create view dd_new_has_spouse as 'SELECT DISTINCT R0.relation_id, id, label
-          FROM has_spouse R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.relation_id, id, label
-          FROM dd_delta_has_spouse R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse" ]
-          input_relations: [
-            has_spouse
-            dd_delta_has_spouse
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_dd_delta_people_mentions_by_ext_people {
-          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM dd_delta_sentences R0
-        
-          """
-          output_relation: "dd_delta_people_mentions"
-          udf: ${APP_HOME}"/udf/ext_people.py"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_sentences
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_has_spouse_candidates_by_ext_has_spouse {
-          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-UNION ALL
-SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-          """
-          output_relation: "dd_delta_has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
-          input_relations: [
-            dd_delta_people_mentions
-            people_mentions
-            dd_new_people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_has_spouse_features_by_ext_has_spouse_features {
-          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-          """
-          output_relation: "dd_delta_has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
-          input_relations: [
-            dd_delta_sentences
-            has_spouse_candidates
-            people_mentions
-            dd_new_sentences
-            dd_delta_has_spouse_candidates
-            dd_new_has_spouse_candidates
-            dd_delta_people_mentions
-            dd_new_people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_istrue_has_spouse {
-          input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_new_has_spouse.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_has_spouse_candidates" ,  "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            dd_new_has_spouse
-            dd_delta_has_spouse_candidates
-            has_spouse_features
-            dd_new_has_spouse_candidates
-            dd_delta_has_spouse_features
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_dd_new_has_spouse_candidates
-  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
-  ext_dd_new_has_spouse
-  ext_dd_delta_has_spouse
-  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
-  ext_dd_new_has_spouse_features
-  ext_dd_delta_people_mentions_by_ext_people
-  ext_dd_new_people_mentions
-  ext_dd_new_sentences
-  ext_dd_new_articles
-]
-deepdive.pipeline.pipelines.inference: [
-  dd_delta_inf_istrue_has_spouse
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_dd_new_has_spouse_candidates
-  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
-  ext_dd_new_has_spouse
-  ext_dd_delta_has_spouse
-  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
-  ext_dd_new_has_spouse_features
-  ext_dd_delta_people_mentions_by_ext_people
-  ext_dd_new_people_mentions
-  ext_dd_new_sentences
-  ext_dd_new_articles
-  dd_delta_inf_istrue_has_spouse
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_articles
-  init_dd_new_people_mentions
-  init_dd_delta_has_spouse_features
-  init_dd_new_articles
-  init_dd_new_has_spouse_candidates
-  init_dd_new_has_spouse_features
-  init_dd_new_sentences
-  init_dd_delta_people_mentions
-  init_dd_delta_has_spouse_candidates
-  init_dd_delta_sentences
-  init_dd_delta_has_spouse
-  init_dd_new_has_spouse
-]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/spouse_example/compile-materialization.expected b/test/expected-output-test/spouse_example/compile-materialization.expected
deleted file mode 100644
index 3a3db96a4..000000000
--- a/test/expected-output-test/spouse_example/compile-materialization.expected
+++ /dev/null
@@ -1,126 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: MATERIALIZATION
-    }
-    
-
-
-      deepdive.schema.variables {
-        has_spouse.label: Boolean
-      }
-    
-
-      deepdive.extraction.extractors.ext_has_spouse {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
-          FROM has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            has_spouse_candidates
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
-          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM sentences R0
-        
-          """
-          output_relation: "people_mentions"
-          udf: ${APP_HOME}"/udf/ext_people.py"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            sentences
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
-          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-          """
-          output_relation: "has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_people_mentions_by_ext_people" ]
-          input_relations: [
-            people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
-          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-          """
-          output_relation: "has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
-          input_relations: [
-            sentences
-            has_spouse_candidates
-            people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.inference.factors.inf_istrue_has_spouse {
-          input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(has_spouse.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            has_spouse
-            has_spouse_candidates
-            has_spouse_features
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_has_spouse
-  ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
-  ext_has_spouse_features_by_ext_has_spouse_features
-]
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_has_spouse
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_has_spouse
-  ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
-  ext_has_spouse_features_by_ext_has_spouse_features
-  inf_istrue_has_spouse
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
diff --git a/test/expected-output-test/spouse_example/compile-merge.expected b/test/expected-output-test/spouse_example/compile-merge.expected
deleted file mode 100644
index dfd4a38b4..000000000
--- a/test/expected-output-test/spouse_example/compile-merge.expected
+++ /dev/null
@@ -1,133 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: MERGE
-    }
-    
-
-
-      deepdive.schema.variables {
-        
-      }
-    
-
-      deepdive.extraction.extractors.ext_sentences {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "sentences"
-	deepdive sql 'INSERT INTO sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM dd_new_sentences R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "sentences"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_sentences
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_has_spouse_candidates {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "has_spouse_candidates"
-	deepdive sql 'INSERT INTO has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM dd_new_has_spouse_candidates R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse_candidates"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_articles {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "articles"
-	deepdive sql 'INSERT INTO articles SELECT R0.article_id, R0.text
-FROM dd_new_articles R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "articles"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_articles
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_has_spouse_features {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "has_spouse_features"
-	deepdive sql 'INSERT INTO has_spouse_features SELECT R0.relation_id, R0.feature
-FROM dd_new_has_spouse_features R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse_features"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_has_spouse_features
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_people_mentions {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "people_mentions"
-	deepdive sql 'INSERT INTO people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM dd_new_people_mentions R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "people_mentions"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            dd_new_people_mentions
-          ]
-      }
-    
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_sentences
-  ext_people_mentions
-  ext_has_spouse_candidates
-  ext_has_spouse_features
-  ext_articles
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_sentences
-  ext_people_mentions
-  ext_has_spouse_candidates
-  ext_has_spouse_features
-  ext_articles
-]
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 5d4b5dbeb..70542e10f 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         has_spouse.label: Boolean
       }
diff --git a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected b/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
deleted file mode 100644
index 4a7ba4173..000000000
--- a/test/expected-output-test/spouse_example_new_feature/compile-incremental.expected
+++ /dev/null
@@ -1,488 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: INCREMENTAL
-    }
-    
-
-      deepdive.schema.keys {
-        dd_delta_has_spouse : [relation_id]
-        dd_new_has_spouse : [relation_id]
-      }
-
-      deepdive.schema.variables {
-        has_spouse.label: Boolean
-dd_delta_has_spouse.label: Boolean
-dd_new_has_spouse.label: Boolean
-      }
-    
-
-          deepdive.extraction.extractors.init_dd_delta_articles {
-            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-            CREATE TABLE
-            dd_delta_articles(article_id text,
-                 text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-            CREATE TABLE
-            dd_new_people_mentions(sentence_id text,
-                      start_position int,
-                      length int,
-                      text text,
-                      mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_features(relation_id text,
-                            feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_articles {
-            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-            CREATE TABLE
-            dd_new_articles(article_id text,
-               text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_candidates(person1_id text,
-                            person2_id text,
-                            sentence_id text,
-                            description text,
-                            relation_id text,
-                            is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_features(relation_id text,
-                          feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-            CREATE TABLE
-            dd_new_sentences(document_id text,
-                sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
-                sentence_offset int,
-                sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-            CREATE TABLE
-            dd_delta_people_mentions(sentence_id text,
-                        start_position int,
-                        length int,
-                        text text,
-                        mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_candidates(person1_id text,
-                              person2_id text,
-                              sentence_id text,
-                              description text,
-                              relation_id text,
-                              is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-            CREATE TABLE
-            dd_delta_sentences(document_id text,
-                  sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
-                  sentence_offset int,
-                  sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse(relation_id text,
-                   id bigint,
-                   label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_articles;
-          TRUNCATE dd_new_people_mentions;
-          TRUNCATE dd_delta_has_spouse_features;
-          TRUNCATE dd_new_articles;
-          TRUNCATE dd_new_has_spouse_candidates;
-          TRUNCATE dd_new_has_spouse_features;
-          TRUNCATE dd_new_sentences;
-          TRUNCATE dd_delta_people_mentions;
-          TRUNCATE dd_delta_has_spouse_candidates;
-          TRUNCATE dd_delta_sentences;
-          TRUNCATE dd_delta_has_spouse;
-          """
-          style: "sql_extractor"
-        }
-
-      deepdive.extraction.extractors.ext_dd_new_people_mentions {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_people_mentions"
-	deepdive sql 'INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM people_mentions R0
-        
-UNION ALL
-SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM dd_delta_people_mentions R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_people_mentions"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
-          input_relations: [
-            people_mentions
-            dd_delta_people_mentions
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_articles {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_articles"
-	deepdive sql 'INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
-FROM articles R0
-        
-UNION ALL
-SELECT R0.article_id, R0.text
-FROM dd_delta_articles R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_articles"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            articles
-            dd_delta_articles
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_has_spouse_candidates"
-	deepdive sql 'INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM has_spouse_candidates R0
-        
-UNION ALL
-SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM dd_delta_has_spouse_candidates R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_has_spouse_candidates"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            has_spouse_candidates
-            dd_delta_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_has_spouse_features"
-	deepdive sql 'INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
-FROM has_spouse_features R0
-        
-UNION ALL
-SELECT R0.relation_id, R0.feature
-FROM dd_delta_has_spouse_features R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_has_spouse_features"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            has_spouse_features
-            dd_delta_has_spouse_features
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_sentences {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_sentences"
-	deepdive sql 'INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM sentences R0
-        
-UNION ALL
-SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM dd_delta_sentences R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_sentences"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            sentences
-            dd_delta_sentences
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_has_spouse {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_has_spouse"
-	deepdive sql 'INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
-          FROM dd_delta_has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            dd_delta_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse {
-        cmd: """
-
-	deepdive create view dd_new_has_spouse as 'SELECT DISTINCT R0.relation_id, id, label
-          FROM has_spouse R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.relation_id, id, label
-          FROM dd_delta_has_spouse R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse" ]
-          input_relations: [
-            has_spouse
-            dd_delta_has_spouse
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_dd_delta_people_mentions_by_ext_people {
-          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM dd_delta_sentences R0
-        
-          """
-          output_relation: "dd_delta_people_mentions"
-          udf: ${APP_HOME}"/udf/ext_people.py"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_sentences
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_has_spouse_candidates_by_ext_has_spouse {
-          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-UNION ALL
-SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-          """
-          output_relation: "dd_delta_has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
-          input_relations: [
-            dd_delta_people_mentions
-            people_mentions
-            dd_new_people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_has_spouse_features_by_ext_has_spouse_features {
-          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-          """
-          output_relation: "dd_delta_has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
-          input_relations: [
-            sentences
-            has_spouse_candidates
-            people_mentions
-            dd_delta_sentences
-            dd_new_sentences
-            dd_delta_has_spouse_candidates
-            dd_new_has_spouse_candidates
-            dd_delta_people_mentions
-            dd_new_people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_istrue_has_spouse {
-          input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_new_has_spouse.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_has_spouse_candidates" ,  "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            dd_new_has_spouse
-            dd_delta_has_spouse_candidates
-            has_spouse_features
-            dd_new_has_spouse_candidates
-            dd_delta_has_spouse_features
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_dd_new_has_spouse_candidates
-  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
-  ext_dd_new_has_spouse
-  ext_dd_delta_has_spouse
-  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
-  ext_dd_new_has_spouse_features
-  ext_dd_delta_people_mentions_by_ext_people
-  ext_dd_new_people_mentions
-  ext_dd_new_sentences
-  ext_dd_new_articles
-]
-deepdive.pipeline.pipelines.inference: [
-  dd_delta_inf_istrue_has_spouse
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_dd_new_has_spouse_candidates
-  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
-  ext_dd_new_has_spouse
-  ext_dd_delta_has_spouse
-  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
-  ext_dd_new_has_spouse_features
-  ext_dd_delta_people_mentions_by_ext_people
-  ext_dd_new_people_mentions
-  ext_dd_new_sentences
-  ext_dd_new_articles
-  dd_delta_inf_istrue_has_spouse
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_articles
-  init_dd_new_people_mentions
-  init_dd_delta_has_spouse_features
-  init_dd_new_articles
-  init_dd_new_has_spouse_candidates
-  init_dd_new_has_spouse_features
-  init_dd_new_sentences
-  init_dd_delta_people_mentions
-  init_dd_delta_has_spouse_candidates
-  init_dd_delta_sentences
-  init_dd_delta_has_spouse
-  init_dd_new_has_spouse
-]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected b/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
deleted file mode 100644
index dd9e085bd..000000000
--- a/test/expected-output-test/spouse_example_new_inference/compile-incremental.expected
+++ /dev/null
@@ -1,500 +0,0 @@
-
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: INCREMENTAL
-    }
-    
-
-      deepdive.schema.keys {
-        dd_delta_has_spouse : [relation_id]
-        dd_new_has_spouse : [relation_id]
-      }
-
-      deepdive.schema.variables {
-        has_spouse.label: Boolean
-dd_delta_has_spouse.label: Boolean
-dd_new_has_spouse.label: Boolean
-      }
-    
-
-          deepdive.extraction.extractors.init_dd_delta_articles {
-            sql: """ DROP TABLE IF EXISTS dd_delta_articles CASCADE;
-            CREATE TABLE
-            dd_delta_articles(article_id text,
-                 text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_new_people_mentions CASCADE;
-            CREATE TABLE
-            dd_new_people_mentions(sentence_id text,
-                      start_position int,
-                      length int,
-                      text text,
-                      mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_features(relation_id text,
-                            feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_articles {
-            sql: """ DROP TABLE IF EXISTS dd_new_articles CASCADE;
-            CREATE TABLE
-            dd_new_articles(article_id text,
-               text text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_candidates(person1_id text,
-                            person2_id text,
-                            sentence_id text,
-                            description text,
-                            relation_id text,
-                            is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_has_spouse_features {
-            sql: """ DROP TABLE IF EXISTS dd_new_has_spouse_features CASCADE;
-            CREATE TABLE
-            dd_new_has_spouse_features(relation_id text,
-                          feature text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_new_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_new_sentences CASCADE;
-            CREATE TABLE
-            dd_new_sentences(document_id text,
-                sentence text,
-                words text[],
-                lemma text[],
-                pos_tags text[],
-                dependencies text[],
-                ner_tags text[],
-                sentence_offset int,
-                sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_people_mentions {
-            sql: """ DROP TABLE IF EXISTS dd_delta_people_mentions CASCADE;
-            CREATE TABLE
-            dd_delta_people_mentions(sentence_id text,
-                        start_position int,
-                        length int,
-                        text text,
-                        mention_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse_candidates {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse_candidates CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse_candidates(person1_id text,
-                              person2_id text,
-                              sentence_id text,
-                              description text,
-                              relation_id text,
-                              is_true boolean)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_sentences {
-            sql: """ DROP TABLE IF EXISTS dd_delta_sentences CASCADE;
-            CREATE TABLE
-            dd_delta_sentences(document_id text,
-                  sentence text,
-                  words text[],
-                  lemma text[],
-                  pos_tags text[],
-                  dependencies text[],
-                  ner_tags text[],
-                  sentence_offset int,
-                  sentence_id text)
-            """
-            style: "sql_extractor"
-          }
-
-          deepdive.extraction.extractors.init_dd_delta_has_spouse {
-            sql: """ DROP TABLE IF EXISTS dd_delta_has_spouse CASCADE;
-            CREATE TABLE
-            dd_delta_has_spouse(relation_id text,
-                   id bigint,
-                   label boolean)
-            """
-            style: "sql_extractor"
-          }
-
-        deepdive.extraction.extractors.cleanup {
-          sql: """
-          TRUNCATE dd_delta_articles;
-          TRUNCATE dd_new_people_mentions;
-          TRUNCATE dd_delta_has_spouse_features;
-          TRUNCATE dd_new_articles;
-          TRUNCATE dd_new_has_spouse_candidates;
-          TRUNCATE dd_new_has_spouse_features;
-          TRUNCATE dd_new_sentences;
-          TRUNCATE dd_delta_people_mentions;
-          TRUNCATE dd_delta_has_spouse_candidates;
-          TRUNCATE dd_delta_sentences;
-          TRUNCATE dd_delta_has_spouse;
-          """
-          style: "sql_extractor"
-        }
-
-      deepdive.extraction.extractors.ext_dd_new_people_mentions {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_people_mentions"
-	deepdive sql 'INSERT INTO dd_new_people_mentions SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM people_mentions R0
-        
-UNION ALL
-SELECT R0.sentence_id, R0.start_position, R0.length, R0.text, R0.mention_id
-FROM dd_delta_people_mentions R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_people_mentions"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ]
-          input_relations: [
-            people_mentions
-            dd_delta_people_mentions
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_articles {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_articles"
-	deepdive sql 'INSERT INTO dd_new_articles SELECT R0.article_id, R0.text
-FROM articles R0
-        
-UNION ALL
-SELECT R0.article_id, R0.text
-FROM dd_delta_articles R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_articles"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            articles
-            dd_delta_articles
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse_candidates {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_has_spouse_candidates"
-	deepdive sql 'INSERT INTO dd_new_has_spouse_candidates SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM has_spouse_candidates R0
-        
-UNION ALL
-SELECT R0.person1_id, R0.person2_id, R0.sentence_id, R0.description, R0.relation_id, R0.is_true
-FROM dd_delta_has_spouse_candidates R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_has_spouse_candidates"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            has_spouse_candidates
-            dd_delta_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse_features {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_has_spouse_features"
-	deepdive sql 'INSERT INTO dd_new_has_spouse_features SELECT R0.relation_id, R0.feature
-FROM has_spouse_features R0
-        
-UNION ALL
-SELECT R0.relation_id, R0.feature
-FROM dd_delta_has_spouse_features R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_has_spouse_features"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            has_spouse_features
-            dd_delta_has_spouse_features
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_sentences {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_new_sentences"
-	deepdive sql 'INSERT INTO dd_new_sentences SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM sentences R0
-        
-UNION ALL
-SELECT R0.document_id, R0.sentence, R0.words, R0.lemma, R0.pos_tags, R0.dependencies, R0.ner_tags, R0.sentence_offset, R0.sentence_id
-FROM dd_delta_sentences R0
-        '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_new_sentences"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            sentences
-            dd_delta_sentences
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_delta_has_spouse {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "dd_delta_has_spouse"
-	deepdive sql 'INSERT INTO dd_delta_has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
-          FROM dd_delta_has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "dd_delta_has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            dd_delta_has_spouse_candidates
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_dd_new_has_spouse {
-        cmd: """
-
-	deepdive create view dd_new_has_spouse as 'SELECT DISTINCT R0.relation_id, id, label
-          FROM has_spouse R0
-        
-          
-UNION ALL
-SELECT DISTINCT R0.relation_id, id, label
-          FROM dd_delta_has_spouse R0
-        
-          '
-	
-        """
-          output_relation: "dd_new_has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_dd_delta_has_spouse" ]
-          input_relations: [
-            has_spouse
-            dd_delta_has_spouse
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_dd_delta_people_mentions_by_ext_people {
-          input: """ SELECT R0.sentence_id AS "dd_delta_sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM dd_delta_sentences R0
-        
-          """
-          output_relation: "dd_delta_people_mentions"
-          udf: ${APP_HOME}"/udf/ext_people.py"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            dd_delta_sentences
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_has_spouse_candidates_by_ext_has_spouse {
-          input: """ SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM dd_delta_people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-UNION ALL
-SELECT R0.sentence_id AS "dd_delta_people_mentions.R0.sentence_id", R0.mention_id AS "dd_delta_people_mentions.R0.mention_id", R0.text AS "dd_delta_people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM dd_new_people_mentions R0, dd_delta_people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-          """
-          output_relation: "dd_delta_has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ]
-          input_relations: [
-            dd_delta_people_mentions
-            people_mentions
-            dd_new_people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_dd_delta_has_spouse_features_by_ext_has_spouse_features {
-          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_delta_sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_delta_has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_delta_people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-UNION ALL
-SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM dd_new_sentences R0, dd_new_has_spouse_candidates R1, dd_new_people_mentions R2, dd_delta_people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-          """
-          output_relation: "dd_delta_has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
-          style: "tsv_extractor" 
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_sentences" ,  "ext_dd_delta_people_mentions_by_ext_people" ,  "ext_dd_new_people_mentions" ,  "ext_dd_new_has_spouse_candidates" ]
-          input_relations: [
-            dd_delta_sentences
-            has_spouse_candidates
-            people_mentions
-            dd_new_sentences
-            dd_delta_has_spouse_candidates
-            dd_new_has_spouse_candidates
-            dd_delta_people_mentions
-            dd_new_people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_istrue_has_spouse {
-          input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM dd_new_has_spouse R0, dd_delta_has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id  UNION ALL 
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM dd_new_has_spouse R0, dd_new_has_spouse_candidates R1, dd_delta_has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(dd_new_has_spouse.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_dd_delta_has_spouse_candidates_by_ext_has_spouse" ,  "ext_dd_new_has_spouse_candidates" ,  "ext_dd_delta_has_spouse_features_by_ext_has_spouse_features" ]
-          input_relations: [
-            dd_new_has_spouse
-            dd_delta_has_spouse_candidates
-            has_spouse_features
-            dd_new_has_spouse_candidates
-            dd_delta_has_spouse_features
-          ]
-        }
-      
-
-        deepdive.inference.factors.dd_delta_inf_equal_has_spouse_has_spouse {
-          input_query: """
-          SELECT R0.id AS "dd_new_has_spouse.R0.id" , R1.id AS "dd_new_has_spouse.R1.id" 
-          FROM dd_new_has_spouse R0, dd_new_has_spouse R1, dd_new_has_spouse_candidates R2, dd_new_has_spouse_candidates R3
-        WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
-          function: "Equal(dd_new_has_spouse.R0.label, dd_new_has_spouse.R1.label)"
-          weight: "3.0"
-          dependencies: [ "ext_dd_new_has_spouse_candidates" ]
-          input_relations: [
-            dd_new_has_spouse
-            dd_new_has_spouse_candidates
-          ]
-        }
-      
-deepdive.pipeline.run: ${PIPELINE}
-deepdive.pipeline.pipelines.extraction: [
-  ext_dd_new_has_spouse_candidates
-  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
-  ext_dd_new_has_spouse
-  ext_dd_delta_has_spouse
-  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
-  ext_dd_new_has_spouse_features
-  ext_dd_delta_people_mentions_by_ext_people
-  ext_dd_new_people_mentions
-  ext_dd_new_sentences
-  ext_dd_new_articles
-]
-deepdive.pipeline.pipelines.inference: [
-  dd_delta_inf_istrue_has_spouse
-  dd_delta_inf_equal_has_spouse_has_spouse
-]
-deepdive.pipeline.pipelines.endtoend: [
-  ext_dd_new_has_spouse_candidates
-  ext_dd_delta_has_spouse_candidates_by_ext_has_spouse
-  ext_dd_new_has_spouse
-  ext_dd_delta_has_spouse
-  ext_dd_delta_has_spouse_features_by_ext_has_spouse_features
-  ext_dd_new_has_spouse_features
-  ext_dd_delta_people_mentions_by_ext_people
-  ext_dd_new_people_mentions
-  ext_dd_new_sentences
-  ext_dd_new_articles
-  dd_delta_inf_istrue_has_spouse
-  dd_delta_inf_equal_has_spouse_has_spouse
-]
-deepdive.pipeline.base_dir: ${BASEDIR}
-deepdive.pipeline.pipelines.initdb: [
-  init_dd_delta_articles
-  init_dd_new_people_mentions
-  init_dd_delta_has_spouse_features
-  init_dd_new_articles
-  init_dd_new_has_spouse_candidates
-  init_dd_new_has_spouse_features
-  init_dd_new_sentences
-  init_dd_delta_people_mentions
-  init_dd_delta_has_spouse_candidates
-  init_dd_delta_sentences
-  init_dd_delta_has_spouse
-  init_dd_new_has_spouse
-]
-deepdive.pipeline.pipelines.cleanup: [
-  cleanup
-]
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 38beb2384..bcbc4579f 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         has_spouse.label: Boolean
       }
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index f738ff7f6..e85b48f77 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         
       }
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index cd650b0fc..51ea9eae8 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -1,17 +1,4 @@
 
-  deepdive.db.default {
-    driver: "org.postgresql.Driver"
-    url: "jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}
-    user: ${PGUSER}
-    password: ${PGPASSWORD}
-    dbname: ${DBNAME}
-    host: ${PGHOST}
-    port: ${PGPORT}
-    incremental_mode: ORIGINAL
-    }
-    
-
-
       deepdive.schema.variables {
         a.label: Boolean
 f.label: Boolean

From 6976fc7af48dc1cdb19b06c9ab0e2ae086c7c7c9 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 01:58:15 -0800
Subject: [PATCH 292/347] Rewrites vars into vals in compiler and some other
 cleanups

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 135 ++++--------------
 1 file changed, 28 insertions(+), 107 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d855b4d32..a97afceca 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -3,61 +3,6 @@ package org.deepdive.ddlog
 // DeepDiveLog compiler
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
-// TODO update the following comment to new syntax.
-/*
- This file parses an extended form of datalog like sugar.
-
- It allows schema declarations
-
- SomeOther(realname, otherattribute)
-
- And queries
-
- Q(x,y) :- R(x,y), SomeOther(y, z)
-
- Using the schema can SQLized as
-
- SELECT R1.x,R2.y
- FROM   R as R1,SomeOther as R2
- WHERE  R1.y = R2.realname
-
- We translate by introducing aliases R1, R2 , etc. to deal with
- repeated symbols.
-
- TODO:
- =================
-
- Our schema needs to know whether a symbol is this a query table (and
- so should contain an _id) field or is a regular table from the
- user.
-
- If a head term is not mentioned in the schema, its assumed it is a
- query table that this code must create.
-
- If one wants to explicilty mention a query table in the schema, they
- do so with a trailing exclamation point as follows
-
- Q(x,y)!;
-
-Consider
-
- Q(x) :- R(x,f) weight=f
-
- ... R is likely *not* a variable table ... we record its translation below.
-
- In contrast, Q(x) :- R(x),S(x) ... coule be treated as variable tables. Hence, the schema has:
-
- R(x,f) // regular table
- R(x,f)! // variable table.
-
- */
-
-/* TODOs:
-
- Refactor schema object and introduce error checking (unsafe queries,
- unordered attributes, etc.).
-*/
-
 import scala.collection.immutable.HashMap
 import org.apache.commons.lang3.StringEscapeUtils
 import scala.collection.mutable.ListBuffer
@@ -72,22 +17,17 @@ object AliasStyle extends Enumeration {
 }
 import AliasStyle._
 
-// This handles the schema statements.
-// It can tell you if a predicate is a "query" predicate or a "ground prediate"
-// and it resolves Variables their correct and true name in the schema, i.e. R(x,y) then x could be Attribute1 declared.
 class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.Config )  {
-    // TODO: refactor the schema into a class that constructs and
-    // manages these maps. Also it should have appropriate
-    // abstractions and error handling for missing values.
-    // ** Start refactor.
-  var schema : Map[ Tuple2[String,Int], String ] = new HashMap[ Tuple2[String,Int], String ]()
-
-  var ground_relations : Map[ String, Boolean ]  = new HashMap[ String, Boolean ]()
-
-  // map relation name -> variable type
-  var variableType : Map[String, VariableType]   = new HashMap[String, VariableType]()
+  val attrNameForRelationAndPosition: Map[ Tuple2[String,Int], String ] =
+    (statements collect {
+      case decl: SchemaDeclaration =>
+        decl.a.terms.zipWithIndex.map { case (n, i) => (decl.a.name, i) -> n }
+    } flatten) toMap
 
-  var function_schema : Map[String, FunctionDeclaration] = new HashMap[ String, FunctionDeclaration]()
+  val functionDeclarationByName: Map[String, FunctionDeclaration] =
+    statements collect {
+      case fdecl: FunctionDeclaration => fdecl.functionName -> fdecl
+    } toMap
 
   // The dependency graph between statements.
   var dependencies : Map[Statement, Set[Statement]] = new HashMap()
@@ -106,20 +46,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   def init() = {
     // generate the statements.
-    statements.foreach {
-      case decl: SchemaDeclaration => {
-        val r = decl.a.name
-        decl.a.terms.zipWithIndex.foreach {
-          case (n, i) =>
-            schema           += { (r, i) -> n }
-            ground_relations += { r -> !decl.isQuery } // record whether a query or a ground term.
-            if (decl.isQuery) variableType += { r -> decl.variableType.get }
-        }
-        if (decl.isQuery) variableTableNames += r
-      }
-      case fdecl : FunctionDeclaration => function_schema += {fdecl.functionName -> fdecl}
-      case _ =>
-    }
     functionCallList = statements collect { case s: FunctionCallRule => s }
     inferenceRules   = statements collect { case s: InferenceRule    => s }
     groupByHead(statements)
@@ -129,6 +55,10 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   init()
 
+  def schemaDeclaration(name: String): Option[SchemaDeclaration] = {
+    schemaDeclarationGroupByHead get (name) map (_(0))
+  }
+
   def error(message: String) {
     throw new RuntimeException(message)
   }
@@ -172,8 +102,8 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   // odd has happened.
   def resolveName( v : Variable ) : String = {
     v match { case Variable(v,relName,i) =>
-      if(schema contains (relName,i)) {
-        schema(relName,i)
+      if(attrNameForRelationAndPosition contains (relName,i)) {
+        attrNameForRelationAndPosition(relName,i)
       } else {
         // for views, columns names are in the form of "column_index"
         return s"column_${i}"
@@ -181,15 +111,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     }
   }
 
-  def resolveFunctionName( v : String ) : FunctionDeclaration = {
-    function_schema(v)
-  }
-
-  // The default is query term.
-  def isQueryTerm( relName : String ): Boolean = {
-    if( ground_relations contains relName ) !ground_relations(relName) else true
-  }
-
   // has schema declared
   def hasSchemaDeclared(relName: String) : Boolean = {
     schemaDeclarationGroupByHead contains relName
@@ -418,7 +339,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
               // expression patterns indicate a filter condition on the column
               case ExprPattern(expr) => {
                 val resolved = compileExpr(expr)
-                val attr = ss.schema(relName, termIndex)
+                val attr = ss.attrNameForRelationAndPosition(relName, termIndex)
                 Some(s"R${bodyIndex}.${attr} = ${resolved}")
               }
             }
@@ -633,7 +554,7 @@ ${if (createTable) {
     var extractors = new ListBuffer[String]()
     for (stmt <- stmts) {
 
-      val function = ss.resolveFunctionName(stmt.function)
+      val function = ss.functionDeclarationByName(stmt.function)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
           s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
@@ -692,7 +613,7 @@ ${if (createTable) {
         // TODO self-join?
         val varInBody = (fakeBody.zipWithIndex flatMap {
           case (x: BodyAtom, i) =>
-            if (ss.variableTableNames contains x.name)
+            if (ss.schemaDeclaration(x.name) map(_.isQuery) getOrElse(false))
               Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
             else
               None
@@ -724,10 +645,11 @@ ${if (createTable) {
             case FactorFunction.Equal()  => "Equal"
             case FactorFunction.Linear() => "Linear"
             case FactorFunction.Ratio()  => "Ratio"
-            case FactorFunction.IsTrue() => ss.variableType get stmt.head.terms(0).name match {
-              case Some(BooleanType())        => "Imply"
-              case Some(MultinomialType(_)) => "Multinomial"
-            }
+            case FactorFunction.IsTrue() =>
+              ss.schemaDeclaration(stmt.head.terms(0).name) map(_.variableType) match {
+                case Some(Some(MultinomialType(_))) => "Multinomial"
+                case _ => "Imply" // TODO fix to IsTrue
+              }
             case FactorFunction.Multinomial() => "Multinomial"
           }
           func = s"""${function}(${funcBody.mkString(", ")})"""
@@ -810,16 +732,15 @@ ${if (createTable) {
     // take an initial pass to analyze the parsed program
     val state = new CompilationState( programToCompile, config )
 
-    val body = new ListBuffer[String]()
-    state.extractionRuleGroupByHead foreach {keyVal => body ++= compileExtractionRules(keyVal._2, state)}
-    state.functionCallList          foreach {func   => body ++= compileFunctionCallRules(List(func), state)}
-    state.inferenceRules            foreach {inf    => body ++= compileInferenceRules(List(inf), state)}
-
     // compile the program into blocks of application.conf
     val blocks = (
       compileVariableSchema(programToCompile, state)
       :::
-      body.toList
+        (state.extractionRuleGroupByHead.values.toList flatMap (compileExtractionRules(_, state)))
+      :::
+        (state.functionCallList flatMap { fncall => compileFunctionCallRules(List(fncall), state)})
+      :::
+        (state.inferenceRules flatMap {inf => compileInferenceRules(List(inf), state)})
       :::
       compilePipelines(state)
     )

From 4dbeea0e6db257667c57960284ccbf48b356113f Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 03:13:33 -0800
Subject: [PATCH 293/347] Rewrites vars to vals in compilation state class

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 150 +++++-------
 .../arrays/compile.expected                   |  16 +-
 .../chunking_example/compile.expected         |  46 ++--
 .../expressions/compile.expected              | 226 +++++++++---------
 .../if-then-else/compile.expected             |  50 ++--
 .../compile.expected                          |  62 ++---
 .../smoke_example/compile.expected            |  24 +-
 .../spouse_example/compile.expected           |  46 ++--
 .../compile.expected                          |  46 ++--
 9 files changed, 312 insertions(+), 354 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a97afceca..2aa66a4a3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -29,35 +29,29 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case fdecl: FunctionDeclaration => fdecl.functionName -> fdecl
     } toMap
 
-  // The dependency graph between statements.
-  var dependencies : Map[Statement, Set[Statement]] = new HashMap()
+  val schemaDeclarationByRelationName: Map[String, SchemaDeclaration] =
+    statements collect {
+      case decl: SchemaDeclaration => decl.a.name -> decl
+    } toMap
 
-  // The statement whether will compile or union to other statements
-  var visible : Set[Statement] = Set()
+  val inferenceRules = statements collect { case s: InferenceRule => s }
 
-  var variableTableNames : Set[String] = Set()
+  val statementsByHeadName: Map[String, List[Statement]] =
+    statements collect {
+      case s: ExtractionRule       => s.headName -> s
+      case s: FunctionCallRule     => s.output -> s
+    } groupBy(_._1) mapValues(_ map {_._2})
 
-  // Mapping head names to the actual statements
-  var schemaDeclarationGroupByHead  : Map[String, List[SchemaDeclaration]] = new HashMap[String, List[SchemaDeclaration]]()
-  var extractionRuleGroupByHead     : Map[String, List[ExtractionRule]] = new HashMap[String, List[ExtractionRule]]()
-  var functionCallRuleGroupByOutput : Map[String, List[FunctionCallRule]] = new HashMap[String, List[FunctionCallRule]]()
-  var functionCallList              : List[FunctionCallRule] = Nil
-  var inferenceRules                : List[InferenceRule] = Nil
+  val statementsByRepresentative: Map[Statement, List[Statement]] =
+    statementsByHeadName map { case (name, stmts) => stmts(0) -> stmts }
 
-  def init() = {
-    // generate the statements.
-    functionCallList = statements collect { case s: FunctionCallRule => s }
-    inferenceRules   = statements collect { case s: InferenceRule    => s }
-    groupByHead(statements)
-    analyzeVisible(statements)
-    analyzeDependency(statements)
-  }
+  val representativeStatements : Set[Statement] =
+    statementsByHeadName.values map { _(0) } toSet
 
-  init()
+  // The dependency graph between statements.
+  var dependencies : Map[Statement, Set[Statement]] = new HashMap()
 
-  def schemaDeclaration(name: String): Option[SchemaDeclaration] = {
-    schemaDeclarationGroupByHead get (name) map (_(0))
-  }
+  analyzeDependency(statements)
 
   def error(message: String) {
     throw new RuntimeException(message)
@@ -74,7 +68,9 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       // Extra numbering is necessary because there can be many function calls to the same head relation
       // XXX This comes right after the prefix to prevent potential collision with user's name
       val functionCallsForSameOutputAndFunction =
-        (functionCallRuleGroupByOutput getOrElse(f.output, Set.empty) toList).filter (_.function == f.function)
+        statementsByHeadName getOrElse(f.output, List.empty) filter {
+          case s:FunctionCallRule => s.function == f.function
+        }
       val idx = functionCallsForSameOutputAndFunction indexOf f
       optionalIndex(idx)
     }_${f.output}_by_${f.function}"
@@ -113,45 +109,16 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // has schema declared
   def hasSchemaDeclared(relName: String) : Boolean = {
-    schemaDeclarationGroupByHead contains relName
-  }
-
-  // Group statements by head
-  def groupByHead(statements: List[Statement]) = {
-    // Compile compilation states by head name based on type
-    val schemaDeclarationToCompile = new ListBuffer[SchemaDeclaration]()
-    val extractionRuleToCompile    = new ListBuffer[ExtractionRule]()
-    val inferenceRuleToCompile     = new ListBuffer[InferenceRule]()
-    val functionCallRuleToCompile  = new ListBuffer[FunctionCallRule]()
-
-    statements foreach (_ match {
-      case s: SchemaDeclaration    => schemaDeclarationToCompile += s
-      case s: ExtractionRule       => extractionRuleToCompile += s
-      case s: FunctionCallRule     => functionCallRuleToCompile += s
-      case s: InferenceRule        => inferenceRuleToCompile += s
-      case _                       =>
-    })
-
-    schemaDeclarationGroupByHead = schemaDeclarationToCompile.toList.groupBy(_.a.name)
-    extractionRuleGroupByHead      = extractionRuleToCompile.toList.groupBy(_.headName)
-    functionCallRuleGroupByOutput  = functionCallRuleToCompile.toList.groupBy(_.output)
-  }
-
-  // Analyze the block visibility among statements
-  def analyzeVisible(statements: List[Statement]) = {
-    extractionRuleGroupByHead.values foreach { visible += _(0) }
-    functionCallList foreach { visible += _ }
+    schemaDeclarationByRelationName contains relName
   }
 
   // Analyze the dependency between statements and construct a graph.
   def analyzeDependency(statements: List[Statement]) = {
-    val stmtByHeadName = (extractionRuleGroupByHead.toSeq ++
-      functionCallRuleGroupByOutput.toSeq).groupBy(_._1).mapValues(_.map(_._2).toList)
 
     def collectUsedRelations(bodies: List[List[Body]]): Set[Statement] = {
       // FIXME need to be recursively defined on QuantifiedBody
       (bodies.flatten collect { case x: BodyAtom => x.name }
-      flatMap (stmtByHeadName get _)).toSet.flatten.flatten
+      flatMap (statementsByHeadName get _)).flatten toSet
     }
 
     // Look at the body of each statement to construct a dependency graph
@@ -169,7 +136,7 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   def generateDependenciesOfCompiledBlockFor(statements: List[Statement]): String = {
     var dependentExtractorBlockNames = Set[String]()
     for (statement <- statements) {
-      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & visible) map resolveExtractorBlockName
+      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & representativeStatements) map resolveExtractorBlockName
     }
     if (dependentExtractorBlockNames.size == 0) "" else {
       val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")
@@ -466,37 +433,21 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
   def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\\\''")}'"
 
-  // Generate schema and cleanup part for database
-  def compileSchemaDeclarations(stmts: List[SchemaDeclaration], ss: CompilationState): CompiledBlocks = {
-    var schemas = new ListBuffer[String]()
-    for (stmt <- stmts) {
-        var columnDecls = stmt.a.terms.zipWithIndex map {
-          case (name,i) => s"${name} ${stmt.a.types(i)}"
-        }
-        if (stmt.isQuery) {
-          val labelColumn = stmt.variableType match {
-            case Some(BooleanType())        => "label boolean"
-            case Some(MultinomialType(_)) => "label int"
-          }
-          columnDecls = columnDecls :+ "id bigint" :+ labelColumn
-        }
-        val indentation = " " * stmt.a.name.length
-        val blockName = ss.resolveExtractorBlockName(stmt)
-        schemas += s"""
-          deepdive.extraction.extractors.${blockName} {
-            sql: \"\"\" DROP TABLE IF EXISTS ${stmt.a.name} CASCADE;
-            CREATE TABLE
-            ${stmt.a.name}(${columnDecls.mkString(",\n" + indentation)})
-            \"\"\"
-            style: "sql_extractor"
-          }"""
-    }
-    schemas.toList
+  def compile(stmt: SchemaDeclaration, ss: CompilationState): CompiledBlocks = {
+    // Nothing to compile
+    List()
   }
 
+  def compile(stmt: FunctionDeclaration, ss: CompilationState): CompiledBlocks = {
+    // Nothing to compile
+    List()
+  }
 
   // Generate extraction rule part for deepdive
-  def compileExtractionRules(stmts: List[ExtractionRule], ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: ExtractionRule, ss: CompilationState): CompiledBlocks = {
+    val stmts = ss.statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
+    if (stmts isEmpty) return List()
+
     var inputQueries = new ListBuffer[String]()
     for (stmt <- stmts) {
       for (cqBody <- stmt.q.bodies) {
@@ -550,7 +501,10 @@ ${if (createTable) {
     List(extractor)
   }
 
-  def compileFunctionCallRules(stmts: List[FunctionCallRule], ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: FunctionCallRule, ss: CompilationState): CompiledBlocks = {
+    val stmts = ss.statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: FunctionCallRule => s }
+    if (stmts isEmpty) return List()
+
     var extractors = new ListBuffer[String]()
     for (stmt <- stmts) {
 
@@ -587,9 +541,10 @@ ${if (createTable) {
   }
 
   // generate inference rule part for deepdive
-  def compileInferenceRules(stmts: List[InferenceRule], ss: CompilationState): CompiledBlocks = {
-    var blocks = List[String]()
-    for (stmt <- stmts) {
+  def compile(stmt: InferenceRule, ss: CompilationState): CompiledBlocks = {
+      val stmts = List(stmt)  // XXX remove this
+
+      var blocks = List[String]()
       var inputQueries = new ListBuffer[String]()
       var func = ""
       var weight = ""
@@ -613,7 +568,7 @@ ${if (createTable) {
         // TODO self-join?
         val varInBody = (fakeBody.zipWithIndex flatMap {
           case (x: BodyAtom, i) =>
-            if (ss.schemaDeclaration(x.name) map(_.isQuery) getOrElse(false))
+            if (ss.schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
               Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
             else
               None
@@ -646,7 +601,7 @@ ${if (createTable) {
             case FactorFunction.Linear() => "Linear"
             case FactorFunction.Ratio()  => "Ratio"
             case FactorFunction.IsTrue() =>
-              ss.schemaDeclaration(stmt.head.terms(0).name) map(_.variableType) match {
+              ss.schemaDeclarationByRelationName get(stmt.head.terms(0).name) map(_.variableType) match {
                 case Some(Some(MultinomialType(_))) => "Multinomial"
                 case _ => "Imply" // TODO fix to IsTrue
               }
@@ -684,15 +639,22 @@ ${if (createTable) {
             ) mkString("\n            ", "\n            ", "\n          ")}]
         }
       """
-    }
     blocks.reverse
   }
 
+  def compile(stmt: Statement, ss: CompilationState): CompiledBlocks = stmt match {
+    case s: SchemaDeclaration => compile(s, ss)
+    case s: FunctionDeclaration => compile(s, ss)
+    case s: ExtractionRule => compile(s, ss)
+    case s: FunctionCallRule => compile(s, ss)
+    case s: InferenceRule => compile(s, ss)
+    case _ => sys.error(s"Compiler does not recognize statement: ${stmt}")
+  }
 
   // generate application.conf pipelines
   def compilePipelines(ss: CompilationState): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
-    val extraction = (ss.visible map {s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
+    val extraction = (ss.representativeStatements map { s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
     val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [\n  ${extraction}\n]" else ""
     val inference = (ss.inferenceRules map {s => ss.resolveInferenceBlockName(s)}).mkString("\n  ")
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [\n  ${inference}\n]" else ""
@@ -736,11 +698,7 @@ ${if (createTable) {
     val blocks = (
       compileVariableSchema(programToCompile, state)
       :::
-        (state.extractionRuleGroupByHead.values.toList flatMap (compileExtractionRules(_, state)))
-      :::
-        (state.functionCallList flatMap { fncall => compileFunctionCallRules(List(fncall), state)})
-      :::
-        (state.inferenceRules flatMap {inf => compileInferenceRules(List(inf), state)})
+      (programToCompile flatMap (compile(_, state)))
       :::
       compilePipelines(state)
     )
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index 4118c4e5f..ee952d842 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -4,15 +4,15 @@
       }
     
 
-      deepdive.extraction.extractors.ext_U {
+      deepdive.extraction.extractors.ext_T {
         cmd: """
 
-	deepdive create view U as 'SELECT R1.x AS column_0
+	deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
 FROM R R0, S R1
-        WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]'
+        WHERE R0.x[1] = R1.y[1] AND R0.x[2] = R1.y[2]'
 	
         """
-          output_relation: "U"
+          output_relation: "T"
         style: "cmd_extractor"
           
           input_relations: [
@@ -22,15 +22,15 @@ FROM R R0, S R1
       }
     
 
-      deepdive.extraction.extractors.ext_T {
+      deepdive.extraction.extractors.ext_U {
         cmd: """
 
-	deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
+	deepdive create view U as 'SELECT R1.x AS column_0
 FROM R R0, S R1
-        WHERE R0.x[1] = R1.y[1] AND R0.x[2] = R1.y[2]'
+        WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]'
 	
         """
-          output_relation: "T"
+          output_relation: "U"
         style: "cmd_extractor"
           
           input_relations: [
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 7f8f93a39..45692ba90 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -4,27 +4,6 @@
       }
     
 
-      deepdive.extraction.extractors.ext_tag {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "tag"
-	deepdive sql 'INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
-          FROM words R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "tag"
-        style: "cmd_extractor"
-          dependencies: [ "ext_words_by_ext_training" ]
-          input_relations: [
-            words
-          ]
-      }
-    
-
         deepdive.extraction.extractors.ext_words_by_ext_training {
           input: """ SELECT R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.tag AS "words_raw.R0.tag"
 FROM words_raw R0
@@ -59,6 +38,27 @@ FROM words R0, words R1
         }
       
 
+      deepdive.extraction.extractors.ext_tag {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "tag"
+	deepdive sql 'INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
+          FROM words R0
+        
+          '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "tag"
+        style: "cmd_extractor"
+          dependencies: [ "ext_words_by_ext_training" ]
+          input_relations: [
+            words
+          ]
+      }
+    
+
         deepdive.inference.factors.inf_istrue_tag {
           input_query: """
           SELECT R0.id AS "tag.R0.id" , R1.feature AS "dd_weight_column_0" 
@@ -75,16 +75,16 @@ FROM words R0, words R1
       
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
-  ext_tag
   ext_words_by_ext_training
+  ext_tag
   ext_word_features_by_ext_features
 ]
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_tag
 ]
 deepdive.pipeline.pipelines.endtoend: [
-  ext_tag
   ext_words_by_ext_training
+  ext_tag
   ext_word_features_by_ext_features
   inf_istrue_tag
 ]
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index db8433a65..45ed0c519 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -4,86 +4,87 @@
       }
     
 
-      deepdive.extraction.extractors.ext_E {
+      deepdive.extraction.extractors.ext_Q {
         cmd: """
 
-	deepdive create view E as 'SELECT (R0.k :: INT) AS column_0
-FROM b R0
-        '
+	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
+FROM a R0, b R1, c R2
+        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))'
 	
         """
-          output_relation: "E"
+          output_relation: "Q"
         style: "cmd_extractor"
           
           input_relations: [
+            a
             b
+            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_X {
+      deepdive.extraction.extractors.ext_P {
         cmd: """
 
-	deepdive create view X as 'SELECT R0.k AS column_0
-FROM b R0, c R1
-        WHERE R1.n = R0.k '
+	deepdive create view P as 'SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
+FROM a R0, b R1
+        WHERE R1.k = R0.k 
+        GROUP BY R1.p, R1.q'
 	
         """
-          output_relation: "X"
+          output_relation: "P"
         style: "cmd_extractor"
           
           input_relations: [
+            a
             b
-            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_N {
+      deepdive.extraction.extractors.ext_A {
         cmd: """
 
-	deepdive create view N as 'SELECT R0.k AS column_0
+	deepdive create view A as 'SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > '\''a'\'')'
+        '
 	
         """
-          output_relation: "N"
+          output_relation: "A"
         style: "cmd_extractor"
           
           input_relations: [
             b
-            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_T {
+      deepdive.extraction.extractors.ext_B {
         cmd: """
 
-	deepdive create view T as 'SELECT R0.k AS column_0
-FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
-        WHERE R1_0.s > R0.p'
+	deepdive create view B as 'SELECT func(R0.k + (R0.r + R0.k)) AS column_0
+FROM b R0
+        '
 	
         """
-          output_relation: "T"
+          output_relation: "B"
         style: "cmd_extractor"
           
           input_relations: [
             b
-            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_J {
+      deepdive.extraction.extractors.ext_C {
         cmd: """
 
-	deepdive create view J as 'SELECT R0.k AS column_0
+	deepdive create view C as 'SELECT func(func(func(R0.k))) AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)'
+        '
 	
         """
-          output_relation: "J"
+          output_relation: "C"
         style: "cmd_extractor"
           
           input_relations: [
@@ -92,33 +93,32 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.ext_U {
+      deepdive.extraction.extractors.ext_D {
         cmd: """
 
-	deepdive create view U as 'SELECT R0_0.k AS column_0
-FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
+	deepdive create view D as 'SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
+FROM b R0
         '
 	
         """
-          output_relation: "U"
+          output_relation: "D"
         style: "cmd_extractor"
           
           input_relations: [
             b
-            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_F {
+      deepdive.extraction.extractors.ext_E {
         cmd: """
 
-	deepdive create view F as 'SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
+	deepdive create view E as 'SELECT (R0.k :: INT) AS column_0
 FROM b R0
         '
 	
         """
-          output_relation: "F"
+          output_relation: "E"
         style: "cmd_extractor"
           
           input_relations: [
@@ -127,15 +127,15 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.ext_A {
+      deepdive.extraction.extractors.ext_F {
         cmd: """
 
-	deepdive create view A as 'SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
+	deepdive create view F as 'SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
 FROM b R0
         '
 	
         """
-          output_relation: "A"
+          output_relation: "F"
         style: "cmd_extractor"
           
           input_relations: [
@@ -144,33 +144,32 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.ext_M {
+      deepdive.extraction.extractors.ext_G {
         cmd: """
 
-	deepdive create view M as 'SELECT R0.k AS column_0
+	deepdive create view G as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )'
+        WHERE (R0.k + R0.r) = 100'
 	
         """
-          output_relation: "M"
+          output_relation: "G"
         style: "cmd_extractor"
           
           input_relations: [
             b
-            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_I {
+      deepdive.extraction.extractors.ext_H {
         cmd: """
 
-	deepdive create view I as 'SELECT R0.k AS column_0
+	deepdive create view H as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
+        WHERE (R0.k + R0.r) = 100 AND R0.k > 50'
 	
         """
-          output_relation: "I"
+          output_relation: "H"
         style: "cmd_extractor"
           
           input_relations: [
@@ -179,15 +178,15 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.ext_G {
+      deepdive.extraction.extractors.ext_I {
         cmd: """
 
-	deepdive create view G as 'SELECT R0.k AS column_0
+	deepdive create view I as 'SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100'
+        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
 	
         """
-          output_relation: "G"
+          output_relation: "I"
         style: "cmd_extractor"
           
           input_relations: [
@@ -196,39 +195,36 @@ FROM b R0
       }
     
 
-      deepdive.extraction.extractors.ext_V {
+      deepdive.extraction.extractors.ext_J {
         cmd: """
 
-	deepdive create view V as 'SELECT R0.n AS column_0
-FROM c R0, a R1
-        WHERE R1.k = R0.n '
+	deepdive create view J as 'SELECT R0.k AS column_0
+FROM b R0
+        WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)'
 	
         """
-          output_relation: "V"
+          output_relation: "J"
         style: "cmd_extractor"
           
           input_relations: [
-            c
-            a
+            b
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_Q {
+      deepdive.extraction.extractors.ext_K {
         cmd: """
 
-	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
-FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))'
+	deepdive create view K as 'SELECT R0.k AS column_0
+FROM b R0
+        WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))'
 	
         """
-          output_relation: "Q"
+          output_relation: "K"
         style: "cmd_extractor"
           
           input_relations: [
-            a
             b
-            c
           ]
       }
     
@@ -251,156 +247,160 @@ LIMIT 100'
       }
     
 
-      deepdive.extraction.extractors.ext_B {
+      deepdive.extraction.extractors.ext_M {
         cmd: """
 
-	deepdive create view B as 'SELECT func(R0.k + (R0.r + R0.k)) AS column_0
+	deepdive create view M as 'SELECT R0.k AS column_0
 FROM b R0
-        '
+        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )'
 	
         """
-          output_relation: "B"
+          output_relation: "M"
         style: "cmd_extractor"
           
           input_relations: [
             b
+            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_P {
+      deepdive.extraction.extractors.ext_N {
         cmd: """
 
-	deepdive create view P as 'SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
-FROM a R0, b R1
-        WHERE R1.k = R0.k 
-        GROUP BY R1.p, R1.q'
+	deepdive create view N as 'SELECT R0.k AS column_0
+FROM b R0
+        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > '\''a'\'')'
 	
         """
-          output_relation: "P"
+          output_relation: "N"
         style: "cmd_extractor"
           
           input_relations: [
-            a
             b
+            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_C {
+      deepdive.extraction.extractors.ext_O {
         cmd: """
 
-	deepdive create view C as 'SELECT func(func(func(R0.k))) AS column_0
+	deepdive create view O as 'SELECT R0.k AS column_0
 FROM b R0
-        '
+        WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )'
 	
         """
-          output_relation: "C"
+          output_relation: "O"
         style: "cmd_extractor"
           
           input_relations: [
             b
+            c
+            a
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_H {
+      deepdive.extraction.extractors.ext_S {
         cmd: """
 
-	deepdive create view H as 'SELECT R0.k AS column_0
-FROM b R0
-        WHERE (R0.k + R0.r) = 100 AND R0.k > 50'
+	deepdive create view S as 'SELECT R0.k AS column_0
+FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
+        '
 	
         """
-          output_relation: "H"
+          output_relation: "S"
         style: "cmd_extractor"
           
           input_relations: [
             b
+            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_W {
+      deepdive.extraction.extractors.ext_T {
         cmd: """
 
-	deepdive create view W as 'SELECT R0.k AS column_0
-FROM a R0
-        WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))'
+	deepdive create view T as 'SELECT R0.k AS column_0
+FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
+        WHERE R1_0.s > R0.p'
 	
         """
-          output_relation: "W"
+          output_relation: "T"
         style: "cmd_extractor"
           
           input_relations: [
-            a
+            b
             c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_K {
+      deepdive.extraction.extractors.ext_U {
         cmd: """
 
-	deepdive create view K as 'SELECT R0.k AS column_0
-FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))'
+	deepdive create view U as 'SELECT R0_0.k AS column_0
+FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
+        '
 	
         """
-          output_relation: "K"
+          output_relation: "U"
         style: "cmd_extractor"
           
           input_relations: [
             b
+            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_O {
+      deepdive.extraction.extractors.ext_W {
         cmd: """
 
-	deepdive create view O as 'SELECT R0.k AS column_0
-FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )'
+	deepdive create view W as 'SELECT R0.k AS column_0
+FROM a R0
+        WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))'
 	
         """
-          output_relation: "O"
+          output_relation: "W"
         style: "cmd_extractor"
           
           input_relations: [
-            b
-            c
             a
+            c
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_D {
+      deepdive.extraction.extractors.ext_V {
         cmd: """
 
-	deepdive create view D as 'SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
-FROM b R0
-        '
+	deepdive create view V as 'SELECT R0.n AS column_0
+FROM c R0, a R1
+        WHERE R1.k = R0.n '
 	
         """
-          output_relation: "D"
+          output_relation: "V"
         style: "cmd_extractor"
           
           input_relations: [
-            b
+            c
+            a
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_S {
+      deepdive.extraction.extractors.ext_X {
         cmd: """
 
-	deepdive create view S as 'SELECT R0.k AS column_0
-FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
-        '
+	deepdive create view X as 'SELECT R0.k AS column_0
+FROM b R0, c R1
+        WHERE R1.n = R0.k '
 	
         """
-          output_relation: "S"
+          output_relation: "X"
         style: "cmd_extractor"
           
           input_relations: [
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 8b3de1708..a62ffb721 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -4,31 +4,6 @@
       }
     
 
-      deepdive.extraction.extractors.ext_labels_resolved {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "labels_resolved"
-	deepdive sql 'INSERT INTO labels_resolved SELECT R0.x AS "labels.R0.x", SUM(
-CASE WHEN R0.l IS NULL THEN 0
-     WHEN R0.l = true THEN 1
-     ELSE -1
-END) AS column_1
-FROM labels R0
-        
-        GROUP BY R0.x'
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "labels_resolved"
-        style: "cmd_extractor"
-          
-          input_relations: [
-            labels
-          ]
-      }
-    
-
       deepdive.extraction.extractors.ext_q {
         cmd: """
 
@@ -80,6 +55,31 @@ FROM labels R0
           ]
       }
     
+
+      deepdive.extraction.extractors.ext_labels_resolved {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "labels_resolved"
+	deepdive sql 'INSERT INTO labels_resolved SELECT R0.x AS "labels.R0.x", SUM(
+CASE WHEN R0.l IS NULL THEN 0
+     WHEN R0.l = true THEN 1
+     ELSE -1
+END) AS column_1
+FROM labels R0
+        
+        GROUP BY R0.x'
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "labels_resolved"
+        style: "cmd_extractor"
+          
+          input_relations: [
+            labels
+          ]
+      }
+    
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
   ext_labels_resolved
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index e49a3062a..10562fdc7 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -47,22 +47,22 @@ FROM S_2 R0
       }
     
 
-      deepdive.extraction.extractors.ext_T__3 {
-        cmd: """
-
-	deepdive create view T__3 as 'SELECT R0.a AS column_0
-FROM T R0
-        '
-	
-        """
-          output_relation: "T__3"
-        style: "cmd_extractor"
-          dependencies: [ "ext_T" ]
+        deepdive.extraction.extractors.ext_T___0_by_f {
+          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+FROM R R0
+        WHERE R0.a > 1000
+          """
+          output_relation: "T___0"
+          udf: ${APP_HOME}"//bin/false"
+          style: "tsv_extractor" 
+          
           input_relations: [
-            T
+            R
           ]
-      }
-    
+          input_batch_size: ${INPUT_BATCH_SIZE}
+          parallelism: ${PARALLELISM}
+        }
+      
 
       deepdive.extraction.extractors.ext_T {
         cmd: """
@@ -99,23 +99,6 @@ FROM T___3 R0
       }
     
 
-        deepdive.extraction.extractors.ext_T___0_by_f {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
-FROM R R0
-        WHERE R0.a > 1000
-          """
-          output_relation: "T___0"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
         deepdive.extraction.extractors.ext_T___1_by_f {
           input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
@@ -279,6 +262,23 @@ FROM R R0
           ]
         }
       
+
+      deepdive.extraction.extractors.ext_T__3 {
+        cmd: """
+
+	deepdive create view T__3 as 'SELECT R0.a AS column_0
+FROM T R0
+        '
+	
+        """
+          output_relation: "T__3"
+        style: "cmd_extractor"
+          dependencies: [ "ext_T" ]
+          input_relations: [
+            T
+          ]
+      }
+    
 deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
   ext_S_1_by_f
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 765f6234c..9a56eff2f 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -5,44 +5,44 @@ cancer.label: Boolean
       }
     
 
-      deepdive.extraction.extractors.ext_cancer {
+      deepdive.extraction.extractors.ext_smoke {
         cmd: """
 
 	# TODO use temporary table
-	deepdive create table "cancer"
-	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
-          FROM person_has_cancer R0
+	deepdive create table "smoke"
+	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
+          FROM person_smokes R0
         
           '
 	# TODO rename temporary table to replace output_relation
 	
         """
-          output_relation: "cancer"
+          output_relation: "smoke"
         style: "cmd_extractor"
           
           input_relations: [
-            person_has_cancer
+            person_smokes
           ]
       }
     
 
-      deepdive.extraction.extractors.ext_smoke {
+      deepdive.extraction.extractors.ext_cancer {
         cmd: """
 
 	# TODO use temporary table
-	deepdive create table "smoke"
-	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
-          FROM person_smokes R0
+	deepdive create table "cancer"
+	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
+          FROM person_has_cancer R0
         
           '
 	# TODO rename temporary table to replace output_relation
 	
         """
-          output_relation: "smoke"
+          output_relation: "cancer"
         style: "cmd_extractor"
           
           input_relations: [
-            person_smokes
+            person_has_cancer
           ]
       }
     
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 70542e10f..5e4310c7e 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -4,27 +4,6 @@
       }
     
 
-      deepdive.extraction.extractors.ext_has_spouse {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
-          FROM has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            has_spouse_candidates
-          ]
-      }
-    
-
         deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
@@ -78,6 +57,27 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
+      deepdive.extraction.extractors.ext_has_spouse {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse"
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+          FROM has_spouse_candidates R0
+        
+          '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "has_spouse"
+        style: "cmd_extractor"
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+          ]
+      }
+    
+
         deepdive.inference.factors.inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
@@ -97,8 +97,8 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
   ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse_candidates_by_ext_has_spouse
 ]
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_has_spouse
@@ -106,7 +106,7 @@ deepdive.pipeline.pipelines.inference: [
 deepdive.pipeline.pipelines.endtoend: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
   ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse_candidates_by_ext_has_spouse
   inf_istrue_has_spouse
 ]
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index bcbc4579f..b04847385 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -4,27 +4,6 @@
       }
     
 
-      deepdive.extraction.extractors.ext_has_spouse {
-        cmd: """
-
-	# TODO use temporary table
-	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
-          FROM has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse"
-        style: "cmd_extractor"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
-          input_relations: [
-            has_spouse_candidates
-          ]
-      }
-    
-
         deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
           input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
@@ -78,6 +57,27 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         }
       
 
+      deepdive.extraction.extractors.ext_has_spouse {
+        cmd: """
+
+	# TODO use temporary table
+	deepdive create table "has_spouse"
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+          FROM has_spouse_candidates R0
+        
+          '
+	# TODO rename temporary table to replace output_relation
+	
+        """
+          output_relation: "has_spouse"
+        style: "cmd_extractor"
+          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
+          input_relations: [
+            has_spouse_candidates
+          ]
+      }
+    
+
         deepdive.inference.factors.inf_istrue_has_spouse {
           input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
@@ -112,8 +112,8 @@ deepdive.pipeline.run: ${PIPELINE}
 deepdive.pipeline.pipelines.extraction: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
   ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse_candidates_by_ext_has_spouse
 ]
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_has_spouse
@@ -122,8 +122,8 @@ deepdive.pipeline.pipelines.inference: [
 deepdive.pipeline.pipelines.endtoend: [
   ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
   ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse_candidates_by_ext_has_spouse
   inf_istrue_has_spouse
   inf_equal_has_spouse_has_spouse
 ]

From 1a57a238fe77fb192a26f884aa36d87b3b3936d7 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 03:19:23 -0800
Subject: [PATCH 294/347] Drops dependencies generation that is superseded by
 input_relations

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 40 -------------------
 .../arrays/compile.expected                   |  2 -
 .../chunking_example/compile.expected         |  4 --
 .../expressions/compile.expected              | 23 -----------
 .../factor_functions/compile.expected         |  2 -
 .../if-then-else/compile.expected             |  3 --
 .../compile.expected                          | 14 -------
 .../ocr_example/compile.expected              |  4 --
 .../smoke_example/compile.expected            |  4 --
 .../spouse_example/compile.expected           |  5 ---
 .../compile.expected                          |  6 ---
 .../views/compile.expected                    |  2 -
 .../weights/compile.expected                  |  5 ---
 13 files changed, 114 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 2aa66a4a3..99e694991 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -48,11 +48,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   val representativeStatements : Set[Statement] =
     statementsByHeadName.values map { _(0) } toSet
 
-  // The dependency graph between statements.
-  var dependencies : Map[Statement, Set[Statement]] = new HashMap()
-
-  analyzeDependency(statements)
-
   def error(message: String) {
     throw new RuntimeException(message)
   }
@@ -112,38 +107,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
     schemaDeclarationByRelationName contains relName
   }
 
-  // Analyze the dependency between statements and construct a graph.
-  def analyzeDependency(statements: List[Statement]) = {
-
-    def collectUsedRelations(bodies: List[List[Body]]): Set[Statement] = {
-      // FIXME need to be recursively defined on QuantifiedBody
-      (bodies.flatten collect { case x: BodyAtom => x.name }
-      flatMap (statementsByHeadName get _)).flatten toSet
-    }
-
-    // Look at the body of each statement to construct a dependency graph
-    statements foreach {
-      case f : FunctionCallRule => dependencies += {
-        f -> collectUsedRelations(f.q.bodies) }
-      case e : ExtractionRule   => dependencies += {
-        e -> collectUsedRelations(e.q.bodies) }
-      case e : InferenceRule    => dependencies += {
-        e -> collectUsedRelations(e.q.bodies) }
-      case _ =>
-    }
-  }
-  // Generates a "dependencies" value for a compiled block of given statement.
-  def generateDependenciesOfCompiledBlockFor(statements: List[Statement]): String = {
-    var dependentExtractorBlockNames = Set[String]()
-    for (statement <- statements) {
-      dependentExtractorBlockNames ++= ((dependencies getOrElse (statement, Set())) & representativeStatements) map resolveExtractorBlockName
-    }
-    if (dependentExtractorBlockNames.size == 0) "" else {
-      val depStr = dependentExtractorBlockNames map {" \"" + _ + "\" "} mkString(", ")
-      s"dependencies: [${depStr}]"
-    }
-  }
-
   def collectUsedRelations1(body: Body): List[String] = body match {
     case a: BodyAtom => List(a.name)
     case q: QuantifiedBody => collectUsedRelations(q.bodies)
@@ -492,7 +455,6 @@ ${if (createTable) {
         \"\"\"
           output_relation: \"${stmts(0).headName}\"
         style: "cmd_extractor"
-          ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
           input_relations: [${
             (stmts flatMap ss.relationNamesUsedByStatement distinct
             ) mkString("\n            ", "\n            ", "\n          ")}]
@@ -527,7 +489,6 @@ ${if (createTable) {
           \"\"\"
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
-          ${ss.generateDependenciesOfCompiledBlockFor(List(stmt))}
           input_relations: [${
             (List(stmt) flatMap ss.relationNamesUsedByStatement distinct
             ) mkString("\n            ", "\n            ", "\n          ")}]
@@ -631,7 +592,6 @@ ${if (createTable) {
           input_query: \"\"\"${inputQueries.mkString(" UNION ALL ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
-          ${ss.generateDependenciesOfCompiledBlockFor(stmts)}
           input_relations: [${
             val relationsInHead = stmts flatMap (_.head.terms map (_.name))
             val relationsInBody = stmts flatMap ss.relationNamesUsedByStatement
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index ee952d842..a6b5da57d 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -14,7 +14,6 @@ FROM R R0, S R1
         """
           output_relation: "T"
         style: "cmd_extractor"
-          
           input_relations: [
             R
             S
@@ -32,7 +31,6 @@ FROM R R0, S R1
         """
           output_relation: "U"
         style: "cmd_extractor"
-          
           input_relations: [
             R
             S
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 45692ba90..f0e812c95 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -12,7 +12,6 @@ FROM words_raw R0
           output_relation: "words"
           udf: ${APP_HOME}"/udf/ext_training.py"
           style: "tsv_extractor" 
-          
           input_relations: [
             words_raw
           ]
@@ -29,7 +28,6 @@ FROM words R0, words R1
           output_relation: "word_features"
           udf: ${APP_HOME}"/udf/ext_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "ext_words_by_ext_training" ]
           input_relations: [
             words
           ]
@@ -52,7 +50,6 @@ FROM words R0, words R1
         """
           output_relation: "tag"
         style: "cmd_extractor"
-          dependencies: [ "ext_words_by_ext_training" ]
           input_relations: [
             words
           ]
@@ -66,7 +63,6 @@ FROM words R0, words R1
         WHERE R1.word_id = R0.word_id """
           function: "Multinomial(tag.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_word_features_by_ext_features" ]
           input_relations: [
             tag
             word_features
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 45ed0c519..c13de53c4 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -14,7 +14,6 @@ FROM a R0, b R1, c R2
         """
           output_relation: "Q"
         style: "cmd_extractor"
-          
           input_relations: [
             a
             b
@@ -34,7 +33,6 @@ FROM a R0, b R1
         """
           output_relation: "P"
         style: "cmd_extractor"
-          
           input_relations: [
             a
             b
@@ -52,7 +50,6 @@ FROM b R0
         """
           output_relation: "A"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -69,7 +66,6 @@ FROM b R0
         """
           output_relation: "B"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -86,7 +82,6 @@ FROM b R0
         """
           output_relation: "C"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -103,7 +98,6 @@ FROM b R0
         """
           output_relation: "D"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -120,7 +114,6 @@ FROM b R0
         """
           output_relation: "E"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -137,7 +130,6 @@ FROM b R0
         """
           output_relation: "F"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -154,7 +146,6 @@ FROM b R0
         """
           output_relation: "G"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -171,7 +162,6 @@ FROM b R0
         """
           output_relation: "H"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -188,7 +178,6 @@ FROM b R0
         """
           output_relation: "I"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -205,7 +194,6 @@ FROM b R0
         """
           output_relation: "J"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -222,7 +210,6 @@ FROM b R0
         """
           output_relation: "K"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -240,7 +227,6 @@ LIMIT 100'
         """
           output_relation: "L"
         style: "cmd_extractor"
-          
           input_relations: [
             b
           ]
@@ -257,7 +243,6 @@ FROM b R0
         """
           output_relation: "M"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
@@ -275,7 +260,6 @@ FROM b R0
         """
           output_relation: "N"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
@@ -293,7 +277,6 @@ FROM b R0
         """
           output_relation: "O"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
@@ -312,7 +295,6 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k
         """
           output_relation: "S"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
@@ -330,7 +312,6 @@ FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         """
           output_relation: "T"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
@@ -348,7 +329,6 @@ FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k
         """
           output_relation: "U"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
@@ -366,7 +346,6 @@ FROM a R0
         """
           output_relation: "W"
         style: "cmd_extractor"
-          
           input_relations: [
             a
             c
@@ -384,7 +363,6 @@ FROM c R0, a R1
         """
           output_relation: "V"
         style: "cmd_extractor"
-          
           input_relations: [
             c
             a
@@ -402,7 +380,6 @@ FROM b R0, c R1
         """
           output_relation: "X"
         style: "cmd_extractor"
-          
           input_relations: [
             b
             c
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index c6fff079a..2f10bd31a 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -12,7 +12,6 @@ Q.label: Boolean
         WHERE R2.a = R0.x  AND R2.b = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          
           input_relations: [
             Q
             R
@@ -27,7 +26,6 @@ Q.label: Boolean
         WHERE R2.a = R0.x  AND R2.b = R1.x """
           function: "Equal(Q.R0.label, !Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          
           input_relations: [
             Q
             R
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index a62ffb721..9774c6e81 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -22,7 +22,6 @@ END AS label
         """
           output_relation: "q"
         style: "cmd_extractor"
-          dependencies: [ "ext_labels_resolved" ]
           input_relations: [
             labels_resolved
           ]
@@ -49,7 +48,6 @@ FROM labels R0
         """
           output_relation: "p"
         style: "cmd_extractor"
-          
           input_relations: [
             labels
           ]
@@ -74,7 +72,6 @@ FROM labels R0
         """
           output_relation: "labels_resolved"
         style: "cmd_extractor"
-          
           input_relations: [
             labels
           ]
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 10562fdc7..d486589ea 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -37,7 +37,6 @@ FROM S_2 R0
         """
           output_relation: "S"
         style: "cmd_extractor"
-          dependencies: [ "ext_S_0_by_f" ,  "ext_S_1_by_f" ,  "ext_S_2_by_f_1" ]
           input_relations: [
             R
             S_0
@@ -55,7 +54,6 @@ FROM R R0
           output_relation: "T___0"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -89,7 +87,6 @@ FROM T___3 R0
         """
           output_relation: "T"
         style: "cmd_extractor"
-          dependencies: [ "ext_T___0_by_f" ,  "ext_T___1_by_f" ,  "ext_T___2_by_f" ,  "ext_T___3_by_f_1" ]
           input_relations: [
             T___0
             T___1
@@ -107,7 +104,6 @@ FROM R R0
           output_relation: "T___1"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -124,7 +120,6 @@ FROM R R0
           output_relation: "T___2"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -141,7 +136,6 @@ FROM R R0
           output_relation: "S_0"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -158,7 +152,6 @@ FROM R R0
           output_relation: "S_1"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -175,7 +168,6 @@ FROM R R0
           output_relation: "T___3"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -192,7 +184,6 @@ FROM R R0
           output_relation: "S_2"
           udf: ${APP_HOME}"//bin/false"
           style: "tsv_extractor" 
-          
           input_relations: [
             R
           ]
@@ -208,7 +199,6 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x > 1000"""
           function: "Imply(Q.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -223,7 +213,6 @@ FROM R R0
         WHERE R1.a = R0.x  AND R0.x = 0"""
           function: "Imply(Q.R0.label)"
           weight: "1.0"
-          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -238,7 +227,6 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -254,7 +242,6 @@ FROM R R0
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
           function: "Imply(Q.R0.label, Q.R1.label)"
           weight: "-10.0"
-          dependencies: [ "ext_S" ]
           input_relations: [
             Q
             S
@@ -273,7 +260,6 @@ FROM T R0
         """
           output_relation: "T__3"
         style: "cmd_extractor"
-          dependencies: [ "ext_T" ]
           input_relations: [
             T
           ]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index dcd4c5cfb..fdd780023 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -19,7 +19,6 @@ q2.label: Boolean
         """
           output_relation: "q1"
         style: "cmd_extractor"
-          
           input_relations: [
             label1
           ]
@@ -40,7 +39,6 @@ q2.label: Boolean
         """
           output_relation: "q2"
         style: "cmd_extractor"
-          
           input_relations: [
             label2
           ]
@@ -54,7 +52,6 @@ q2.label: Boolean
         WHERE R1.word_id = R0.wid """
           function: "Imply(q1.R0.label)"
           weight: "?(dd_weight_column_0)"
-          
           input_relations: [
             q1
             features
@@ -69,7 +66,6 @@ q2.label: Boolean
         WHERE R1.word_id = R0.wid """
           function: "Imply(q2.R0.label)"
           weight: "?(dd_weight_column_0)"
-          
           input_relations: [
             q2
             features
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 9a56eff2f..baebffdfb 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -19,7 +19,6 @@ cancer.label: Boolean
         """
           output_relation: "smoke"
         style: "cmd_extractor"
-          
           input_relations: [
             person_smokes
           ]
@@ -40,7 +39,6 @@ cancer.label: Boolean
         """
           output_relation: "cancer"
         style: "cmd_extractor"
-          
           input_relations: [
             person_has_cancer
           ]
@@ -54,7 +52,6 @@ cancer.label: Boolean
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
           function: "Imply(smoke.R0.label, cancer.R1.label)"
           weight: "0.5"
-          
           input_relations: [
             smoke
             cancer
@@ -70,7 +67,6 @@ cancer.label: Boolean
         WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
           function: "Imply(smoke.R0.label, smoke.R1.label)"
           weight: "0.4"
-          
           input_relations: [
             smoke
             friends
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 5e4310c7e..f8dc85d4f 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -12,7 +12,6 @@ FROM sentences R0
           output_relation: "people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          
           input_relations: [
             sentences
           ]
@@ -29,7 +28,6 @@ FROM people_mentions R0, people_mentions R1
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "ext_people_mentions_by_ext_people" ]
           input_relations: [
             people_mentions
           ]
@@ -46,7 +44,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
           input_relations: [
             sentences
             has_spouse_candidates
@@ -71,7 +68,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         """
           output_relation: "has_spouse"
         style: "cmd_extractor"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
           ]
@@ -85,7 +81,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_has_spouse_features_by_ext_has_spouse_features" ]
           input_relations: [
             has_spouse
             has_spouse_candidates
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index b04847385..a84b4b658 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -12,7 +12,6 @@ FROM sentences R0
           output_relation: "people_mentions"
           udf: ${APP_HOME}"/udf/ext_people.py"
           style: "tsv_extractor" 
-          
           input_relations: [
             sentences
           ]
@@ -29,7 +28,6 @@ FROM people_mentions R0, people_mentions R1
           output_relation: "has_spouse_candidates"
           udf: ${APP_HOME}"/udf/ext_has_spouse.py"
           style: "tsv_extractor" 
-          dependencies: [ "ext_people_mentions_by_ext_people" ]
           input_relations: [
             people_mentions
           ]
@@ -46,7 +44,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
           output_relation: "has_spouse_features"
           udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
           style: "tsv_extractor" 
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_people_mentions_by_ext_people" ]
           input_relations: [
             sentences
             has_spouse_candidates
@@ -71,7 +68,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         """
           output_relation: "has_spouse"
         style: "cmd_extractor"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse_candidates
           ]
@@ -85,7 +81,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
           function: "Imply(has_spouse.R0.label)"
           weight: "?(dd_weight_column_0)"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ,  "ext_has_spouse_features_by_ext_has_spouse_features" ]
           input_relations: [
             has_spouse
             has_spouse_candidates
@@ -101,7 +96,6 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
           function: "Equal(has_spouse.R0.label, has_spouse.R1.label)"
           weight: "3.0"
-          dependencies: [ "ext_has_spouse_candidates_by_ext_has_spouse" ]
           input_relations: [
             has_spouse
             has_spouse_candidates
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index e85b48f77..78e218a77 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -14,7 +14,6 @@ FROM R R0
         """
           output_relation: "A"
         style: "cmd_extractor"
-          
           input_relations: [
             R
           ]
@@ -31,7 +30,6 @@ FROM A R0, R R1
         """
           output_relation: "B"
         style: "cmd_extractor"
-          dependencies: [ "ext_A" ]
           input_relations: [
             A
             R
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 51ea9eae8..cb0f0ef29 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -15,7 +15,6 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(a.R0.label)"
           weight: "?(dd_weight_column_0)"
-          
           input_relations: [
             a
             b
@@ -30,7 +29,6 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(c.R0.label)"
           weight: "?"
-          
           input_relations: [
             c
             b
@@ -45,7 +43,6 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(d.R0.label)"
           weight: "?(dd_weight_column_0, dd_weight_column_1)"
-          
           input_relations: [
             d
             b
@@ -60,7 +57,6 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(e.R0.label)"
           weight: "-10"
-          
           input_relations: [
             e
             b
@@ -75,7 +71,6 @@ c.label: Boolean
         WHERE R1.k = R0.k """
           function: "Imply(f.R0.label)"
           weight: "-0.3"
-          
           input_relations: [
             f
             b

From d1c29c81d3d7cb4b3c98070d7e6415d603ca1fd0 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 03:19:59 -0800
Subject: [PATCH 295/347] Replaces with sys.error

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 8 ++------
 .../org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala      | 2 +-
 .../org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala   | 3 +--
 3 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 99e694991..5fb0267d3 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -48,10 +48,6 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
   val representativeStatements : Set[Statement] =
     statementsByHeadName.values map { _(0) } toSet
 
-  def error(message: String) {
-    throw new RuntimeException(message)
-  }
-
   def optionalIndex(idx: Int) =
     if (idx < 1) "" else s"${idx}"
 
@@ -419,7 +415,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
         val qc              = new QueryCompiler(tmpCq, ss)
 
         if (stmt.supervision != None) {
-          if (stmt.q.bodies.length > 1) ss.error(s"Scoping rule does not allow disjunction.\n")
+          if (stmt.q.bodies.length > 1) sys.error(s"Scoping rule does not allow disjunction.\n")
           val headStr = qc.generateSQLHead(NoAlias)
           val labelCol = qc.compileExpr(stmt.supervision.get)
           inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
@@ -478,7 +474,7 @@ ${if (createTable) {
       })
 
       if (udfDetails.isEmpty)
-        ss.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
+        sys.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
           + (function.implementations mkString "\n  "))
 
       val blockName = ss.resolveExtractorBlockName(stmt)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
index 87b80bc25..cf09438b8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
@@ -39,7 +39,7 @@ object DeepDiveLogDeltaDeriver extends DeepDiveLogHandler {
       // We don't support deriving delta rules for modifiers
       bodies foreach {
         case _: Cond | _: BodyAtom => // supported
-        case _ => throw new RuntimeException("Deriving delta rules for modifier atom is not supported!")
+        case _ => sys.error("Deriving delta rules for modifier atom is not supported!")
       }
       // Delta body
       val incDeltaBody = bodies collect {
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index e7c0fbccd..3209ce19c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -269,8 +269,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
 
   // throw exception
   def error(stmt: Statement, message: String) {
-    val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
-    throw new RuntimeException(message + s"\n${stmtStr}")
+    sys.error(message + s"\n${DeepDiveLogPrettyPrinter.print(stmt)}")
   }
 
   // run the checker

From 99c72a378a12a6d3ac465a126c415fb93584924b Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 03:37:19 -0800
Subject: [PATCH 296/347] Rewrites all vars to vals in Semantic Checker

---
 .../ddlog/DeepDiveLogQueryCompiler.scala      |   2 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 213 +++++++++---------
 2 files changed, 108 insertions(+), 107 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index 41b583db7..6eeca9b79 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -8,7 +8,7 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
     val (query, extraRules) = (new DeepDiveLogParser).parseQuery(config.query)
 
     // make sure extraRules don't have name clashes with the program
-    DeepDiveLogSemanticChecker.checkNoRedefinition(program, extraRules)
+    new DeepDiveLogSemanticChecker(program).checkNoRedefinition(program, extraRules)
 
     // run typical checks for correct semantics
     val programToCheck = ExtractionRule(q = query, headName = "") :: extraRules ++ program
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 3209ce19c..3f6dbe88f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -4,26 +4,32 @@ import scala.collection.immutable.HashMap
 import scala.collection.immutable.HashSet
 
 // semantic checker for ddlog
-object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
+class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
 
-  // initialize the checker
-  def init(program: DeepDiveLog.Program) {
-    program foreach {
-      case s: SchemaDeclaration => {
-        heads += s.a.name
-        schemaDeclaration += { s.a.name -> s }
-      }
-      case s: ExtractionRule => {
-        if (s.supervision == None) heads += s.headName
-      }
-      case s: FunctionDeclaration => {
-        functionDeclaration += { s.functionName -> s }
-      }
-      case s: FunctionCallRule => {
-        heads += s.output
-      }
-      case _ =>
-    }
+  val namesUsedInHead: Set[String] =
+    program collect {
+      case s: SchemaDeclaration => s.a.name
+      case s: ExtractionRule if s.supervision isEmpty => s.headName
+      case s: FunctionCallRule => s.output
+    } toSet
+
+  val schemaDeclarationByName: Map[String, SchemaDeclaration] =
+    program collect {
+      case s: SchemaDeclaration => s.a.name -> s
+    } toMap
+
+  val functionDeclarationByName: Map[String, FunctionDeclaration] =
+    program collect {
+      case s: FunctionDeclaration => s.functionName -> s
+    } toMap
+
+  def check(): Unit = {
+    program foreach check
+  }
+
+  // throw exception
+  def error(stmt: Statement, message: String) {
+    sys.error(message + s"\n${DeepDiveLogPrettyPrinter.print(stmt)}")
   }
 
   // check a statement
@@ -51,7 +57,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkRelationDefined(stmt: Statement) {
     val stmtStr = DeepDiveLogPrettyPrinter.print(stmt)
     def checkRelation(name: String) {
-      if (!(heads contains name))
+      if (!(namesUsedInHead contains name))
         error(stmt, s"""relation "${name}" is not defined""")
     }
     def checkAtom(a: BodyAtom) = checkRelation(a.name)
@@ -60,7 +66,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       case s: ExtractionRule => s.q.bodies foreach check
       case s: InferenceRule => {
         s.q.bodies foreach check
-        s.head.terms map(_.name) foreach checkRelation
+        s.head.terms map (_.name) foreach checkRelation
       }
       case s: FunctionCallRule => s.q.bodies foreach check
       case _ =>
@@ -71,7 +77,7 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   def checkFunctionDefined(stmt: Statement) {
     stmt match {
       case s: FunctionCallRule => {
-        if (!(functionDeclaration.keySet contains s.function))
+        if (!(functionDeclarationByName.keySet contains s.function))
           error(stmt, s"""function "${s.function}" is not defined""")
       }
       case _ =>
@@ -97,8 +103,8 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   // check if the number of columns match schema declaration
   def checkNumberOfColumns(stmt: Statement) {
     def check(name: String, size: Int) {
-      if ((schemaDeclaration.keySet contains name) &&
-        (size != schemaDeclaration(name).a.terms.size))
+      if ((schemaDeclarationByName.keySet contains name) &&
+        (size != schemaDeclarationByName(name).a.terms.size))
         error(stmt, s""""${name}": number of columns in the query does not match number of columns in the schema""")
     }
     def checkBodyAtom(a: BodyAtom) = check(a.name, a.terms.size)
@@ -107,11 +113,11 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
       cq.bodies foreach checkBodyAtoms(checkBodyAtom)
     }
     stmt match {
-      case s: ExtractionRule   => {
+      case s: ExtractionRule => {
         check(s.headName, s.q.headTerms.size)
         checkCq(s.q)
       }
-      case s: InferenceRule    => {
+      case s: InferenceRule => {
         s.head.terms foreach checkHeadAtom
         checkCq(s.q)
       }
@@ -158,34 +164,34 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, b: BodyAtom) {
-    if (schemaDeclaration contains b.name)
-    b.terms.zipWithIndex.foreach {
-      case (`supVariable`, index) => {
-        val expColumnType = expType match {
-          case BooleanType() => "boolean"
-          case MultinomialType(_) => "int"
-        }
-        if (schemaDeclaration(b.name).a.types(index).toLowerCase != expColumnType) {
-          val actualColumnType = schemaDeclaration(b.name).a.types(index).toLowerCase
-          error(s, s"Supervision column ${supVariable.name} should be ${expColumnType} type, but is ${actualColumnType} type")
+    if (schemaDeclarationByName contains b.name)
+      b.terms.zipWithIndex.foreach {
+        case (`supVariable`, index) => {
+          val expColumnType = expType match {
+            case BooleanType() => "boolean"
+            case MultinomialType(_) => "int"
+          }
+          if (schemaDeclarationByName(b.name).a.types(index).toLowerCase != expColumnType) {
+            val actualColumnType = schemaDeclarationByName(b.name).a.types(index).toLowerCase
+            error(s, s"Supervision column ${supVariable.name} should be ${expColumnType} type, but is ${actualColumnType} type")
+          }
         }
+        case _ =>
       }
-      case _ =>
-    }
   }
 
   def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, body: Body) {
     body match {
-      case qb: QuantifiedBody => qb.bodies.foreach { b => checkSupervisionLabelType(s, expType, supVariable, b)}
-      case b: BodyAtom =>  checkSupervisionLabelType(s, expType, supVariable, b)
+      case qb: QuantifiedBody => qb.bodies.foreach { b => checkSupervisionLabelType(s, expType, supVariable, b) }
+      case b: BodyAtom => checkSupervisionLabelType(s, expType, supVariable, b)
       case _ =>
     }
   }
 
   def checkSupervisionLabelType(stmt: Statement) {
     stmt match {
-      case s: ExtractionRule if (schemaDeclaration contains s.headName) && (schemaDeclaration(s.headName).variableType nonEmpty) => {
-        val headType = schemaDeclaration(s.headName).variableType.get
+      case s: ExtractionRule if (schemaDeclarationByName contains s.headName) && (schemaDeclarationByName(s.headName).variableType nonEmpty) => {
+        val headType = schemaDeclarationByName(s.headName).variableType.get
         s.supervision foreach {
           case b: BooleanConst => {
             if (headType != BooleanType) {
@@ -195,18 +201,64 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
           case VarExpr(varname) =>
             s.q.bodies.foreach { bodies: List[Body] =>
               bodies.foreach { b =>
-                checkSupervisionLabelType(s, headType, VarPattern(varname), b) }
+                checkSupervisionLabelType(s, headType, VarPattern(varname), b)
+              }
             }
           case _ =>
-            // XXX assume the rest of the expressions are correct
+          // XXX assume the rest of the expressions are correct
         }
       }
       case _ =>
     }
   }
 
+  // check if variables have bindings in the body
+  def checkVariableBindings(stmt: Statement) {
+    // check variable bindings in a conjunctive query
+    def checkCq(cq: ConjunctiveQuery, additionalUsedVars: Set[String] = Set()) {
+      // collect variable definitions and usages
+      val varDefs = cq.bodies flatMap (_ flatMap DeepDiveLogSemanticChecker.collectDefinedVars) toSet
+      val varUses = (cq.bodies flatMap (_ flatMap DeepDiveLogSemanticChecker.collectUsedVars) toSet) ++
+        (cq.headTerms flatMap DeepDiveLogSemanticChecker.collectUsedVars) ++
+        (additionalUsedVars)
+      val varUndefined = varUses -- varDefs
+      if (varUndefined nonEmpty) error(stmt, s"Variable ${varUndefined mkString (", ")} must have bindings")
+    }
+    stmt match {
+      case s: ExtractionRule => checkCq(s.q, (s.supervision.toSet flatMap { e: Expr => DeepDiveLogSemanticChecker.collectUsedVars(e) }))
+      case s: InferenceRule => checkCq(s.q, (s.weights.variables flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet))
+      case _ =>
+    }
+  }
+
+  // partial function that returns relation name defined by the rule
+  def definedRelationName(rule: Statement): Option[String] = rule match {
+    case decl: SchemaDeclaration => Some(decl.a.name)
+    case rule: ExtractionRule => Some(rule.headName)
+    case fncall: FunctionCallRule => Some(fncall.output)
+    case _ => None
+  }
+
+  // shorthand for checking if a set of more rules redefine anything in existing rules
+  // (useful for checking queries against a program)
+  def checkNoRedefinition(existingRules: List[Statement], moreRules: List[Statement]) = {
+    val relationsDefinedByProgram = existingRules flatMap definedRelationName
+    val relationsDefinedByExtraRules = moreRules flatMap definedRelationName
+    val relationsRedefinedByExtraRules = relationsDefinedByExtraRules intersect relationsDefinedByProgram
+    if (relationsRedefinedByExtraRules nonEmpty)
+      sys.error(s"Following relations must not be redefined: ${
+        relationsRedefinedByExtraRules map {
+          "'" + _ + "'"
+        } mkString (", ")
+      }")
+  }
+
+}
+
+object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
+
   // collect variables used in the expression
-  def collectUsedVars(expr: Expr) : Set[String] = expr match {
+  def collectUsedVars(expr: Expr): Set[String] = expr match {
     case VarExpr(name) => Set(name)
     case FuncExpr(function, args, agg) => args flatMap collectUsedVars toSet
     case BinaryOpExpr(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
@@ -214,94 +266,43 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
     case IfThenElseExpr(ifCondThenExprs, optElseExpr) =>
       (ifCondThenExprs flatMap { case (ifCond, thenExpr) =>
         collectUsedVars(ifCond) ++ collectUsedVars(thenExpr)
-      } toSet) ++ (optElseExpr.toSet flatMap { e:Expr => collectUsedVars(e) })
+      } toSet) ++ (optElseExpr.toSet flatMap { e: Expr => collectUsedVars(e) })
     case ArrayElementExpr(array, index) => collectUsedVars(array) ++ collectUsedVars(index)
     case _ => Set()
   }
 
-  def collectUsedVars(pattern: Pattern) : Set[String] = pattern match {
+  def collectUsedVars(pattern: Pattern): Set[String] = pattern match {
     case VarPattern(name) => Set(name)
     case ExprPattern(e) => collectUsedVars(e)
     case PlaceholderPattern() => Set()
   }
 
-  def collectDefinedVars(pattern: Pattern) : Set[String] = pattern match {
+  def collectDefinedVars(pattern: Pattern): Set[String] = pattern match {
     case VarPattern(name) => Set(name)
     case _ => Set()
   }
 
-  def collectUsedVars(cond: Cond) : Set[String] = cond match {
-    case ExprCond(e)                  => collectUsedVars(e)
-    case CompoundCond(lhs, op, rhs)   => collectUsedVars(lhs) ++ collectUsedVars(rhs)
-    case NegationCond(c)              => collectUsedVars(c)
+  def collectUsedVars(cond: Cond): Set[String] = cond match {
+    case ExprCond(e) => collectUsedVars(e)
+    case CompoundCond(lhs, op, rhs) => collectUsedVars(lhs) ++ collectUsedVars(rhs)
+    case NegationCond(c) => collectUsedVars(c)
   }
 
-  def collectUsedVars(body: Body) : Set[String] = body match {
+  def collectUsedVars(body: Body): Set[String] = body match {
     case a: BodyAtom => a.terms flatMap collectUsedVars toSet
     case a: QuantifiedBody => a.bodies flatMap collectUsedVars toSet
     case a: Cond => collectUsedVars(a)
   }
 
-  def collectDefinedVars(body: Body) : Set[String] = body match {
+  def collectDefinedVars(body: Body): Set[String] = body match {
     case a: BodyAtom => a.terms flatMap collectDefinedVars toSet
     case a: QuantifiedBody => a.bodies flatMap collectDefinedVars toSet
     case a: Cond => Set()
   }
 
-  // check if variables have bindings in the body
-  def checkVariableBindings(stmt: Statement) {
-    // check variable bindings in a conjunctive query
-    def checkCq(cq: ConjunctiveQuery, additionalUsedVars: Set[String] = Set()) {
-      // collect variable definitions and usages
-      var varDefs = cq.bodies flatMap (_ flatMap collectDefinedVars) toSet
-      val varUses = (cq.bodies flatMap (_ flatMap collectUsedVars) toSet) ++
-        (cq.headTerms flatMap collectUsedVars) ++
-        (additionalUsedVars)
-      val varUndefined = varUses -- varDefs
-      if (varUndefined nonEmpty) error(stmt, s"Variable ${varUndefined mkString(", ")} must have bindings")
-    }
-    stmt match {
-      case s: ExtractionRule => checkCq(s.q, (s.supervision.toSet flatMap { e:Expr => collectUsedVars(e) }))
-      case s: InferenceRule  => checkCq(s.q, (s.weights.variables flatMap collectUsedVars toSet))
-      case _ =>
-    }
-  }
-
-  // throw exception
-  def error(stmt: Statement, message: String) {
-    sys.error(message + s"\n${DeepDiveLogPrettyPrinter.print(stmt)}")
-  }
-
   // run the checker
   override def run(program: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    init(program)
-    program foreach check
-  }
-
-  // schema declaration
-  var heads  : Set[String]                       = new HashSet[String]()
-  // schema
-  var schemaDeclaration : Map[String, SchemaDeclaration] = new HashMap[String, SchemaDeclaration]()
-  // function declaration
-  var functionDeclaration : Map[String, FunctionDeclaration] = new HashMap[String, FunctionDeclaration]()
-
-  // partial function that returns relation name defined by the rule
-  def definedRelationName(rule: Statement): Option[String] = rule match {
-    case decl: SchemaDeclaration  => Some(decl.a.name)
-    case rule: ExtractionRule     => Some(rule.headName)
-    case fncall: FunctionCallRule => Some(fncall.output)
-    case _                        => None
-  }
-
-  // shorthand for checking if a set of more rules redefine anything in existing rules
-  // (useful for checking queries against a program)
-  def checkNoRedefinition(existingRules: List[Statement], moreRules: List[Statement]) = {
-    val relationsDefinedByProgram = existingRules flatMap definedRelationName
-    val relationsDefinedByExtraRules =  moreRules flatMap definedRelationName
-    val relationsRedefinedByExtraRules = relationsDefinedByExtraRules intersect relationsDefinedByProgram
-    if (relationsRedefinedByExtraRules nonEmpty)
-      sys.error(s"Following relations must not be redefined: ${
-        relationsRedefinedByExtraRules map {"'"+_+"'"} mkString(", ")}")
+    new DeepDiveLogSemanticChecker(program).check()
   }
 
 }

From f18447b2db870382a7080c3b0193b3fb32231f93 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 04:10:57 -0800
Subject: [PATCH 297/347] Eliminates vars further from compiler

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 150 ++++++++----------
 .../weights/compile.expected                  |   8 +-
 2 files changed, 73 insertions(+), 85 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 5fb0267d3..9bf7bb8bd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -124,7 +124,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   // conditions, select, etc.)
   var query_schema = new HashMap[ String, Tuple2[String,Variable] ]()
 
-  // maps each variable name to a canonical version of itself (first occurence in body in left-to-right order)
+  // maps each variable name to a canonical version of itself (first occurrence in body in left-to-right order)
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
   def generateCanonicalVar()  = {
@@ -407,9 +407,8 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     val stmts = ss.statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
     if (stmts isEmpty) return List()
 
-    var inputQueries = new ListBuffer[String]()
-    for (stmt <- stmts) {
-      for (cqBody <- stmt.q.bodies) {
+    val inputQueries = stmts flatMap { case stmt =>
+      stmt.q.bodies map { case cqBody =>
         val tmpCq = stmt.q.copy(bodies = List(cqBody))
         // Generate the body of the query.
         val qc              = new QueryCompiler(tmpCq, ss)
@@ -418,7 +417,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           if (stmt.q.bodies.length > 1) sys.error(s"Scoping rule does not allow disjunction.\n")
           val headStr = qc.generateSQLHead(NoAlias)
           val labelCol = qc.compileExpr(stmt.supervision.get)
-          inputQueries += s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
+          s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
         } else {
@@ -427,7 +426,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           // views uses view alias
           val aliasStyle = if (!ss.hasSchemaDeclared(stmt.headName)) ViewAlias
               else TableAlias
-          inputQueries += qc.generateSQL(aliasStyle)
+          qc.generateSQL(aliasStyle)
         }
       }
     }
@@ -463,9 +462,7 @@ ${if (createTable) {
     val stmts = ss.statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: FunctionCallRule => s }
     if (stmts isEmpty) return List()
 
-    var extractors = new ListBuffer[String]()
-    for (stmt <- stmts) {
-
+    stmts map { case stmt =>
       val function = ss.functionDeclarationByName(stmt.function)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
@@ -479,7 +476,7 @@ ${if (createTable) {
 
       val blockName = ss.resolveExtractorBlockName(stmt)
       val parallelism = stmt.parallelism getOrElse("${PARALLELISM}")
-      val extractor = s"""
+      s"""
         deepdive.extraction.extractors.${blockName} {
           input: \"\"\" ${new QueryCompiler(stmt.q, ss).generateSQL(TableAlias)}
           \"\"\"
@@ -492,30 +489,25 @@ ${if (createTable) {
           parallelism: ${parallelism}
         }
       """
-      extractors += extractor
     }
-    extractors.toList
   }
 
   // generate inference rule part for deepdive
   def compile(stmt: InferenceRule, ss: CompilationState): CompiledBlocks = {
-      val stmts = List(stmt)  // XXX remove this
+    val headAsBody = stmt.head.terms map { x =>
+      BodyAtom(x.name, x.terms map {
+        case x: VarExpr => VarPattern(x.name)
+        case x: Expr    => ExprPattern(x)
+      })
+    }
 
-      var blocks = List[String]()
-      var inputQueries = new ListBuffer[String]()
-      var func = ""
-      var weight = ""
-      for (cqBody <- stmt.q.bodies) {
+    val inputQueries =
+      stmt.q.bodies map { case cqBody =>
         // edge query
         // Here we need to select from the bodies atoms as well as the head atoms,
         // which are the variable relations.
         // This is achieved by puting head atoms into the body.
-        val headAsBody = stmt.head.terms map { x =>
-          BodyAtom(x.name, x.terms map {
-            case x: VarExpr => VarPattern(x.name)
-            case x: Expr    => ExprPattern(x)
-          })
-        }
+
         val fakeBody        = headAsBody ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
         val fakeBodyAtoms   = fakeBody.collect { case x: BodyAtom => x }
@@ -541,61 +533,63 @@ ${if (createTable) {
         val selectStr = List(varInBody, uwStr).filterNot(_.isEmpty).mkString(", ")
 
         // factor input query
-        inputQueries += s"""
+        s"""
           SELECT ${selectStr}
           ${ qc.generateSQLBody(fakeBody) }"""
-        // factor function
-        if (func.length == 0) {
-          val funcBody = (headAsBody zip stmt.head.terms map { case(x, y) =>
-            s"""${if (y.isNegated) "!" else ""}${x.name}.R${fakeBody indexOf x}.label"""
-          })
-
-          val function = stmt.head.function match {
-            case FactorFunction.Imply()  => "Imply"
-            case FactorFunction.And()    => "And"
-            case FactorFunction.Or()     => "Or"
-            case FactorFunction.Equal()  => "Equal"
-            case FactorFunction.Linear() => "Linear"
-            case FactorFunction.Ratio()  => "Ratio"
-            case FactorFunction.IsTrue() =>
-              ss.schemaDeclarationByRelationName get(stmt.head.terms(0).name) map(_.variableType) match {
-                case Some(Some(MultinomialType(_))) => "Multinomial"
-                case _ => "Imply" // TODO fix to IsTrue
-              }
-            case FactorFunction.Multinomial() => "Multinomial"
-          }
-          func = s"""${function}(${funcBody.mkString(", ")})"""
-        }
-        // weight
-        if (weight.length == 0) {
-          // note error cases should be handled in semantic checker
-          weight = stmt.weights.variables(0) match {
-            case IntConst(value) => value.toString
-            case DoubleConst(value) => value.toString
-            case StringConst(value) => "?"
-            case _ => {
-              val weightVars = stmt.weights.variables.zipWithIndex.flatMap {
-                case(s: Expr, i) => Some(s"dd_weight_column_${i}")
-              } mkString(", ")
-              s"?(${weightVars})"
-            }
+      }
+
+    // factor function
+    val func = {
+      val funcBody = (headAsBody zip stmt.head.terms map { case(x, y) =>
+        s"""${if (y.isNegated) "!" else ""}${x.name}.R${headAsBody indexOf x}.label"""
+      })
+
+      val function = stmt.head.function match {
+        case FactorFunction.Imply()  => "Imply"
+        case FactorFunction.And()    => "And"
+        case FactorFunction.Or()     => "Or"
+        case FactorFunction.Equal()  => "Equal"
+        case FactorFunction.Linear() => "Linear"
+        case FactorFunction.Ratio()  => "Ratio"
+        case FactorFunction.IsTrue() =>
+          ss.schemaDeclarationByRelationName get(stmt.head.terms(0).name) map(_.variableType) match {
+            case Some(Some(MultinomialType(_))) => "Multinomial"
+            case _ => "Imply" // TODO fix to IsTrue
           }
+        case FactorFunction.Multinomial() => "Multinomial"
+      }
+      s"""${function}(${funcBody.mkString(", ")})"""
+    }
+
+    // weight
+    val weight = {
+      // note error cases should be handled in semantic checker
+      // FIXME check if all weights.variables are ConstExpr to determine whether it's a fixed or unknown weight
+      stmt.weights.variables(0) match {
+        case IntConst(value) => value.toString
+        case DoubleConst(value) => value.toString
+        case StringConst(value) => "?"
+        case _ => {
+          val weightVars = stmt.weights.variables.zipWithIndex.flatMap {
+            case(s: Expr, i) => Some(s"dd_weight_column_${i}")
+          } mkString(", ")
+          s"?(${weightVars})"
         }
       }
-      val blockName = ss.resolveInferenceBlockName(stmt)
-      blocks ::= s"""
-        deepdive.inference.factors.${blockName} {
+    }
+
+    List(s"""
+        deepdive.inference.factors.${ss.resolveInferenceBlockName(stmt)} {
           input_query: \"\"\"${inputQueries.mkString(" UNION ALL ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
           input_relations: [${
-            val relationsInHead = stmts flatMap (_.head.terms map (_.name))
-            val relationsInBody = stmts flatMap ss.relationNamesUsedByStatement
+            val relationsInHead = stmt.head.terms map (_.name)
+            val relationsInBody = ss.relationNamesUsedByStatement getOrElse(stmt, List.empty)
             ((relationsInHead ++ relationsInBody) distinct
             ) mkString("\n            ", "\n            ", "\n          ")}]
         }
-      """
-    blocks.reverse
+      """)
   }
 
   def compile(stmt: Statement, ss: CompilationState): CompiledBlocks = stmt match {
@@ -621,25 +615,19 @@ ${if (createTable) {
 
   // generate variable schema statements
   def compileVariableSchema(statements: DeepDiveLog.Program, ss: CompilationState): CompiledBlocks = {
-    var schema = Set[String]()
     // generate the statements.
-    statements.foreach {
-      case decl: SchemaDeclaration =>
-        if (decl.isQuery) {
+    List(s"""
+      deepdive.schema.variables {
+    ${statements collect {
+      case decl: SchemaDeclaration if decl.isQuery =>
           val variableTypeDecl = decl.variableType match {
-            case Some(BooleanType())        => "Boolean"
             case Some(MultinomialType(x)) => s"Categorical(${x})"
+            case _ => "Boolean"
           }
-          schema += s"${decl.a.name}.label: ${variableTypeDecl}"
-        }
-      case _ => ()
-    }
-    val ddSchema = s"""
-      deepdive.schema.variables {
-        ${schema.mkString("\n")}
+          s"${decl.a.name}.label: ${variableTypeDecl}"
+    } mkString("\n")}
       }
-    """
-    List(ddSchema)
+    """)
   }
 
   // entry point for compilation
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index cb0f0ef29..73e9d3b20 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -1,10 +1,10 @@
 
       deepdive.schema.variables {
-        a.label: Boolean
-f.label: Boolean
-e.label: Boolean
-d.label: Boolean
+    a.label: Boolean
 c.label: Boolean
+d.label: Boolean
+e.label: Boolean
+f.label: Boolean
       }
     
 

From af03f2fe74622959e46219b6fe4cd8b8b4b6e474 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 04:33:52 -0800
Subject: [PATCH 298/347] Renames CompilationState to DeepDiveCompiler and
 turns QueryCompiler into an inner class

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 133 ++++++++++--------
 .../ddlog/DeepDiveLogQueryCompiler.scala      |  10 +-
 2 files changed, 76 insertions(+), 67 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9bf7bb8bd..aae1ef0ab 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -9,15 +9,13 @@ import scala.collection.mutable.ListBuffer
 import org.deepdive.ddlog.DeepDiveLog.Mode._
 import scala.language.postfixOps
 
-object AliasStyle extends Enumeration {
-  type AliasStyle = Value
-  // TableStyle: tableName.R{tableIndex}.columnName
-  // ViewStyle: column_{columnIndex}
-  val ViewAlias, TableAlias, NoAlias, UseVariableAsAlias = Value
-}
-import AliasStyle._
+// Compiler that takes parsed program as input and turns into blocks of deepdive.conf
+class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.Config )  {
+  type CompiledBlock = String
+  type CompiledBlocks = List[CompiledBlock]
+
+  val statements = program
 
-class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.Config )  {
   val attrNameForRelationAndPosition: Map[ Tuple2[String,Int], String ] =
     (statements collect {
       case decl: SchemaDeclaration =>
@@ -114,10 +112,20 @@ class CompilationState( statements : DeepDiveLog.Program, config : DeepDiveLog.C
       case e : ExtractionRule   => e -> (e.q.bodies flatMap collectUsedRelations distinct)
       case e : InferenceRule    => e -> (e.q.bodies flatMap collectUsedRelations distinct)
     } toMap
-}
 
-// This is responsible for compiling a single conjunctive query
-class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
+
+  sealed trait AliasStyle
+  // ViewStyle: column_{columnIndex}
+  case object ViewAlias extends AliasStyle
+  // TableStyle: tableName.R{tableIndex}.columnName
+  case object TableAlias extends AliasStyle
+  case object NoAlias extends AliasStyle
+  case object UseVariableAsAlias extends AliasStyle
+
+
+  // This is responsible for compiling a single conjunctive query
+class QueryCompiler(cq : ConjunctiveQuery) {
+  // TODO remove var and make the generate* stuff below side-effect free
   // This is responsible for schema elements within a given query, e.g.,
   // what is the canonical version of x? (i.e., the first time it is
   // mentioned in the body. This is useful to translate to SQL (join
@@ -159,7 +167,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
   // compile a variable name to its canonical relation and column in R{index}.{name} style
   def compileVariable(v: String) = {
     val index = getBodyIndex(v)
-    val name  = ss.resolveName(getVar(v))
+    val name  = resolveName(getVar(v))
     s"R${index}.${name}"
   }
 
@@ -170,7 +178,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
       case VarExpr(v) => {
         val index = getBodyIndex(v)
         val variable = getVar(v)
-        val name  = ss.resolveName(variable)
+        val name  = resolveName(variable)
         val relation = variable.relName
         s""" AS "${relation}.R${index}.${name}"""" //"
       }
@@ -256,8 +264,8 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
               case VarPattern(varName) => {
                 val canonical_body_index = getBodyIndex(varName)
                 if (canonical_body_index != bodyIndex) {
-                  val real_attr_name1 = ss.resolveName( Variable(varName, relName, termIndex) )
-                  val real_attr_name2 = ss.resolveName( getVar(varName))
+                  val real_attr_name1 = resolveName( Variable(varName, relName, termIndex) )
+                  val real_attr_name2 = resolveName( getVar(varName))
                   Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
                 } else { None }
               }
@@ -265,7 +273,7 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
               // expression patterns indicate a filter condition on the column
               case ExprPattern(expr) => {
                 val resolved = compileExpr(expr)
-                val attr = ss.attrNameForRelationAndPosition(relName, termIndex)
+                val attr = attrNameForRelationAndPosition(relName, termIndex)
                 Some(s"R${bodyIndex}.${attr} = ${resolved}")
               }
             }
@@ -384,34 +392,28 @@ class QueryCompiler(cq : ConjunctiveQuery, ss: CompilationState) {
 
 }
 
-
-// Compiler that takes parsed program as input and prints blocks of application.conf
-object DeepDiveLogCompiler extends DeepDiveLogHandler {
-  type CompiledBlock = String
-  type CompiledBlocks = List[CompiledBlock]
-
   def escape4sh(arg: String): String = s"'${arg.replaceAll("'", "'\\\\''")}'"
 
-  def compile(stmt: SchemaDeclaration, ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: SchemaDeclaration): CompiledBlocks = {
     // Nothing to compile
     List()
   }
 
-  def compile(stmt: FunctionDeclaration, ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: FunctionDeclaration): CompiledBlocks = {
     // Nothing to compile
     List()
   }
 
   // Generate extraction rule part for deepdive
-  def compile(stmt: ExtractionRule, ss: CompilationState): CompiledBlocks = {
-    val stmts = ss.statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
+  def compile(stmt: ExtractionRule): CompiledBlocks = {
+    val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
     if (stmts isEmpty) return List()
 
     val inputQueries = stmts flatMap { case stmt =>
       stmt.q.bodies map { case cqBody =>
         val tmpCq = stmt.q.copy(bodies = List(cqBody))
         // Generate the body of the query.
-        val qc              = new QueryCompiler(tmpCq, ss)
+        val qc              = new QueryCompiler(tmpCq)
 
         if (stmt.supervision != None) {
           if (stmt.q.bodies.length > 1) sys.error(s"Scoping rule does not allow disjunction.\n")
@@ -424,14 +426,14 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
           // variable columns
           // dd_new_ tale only need original column name to make sure the schema is the same with original table
           // views uses view alias
-          val aliasStyle = if (!ss.hasSchemaDeclared(stmt.headName)) ViewAlias
+          val aliasStyle = if (!hasSchemaDeclared(stmt.headName)) ViewAlias
               else TableAlias
           qc.generateSQL(aliasStyle)
         }
       }
     }
-    val blockName = ss.resolveExtractorBlockName(stmts(0))
-    val createTable = ss.hasSchemaDeclared(stmts(0).headName)
+    val blockName = resolveExtractorBlockName(stmts(0))
+    val createTable = hasSchemaDeclared(stmts(0).headName)
     val extractor = s"""
       deepdive.extraction.extractors.${blockName} {
         cmd: \"\"\"
@@ -451,19 +453,19 @@ ${if (createTable) {
           output_relation: \"${stmts(0).headName}\"
         style: "cmd_extractor"
           input_relations: [${
-            (stmts flatMap ss.relationNamesUsedByStatement distinct
+            (stmts flatMap relationNamesUsedByStatement distinct
             ) mkString("\n            ", "\n            ", "\n          ")}]
       }
     """
     List(extractor)
   }
 
-  def compile(stmt: FunctionCallRule, ss: CompilationState): CompiledBlocks = {
-    val stmts = ss.statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: FunctionCallRule => s }
+  def compile(stmt: FunctionCallRule): CompiledBlocks = {
+    val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: FunctionCallRule => s }
     if (stmts isEmpty) return List()
 
     stmts map { case stmt =>
-      val function = ss.functionDeclarationByName(stmt.function)
+      val function = functionDeclarationByName(stmt.function)
       val udfDetails = (function.implementations collectFirst {
         case impl: RowWiseLineHandler =>
           s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
@@ -474,16 +476,16 @@ ${if (createTable) {
         sys.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
           + (function.implementations mkString "\n  "))
 
-      val blockName = ss.resolveExtractorBlockName(stmt)
+      val blockName = resolveExtractorBlockName(stmt)
       val parallelism = stmt.parallelism getOrElse("${PARALLELISM}")
       s"""
         deepdive.extraction.extractors.${blockName} {
-          input: \"\"\" ${new QueryCompiler(stmt.q, ss).generateSQL(TableAlias)}
+          input: \"\"\" ${new QueryCompiler(stmt.q).generateSQL(TableAlias)}
           \"\"\"
           output_relation: \"${stmt.output}\"
           ${udfDetails.get}
           input_relations: [${
-            (List(stmt) flatMap ss.relationNamesUsedByStatement distinct
+            (List(stmt) flatMap relationNamesUsedByStatement distinct
             ) mkString("\n            ", "\n            ", "\n          ")}]
           input_batch_size: $${INPUT_BATCH_SIZE}
           parallelism: ${parallelism}
@@ -493,7 +495,7 @@ ${if (createTable) {
   }
 
   // generate inference rule part for deepdive
-  def compile(stmt: InferenceRule, ss: CompilationState): CompiledBlocks = {
+  def compile(stmt: InferenceRule): CompiledBlocks = {
     val headAsBody = stmt.head.terms map { x =>
       BodyAtom(x.name, x.terms map {
         case x: VarExpr => VarPattern(x.name)
@@ -513,11 +515,11 @@ ${if (createTable) {
         val fakeBodyAtoms   = fakeBody.collect { case x: BodyAtom => x }
 
         val index = cqBody.length + 1
-        val qc = new QueryCompiler(fakeCQ, ss)
+        val qc = new QueryCompiler(fakeCQ)
         // TODO self-join?
         val varInBody = (fakeBody.zipWithIndex flatMap {
           case (x: BodyAtom, i) =>
-            if (ss.schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
+            if (schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
               Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
             else
               None
@@ -552,7 +554,7 @@ ${if (createTable) {
         case FactorFunction.Linear() => "Linear"
         case FactorFunction.Ratio()  => "Ratio"
         case FactorFunction.IsTrue() =>
-          ss.schemaDeclarationByRelationName get(stmt.head.terms(0).name) map(_.variableType) match {
+          schemaDeclarationByRelationName get(stmt.head.terms(0).name) map(_.variableType) match {
             case Some(Some(MultinomialType(_))) => "Multinomial"
             case _ => "Imply" // TODO fix to IsTrue
           }
@@ -579,34 +581,34 @@ ${if (createTable) {
     }
 
     List(s"""
-        deepdive.inference.factors.${ss.resolveInferenceBlockName(stmt)} {
+        deepdive.inference.factors.${resolveInferenceBlockName(stmt)} {
           input_query: \"\"\"${inputQueries.mkString(" UNION ALL ")}\"\"\"
           function: "${func}"
           weight: "${weight}"
           input_relations: [${
             val relationsInHead = stmt.head.terms map (_.name)
-            val relationsInBody = ss.relationNamesUsedByStatement getOrElse(stmt, List.empty)
+            val relationsInBody = relationNamesUsedByStatement getOrElse(stmt, List.empty)
             ((relationsInHead ++ relationsInBody) distinct
             ) mkString("\n            ", "\n            ", "\n          ")}]
         }
       """)
   }
 
-  def compile(stmt: Statement, ss: CompilationState): CompiledBlocks = stmt match {
-    case s: SchemaDeclaration => compile(s, ss)
-    case s: FunctionDeclaration => compile(s, ss)
-    case s: ExtractionRule => compile(s, ss)
-    case s: FunctionCallRule => compile(s, ss)
-    case s: InferenceRule => compile(s, ss)
+  def compile(stmt: Statement): CompiledBlocks = stmt match {
+    case s: SchemaDeclaration => compile(s)
+    case s: FunctionDeclaration => compile(s)
+    case s: ExtractionRule => compile(s)
+    case s: FunctionCallRule => compile(s)
+    case s: InferenceRule => compile(s)
     case _ => sys.error(s"Compiler does not recognize statement: ${stmt}")
   }
 
   // generate application.conf pipelines
-  def compilePipelines(ss: CompilationState): CompiledBlocks = {
+  def compilePipelines(): CompiledBlocks = {
     val run = "deepdive.pipeline.run: ${PIPELINE}"
-    val extraction = (ss.representativeStatements map { s => ss.resolveExtractorBlockName(s)}).mkString("\n  ")
+    val extraction = (representativeStatements map { s => resolveExtractorBlockName(s)}).mkString("\n  ")
     val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [\n  ${extraction}\n]" else ""
-    val inference = (ss.inferenceRules map {s => ss.resolveInferenceBlockName(s)}).mkString("\n  ")
+    val inference = (inferenceRules map {s => resolveInferenceBlockName(s)}).mkString("\n  ")
     val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [\n  ${inference}\n]" else ""
     val endtoend = List(extraction, inference).filter(_ != "").mkString("\n  ")
     val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [\n  ${endtoend}\n]" else ""
@@ -614,7 +616,7 @@ ${if (createTable) {
   }
 
   // generate variable schema statements
-  def compileVariableSchema(statements: DeepDiveLog.Program, ss: CompilationState): CompiledBlocks = {
+  def compileVariableSchema(): CompiledBlocks = {
     // generate the statements.
     List(s"""
       deepdive.schema.variables {
@@ -630,22 +632,29 @@ ${if (createTable) {
     """)
   }
 
+  def compile(): CompiledBlocks = (
+    compileVariableSchema()
+    :::
+    (statements flatMap compile)
+    :::
+    compilePipelines()
+  )
+
+}
+
+object DeepDiveLogCompiler extends DeepDiveLogHandler {
+
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
-    // semantic checking
+    // don't compile if it doesn't pass all semantic checks
     DeepDiveLogSemanticChecker.run(parsedProgram, config)
     val programToCompile = parsedProgram
+
     // take an initial pass to analyze the parsed program
-    val state = new CompilationState( programToCompile, config )
+    val compiler = new DeepDiveLogCompiler( programToCompile, config )
 
     // compile the program into blocks of application.conf
-    val blocks = (
-      compileVariableSchema(programToCompile, state)
-      :::
-      (programToCompile flatMap (compile(_, state)))
-      :::
-      compilePipelines(state)
-    )
+    val blocks = compiler.compile()
 
     // emit the generated code
     blocks foreach println
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index 6eeca9b79..2751dbbf8 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -15,19 +15,19 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
     DeepDiveLogSemanticChecker.run(programToCheck, config)
 
     // use schema declarations, etc. in given program
-    val compilationState = new CompilationState(
+    val compiler = new DeepDiveLogCompiler(
       config = config,
-      statements = extraRules ++ program
+      program = extraRules ++ program
     )
     val sql = (extraRules collect {
       // compile supporting rules as CREATE TEMP TABLE queries
       case rule: ExtractionRule =>
-        val qc = new QueryCompiler(rule.q, compilationState)
+        val qc = new compiler.QueryCompiler(rule.q)
         s"""CREATE TEMPORARY TABLE ${rule.headName} AS\n${
-          qc.generateSQL(AliasStyle.ViewAlias)}"""
+          qc.generateSQL(compiler.ViewAlias)}"""
     }) ++ List({
       // compile the query
-      s"""${new QueryCompiler(query, compilationState).generateSQL(AliasStyle.UseVariableAsAlias)}"""
+      s"""${new compiler.QueryCompiler(query).generateSQL(compiler.UseVariableAsAlias)}"""
     }) mkString(";\n\n")
     println(sql)
   }

From 2edca9dbc3b35e1d2fa5b818443602e44dc51236 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 06:31:07 -0800
Subject: [PATCH 299/347] Redefines CompiledBlocks to bring more structure to
 compiler

and separates HOCON codegen to save compiler from falling into a string
manipulation hell
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 164 ++---
 .../arrays/compile.expected                   |  62 +-
 .../chunking_example/compile.expected         | 110 ++--
 .../expressions/compile.expected              | 602 ++++++++----------
 .../factor_functions/compile.expected         |  55 +-
 .../if-then-else/compile.expected             |  77 ++-
 .../compile.expected                          | 409 ++++++------
 .../ocr_example/compile.expected              |  94 +--
 .../smoke_example/compile.expected            | 100 +--
 .../spouse_example/compile.expected           | 155 +++--
 .../compile.expected                          | 177 +++--
 .../views/compile.expected                    |  56 +-
 .../weights/compile.expected                  | 113 ++--
 13 files changed, 1064 insertions(+), 1110 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index aae1ef0ab..2caf02620 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -4,15 +4,13 @@ package org.deepdive.ddlog
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
 import scala.collection.immutable.HashMap
-import org.apache.commons.lang3.StringEscapeUtils
-import scala.collection.mutable.ListBuffer
-import org.deepdive.ddlog.DeepDiveLog.Mode._
 import scala.language.postfixOps
 
 // Compiler that takes parsed program as input and turns into blocks of deepdive.conf
-class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.Config )  {
-  type CompiledBlock = String
-  type CompiledBlocks = List[CompiledBlock]
+class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.Config ) {
+  type CompiledBlocks = List[(String, Any)]  // TODO be more specific
+
+  case class QuotedString(value: String)
 
   val statements = program
 
@@ -396,18 +394,18 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
   def compile(stmt: SchemaDeclaration): CompiledBlocks = {
     // Nothing to compile
-    List()
+    List.empty
   }
 
   def compile(stmt: FunctionDeclaration): CompiledBlocks = {
     // Nothing to compile
-    List()
+    List.empty
   }
 
   // Generate extraction rule part for deepdive
   def compile(stmt: ExtractionRule): CompiledBlocks = {
     val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
-    if (stmts isEmpty) return List()
+    if (stmts isEmpty) return List.empty
 
     val inputQueries = stmts flatMap { case stmt =>
       stmt.q.bodies map { case cqBody =>
@@ -434,10 +432,8 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     }
     val blockName = resolveExtractorBlockName(stmts(0))
     val createTable = hasSchemaDeclared(stmts(0).headName)
-    val extractor = s"""
-      deepdive.extraction.extractors.${blockName} {
-        cmd: \"\"\"
-${if (createTable) {
+    List(s"deepdive.extraction.extractors.${blockName}" -> Map(
+      "cmd" -> QuotedString(if (createTable) {
 	s"""
 	# TODO use temporary table
 	deepdive create table "${stmts(0).headName}"
@@ -448,29 +444,25 @@ ${if (createTable) {
 	s"""
 	deepdive create view ${stmts(0).headName} as ${escape4sh(inputQueries.mkString("\nUNION ALL\n"))}
 	"""
-}}
-        \"\"\"
-          output_relation: \"${stmts(0).headName}\"
-        style: "cmd_extractor"
-          input_relations: [${
-            (stmts flatMap relationNamesUsedByStatement distinct
-            ) mkString("\n            ", "\n            ", "\n          ")}]
-      }
-    """
-    List(extractor)
+}),
+      "output_relation" -> stmts(0).headName,
+      "style" -> "cmd_extractor",
+      "input_relations" -> (stmts flatMap relationNamesUsedByStatement distinct)
+    ))
   }
 
   def compile(stmt: FunctionCallRule): CompiledBlocks = {
     val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: FunctionCallRule => s }
-    if (stmts isEmpty) return List()
+    if (stmts isEmpty) return List.empty
 
     stmts map { case stmt =>
       val function = functionDeclarationByName(stmt.function)
-      val udfDetails = (function.implementations collectFirst {
-        case impl: RowWiseLineHandler =>
-          s"""udf: $${APP_HOME}\"/${StringEscapeUtils.escapeJava(impl.command)}\"
-          style: \"${impl.style}_extractor\" """
-      })
+      val udfDetails = function.implementations collectFirst {
+        case impl: RowWiseLineHandler => List(
+            "udf" -> QuotedString(impl.command),
+            "style" -> s"${impl.style}_extractor"
+          )
+      }
 
       if (udfDetails.isEmpty)
         sys.error(s"Cannot find compilable implementation for function ${stmt.function} among:\n  "
@@ -478,19 +470,13 @@ ${if (createTable) {
 
       val blockName = resolveExtractorBlockName(stmt)
       val parallelism = stmt.parallelism getOrElse("${PARALLELISM}")
-      s"""
-        deepdive.extraction.extractors.${blockName} {
-          input: \"\"\" ${new QueryCompiler(stmt.q).generateSQL(TableAlias)}
-          \"\"\"
-          output_relation: \"${stmt.output}\"
-          ${udfDetails.get}
-          input_relations: [${
-            (List(stmt) flatMap relationNamesUsedByStatement distinct
-            ) mkString("\n            ", "\n            ", "\n          ")}]
-          input_batch_size: $${INPUT_BATCH_SIZE}
-          parallelism: ${parallelism}
-        }
-      """
+      s"deepdive.extraction.extractors.${blockName}" -> (Map(
+        "input" -> QuotedString(new QueryCompiler(stmt.q).generateSQL(TableAlias)),
+        "output_relation" -> stmt.output,
+        "input_relations" -> (List(stmt) flatMap relationNamesUsedByStatement distinct),
+        "input_batch_size" -> "${INPUT_BATCH_SIZE}",
+        "parallelism" -> parallelism
+        ) ++ udfDetails.get)
     }
   }
 
@@ -580,18 +566,16 @@ ${if (createTable) {
       }
     }
 
-    List(s"""
-        deepdive.inference.factors.${resolveInferenceBlockName(stmt)} {
-          input_query: \"\"\"${inputQueries.mkString(" UNION ALL ")}\"\"\"
-          function: "${func}"
-          weight: "${weight}"
-          input_relations: [${
-            val relationsInHead = stmt.head.terms map (_.name)
-            val relationsInBody = relationNamesUsedByStatement getOrElse(stmt, List.empty)
-            ((relationsInHead ++ relationsInBody) distinct
-            ) mkString("\n            ", "\n            ", "\n          ")}]
+    List(s"deepdive.inference.factors.${resolveInferenceBlockName(stmt)}" -> Map(
+        "input_query" -> QuotedString(inputQueries.mkString(" UNION ALL ")),
+        "function" -> QuotedString(func),
+        "weight" -> QuotedString(weight),
+        "input_relations" -> {
+          val relationsInHead = stmt.head.terms map (_.name)
+          val relationsInBody = relationNamesUsedByStatement getOrElse(stmt, List.empty)
+          (relationsInHead ++ relationsInBody) distinct
         }
-      """)
+    ))
   }
 
   def compile(stmt: Statement): CompiledBlocks = stmt match {
@@ -605,38 +589,35 @@ ${if (createTable) {
 
   // generate application.conf pipelines
   def compilePipelines(): CompiledBlocks = {
-    val run = "deepdive.pipeline.run: ${PIPELINE}"
-    val extraction = (representativeStatements map { s => resolveExtractorBlockName(s)}).mkString("\n  ")
-    val extraction_pipeline = if (extraction.length > 0) s"deepdive.pipeline.pipelines.extraction: [\n  ${extraction}\n]" else ""
-    val inference = (inferenceRules map {s => resolveInferenceBlockName(s)}).mkString("\n  ")
-    val inference_pipeline = if (inference.length > 0) s"deepdive.pipeline.pipelines.inference: [\n  ${inference}\n]" else ""
-    val endtoend = List(extraction, inference).filter(_ != "").mkString("\n  ")
-    val endtoend_pipeline = if (endtoend.length > 0) s"deepdive.pipeline.pipelines.endtoend: [\n  ${endtoend}\n]" else ""
-    List(run, extraction_pipeline, inference_pipeline, endtoend_pipeline).filter(_ != "")
+    val run = List("deepdive.pipeline.run" -> "${PIPELINE}")
+    val extraction = statements filter(representativeStatements contains _) map resolveExtractorBlockName
+    val extraction_pipeline = if (extraction nonEmpty) List("deepdive.pipeline.pipelines.extraction" -> extraction) else List.empty
+    val inference = inferenceRules map resolveInferenceBlockName
+    val inference_pipeline = if (inference nonEmpty) List("deepdive.pipeline.pipelines.inference" -> inference) else List.empty
+    val endtoend = extraction ++ inference
+    val endtoend_pipeline = if (endtoend nonEmpty) List("deepdive.pipeline.pipelines.endtoend" -> endtoend) else List.empty
+
+    run ++ extraction_pipeline ++ inference_pipeline ++ endtoend_pipeline
   }
 
   // generate variable schema statements
   def compileVariableSchema(): CompiledBlocks = {
     // generate the statements.
-    List(s"""
-      deepdive.schema.variables {
-    ${statements collect {
+    List("deepdive.schema.variables" -> (statements collect {
       case decl: SchemaDeclaration if decl.isQuery =>
-          val variableTypeDecl = decl.variableType match {
-            case Some(MultinomialType(x)) => s"Categorical(${x})"
-            case _ => "Boolean"
-          }
-          s"${decl.a.name}.label: ${variableTypeDecl}"
-    } mkString("\n")}
-      }
-    """)
+        s"${decl.a.name}.label" -> (decl.variableType match {
+          case Some(MultinomialType(x)) => s"Categorical(${x})"
+          case _ => "Boolean"
+        })
+      } toMap)
+    )
   }
 
   def compile(): CompiledBlocks = (
     compileVariableSchema()
-    :::
+    ++
     (statements flatMap compile)
-    :::
+    ++
     compilePipelines()
   )
 
@@ -653,10 +634,39 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // take an initial pass to analyze the parsed program
     val compiler = new DeepDiveLogCompiler( programToCompile, config )
 
-    // compile the program into blocks of application.conf
+    // compile the program into blocks of deepdive.conf
     val blocks = compiler.compile()
 
-    // emit the generated code
-    blocks foreach println
+    // codegen HOCON
+    def codegenValue(value: Any): String = value match {
+      case compiler.QuotedString(s) => // multi-line string
+        s"""\"\"\"${s replaceAll("\"\"\"", "\\\"\\\"\\\"")}\"\"\""""
+      case _ =>
+        value.toString
+    }
+    def codegen(key: String, value: Any): String = value match {
+      case m: Map[_, _] => // map
+        s"""${key} {
+           |${m map { case (k, v) => codegen(k.toString, v) } mkString("")}
+           |}
+           |""".stripMargin
+
+      case l: List[_] => // lists
+        s"""${key}: [${l map codegenValue mkString("\n  ", "\n  ", "")}
+           |]
+           |""".stripMargin
+      case l: Set[_] => // sets
+        s"""${key}: [${l map codegenValue mkString("\n  ", "\n  ", "")}
+           |]
+           |""".stripMargin
+
+      case _ =>
+        s"""${key}: ${codegenValue(value)}
+           |""".stripMargin
+
+    }
+
+    blocks foreach { case (key, value) => println(codegen(key, value)) }
   }
+
 }
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index a6b5da57d..0ce74f141 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -1,48 +1,46 @@
+deepdive.schema.variables {
 
-      deepdive.schema.variables {
-        
-      }
-    
-
-      deepdive.extraction.extractors.ext_T {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_T {
+cmd: """
 	deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
 FROM R R0, S R1
         WHERE R0.x[1] = R1.y[1] AND R0.x[2] = R1.y[2]'
-	
-        """
-          output_relation: "T"
-        style: "cmd_extractor"
-          input_relations: [
-            R
-            S
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_U {
-        cmd: """
+	"""
+output_relation: T
+style: cmd_extractor
+input_relations: [
+  R
+  S
+]
 
+}
+
+deepdive.extraction.extractors.ext_U {
+cmd: """
 	deepdive create view U as 'SELECT R1.x AS column_0
 FROM R R0, S R1
         WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]'
-	
-        """
-          output_relation: "U"
-        style: "cmd_extractor"
-          input_relations: [
-            R
-            S
-          ]
-      }
-    
+	"""
+output_relation: U
+style: cmd_extractor
+input_relations: [
+  R
+  S
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_U
   ext_T
+  ext_U
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_U
   ext_T
+  ext_U
 ]
+
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index f0e812c95..aa9ddea5a 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -1,44 +1,40 @@
+deepdive.schema.variables {
+tag.label: Categorical(13)
 
-      deepdive.schema.variables {
-        tag.label: Categorical(13)
-      }
-    
+}
 
-        deepdive.extraction.extractors.ext_words_by_ext_training {
-          input: """ SELECT R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.tag AS "words_raw.R0.tag"
+deepdive.extraction.extractors.ext_words_by_ext_training {
+parallelism: ${PARALLELISM}
+input_relations: [
+  words_raw
+]
+style: tsv_extractor
+output_relation: words
+udf: """udf/ext_training.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.tag AS "words_raw.R0.tag"
 FROM words_raw R0
-        
-          """
-          output_relation: "words"
-          udf: ${APP_HOME}"/udf/ext_training.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            words_raw
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
+        """
 
-        deepdive.extraction.extractors.ext_word_features_by_ext_features {
-          input: """ SELECT R0.word_id AS "words.R0.word_id", R0.word AS "words.R0.word", R0.pos AS "words.R0.pos", R1.word AS "words.R1.word", R1.pos AS "words.R1.pos"
+}
+
+deepdive.extraction.extractors.ext_word_features_by_ext_features {
+parallelism: ${PARALLELISM}
+input_relations: [
+  words
+]
+style: tsv_extractor
+output_relation: word_features
+udf: """udf/ext_features.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.word_id AS "words.R0.word_id", R0.word AS "words.R0.word", R0.pos AS "words.R0.pos", R1.word AS "words.R1.word", R1.pos AS "words.R1.pos"
 FROM words R0, words R1
-        WHERE R1.sent_id = R0.sent_id 
-          """
-          output_relation: "word_features"
-          udf: ${APP_HOME}"/udf/ext_features.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            words
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
+        WHERE R1.sent_id = R0.sent_id """
 
-      deepdive.extraction.extractors.ext_tag {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_tag {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "tag"
 	deepdive sql 'INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
@@ -46,41 +42,45 @@ FROM words R0, words R1
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "tag"
-        style: "cmd_extractor"
-          input_relations: [
-            words
-          ]
-      }
-    
+	"""
+output_relation: tag
+style: cmd_extractor
+input_relations: [
+  words
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_tag {
-          input_query: """
+deepdive.inference.factors.inf_istrue_tag {
+input_query: """
           SELECT R0.id AS "tag.R0.id" , R1.feature AS "dd_weight_column_0" 
           FROM tag R0, word_features R1
         WHERE R1.word_id = R0.word_id """
-          function: "Multinomial(tag.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            tag
-            word_features
-          ]
-        }
-      
+function: """Multinomial(tag.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  tag
+  word_features
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
   ext_words_by_ext_training
-  ext_tag
   ext_word_features_by_ext_features
+  ext_tag
 ]
+
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_tag
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
   ext_words_by_ext_training
-  ext_tag
   ext_word_features_by_ext_features
+  ext_tag
   inf_istrue_tag
 ]
+
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index c13de53c4..3500847d7 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -1,439 +1,395 @@
+deepdive.schema.variables {
 
-      deepdive.schema.variables {
-        
-      }
-    
-
-      deepdive.extraction.extractors.ext_Q {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_Q {
+cmd: """
 	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
 FROM a R0, b R1, c R2
         WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))'
-	
-        """
-          output_relation: "Q"
-        style: "cmd_extractor"
-          input_relations: [
-            a
-            b
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_P {
-        cmd: """
+	"""
+output_relation: Q
+style: cmd_extractor
+input_relations: [
+  a
+  b
+  c
+]
+
+}
 
+deepdive.extraction.extractors.ext_P {
+cmd: """
 	deepdive create view P as 'SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
 FROM a R0, b R1
         WHERE R1.k = R0.k 
         GROUP BY R1.p, R1.q'
-	
-        """
-          output_relation: "P"
-        style: "cmd_extractor"
-          input_relations: [
-            a
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_A {
-        cmd: """
+	"""
+output_relation: P
+style: cmd_extractor
+input_relations: [
+  a
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_A {
+cmd: """
 	deepdive create view A as 'SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
 FROM b R0
         '
-	
-        """
-          output_relation: "A"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_B {
-        cmd: """
+	"""
+output_relation: A
+style: cmd_extractor
+input_relations: [
+  b
+]
 
+}
+
+deepdive.extraction.extractors.ext_B {
+cmd: """
 	deepdive create view B as 'SELECT func(R0.k + (R0.r + R0.k)) AS column_0
 FROM b R0
         '
-	
-        """
-          output_relation: "B"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_C {
-        cmd: """
+	"""
+output_relation: B
+style: cmd_extractor
+input_relations: [
+  b
+]
 
+}
+
+deepdive.extraction.extractors.ext_C {
+cmd: """
 	deepdive create view C as 'SELECT func(func(func(R0.k))) AS column_0
 FROM b R0
         '
-	
-        """
-          output_relation: "C"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_D {
-        cmd: """
+	"""
+output_relation: C
+style: cmd_extractor
+input_relations: [
+  b
+]
 
+}
+
+deepdive.extraction.extractors.ext_D {
+cmd: """
 	deepdive create view D as 'SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
 FROM b R0
         '
-	
-        """
-          output_relation: "D"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_E {
-        cmd: """
+	"""
+output_relation: D
+style: cmd_extractor
+input_relations: [
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_E {
+cmd: """
 	deepdive create view E as 'SELECT (R0.k :: INT) AS column_0
 FROM b R0
         '
-	
-        """
-          output_relation: "E"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_F {
-        cmd: """
+	"""
+output_relation: E
+style: cmd_extractor
+input_relations: [
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_F {
+cmd: """
 	deepdive create view F as 'SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
 FROM b R0
         '
-	
-        """
-          output_relation: "F"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_G {
-        cmd: """
+	"""
+output_relation: F
+style: cmd_extractor
+input_relations: [
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_G {
+cmd: """
 	deepdive create view G as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE (R0.k + R0.r) = 100'
-	
-        """
-          output_relation: "G"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_H {
-        cmd: """
+	"""
+output_relation: G
+style: cmd_extractor
+input_relations: [
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_H {
+cmd: """
 	deepdive create view H as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE (R0.k + R0.r) = 100 AND R0.k > 50'
-	
-        """
-          output_relation: "H"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_I {
-        cmd: """
+	"""
+output_relation: H
+style: cmd_extractor
+input_relations: [
+  b
+]
 
+}
+
+deepdive.extraction.extractors.ext_I {
+cmd: """
 	deepdive create view I as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
-	
-        """
-          output_relation: "I"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_J {
-        cmd: """
+	"""
+output_relation: I
+style: cmd_extractor
+input_relations: [
+  b
+]
 
+}
+
+deepdive.extraction.extractors.ext_J {
+cmd: """
 	deepdive create view J as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)'
-	
-        """
-          output_relation: "J"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_K {
-        cmd: """
+	"""
+output_relation: J
+style: cmd_extractor
+input_relations: [
+  b
+]
 
+}
+
+deepdive.extraction.extractors.ext_K {
+cmd: """
 	deepdive create view K as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))'
-	
-        """
-          output_relation: "K"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_L {
-        cmd: """
+	"""
+output_relation: K
+style: cmd_extractor
+input_relations: [
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_L {
+cmd: """
 	deepdive create view L as 'SELECT DISTINCT R0.k AS column_0
 FROM b R0
         
 LIMIT 100'
-	
-        """
-          output_relation: "L"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_M {
-        cmd: """
+	"""
+output_relation: L
+style: cmd_extractor
+input_relations: [
+  b
+]
+
+}
 
+deepdive.extraction.extractors.ext_M {
+cmd: """
 	deepdive create view M as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )'
-	
-        """
-          output_relation: "M"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_N {
-        cmd: """
+	"""
+output_relation: M
+style: cmd_extractor
+input_relations: [
+  b
+  c
+]
+
+}
 
+deepdive.extraction.extractors.ext_N {
+cmd: """
 	deepdive create view N as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > '\''a'\'')'
-	
-        """
-          output_relation: "N"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_O {
-        cmd: """
+	"""
+output_relation: N
+style: cmd_extractor
+input_relations: [
+  b
+  c
+]
+
+}
 
+deepdive.extraction.extractors.ext_O {
+cmd: """
 	deepdive create view O as 'SELECT R0.k AS column_0
 FROM b R0
         WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )'
-	
-        """
-          output_relation: "O"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-            a
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_S {
-        cmd: """
+	"""
+output_relation: O
+style: cmd_extractor
+input_relations: [
+  b
+  c
+  a
+]
 
+}
+
+deepdive.extraction.extractors.ext_S {
+cmd: """
 	deepdive create view S as 'SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
         '
-	
-        """
-          output_relation: "S"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_T {
-        cmd: """
+	"""
+output_relation: S
+style: cmd_extractor
+input_relations: [
+  b
+  c
+]
 
+}
+
+deepdive.extraction.extractors.ext_T {
+cmd: """
 	deepdive create view T as 'SELECT R0.k AS column_0
 FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
         WHERE R1_0.s > R0.p'
-	
-        """
-          output_relation: "T"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_U {
-        cmd: """
+	"""
+output_relation: T
+style: cmd_extractor
+input_relations: [
+  b
+  c
+]
 
+}
+
+deepdive.extraction.extractors.ext_U {
+cmd: """
 	deepdive create view U as 'SELECT R0_0.k AS column_0
 FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
         '
-	
-        """
-          output_relation: "U"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_W {
-        cmd: """
+	"""
+output_relation: U
+style: cmd_extractor
+input_relations: [
+  b
+  c
+]
+
+}
 
+deepdive.extraction.extractors.ext_W {
+cmd: """
 	deepdive create view W as 'SELECT R0.k AS column_0
 FROM a R0
         WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))'
-	
-        """
-          output_relation: "W"
-        style: "cmd_extractor"
-          input_relations: [
-            a
-            c
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_V {
-        cmd: """
+	"""
+output_relation: W
+style: cmd_extractor
+input_relations: [
+  a
+  c
+]
+
+}
 
+deepdive.extraction.extractors.ext_V {
+cmd: """
 	deepdive create view V as 'SELECT R0.n AS column_0
 FROM c R0, a R1
         WHERE R1.k = R0.n '
-	
-        """
-          output_relation: "V"
-        style: "cmd_extractor"
-          input_relations: [
-            c
-            a
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_X {
-        cmd: """
+	"""
+output_relation: V
+style: cmd_extractor
+input_relations: [
+  c
+  a
+]
+
+}
 
+deepdive.extraction.extractors.ext_X {
+cmd: """
 	deepdive create view X as 'SELECT R0.k AS column_0
 FROM b R0, c R1
         WHERE R1.n = R0.k '
-	
-        """
-          output_relation: "X"
-        style: "cmd_extractor"
-          input_relations: [
-            b
-            c
-          ]
-      }
-    
+	"""
+output_relation: X
+style: cmd_extractor
+input_relations: [
+  b
+  c
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_M
   ext_Q
+  ext_P
+  ext_A
   ext_B
-  ext_U
+  ext_C
+  ext_D
+  ext_E
   ext_F
+  ext_G
+  ext_H
   ext_I
-  ext_N
-  ext_T
-  ext_A
-  ext_P
-  ext_K
-  ext_E
-  ext_W
   ext_J
-  ext_D
-  ext_O
+  ext_K
   ext_L
-  ext_G
-  ext_X
+  ext_M
+  ext_N
+  ext_O
   ext_S
-  ext_C
+  ext_T
+  ext_U
+  ext_W
   ext_V
-  ext_H
+  ext_X
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_M
   ext_Q
+  ext_P
+  ext_A
   ext_B
-  ext_U
+  ext_C
+  ext_D
+  ext_E
   ext_F
+  ext_G
+  ext_H
   ext_I
-  ext_N
-  ext_T
-  ext_A
-  ext_P
-  ext_K
-  ext_E
-  ext_W
   ext_J
-  ext_D
-  ext_O
+  ext_K
   ext_L
-  ext_G
-  ext_X
+  ext_M
+  ext_N
+  ext_O
   ext_S
-  ext_C
+  ext_T
+  ext_U
+  ext_W
   ext_V
-  ext_H
+  ext_X
 ]
+
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 2f10bd31a..a5631d8f7 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -1,43 +1,46 @@
-
-      deepdive.schema.variables {
-        S.label: Boolean
+deepdive.schema.variables {
+S.label: Boolean
 Q.label: Boolean
-      }
-    
 
-        deepdive.inference.factors.inf_imply_Q_Q {
-          input_query: """
+}
+
+deepdive.inference.factors.inf_imply_Q_Q {
+input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
           FROM Q R0, Q R1, R R2
         WHERE R2.a = R0.x  AND R2.b = R1.x """
-          function: "Imply(Q.R0.label, Q.R1.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            Q
-            R
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf_equal_Q_Q {
-          input_query: """
+function: """Imply(Q.R0.label, Q.R1.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  Q
+  R
+]
+
+}
+
+deepdive.inference.factors.inf_equal_Q_Q {
+input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
           FROM Q R0, Q R1, R R2
         WHERE R2.a = R0.x  AND R2.b = R1.x """
-          function: "Equal(Q.R0.label, !Q.R1.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            Q
-            R
-          ]
-        }
-      
+function: """Equal(Q.R0.label, !Q.R1.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  Q
+  R
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.inference: [
   inf_imply_Q_Q
   inf_equal_Q_Q
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
   inf_imply_Q_Q
   inf_equal_Q_Q
 ]
+
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 9774c6e81..8e5b7ce81 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -1,12 +1,10 @@
+deepdive.schema.variables {
+q.label: Boolean
 
-      deepdive.schema.variables {
-        q.label: Boolean
-      }
-    
-
-      deepdive.extraction.extractors.ext_q {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_q {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "q"
 	deepdive sql 'INSERT INTO q SELECT DISTINCT R0.x, 0 AS id, 
@@ -18,19 +16,17 @@ END AS label
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "q"
-        style: "cmd_extractor"
-          input_relations: [
-            labels_resolved
-          ]
-      }
-    
+	"""
+output_relation: q
+style: cmd_extractor
+input_relations: [
+  labels_resolved
+]
 
-      deepdive.extraction.extractors.ext_p {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_p {
+cmd: """
 	deepdive create view p as 'SELECT R0.x AS column_0, 
 CASE WHEN abs(R0.l) > 10 THEN true
      ELSE false
@@ -44,19 +40,17 @@ CASE WHEN (R0.x % 10) = 0 THEN false
 END AS column_1
 FROM labels R0
         '
-	
-        """
-          output_relation: "p"
-        style: "cmd_extractor"
-          input_relations: [
-            labels
-          ]
-      }
-    
+	"""
+output_relation: p
+style: cmd_extractor
+input_relations: [
+  labels
+]
 
-      deepdive.extraction.extractors.ext_labels_resolved {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_labels_resolved {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "labels_resolved"
 	deepdive sql 'INSERT INTO labels_resolved SELECT R0.x AS "labels.R0.x", SUM(
@@ -68,23 +62,26 @@ FROM labels R0
         
         GROUP BY R0.x'
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "labels_resolved"
-        style: "cmd_extractor"
-          input_relations: [
-            labels
-          ]
-      }
-    
+	"""
+output_relation: labels_resolved
+style: cmd_extractor
+input_relations: [
+  labels
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_labels_resolved
   ext_q
   ext_p
+  ext_labels_resolved
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_labels_resolved
   ext_q
   ext_p
+  ext_labels_resolved
 ]
+
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index d486589ea..1fb8cc7e9 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -1,12 +1,10 @@
+deepdive.schema.variables {
+Q.label: Boolean
 
-      deepdive.schema.variables {
-        Q.label: Boolean
-      }
-    
-
-      deepdive.extraction.extractors.ext_S {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_S {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "S"
 	deepdive sql 'INSERT INTO S SELECT R0.a AS "R.R0.a"
@@ -33,38 +31,35 @@ SELECT R0.a AS "S_2.R0.a"
 FROM S_2 R0
         '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "S"
-        style: "cmd_extractor"
-          input_relations: [
-            R
-            S_0
-            S_1
-            S_2
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_T___0_by_f {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+	"""
+output_relation: S
+style: cmd_extractor
+input_relations: [
+  R
+  S_0
+  S_1
+  S_2
+]
+
+}
+
+deepdive.extraction.extractors.ext_T___0_by_f {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: T___0
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE R0.a > 1000
-          """
-          output_relation: "T___0"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-      deepdive.extraction.extractors.ext_T {
-        cmd: """
+        WHERE R0.a > 1000"""
+
+}
 
+deepdive.extraction.extractors.ext_T {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "T"
 	deepdive sql 'INSERT INTO T SELECT R0.a AS "T___0.R0.a"
@@ -83,220 +78,216 @@ SELECT R0.a AS "T___3.R0.a"
 FROM T___3 R0
         '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "T"
-        style: "cmd_extractor"
-          input_relations: [
-            T___0
-            T___1
-            T___2
-            T___3
-          ]
-      }
-    
-
-        deepdive.extraction.extractors.ext_T___1_by_f {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+	"""
+output_relation: T
+style: cmd_extractor
+input_relations: [
+  T___0
+  T___1
+  T___2
+  T___3
+]
+
+}
+
+deepdive.extraction.extractors.ext_T___1_by_f {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: T___1
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE 10 < R0.a AND R0.a < 20
-          """
-          output_relation: "T___1"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_T___2_by_f {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+        WHERE 10 < R0.a AND R0.a < 20"""
+
+}
+
+deepdive.extraction.extractors.ext_T___2_by_f {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: T___2
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE 100 < R0.a AND R0.a < 200
-          """
-          output_relation: "T___2"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_S_0_by_f {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+        WHERE 100 < R0.a AND R0.a < 200"""
+
+}
+
+deepdive.extraction.extractors.ext_S_0_by_f {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: S_0
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE R0.a < 0
-          """
-          output_relation: "S_0"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_S_1_by_f {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+        WHERE R0.a < 0"""
+
+}
+
+deepdive.extraction.extractors.ext_S_1_by_f {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: S_1
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE R0.a > 0
-          """
-          output_relation: "S_1"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_T___3_by_f_1 {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+        WHERE R0.a > 0"""
+
+}
+
+deepdive.extraction.extractors.ext_T___3_by_f_1 {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: T___3
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        
-          """
-          output_relation: "T___3"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_S_2_by_f_1 {
-          input: """ SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+        """
+
+}
+
+deepdive.extraction.extractors.ext_S_2_by_f_1 {
+parallelism: ${PARALLELISM}
+input_relations: [
+  R
+]
+style: tsv_extractor
+output_relation: S_2
+udf: """/bin/false"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
 FROM R R0
-        WHERE R0.a > 0
-          """
-          output_relation: "S_2"
-          udf: ${APP_HOME}"//bin/false"
-          style: "tsv_extractor" 
-          input_relations: [
-            R
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.inference.factors.inf_istrue_Q {
-          input_query: """
+        WHERE R0.a > 0"""
+
+}
+
+deepdive.inference.factors.inf_istrue_Q {
+input_query: """
           SELECT R0.id AS "Q.R0.id" , R0.x AS "dd_weight_column_0" 
           FROM Q R0, S R1
         WHERE R1.a = R0.x  AND R0.x > 1000"""
-          function: "Imply(Q.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            Q
-            S
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf1_istrue_Q {
-          input_query: """
+function: """Imply(Q.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  Q
+  S
+]
+
+}
+
+deepdive.inference.factors.inf1_istrue_Q {
+input_query: """
           SELECT R0.id AS "Q.R0.id" 
           FROM Q R0, S R1
         WHERE R1.a = R0.x  AND R0.x = 0"""
-          function: "Imply(Q.R0.label)"
-          weight: "1.0"
-          input_relations: [
-            Q
-            S
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf_imply_Q_Q {
-          input_query: """
+function: """Imply(Q.R0.label)"""
+weight: """1.0"""
+input_relations: [
+  Q
+  S
+]
+
+}
+
+deepdive.inference.factors.inf_imply_Q_Q {
+input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R0.x AS "dd_weight_column_0" 
           FROM Q R0, Q R1, S R2, R R3, S R4
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
-          function: "Imply(Q.R0.label, Q.R1.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            Q
-            S
-            R
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf1_imply_Q_Q {
-          input_query: """
+function: """Imply(Q.R0.label, Q.R1.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  Q
+  S
+  R
+]
+
+}
+
+deepdive.inference.factors.inf1_imply_Q_Q {
+input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
           FROM Q R0, Q R1, S R2, R R3, S R4
         WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
-          function: "Imply(Q.R0.label, Q.R1.label)"
-          weight: "-10.0"
-          input_relations: [
-            Q
-            S
-            R
-          ]
-        }
-      
-
-      deepdive.extraction.extractors.ext_T__3 {
-        cmd: """
+function: """Imply(Q.R0.label, Q.R1.label)"""
+weight: """-10.0"""
+input_relations: [
+  Q
+  S
+  R
+]
+
+}
 
+deepdive.extraction.extractors.ext_T__3 {
+cmd: """
 	deepdive create view T__3 as 'SELECT R0.a AS column_0
 FROM T R0
         '
-	
-        """
-          output_relation: "T__3"
-        style: "cmd_extractor"
-          input_relations: [
-            T
-          ]
-      }
-    
+	"""
+output_relation: T__3
+style: cmd_extractor
+input_relations: [
+  T
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_S_1_by_f
+  ext_S
+  ext_T___0_by_f
   ext_T
-  ext_S_2_by_f_1
+  ext_T___1_by_f
+  ext_T___2_by_f
   ext_S_0_by_f
+  ext_S_1_by_f
   ext_T___3_by_f_1
+  ext_S_2_by_f_1
   ext_T__3
-  ext_T___2_by_f
-  ext_T___0_by_f
-  ext_S
-  ext_T___1_by_f
 ]
+
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_Q
   inf1_istrue_Q
   inf_imply_Q_Q
   inf1_imply_Q_Q
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_S_1_by_f
+  ext_S
+  ext_T___0_by_f
   ext_T
-  ext_S_2_by_f_1
+  ext_T___1_by_f
+  ext_T___2_by_f
   ext_S_0_by_f
+  ext_S_1_by_f
   ext_T___3_by_f_1
+  ext_S_2_by_f_1
   ext_T__3
-  ext_T___2_by_f
-  ext_T___0_by_f
-  ext_S
-  ext_T___1_by_f
   inf_istrue_Q
   inf1_istrue_Q
   inf_imply_Q_Q
   inf1_imply_Q_Q
 ]
+
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index fdd780023..e19233af0 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -1,13 +1,11 @@
-
-      deepdive.schema.variables {
-        q1.label: Boolean
+deepdive.schema.variables {
+q1.label: Boolean
 q2.label: Boolean
-      }
-    
 
-      deepdive.extraction.extractors.ext_q1 {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_q1 {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "q1"
 	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
@@ -15,19 +13,17 @@ q2.label: Boolean
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "q1"
-        style: "cmd_extractor"
-          input_relations: [
-            label1
-          ]
-      }
-    
+	"""
+output_relation: q1
+style: cmd_extractor
+input_relations: [
+  label1
+]
 
-      deepdive.extraction.extractors.ext_q2 {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_q2 {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "q2"
 	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
@@ -35,55 +31,59 @@ q2.label: Boolean
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "q2"
-        style: "cmd_extractor"
-          input_relations: [
-            label2
-          ]
-      }
-    
+	"""
+output_relation: q2
+style: cmd_extractor
+input_relations: [
+  label2
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_q1 {
-          input_query: """
+deepdive.inference.factors.inf_istrue_q1 {
+input_query: """
           SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q1 R0, features R1
         WHERE R1.word_id = R0.wid """
-          function: "Imply(q1.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            q1
-            features
-          ]
-        }
-      
+function: """Imply(q1.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  q1
+  features
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_q2 {
-          input_query: """
+deepdive.inference.factors.inf_istrue_q2 {
+input_query: """
           SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
           FROM q2 R0, features R1
         WHERE R1.word_id = R0.wid """
-          function: "Imply(q2.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            q2
-            features
-          ]
-        }
-      
+function: """Imply(q2.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  q2
+  features
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
   ext_q1
   ext_q2
 ]
+
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_q1
   inf_istrue_q2
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
   ext_q1
   ext_q2
   inf_istrue_q1
   inf_istrue_q2
 ]
+
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index baebffdfb..7ea48be66 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -1,13 +1,11 @@
-
-      deepdive.schema.variables {
-        smoke.label: Boolean
+deepdive.schema.variables {
+smoke.label: Boolean
 cancer.label: Boolean
-      }
-    
 
-      deepdive.extraction.extractors.ext_smoke {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_smoke {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "smoke"
 	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
@@ -15,19 +13,17 @@ cancer.label: Boolean
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "smoke"
-        style: "cmd_extractor"
-          input_relations: [
-            person_smokes
-          ]
-      }
-    
+	"""
+output_relation: smoke
+style: cmd_extractor
+input_relations: [
+  person_smokes
+]
 
-      deepdive.extraction.extractors.ext_cancer {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_cancer {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "cancer"
 	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
@@ -35,56 +31,60 @@ cancer.label: Boolean
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "cancer"
-        style: "cmd_extractor"
-          input_relations: [
-            person_has_cancer
-          ]
-      }
-    
+	"""
+output_relation: cancer
+style: cmd_extractor
+input_relations: [
+  person_has_cancer
+]
 
-        deepdive.inference.factors.inf_imply_smoke_cancer {
-          input_query: """
+}
+
+deepdive.inference.factors.inf_imply_smoke_cancer {
+input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
           FROM smoke R0, cancer R1, person_smokes R2
         WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
-          function: "Imply(smoke.R0.label, cancer.R1.label)"
-          weight: "0.5"
-          input_relations: [
-            smoke
-            cancer
-            person_smokes
-          ]
-        }
-      
+function: """Imply(smoke.R0.label, cancer.R1.label)"""
+weight: """0.5"""
+input_relations: [
+  smoke
+  cancer
+  person_smokes
+]
 
-        deepdive.inference.factors.inf_imply_smoke_smoke {
-          input_query: """
+}
+
+deepdive.inference.factors.inf_imply_smoke_smoke {
+input_query: """
           SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
           FROM smoke R0, smoke R1, friends R2
         WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
-          function: "Imply(smoke.R0.label, smoke.R1.label)"
-          weight: "0.4"
-          input_relations: [
-            smoke
-            friends
-          ]
-        }
-      
+function: """Imply(smoke.R0.label, smoke.R1.label)"""
+weight: """0.4"""
+input_relations: [
+  smoke
+  friends
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_cancer
   ext_smoke
+  ext_cancer
 ]
+
 deepdive.pipeline.pipelines.inference: [
   inf_imply_smoke_cancer
   inf_imply_smoke_smoke
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_cancer
   ext_smoke
+  ext_cancer
   inf_imply_smoke_cancer
   inf_imply_smoke_smoke
 ]
+
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index f8dc85d4f..18fb269f4 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -1,62 +1,57 @@
+deepdive.schema.variables {
+has_spouse.label: Boolean
 
-      deepdive.schema.variables {
-        has_spouse.label: Boolean
-      }
-    
+}
 
-        deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
-          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
+deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
+parallelism: ${PARALLELISM}
+input_relations: [
+  sentences
+]
+style: tsv_extractor
+output_relation: people_mentions
+udf: """udf/ext_people.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
-        
-          """
-          output_relation: "people_mentions"
-          udf: ${APP_HOME}"/udf/ext_people.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            sentences
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
-          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
+        """
+
+}
+
+deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
+parallelism: ${PARALLELISM}
+input_relations: [
+  people_mentions
+]
+style: tsv_extractor
+output_relation: has_spouse_candidates
+udf: """udf/ext_has_spouse.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-          """
-          output_relation: "has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
-          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
+        WHERE R1.sentence_id = R0.sentence_id """
+
+}
+
+deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
+parallelism: ${PARALLELISM}
+input_relations: [
+  sentences
+  has_spouse_candidates
+  people_mentions
+]
+style: tsv_extractor
+output_relation: has_spouse_features
+udf: """udf/ext_has_spouse_features.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-          """
-          output_relation: "has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            sentences
-            has_spouse_candidates
-            people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-      deepdive.extraction.extractors.ext_has_spouse {
-        cmd: """
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id """
+
+}
 
+deepdive.extraction.extractors.ext_has_spouse {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "has_spouse"
 	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
@@ -64,44 +59,48 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse"
-        style: "cmd_extractor"
-          input_relations: [
-            has_spouse_candidates
-          ]
-      }
-    
-
-        deepdive.inference.factors.inf_istrue_has_spouse {
-          input_query: """
+	"""
+output_relation: has_spouse
+style: cmd_extractor
+input_relations: [
+  has_spouse_candidates
+]
+
+}
+
+deepdive.inference.factors.inf_istrue_has_spouse {
+input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(has_spouse.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            has_spouse
-            has_spouse_candidates
-            has_spouse_features
-          ]
-        }
-      
+function: """Imply(has_spouse.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  has_spouse
+  has_spouse_candidates
+  has_spouse_features
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_features_by_ext_has_spouse_features
   ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse
 ]
+
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_has_spouse
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_features_by_ext_has_spouse_features
   ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse
   inf_istrue_has_spouse
 ]
+
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index a84b4b658..2ea1fd2b8 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -1,62 +1,57 @@
+deepdive.schema.variables {
+has_spouse.label: Boolean
 
-      deepdive.schema.variables {
-        has_spouse.label: Boolean
-      }
-    
+}
 
-        deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
-          input: """ SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
+deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
+parallelism: ${PARALLELISM}
+input_relations: [
+  sentences
+]
+style: tsv_extractor
+output_relation: people_mentions
+udf: """udf/ext_people.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
 FROM sentences R0
-        
-          """
-          output_relation: "people_mentions"
-          udf: ${APP_HOME}"/udf/ext_people.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            sentences
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
-          input: """ SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
+        """
+
+}
+
+deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
+parallelism: ${PARALLELISM}
+input_relations: [
+  people_mentions
+]
+style: tsv_extractor
+output_relation: has_spouse_candidates
+udf: """udf/ext_has_spouse.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
 FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id 
-          """
-          output_relation: "has_spouse_candidates"
-          udf: ${APP_HOME}"/udf/ext_has_spouse.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-        deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
-          input: """ SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
+        WHERE R1.sentence_id = R0.sentence_id """
+
+}
+
+deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
+parallelism: ${PARALLELISM}
+input_relations: [
+  sentences
+  has_spouse_candidates
+  people_mentions
+]
+style: tsv_extractor
+output_relation: has_spouse_features
+udf: """udf/ext_has_spouse_features.py"""
+input_batch_size: ${INPUT_BATCH_SIZE}
+input: """SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
 FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id 
-          """
-          output_relation: "has_spouse_features"
-          udf: ${APP_HOME}"/udf/ext_has_spouse_features.py"
-          style: "tsv_extractor" 
-          input_relations: [
-            sentences
-            has_spouse_candidates
-            people_mentions
-          ]
-          input_batch_size: ${INPUT_BATCH_SIZE}
-          parallelism: ${PARALLELISM}
-        }
-      
-
-      deepdive.extraction.extractors.ext_has_spouse {
-        cmd: """
+        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id """
+
+}
 
+deepdive.extraction.extractors.ext_has_spouse {
+cmd: """
 	# TODO use temporary table
 	deepdive create table "has_spouse"
 	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
@@ -64,60 +59,64 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
         
           '
 	# TODO rename temporary table to replace output_relation
-	
-        """
-          output_relation: "has_spouse"
-        style: "cmd_extractor"
-          input_relations: [
-            has_spouse_candidates
-          ]
-      }
-    
-
-        deepdive.inference.factors.inf_istrue_has_spouse {
-          input_query: """
+	"""
+output_relation: has_spouse
+style: cmd_extractor
+input_relations: [
+  has_spouse_candidates
+]
+
+}
+
+deepdive.inference.factors.inf_istrue_has_spouse {
+input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
           FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
         WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-          function: "Imply(has_spouse.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            has_spouse
-            has_spouse_candidates
-            has_spouse_features
-          ]
-        }
-      
-
-        deepdive.inference.factors.inf_equal_has_spouse_has_spouse {
-          input_query: """
+function: """Imply(has_spouse.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  has_spouse
+  has_spouse_candidates
+  has_spouse_features
+]
+
+}
+
+deepdive.inference.factors.inf_equal_has_spouse_has_spouse {
+input_query: """
           SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
           FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
         WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
-          function: "Equal(has_spouse.R0.label, has_spouse.R1.label)"
-          weight: "3.0"
-          input_relations: [
-            has_spouse
-            has_spouse_candidates
-          ]
-        }
-      
+function: """Equal(has_spouse.R0.label, has_spouse.R1.label)"""
+weight: """3.0"""
+input_relations: [
+  has_spouse
+  has_spouse_candidates
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
-  ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_features_by_ext_has_spouse_features
   ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse
 ]
+
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_has_spouse
   inf_equal_has_spouse_has_spouse
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
-  ext_has_spouse
   ext_people_mentions_by_ext_people
-  ext_has_spouse_features_by_ext_has_spouse_features
   ext_has_spouse_candidates_by_ext_has_spouse
+  ext_has_spouse_features_by_ext_has_spouse_features
+  ext_has_spouse
   inf_istrue_has_spouse
   inf_equal_has_spouse_has_spouse
 ]
+
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 78e218a77..53e52222a 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -1,47 +1,45 @@
+deepdive.schema.variables {
 
-      deepdive.schema.variables {
-        
-      }
-    
-
-      deepdive.extraction.extractors.ext_A {
-        cmd: """
+}
 
+deepdive.extraction.extractors.ext_A {
+cmd: """
 	deepdive create view A as 'SELECT R0.a AS column_0, R0.a + R0.b AS column_1
 FROM R R0
         '
-	
-        """
-          output_relation: "A"
-        style: "cmd_extractor"
-          input_relations: [
-            R
-          ]
-      }
-    
-
-      deepdive.extraction.extractors.ext_B {
-        cmd: """
+	"""
+output_relation: A
+style: cmd_extractor
+input_relations: [
+  R
+]
+
+}
 
+deepdive.extraction.extractors.ext_B {
+cmd: """
 	deepdive create view B as 'SELECT R0.column_0 AS column_0, R1.b AS column_1
 FROM A R0, R R1
         WHERE R1.a = R0.column_1 '
-	
-        """
-          output_relation: "B"
-        style: "cmd_extractor"
-          input_relations: [
-            A
-            R
-          ]
-      }
-    
+	"""
+output_relation: B
+style: cmd_extractor
+input_relations: [
+  A
+  R
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.extraction: [
   ext_A
   ext_B
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
   ext_A
   ext_B
 ]
+
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 73e9d3b20..7926d6493 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -1,83 +1,84 @@
-
-      deepdive.schema.variables {
-    a.label: Boolean
+deepdive.schema.variables {
 c.label: Boolean
 d.label: Boolean
+a.label: Boolean
 e.label: Boolean
 f.label: Boolean
-      }
-    
 
-        deepdive.inference.factors.inf_istrue_a {
-          input_query: """
+}
+
+deepdive.inference.factors.inf_istrue_a {
+input_query: """
           SELECT R0.id AS "a.R0.id" , R0.k + R1.p AS "dd_weight_column_0" 
           FROM a R0, b R1
         WHERE R1.k = R0.k """
-          function: "Imply(a.R0.label)"
-          weight: "?(dd_weight_column_0)"
-          input_relations: [
-            a
-            b
-          ]
-        }
-      
+function: """Imply(a.R0.label)"""
+weight: """?(dd_weight_column_0)"""
+input_relations: [
+  a
+  b
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_c {
-          input_query: """
+deepdive.inference.factors.inf_istrue_c {
+input_query: """
           SELECT R0.id AS "c.R0.id" 
           FROM c R0, b R1
         WHERE R1.k = R0.k """
-          function: "Imply(c.R0.label)"
-          weight: "?"
-          input_relations: [
-            c
-            b
-          ]
-        }
-      
+function: """Imply(c.R0.label)"""
+weight: """?"""
+input_relations: [
+  c
+  b
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_d {
-          input_query: """
+deepdive.inference.factors.inf_istrue_d {
+input_query: """
           SELECT R0.id AS "d.R0.id" , R0.k AS "dd_weight_column_0" , R1.p AS "dd_weight_column_1" 
           FROM d R0, b R1
         WHERE R1.k = R0.k """
-          function: "Imply(d.R0.label)"
-          weight: "?(dd_weight_column_0, dd_weight_column_1)"
-          input_relations: [
-            d
-            b
-          ]
-        }
-      
+function: """Imply(d.R0.label)"""
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
+input_relations: [
+  d
+  b
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_e {
-          input_query: """
+deepdive.inference.factors.inf_istrue_e {
+input_query: """
           SELECT R0.id AS "e.R0.id" 
           FROM e R0, b R1
         WHERE R1.k = R0.k """
-          function: "Imply(e.R0.label)"
-          weight: "-10"
-          input_relations: [
-            e
-            b
-          ]
-        }
-      
+function: """Imply(e.R0.label)"""
+weight: """-10"""
+input_relations: [
+  e
+  b
+]
+
+}
 
-        deepdive.inference.factors.inf_istrue_f {
-          input_query: """
+deepdive.inference.factors.inf_istrue_f {
+input_query: """
           SELECT R0.id AS "f.R0.id" 
           FROM f R0, b R1
         WHERE R1.k = R0.k """
-          function: "Imply(f.R0.label)"
-          weight: "-0.3"
-          input_relations: [
-            f
-            b
-          ]
-        }
-      
+function: """Imply(f.R0.label)"""
+weight: """-0.3"""
+input_relations: [
+  f
+  b
+]
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
+
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_a
   inf_istrue_c
@@ -85,6 +86,7 @@ deepdive.pipeline.pipelines.inference: [
   inf_istrue_e
   inf_istrue_f
 ]
+
 deepdive.pipeline.pipelines.endtoend: [
   inf_istrue_a
   inf_istrue_c
@@ -92,3 +94,4 @@ deepdive.pipeline.pipelines.endtoend: [
   inf_istrue_e
   inf_istrue_f
 ]
+

From 8527a60e5e5b263b025e35142608ef0c4ad19ca7 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 10:50:46 -0800
Subject: [PATCH 300/347] Updates travis scala version as well

to see if it helps the out of memory error Scala compiler build
---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 25f64fbe8..a41c19f7c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,6 @@
 language: scala
 scala:
-    - "2.11.1"
+    - "2.11.7"
 
 sudo: false  # to use container-based infrastructure
 addons:

From 89007ec4b58eca8a23b87db8c70f538f43a02d86 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Mon, 29 Feb 2016 12:04:43 -0800
Subject: [PATCH 301/347] Declares oraclejdk8 to see if Travis Scala build
 error goes away

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index a41c19f7c..fa337b508 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,8 @@
 language: scala
 scala:
     - "2.11.7"
+jdk:
+    - oraclejdk8
 
 sudo: false  # to use container-based infrastructure
 addons:

From 4aeb752554e5fba7d8710da177136e44dd20a7b0 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Tue, 1 Mar 2016 03:55:17 -0800
Subject: [PATCH 302/347] Switches syntax for categorical variables

to recognize `@key` column annotations on variable relations and treat
the rest of the columns that aren't annotated with `@key` as defining
the possible categories for the variable.

- Updates chunking example
- Drops supervision label column type checker
- Adjusts expected test outputs as we drop the `Categorical(N)` syntax.
---
 examples/chunking.ddlog                       |  83 ++++++++----
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  45 ++++---
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  41 ++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |   1 -
 .../ddlog/DeepDiveLogSchemaExporter.scala     |  15 +--
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  64 ++-------
 .../supervision_multinomial/input.ddlog       |   4 +-
 .../compile-error.expected                    |   7 +
 .../input.ddlog                               |   8 ++
 .../compile-error.expected                    |   4 -
 .../input.ddlog                               |   4 -
 .../annotations/export-schema.expected        |   2 +-
 .../chunking_example/compile.expected         | 127 ++++++++++++------
 13 files changed, 229 insertions(+), 176 deletions(-)
 create mode 100644 test/compile-error-test/composing_boolean_categorical_vars/compile-error.expected
 create mode 100644 test/compile-error-test/composing_boolean_categorical_vars/input.ddlog
 delete mode 100644 test/compile-error-test/supervision_label_type_mismatch/compile-error.expected
 delete mode 100644 test/compile-error-test/supervision_label_type_mismatch/input.ddlog

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index 2b07f7eba..f17d83f26 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -1,44 +1,81 @@
-// chunking example
-// https://github.com/HazyResearch/deepdive/tree/master/examples/chunking
+chunk?(
+    @key sent_id bigint,
+    @key word_id bigint,
+    tag text
+).
+tags(tag text).
 
+# input data ##################################################################
 words_raw(
-  word_id bigserial,
+  sent_id bigint,
+  word_id bigint,
   word text,
   pos text,
-  tag text).
+  true_tag text
+).
 
 words(
   sent_id bigint,
   word_id bigint,
   word text,
   pos text,
-  true_tag int).
-
-word_features(
-  word_id bigint,
-  feature text).
+  true_tag text,
+  tag text
+).
 
-tag?(word_id bigint) Categorical(13).
+# supervision / scope of tags #################################################
+chunk(s, word, tag) = (
+  if tag = tag_supervised then TRUE
+                          else NULL
+  end
+) :-
+  words(s, word, _, _, _, tag_supervised),
+  tags(tag).
 
-function ext_training
-  over rows like words_raw
-  returns rows like words
-  implementation "udf/ext_training.py" handles tsv lines.
+# TODO the following if-then-else can go directly to the supervision rule once DDlog supports true unification (tag_supervised = if ... end in the body)
+words(sent_id, word_id, word, pos, true_tag,
+             if true_tag = "B-UCP"        then NULL
+        else if true_tag = "I-UCP"        then NULL
+        else if strpos(true_tag, "-") > 0 then split_part(true_tag, "-", 2)
+        else if true_tag = "O"            then "O"
+        else                                   NULL
+        end) :-
+  words_raw(sent_id, word_id, word, pos, true_tag).
 
-words +=
-  ext_training(wid, word, pos, tag) :- words_raw(wid, word, pos, tag).
+# features ####################################################################
+word_features(
+  sent_id bigint,
+  word_id bigint,
+  feature text
+).
 
 function ext_features
-  over (word_id1 bigint, word1 text, pos1 text, word2 text, pos2 text)
+  over (sent_id bigint, word_id1 bigint, word1 text, pos1 text, word2 text, pos2 text)
   returns rows like word_features
   implementation "udf/ext_features.py" handles tsv lines.
 
 word_features +=
-  ext_features(word_id1, word1, pos1, word2, pos2) :-
-  words(sent_id, word_id1, word1, pos1, tag1),
-  words(sent_id, word_id2, word2, pos2, tag2).
+  ext_features(s, w1, word1, pos1, word2, pos2) :-
+  words(s, w1, word1, pos1, _, _),
+  words(s, w2, word2, pos2, _, _),
+  [w1 = w2 + 1],
+  word1 IS NOT NULL.
+
+@weight(f, tag)
+chunk(s, w, tag) :-
+                      words(s, w, _, _, _, _), tags(tag), # XXX just to make it compile. remove after fixing https://github.com/HazyResearch/ddlog/issues/72
+  word_features(s, w, f).
 
-tag(word_id) = tag :- words(word_id, a, b, c, tag).
+# linear chains ###############################################################
+@weight(tag1, tag2)
+chunk(s, w1, tag1) ^ chunk(s, w2, tag2) :-
+                      words(s, w1, _, _, _, _), words(s, w2, _, _, _, _), tags(tag1), tags(tag2), # XXX just to make it compile. remove after fixing https://github.com/HazyResearch/ddlog/issues/72
+  w2 = w1 + 1.
 
-@weight(f)
-tag(word_id) :- word_features(word_id, f).
+# skip chain ##################################################################
+@weight(tag1, tag2)
+chunk(s, w1, tag1) ^ chunk(s, w2, tag2) :-
+  words(s, w1, _, _, _, tag),
+                      words(s, w2, _, _, _, _), tags(tag1), tags(tag2), # XXX just to make it compile. remove after fixing https://github.com/HazyResearch/ddlog/issues/72
+  tag IS NOT NULL,
+  w1 < w2.
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 2caf02620..988b121e1 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -30,6 +30,9 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
       case decl: SchemaDeclaration => decl.a.name -> decl
     } toMap
 
+  def isCategoricalRelation(name: String): Boolean =
+    schemaDeclarationByRelationName get(name) map (_.categoricalColumns.size > 0) getOrElse(false)
+
   val inferenceRules = statements collect { case s: InferenceRule => s }
 
   val statementsByHeadName: Map[String, List[Statement]] =
@@ -532,19 +535,29 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         s"""${if (y.isNegated) "!" else ""}${x.name}.R${headAsBody indexOf x}.label"""
       })
 
-      val function = stmt.head.function match {
-        case FactorFunction.Imply()  => "Imply"
-        case FactorFunction.And()    => "And"
-        case FactorFunction.Or()     => "Or"
-        case FactorFunction.Equal()  => "Equal"
-        case FactorFunction.Linear() => "Linear"
-        case FactorFunction.Ratio()  => "Ratio"
-        case FactorFunction.IsTrue() =>
-          schemaDeclarationByRelationName get(stmt.head.terms(0).name) map(_.variableType) match {
-            case Some(Some(MultinomialType(_))) => "Multinomial"
-            case _ => "Imply" // TODO fix to IsTrue
+      val categoricalVars = stmt.head.terms filter { t => isCategoricalRelation(t.name) }
+      val isMultinomialFactor =
+        if (categoricalVars.size == 0 || stmt.head.terms.size == categoricalVars.size)
+          categoricalVars.size > 0
+        else
+          sys.error("None or all variables must be categorical")
+
+      val function =
+        if (isMultinomialFactor) {
+          stmt.head.function match {
+            case FactorFunction.IsTrue() | FactorFunction.And() => "Multinomial"
+            case f => sys.error(s"Unsupported factor over categorical variables: ${f}")
+          }
+        } else { // Boolean
+          stmt.head.function match {
+            case FactorFunction.Imply()  => "Imply"
+            case FactorFunction.And()    => "And"
+            case FactorFunction.Or()     => "Or"
+            case FactorFunction.Equal()  => "Equal"
+            case FactorFunction.Linear() => "Linear"
+            case FactorFunction.Ratio()  => "Ratio"
+            case FactorFunction.IsTrue() => "Imply" // TODO fix to IsTrue
           }
-        case FactorFunction.Multinomial() => "Multinomial"
       }
       s"""${function}(${funcBody.mkString(", ")})"""
     }
@@ -605,10 +618,10 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     // generate the statements.
     List("deepdive.schema.variables" -> (statements collect {
       case decl: SchemaDeclaration if decl.isQuery =>
-        s"${decl.a.name}.label" -> (decl.variableType match {
-          case Some(MultinomialType(x)) => s"Categorical(${x})"
-          case _ => "Boolean"
-        })
+        if (isCategoricalRelation(decl.a.name)) {
+          decl.a.name -> (decl.categoricalColumns map (_ -> "Categorical") toMap)
+        } else // Boolean variables
+          s"${decl.a.name}.label" -> "Boolean"
       } toMap)
     )
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index aaccae70e..e992fd915 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -70,17 +70,6 @@ object LogicOperator {
   case class OR() extends LogicOperator
 }
 
-// variable type
-sealed trait VariableType {
-  def cardinality: Long
-}
-case class BooleanType() extends VariableType {
-  def cardinality = 2
-}
-case class MultinomialType(numCategories: Int) extends VariableType {
-  def cardinality = numCategories
-}
-
 case class FactorWeight(variables: List[Expr])
 
 // factor function
@@ -91,7 +80,6 @@ object FactorFunction {
   case class Or()          extends FactorFunction
   case class And()         extends FactorFunction
   case class Equal()       extends FactorFunction
-  case class Multinomial() extends FactorFunction
   case class Linear()      extends FactorFunction
   case class Ratio()       extends FactorFunction
 }
@@ -110,9 +98,19 @@ case class RowWiseLineHandler(style: String, command: String) extends FunctionIm
 trait Statement
 case class SchemaDeclaration( a : Attribute
                             , isQuery : Boolean
-                            , variableType : Option[VariableType]
                             , annotation : List[Annotation] = List.empty // optional annotation
                             ) extends Statement // atom and whether this is a query relation.
+{
+  // infer whether this is a categorical variable based on column annotations
+  val categoricalColumns =
+    if (isQuery) {
+      val keyColumns = a.terms.zip(a.annotations) collect {
+        case (term, annos) if annos exists (_.name == "key") => term
+      }
+      if (keyColumns isEmpty) List.empty  // treat all columns as key if none were annotated
+      else a.terms diff keyColumns toList  // otherwise, the rest of the columns define categories
+    } else List.empty
+}
 case class FunctionDeclaration( functionName: String, inputType: FunctionInputOutputType,
   outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration]) extends Statement
 case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[Expr] = None) extends Statement // Extraction rule
@@ -190,22 +188,14 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case(anno ~ name ~ ty) => Column(name, ty, anno)
     }
 
-  def CategoricalParser = "Categorical" ~> "(" ~> """\d+""".r <~ ")" ^^ { n => MultinomialType(n.toInt) }
-  def BooleanParser = "Boolean" ^^ { s => BooleanType() }
-  def dataType = CategoricalParser | BooleanParser
-
   def schemaDeclaration: Parser[SchemaDeclaration] =
     rep(annotation) ~
-    relationName ~ opt("?") ~ "(" ~ rep1sep(columnDeclaration, ",") ~ ")" ~ opt(dataType) ^^ {
-      case (anno ~ r ~ isQuery ~ "(" ~ attrs ~ ")" ~ vType) => {
+    relationName ~ opt("?") ~ ("(" ~> rep1sep(columnDeclaration, ",") <~ ")") ^^ {
+      case (anno ~ r ~ isQuery ~ attrs) => {
         val vars = attrs map (_.name)
         var types = attrs map (_.t)
         val annos = attrs map (_.annotation)
-        val variableType = vType match {
-          case None => if (isQuery != None) Some(BooleanType()) else None
-          case Some(s) => Some(s)
-        }
-        SchemaDeclaration(Attribute(r, vars, types, annos), (isQuery != None), variableType, anno)
+        SchemaDeclaration(Attribute(r, vars, types, annos), (isQuery != None), anno)
       }
     }
 
@@ -403,9 +393,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
   | headAtom ~ "v" ~ rep1sep(headAtom, "v") ^^ { case (a ~ _ ~ b) =>
       InferenceRuleHead(FactorFunction.Or(), a +: b)
     }
-  | "Multinomial" ~> "(" ~> rep1sep(headAtom, ",") <~ ")" ^^ {
-      InferenceRuleHead(FactorFunction.Multinomial(), _)
-    }
   | headAtom ^^ {
       x => InferenceRuleHead(FactorFunction.IsTrue(), List(x))
     }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 96ee0f2a6..877f8df90 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -176,7 +176,6 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
       case FactorFunction.Or()     => printHead(head.terms, " v ")
       case FactorFunction.Equal()  => printHead(head.terms, " = ")
       case FactorFunction.IsTrue() => printHead(head.terms, "")
-      case FactorFunction.Multinomial() => s"""Multinomial(${printHead(head.terms, ", ")})"""
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index c31e8516b..f3cab12dc 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -32,14 +32,10 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
       schema += "annotations" -> exportAnnotations(decl.annotation)
     // what type of random variable this relation is
     if (decl.isQuery)
-      decl.variableType getOrElse { BooleanType() } match {
-        case ty =>
-          schema += "variable_type" -> (ty match {
-            case BooleanType()      => "boolean"
-            case MultinomialType(n) => "multinomial"
-          })
-          schema += "variable_cardinality" -> ty.cardinality
-      }
+      schema += "variable_type" -> (
+        if (decl.categoricalColumns.size > 0) "multinomial"
+        else "boolean"
+      )
 
     // finally, mapping for this relation
     decl.a.name -> JSONObject(schema)
@@ -79,8 +75,7 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
                   types = rule.q.headTerms map { _ => "UNKNOWN" },
                   annotations = rule.q.headTerms map { _ => List.empty }
                 ),
-                isQuery = false,
-                variableType = None
+                isQuery = false
               ),
               "type" -> "view"
             )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 3f6dbe88f..ce6945b59 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -37,11 +37,11 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
     checkRelationDefined(stmt)
     checkFunctionDefined(stmt)
     checkVariableRelationSchema(stmt)
+    checkMultinomialFactors(stmt)
     checkNumberOfColumns(stmt)
     checkQuantifiedBody(stmt)
     checkWeight(stmt)
     checkVariableBindings(stmt)
-    checkSupervisionLabelType(stmt)
   }
 
   // iterate over all atoms contained in the body list and apply the checker
@@ -94,12 +94,25 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
             if (reservedSet contains name)
               error(stmt, s"""variable relation contains reserved column "${name}" """)
           }
+          // TODO check if none or all columns are annotated with @key
         }
       }
       case _ =>
     }
   }
 
+  // TODO check if all factors have only isQuery relations in their heads
+
+  // check if any factors are defined across categorical and Boolean variables
+  def checkMultinomialFactors(stmt: Statement) = stmt match {
+    case s: InferenceRule =>
+      val categoricalVars = s.head.terms filter { t =>
+        schemaDeclarationByName get(t.name) map(_.categoricalColumns nonEmpty) getOrElse(false) }
+      if (! (categoricalVars.size == 0 || s.head.terms.size == categoricalVars.size))
+        error(s, "None or all variables must be categorical")
+    case _ =>
+  }
+
   // check if the number of columns match schema declaration
   def checkNumberOfColumns(stmt: Statement) {
     def check(name: String, size: Int) {
@@ -163,55 +176,6 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
     }
   }
 
-  def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, b: BodyAtom) {
-    if (schemaDeclarationByName contains b.name)
-      b.terms.zipWithIndex.foreach {
-        case (`supVariable`, index) => {
-          val expColumnType = expType match {
-            case BooleanType() => "boolean"
-            case MultinomialType(_) => "int"
-          }
-          if (schemaDeclarationByName(b.name).a.types(index).toLowerCase != expColumnType) {
-            val actualColumnType = schemaDeclarationByName(b.name).a.types(index).toLowerCase
-            error(s, s"Supervision column ${supVariable.name} should be ${expColumnType} type, but is ${actualColumnType} type")
-          }
-        }
-        case _ =>
-      }
-  }
-
-  def checkSupervisionLabelType(s: ExtractionRule, expType: VariableType, supVariable: VarPattern, body: Body) {
-    body match {
-      case qb: QuantifiedBody => qb.bodies.foreach { b => checkSupervisionLabelType(s, expType, supVariable, b) }
-      case b: BodyAtom => checkSupervisionLabelType(s, expType, supVariable, b)
-      case _ =>
-    }
-  }
-
-  def checkSupervisionLabelType(stmt: Statement) {
-    stmt match {
-      case s: ExtractionRule if (schemaDeclarationByName contains s.headName) && (schemaDeclarationByName(s.headName).variableType nonEmpty) => {
-        val headType = schemaDeclarationByName(s.headName).variableType.get
-        s.supervision foreach {
-          case b: BooleanConst => {
-            if (headType != BooleanType) {
-              error(s, s"Supervision column ${s.supervision} should be boolean type but is ${headType} type")
-            }
-          }
-          case VarExpr(varname) =>
-            s.q.bodies.foreach { bodies: List[Body] =>
-              bodies.foreach { b =>
-                checkSupervisionLabelType(s, headType, VarPattern(varname), b)
-              }
-            }
-          case _ =>
-          // XXX assume the rest of the expressions are correct
-        }
-      }
-      case _ =>
-    }
-  }
-
   // check if variables have bindings in the body
   def checkVariableBindings(stmt: Statement) {
     // check variable bindings in a conjunctive query
diff --git a/test/checker-test/supervision_multinomial/input.ddlog b/test/checker-test/supervision_multinomial/input.ddlog
index 3b8a4ab70..abac852f8 100644
--- a/test/checker-test/supervision_multinomial/input.ddlog
+++ b/test/checker-test/supervision_multinomial/input.ddlog
@@ -1,4 +1,4 @@
-Q?(x int) Categorical(10).
+Q?(@key x int, category int).
 R(x int, label int).
 
-Q(x) = label :- R(x, label).
+Q(x, label) = TRUE :- R(x, label).
diff --git a/test/compile-error-test/composing_boolean_categorical_vars/compile-error.expected b/test/compile-error-test/composing_boolean_categorical_vars/compile-error.expected
new file mode 100644
index 000000000..5b818bdc5
--- /dev/null
+++ b/test/compile-error-test/composing_boolean_categorical_vars/compile-error.expected
@@ -0,0 +1,7 @@
+[error] None or all variables must be categorical
+@weight(1.0)
+P(x) => Q(y, c) :-
+    R(x),
+    R(y),
+    C(c).
+
diff --git a/test/compile-error-test/composing_boolean_categorical_vars/input.ddlog b/test/compile-error-test/composing_boolean_categorical_vars/input.ddlog
new file mode 100644
index 000000000..97b19817c
--- /dev/null
+++ b/test/compile-error-test/composing_boolean_categorical_vars/input.ddlog
@@ -0,0 +1,8 @@
+P?(x int).
+Q?(@key y int, category text).
+
+@weight(1.0)
+P(x) => Q(y, c) :- R(x), R(y), C(c).
+
+R(x int).
+C(c text).
diff --git a/test/compile-error-test/supervision_label_type_mismatch/compile-error.expected b/test/compile-error-test/supervision_label_type_mismatch/compile-error.expected
deleted file mode 100644
index a93055da1..000000000
--- a/test/compile-error-test/supervision_label_type_mismatch/compile-error.expected
+++ /dev/null
@@ -1,4 +0,0 @@
-[error] Supervision column label should be boolean type, but is text type
-Q(x) = label :-
-    R(x, label).
-
diff --git a/test/compile-error-test/supervision_label_type_mismatch/input.ddlog b/test/compile-error-test/supervision_label_type_mismatch/input.ddlog
deleted file mode 100644
index 24750149f..000000000
--- a/test/compile-error-test/supervision_label_type_mismatch/input.ddlog
+++ /dev/null
@@ -1,4 +0,0 @@
-Q?(x int).
-R(x int, label text).
-
-Q(x) = label :- R(x, label).
diff --git a/test/expected-output-test/annotations/export-schema.expected b/test/expected-output-test/annotations/export-schema.expected
index cb9142969..e25c94f71 100644
--- a/test/expected-output-test/annotations/export-schema.expected
+++ b/test/expected-output-test/annotations/export-schema.expected
@@ -1 +1 @@
-{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text", "index" : 0}, "start_pos" : {"type" : "int", "index" : 1, "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "index" : 2, "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text", "index" : 0}, "q" : {"type" : "int", "index" : 1}, "r" : {"type" : "float", "index" : 2, "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}, "has_spouse" : {"columns" : {"couple_id" : {"type" : "text", "index" : 0, "annotations" : [{"name" : "key"}, {"name" : "references", "args" : {"relation" : "couples", "column" : "id"}}]}}, "annotations" : [{"name" : "fact"}], "variable_type" : "boolean", "variable_cardinality" : 2}}}
+{"relations" : {"mention_candidate" : {"columns" : {"doc_id" : {"type" : "text", "index" : 0}, "start_pos" : {"type" : "int", "index" : 1, "annotations" : [{"name" : "textspan_start"}]}, "len" : {"type" : "int", "index" : 2, "annotations" : [{"name" : "textspan_length"}]}}, "annotations" : [{"name" : "textspan", "args" : {"from" : "start_pos", "length" : "len"}}]}, "R" : {"columns" : {"p" : {"type" : "text", "index" : 0}, "q" : {"type" : "int", "index" : 1}, "r" : {"type" : "float", "index" : 2, "annotations" : [{"name" : "empty_args", "args" : {}}]}}, "annotations" : [{"name" : "foo"}, {"name" : "bar", "args" : {"x" : 1}}, {"name" : "qux", "args" : {"y" : 2.345}}, {"name" : "unnamed_args_list", "args" : [1, "two", 3.0]}, {"name" : "unnamed_args_list", "args" : ["four", 5.6, 7]}]}, "has_spouse" : {"columns" : {"couple_id" : {"type" : "text", "index" : 0, "annotations" : [{"name" : "key"}, {"name" : "references", "args" : {"relation" : "couples", "column" : "id"}}]}}, "annotations" : [{"name" : "fact"}], "variable_type" : "boolean"}}}
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index aa9ddea5a..f5607abd8 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -1,20 +1,53 @@
 deepdive.schema.variables {
-tag.label: Categorical(13)
+chunk {
+tag: Categorical
 
 }
 
-deepdive.extraction.extractors.ext_words_by_ext_training {
-parallelism: ${PARALLELISM}
+}
+
+deepdive.extraction.extractors.ext_chunk {
+cmd: """
+	# TODO use temporary table
+	deepdive create table "chunk"
+	deepdive sql 'INSERT INTO chunk SELECT DISTINCT R0.sent_id, R0.word_id, R1.tag, 0 AS id, 
+CASE WHEN R1.tag = R0.tag THEN true
+     ELSE NULL
+END AS label
+          FROM words R0, tags R1
+        
+          '
+	# TODO rename temporary table to replace output_relation
+	"""
+output_relation: chunk
+style: cmd_extractor
 input_relations: [
-  words_raw
+  words
+  tags
 ]
-style: tsv_extractor
-output_relation: words
-udf: """udf/ext_training.py"""
-input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.tag AS "words_raw.R0.tag"
+
+}
+
+deepdive.extraction.extractors.ext_words {
+cmd: """
+	# TODO use temporary table
+	deepdive create table "words"
+	deepdive sql 'INSERT INTO words SELECT R0.sent_id AS "words_raw.R0.sent_id", R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.true_tag AS "words_raw.R0.true_tag", 
+CASE WHEN R0.true_tag = '\''B-UCP'\'' THEN NULL
+     WHEN R0.true_tag = '\''I-UCP'\'' THEN NULL
+     WHEN strpos(R0.true_tag, '\''-'\'') > 0 THEN split_part(R0.true_tag, '\''-'\'', 2)
+     WHEN R0.true_tag = '\''O'\'' THEN '\''O'\''
+     ELSE NULL
+END AS column_5
 FROM words_raw R0
-        """
+        '
+	# TODO rename temporary table to replace output_relation
+	"""
+output_relation: words
+style: cmd_extractor
+input_relations: [
+  words_raw
+]
 
 }
 
@@ -27,40 +60,54 @@ style: tsv_extractor
 output_relation: word_features
 udf: """udf/ext_features.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.word_id AS "words.R0.word_id", R0.word AS "words.R0.word", R0.pos AS "words.R0.pos", R1.word AS "words.R1.word", R1.pos AS "words.R1.pos"
+input: """SELECT R0.sent_id AS "words.R0.sent_id", R0.word_id AS "words.R0.word_id", R0.word AS "words.R0.word", R0.pos AS "words.R0.pos", R1.word AS "words.R1.word", R1.pos AS "words.R1.pos"
 FROM words R0, words R1
-        WHERE R1.sent_id = R0.sent_id """
+        WHERE R1.sent_id = R0.sent_id  AND R0.word_id = (R1.word_id + 1) AND R0.word IS NOT NULL"""
 
 }
 
-deepdive.extraction.extractors.ext_tag {
-cmd: """
-	# TODO use temporary table
-	deepdive create table "tag"
-	deepdive sql 'INSERT INTO tag SELECT DISTINCT R0.sent_id, 0 AS id, R0.true_tag AS label
-          FROM words R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
-output_relation: tag
-style: cmd_extractor
+deepdive.inference.factors.inf_istrue_chunk {
+input_query: """
+          SELECT R0.id AS "chunk.R0.id" , R3.feature AS "dd_weight_column_0" , R0.tag AS "dd_weight_column_1" 
+          FROM chunk R0, words R1, tags R2, word_features R3
+        WHERE R1.sent_id = R0.sent_id  AND R1.word_id = R0.word_id  AND R2.tag = R0.tag  AND R3.sent_id = R0.sent_id  AND R3.word_id = R0.word_id """
+function: """Multinomial(chunk.R0.label)"""
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
+  chunk
   words
+  tags
+  word_features
 ]
 
 }
 
-deepdive.inference.factors.inf_istrue_tag {
+deepdive.inference.factors.inf_and_chunk_chunk {
 input_query: """
-          SELECT R0.id AS "tag.R0.id" , R1.feature AS "dd_weight_column_0" 
-          FROM tag R0, word_features R1
-        WHERE R1.word_id = R0.word_id """
-function: """Multinomial(tag.R0.label)"""
-weight: """?(dd_weight_column_0)"""
+          SELECT R0.id AS "chunk.R0.id" , R1.id AS "chunk.R1.id" , R0.tag AS "dd_weight_column_0" , R1.tag AS "dd_weight_column_1" 
+          FROM chunk R0, chunk R1, words R2, words R3, tags R4, tags R5
+        WHERE R1.sent_id = R0.sent_id  AND R2.sent_id = R0.sent_id  AND R2.word_id = R0.word_id  AND R3.sent_id = R0.sent_id  AND R3.word_id = R1.word_id  AND R4.tag = R0.tag  AND R5.tag = R1.tag  AND R1.word_id = (R0.word_id + 1)"""
+function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
-  tag
-  word_features
+  chunk
+  words
+  tags
+]
+
+}
+
+deepdive.inference.factors.inf1_and_chunk_chunk {
+input_query: """
+          SELECT R0.id AS "chunk.R0.id" , R1.id AS "chunk.R1.id" , R0.tag AS "dd_weight_column_0" , R1.tag AS "dd_weight_column_1" 
+          FROM chunk R0, chunk R1, words R2, words R3, tags R4, tags R5
+        WHERE R1.sent_id = R0.sent_id  AND R2.sent_id = R0.sent_id  AND R2.word_id = R0.word_id  AND R3.sent_id = R0.sent_id  AND R3.word_id = R1.word_id  AND R4.tag = R0.tag  AND R5.tag = R1.tag  AND R2.tag IS NOT NULL AND R0.word_id < R1.word_id"""
+function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
+input_relations: [
+  chunk
+  words
+  tags
 ]
 
 }
@@ -68,19 +115,23 @@ input_relations: [
 deepdive.pipeline.run: ${PIPELINE}
 
 deepdive.pipeline.pipelines.extraction: [
-  ext_words_by_ext_training
+  ext_chunk
+  ext_words
   ext_word_features_by_ext_features
-  ext_tag
 ]
 
 deepdive.pipeline.pipelines.inference: [
-  inf_istrue_tag
+  inf_istrue_chunk
+  inf_and_chunk_chunk
+  inf1_and_chunk_chunk
 ]
 
 deepdive.pipeline.pipelines.endtoend: [
-  ext_words_by_ext_training
+  ext_chunk
+  ext_words
   ext_word_features_by_ext_features
-  ext_tag
-  inf_istrue_tag
+  inf_istrue_chunk
+  inf_and_chunk_chunk
+  inf1_and_chunk_chunk
 ]
 

From ab6f796762ce62477ec1e2918c163ad853f593db Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 2 Mar 2016 04:45:57 -0800
Subject: [PATCH 303/347] Drops id columns from variable tables

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala   | 2 +-
 test/expected-output-test/chunking_example/compile.expected   | 2 +-
 test/expected-output-test/if-then-else/compile.expected       | 2 +-
 test/expected-output-test/ocr_example/compile.expected        | 4 ++--
 test/expected-output-test/smoke_example/compile.expected      | 4 ++--
 test/expected-output-test/spouse_example/compile.expected     | 2 +-
 .../spouse_example_new_inference/compile.expected             | 2 +-
 7 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 988b121e1..bd1dccc22 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -420,7 +420,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
           if (stmt.q.bodies.length > 1) sys.error(s"Scoping rule does not allow disjunction.\n")
           val headStr = qc.generateSQLHead(NoAlias)
           val labelCol = qc.compileExpr(stmt.supervision.get)
-          s"""SELECT DISTINCT ${ headStr }, 0 AS id, ${labelCol} AS label
+          s"""SELECT DISTINCT ${ headStr }, ${labelCol} AS label
           ${ qc.generateSQLBody(cqBody) }
           """
         } else {
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index f5607abd8..d4bd9ec03 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -10,7 +10,7 @@ deepdive.extraction.extractors.ext_chunk {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "chunk"
-	deepdive sql 'INSERT INTO chunk SELECT DISTINCT R0.sent_id, R0.word_id, R1.tag, 0 AS id, 
+	deepdive sql 'INSERT INTO chunk SELECT DISTINCT R0.sent_id, R0.word_id, R1.tag, 
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS label
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 8e5b7ce81..1b603bf0a 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -7,7 +7,7 @@ deepdive.extraction.extractors.ext_q {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "q"
-	deepdive sql 'INSERT INTO q SELECT DISTINCT R0.x, 0 AS id, 
+	deepdive sql 'INSERT INTO q SELECT DISTINCT R0.x, 
 CASE WHEN R0.l > 0 THEN true
      WHEN R0.l < 0 THEN false
      ELSE NULL
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index e19233af0..1d0c6dd0b 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -8,7 +8,7 @@ deepdive.extraction.extractors.ext_q1 {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "q1"
-	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, R0.val AS label
           FROM label1 R0
         
           '
@@ -26,7 +26,7 @@ deepdive.extraction.extractors.ext_q2 {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "q2"
-	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, 0 AS id, R0.val AS label
+	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, R0.val AS label
           FROM label2 R0
         
           '
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 7ea48be66..ff67f79ca 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -8,7 +8,7 @@ deepdive.extraction.extractors.ext_smoke {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "smoke"
-	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, 0 AS id, R0.smokes AS label
+	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, R0.smokes AS label
           FROM person_smokes R0
         
           '
@@ -26,7 +26,7 @@ deepdive.extraction.extractors.ext_cancer {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "cancer"
-	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, 0 AS id, R0.has_cancer AS label
+	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, R0.has_cancer AS label
           FROM person_has_cancer R0
         
           '
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 18fb269f4..e4c2f5401 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -54,7 +54,7 @@ deepdive.extraction.extractors.ext_has_spouse {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           '
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
index 2ea1fd2b8..533ae67f5 100644
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ b/test/expected-output-test/spouse_example_new_inference/compile.expected
@@ -54,7 +54,7 @@ deepdive.extraction.extractors.ext_has_spouse {
 cmd: """
 	# TODO use temporary table
 	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, 0 AS id, R0.is_true AS label
+	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, R0.is_true AS label
           FROM has_spouse_candidates R0
         
           '

From 5abebc98d5a0724daaa93f9c8a48a979ca5d93c2 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Sun, 28 Feb 2016 23:24:59 -0800
Subject: [PATCH 304/347] Changes annotations to hold Expr not Any values

---
 .../org/deepdive/ddlog/DeepDiveLogParser.scala  |  9 ++++-----
 .../ddlog/DeepDiveLogSchemaExporter.scala       | 17 +++++++++++++++--
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index e992fd915..23626cedd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -53,7 +53,7 @@ case class Column(name : String // name of the column
                  )
 
 case class Annotation( name : String // name of the annotation
-                     , args : Option[Either[Map[String, Any],List[Any]]] = None // optional, named arguments map or unnamed list
+                     , args : Option[Either[Map[String,Expr],List[Expr]]] = None // optional, named arguments map or unnamed list
                      )
 case class RuleAnnotation(name: String, args: List[String])
 
@@ -164,7 +164,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       case (_ ~ name ~ optArgs) => Annotation(name, optArgs)
     }
 
-  def annotationArguments: Parser[Either[Map[String, Any], List[Any]]] =
+  def annotationArguments: Parser[Either[Map[String, Expr], List[Expr]]] =
     "(" ~> (
       // XXX rep1sep must be above repsep to parse "()"
       rep1sep(annotationArgumentValue, ",") ^^ {
@@ -175,12 +175,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
         case namedArgs => Left(namedArgs toMap)
       }
     ) <~ ")"
-  def annotationNamedArgument: Parser[(String, Any)] =
+  def annotationNamedArgument: Parser[(String, Expr)] =
     annotationArgumentName ~ "=" ~ annotationArgumentValue ^^ {
       case name ~ _ ~ value => name -> value
     }
-  def annotationArgumentValue: Parser[Any] =
-    stringLiteralAsString | double | integer
+  def annotationArgumentValue: Parser[Expr] = expr
 
   def columnDeclaration: Parser[Column] =
     rep(annotation) ~
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index f3cab12dc..2a2e49555 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -48,8 +48,21 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
     var a = jsonMap(
       "name" -> anno.name
     )
-    if (anno.args nonEmpty)
-      a += "args" -> (anno.args.get fold (JSONObject, JSONArray))
+    if (anno.args nonEmpty) {
+      def toValue(e: Expr): Any = e match {
+        case IntConst(v) => v
+        case StringConst(v) => v
+        case DoubleConst(v) => v
+        case BooleanConst(v) => v
+        case NullConst() => null
+        case _ => sys.error(s"Cannot export non-constant value in annotation: ${DeepDiveLogPrettyPrinter.printAnnotations(List(anno))}")
+      }
+      def toJSONObject(nameExprMap: Map[String,Expr]) = {
+        JSONObject (nameExprMap mapValues toValue)
+      }
+      def toJSONArray(exprs: List[Expr]) = JSONArray(exprs map toValue)
+      a += "args" -> (anno.args.get fold (toJSONObject, toJSONArray))
+    }
     JSONObject(a)
   }
 

From ca2fee1589714978daa7e7dcb834b5db592e1e3b Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 3 Mar 2016 06:10:45 -0800
Subject: [PATCH 305/347] Improves make actual-expected to ignore spaces

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 1546ecabe..b242f49b4 100644
--- a/Makefile
+++ b/Makefile
@@ -53,7 +53,7 @@ actual-expected:
 	        *)                actual=$${expected%.expected}.actual      ;; \
 	    esac; \
 	    [[ "$$actual" -nt "$$expected" ]] && \
-	    ! diff -q "$$actual" "$$expected" || continue; \
+	    ! diff -q --ignore-all-space "$$actual" "$$expected" || continue; \
 	    cp -vf "$$actual" "$$expected"; \
 	done
 

From f0c2ae0dd90a59423f7f89b9e7cfa101448d766c Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 3 Mar 2016 06:11:07 -0800
Subject: [PATCH 306/347] Enable scalac -feature

---
 build.sbt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/build.sbt b/build.sbt
index 265de9a01..4fd760f9b 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,5 +1,7 @@
 scalaVersion := "2.11.7"
 
+scalacOptions ++= Seq("-feature")
+
 libraryDependencies += "org.scala-lang.modules" %% "scala-parser-combinators" % "1.0.4"
 
 libraryDependencies += "org.apache.commons" % "commons-lang3" % "3.4"

From 8cea0a1adf8421608ba91a72fe24de6d393273f0 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 3 Mar 2016 06:35:45 -0800
Subject: [PATCH 307/347] Cleans up parser's special cases with general
 annotation handling

Also drops DeepDiveLogDeltaDeriver since it's difficult to understand,
and not so valuable to maintain with so much pain..
---
 .../org/deepdive/ddlog/DeepDiveLog.scala      |   1 -
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 129 +++---
 .../ddlog/DeepDiveLogDeltaDeriver.scala       | 176 --------
 .../ddlog/DeepDiveLogDesugarRewriter.scala    |   2 +
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 419 ++++++++++--------
 .../ddlog/DeepDiveLogPrettyPrinter.scala      |  33 +-
 .../ddlog/DeepDiveLogQueryCompiler.scala      |   2 +-
 .../ddlog/DeepDiveLogSchemaExporter.scala     |   8 +-
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  31 +-
 .../compile-error.expected                    |   4 +-
 .../invalid_variable_schema/input.ddlog       |   4 +-
 .../many_joins/print-incremental.expected     |  57 ---
 .../ocr_example/print-incremental.expected    |  79 ----
 .../smoke_example/print-incremental.expected  |  86 ----
 .../spouse_example/print-incremental.expected | 172 -------
 .../spouse_example_new_feature/input.ddlog    |  71 ---
 .../print-incremental.expected                | 176 --------
 .../compile.expected                          | 122 -----
 .../spouse_example_new_inference/input.ddlog  |  76 ----
 .../print-incremental.expected                | 177 --------
 .../print.expected                            |  76 ----
 .../annotation_mode/input.ddlog               |   3 -
 .../annotation_mode/parse-error.expected      |   5 -
 .../annotation_semantics/parse-error.expected |   6 +-
 24 files changed, 358 insertions(+), 1557 deletions(-)
 delete mode 100644 src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
 delete mode 100644 test/expected-output-test/many_joins/print-incremental.expected
 delete mode 100644 test/expected-output-test/ocr_example/print-incremental.expected
 delete mode 100644 test/expected-output-test/smoke_example/print-incremental.expected
 delete mode 100644 test/expected-output-test/spouse_example/print-incremental.expected
 delete mode 100644 test/expected-output-test/spouse_example_new_feature/input.ddlog
 delete mode 100644 test/expected-output-test/spouse_example_new_feature/print-incremental.expected
 delete mode 100644 test/expected-output-test/spouse_example_new_inference/compile.expected
 delete mode 100644 test/expected-output-test/spouse_example_new_inference/input.ddlog
 delete mode 100644 test/expected-output-test/spouse_example_new_inference/print-incremental.expected
 delete mode 100644 test/expected-output-test/spouse_example_new_inference/print.expected
 delete mode 100644 test/parse-error-test/annotation_mode/input.ddlog
 delete mode 100644 test/parse-error-test/annotation_mode/parse-error.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
index 9ee4b8543..c06fbcd43 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLog.scala
@@ -33,7 +33,6 @@ object DeepDiveLog {
       )
     cmd("compile")                     required() action { (_, c) => c.copy(handler = DeepDiveLogCompiler)        } text("Compiles a deepdive.conf")
     cmd("print")                       required() action { (_, c) => c.copy(handler = DeepDiveLogPrettyPrinter)   } text("Prints given program after parsing")
-    cmd("print-incremental")           required() action { (_, c) => c.copy(handler = DeepDiveLogDeltaDeriver)    } text("Prints delta rules after parsing given program")
     cmd("check")                       required() action { (_, c) => c.copy(handler = DeepDiveLogSemanticChecker) } text("Checks if given program is valid")
     cmd("export-schema")               required() action { (_, c) => c.copy(handler = DeepDiveLogSchemaExporter)  } text("Exports given program in JSON")
     opt[Unit]("skip-desugar")          optional() action { (_, c) => c.copy(skipDesugar = true)                   } text("Whether to skip desugaring and assume no sugar")
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index bd1dccc22..9feb5aeb7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -37,8 +37,9 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
 
   val statementsByHeadName: Map[String, List[Statement]] =
     statements collect {
-      case s: ExtractionRule       => s.headName -> s
       case s: FunctionCallRule     => s.output -> s
+      case s: ExtractionRule       => s.headName -> s
+      case s: SupervisionRule      => s.headName -> s
     } groupBy(_._1) mapValues(_ map {_._2})
 
   val statementsByRepresentative: Map[Statement, List[Statement]] =
@@ -53,17 +54,19 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   // Given a statement, resolve its name for the compiled extractor block.
   def resolveExtractorBlockName(s: Statement): String = s match {
     case d: SchemaDeclaration => s"init_${d.a.name}"
-    case e: ExtractionRule => s"ext_${e.headName}"
     case f: FunctionCallRule => s"ext${
       // Extra numbering is necessary because there can be many function calls to the same head relation
       // XXX This comes right after the prefix to prevent potential collision with user's name
       val functionCallsForSameOutputAndFunction =
         statementsByHeadName getOrElse(f.output, List.empty) filter {
           case s:FunctionCallRule => s.function == f.function
+          case _ => false
         }
       val idx = functionCallsForSameOutputAndFunction indexOf f
       optionalIndex(idx)
     }_${f.output}_by_${f.function}"
+    case e: ExtractionRule => s"ext_${e.headName}"
+    case s: SupervisionRule => s"ext_${s.headName}"
     case _ => sys.error(s"${s}: Cannot determine extractor block name for rule")
   }
 
@@ -97,20 +100,16 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
     }
   }
 
-  // has schema declared
-  def hasSchemaDeclared(relName: String) : Boolean = {
-    schemaDeclarationByRelationName contains relName
-  }
-
   def collectUsedRelations1(body: Body): List[String] = body match {
     case a: BodyAtom => List(a.name)
     case q: QuantifiedBody => collectUsedRelations(q.bodies)
     case _ => List.empty
   }
   def collectUsedRelations(bodies: List[Body]): List[String] = bodies flatMap collectUsedRelations1
-  val relationNamesUsedByStatement = statements collect {
+  val relationNamesUsedByStatement: Map[Statement, List[String]] = statements collect {
       case f : FunctionCallRule => f -> (f.q.bodies flatMap collectUsedRelations distinct)
       case e : ExtractionRule   => e -> (e.q.bodies flatMap collectUsedRelations distinct)
+      case e : SupervisionRule  => e -> (e.q.bodies flatMap collectUsedRelations distinct)
       case e : InferenceRule    => e -> (e.q.bodies flatMap collectUsedRelations distinct)
     } toMap
 
@@ -122,6 +121,7 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   case object TableAlias extends AliasStyle
   case object NoAlias extends AliasStyle
   case object UseVariableAsAlias extends AliasStyle
+  case object SupervisionRuleAlias extends AliasStyle
 
 
   // This is responsible for compiling a single conjunctive query
@@ -173,7 +173,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   }
 
   // compile alias
-  def compileAlias(e: Expr, aliasStyle: AliasStyle) = aliasStyle match {
+  def compileAlias(e: Expr, a: Option[String], aliasStyle: AliasStyle) = aliasStyle match {
     case NoAlias => ""
     case TableAlias => e match {
       case VarExpr(v) => {
@@ -187,6 +187,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     }
     case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
     case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}"""" //" fix sublime highlighting
+    case SupervisionRuleAlias => a map (" AS " + _) getOrElse ""
   }
 
   // resolve an expression
@@ -244,8 +245,9 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
   // generate SQL SELECT cluase
   def generateSQLHead(aliasStyle: AliasStyle) = {
-    val head = if (cq.headTerms isEmpty) "*" else cq.headTerms map { expr =>
-      compileExpr(expr) + compileAlias(expr, aliasStyle)
+    val head = if (cq.headTerms isEmpty) "*" else cq.headTerms.zip(
+      cq.headTermAliases getOrElse {cq.headTerms map {_ => None}}) map { case (expr, alias) =>
+      compileExpr(expr) + compileAlias(expr, alias, aliasStyle)
     } mkString(", ")
     val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
     s"${distinctStr}${head}"
@@ -354,27 +356,15 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     val orderbyStr =
       if (cq.headTermAnnotations.size != cq.headTerms.size) "" // invalid annotations
       else {
-        val ORDER_BY_ANNOTATION_NAMES = Set("order_by")
-        val orderByAnnos = cq.headTermAnnotations map {
-          case annos => annos collectFirst {
-            case anno if ORDER_BY_ANNOTATION_NAMES contains anno.name => anno
-          }
-        }
+        val orderByAnnos = cq.headTermAnnotations map (_ find (_ named "order_by"))
         val orderByExprs = cq.headTerms.zip(orderByAnnos).zipWithIndex collect {
           case ((e, Some(orderByAnno)), i) =>
-            // TODO factor out annotation argument handling
             val isAscending = // the "dir" or first argument of the annotation decides the sort order, defaulting to ASCending
-              orderByAnno.args collect {
-                case Left(argsMap) => (argsMap getOrElse("dir", "ASC")).toString == "ASC"
-                case Right(dir :: _) => dir.toString == "ASC"
-              } getOrElse(true)
+              (orderByAnno.valueAt("dir", 0) getOrElse "ASC") == "ASC"
             val priority = // the priority or second argument decides the key index
-              orderByAnno.args collect {
-                case Left(argsMap) => (argsMap getOrElse("priority", i+1)).toString.toInt
-                case Right(_ :: priority :: _) => priority.toString.toInt
-              } getOrElse(i+1)
+              orderByAnno.valueAt("priority", 1) map (_.toString.toInt) getOrElse (i+1)
             (e, isAscending, priority)
-        } sortBy { _._3 }
+        } sortBy (_._3)
         optionalClause("\nORDER BY", orderByExprs map {
             case (e, isAscending, _) => s"${compileExpr(e)} ${if (isAscending) "ASC" else "DESC"}"
           } mkString(", ")
@@ -405,55 +395,60 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     List.empty
   }
 
+  def generateUnionAllSQL(cqs: List[ConjunctiveQuery], aliasStyle: AliasStyle): String = {
+    cqs map { q => new QueryCompiler(q).generateSQL(aliasStyle) } mkString("\nUNION ALL\n")
+  }
+
   // Generate extraction rule part for deepdive
   def compile(stmt: ExtractionRule): CompiledBlocks = {
     val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
     if (stmts isEmpty) return List.empty
 
-    val inputQueries = stmts flatMap { case stmt =>
-      stmt.q.bodies map { case cqBody =>
-        val tmpCq = stmt.q.copy(bodies = List(cqBody))
-        // Generate the body of the query.
-        val qc              = new QueryCompiler(tmpCq)
-
-        if (stmt.supervision != None) {
-          if (stmt.q.bodies.length > 1) sys.error(s"Scoping rule does not allow disjunction.\n")
-          val headStr = qc.generateSQLHead(NoAlias)
-          val labelCol = qc.compileExpr(stmt.supervision.get)
-          s"""SELECT DISTINCT ${ headStr }, ${labelCol} AS label
-          ${ qc.generateSQLBody(cqBody) }
-          """
+    val hasSchemaDeclared = schemaDeclarationByRelationName contains stmt.headName
+    val aliasStyle = if (hasSchemaDeclared) TableAlias else ViewAlias
+    compileExtractorBlock(resolveExtractorBlockName(stmt), stmt.headName, stmts,
+      generateUnionAllSQL(stmts map (_.q), aliasStyle))
+  }
+
+  def compileExtractorBlock(extractorName: String, outputRelation: String, stmts: List[Statement], sql: String): CompiledBlocks = {
+    val shouldMaterialize = schemaDeclarationByRelationName contains outputRelation
+
+    List(s"deepdive.extraction.extractors.${extractorName}" -> Map(
+      "cmd" -> QuotedString(
+        if (shouldMaterialize) {
+          s"""
+          |# TODO use temporary table
+          |deepdive create table "${outputRelation}"
+          |deepdive sql ${escape4sh(s"INSERT INTO ${outputRelation} $sql")}
+          |# TODO rename temporary table to replace output_relation
+          |""".stripMargin
         } else {
-          // variable columns
-          // dd_new_ tale only need original column name to make sure the schema is the same with original table
-          // views uses view alias
-          val aliasStyle = if (!hasSchemaDeclared(stmt.headName)) ViewAlias
-              else TableAlias
-          qc.generateSQL(aliasStyle)
+          s"""
+          |deepdive create view ${outputRelation} as ${escape4sh(sql)}
+          |""".stripMargin
         }
-      }
-    }
-    val blockName = resolveExtractorBlockName(stmts(0))
-    val createTable = hasSchemaDeclared(stmts(0).headName)
-    List(s"deepdive.extraction.extractors.${blockName}" -> Map(
-      "cmd" -> QuotedString(if (createTable) {
-	s"""
-	# TODO use temporary table
-	deepdive create table "${stmts(0).headName}"
-	deepdive sql ${escape4sh(s"INSERT INTO ${stmts(0).headName} ${inputQueries.mkString("\nUNION ALL\n")}")}
-	# TODO rename temporary table to replace output_relation
-	"""
-} else {
-	s"""
-	deepdive create view ${stmts(0).headName} as ${escape4sh(inputQueries.mkString("\nUNION ALL\n"))}
-	"""
-}),
-      "output_relation" -> stmts(0).headName,
+      ),
+      "output_relation" -> outputRelation,
       "style" -> "cmd_extractor",
       "input_relations" -> (stmts flatMap relationNamesUsedByStatement distinct)
     ))
   }
 
+  def compile(stmt: SupervisionRule): CompiledBlocks = {
+    val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: SupervisionRule => s }
+    if (stmts isEmpty) return List.empty
+
+    compileExtractorBlock(resolveExtractorBlockName(stmt), stmt.headName, stmts,
+      generateUnionAllSQL(stmts map { case stmt => stmt.q.copy(
+        headTerms = stmt.q.headTerms :+ stmt.supervision,
+        headTermAliases = {
+          stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ :+ Some("label") }
+        },
+        isDistinct = true
+      ) }, SupervisionRuleAlias)
+    )
+  }
+
   def compile(stmt: FunctionCallRule): CompiledBlocks = {
     val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: FunctionCallRule => s }
     if (stmts isEmpty) return List.empty
@@ -472,7 +467,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
           + (function.implementations mkString "\n  "))
 
       val blockName = resolveExtractorBlockName(stmt)
-      val parallelism = stmt.parallelism getOrElse("${PARALLELISM}")
+      val parallelism = stmt.annotations find (_ named "parallelism") flatMap (_.value) getOrElse("${PARALLELISM}")
       s"deepdive.extraction.extractors.${blockName}" -> (Map(
         "input" -> QuotedString(new QueryCompiler(stmt.q).generateSQL(TableAlias)),
         "output_relation" -> stmt.output,
@@ -485,6 +480,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
   // generate inference rule part for deepdive
   def compile(stmt: InferenceRule): CompiledBlocks = {
+    // FIXME change stmt.head.terms to be List[BodyAtom] in the parser
     val headAsBody = stmt.head.terms map { x =>
       BodyAtom(x.name, x.terms map {
         case x: VarExpr => VarPattern(x.name)
@@ -594,8 +590,9 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   def compile(stmt: Statement): CompiledBlocks = stmt match {
     case s: SchemaDeclaration => compile(s)
     case s: FunctionDeclaration => compile(s)
-    case s: ExtractionRule => compile(s)
     case s: FunctionCallRule => compile(s)
+    case s: ExtractionRule => compile(s)
+    case s: SupervisionRule => compile(s)
     case s: InferenceRule => compile(s)
     case _ => sys.error(s"Compiler does not recognize statement: ${stmt}")
   }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
deleted file mode 100644
index cf09438b8..000000000
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDeltaDeriver.scala
+++ /dev/null
@@ -1,176 +0,0 @@
-package org.deepdive.ddlog
-
-import org.deepdive.ddlog.DeepDiveLog.{Config, Program}
-
-import scala.collection.mutable.ListBuffer
-
-
-object Mode extends Enumeration {
-  type Mode = Value
-  // NewInference: a new inference rule
-  // NewFunction: a new function call
-  // Normal: existing rules
-  val NewInference, NewFunction, Normal = Value
-}
-import Mode._
-
-object DeepDiveLogDeltaDeriver extends DeepDiveLogHandler {
-
-  // Default prefix for incremental tables
-  val deltaPrefix = "dd_delta_"
-  val newPrefix = "dd_new_"
-
-  def transform(stmt: Statement): List[Statement] = stmt match {
-    case s: SchemaDeclaration   => transform(s)
-    case s: FunctionDeclaration => transform(s)
-    case s: ExtractionRule      => transform(s)
-    case s: FunctionCallRule    => transform(s)
-    case s: InferenceRule       => transform(s)
-  }
-
-  def transform(headName: String, cq: ConjunctiveQuery, mode: Mode): ConjunctiveQuery = {
-
-    // New head
-    val incCqHead = transform(headName)
-
-    var incCqBodies = new ListBuffer[List[Body]]()
-    // New incremental bodies
-    cq.bodies foreach { bodies =>
-      // We don't support deriving delta rules for modifiers
-      bodies foreach {
-        case _: Cond | _: BodyAtom => // supported
-        case _ => sys.error("Deriving delta rules for modifier atom is not supported!")
-      }
-      // Delta body
-      val incDeltaBody = bodies collect {
-        case a: BodyAtom => a.copy(name = deltaPrefix + a.name)
-        case a: Cond => a
-      }
-      // New body
-      val incNewBody = bodies collect {
-        case a: BodyAtom => a.copy(name = newPrefix + a.name)
-        case a: Cond => a
-      }
-      val bodyAtoms         = bodies       collect { case a: BodyAtom => a }
-      val bodyConds         = bodies       collect { case a: Cond => a }
-      val incDeltaBodyAtoms = incDeltaBody collect { case a: BodyAtom => a }
-      val incNewBodyAtoms   = incNewBody   collect { case a: BodyAtom => a }
-
-      if (mode == NewInference) {
-        incCqBodies += incNewBody
-      } else {
-        var i = 0
-        var j = 0
-        val index = if (mode == NewFunction) -1 else 0
-        for (i <- index to (bodyAtoms.length - 1)) {
-          var newBody = new ListBuffer[Body]()
-          for (j <- 0 to (bodyAtoms.length - 1)) {
-            if (j > i)
-              newBody += bodyAtoms(j)
-            else if (j < i)
-              newBody += incNewBodyAtoms(j)
-            else if (j == i)
-              newBody += incDeltaBodyAtoms(j)
-          }
-          newBody = newBody ++ bodyConds
-          incCqBodies += newBody.toList
-        }
-      }
-    }
-
-    cq.copy(bodies = incCqBodies.toList)
-  }
-
-  def transform(headName: String) : String = deltaPrefix + headName
-
-  def transform(a: HeadAtom) : HeadAtom = a.copy(name = newPrefix + a.name)
-
-  // Incremental scheme declaration,
-  // keep the original scheme and create one delta scheme
-  def transform(stmt: SchemaDeclaration): List[Statement] = {
-    var incrementalStatement = new ListBuffer[Statement]()
-    // Incremental table
-    incrementalStatement += stmt
-
-    // Delta table
-    var incDeltaStmt = stmt.copy(
-      a = stmt.a.copy(
-        name = deltaPrefix + stmt.a.name
-      )
-    )
-    incrementalStatement += incDeltaStmt
-
-    // New table
-    var incNewStmt = stmt.copy(
-      a = stmt.a.copy(
-        name = newPrefix + stmt.a.name
-      )
-    )
-    incrementalStatement += incNewStmt
-
-    incrementalStatement += ExtractionRule(incNewStmt.a.name,
-      ConjunctiveQuery(incNewStmt.a.terms map { VarExpr(_) },
-      List(List(BodyAtom(stmt.a.name, stmt.a.terms map { VarPattern(_) })),
-      List(BodyAtom(incDeltaStmt.a.name, incDeltaStmt.a.terms map { VarPattern(_) }))),
-      false, None))
-
-    incrementalStatement.toList
-  }
-
-  // Incremental function declaration,
-  // create one delta function scheme based on original function scheme
-  def transform(stmt: FunctionDeclaration): List[Statement] = {
-    List(stmt.copy(
-      inputType = stmt.inputType match {
-        case inTy: RelationTypeDeclaration => inTy
-        case inTy: RelationTypeAlias =>
-          inTy.copy(likeRelationName = deltaPrefix + inTy.likeRelationName)
-      },
-      outputType = stmt.outputType match {
-        case outTy: RelationTypeDeclaration => outTy
-        case outTy: RelationTypeAlias =>
-          outTy.copy(likeRelationName = deltaPrefix + outTy.likeRelationName)
-      }
-    ))
-  }
-
-  // Incremental extraction rule,
-  // create delta rules based on original extraction rule
-  def transform(stmt: ExtractionRule): List[Statement] = {
-    List(stmt.copy(
-      headName = transform(stmt.headName),
-      q = transform(stmt.headName, stmt.q, Normal)))
-  }
-
-  // Incremental function call rule,
-  // modify function input and output
-  def transform(stmt: FunctionCallRule): List[Statement] = {
-    val mode = if (stmt.mode == Some("inc")) NewFunction else Normal
-    List(stmt.copy(
-      output = transform(stmt.output),
-      q = transform(stmt.output, stmt.q, mode),
-      mode = None))
-  }
-
-  // Incremental inference rule,
-  // create delta rules based on original extraction rule
-  def transform(stmt: InferenceRule): List[Statement] = {
-    val mode = if (stmt.mode == Some("inc")) NewInference else Normal
-    List(stmt.copy(head = stmt.head.copy(terms = stmt.head.terms map transform),
-      q = transform("", stmt.q, mode), mode = None))
-  }
-
-  def derive(program: DeepDiveLog.Program): DeepDiveLog.Program = {
-    var incrementalProgram = new ListBuffer[Statement]()
-
-    for (x <- program) {
-      incrementalProgram = incrementalProgram ++ transform(x)
-    }
-    incrementalProgram.toList
-  }
-
-  override def run(program: Program, config: Config): Unit = {
-    DeepDiveLogPrettyPrinter.run(derive(program), config)
-  }
-
-}
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
index b06f5b1d6..8d49af363 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
@@ -1,5 +1,7 @@
 package org.deepdive.ddlog
 
+import scala.language.postfixOps
+
 object DeepDiveLogDesugarRewriter {
 
   // Rewrite function call rules whose output coincides with normal rules.
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 23626cedd..fd3636a2e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -3,9 +3,10 @@ package org.deepdive.ddlog
 // DeepDiveLog syntax
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
-import scala.util.parsing.combinator._
 import org.apache.commons.lang3.StringEscapeUtils
-import scala.util.Try
+
+import scala.language.postfixOps
+import scala.util.parsing.combinator._
 
 // ***************************************
 // * The union types for for the parser. *
@@ -16,11 +17,14 @@ sealed trait Expr
 case class VarExpr(name: String) extends Expr
 case class ArrayElementExpr(array: Expr, index: Expr) extends Expr
 sealed trait ConstExpr extends Expr
+{
+  def value: Any
+}
 case class StringConst(value: String) extends ConstExpr
 case class IntConst(value: Int) extends ConstExpr
 case class DoubleConst(value: Double) extends ConstExpr
 case class BooleanConst(value: Boolean) extends ConstExpr
-case class NullConst() extends ConstExpr
+case class NullConst() extends ConstExpr { def value = null }
 case class FuncExpr(function: String, args: List[Expr], isAggregation: Boolean) extends Expr
 case class BinaryOpExpr(lhs: Expr, op: String, rhs: Expr) extends Expr
 case class TypecastExpr(lhs: Expr, rhs: String) extends Expr
@@ -41,21 +45,34 @@ case class OuterModifier() extends BodyModifier
 case class AllModifier() extends BodyModifier
 
 case class Attribute(name : String, terms : List[String], types : List[String], annotations : List[List[Annotation]])
-case class ConjunctiveQuery(headTerms: List[Expr], bodies: List[List[Body]], isDistinct: Boolean = false, limit: Option[Int] = None,
+case class ConjunctiveQuery(headTerms: List[Expr],
+                            bodies: List[List[Body]],
+                            isDistinct: Boolean = false,
+                            limit: Option[Int] = None,
                             // optional annotations for head terms
                             headTermAnnotations: List[List[Annotation]] = List.empty,
+                            headTermAliases: Option[List[Option[String]]] = None,
                             // XXX This flag is not ideal, but minimizes the impact of query treatment when compared to creating another case class
                             isForQuery: Boolean = false
                            )
-case class Column(name : String // name of the column
-                 , t : String // type of the column
-                 , annotation: List[Annotation] = List.empty // optional annotation
-                 )
 
 case class Annotation( name : String // name of the annotation
                      , args : Option[Either[Map[String,Expr],List[Expr]]] = None // optional, named arguments map or unnamed list
                      )
-case class RuleAnnotation(name: String, args: List[String])
+{
+  def named(n: String): Boolean = name.toLowerCase == n.toLowerCase
+
+  def exprs: List[Expr] = args map (_ fold (_.values toList, es => es)) getOrElse List.empty
+  def values: List[Any] = exprs collect { case e: ConstExpr => e.value }
+
+  def expr: Option[Expr] = exprs headOption
+  def value: Option[Any] = values headOption
+
+  def exprAt(namedArg: String, positionalArg: Int): Option[Expr] =
+    args flatMap (_ fold (_ get namedArg, _ lift positionalArg))
+  def valueAt(namedArg: String, positionalArg: Int): Option[Any] =
+    exprAt(namedArg, positionalArg) collect { case e: ConstExpr => e.value }
+}
 
 // condition
 sealed trait Cond extends Body
@@ -87,18 +104,21 @@ case class HeadAtom(name : String, terms : List[Expr], isNegated: Boolean = fals
 case class InferenceRuleHead(function: FactorFunction.FactorFunction, terms: List[HeadAtom])
 
 
-trait FunctionInputOutputType
+sealed trait FunctionInputOutputType
 case class RelationTypeDeclaration(names: List[String], types: List[String]) extends FunctionInputOutputType
 case class RelationTypeAlias(likeRelationName: String) extends FunctionInputOutputType
 
-trait FunctionImplementationDeclaration
+sealed trait FunctionImplementationDeclaration
 case class RowWiseLineHandler(style: String, command: String) extends FunctionImplementationDeclaration
 
 // Statements that will be parsed and compiled
-trait Statement
-case class SchemaDeclaration( a : Attribute
-                            , isQuery : Boolean
-                            , annotation : List[Annotation] = List.empty // optional annotation
+sealed trait Statement
+{
+  val annotations: List[Annotation]
+}
+case class SchemaDeclaration(a: Attribute,
+                             isQuery: Boolean,
+                             annotations: List[Annotation] = List.empty
                             ) extends Statement // atom and whether this is a query relation.
 {
   // infer whether this is a categorical variable based on column annotations
@@ -111,13 +131,32 @@ case class SchemaDeclaration( a : Attribute
       else a.terms diff keyColumns toList  // otherwise, the rest of the columns define categories
     } else List.empty
 }
-case class FunctionDeclaration( functionName: String, inputType: FunctionInputOutputType,
-  outputType: FunctionInputOutputType, implementations: List[FunctionImplementationDeclaration]) extends Statement
-case class ExtractionRule(headName: String, q : ConjunctiveQuery, supervision: Option[Expr] = None) extends Statement // Extraction rule
-case class FunctionCallRule(output: String, function: String, q : ConjunctiveQuery, mode: Option[String], parallelism: Option[Int]) extends Statement // Extraction rule
-case class InferenceRule(head: InferenceRuleHead, q : ConjunctiveQuery, weights : FactorWeight, mode: Option[String] = None) extends Statement // Weighted rule
-
-
+case class FunctionDeclaration(functionName: String,
+                               inputType: FunctionInputOutputType,
+                               outputType: FunctionInputOutputType,
+                               implementations: List[FunctionImplementationDeclaration],
+                               annotations: List[Annotation] = List.empty
+                              ) extends Statement
+sealed trait RuleWithConjunctiveQuery extends Statement { val q: ConjunctiveQuery }
+case class ExtractionRule(headName: String,
+                          q: ConjunctiveQuery,
+                          annotations: List[Annotation] = List.empty
+                         ) extends RuleWithConjunctiveQuery
+case class FunctionCallRule(output: String,
+                            function: String,
+                            q: ConjunctiveQuery,
+                            annotations: List[Annotation] = List.empty
+                           ) extends RuleWithConjunctiveQuery
+case class SupervisionRule(headName: String,
+                           supervision: Expr,
+                           q: ConjunctiveQuery,
+                           annotations: List[Annotation] = List.empty
+                          ) extends RuleWithConjunctiveQuery
+case class InferenceRule(head: InferenceRuleHead,
+                         q: ConjunctiveQuery,
+                         weights: FactorWeight = null,
+                         annotations: List[Annotation] = List.empty
+                        ) extends RuleWithConjunctiveQuery
 
 
 
@@ -147,22 +186,22 @@ class DeepDiveLogParser extends JavaTokenParsers {
   protected override val whiteSpace = """(?:(?:^|\s+)#.*|//.*|\s)+""".r
 
   // We just use Java identifiers to parse various names
-  def relationName = ident
-  def columnName   = ident
+  def relationName = ident named "relation name"
+  def columnName   = ident named "column name"
   def columnType   = ident ~ ("[]"?) ^^ {
       case ty ~ isArrayType => ty + isArrayType.getOrElse("")
-    }
-  def variableName = ident
-  def functionName = ident
+    } named "column type"
+  def variableName = ident named "variable name"
+  def functionName = ident named "function name"
   def functionModeType = stringLiteralAsString
   def inferenceModeType = stringLiteralAsString
-  def annotationName = ident
-  def annotationArgumentName = ident
+  def annotationName = ident named "annotation name"
+  def annotationArgumentName = ident named "annotation argument name"
 
   def annotation: Parser[Annotation] =
     "@" ~ annotationName ~ opt(annotationArguments) ^^ {
       case (_ ~ name ~ optArgs) => Annotation(name, optArgs)
-    }
+    } named "annotation"
 
   def annotationArguments: Parser[Either[Map[String, Expr], List[Expr]]] =
     "(" ~> (
@@ -170,36 +209,63 @@ class DeepDiveLogParser extends JavaTokenParsers {
       rep1sep(annotationArgumentValue, ",") ^^ {
         case values => Right(values)
       }
-    |
+    |||
       repsep(annotationNamedArgument, ",") ^^ {
         case namedArgs => Left(namedArgs toMap)
       }
-    ) <~ ")"
+    ) <~ ")" named "annotation arguments"
   def annotationNamedArgument: Parser[(String, Expr)] =
     annotationArgumentName ~ "=" ~ annotationArgumentValue ^^ {
       case name ~ _ ~ value => name -> value
-    }
-  def annotationArgumentValue: Parser[Expr] = expr
+    } named "annotation named arguments"
+  def annotationArgumentValue: Parser[Expr] = expr named "annotation argument value"
 
-  def columnDeclaration: Parser[Column] =
+  def columnDeclaration: Parser[(String, String, List[Annotation])] =
     rep(annotation) ~
     columnName ~ columnType ^^ {
-      case(anno ~ name ~ ty) => Column(name, ty, anno)
-    }
+      case(anno ~ name ~ ty) => (name, ty, anno)
+    } named "column declaration"
 
   def schemaDeclaration: Parser[SchemaDeclaration] =
-    rep(annotation) ~
     relationName ~ opt("?") ~ ("(" ~> rep1sep(columnDeclaration, ",") <~ ")") ^^ {
-      case (anno ~ r ~ isQuery ~ attrs) => {
-        val vars = attrs map (_.name)
-        var types = attrs map (_.t)
-        val annos = attrs map (_.annotation)
-        SchemaDeclaration(Attribute(r, vars, types, annos), (isQuery != None), anno)
+      case (r ~ isQuery ~ attrs) =>
+        attrs unzip3 match { case (vars, types, annos) =>
+          SchemaDeclaration(Attribute(r, vars, types, annos), isQuery != None)
+        }
+    } named "schema declaration"
+
+  def functionInputOutputType: Parser[FunctionInputOutputType] =
+    ( "rows" ~> "like" ~> relationName ^^ RelationTypeAlias
+    | "(" ~> rep1sep(columnDeclaration, ",") <~ ")" ^^ { attrs =>
+        attrs unzip3 match { case (names, types, annos) =>
+          RelationTypeDeclaration(names, types)
+        }
       }
-    }
+    ) named "function input/output type declaration"
+
+  def functionImplementation : Parser[FunctionImplementationDeclaration] =
+    ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
+        case (_ ~ command ~ _ ~ style ~ _) => RowWiseLineHandler(command=command, style=style)
+      }
+    | "implementation" ~ stringLiteralAsString ~ "runs" ~ "as" ~ "plpy" ^^ {
+        case (_ ~ command ~ _ ~ _ ~ style) => RowWiseLineHandler(command=command, style=style)
+      }
+    ) named "function implementation declaration"
+
+  def functionDeclaration : Parser[FunctionDeclaration] =
+    ( "function" ~ functionName ~ "over" ~ functionInputOutputType
+    ~ "returns" ~ functionInputOutputType
+    ~ (functionImplementation+)
+    ) ^^ {
+      case ("function" ~ a ~ "over" ~ inTy
+        ~ "returns" ~ outTy
+        ~ implementationDecls) =>
+        FunctionDeclaration(a, inTy, outTy, implementationDecls)
+    } named "function declaration"
+
 
   def operator =
-    ( "||" | "+" | "-" | "*" | "/" | "&" | "%" )
+    ( "||" | "+" | "-" | "*" | "/" | "&" | "%" ) named "operator"
   def typeOperator = "::"
   val aggregationFunctions = Set("MAX", "SUM", "MIN", "ARRAY_ACCUM", "ARRAY_AGG", "COUNT")
 
@@ -209,7 +275,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | lexpr ~ operator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
     | lexpr ~ typeOperator ~ columnType ^^ { case (lhs ~ _ ~ rhs) => TypecastExpr(lhs, rhs) }
     | lexpr
-    )
+    ) named "expression"
 
   def cexpr =
     ( expr ~ compareOperator ~ expr ^^ { case (lhs ~ op ~ rhs) => BinaryOpExpr(lhs, op, rhs) }
@@ -221,15 +287,15 @@ class DeepDiveLogParser extends JavaTokenParsers {
         case (ifCond ~ thenExpr ~ elseIfs ~ optElseExpr) =>
           IfThenElseExpr((ifCond, thenExpr) :: elseIfs, optElseExpr)
       }
-    | stringLiteralAsString ^^ { StringConst(_) }
-    | double ^^ { DoubleConst(_) }
-    | integer ^^ { IntConst(_) }
+    | stringLiteralAsString ^^ StringConst
+    | double ^^ DoubleConst
+    | integer ^^ IntConst
     | ("TRUE" | "FALSE") ^^ { x => BooleanConst(x.toBoolean) }
     | "NULL" ^^ { _ => NullConst() }
     | functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
-        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, (aggregationFunctions contains name))
+        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, aggregationFunctions contains name)
       }
-    | variableName ^^ { VarExpr(_) }
+    | variableName ^^ VarExpr
     | "(" ~> expr <~ ")"
     )
 
@@ -239,21 +305,21 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   // conditional expressions
-  def compareOperator = "LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" ~ "NOT" ^^ { _ => "IS NOT" } | "IS"
+  def compareOperator = ("LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" ~ "NOT" ^^ { _ => "IS NOT" } | "IS") named "compare operator"
 
   def cond : Parser[Cond] =
-    ( acond ~ (";") ~ cond ^^ { case (lhs ~ op ~ rhs) =>
+    ( acond ~ ";" ~ cond ^^ { case (lhs ~ op ~ rhs) =>
         CompoundCond(lhs, LogicOperator.OR(), rhs)
       }
     | acond
-    )
+    ) named "conditional expression"
   def acond : Parser[Cond] =
-    ( lcond ~ (",") ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND(), rhs) }
+    ( lcond ~ "," ~ acond ^^ { case (lhs ~ op ~ rhs) => CompoundCond(lhs, LogicOperator.AND(), rhs) }
     | lcond
     )
   // ! has higher priority...
   def lcond : Parser[Cond] =
-    ( "!" ~> bcond ^^ { NegationCond(_) }
+    ( "!" ~> bcond ^^ NegationCond
     | bcond
     )
   def bcond : Parser[Cond] =
@@ -267,7 +333,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
         case VarExpr(x) => VarPattern(x)
         case x: Expr => ExprPattern(x)
       }
-    )
+    ) named "pattern"
 
   def atom = relationName ~ "(" ~ rep1sep(pattern, ",") ~ ")" ^^ {
     case (r ~ _ ~ patterns ~ _) => BodyAtom(r, patterns)
@@ -281,152 +347,141 @@ class DeepDiveLogParser extends JavaTokenParsers {
     QuantifiedBody(modifier, b)
   }
 
-  def functionInputOutputType: Parser[FunctionInputOutputType] =
-    ( "rows" ~> "like" ~> relationName ^^ { RelationTypeAlias(_) }
-    | "(" ~> rep1sep(columnDeclaration, ",") <~ ")" ^^ {
-        attrs => RelationTypeDeclaration(attrs map { _.name }, attrs map { _.t })
-      }
-    )
-
-  def ruleAnnotation = "@" ~> annotationName ~ ("(" ~> rep1sep(ident, ",") <~ ")") ^^ {
-    case (name ~ args) => RuleAnnotation(name, args)
-  }
-
-  def ruleAnnotations = rep(ruleAnnotation)
-
-  def getArg(annos: List[RuleAnnotation], name: String)  = {
-    annos.find(_.name == name) map (_.args) map (_(0))
-  }
-
-  def functionImplementation : Parser[FunctionImplementationDeclaration] =
-    ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
-        case (_ ~ command ~ _ ~ style ~ _) => RowWiseLineHandler(command=command, style=style)
-      }
-    | "implementation" ~ stringLiteralAsString ~ "runs" ~ "as" ~ "plpy" ^^ {
-        case (_ ~ command ~ _ ~ _ ~ style) => RowWiseLineHandler(command=command, style=style)
-      }
-    )
-
-  def functionDeclaration : Parser[FunctionDeclaration] =
-    ( "function" ~ functionName ~ "over" ~ functionInputOutputType
-                             ~ "returns" ~ functionInputOutputType
-                 ~ (functionImplementation+)
-    ) ^^ {
-      case ("function" ~ a ~ "over" ~ inTy
-                           ~ "returns" ~ outTy
-                       ~ implementationDecls) =>
-             FunctionDeclaration(a, inTy, outTy, implementationDecls)
-    }
-
   def cqBody: Parser[Body] = quantifiedBody | atom | lcond
 
   def cqConjunctiveBody: Parser[List[Body]] = rep1sep(cqBody, ",")
 
-  def cqHeadTerms = "(" ~> rep1sep(expr, ",") <~ ")"
-
   def conjunctiveQueryBody(separator: Parser[_] = ":-") : Parser[ConjunctiveQuery] =
     opt("*") ~ opt("|" ~> decimalNumber) ~ separator ~ rep1sep(cqConjunctiveBody, ";") ^^ {
       case (isDistinct ~ limit ~ _ ~ disjunctiveBodies) =>
-        ConjunctiveQuery(List.empty, disjunctiveBodies, isDistinct != None, limit map (_.toInt))
+        ConjunctiveQuery(List.empty, disjunctiveBodies, isDistinct isDefined, limit map (_.toInt))
     }
 
+  def conjunctiveQueryHeadTerms = "(" ~> rep1sep(expr, ",") <~ ")"
+
   def conjunctiveQuery : Parser[ConjunctiveQuery] =
     // TODO fill headTermAnnotations as done in queryWithOptionalHeadTerms to support @order_by
-    cqHeadTerms ~ conjunctiveQueryBody() ^^ {
+    conjunctiveQueryHeadTerms ~ conjunctiveQueryBody() ^^ {
       case (head ~ cq) => cq.copy(headTerms = head)
     }
 
-  def functionMode = "@mode" ~> commit("(" ~> functionModeType <~ ")" ^? ({
-    case "inc" => "inc"
-  }, (s) => s"${s}: unrecognized mode"))
-
-  def parallelism = "@parallelism" ~> "(" ~> integer <~ ")"
-
-  def functionCallRule : Parser[FunctionCallRule] =
-    opt(functionMode) ~ opt(parallelism) ~ relationName ~ "+=" ~ functionName ~ conjunctiveQuery ^^ {
-      case (mode ~ parallelism ~ out ~ _ ~ func ~ cq) => FunctionCallRule(out, func, cq, mode, parallelism)
-    }
-
-  def supervisionAnnotation = "@label" ~> "(" ~> expr <~ ")"
-
-  def extractionRule =
-    ( opt(supervisionAnnotation) ~ relationName ~ conjunctiveQuery ^^ {
-        case (sup ~ head ~ cq) => ExtractionRule(head, cq, sup)
+  def ruleWithConjunctiveQuery: Parser[RuleWithConjunctiveQuery] =
+    ( // normal derivation rule (or could also be IsTrue factor rule when @weight annotation is present which is handled later)
+      relationName ~ conjunctiveQuery ^^ {
+        case head ~ cq =>
+          ExtractionRule(headName = head, q = cq)
+      }
+    | // inference rule with special syntax in head for designated factors
+      inferenceRuleHead ~ conjunctiveQueryBody() ^^ {
+        case head ~ cq =>
+          InferenceRule(head = head, q = cq)
       }
-    | relationName ~ cqHeadTerms ~ ("=" ~> expr) ~ conjunctiveQueryBody() ^^ {
-        case (head ~ headTerms ~ sup ~ cq) =>
-          ExtractionRule(head, cq.copy(headTerms = headTerms), Some(sup))
+    | // supervision rule with equal sign
+      relationName ~ conjunctiveQueryHeadTerms ~ ("=" ~> expr) ~ conjunctiveQueryBody() ^^ {
+        case h ~ ts ~ sup ~ cq =>
+          SupervisionRule(headName = h, supervision = sup, q = cq.copy(headTerms = ts))
+      }
+    | // function call with += sign between head and function call
+      relationName ~ ("+=" ~> functionName) ~ conjunctiveQuery ^^ {
+        case out ~ func ~ cq =>
+          FunctionCallRule(output = out, function = func, q = cq)
       }
     )
 
-  def factorWeight = "@weight" ~> "(" ~> rep1sep(expr, ",") <~ ")" ^^ { FactorWeight(_) }
-  def inferenceMode = "@mode" ~> commit("(" ~> inferenceModeType <~ ")" ^? ({
-    case "inc" => "inc"
-  }, (s) => s"${s}: unrecognized mode"))
-
   // factor functions
-  def headAtom = opt("!") ~ relationName ~ ("(" ~> rep1sep(expr, ",") <~ ")") ^^ {
-    case (isNegated ~ r ~ expressions) => HeadAtom(r, expressions, isNegated != None)
-  }
-
-  def implyHeadAtoms = rep1sep(headAtom, ",") ~ "=>" ~ headAtom ^^ {
-    case (a ~ _ ~ b) => a :+ b
-  }
-
   def inferenceRuleHead =
-  ( implyHeadAtoms ^^ {
-      InferenceRuleHead(FactorFunction.Imply(), _)
-    }
-  | "@semantics" ~> commit("(" ~> stringLiteralAsString <~ ")" ^? ({
-      case "linear" => FactorFunction.Linear()
-      case "ratio"  => FactorFunction.Ratio()
-    }, (s) => s"${s}: unrecognized semantics")) ~ implyHeadAtoms ^^ {
-      case (s ~ h) => InferenceRuleHead(s, h)
-    }
-  | headAtom ~ "=" ~ rep1sep(headAtom, "=") ^^ { case (a ~ _ ~ b) =>
-      InferenceRuleHead(FactorFunction.Equal(), a +: b)
-    }
-  | headAtom ~ "^" ~ rep1sep(headAtom, "^") ^^ { case (a ~ _ ~ b) =>
-      InferenceRuleHead(FactorFunction.And(), a +: b)
-    }
-  | headAtom ~ "v" ~ rep1sep(headAtom, "v") ^^ { case (a ~ _ ~ b) =>
-      InferenceRuleHead(FactorFunction.Or(), a +: b)
+    ( rep1sep(headAtom, ",") ~ ("=>" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.Imply() ,  a :+ b) }
+    |         headAtom    ~ rep1("=" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.Equal() ,  a +: b) }
+    |         headAtom    ~ rep1("^" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.And()   ,  a +: b) }
+    |         headAtom    ~ rep1("v" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.Or()    ,  a +: b) }
+    |         headAtom                            ^^ { case       a => InferenceRuleHead(FactorFunction.IsTrue(), List(a)) }
+    )
+  def headAtom =
+    opt("!") ~ relationName ~ conjunctiveQueryHeadTerms ^^ {
+      case (isNegated ~ varName ~ expressions) => HeadAtom(varName, expressions, isNegated isDefined)
     }
-  | headAtom ^^ {
-      x => InferenceRuleHead(FactorFunction.IsTrue(), List(x))
+
+  // rules or schema elements in arbitrary order
+  def statement : Parser[Statement] = (
+    rep(annotation) ~
+      ( schemaDeclaration
+      | functionDeclaration
+      | ruleWithConjunctiveQuery
+      )
+    ) ^^ {
+    case annos ~ stmt if annos isEmpty => stmt
+    case annos ~ stmt => stmt match {
+      case s: SchemaDeclaration   => s.copy(annotations = annos)
+      case s: FunctionDeclaration => s.copy(annotations = annos)
+      case s: FunctionCallRule    => s.copy(annotations = annos)
+      case s: ExtractionRule      => s.copy(annotations = annos)
+      case s: SupervisionRule     => s.copy(annotations = annos)
+      case s: InferenceRule       => s.copy(annotations = annos)
     }
-  )
 
-  def inferenceConjunctiveQuery : Parser[ConjunctiveQuery] =
-    ":-" ~> rep1sep(cqConjunctiveBody, ";") ^^ {
-      ConjunctiveQuery(List(), _, false, None)
-  }
+  } ^? {
+    // adjust parse result based on annotations
+    case decl: SchemaDeclaration => decl
+    case decl: FunctionDeclaration => decl
+    case fncall: FunctionCallRule => fncall
+    case supvis: SupervisionRule => supvis
+
+    // treat @weight annotations
+    case rule: RuleWithConjunctiveQuery if rule.annotations exists {
+      anno => (anno named "weight") && (anno.args isDefined)
+    } =>
+      val weights = FactorWeight(rule.annotations find (_ named "weight") map (_ exprs) get)
+      rule match {
+        case extrRule: ExtractionRule =>
+          // turn normal derivation rules to IsTrue factors
+          val headAtom = HeadAtom(name = extrRule.headName, terms = extrRule.q.headTerms, isNegated = false)
+          InferenceRule(
+            head = InferenceRuleHead(FactorFunction.IsTrue(), List(headAtom)),
+            q = extrRule.q.copy(headTerms = List.empty),
+            weights = weights,
+            annotations = extrRule.annotations
+          )
+        case infrRule: InferenceRule =>
+          infrRule.copy(weights = weights)
+        case _ => sys.error(s"Invalid usage of @weight:\n${DeepDiveLogPrettyPrinter.print(rule)}")
+      }
+
+    // treat @label annotation
+    case rule: ExtractionRule if rule.annotations exists {
+      anno => (anno named "label") && (anno.exprs.size == 1)
+    } =>
+      val labelExpr = (rule.annotations find (_ named "label") flatMap (_ expr) get)
+      SupervisionRule(headName = rule.headName, supervision = labelExpr, q = rule.q,
+        annotations = rule.annotations filterNot (_ named "label"))
+
+    case rule: ExtractionRule => rule
+    // otherwise (InferenceRule without @weight), it's an error
+
+  } ^? {
+    // treat @semantics annotation
+    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _) if rule.annotations exists {
+      anno => (anno named "semantics") && (anno.exprs.size == 1)
+    } =>
+      rule.annotations find (_ named "semantics") flatMap (_ value) collect {
+        case s: String => s.toLowerCase match {
+          case "linear" => FactorFunction.Linear()
+          case "ratio" => FactorFunction.Ratio()
+          case "logical" => FactorFunction.Imply()
+          case _ => sys.error(s"$s: unrecognized @semantics value")
+        }
+        case v => sys.error(s"${v}: unrecognized @semantics")
+      } map {
+        case factor => rule.copy(head = rule.head.copy(function = factor))
+      } get
+    case rule: Statement if !rule.isInstanceOf[InferenceRule] ||
+      !(rule.annotations exists (_ named "semantics")) => rule
 
-  def inferenceRule =
-    opt(inferenceMode) ~ factorWeight ~ inferenceRuleHead ~ inferenceConjunctiveQuery ^^ {
-      case (mode ~ weight ~ head ~ cq) => InferenceRule(head, cq, weight, mode)
   }
 
-  // rules or schema elements in arbitrary order
-  def statement : Parser[Statement] = ( inferenceRule
-                                      | schemaDeclaration
-                                      | extractionRule
-                                      | functionDeclaration
-                                      | functionCallRule
-                                      )
   def program : Parser[DeepDiveLog.Program] = phrase(rep1(statement <~ "."))
 
-  def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
-    val result = parse(program, inputProgram)
-    if (result successful) result.get
-    else sys.error(fileName.getOrElse("") + result.toString)
-  }
 
-  def parseProgramFile(fileName: String): List[Statement] = {
-    val source = scala.io.Source.fromFile(fileName)
-    try parseProgram(source.getLines mkString "\n", Some(fileName))
-    finally source.close()
-  }
+
 
   // query is a conjunctive query with optional projection and extraction rules
   def query : Parser[DeepDiveLog.Query] =
@@ -458,6 +513,22 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   def annotatedHeadTerm = rep(annotation) ~ expr ^^ { case anno ~ e => (e, anno) }
 
+
+
+
+
+  def parseProgram(inputProgram: CharSequence, fileName: Option[String] = None): List[Statement] = {
+    val result = parse(program, inputProgram)
+    if (result successful) result.get
+    else sys.error(fileName.getOrElse("") + result.toString)
+  }
+
+  def parseProgramFile(fileName: String): List[Statement] = {
+    val source = scala.io.Source.fromFile(fileName)
+    try parseProgram(source.getLines mkString "\n", Some(fileName))
+    finally source.close()
+  }
+
   def parseQuery(inputQuery: String): DeepDiveLog.Query = {
     val result = parse(phrase(query), inputQuery)
     if (result successful) result.get
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 877f8df90..6ddcb7e1e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -1,7 +1,8 @@
 package org.deepdive.ddlog
 
 import org.apache.commons.lang3.StringEscapeUtils
-import org.deepdive.ddlog.DeepDiveLog.Mode._
+
+import scala.language.postfixOps
 
 // Pretty printer that simply prints the parsed input
 object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
@@ -12,6 +13,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     case s: FunctionDeclaration => print(s)
     case s: ExtractionRule      => print(s)
     case s: FunctionCallRule    => print(s)
+    case s: SupervisionRule     => print(s)
     case s: InferenceRule       => print(s)
   }
 
@@ -22,9 +24,9 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
           if (anno.args isEmpty) ""
           else s"(${anno.args.get fold (
             // named arguments case
-            {_ map { case (name, value) => s"${name}=${printLiteral(value)}" }},
+            {_ map { case (name, value) => s"${name}=${print(value)}" }},
             // unnamed argument list case
-            {_ map printLiteral}
+            {_ map print}
           ) mkString(", ") })"
         }" + ("\n" + indentation)
     } mkString
@@ -38,7 +40,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         printAnnotations(stmt.a.annotations(i), indentation) +
         s"${name} ${stmt.a.types(i)}"
     }
-    printAnnotations(stmt.annotation) +
+    printAnnotations(stmt.annotations) +
     s"""${prefix}${columnDecls.mkString(",\n" + indentation)}).
        |""".stripMargin
   }
@@ -60,6 +62,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
         "\"" + StringEscapeUtils.escapeJava(impl.command) + "\"" + styleStr
       }
     }
+    printAnnotations(stmt.annotations) +
     s"""function ${stmt.functionName}
        |    over ${inputType}
        | returns ${outputType}
@@ -170,8 +173,8 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     def printHead(a: List[HeadAtom], delim: String) : String = a map print mkString(delim)
     head.function match {
       case FactorFunction.Imply()  => printImplyHead
-      case FactorFunction.Linear() => s"""@semantics("linear")\n${printImplyHead}"""
-      case FactorFunction.Ratio()  => s"""@semantics("ratio")\n${printImplyHead}"""
+      case FactorFunction.Linear() => printImplyHead
+      case FactorFunction.Ratio()  => printImplyHead
       case FactorFunction.And()    => printHead(head.terms, " ^ ")
       case FactorFunction.Or()     => printHead(head.terms, " v ")
       case FactorFunction.Equal()  => printHead(head.terms, " = ")
@@ -180,24 +183,28 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(stmt: ExtractionRule): String = {
-    stmt.headName + print(stmt.q, stmt.supervision) + ".\n"
+    printAnnotations(stmt.annotations) +
+    stmt.headName + print(stmt.q) + ".\n"
+  }
+
+  def print(stmt: SupervisionRule): String = {
+    printAnnotations(stmt.annotations) +
+    stmt.headName + print(stmt.q, Some(stmt.supervision)) + ".\n"
   }
 
   def print(stmt: FunctionCallRule): String = {
-    ( stmt.mode map (s => s"""@mode("${s}")\n""") getOrElse("") ) +
-    ( stmt.parallelism map (s => s"@parallelism($s)\n") getOrElse("") ) +
+    printAnnotations(stmt.annotations) +
     s"${stmt.output} += ${stmt.function}${print(stmt.q)}.\n"
   }
 
   def print(stmt: InferenceRule): String = {
-    ( stmt.mode map (s => s"""@mode("${s}")\n""") getOrElse "" ) +
-    ( s"@weight(${stmt.weights.variables map print mkString(", ")})\n"
-    ) + print(stmt.head) + print(stmt.q) + ".\n"
+    printAnnotations(stmt.annotations) +
+    print(stmt.head) + print(stmt.q) + ".\n"
   }
 
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     val programToPrint = parsedProgram
     // pretty print in original syntax
-    programToPrint foreach {stmt => println(print(stmt))}
+    programToPrint foreach { stmt => println(print(stmt)) }
   }
 }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index 2751dbbf8..937a115e6 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -28,7 +28,7 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
     }) ++ List({
       // compile the query
       s"""${new compiler.QueryCompiler(query).generateSQL(compiler.UseVariableAsAlias)}"""
-    }) mkString(";\n\n")
+    }) mkString ";\n\n"
     println(sql)
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 2a2e49555..7b3d99f61 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -1,8 +1,6 @@
 package org.deepdive.ddlog
 
-import org.apache.commons.lang3.StringEscapeUtils
-import org.deepdive.ddlog.DeepDiveLog.Mode._
-
+import scala.language.postfixOps
 import scala.util.parsing.json.{JSONArray, JSONObject}
 
 // Schema exporter that dumps column names and types of every relation as well as their annotations
@@ -28,8 +26,8 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
           (name, JSONObject(columnSchema))
       } toMap)
     // relation annotations are omitted when not present
-    if (decl.annotation nonEmpty)
-      schema += "annotations" -> exportAnnotations(decl.annotation)
+    if (decl.annotations nonEmpty)
+      schema += "annotations" -> exportAnnotations(decl.annotations)
     // what type of random variable this relation is
     if (decl.isQuery)
       schema += "variable_type" -> (
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index ce6945b59..2bcc18993 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -1,7 +1,6 @@
 package org.deepdive.ddlog
 
-import scala.collection.immutable.HashMap
-import scala.collection.immutable.HashSet
+import scala.language.postfixOps
 
 // semantic checker for ddlog
 class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
@@ -9,7 +8,8 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
   val namesUsedInHead: Set[String] =
     program collect {
       case s: SchemaDeclaration => s.a.name
-      case s: ExtractionRule if s.supervision isEmpty => s.headName
+      case s: SupervisionRule => s.headName
+      case s: ExtractionRule => s.headName
       case s: FunctionCallRule => s.output
     } toSet
 
@@ -86,7 +86,7 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
 
   // check if the user use reserved column names
   def checkVariableRelationSchema(stmt: Statement) {
-    val reservedSet = Set("id", "label")
+    val reservedSet = Set("label")
     stmt match {
       case decl: SchemaDeclaration => {
         if (decl.isQuery) {
@@ -107,8 +107,8 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
   def checkMultinomialFactors(stmt: Statement) = stmt match {
     case s: InferenceRule =>
       val categoricalVars = s.head.terms filter { t =>
-        schemaDeclarationByName get(t.name) map(_.categoricalColumns nonEmpty) getOrElse(false) }
-      if (! (categoricalVars.size == 0 || s.head.terms.size == categoricalVars.size))
+        schemaDeclarationByName get t.name map(_.categoricalColumns nonEmpty) getOrElse(false) }
+      if (! (categoricalVars.isEmpty || s.head.terms.size == categoricalVars.size))
         error(s, "None or all variables must be categorical")
     case _ =>
   }
@@ -130,6 +130,10 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
         check(s.headName, s.q.headTerms.size)
         checkCq(s.q)
       }
+      case s: SupervisionRule => {
+        check(s.headName, s.q.headTerms.size)
+        checkCq(s.q)
+      }
       case s: InferenceRule => {
         s.head.terms foreach checkHeadAtom
         checkCq(s.q)
@@ -148,10 +152,10 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
               if ((b.bodies collect { case x: BodyAtom => 1 }).size != 1)
                 error(stmt, s"One and only one atom should be supplied in OPTIONAL modifier")
             case ExistModifier(_) =>
-              if ((b.bodies collect { case x: BodyAtom => 1 }).size == 0)
+              if ((b.bodies collect { case x: BodyAtom => 1 }) isEmpty)
                 error(stmt, s"At least one atom should be supplied in EXISTS modifier")
             case AllModifier() =>
-              if ((b.bodies collect { case x: BodyAtom => 1 }).size == 0)
+              if ((b.bodies collect { case x: BodyAtom => 1 }) isEmpty)
                 error(stmt, s"At least one atom should be supplied in ALL modifier")
           }
         }
@@ -160,6 +164,7 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
     }
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach checkBody
+      case s: SupervisionRule => s.q.bodies foreach checkBody
       case s: InferenceRule => s.q.bodies foreach checkBody
       case _ =>
     }
@@ -186,11 +191,12 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
         (cq.headTerms flatMap DeepDiveLogSemanticChecker.collectUsedVars) ++
         (additionalUsedVars)
       val varUndefined = varUses -- varDefs
-      if (varUndefined nonEmpty) error(stmt, s"Variable ${varUndefined mkString (", ")} must have bindings")
+      if (varUndefined nonEmpty) error(stmt, s"Variable ${varUndefined mkString ", "} must have bindings")
     }
     stmt match {
-      case s: ExtractionRule => checkCq(s.q, (s.supervision.toSet flatMap { e: Expr => DeepDiveLogSemanticChecker.collectUsedVars(e) }))
-      case s: InferenceRule => checkCq(s.q, (s.weights.variables flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet))
+      case s: ExtractionRule => checkCq(s.q)
+      case s: SupervisionRule => checkCq(s.q, List(s.supervision) flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet)
+      case s: InferenceRule => checkCq(s.q, s.weights.variables flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet)
       case _ =>
     }
   }
@@ -200,6 +206,7 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
     case decl: SchemaDeclaration => Some(decl.a.name)
     case rule: ExtractionRule => Some(rule.headName)
     case fncall: FunctionCallRule => Some(fncall.output)
+    case rule: SupervisionRule => Some(rule.headName)
     case _ => None
   }
 
@@ -213,7 +220,7 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
       sys.error(s"Following relations must not be redefined: ${
         relationsRedefinedByExtraRules map {
           "'" + _ + "'"
-        } mkString (", ")
+        } mkString ", "
       }")
   }
 
diff --git a/test/compile-error-test/invalid_variable_schema/compile-error.expected b/test/compile-error-test/invalid_variable_schema/compile-error.expected
index c74cc14ed..09335356f 100644
--- a/test/compile-error-test/invalid_variable_schema/compile-error.expected
+++ b/test/compile-error-test/invalid_variable_schema/compile-error.expected
@@ -1,5 +1,5 @@
-[error] variable relation contains reserved column "id" 
-c?(id int,
+[error] variable relation contains reserved column "label" 
+c?(label int,
    s text,
    n int,
    t text).
diff --git a/test/compile-error-test/invalid_variable_schema/input.ddlog b/test/compile-error-test/invalid_variable_schema/input.ddlog
index d9254a628..61f225b66 100644
--- a/test/compile-error-test/invalid_variable_schema/input.ddlog
+++ b/test/compile-error-test/invalid_variable_schema/input.ddlog
@@ -1,5 +1,5 @@
 a(k int).
 b(k int, p text, q text, r int).
-c?(id int, s text, n int, t text).
+c?(label int, s text, n int, t text).
 
-Q(y, z) :- a(x), d(x,y,z,w).
\ No newline at end of file
+Q(y, z) :- a(x), d(x,y,z,w).
diff --git a/test/expected-output-test/many_joins/print-incremental.expected b/test/expected-output-test/many_joins/print-incremental.expected
deleted file mode 100644
index 6edb3d0f8..000000000
--- a/test/expected-output-test/many_joins/print-incremental.expected
+++ /dev/null
@@ -1,57 +0,0 @@
-R?(x text).
-
-dd_delta_R?(x text).
-
-dd_new_R?(x text).
-
-dd_new_R(x) :-
-    R(x);
-    dd_delta_R(x).
-
-S(x text).
-
-dd_delta_S(x text).
-
-dd_new_S(x text).
-
-dd_new_S(x) :-
-    S(x);
-    dd_delta_S(x).
-
-T(x text,
-  f text).
-
-dd_delta_T(x text,
-           f text).
-
-dd_new_T(x text,
-         f text).
-
-dd_new_T(x, f) :-
-    T(x, f);
-    dd_delta_T(x, f).
-
-U(x text,
-  l text).
-
-dd_delta_U(x text,
-           l text).
-
-dd_new_U(x text,
-         l text).
-
-dd_new_U(x, l) :-
-    U(x, l);
-    dd_delta_U(x, l).
-
-dd_delta_R(x) :-
-    dd_delta_S(x),
-    T(x, f),
-    U(x, l);
-    dd_new_S(x),
-    dd_delta_T(x, f),
-    U(x, l);
-    dd_new_S(x),
-    dd_new_T(x, f),
-    dd_delta_U(x, l).
-
diff --git a/test/expected-output-test/ocr_example/print-incremental.expected b/test/expected-output-test/ocr_example/print-incremental.expected
deleted file mode 100644
index a7fb4bca8..000000000
--- a/test/expected-output-test/ocr_example/print-incremental.expected
+++ /dev/null
@@ -1,79 +0,0 @@
-features(id BIGSERIAL,
-         word_id INT,
-         feature_id INT,
-         feature_val BOOLEAN).
-
-dd_delta_features(id BIGSERIAL,
-                  word_id INT,
-                  feature_id INT,
-                  feature_val BOOLEAN).
-
-dd_new_features(id BIGSERIAL,
-                word_id INT,
-                feature_id INT,
-                feature_val BOOLEAN).
-
-dd_new_features(id, word_id, feature_id, feature_val) :-
-    features(id, word_id, feature_id, feature_val);
-    dd_delta_features(id, word_id, feature_id, feature_val).
-
-label1(wid INT,
-       val BOOLEAN).
-
-dd_delta_label1(wid INT,
-                val BOOLEAN).
-
-dd_new_label1(wid INT,
-              val BOOLEAN).
-
-dd_new_label1(wid, val) :-
-    label1(wid, val);
-    dd_delta_label1(wid, val).
-
-label2(wid INT,
-       val BOOLEAN).
-
-dd_delta_label2(wid INT,
-                val BOOLEAN).
-
-dd_new_label2(wid INT,
-              val BOOLEAN).
-
-dd_new_label2(wid, val) :-
-    label2(wid, val);
-    dd_delta_label2(wid, val).
-
-q1?(wid INT).
-
-dd_delta_q1?(wid INT).
-
-dd_new_q1?(wid INT).
-
-dd_new_q1(wid) :-
-    q1(wid);
-    dd_delta_q1(wid).
-
-q2?(wid INT).
-
-dd_delta_q2?(wid INT).
-
-dd_new_q2?(wid INT).
-
-dd_new_q2(wid) :-
-    q2(wid);
-    dd_delta_q2(wid).
-
-dd_delta_q1(wid) = val :-
-    dd_delta_label1(wid, val).
-
-dd_delta_q2(wid) = val :-
-    dd_delta_label2(wid, val).
-
-@weight(fid)
-dd_new_q1(wid) :-
-    dd_delta_features(id, wid, fid, fval).
-
-@weight(fid)
-dd_new_q2(wid) :-
-    dd_delta_features(id, wid, fid, fval).
-
diff --git a/test/expected-output-test/smoke_example/print-incremental.expected b/test/expected-output-test/smoke_example/print-incremental.expected
deleted file mode 100644
index 594b54980..000000000
--- a/test/expected-output-test/smoke_example/print-incremental.expected
+++ /dev/null
@@ -1,86 +0,0 @@
-person(person_id bigint,
-       name text).
-
-dd_delta_person(person_id bigint,
-                name text).
-
-dd_new_person(person_id bigint,
-              name text).
-
-dd_new_person(person_id, name) :-
-    person(person_id, name);
-    dd_delta_person(person_id, name).
-
-person_has_cancer(person_id bigint,
-                  has_cancer boolean).
-
-dd_delta_person_has_cancer(person_id bigint,
-                           has_cancer boolean).
-
-dd_new_person_has_cancer(person_id bigint,
-                         has_cancer boolean).
-
-dd_new_person_has_cancer(person_id, has_cancer) :-
-    person_has_cancer(person_id, has_cancer);
-    dd_delta_person_has_cancer(person_id, has_cancer).
-
-person_smokes(person_id bigint,
-              smokes boolean).
-
-dd_delta_person_smokes(person_id bigint,
-                       smokes boolean).
-
-dd_new_person_smokes(person_id bigint,
-                     smokes boolean).
-
-dd_new_person_smokes(person_id, smokes) :-
-    person_smokes(person_id, smokes);
-    dd_delta_person_smokes(person_id, smokes).
-
-friends(person_id bigint,
-        friend_id bigint).
-
-dd_delta_friends(person_id bigint,
-                 friend_id bigint).
-
-dd_new_friends(person_id bigint,
-               friend_id bigint).
-
-dd_new_friends(person_id, friend_id) :-
-    friends(person_id, friend_id);
-    dd_delta_friends(person_id, friend_id).
-
-smoke?(person_id bigint).
-
-dd_delta_smoke?(person_id bigint).
-
-dd_new_smoke?(person_id bigint).
-
-dd_new_smoke(person_id) :-
-    smoke(person_id);
-    dd_delta_smoke(person_id).
-
-cancer?(person_id bigint).
-
-dd_delta_cancer?(person_id bigint).
-
-dd_new_cancer?(person_id bigint).
-
-dd_new_cancer(person_id) :-
-    cancer(person_id);
-    dd_delta_cancer(person_id).
-
-dd_delta_smoke(pid) = l :-
-    dd_delta_person_smokes(pid, l).
-
-dd_delta_cancer(pid) = l :-
-    dd_delta_person_has_cancer(pid, l).
-
-@weight(0.5)
-dd_new_smoke(pid) => dd_new_cancer(pid) :-
-    dd_delta_person_smokes(pid, l).
-
-@weight(0.4)
-dd_new_smoke(pid1) => dd_new_smoke(pid) :-
-    dd_delta_friends(pid1, pid).
-
diff --git a/test/expected-output-test/spouse_example/print-incremental.expected b/test/expected-output-test/spouse_example/print-incremental.expected
deleted file mode 100644
index 0faf7c26e..000000000
--- a/test/expected-output-test/spouse_example/print-incremental.expected
+++ /dev/null
@@ -1,172 +0,0 @@
-articles(article_id text,
-         text text).
-
-dd_delta_articles(article_id text,
-                  text text).
-
-dd_new_articles(article_id text,
-                text text).
-
-dd_new_articles(article_id, text) :-
-    articles(article_id, text);
-    dd_delta_articles(article_id, text).
-
-sentences(document_id text,
-          sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
-          sentence_offset int,
-          sentence_id text).
-
-dd_delta_sentences(document_id text,
-                   sentence text,
-                   words text[],
-                   lemma text[],
-                   pos_tags text[],
-                   dependencies text[],
-                   ner_tags text[],
-                   sentence_offset int,
-                   sentence_id text).
-
-dd_new_sentences(document_id text,
-                 sentence text,
-                 words text[],
-                 lemma text[],
-                 pos_tags text[],
-                 dependencies text[],
-                 ner_tags text[],
-                 sentence_offset int,
-                 sentence_id text).
-
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
-    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
-    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
-
-people_mentions(sentence_id text,
-                start_position int,
-                length int,
-                text text,
-                mention_id text).
-
-dd_delta_people_mentions(sentence_id text,
-                         start_position int,
-                         length int,
-                         text text,
-                         mention_id text).
-
-dd_new_people_mentions(sentence_id text,
-                       start_position int,
-                       length int,
-                       text text,
-                       mention_id text).
-
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
-    people_mentions(sentence_id, start_position, length, text, mention_id);
-    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
-
-has_spouse_candidates(person1_id text,
-                      person2_id text,
-                      sentence_id text,
-                      description text,
-                      relation_id text,
-                      is_true boolean).
-
-dd_delta_has_spouse_candidates(person1_id text,
-                               person2_id text,
-                               sentence_id text,
-                               description text,
-                               relation_id text,
-                               is_true boolean).
-
-dd_new_has_spouse_candidates(person1_id text,
-                             person2_id text,
-                             sentence_id text,
-                             description text,
-                             relation_id text,
-                             is_true boolean).
-
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
-    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
-    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
-
-has_spouse_features(relation_id text,
-                    feature text).
-
-dd_delta_has_spouse_features(relation_id text,
-                             feature text).
-
-dd_new_has_spouse_features(relation_id text,
-                           feature text).
-
-dd_new_has_spouse_features(relation_id, feature) :-
-    has_spouse_features(relation_id, feature);
-    dd_delta_has_spouse_features(relation_id, feature).
-
-has_spouse?(relation_id text).
-
-dd_delta_has_spouse?(relation_id text).
-
-dd_new_has_spouse?(relation_id text).
-
-dd_new_has_spouse(relation_id) :-
-    has_spouse(relation_id);
-    dd_delta_has_spouse(relation_id).
-
-function ext_people
-    over (sentence_id text, words text, ner_tags text)
- returns rows like dd_delta_people_mentions
- implementation "udf/ext_people.py"
-        handles tsv lines.
-
-dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
-    dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
-
-function ext_has_spouse
-    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
- returns rows like dd_delta_has_spouse_candidates
- implementation "udf/ext_has_spouse.py"
-        handles tsv lines.
-
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, _, _, p1_text, p1_id),
-    people_mentions(s, _, _, p2_text, p2_id);
-    dd_new_people_mentions(s, _, _, p1_text, p1_id),
-    dd_delta_people_mentions(s, _, _, p2_text, p2_id).
-
-function ext_has_spouse_features
-    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
- returns rows like dd_delta_has_spouse_features
- implementation "udf/ext_has_spouse_features.py"
-        handles tsv lines.
-
-dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(_, _, words, _, _, _, _, _, s),
-    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    dd_delta_people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
-
-dd_delta_has_spouse(rid) = l :-
-    dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
-
-@weight(f)
-dd_new_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(_, _, _, _, rid, _),
-    has_spouse_features(rid, f);
-    dd_new_has_spouse_candidates(_, _, _, _, rid, _),
-    dd_delta_has_spouse_features(rid, f).
-
diff --git a/test/expected-output-test/spouse_example_new_feature/input.ddlog b/test/expected-output-test/spouse_example_new_feature/input.ddlog
deleted file mode 100644
index 30fcae415..000000000
--- a/test/expected-output-test/spouse_example_new_feature/input.ddlog
+++ /dev/null
@@ -1,71 +0,0 @@
-articles(
-  article_id text,
-  text       text).
-
-sentences(
-  document_id     text,
-  sentence        text,
-  words           text[],
-  lemma           text[],
-  pos_tags        text[],
-  dependencies    text[],
-  ner_tags        text[],
-  sentence_offset int,
-  sentence_id     text).
-
-people_mentions(
-  sentence_id    text,
-  start_position int,
-  length         int,
-  text           text,
-  mention_id     text).
-
-has_spouse_candidates(
-  person1_id  text,
-  person2_id  text,
-  sentence_id text,
-  description text,
-  relation_id text,
-  is_true boolean).
-
-has_spouse_features(
-  relation_id text,
-  feature     text).
-
-has_spouse?(relation_id text).
-
-function ext_people over (sentence_id text, words text, ner_tags text)
-                 returns rows like people_mentions
-  implementation "udf/ext_people.py" handles tsv lines.
-
-people_mentions +=
-  ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
-  sentences(_, _, words, _, _, _, ner_tags, _, s).
-
-function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
-                     returns rows like has_spouse_candidates
-  implementation "udf/ext_has_spouse.py" handles tsv lines.
-
-has_spouse_candidates +=
-  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, _, _, p1_text, p1_id),
-  people_mentions(s, _, _, p2_text, p2_id).
-
-function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
-                              returns rows like has_spouse_features
-  implementation "udf/ext_has_spouse_features.py" handles tsv lines.
-
-@mode("inc")
-has_spouse_features +=
-  ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(_, _, words, _, _, _, _, _, s),
-  has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-  people_mentions(s, p1idx, p1len, _, person1_id),
-  people_mentions(s, p2idx, p2len, _, person2_id).
-
-has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
-
-@weight(f)
-has_spouse(rid) :-
-  has_spouse_candidates(_, _, _, _, rid, _),
-  has_spouse_features(rid, f).
diff --git a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected b/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
deleted file mode 100644
index 2a57231de..000000000
--- a/test/expected-output-test/spouse_example_new_feature/print-incremental.expected
+++ /dev/null
@@ -1,176 +0,0 @@
-articles(article_id text,
-         text text).
-
-dd_delta_articles(article_id text,
-                  text text).
-
-dd_new_articles(article_id text,
-                text text).
-
-dd_new_articles(article_id, text) :-
-    articles(article_id, text);
-    dd_delta_articles(article_id, text).
-
-sentences(document_id text,
-          sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
-          sentence_offset int,
-          sentence_id text).
-
-dd_delta_sentences(document_id text,
-                   sentence text,
-                   words text[],
-                   lemma text[],
-                   pos_tags text[],
-                   dependencies text[],
-                   ner_tags text[],
-                   sentence_offset int,
-                   sentence_id text).
-
-dd_new_sentences(document_id text,
-                 sentence text,
-                 words text[],
-                 lemma text[],
-                 pos_tags text[],
-                 dependencies text[],
-                 ner_tags text[],
-                 sentence_offset int,
-                 sentence_id text).
-
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
-    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
-    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
-
-people_mentions(sentence_id text,
-                start_position int,
-                length int,
-                text text,
-                mention_id text).
-
-dd_delta_people_mentions(sentence_id text,
-                         start_position int,
-                         length int,
-                         text text,
-                         mention_id text).
-
-dd_new_people_mentions(sentence_id text,
-                       start_position int,
-                       length int,
-                       text text,
-                       mention_id text).
-
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
-    people_mentions(sentence_id, start_position, length, text, mention_id);
-    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
-
-has_spouse_candidates(person1_id text,
-                      person2_id text,
-                      sentence_id text,
-                      description text,
-                      relation_id text,
-                      is_true boolean).
-
-dd_delta_has_spouse_candidates(person1_id text,
-                               person2_id text,
-                               sentence_id text,
-                               description text,
-                               relation_id text,
-                               is_true boolean).
-
-dd_new_has_spouse_candidates(person1_id text,
-                             person2_id text,
-                             sentence_id text,
-                             description text,
-                             relation_id text,
-                             is_true boolean).
-
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
-    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
-    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
-
-has_spouse_features(relation_id text,
-                    feature text).
-
-dd_delta_has_spouse_features(relation_id text,
-                             feature text).
-
-dd_new_has_spouse_features(relation_id text,
-                           feature text).
-
-dd_new_has_spouse_features(relation_id, feature) :-
-    has_spouse_features(relation_id, feature);
-    dd_delta_has_spouse_features(relation_id, feature).
-
-has_spouse?(relation_id text).
-
-dd_delta_has_spouse?(relation_id text).
-
-dd_new_has_spouse?(relation_id text).
-
-dd_new_has_spouse(relation_id) :-
-    has_spouse(relation_id);
-    dd_delta_has_spouse(relation_id).
-
-function ext_people
-    over (sentence_id text, words text, ner_tags text)
- returns rows like dd_delta_people_mentions
- implementation "udf/ext_people.py"
-        handles tsv lines.
-
-dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
-    dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
-
-function ext_has_spouse
-    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
- returns rows like dd_delta_has_spouse_candidates
- implementation "udf/ext_has_spouse.py"
-        handles tsv lines.
-
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, _, _, p1_text, p1_id),
-    people_mentions(s, _, _, p2_text, p2_id);
-    dd_new_people_mentions(s, _, _, p1_text, p1_id),
-    dd_delta_people_mentions(s, _, _, p2_text, p2_id).
-
-function ext_has_spouse_features
-    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
- returns rows like dd_delta_has_spouse_features
- implementation "udf/ext_has_spouse_features.py"
-        handles tsv lines.
-
-dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(_, _, words, _, _, _, _, _, s),
-    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_delta_sentences(_, _, words, _, _, _, _, _, s),
-    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    dd_delta_people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
-
-dd_delta_has_spouse(rid) = l :-
-    dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
-
-@weight(f)
-dd_new_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(_, _, _, _, rid, _),
-    has_spouse_features(rid, f);
-    dd_new_has_spouse_candidates(_, _, _, _, rid, _),
-    dd_delta_has_spouse_features(rid, f).
-
diff --git a/test/expected-output-test/spouse_example_new_inference/compile.expected b/test/expected-output-test/spouse_example_new_inference/compile.expected
deleted file mode 100644
index 533ae67f5..000000000
--- a/test/expected-output-test/spouse_example_new_inference/compile.expected
+++ /dev/null
@@ -1,122 +0,0 @@
-deepdive.schema.variables {
-has_spouse.label: Boolean
-
-}
-
-deepdive.extraction.extractors.ext_people_mentions_by_ext_people {
-parallelism: ${PARALLELISM}
-input_relations: [
-  sentences
-]
-style: tsv_extractor
-output_relation: people_mentions
-udf: """udf/ext_people.py"""
-input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM sentences R0
-        """
-
-}
-
-deepdive.extraction.extractors.ext_has_spouse_candidates_by_ext_has_spouse {
-parallelism: ${PARALLELISM}
-input_relations: [
-  people_mentions
-]
-style: tsv_extractor
-output_relation: has_spouse_candidates
-udf: """udf/ext_has_spouse.py"""
-input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id """
-
-}
-
-deepdive.extraction.extractors.ext_has_spouse_features_by_ext_has_spouse_features {
-parallelism: ${PARALLELISM}
-input_relations: [
-  sentences
-  has_spouse_candidates
-  people_mentions
-]
-style: tsv_extractor
-output_relation: has_spouse_features
-udf: """udf/ext_has_spouse_features.py"""
-input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id """
-
-}
-
-deepdive.extraction.extractors.ext_has_spouse {
-cmd: """
-	# TODO use temporary table
-	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, R0.is_true AS label
-          FROM has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
-output_relation: has_spouse
-style: cmd_extractor
-input_relations: [
-  has_spouse_candidates
-]
-
-}
-
-deepdive.inference.factors.inf_istrue_has_spouse {
-input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
-function: """Imply(has_spouse.R0.label)"""
-weight: """?(dd_weight_column_0)"""
-input_relations: [
-  has_spouse
-  has_spouse_candidates
-  has_spouse_features
-]
-
-}
-
-deepdive.inference.factors.inf_equal_has_spouse_has_spouse {
-input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R1.id AS "has_spouse.R1.id" 
-          FROM has_spouse R0, has_spouse R1, has_spouse_candidates R2, has_spouse_candidates R3
-        WHERE R2.relation_id = R1.relation_id  AND R3.person1_id = R2.person2_id  AND R3.person2_id = R2.person1_id  AND R3.relation_id = R0.relation_id """
-function: """Equal(has_spouse.R0.label, has_spouse.R1.label)"""
-weight: """3.0"""
-input_relations: [
-  has_spouse
-  has_spouse_candidates
-]
-
-}
-
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
-  ext_has_spouse_features_by_ext_has_spouse_features
-  ext_has_spouse
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_has_spouse
-  inf_equal_has_spouse_has_spouse
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
-  ext_has_spouse_features_by_ext_has_spouse_features
-  ext_has_spouse
-  inf_istrue_has_spouse
-  inf_equal_has_spouse_has_spouse
-]
-
diff --git a/test/expected-output-test/spouse_example_new_inference/input.ddlog b/test/expected-output-test/spouse_example_new_inference/input.ddlog
deleted file mode 100644
index 15cfd39c6..000000000
--- a/test/expected-output-test/spouse_example_new_inference/input.ddlog
+++ /dev/null
@@ -1,76 +0,0 @@
-articles(
-  article_id text,
-  text       text).
-
-sentences(
-  document_id     text,
-  sentence        text,
-  words           text[],
-  lemma           text[],
-  pos_tags        text[],
-  dependencies    text[],
-  ner_tags        text[],
-  sentence_offset int,
-  sentence_id     text).
-
-people_mentions(
-  sentence_id    text,
-  start_position int,
-  length         int,
-  text           text,
-  mention_id     text).
-
-has_spouse_candidates(
-  person1_id  text,
-  person2_id  text,
-  sentence_id text,
-  description text,
-  relation_id text,
-  is_true boolean).
-
-has_spouse_features(
-  relation_id text,
-  feature     text).
-
-has_spouse?(relation_id text).
-
-function ext_people over (sentence_id text, words text, ner_tags text)
-                 returns rows like people_mentions
-  implementation "udf/ext_people.py" handles tsv lines.
-
-people_mentions +=
-  ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
-  sentences(_, _, words, _, _, _, ner_tags, _, s).
-
-function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
-                     returns rows like has_spouse_candidates
-  implementation "udf/ext_has_spouse.py" handles tsv lines.
-
-has_spouse_candidates +=
-  ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-  people_mentions(s, _, _, p1_text, p1_id),
-  people_mentions(s, _, _, p2_text, p2_id).
-
-function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
-                              returns rows like has_spouse_features
-  implementation "udf/ext_has_spouse_features.py" handles tsv lines.
-
-has_spouse_features +=
-  ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
-  sentences(_, _, words, _, _, _, _, _, s),
-  has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-  people_mentions(s, p1idx, p1len, _, person1_id),
-  people_mentions(s, p2idx, p2len, _, person2_id).
-
-has_spouse(rid) = l :- has_spouse_candidates(_, _, _, _, rid, l).
-
-@weight(f)
-has_spouse(rid) :-
-  has_spouse_candidates(_, _, _, _, rid, _),
-  has_spouse_features(rid, f).
-
-@mode("inc")
-@weight(3.0)
-has_spouse(rid2) = has_spouse(rid) :-
-  has_spouse_candidates(a1, b1, _, _, rid, _),
-  has_spouse_candidates(b1, a1, _, _, rid2, _).
diff --git a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected b/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
deleted file mode 100644
index c924799cb..000000000
--- a/test/expected-output-test/spouse_example_new_inference/print-incremental.expected
+++ /dev/null
@@ -1,177 +0,0 @@
-articles(article_id text,
-         text text).
-
-dd_delta_articles(article_id text,
-                  text text).
-
-dd_new_articles(article_id text,
-                text text).
-
-dd_new_articles(article_id, text) :-
-    articles(article_id, text);
-    dd_delta_articles(article_id, text).
-
-sentences(document_id text,
-          sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
-          sentence_offset int,
-          sentence_id text).
-
-dd_delta_sentences(document_id text,
-                   sentence text,
-                   words text[],
-                   lemma text[],
-                   pos_tags text[],
-                   dependencies text[],
-                   ner_tags text[],
-                   sentence_offset int,
-                   sentence_id text).
-
-dd_new_sentences(document_id text,
-                 sentence text,
-                 words text[],
-                 lemma text[],
-                 pos_tags text[],
-                 dependencies text[],
-                 ner_tags text[],
-                 sentence_offset int,
-                 sentence_id text).
-
-dd_new_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id) :-
-    sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id);
-    dd_delta_sentences(document_id, sentence, words, lemma, pos_tags, dependencies, ner_tags, sentence_offset, sentence_id).
-
-people_mentions(sentence_id text,
-                start_position int,
-                length int,
-                text text,
-                mention_id text).
-
-dd_delta_people_mentions(sentence_id text,
-                         start_position int,
-                         length int,
-                         text text,
-                         mention_id text).
-
-dd_new_people_mentions(sentence_id text,
-                       start_position int,
-                       length int,
-                       text text,
-                       mention_id text).
-
-dd_new_people_mentions(sentence_id, start_position, length, text, mention_id) :-
-    people_mentions(sentence_id, start_position, length, text, mention_id);
-    dd_delta_people_mentions(sentence_id, start_position, length, text, mention_id).
-
-has_spouse_candidates(person1_id text,
-                      person2_id text,
-                      sentence_id text,
-                      description text,
-                      relation_id text,
-                      is_true boolean).
-
-dd_delta_has_spouse_candidates(person1_id text,
-                               person2_id text,
-                               sentence_id text,
-                               description text,
-                               relation_id text,
-                               is_true boolean).
-
-dd_new_has_spouse_candidates(person1_id text,
-                             person2_id text,
-                             sentence_id text,
-                             description text,
-                             relation_id text,
-                             is_true boolean).
-
-dd_new_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true) :-
-    has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true);
-    dd_delta_has_spouse_candidates(person1_id, person2_id, sentence_id, description, relation_id, is_true).
-
-has_spouse_features(relation_id text,
-                    feature text).
-
-dd_delta_has_spouse_features(relation_id text,
-                             feature text).
-
-dd_new_has_spouse_features(relation_id text,
-                           feature text).
-
-dd_new_has_spouse_features(relation_id, feature) :-
-    has_spouse_features(relation_id, feature);
-    dd_delta_has_spouse_features(relation_id, feature).
-
-has_spouse?(relation_id text).
-
-dd_delta_has_spouse?(relation_id text).
-
-dd_new_has_spouse?(relation_id text).
-
-dd_new_has_spouse(relation_id) :-
-    has_spouse(relation_id);
-    dd_delta_has_spouse(relation_id).
-
-function ext_people
-    over (sentence_id text, words text, ner_tags text)
- returns rows like dd_delta_people_mentions
- implementation "udf/ext_people.py"
-        handles tsv lines.
-
-dd_delta_people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
-    dd_delta_sentences(_, _, words, _, _, _, ner_tags, _, s).
-
-function ext_has_spouse
-    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
- returns rows like dd_delta_has_spouse_candidates
- implementation "udf/ext_has_spouse.py"
-        handles tsv lines.
-
-dd_delta_has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    dd_delta_people_mentions(s, _, _, p1_text, p1_id),
-    people_mentions(s, _, _, p2_text, p2_id);
-    dd_new_people_mentions(s, _, _, p1_text, p1_id),
-    dd_delta_people_mentions(s, _, _, p2_text, p2_id).
-
-function ext_has_spouse_features
-    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
- returns rows like dd_delta_has_spouse_features
- implementation "udf/ext_has_spouse_features.py"
-        handles tsv lines.
-
-dd_delta_has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
-    dd_delta_sentences(_, _, words, _, _, _, _, _, s),
-    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_delta_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    dd_delta_people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id);
-    dd_new_sentences(_, _, words, _, _, _, _, _, s),
-    dd_new_has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    dd_new_people_mentions(s, p1idx, p1len, _, person1_id),
-    dd_delta_people_mentions(s, p2idx, p2len, _, person2_id).
-
-dd_delta_has_spouse(rid) = l :-
-    dd_delta_has_spouse_candidates(_, _, _, _, rid, l).
-
-@weight(f)
-dd_new_has_spouse(rid) :-
-    dd_delta_has_spouse_candidates(_, _, _, _, rid, _),
-    has_spouse_features(rid, f);
-    dd_new_has_spouse_candidates(_, _, _, _, rid, _),
-    dd_delta_has_spouse_features(rid, f).
-
-@weight(3.0)
-dd_new_has_spouse(rid2) = dd_new_has_spouse(rid) :-
-    dd_new_has_spouse_candidates(a1, b1, _, _, rid, _),
-    dd_new_has_spouse_candidates(b1, a1, _, _, rid2, _).
-
diff --git a/test/expected-output-test/spouse_example_new_inference/print.expected b/test/expected-output-test/spouse_example_new_inference/print.expected
deleted file mode 100644
index 20d6f1ecb..000000000
--- a/test/expected-output-test/spouse_example_new_inference/print.expected
+++ /dev/null
@@ -1,76 +0,0 @@
-articles(article_id text,
-         text text).
-
-sentences(document_id text,
-          sentence text,
-          words text[],
-          lemma text[],
-          pos_tags text[],
-          dependencies text[],
-          ner_tags text[],
-          sentence_offset int,
-          sentence_id text).
-
-people_mentions(sentence_id text,
-                start_position int,
-                length int,
-                text text,
-                mention_id text).
-
-has_spouse_candidates(person1_id text,
-                      person2_id text,
-                      sentence_id text,
-                      description text,
-                      relation_id text,
-                      is_true boolean).
-
-has_spouse_features(relation_id text,
-                    feature text).
-
-has_spouse?(relation_id text).
-
-function ext_people
-    over (sentence_id text, words text, ner_tags text)
- returns rows like people_mentions
- implementation "udf/ext_people.py"
-        handles tsv lines.
-
-people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
-    sentences(_, _, words, _, _, _, ner_tags, _, s).
-
-function ext_has_spouse
-    over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
- returns rows like has_spouse_candidates
- implementation "udf/ext_has_spouse.py"
-        handles tsv lines.
-
-has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
-    people_mentions(s, _, _, p1_text, p1_id),
-    people_mentions(s, _, _, p2_text, p2_id).
-
-function ext_has_spouse_features
-    over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
- returns rows like has_spouse_features
- implementation "udf/ext_has_spouse_features.py"
-        handles tsv lines.
-
-has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
-    sentences(_, _, words, _, _, _, _, _, s),
-    has_spouse_candidates(person1_id, person2_id, s, _, rid, _),
-    people_mentions(s, p1idx, p1len, _, person1_id),
-    people_mentions(s, p2idx, p2len, _, person2_id).
-
-has_spouse(rid) = l :-
-    has_spouse_candidates(_, _, _, _, rid, l).
-
-@weight(f)
-has_spouse(rid) :-
-    has_spouse_candidates(_, _, _, _, rid, _),
-    has_spouse_features(rid, f).
-
-@mode("inc")
-@weight(3.0)
-has_spouse(rid2) = has_spouse(rid) :-
-    has_spouse_candidates(a1, b1, _, _, rid, _),
-    has_spouse_candidates(b1, a1, _, _, rid2, _).
-
diff --git a/test/parse-error-test/annotation_mode/input.ddlog b/test/parse-error-test/annotation_mode/input.ddlog
deleted file mode 100644
index 4d59175af..000000000
--- a/test/parse-error-test/annotation_mode/input.ddlog
+++ /dev/null
@@ -1,3 +0,0 @@
-@mode("unknown")
-@weight(3)
-Q(x) :- R(x).
diff --git a/test/parse-error-test/annotation_mode/parse-error.expected b/test/parse-error-test/annotation_mode/parse-error.expected
deleted file mode 100644
index 56d929dca..000000000
--- a/test/parse-error-test/annotation_mode/parse-error.expected
+++ /dev/null
@@ -1,5 +0,0 @@
-[error] test/parse-error-test/annotation_mode/input.ddlog[1.17] error: unknown: unrecognized mode
-
-@mode("unknown")
-
-                ^
diff --git a/test/parse-error-test/annotation_semantics/parse-error.expected b/test/parse-error-test/annotation_semantics/parse-error.expected
index 8679133fb..50a28efd9 100644
--- a/test/parse-error-test/annotation_semantics/parse-error.expected
+++ b/test/parse-error-test/annotation_semantics/parse-error.expected
@@ -1,5 +1 @@
-[error] test/parse-error-test/annotation_semantics/input.ddlog[2.22] error: unknown: unrecognized semantics
-
-@semantics("unknown")
-
-                     ^
+[error] unknown: unrecognized @semantics value

From 02b485b6c84f43bb7b88eda700bc4cbfb40fa551 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 3 Mar 2016 06:43:11 -0800
Subject: [PATCH 308/347] Defaults to view and adds `@materialize` annotation

so users can mark which relations to create tables for
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  3 +-
 .../chunking_example/compile.expected         | 19 ++--
 .../if-then-else/compile.expected             | 23 ++---
 .../materialize_annotation/compile.expected   | 87 +++++++++++++++++++
 .../materialize_annotation/input.ddlog        | 22 +++++
 .../compile.expected                          | 18 ++--
 .../ocr_example/compile.expected              | 24 ++---
 .../smoke_example/compile.expected            | 24 ++---
 .../spouse_example/compile.expected           | 12 +--
 9 files changed, 151 insertions(+), 81 deletions(-)
 create mode 100644 test/expected-output-test/materialize_annotation/compile.expected
 create mode 100644 test/expected-output-test/materialize_annotation/input.ddlog

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 9feb5aeb7..a327d416f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -411,7 +411,8 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   }
 
   def compileExtractorBlock(extractorName: String, outputRelation: String, stmts: List[Statement], sql: String): CompiledBlocks = {
-    val shouldMaterialize = schemaDeclarationByRelationName contains outputRelation
+    // look for @materialize annotation on any rule defining the same head
+    val shouldMaterialize = stmts flatMap (_.annotations) exists (_ named "materialize")
 
     List(s"deepdive.extraction.extractors.${extractorName}" -> Map(
       "cmd" -> QuotedString(
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index d4bd9ec03..361aa86b3 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -8,17 +8,13 @@ tag: Categorical
 
 deepdive.extraction.extractors.ext_chunk {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "chunk"
-	deepdive sql 'INSERT INTO chunk SELECT DISTINCT R0.sent_id, R0.word_id, R1.tag, 
+deepdive create view chunk as 'SELECT DISTINCT R0.sent_id, R0.word_id, R1.tag, 
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS label
-          FROM words R0, tags R1
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+FROM words R0, tags R1
+        '
+"""
 output_relation: chunk
 style: cmd_extractor
 input_relations: [
@@ -30,9 +26,7 @@ input_relations: [
 
 deepdive.extraction.extractors.ext_words {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "words"
-	deepdive sql 'INSERT INTO words SELECT R0.sent_id AS "words_raw.R0.sent_id", R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.true_tag AS "words_raw.R0.true_tag", 
+deepdive create view words as 'SELECT R0.sent_id AS "words_raw.R0.sent_id", R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.true_tag AS "words_raw.R0.true_tag", 
 CASE WHEN R0.true_tag = '\''B-UCP'\'' THEN NULL
      WHEN R0.true_tag = '\''I-UCP'\'' THEN NULL
      WHEN strpos(R0.true_tag, '\''-'\'') > 0 THEN split_part(R0.true_tag, '\''-'\'', 2)
@@ -41,8 +35,7 @@ CASE WHEN R0.true_tag = '\''B-UCP'\'' THEN NULL
 END AS column_5
 FROM words_raw R0
         '
-	# TODO rename temporary table to replace output_relation
-	"""
+"""
 output_relation: words
 style: cmd_extractor
 input_relations: [
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 1b603bf0a..a301153a2 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -5,18 +5,14 @@ q.label: Boolean
 
 deepdive.extraction.extractors.ext_q {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "q"
-	deepdive sql 'INSERT INTO q SELECT DISTINCT R0.x, 
+deepdive create view q as 'SELECT DISTINCT R0.x, 
 CASE WHEN R0.l > 0 THEN true
      WHEN R0.l < 0 THEN false
      ELSE NULL
 END AS label
-          FROM labels_resolved R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+FROM labels_resolved R0
+        '
+"""
 output_relation: q
 style: cmd_extractor
 input_relations: [
@@ -27,7 +23,7 @@ input_relations: [
 
 deepdive.extraction.extractors.ext_p {
 cmd: """
-	deepdive create view p as 'SELECT R0.x AS column_0, 
+deepdive create view p as 'SELECT R0.x AS column_0, 
 CASE WHEN abs(R0.l) > 10 THEN true
      ELSE false
 END AS column_1
@@ -40,7 +36,7 @@ CASE WHEN (R0.x % 10) = 0 THEN false
 END AS column_1
 FROM labels R0
         '
-	"""
+"""
 output_relation: p
 style: cmd_extractor
 input_relations: [
@@ -51,9 +47,7 @@ input_relations: [
 
 deepdive.extraction.extractors.ext_labels_resolved {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "labels_resolved"
-	deepdive sql 'INSERT INTO labels_resolved SELECT R0.x AS "labels.R0.x", SUM(
+deepdive create view labels_resolved as 'SELECT R0.x AS "labels.R0.x", SUM(
 CASE WHEN R0.l IS NULL THEN 0
      WHEN R0.l = true THEN 1
      ELSE -1
@@ -61,8 +55,7 @@ END) AS column_1
 FROM labels R0
         
         GROUP BY R0.x'
-	# TODO rename temporary table to replace output_relation
-	"""
+"""
 output_relation: labels_resolved
 style: cmd_extractor
 input_relations: [
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
new file mode 100644
index 000000000..3bc84cce3
--- /dev/null
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -0,0 +1,87 @@
+deepdive.schema.variables {
+VQ.label: Boolean
+TQ.label: Boolean
+
+}
+
+deepdive.extraction.extractors.ext_V {
+cmd: """
+deepdive create view V as 'SELECT R0.x AS "D.R0.x"
+FROM D R0
+        '
+"""
+output_relation: V
+style: cmd_extractor
+input_relations: [
+  D
+]
+
+}
+
+deepdive.extraction.extractors.ext_VQ {
+cmd: """
+deepdive create view VQ as 'SELECT DISTINCT R0.x, true AS label
+FROM D R0
+        '
+"""
+output_relation: VQ
+style: cmd_extractor
+input_relations: [
+  D
+]
+
+}
+
+deepdive.extraction.extractors.ext_T {
+cmd: """
+# TODO use temporary table
+deepdive create table "T"
+deepdive sql 'INSERT INTO T SELECT R0.x AS "D.R0.x"
+FROM D R0
+        '
+# TODO rename temporary table to replace output_relation
+"""
+output_relation: T
+style: cmd_extractor
+input_relations: [
+  D
+]
+
+}
+
+deepdive.extraction.extractors.ext_TQ {
+cmd: """
+# TODO use temporary table
+deepdive create table "TQ"
+deepdive sql 'INSERT INTO TQ SELECT DISTINCT R0.x, 
+CASE WHEN length(R0.x) > 5 THEN true
+     ELSE NULL
+END AS label
+FROM D R0
+        '
+# TODO rename temporary table to replace output_relation
+"""
+output_relation: TQ
+style: cmd_extractor
+input_relations: [
+  D
+]
+
+}
+
+deepdive.pipeline.run: ${PIPELINE}
+
+deepdive.pipeline.pipelines.extraction: [
+  ext_V
+  ext_VQ
+  ext_T
+  ext_TQ
+]
+
+deepdive.pipeline.pipelines.endtoend: [
+  ext_V
+  ext_VQ
+  ext_T
+  ext_TQ
+]
+
diff --git a/test/expected-output-test/materialize_annotation/input.ddlog b/test/expected-output-test/materialize_annotation/input.ddlog
new file mode 100644
index 000000000..7a07e1d41
--- /dev/null
+++ b/test/expected-output-test/materialize_annotation/input.ddlog
@@ -0,0 +1,22 @@
+# test for @materialize annotation
+
+# defaults to view
+V(x) :- D(x).
+VQ(x) = TRUE :- D(x).
+
+V(x text).
+VQ?(x text).
+
+
+# with @materialize annotation on the rule, can be materialized as table
+@materialize
+T(x) :- D(x).
+
+@materialize
+TQ(x) = (if length(x) > 5 then TRUE else NULL end) :- D(x).
+
+T(x text).
+TQ?(x text).
+
+# base table
+D(x text).
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 1fb8cc7e9..2e4b8ac7b 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -5,9 +5,7 @@ Q.label: Boolean
 
 deepdive.extraction.extractors.ext_S {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "S"
-	deepdive sql 'INSERT INTO S SELECT R0.a AS "R.R0.a"
+deepdive create view S as 'SELECT R0.a AS "R.R0.a"
 FROM R R0, R R1
         WHERE R1.a = R0.b  AND R0.a > 100
 UNION ALL
@@ -30,8 +28,7 @@ UNION ALL
 SELECT R0.a AS "S_2.R0.a"
 FROM S_2 R0
         '
-	# TODO rename temporary table to replace output_relation
-	"""
+"""
 output_relation: S
 style: cmd_extractor
 input_relations: [
@@ -60,9 +57,7 @@ FROM R R0
 
 deepdive.extraction.extractors.ext_T {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "T"
-	deepdive sql 'INSERT INTO T SELECT R0.a AS "T___0.R0.a"
+deepdive create view T as 'SELECT R0.a AS "T___0.R0.a"
 FROM T___0 R0
         
 UNION ALL
@@ -77,8 +72,7 @@ UNION ALL
 SELECT R0.a AS "T___3.R0.a"
 FROM T___3 R0
         '
-	# TODO rename temporary table to replace output_relation
-	"""
+"""
 output_relation: T
 style: cmd_extractor
 input_relations: [
@@ -240,10 +234,10 @@ input_relations: [
 
 deepdive.extraction.extractors.ext_T__3 {
 cmd: """
-	deepdive create view T__3 as 'SELECT R0.a AS column_0
+deepdive create view T__3 as 'SELECT R0.a AS column_0
 FROM T R0
         '
-	"""
+"""
 output_relation: T__3
 style: cmd_extractor
 input_relations: [
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 1d0c6dd0b..eff2c3e4e 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -6,14 +6,10 @@ q2.label: Boolean
 
 deepdive.extraction.extractors.ext_q1 {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "q1"
-	deepdive sql 'INSERT INTO q1 SELECT DISTINCT R0.wid, R0.val AS label
-          FROM label1 R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+deepdive create view q1 as 'SELECT DISTINCT R0.wid, R0.val AS label
+FROM label1 R0
+        '
+"""
 output_relation: q1
 style: cmd_extractor
 input_relations: [
@@ -24,14 +20,10 @@ input_relations: [
 
 deepdive.extraction.extractors.ext_q2 {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "q2"
-	deepdive sql 'INSERT INTO q2 SELECT DISTINCT R0.wid, R0.val AS label
-          FROM label2 R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+deepdive create view q2 as 'SELECT DISTINCT R0.wid, R0.val AS label
+FROM label2 R0
+        '
+"""
 output_relation: q2
 style: cmd_extractor
 input_relations: [
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index ff67f79ca..03835a579 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -6,14 +6,10 @@ cancer.label: Boolean
 
 deepdive.extraction.extractors.ext_smoke {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "smoke"
-	deepdive sql 'INSERT INTO smoke SELECT DISTINCT R0.person_id, R0.smokes AS label
-          FROM person_smokes R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+deepdive create view smoke as 'SELECT DISTINCT R0.person_id, R0.smokes AS label
+FROM person_smokes R0
+        '
+"""
 output_relation: smoke
 style: cmd_extractor
 input_relations: [
@@ -24,14 +20,10 @@ input_relations: [
 
 deepdive.extraction.extractors.ext_cancer {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "cancer"
-	deepdive sql 'INSERT INTO cancer SELECT DISTINCT R0.person_id, R0.has_cancer AS label
-          FROM person_has_cancer R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+deepdive create view cancer as 'SELECT DISTINCT R0.person_id, R0.has_cancer AS label
+FROM person_has_cancer R0
+        '
+"""
 output_relation: cancer
 style: cmd_extractor
 input_relations: [
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index e4c2f5401..f55e621bd 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -52,14 +52,10 @@ FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions
 
 deepdive.extraction.extractors.ext_has_spouse {
 cmd: """
-	# TODO use temporary table
-	deepdive create table "has_spouse"
-	deepdive sql 'INSERT INTO has_spouse SELECT DISTINCT R0.relation_id, R0.is_true AS label
-          FROM has_spouse_candidates R0
-        
-          '
-	# TODO rename temporary table to replace output_relation
-	"""
+deepdive create view has_spouse as 'SELECT DISTINCT R0.relation_id, R0.is_true AS label
+FROM has_spouse_candidates R0
+        '
+"""
 output_relation: has_spouse
 style: cmd_extractor
 input_relations: [

From 0435f480d714c072d1d854d52dd028a23c04f1d3 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 3 Mar 2016 23:41:27 -0800
Subject: [PATCH 309/347] Simplifies table/view SQL compilation by offloading
 to DeepDive

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 70 +++++++------------
 .../ddlog/DeepDiveLogQueryCompiler.scala      |  2 +-
 2 files changed, 27 insertions(+), 45 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a327d416f..43adf83fd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -119,9 +119,8 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   case object ViewAlias extends AliasStyle
   // TableStyle: tableName.R{tableIndex}.columnName
   case object TableAlias extends AliasStyle
-  case object NoAlias extends AliasStyle
+  // UseVariableAsAlias: to use the expression
   case object UseVariableAsAlias extends AliasStyle
-  case object SupervisionRuleAlias extends AliasStyle
 
 
   // This is responsible for compiling a single conjunctive query
@@ -174,7 +173,6 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
   // compile alias
   def compileAlias(e: Expr, a: Option[String], aliasStyle: AliasStyle) = aliasStyle match {
-    case NoAlias => ""
     case TableAlias => e match {
       case VarExpr(v) => {
         val index = getBodyIndex(v)
@@ -187,7 +185,6 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     }
     case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
     case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}"""" //" fix sublime highlighting
-    case SupervisionRuleAlias => a map (" AS " + _) getOrElse ""
   }
 
   // resolve an expression
@@ -248,7 +245,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     val head = if (cq.headTerms isEmpty) "*" else cq.headTerms.zip(
       cq.headTermAliases getOrElse {cq.headTerms map {_ => None}}) map { case (expr, alias) =>
       compileExpr(expr) + compileAlias(expr, alias, aliasStyle)
-    } mkString(", ")
+    } mkString("\n     , ")
     val distinctStr = if (cq.isDistinct) "DISTINCT " else ""
     s"${distinctStr}${head}"
   }
@@ -294,7 +291,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
           }
         }
       }
-      conditions.mkString(" AND ")
+      conditions.mkString("\n  AND ")
     }
 
     def generateFromClause(bodies: List[Body], indexPrefix: String) : String = {
@@ -309,7 +306,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
             case OuterModifier() => {
               val from = generateFromClause(x.bodies, newIndexPrefix)
               val joinCond = generateWhereClause(x.bodies, newIndexPrefix)
-              Some(s"${from} ON ${joinCond}")
+              Some(s"${from}\n  ON ${joinCond}")
             }
             case _ => None
           }
@@ -318,9 +315,9 @@ class QueryCompiler(cq : ConjunctiveQuery) {
       }
       // full outer join
       if (atoms isEmpty) {
-        outers.mkString(" FULL OUTER JOIN ")
+        outers.mkString("\nFULL OUTER JOIN ")
       } else {
-        (atoms.mkString(", ") +: outers).mkString(" LEFT OUTER JOIN ")
+        (atoms.mkString("\n   , ") +: outers).mkString("\nLEFT OUTER JOIN ")
       }
     }
 
@@ -346,7 +343,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     val groupbyStr = if (groupbyTerms.size == cq.headTerms.size || groupbyTerms.isEmpty) {
       ""
     } else {
-      s"\n        GROUP BY ${groupbyTerms.mkString(", ")}"
+      s"\nGROUP BY ${groupbyTerms.mkString("\n    , ")}"
     }
 
     // limit clause
@@ -367,12 +364,16 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         } sortBy (_._3)
         optionalClause("\nORDER BY", orderByExprs map {
             case (e, isAscending, _) => s"${compileExpr(e)} ${if (isAscending) "ASC" else "DESC"}"
-          } mkString(", ")
+          } mkString("\n    , ")
         )
       }
 
-    s"""FROM ${ generateFromClause(body, "") }
-        ${ optionalClause("WHERE", generateWhereClause(body, "")) }${groupbyStr}${orderbyStr}${limitStr}"""
+    s"""FROM ${ generateFromClause(body, "")
+    }${optionalClause("\nWHERE", generateWhereClause(body, ""))
+    }${groupbyStr
+    }${orderbyStr
+    }${limitStr
+    }"""
   }
 
   def generateSQL(aliasStyle: AliasStyle = ViewAlias) = {
@@ -395,43 +396,23 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     List.empty
   }
 
-  def generateUnionAllSQL(cqs: List[ConjunctiveQuery], aliasStyle: AliasStyle): String = {
-    cqs map { q => new QueryCompiler(q).generateSQL(aliasStyle) } mkString("\nUNION ALL\n")
-  }
-
   // Generate extraction rule part for deepdive
   def compile(stmt: ExtractionRule): CompiledBlocks = {
     val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: ExtractionRule => s }
     if (stmts isEmpty) return List.empty
 
-    val hasSchemaDeclared = schemaDeclarationByRelationName contains stmt.headName
-    val aliasStyle = if (hasSchemaDeclared) TableAlias else ViewAlias
-    compileExtractorBlock(resolveExtractorBlockName(stmt), stmt.headName, stmts,
-      generateUnionAllSQL(stmts map (_.q), aliasStyle))
+    compileExtractorBlock(stmt, stmts, stmt.headName, stmts map (_.q))
   }
 
-  def compileExtractorBlock(extractorName: String, outputRelation: String, stmts: List[Statement], sql: String): CompiledBlocks = {
+  def compileExtractorBlock(stmt: Statement, stmts: List[Statement], outputRelation: String, cqs: List[ConjunctiveQuery]): CompiledBlocks = {
     // look for @materialize annotation on any rule defining the same head
     val shouldMaterialize = stmts flatMap (_.annotations) exists (_ named "materialize")
-
-    List(s"deepdive.extraction.extractors.${extractorName}" -> Map(
-      "cmd" -> QuotedString(
-        if (shouldMaterialize) {
-          s"""
-          |# TODO use temporary table
-          |deepdive create table "${outputRelation}"
-          |deepdive sql ${escape4sh(s"INSERT INTO ${outputRelation} $sql")}
-          |# TODO rename temporary table to replace output_relation
-          |""".stripMargin
-        } else {
-          s"""
-          |deepdive create view ${outputRelation} as ${escape4sh(sql)}
-          |""".stripMargin
-        }
-      ),
+    List(s"deepdive.extraction.extractors.${resolveExtractorBlockName(stmt)}" -> Map(
+      "style" -> "sql_extractor",
+      "input_relations" -> (stmts flatMap relationNamesUsedByStatement distinct),
       "output_relation" -> outputRelation,
-      "style" -> "cmd_extractor",
-      "input_relations" -> (stmts flatMap relationNamesUsedByStatement distinct)
+      "materialize" -> shouldMaterialize,
+      "sql" -> QuotedString(cqs map { q => new QueryCompiler(q).generateSQL() } mkString("\nUNION ALL\n"))
     ))
   }
 
@@ -439,14 +420,14 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     val stmts = statementsByRepresentative getOrElse(stmt, List.empty) collect { case s: SupervisionRule => s }
     if (stmts isEmpty) return List.empty
 
-    compileExtractorBlock(resolveExtractorBlockName(stmt), stmt.headName, stmts,
-      generateUnionAllSQL(stmts map { case stmt => stmt.q.copy(
+    compileExtractorBlock(stmt, stmts, stmt.headName,
+      stmts map { case stmt => stmt.q.copy(
         headTerms = stmt.q.headTerms :+ stmt.supervision,
         headTermAliases = {
           stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ :+ Some("label") }
         },
         isDistinct = true
-      ) }, SupervisionRuleAlias)
+      ) }
     )
   }
 
@@ -470,7 +451,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
       val blockName = resolveExtractorBlockName(stmt)
       val parallelism = stmt.annotations find (_ named "parallelism") flatMap (_.value) getOrElse("${PARALLELISM}")
       s"deepdive.extraction.extractors.${blockName}" -> (Map(
-        "input" -> QuotedString(new QueryCompiler(stmt.q).generateSQL(TableAlias)),
+        "input" -> QuotedString(new QueryCompiler(stmt.q).generateSQL()),
         "output_relation" -> stmt.output,
         "input_relations" -> (List(stmt) flatMap relationNamesUsedByStatement distinct),
         "input_batch_size" -> "${INPUT_BATCH_SIZE}",
@@ -506,6 +487,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         val varInBody = (fakeBody.zipWithIndex flatMap {
           case (x: BodyAtom, i) =>
             if (schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
+              // TODO maybe TableAlias can be useful here or we can completely get rid of it?
               Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
             else
               None
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
index 937a115e6..419a6c313 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogQueryCompiler.scala
@@ -24,7 +24,7 @@ object DeepDiveLogQueryCompiler extends DeepDiveLogHandler {
       case rule: ExtractionRule =>
         val qc = new compiler.QueryCompiler(rule.q)
         s"""CREATE TEMPORARY TABLE ${rule.headName} AS\n${
-          qc.generateSQL(compiler.ViewAlias)}"""
+          qc.generateSQL()}"""
     }) ++ List({
       // compile the query
       s"""${new compiler.QueryCompiler(query).generateSQL(compiler.UseVariableAsAlias)}"""

From 34a113fe800ceb6a8761dbf1b72731805439a73f Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 3 Mar 2016 23:45:30 -0800
Subject: [PATCH 310/347] Turns off automatic DISTINCT for supervision/scoping
 rules

since DeepDive will do it anyway
---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 43adf83fd..e48413968 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -426,7 +426,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         headTermAliases = {
           stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ :+ Some("label") }
         },
-        isDistinct = true
+        isDistinct = false // XXX no need to take DISTINCT here since DeepDive will have to do it anyway
       ) }
     )
   }

From 2c9c29c0cf11f77dfdb5d4b78ae466445298ef27 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 4 Mar 2016 01:40:20 -0800
Subject: [PATCH 311/347] Fixes compiled SQL to use column_N aliases in most
 cases

and a bunch of spaces/linebreaks in the compiled SQL for readability
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  18 +-
 .../arrays/compile.expected                   |  30 +-
 .../chunking_example/compile.expected         | 115 +++++--
 .../expressions/compile.expected              | 301 +++++++++---------
 .../factor_functions/compile.expected         |  22 +-
 .../if-then-else/compile.expected             |  45 ++-
 .../materialize_annotation/compile.expected   |  58 ++--
 .../compile.expected                          | 162 +++++-----
 .../ocr_example/compile.expected              |  42 ++-
 .../smoke_example/compile.expected            |  48 +--
 .../spouse_example/compile.expected           |  59 ++--
 .../views/compile.expected                    |  28 +-
 .../weights/compile.expected                  |  41 +--
 .../article_ids-filtered.ddlogq.expected      |   5 +-
 ...ticle_ids-ordered-revsered.ddlogq.expected |   1 -
 ...icle_ids-ordered-revsered2.ddlogq.expected |   1 -
 .../article_ids-ordered.ddlogq.expected       |   1 -
 .../article_ids-parens.ddlogq.expected        |   1 -
 ...article_ids-without_parens.ddlogq.expected |   1 -
 .../article_ids.ddlogq.expected               |   1 -
 .../count-has_spouse.ddlogq.expected          |   1 -
 ...idates-per-article-ordered.ddlogq.expected |  16 +-
 ...r-article-ordered_multikey.ddlogq.expected |  19 +-
 ...num_candidates-per-article.ddlogq.expected |  16 +-
 .../histogram-supervision.ddlogq.expected     |   6 +-
 .../repeated-vars.ddlogq.expected             |   9 +-
 .../union-no-common-vars.ddlogq.expected      |   2 -
 .../spouse_example/union.ddlogq.expected      |   4 +-
 28 files changed, 565 insertions(+), 488 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index e48413968..e3d7fa5b2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -179,12 +179,12 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         val variable = getVar(v)
         val name  = resolveName(variable)
         val relation = variable.relName
-        s""" AS "${relation}.R${index}.${name}"""" //"
+        s""" AS "${relation}.R${index}.${name}\""""
       }
       case _ => s" AS column_${cq.headTerms indexOf e}"
     }
     case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
-    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}"""" //" fix sublime highlighting
+    case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}\""""
   }
 
   // resolve an expression
@@ -266,7 +266,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
                 if (canonical_body_index != bodyIndex) {
                   val real_attr_name1 = resolveName( Variable(varName, relName, termIndex) )
                   val real_attr_name2 = resolveName( getVar(varName))
-                  Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 } ")
+                  Some(s"R${ bodyIndex }.${ real_attr_name1 } = R${ canonical_body_index }.${ real_attr_name2 }")
                 } else { None }
               }
               case PlaceholderPattern() => None
@@ -488,24 +488,22 @@ class QueryCompiler(cq : ConjunctiveQuery) {
           case (x: BodyAtom, i) =>
             if (schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
               // TODO maybe TableAlias can be useful here or we can completely get rid of it?
-              Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id" """)
+              Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id\"""")
             else
               None
           case _ => None
-        }) mkString(", ")
+        }) mkString("\n     , ")
 
         // weight string
         val uwStr = stmt.weights.variables.zipWithIndex.flatMap {
           case(s: ConstExpr, i) => None
-          case(s: Expr, i) => Some(qc.compileExpr(s) + s""" AS "dd_weight_column_${i}" """)
-        } mkString(", ")
+          case(s: Expr, i) => Some(qc.compileExpr(s) + s""" AS "dd_weight_column_${i}\"""")
+        } mkString("\n     , ")
 
         val selectStr = List(varInBody, uwStr).filterNot(_.isEmpty).mkString(", ")
 
         // factor input query
-        s"""
-          SELECT ${selectStr}
-          ${ qc.generateSQLBody(fakeBody) }"""
+        s"""SELECT ${selectStr}\n${qc.generateSQLBody(fakeBody) }"""
       }
 
     // factor function
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index 0ce74f141..545b51c7b 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -3,32 +3,34 @@ deepdive.schema.variables {
 }
 
 deepdive.extraction.extractors.ext_T {
-cmd: """
-	deepdive create view T as 'SELECT R0.x[3] AS column_0, R1.x AS column_1
-FROM R R0, S R1
-        WHERE R0.x[1] = R1.y[1] AND R0.x[2] = R1.y[2]'
-	"""
-output_relation: T
-style: cmd_extractor
+sql: """SELECT R0.x[3] AS column_0
+     , R1.x AS column_1
+FROM R R0
+   , S R1
+WHERE R0.x[1] = R1.y[1]
+  AND R0.x[2] = R1.y[2]"""
 input_relations: [
   R
   S
 ]
+style: sql_extractor
+output_relation: T
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_U {
-cmd: """
-	deepdive create view U as 'SELECT R1.x AS column_0
-FROM R R0, S R1
-        WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]'
-	"""
-output_relation: U
-style: cmd_extractor
+sql: """SELECT R1.x AS column_0
+FROM R R0
+   , S R1
+WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]"""
 input_relations: [
   R
   S
 ]
+style: sql_extractor
+output_relation: U
+materialize: false
 
 }
 
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 361aa86b3..0417a607b 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -7,40 +7,45 @@ tag: Categorical
 }
 
 deepdive.extraction.extractors.ext_chunk {
-cmd: """
-deepdive create view chunk as 'SELECT DISTINCT R0.sent_id, R0.word_id, R1.tag, 
+sql: """SELECT R0.sent_id AS column_0
+     , R0.word_id AS column_1
+     , R1.tag AS column_2
+     , 
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
-END AS label
-FROM words R0, tags R1
-        '
-"""
-output_relation: chunk
-style: cmd_extractor
+END AS column_3
+FROM words R0
+   , tags R1"""
 input_relations: [
   words
   tags
 ]
+style: sql_extractor
+output_relation: chunk
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_words {
-cmd: """
-deepdive create view words as 'SELECT R0.sent_id AS "words_raw.R0.sent_id", R0.word_id AS "words_raw.R0.word_id", R0.word AS "words_raw.R0.word", R0.pos AS "words_raw.R0.pos", R0.true_tag AS "words_raw.R0.true_tag", 
-CASE WHEN R0.true_tag = '\''B-UCP'\'' THEN NULL
-     WHEN R0.true_tag = '\''I-UCP'\'' THEN NULL
-     WHEN strpos(R0.true_tag, '\''-'\'') > 0 THEN split_part(R0.true_tag, '\''-'\'', 2)
-     WHEN R0.true_tag = '\''O'\'' THEN '\''O'\''
+sql: """SELECT R0.sent_id AS column_0
+     , R0.word_id AS column_1
+     , R0.word AS column_2
+     , R0.pos AS column_3
+     , R0.true_tag AS column_4
+     , 
+CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
+     WHEN R0.true_tag = 'I-UCP' THEN NULL
+     WHEN strpos(R0.true_tag, '-') > 0 THEN split_part(R0.true_tag, '-', 2)
+     WHEN R0.true_tag = 'O' THEN 'O'
      ELSE NULL
 END AS column_5
-FROM words_raw R0
-        '
-"""
-output_relation: words
-style: cmd_extractor
+FROM words_raw R0"""
 input_relations: [
   words_raw
 ]
+style: sql_extractor
+output_relation: words
+materialize: false
 
 }
 
@@ -53,17 +58,32 @@ style: tsv_extractor
 output_relation: word_features
 udf: """udf/ext_features.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sent_id AS "words.R0.sent_id", R0.word_id AS "words.R0.word_id", R0.word AS "words.R0.word", R0.pos AS "words.R0.pos", R1.word AS "words.R1.word", R1.pos AS "words.R1.pos"
-FROM words R0, words R1
-        WHERE R1.sent_id = R0.sent_id  AND R0.word_id = (R1.word_id + 1) AND R0.word IS NOT NULL"""
+input: """SELECT R0.sent_id AS column_0
+     , R0.word_id AS column_1
+     , R0.word AS column_2
+     , R0.pos AS column_3
+     , R1.word AS column_4
+     , R1.pos AS column_5
+FROM words R0
+   , words R1
+WHERE R1.sent_id = R0.sent_id
+  AND R0.word_id = (R1.word_id + 1)
+  AND R0.word IS NOT NULL"""
 
 }
 
 deepdive.inference.factors.inf_istrue_chunk {
-input_query: """
-          SELECT R0.id AS "chunk.R0.id" , R3.feature AS "dd_weight_column_0" , R0.tag AS "dd_weight_column_1" 
-          FROM chunk R0, words R1, tags R2, word_features R3
-        WHERE R1.sent_id = R0.sent_id  AND R1.word_id = R0.word_id  AND R2.tag = R0.tag  AND R3.sent_id = R0.sent_id  AND R3.word_id = R0.word_id """
+input_query: """SELECT R0.id AS "chunk.R0.id", R3.feature AS "dd_weight_column_0"
+     , R0.tag AS "dd_weight_column_1"
+FROM chunk R0
+   , words R1
+   , tags R2
+   , word_features R3
+WHERE R1.sent_id = R0.sent_id
+  AND R1.word_id = R0.word_id
+  AND R2.tag = R0.tag
+  AND R3.sent_id = R0.sent_id
+  AND R3.word_id = R0.word_id"""
 function: """Multinomial(chunk.R0.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
@@ -76,10 +96,23 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_and_chunk_chunk {
-input_query: """
-          SELECT R0.id AS "chunk.R0.id" , R1.id AS "chunk.R1.id" , R0.tag AS "dd_weight_column_0" , R1.tag AS "dd_weight_column_1" 
-          FROM chunk R0, chunk R1, words R2, words R3, tags R4, tags R5
-        WHERE R1.sent_id = R0.sent_id  AND R2.sent_id = R0.sent_id  AND R2.word_id = R0.word_id  AND R3.sent_id = R0.sent_id  AND R3.word_id = R1.word_id  AND R4.tag = R0.tag  AND R5.tag = R1.tag  AND R1.word_id = (R0.word_id + 1)"""
+input_query: """SELECT R0.id AS "chunk.R0.id"
+     , R1.id AS "chunk.R1.id", R0.tag AS "dd_weight_column_0"
+     , R1.tag AS "dd_weight_column_1"
+FROM chunk R0
+   , chunk R1
+   , words R2
+   , words R3
+   , tags R4
+   , tags R5
+WHERE R1.sent_id = R0.sent_id
+  AND R2.sent_id = R0.sent_id
+  AND R2.word_id = R0.word_id
+  AND R3.sent_id = R0.sent_id
+  AND R3.word_id = R1.word_id
+  AND R4.tag = R0.tag
+  AND R5.tag = R1.tag
+  AND R1.word_id = (R0.word_id + 1)"""
 function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
@@ -91,10 +124,24 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf1_and_chunk_chunk {
-input_query: """
-          SELECT R0.id AS "chunk.R0.id" , R1.id AS "chunk.R1.id" , R0.tag AS "dd_weight_column_0" , R1.tag AS "dd_weight_column_1" 
-          FROM chunk R0, chunk R1, words R2, words R3, tags R4, tags R5
-        WHERE R1.sent_id = R0.sent_id  AND R2.sent_id = R0.sent_id  AND R2.word_id = R0.word_id  AND R3.sent_id = R0.sent_id  AND R3.word_id = R1.word_id  AND R4.tag = R0.tag  AND R5.tag = R1.tag  AND R2.tag IS NOT NULL AND R0.word_id < R1.word_id"""
+input_query: """SELECT R0.id AS "chunk.R0.id"
+     , R1.id AS "chunk.R1.id", R0.tag AS "dd_weight_column_0"
+     , R1.tag AS "dd_weight_column_1"
+FROM chunk R0
+   , chunk R1
+   , words R2
+   , words R3
+   , tags R4
+   , tags R5
+WHERE R1.sent_id = R0.sent_id
+  AND R2.sent_id = R0.sent_id
+  AND R2.word_id = R0.word_id
+  AND R3.sent_id = R0.sent_id
+  AND R3.word_id = R1.word_id
+  AND R4.tag = R0.tag
+  AND R5.tag = R1.tag
+  AND R2.tag IS NOT NULL
+  AND R0.word_id < R1.word_id"""
 function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 3500847d7..595f69334 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -3,339 +3,334 @@ deepdive.schema.variables {
 }
 
 deepdive.extraction.extractors.ext_Q {
-cmd: """
-	deepdive create view Q as 'SELECT DISTINCT ('\''test'\'' :: TEXT) AS column_0, 123 AS column_1, R0.k AS column_2, unnest(R1.q) AS column_3
-FROM a R0, b R1, c R2
-        WHERE R1.k = R0.k  AND R2.s = R1.p || R1.q AND R2.n = 10 AND R2.t = '\''foo'\'' AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))'
-	"""
-output_relation: Q
-style: cmd_extractor
+sql: """SELECT DISTINCT ('test' :: TEXT) AS column_0
+     , 123 AS column_1
+     , R0.k AS column_2
+     , unnest(R1.q) AS column_3
+FROM a R0
+   , b R1
+   , c R2
+WHERE R1.k = R0.k
+  AND R2.s = R1.p || R1.q
+  AND R2.n = 10
+  AND R2.t = 'foo'
+  AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))"""
 input_relations: [
   a
   b
   c
 ]
+style: sql_extractor
+output_relation: Q
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_P {
-cmd: """
-	deepdive create view P as 'SELECT R1.p AS column_0, R1.q AS column_1, MAX(R1.r) AS column_2
-FROM a R0, b R1
-        WHERE R1.k = R0.k 
-        GROUP BY R1.p, R1.q'
-	"""
-output_relation: P
-style: cmd_extractor
+sql: """SELECT R1.p AS column_0
+     , R1.q AS column_1
+     , MAX(R1.r) AS column_2
+FROM a R0
+   , b R1
+WHERE R1.k = R0.k
+GROUP BY R1.p
+    , R1.q"""
 input_relations: [
   a
   b
 ]
+style: sql_extractor
+output_relation: P
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_A {
-cmd: """
-	deepdive create view A as 'SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
-FROM b R0
-        '
-	"""
-output_relation: A
-style: cmd_extractor
+sql: """SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
+FROM b R0"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: A
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_B {
-cmd: """
-	deepdive create view B as 'SELECT func(R0.k + (R0.r + R0.k)) AS column_0
-FROM b R0
-        '
-	"""
-output_relation: B
-style: cmd_extractor
+sql: """SELECT func(R0.k + (R0.r + R0.k)) AS column_0
+FROM b R0"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: B
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_C {
-cmd: """
-	deepdive create view C as 'SELECT func(func(func(R0.k))) AS column_0
-FROM b R0
-        '
-	"""
-output_relation: C
-style: cmd_extractor
+sql: """SELECT func(func(func(R0.k))) AS column_0
+FROM b R0"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: C
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_D {
-cmd: """
-	deepdive create view D as 'SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
-FROM b R0
-        '
-	"""
-output_relation: D
-style: cmd_extractor
+sql: """SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
+FROM b R0"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: D
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_E {
-cmd: """
-	deepdive create view E as 'SELECT (R0.k :: INT) AS column_0
-FROM b R0
-        '
-	"""
-output_relation: E
-style: cmd_extractor
+sql: """SELECT (R0.k :: INT) AS column_0
+FROM b R0"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: E
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_F {
-cmd: """
-	deepdive create view F as 'SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
-FROM b R0
-        '
-	"""
-output_relation: F
-style: cmd_extractor
+sql: """SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
+FROM b R0"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: F
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_G {
-cmd: """
-	deepdive create view G as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100'
-	"""
-output_relation: G
-style: cmd_extractor
+WHERE (R0.k + R0.r) = 100"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: G
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_H {
-cmd: """
-	deepdive create view H as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE (R0.k + R0.r) = 100 AND R0.k > 50'
-	"""
-output_relation: H
-style: cmd_extractor
+WHERE (R0.k + R0.r) = 100
+  AND R0.k > 50"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: H
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_I {
-cmd: """
-	deepdive create view I as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))'
-	"""
-output_relation: I
-style: cmd_extractor
+WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: I
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_J {
-cmd: """
-	deepdive create view J as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)'
-	"""
-output_relation: J
-style: cmd_extractor
+WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: J
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_K {
-cmd: """
-	deepdive create view K as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))'
-	"""
-output_relation: K
-style: cmd_extractor
+WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: K
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_L {
-cmd: """
-	deepdive create view L as 'SELECT DISTINCT R0.k AS column_0
+sql: """SELECT DISTINCT R0.k AS column_0
 FROM b R0
-        
-LIMIT 100'
-	"""
-output_relation: L
-style: cmd_extractor
+LIMIT 100"""
 input_relations: [
   b
 ]
+style: sql_extractor
+output_relation: L
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_M {
-cmd: """
-	deepdive create view M as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k )'
-	"""
-output_relation: M
-style: cmd_extractor
+WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k)"""
 input_relations: [
   b
   c
 ]
+style: sql_extractor
+output_relation: M
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_N {
-cmd: """
-	deepdive create view N as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k  AND R1_0.s > '\''a'\'')'
-	"""
-output_relation: N
-style: cmd_extractor
+WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k
+  AND R1_0.s > 'a')"""
 input_relations: [
   b
   c
 ]
+style: sql_extractor
+output_relation: N
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_O {
-cmd: """
-	deepdive create view O as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM b R0
-        WHERE EXISTS (SELECT 1 FROM c R1_0, a R1_1 WHERE R1_0.n = R0.k  AND R1_1.k = R0.k )'
-	"""
-output_relation: O
-style: cmd_extractor
+WHERE EXISTS (SELECT 1 FROM c R1_0
+   , a R1_1 WHERE R1_0.n = R0.k
+  AND R1_1.k = R0.k)"""
 input_relations: [
   b
   c
   a
 ]
+style: sql_extractor
+output_relation: O
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_S {
-cmd: """
-	deepdive create view S as 'SELECT R0.k AS column_0
-FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k 
-        '
-	"""
-output_relation: S
-style: cmd_extractor
+sql: """SELECT R0.k AS column_0
+FROM b R0
+LEFT OUTER JOIN c R1_0
+  ON R1_0.n = R0.k"""
 input_relations: [
   b
   c
 ]
+style: sql_extractor
+output_relation: S
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_T {
-cmd: """
-	deepdive create view T as 'SELECT R0.k AS column_0
-FROM b R0 LEFT OUTER JOIN c R1_0 ON R1_0.n = R0.k  AND R1_0.s > R0.p
-        WHERE R1_0.s > R0.p'
-	"""
-output_relation: T
-style: cmd_extractor
+sql: """SELECT R0.k AS column_0
+FROM b R0
+LEFT OUTER JOIN c R1_0
+  ON R1_0.n = R0.k
+  AND R1_0.s > R0.p
+WHERE R1_0.s > R0.p"""
 input_relations: [
   b
   c
 ]
+style: sql_extractor
+output_relation: T
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_U {
-cmd: """
-	deepdive create view U as 'SELECT R0_0.k AS column_0
-FROM b R0_0 ON  FULL OUTER JOIN c R1_0 ON R1_0.n = R0_0.k 
-        '
-	"""
-output_relation: U
-style: cmd_extractor
+sql: """SELECT R0_0.k AS column_0
+FROM b R0_0
+  ON 
+FULL OUTER JOIN c R1_0
+  ON R1_0.n = R0_0.k"""
 input_relations: [
   b
   c
 ]
+style: sql_extractor
+output_relation: U
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_W {
-cmd: """
-	deepdive create view W as 'SELECT R0.k AS column_0
+sql: """SELECT R0.k AS column_0
 FROM a R0
-        WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))'
-	"""
-output_relation: W
-style: cmd_extractor
+WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))"""
 input_relations: [
   a
   c
 ]
+style: sql_extractor
+output_relation: W
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_V {
-cmd: """
-	deepdive create view V as 'SELECT R0.n AS column_0
-FROM c R0, a R1
-        WHERE R1.k = R0.n '
-	"""
-output_relation: V
-style: cmd_extractor
+sql: """SELECT R0.n AS column_0
+FROM c R0
+   , a R1
+WHERE R1.k = R0.n"""
 input_relations: [
   c
   a
 ]
+style: sql_extractor
+output_relation: V
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_X {
-cmd: """
-	deepdive create view X as 'SELECT R0.k AS column_0
-FROM b R0, c R1
-        WHERE R1.n = R0.k '
-	"""
-output_relation: X
-style: cmd_extractor
+sql: """SELECT R0.k AS column_0
+FROM b R0
+   , c R1
+WHERE R1.n = R0.k"""
 input_relations: [
   b
   c
 ]
+style: sql_extractor
+output_relation: X
+materialize: false
 
 }
 
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index a5631d8f7..ef3425b89 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -5,10 +5,13 @@ Q.label: Boolean
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
-input_query: """
-          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
-          FROM Q R0, Q R1, R R2
-        WHERE R2.a = R0.x  AND R2.b = R1.x """
+input_query: """SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id", R1.x AS "dd_weight_column_0"
+FROM Q R0
+   , Q R1
+   , R R2
+WHERE R2.a = R0.x
+  AND R2.b = R1.x"""
 function: """Imply(Q.R0.label, Q.R1.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -19,10 +22,13 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_equal_Q_Q {
-input_query: """
-          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
-          FROM Q R0, Q R1, R R2
-        WHERE R2.a = R0.x  AND R2.b = R1.x """
+input_query: """SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id", R1.x AS "dd_weight_column_0"
+FROM Q R0
+   , Q R1
+   , R R2
+WHERE R2.a = R0.x
+  AND R2.b = R1.x"""
 function: """Equal(Q.R0.label, !Q.R1.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index a301153a2..570f9642f 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -4,63 +4,60 @@ q.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_q {
-cmd: """
-deepdive create view q as 'SELECT DISTINCT R0.x, 
+sql: """SELECT R0.x AS column_0
+     , 
 CASE WHEN R0.l > 0 THEN true
      WHEN R0.l < 0 THEN false
      ELSE NULL
-END AS label
-FROM labels_resolved R0
-        '
-"""
-output_relation: q
-style: cmd_extractor
+END AS column_1
+FROM labels_resolved R0"""
 input_relations: [
   labels_resolved
 ]
+style: sql_extractor
+output_relation: q
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_p {
-cmd: """
-deepdive create view p as 'SELECT R0.x AS column_0, 
+sql: """SELECT R0.x AS column_0
+     , 
 CASE WHEN abs(R0.l) > 10 THEN true
      ELSE false
 END AS column_1
 FROM labels R0
-        
 UNION ALL
-SELECT R0.x AS column_0, 
+SELECT R0.x AS column_0
+     , 
 CASE WHEN (R0.x % 10) = 0 THEN false
      ELSE 
 END AS column_1
-FROM labels R0
-        '
-"""
-output_relation: p
-style: cmd_extractor
+FROM labels R0"""
 input_relations: [
   labels
 ]
+style: sql_extractor
+output_relation: p
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_labels_resolved {
-cmd: """
-deepdive create view labels_resolved as 'SELECT R0.x AS "labels.R0.x", SUM(
+sql: """SELECT R0.x AS column_0
+     , SUM(
 CASE WHEN R0.l IS NULL THEN 0
      WHEN R0.l = true THEN 1
      ELSE -1
 END) AS column_1
 FROM labels R0
-        
-        GROUP BY R0.x'
-"""
-output_relation: labels_resolved
-style: cmd_extractor
+GROUP BY R0.x"""
 input_relations: [
   labels
 ]
+style: sql_extractor
+output_relation: labels_resolved
+materialize: false
 
 }
 
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index 3bc84cce3..80efcfe26 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -5,67 +5,55 @@ TQ.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_V {
-cmd: """
-deepdive create view V as 'SELECT R0.x AS "D.R0.x"
-FROM D R0
-        '
-"""
-output_relation: V
-style: cmd_extractor
+sql: """SELECT R0.x AS column_0
+FROM D R0"""
 input_relations: [
   D
 ]
+style: sql_extractor
+output_relation: V
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_VQ {
-cmd: """
-deepdive create view VQ as 'SELECT DISTINCT R0.x, true AS label
-FROM D R0
-        '
-"""
-output_relation: VQ
-style: cmd_extractor
+sql: """SELECT R0.x AS column_0
+     , true AS column_1
+FROM D R0"""
 input_relations: [
   D
 ]
+style: sql_extractor
+output_relation: VQ
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_T {
-cmd: """
-# TODO use temporary table
-deepdive create table "T"
-deepdive sql 'INSERT INTO T SELECT R0.x AS "D.R0.x"
-FROM D R0
-        '
-# TODO rename temporary table to replace output_relation
-"""
-output_relation: T
-style: cmd_extractor
+sql: """SELECT R0.x AS column_0
+FROM D R0"""
 input_relations: [
   D
 ]
+style: sql_extractor
+output_relation: T
+materialize: true
 
 }
 
 deepdive.extraction.extractors.ext_TQ {
-cmd: """
-# TODO use temporary table
-deepdive create table "TQ"
-deepdive sql 'INSERT INTO TQ SELECT DISTINCT R0.x, 
+sql: """SELECT R0.x AS column_0
+     , 
 CASE WHEN length(R0.x) > 5 THEN true
      ELSE NULL
-END AS label
-FROM D R0
-        '
-# TODO rename temporary table to replace output_relation
-"""
-output_relation: TQ
-style: cmd_extractor
+END AS column_1
+FROM D R0"""
 input_relations: [
   D
 ]
+style: sql_extractor
+output_relation: TQ
+materialize: true
 
 }
 
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 2e4b8ac7b..33b89e6d6 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -4,39 +4,41 @@ Q.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_S {
-cmd: """
-deepdive create view S as 'SELECT R0.a AS "R.R0.a"
-FROM R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a > 100
+sql: """SELECT R0.a AS column_0
+FROM R R0
+   , R R1
+WHERE R1.a = R0.b
+  AND R0.a > 100
 UNION ALL
-SELECT R0.a AS "R.R0.a"
-FROM R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a < -100
+SELECT R0.a AS column_0
+FROM R R0
+   , R R1
+WHERE R1.a = R0.b
+  AND R0.a < -100
 UNION ALL
-SELECT R0.a AS "R.R0.a"
-FROM R R0, R R1
-        WHERE R1.a = R0.b  AND R0.a = 0
+SELECT R0.a AS column_0
+FROM R R0
+   , R R1
+WHERE R1.a = R0.b
+  AND R0.a = 0
 UNION ALL
-SELECT R0.a AS "S_0.R0.a"
+SELECT R0.a AS column_0
 FROM S_0 R0
-        
 UNION ALL
-SELECT R0.a AS "S_1.R0.a"
+SELECT R0.a AS column_0
 FROM S_1 R0
-        
 UNION ALL
-SELECT R0.a AS "S_2.R0.a"
-FROM S_2 R0
-        '
-"""
-output_relation: S
-style: cmd_extractor
+SELECT R0.a AS column_0
+FROM S_2 R0"""
 input_relations: [
   R
   S_0
   S_1
   S_2
 ]
+style: sql_extractor
+output_relation: S
+materialize: false
 
 }
 
@@ -49,38 +51,34 @@ style: tsv_extractor
 output_relation: T___0
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
 FROM R R0
-        WHERE R0.a > 1000"""
+WHERE R0.a > 1000"""
 
 }
 
 deepdive.extraction.extractors.ext_T {
-cmd: """
-deepdive create view T as 'SELECT R0.a AS "T___0.R0.a"
+sql: """SELECT R0.a AS column_0
 FROM T___0 R0
-        
 UNION ALL
-SELECT R0.a AS "T___1.R0.a"
+SELECT R0.a AS column_0
 FROM T___1 R0
-        
 UNION ALL
-SELECT R0.a AS "T___2.R0.a"
+SELECT R0.a AS column_0
 FROM T___2 R0
-        
 UNION ALL
-SELECT R0.a AS "T___3.R0.a"
-FROM T___3 R0
-        '
-"""
-output_relation: T
-style: cmd_extractor
+SELECT R0.a AS column_0
+FROM T___3 R0"""
 input_relations: [
   T___0
   T___1
   T___2
   T___3
 ]
+style: sql_extractor
+output_relation: T
+materialize: false
 
 }
 
@@ -93,9 +91,11 @@ style: tsv_extractor
 output_relation: T___1
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
 FROM R R0
-        WHERE 10 < R0.a AND R0.a < 20"""
+WHERE 10 < R0.a
+  AND R0.a < 20"""
 
 }
 
@@ -108,9 +108,11 @@ style: tsv_extractor
 output_relation: T___2
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
 FROM R R0
-        WHERE 100 < R0.a AND R0.a < 200"""
+WHERE 100 < R0.a
+  AND R0.a < 200"""
 
 }
 
@@ -123,9 +125,10 @@ style: tsv_extractor
 output_relation: S_0
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
 FROM R R0
-        WHERE R0.a < 0"""
+WHERE R0.a < 0"""
 
 }
 
@@ -138,9 +141,10 @@ style: tsv_extractor
 output_relation: S_1
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
 FROM R R0
-        WHERE R0.a > 0"""
+WHERE R0.a > 0"""
 
 }
 
@@ -153,9 +157,9 @@ style: tsv_extractor
 output_relation: T___3
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
-FROM R R0
-        """
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
+FROM R R0"""
 
 }
 
@@ -168,17 +172,19 @@ style: tsv_extractor
 output_relation: S_2
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS "R.R0.a", R0.b AS "R.R0.b"
+input: """SELECT R0.a AS column_0
+     , R0.b AS column_1
 FROM R R0
-        WHERE R0.a > 0"""
+WHERE R0.a > 0"""
 
 }
 
 deepdive.inference.factors.inf_istrue_Q {
-input_query: """
-          SELECT R0.id AS "Q.R0.id" , R0.x AS "dd_weight_column_0" 
-          FROM Q R0, S R1
-        WHERE R1.a = R0.x  AND R0.x > 1000"""
+input_query: """SELECT R0.id AS "Q.R0.id", R0.x AS "dd_weight_column_0"
+FROM Q R0
+   , S R1
+WHERE R1.a = R0.x
+  AND R0.x > 1000"""
 function: """Imply(Q.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -189,10 +195,11 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf1_istrue_Q {
-input_query: """
-          SELECT R0.id AS "Q.R0.id" 
-          FROM Q R0, S R1
-        WHERE R1.a = R0.x  AND R0.x = 0"""
+input_query: """SELECT R0.id AS "Q.R0.id"
+FROM Q R0
+   , S R1
+WHERE R1.a = R0.x
+  AND R0.x = 0"""
 function: """Imply(Q.R0.label)"""
 weight: """1.0"""
 input_relations: [
@@ -203,10 +210,17 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
-input_query: """
-          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R0.x AS "dd_weight_column_0" 
-          FROM Q R0, Q R1, S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x """
+input_query: """SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id", R0.x AS "dd_weight_column_0"
+FROM Q R0
+   , Q R1
+   , S R2
+   , R R3
+   , S R4
+WHERE R2.a = R0.x
+  AND R3.a = R0.x
+  AND R3.b = R1.x
+  AND R4.a = R1.x"""
 function: """Imply(Q.R0.label, Q.R1.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -218,10 +232,18 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf1_imply_Q_Q {
-input_query: """
-          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
-          FROM Q R0, Q R1, S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) < 1000"""
+input_query: """SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id"
+FROM Q R0
+   , Q R1
+   , S R2
+   , R R3
+   , S R4
+WHERE R2.a = R0.x
+  AND R3.a = R0.x
+  AND R3.b = R1.x
+  AND R4.a = R1.x
+  AND (R0.x + R1.x) < 1000"""
 function: """Imply(Q.R0.label, Q.R1.label)"""
 weight: """-10.0"""
 input_relations: [
@@ -233,16 +255,14 @@ input_relations: [
 }
 
 deepdive.extraction.extractors.ext_T__3 {
-cmd: """
-deepdive create view T__3 as 'SELECT R0.a AS column_0
-FROM T R0
-        '
-"""
-output_relation: T__3
-style: cmd_extractor
+sql: """SELECT R0.a AS column_0
+FROM T R0"""
 input_relations: [
   T
 ]
+style: sql_extractor
+output_relation: T__3
+materialize: false
 
 }
 
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index eff2c3e4e..377356988 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -5,38 +5,36 @@ q2.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_q1 {
-cmd: """
-deepdive create view q1 as 'SELECT DISTINCT R0.wid, R0.val AS label
-FROM label1 R0
-        '
-"""
-output_relation: q1
-style: cmd_extractor
+sql: """SELECT R0.wid AS column_0
+     , R0.val AS column_1
+FROM label1 R0"""
 input_relations: [
   label1
 ]
+style: sql_extractor
+output_relation: q1
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_q2 {
-cmd: """
-deepdive create view q2 as 'SELECT DISTINCT R0.wid, R0.val AS label
-FROM label2 R0
-        '
-"""
-output_relation: q2
-style: cmd_extractor
+sql: """SELECT R0.wid AS column_0
+     , R0.val AS column_1
+FROM label2 R0"""
 input_relations: [
   label2
 ]
+style: sql_extractor
+output_relation: q2
+materialize: false
 
 }
 
 deepdive.inference.factors.inf_istrue_q1 {
-input_query: """
-          SELECT R0.id AS "q1.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM q1 R0, features R1
-        WHERE R1.word_id = R0.wid """
+input_query: """SELECT R0.id AS "q1.R0.id", R1.feature_id AS "dd_weight_column_0"
+FROM q1 R0
+   , features R1
+WHERE R1.word_id = R0.wid"""
 function: """Imply(q1.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -47,10 +45,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_q2 {
-input_query: """
-          SELECT R0.id AS "q2.R0.id" , R1.feature_id AS "dd_weight_column_0" 
-          FROM q2 R0, features R1
-        WHERE R1.word_id = R0.wid """
+input_query: """SELECT R0.id AS "q2.R0.id", R1.feature_id AS "dd_weight_column_0"
+FROM q2 R0
+   , features R1
+WHERE R1.word_id = R0.wid"""
 function: """Imply(q2.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 03835a579..3840faf69 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -5,38 +5,39 @@ cancer.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_smoke {
-cmd: """
-deepdive create view smoke as 'SELECT DISTINCT R0.person_id, R0.smokes AS label
-FROM person_smokes R0
-        '
-"""
-output_relation: smoke
-style: cmd_extractor
+sql: """SELECT R0.person_id AS column_0
+     , R0.smokes AS column_1
+FROM person_smokes R0"""
 input_relations: [
   person_smokes
 ]
+style: sql_extractor
+output_relation: smoke
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_cancer {
-cmd: """
-deepdive create view cancer as 'SELECT DISTINCT R0.person_id, R0.has_cancer AS label
-FROM person_has_cancer R0
-        '
-"""
-output_relation: cancer
-style: cmd_extractor
+sql: """SELECT R0.person_id AS column_0
+     , R0.has_cancer AS column_1
+FROM person_has_cancer R0"""
 input_relations: [
   person_has_cancer
 ]
+style: sql_extractor
+output_relation: cancer
+materialize: false
 
 }
 
 deepdive.inference.factors.inf_imply_smoke_cancer {
-input_query: """
-          SELECT R0.id AS "smoke.R0.id" , R1.id AS "cancer.R1.id" 
-          FROM smoke R0, cancer R1, person_smokes R2
-        WHERE R1.person_id = R0.person_id  AND R2.person_id = R0.person_id """
+input_query: """SELECT R0.id AS "smoke.R0.id"
+     , R1.id AS "cancer.R1.id"
+FROM smoke R0
+   , cancer R1
+   , person_smokes R2
+WHERE R1.person_id = R0.person_id
+  AND R2.person_id = R0.person_id"""
 function: """Imply(smoke.R0.label, cancer.R1.label)"""
 weight: """0.5"""
 input_relations: [
@@ -48,10 +49,13 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_imply_smoke_smoke {
-input_query: """
-          SELECT R0.id AS "smoke.R0.id" , R1.id AS "smoke.R1.id" 
-          FROM smoke R0, smoke R1, friends R2
-        WHERE R2.person_id = R0.person_id  AND R2.friend_id = R1.person_id """
+input_query: """SELECT R0.id AS "smoke.R0.id"
+     , R1.id AS "smoke.R1.id"
+FROM smoke R0
+   , smoke R1
+   , friends R2
+WHERE R2.person_id = R0.person_id
+  AND R2.friend_id = R1.person_id"""
 function: """Imply(smoke.R0.label, smoke.R1.label)"""
 weight: """0.4"""
 input_relations: [
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index f55e621bd..9a22bc542 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -12,9 +12,10 @@ style: tsv_extractor
 output_relation: people_mentions
 udf: """udf/ext_people.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sentence_id AS "sentences.R0.sentence_id", ARRAY_TO_STRING(R0.words, '~^~') AS column_1, ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM sentences R0
-        """
+input: """SELECT R0.sentence_id AS column_0
+     , ARRAY_TO_STRING(R0.words, '~^~') AS column_1
+     , ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
+FROM sentences R0"""
 
 }
 
@@ -27,9 +28,14 @@ style: tsv_extractor
 output_relation: has_spouse_candidates
 udf: """udf/ext_has_spouse.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sentence_id AS "people_mentions.R0.sentence_id", R0.mention_id AS "people_mentions.R0.mention_id", R0.text AS "people_mentions.R0.text", R1.mention_id AS "people_mentions.R1.mention_id", R1.text AS "people_mentions.R1.text"
-FROM people_mentions R0, people_mentions R1
-        WHERE R1.sentence_id = R0.sentence_id """
+input: """SELECT R0.sentence_id AS column_0
+     , R0.mention_id AS column_1
+     , R0.text AS column_2
+     , R1.mention_id AS column_3
+     , R1.text AS column_4
+FROM people_mentions R0
+   , people_mentions R1
+WHERE R1.sentence_id = R0.sentence_id"""
 
 }
 
@@ -44,31 +50,44 @@ style: tsv_extractor
 output_relation: has_spouse_features
 udf: """udf/ext_has_spouse_features.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0, R1.relation_id AS "has_spouse_candidates.R1.relation_id", R2.start_position AS "people_mentions.R2.start_position", R2.length AS "people_mentions.R2.length", R3.start_position AS "people_mentions.R3.start_position", R3.length AS "people_mentions.R3.length"
-FROM sentences R0, has_spouse_candidates R1, people_mentions R2, people_mentions R3
-        WHERE R1.sentence_id = R0.sentence_id  AND R2.sentence_id = R0.sentence_id  AND R2.mention_id = R1.person1_id  AND R3.sentence_id = R0.sentence_id  AND R3.mention_id = R1.person2_id """
+input: """SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0
+     , R1.relation_id AS column_1
+     , R2.start_position AS column_2
+     , R2.length AS column_3
+     , R3.start_position AS column_4
+     , R3.length AS column_5
+FROM sentences R0
+   , has_spouse_candidates R1
+   , people_mentions R2
+   , people_mentions R3
+WHERE R1.sentence_id = R0.sentence_id
+  AND R2.sentence_id = R0.sentence_id
+  AND R2.mention_id = R1.person1_id
+  AND R3.sentence_id = R0.sentence_id
+  AND R3.mention_id = R1.person2_id"""
 
 }
 
 deepdive.extraction.extractors.ext_has_spouse {
-cmd: """
-deepdive create view has_spouse as 'SELECT DISTINCT R0.relation_id, R0.is_true AS label
-FROM has_spouse_candidates R0
-        '
-"""
-output_relation: has_spouse
-style: cmd_extractor
+sql: """SELECT R0.relation_id AS column_0
+     , R0.is_true AS column_1
+FROM has_spouse_candidates R0"""
 input_relations: [
   has_spouse_candidates
 ]
+style: sql_extractor
+output_relation: has_spouse
+materialize: false
 
 }
 
 deepdive.inference.factors.inf_istrue_has_spouse {
-input_query: """
-          SELECT R0.id AS "has_spouse.R0.id" , R2.feature AS "dd_weight_column_0" 
-          FROM has_spouse R0, has_spouse_candidates R1, has_spouse_features R2
-        WHERE R1.relation_id = R0.relation_id  AND R2.relation_id = R0.relation_id """
+input_query: """SELECT R0.id AS "has_spouse.R0.id", R2.feature AS "dd_weight_column_0"
+FROM has_spouse R0
+   , has_spouse_candidates R1
+   , has_spouse_features R2
+WHERE R1.relation_id = R0.relation_id
+  AND R2.relation_id = R0.relation_id"""
 function: """Imply(has_spouse.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 53e52222a..5607f956b 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -3,31 +3,31 @@ deepdive.schema.variables {
 }
 
 deepdive.extraction.extractors.ext_A {
-cmd: """
-	deepdive create view A as 'SELECT R0.a AS column_0, R0.a + R0.b AS column_1
-FROM R R0
-        '
-	"""
-output_relation: A
-style: cmd_extractor
+sql: """SELECT R0.a AS column_0
+     , R0.a + R0.b AS column_1
+FROM R R0"""
 input_relations: [
   R
 ]
+style: sql_extractor
+output_relation: A
+materialize: false
 
 }
 
 deepdive.extraction.extractors.ext_B {
-cmd: """
-	deepdive create view B as 'SELECT R0.column_0 AS column_0, R1.b AS column_1
-FROM A R0, R R1
-        WHERE R1.a = R0.column_1 '
-	"""
-output_relation: B
-style: cmd_extractor
+sql: """SELECT R0.column_0 AS column_0
+     , R1.b AS column_1
+FROM A R0
+   , R R1
+WHERE R1.a = R0.column_1"""
 input_relations: [
   A
   R
 ]
+style: sql_extractor
+output_relation: B
+materialize: false
 
 }
 
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 7926d6493..515326352 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -8,10 +8,10 @@ f.label: Boolean
 }
 
 deepdive.inference.factors.inf_istrue_a {
-input_query: """
-          SELECT R0.id AS "a.R0.id" , R0.k + R1.p AS "dd_weight_column_0" 
-          FROM a R0, b R1
-        WHERE R1.k = R0.k """
+input_query: """SELECT R0.id AS "a.R0.id", R0.k + R1.p AS "dd_weight_column_0"
+FROM a R0
+   , b R1
+WHERE R1.k = R0.k"""
 function: """Imply(a.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -22,10 +22,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_c {
-input_query: """
-          SELECT R0.id AS "c.R0.id" 
-          FROM c R0, b R1
-        WHERE R1.k = R0.k """
+input_query: """SELECT R0.id AS "c.R0.id"
+FROM c R0
+   , b R1
+WHERE R1.k = R0.k"""
 function: """Imply(c.R0.label)"""
 weight: """?"""
 input_relations: [
@@ -36,10 +36,11 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_d {
-input_query: """
-          SELECT R0.id AS "d.R0.id" , R0.k AS "dd_weight_column_0" , R1.p AS "dd_weight_column_1" 
-          FROM d R0, b R1
-        WHERE R1.k = R0.k """
+input_query: """SELECT R0.id AS "d.R0.id", R0.k AS "dd_weight_column_0"
+     , R1.p AS "dd_weight_column_1"
+FROM d R0
+   , b R1
+WHERE R1.k = R0.k"""
 function: """Imply(d.R0.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
@@ -50,10 +51,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_e {
-input_query: """
-          SELECT R0.id AS "e.R0.id" 
-          FROM e R0, b R1
-        WHERE R1.k = R0.k """
+input_query: """SELECT R0.id AS "e.R0.id"
+FROM e R0
+   , b R1
+WHERE R1.k = R0.k"""
 function: """Imply(e.R0.label)"""
 weight: """-10"""
 input_relations: [
@@ -64,10 +65,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_f {
-input_query: """
-          SELECT R0.id AS "f.R0.id" 
-          FROM f R0, b R1
-        WHERE R1.k = R0.k """
+input_query: """SELECT R0.id AS "f.R0.id"
+FROM f R0
+   , b R1
+WHERE R1.k = R0.k"""
 function: """Imply(f.R0.label)"""
 weight: """-0.3"""
 input_relations: [
diff --git a/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected b/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected
index 41eb2b81c..9246bafb5 100644
--- a/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids-filtered.ddlogq.expected
@@ -1,3 +1,4 @@
-SELECT R0.article_id AS "id", R0.text AS "content"
+SELECT R0.article_id AS "id"
+     , R0.text AS "content"
 FROM articles R0
-        WHERE R0.text LIKE '% wife %'
+WHERE R0.text LIKE '% wife %'
diff --git a/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected b/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected
index 71294268d..e023d9598 100644
--- a/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids-ordered-revsered.ddlogq.expected
@@ -1,4 +1,3 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        
 ORDER BY R0.article_id DESC
diff --git a/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected b/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected
index 71294268d..e023d9598 100644
--- a/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids-ordered-revsered2.ddlogq.expected
@@ -1,4 +1,3 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        
 ORDER BY R0.article_id DESC
diff --git a/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected b/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected
index d52f31ca1..77f5c1805 100644
--- a/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids-ordered.ddlogq.expected
@@ -1,4 +1,3 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        
 ORDER BY R0.article_id ASC
diff --git a/test/query-test/spouse_example/article_ids-parens.ddlogq.expected b/test/query-test/spouse_example/article_ids-parens.ddlogq.expected
index 54b58a592..cc32b7062 100644
--- a/test/query-test/spouse_example/article_ids-parens.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids-parens.ddlogq.expected
@@ -1,3 +1,2 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        
diff --git a/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected b/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected
index 54b58a592..cc32b7062 100644
--- a/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids-without_parens.ddlogq.expected
@@ -1,3 +1,2 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        
diff --git a/test/query-test/spouse_example/article_ids.ddlogq.expected b/test/query-test/spouse_example/article_ids.ddlogq.expected
index 54b58a592..cc32b7062 100644
--- a/test/query-test/spouse_example/article_ids.ddlogq.expected
+++ b/test/query-test/spouse_example/article_ids.ddlogq.expected
@@ -1,3 +1,2 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        
diff --git a/test/query-test/spouse_example/count-has_spouse.ddlogq.expected b/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
index 66a016932..ab1044003 100644
--- a/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
+++ b/test/query-test/spouse_example/count-has_spouse.ddlogq.expected
@@ -1,3 +1,2 @@
 SELECT COUNT(R0.relation_id) AS "COUNT(r)"
 FROM has_spouse R0
-        
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected
index a819951cf..a9cec8d19 100644
--- a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered.ddlogq.expected
@@ -1,11 +1,13 @@
 CREATE TEMPORARY TABLE num_candidates_by_doc AS
-SELECT R1.document_id AS column_0, COUNT(R0.relation_id) AS column_1
-FROM has_spouse_candidates R0, sentences R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        GROUP BY R1.document_id;
+SELECT R1.document_id AS column_0
+     , COUNT(R0.relation_id) AS column_1
+FROM has_spouse_candidates R0
+   , sentences R1
+WHERE R1.sentence_id = R0.sentence_id
+GROUP BY R1.document_id;
 
-SELECT R0.column_1 AS "num_candidates", COUNT(R0.column_0) AS "COUNT(doc)"
+SELECT R0.column_1 AS "num_candidates"
+     , COUNT(R0.column_0) AS "COUNT(doc)"
 FROM num_candidates_by_doc R0
-        
-        GROUP BY R0.column_1
+GROUP BY R0.column_1
 ORDER BY R0.column_1 ASC
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected
index 2783ab53c..6a6af469e 100644
--- a/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article-ordered_multikey.ddlogq.expected
@@ -1,11 +1,14 @@
 CREATE TEMPORARY TABLE num_candidates_by_doc AS
-SELECT R1.document_id AS column_0, COUNT(R0.relation_id) AS column_1
-FROM has_spouse_candidates R0, sentences R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        GROUP BY R1.document_id;
+SELECT R1.document_id AS column_0
+     , COUNT(R0.relation_id) AS column_1
+FROM has_spouse_candidates R0
+   , sentences R1
+WHERE R1.sentence_id = R0.sentence_id
+GROUP BY R1.document_id;
 
-SELECT R0.column_1 AS "num_candidates", COUNT(R0.column_0) AS "COUNT(doc)"
+SELECT R0.column_1 AS "num_candidates"
+     , COUNT(R0.column_0) AS "COUNT(doc)"
 FROM num_candidates_by_doc R0
-        
-        GROUP BY R0.column_1
-ORDER BY COUNT(R0.column_0) DESC, R0.column_1 ASC
+GROUP BY R0.column_1
+ORDER BY COUNT(R0.column_0) DESC
+    , R0.column_1 ASC
diff --git a/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected b/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected
index 9c3604bdf..d9446dd45 100644
--- a/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected
+++ b/test/query-test/spouse_example/histogram-num_candidates-per-article.ddlogq.expected
@@ -1,10 +1,12 @@
 CREATE TEMPORARY TABLE num_candidates_by_doc AS
-SELECT R1.document_id AS column_0, COUNT(R0.relation_id) AS column_1
-FROM has_spouse_candidates R0, sentences R1
-        WHERE R1.sentence_id = R0.sentence_id 
-        GROUP BY R1.document_id;
+SELECT R1.document_id AS column_0
+     , COUNT(R0.relation_id) AS column_1
+FROM has_spouse_candidates R0
+   , sentences R1
+WHERE R1.sentence_id = R0.sentence_id
+GROUP BY R1.document_id;
 
-SELECT R0.column_1 AS "num_candidates", COUNT(R0.column_0) AS "COUNT(doc)"
+SELECT R0.column_1 AS "num_candidates"
+     , COUNT(R0.column_0) AS "COUNT(doc)"
 FROM num_candidates_by_doc R0
-        
-        GROUP BY R0.column_1
+GROUP BY R0.column_1
diff --git a/test/query-test/spouse_example/histogram-supervision.ddlogq.expected b/test/query-test/spouse_example/histogram-supervision.ddlogq.expected
index a36539961..1e266c41b 100644
--- a/test/query-test/spouse_example/histogram-supervision.ddlogq.expected
+++ b/test/query-test/spouse_example/histogram-supervision.ddlogq.expected
@@ -1,4 +1,4 @@
-SELECT R0.is_true AS "label", COUNT(R0.person1_id) AS "COUNT(candidate)"
+SELECT R0.is_true AS "label"
+     , COUNT(R0.person1_id) AS "COUNT(candidate)"
 FROM has_spouse_candidates R0
-        
-        GROUP BY R0.is_true
+GROUP BY R0.is_true
diff --git a/test/query-test/spouse_example/repeated-vars.ddlogq.expected b/test/query-test/spouse_example/repeated-vars.ddlogq.expected
index bebfd043d..a29a0d6d6 100644
--- a/test/query-test/spouse_example/repeated-vars.ddlogq.expected
+++ b/test/query-test/spouse_example/repeated-vars.ddlogq.expected
@@ -1,3 +1,6 @@
-SELECT R0.article_id AS "id1", R0.text AS "content", R1.article_id AS "id2"
-FROM articles R0, articles R1
-        WHERE R1.text = R0.text 
+SELECT R0.article_id AS "id1"
+     , R0.text AS "content"
+     , R1.article_id AS "id2"
+FROM articles R0
+   , articles R1
+WHERE R1.text = R0.text
diff --git a/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected b/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected
index 79d695ca2..d19f366e5 100644
--- a/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected
+++ b/test/query-test/spouse_example/union-no-common-vars.ddlogq.expected
@@ -1,7 +1,5 @@
 SELECT *
 FROM articles R0
-        
 UNION ALL
 SELECT *
 FROM articles R0
-        
diff --git a/test/query-test/spouse_example/union.ddlogq.expected b/test/query-test/spouse_example/union.ddlogq.expected
index 36c73977c..e0b150190 100644
--- a/test/query-test/spouse_example/union.ddlogq.expected
+++ b/test/query-test/spouse_example/union.ddlogq.expected
@@ -1,7 +1,7 @@
 SELECT R0.article_id AS "id"
 FROM articles R0
-        WHERE R0.article_id < 100
+WHERE R0.article_id < 100
 UNION ALL
 SELECT R0.article_id AS "id"
 FROM articles R0
-        WHERE R0.article_id > 100000
+WHERE R0.article_id > 100000

From f461168dc8353710afbaae5dc7f6c7edf11b694e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 4 Mar 2016 05:25:37 -0800
Subject: [PATCH 312/347] Fixes to accept purely logical inference rules

that describe relation between variables and joins with no other data.
Done by treating head atoms of inference rules just like body atoms and
taking the heads into account while checking variable bindings.

(Fixes #72) Joins with the heads were always being compiled but their
variables were not counting, so those variables had to come from another
relation in the body, causing unnecessary joins to be written.  Now this
can be avoided and putting a `:- TRUE.` body (which will become optional
in the future).
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 32 ++++-----
 .../ddlog/DeepDiveLogDesugarRewriter.scala    |  2 +-
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 28 ++++----
 .../ddlog/DeepDiveLogPrettyPrinter.scala      | 17 +++--
 .../ddlog/DeepDiveLogSemanticChecker.scala    | 34 +++++-----
 .../unbound_variable_5/compile-error.expected |  5 ++
 .../unbound_variable_5/input.ddlog            | 12 ++++
 .../logical_rules/compile.expected            | 65 +++++++++++++++++++
 .../logical_rules/input.ddlog                 |  9 +++
 .../logical_rules/print.expected              | 17 +++++
 10 files changed, 164 insertions(+), 57 deletions(-)
 create mode 100644 test/compile-error-test/unbound_variable_5/compile-error.expected
 create mode 100644 test/compile-error-test/unbound_variable_5/input.ddlog
 create mode 100644 test/expected-output-test/logical_rules/compile.expected
 create mode 100644 test/expected-output-test/logical_rules/input.ddlog
 create mode 100644 test/expected-output-test/logical_rules/print.expected

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index e3d7fa5b2..bb1730901 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -82,7 +82,7 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
         factorFuncName
       }_${
         // followed by variable names
-        s.head.terms map {_.name} mkString("_")
+        s.head.variables map (_.atom.name) mkString("_")
       }"
   }
 
@@ -101,7 +101,7 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   }
 
   def collectUsedRelations1(body: Body): List[String] = body match {
-    case a: BodyAtom => List(a.name)
+    case a: Atom => List(a.name)
     case q: QuantifiedBody => collectUsedRelations(q.bodies)
     case _ => List.empty
   }
@@ -136,7 +136,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
   def generateCanonicalVar()  = {
-    def generateCanonicalVarFromAtom(a: BodyAtom, index: String) {
+    def generateCanonicalVarFromAtom(a: Atom, index: String) {
       a.terms.zipWithIndex.foreach { case (expr, i) =>
         expr match {
           case VarPattern(v) =>
@@ -149,7 +149,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     // For quantified body, we need to recursively add variables from the atoms inside the quantified body
     def generateCanonicalVarFromBodies(bodies: List[Body], indexPrefix: String) {
       bodies.zipWithIndex.foreach {
-        case (a: BodyAtom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
+        case (a: Atom, index) => generateCanonicalVarFromAtom(a, s"${indexPrefix}${index}")
         // we need to recursively handle the atoms inside the modifier
         case (a: QuantifiedBody, index) => generateCanonicalVarFromBodies(a.bodies, s"${indexPrefix}${index}_")
         case _ =>
@@ -256,7 +256,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     // generate where clause from unification and conditions
     def generateWhereClause(bodies: List[Body], indexPrefix: String) : String = {
       val conditions = bodies.zipWithIndex.flatMap {
-        case (BodyAtom(relName, terms), index) => {
+        case (Atom(relName, terms), index) => {
           val bodyIndex = s"${indexPrefix}${index}"
           terms.zipWithIndex flatMap { case (pattern, termIndex) =>
             pattern match {
@@ -296,7 +296,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
     def generateFromClause(bodies: List[Body], indexPrefix: String) : String = {
       val atoms = bodies.zipWithIndex flatMap {
-        case (x:BodyAtom,i) => Some(s"${x.name} R${indexPrefix}${i}")
+        case (x:Atom,i) => Some(s"${x.name} R${indexPrefix}${i}")
         case _ => None
       }
       val outers = bodies.zipWithIndex flatMap {
@@ -462,13 +462,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
   // generate inference rule part for deepdive
   def compile(stmt: InferenceRule): CompiledBlocks = {
-    // FIXME change stmt.head.terms to be List[BodyAtom] in the parser
-    val headAsBody = stmt.head.terms map { x =>
-      BodyAtom(x.name, x.terms map {
-        case x: VarExpr => VarPattern(x.name)
-        case x: Expr    => ExprPattern(x)
-      })
-    }
+    val headAsBody = stmt.head.variables map (_.atom)
 
     val inputQueries =
       stmt.q.bodies map { case cqBody =>
@@ -479,13 +473,13 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
         val fakeBody        = headAsBody ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
-        val fakeBodyAtoms   = fakeBody.collect { case x: BodyAtom => x }
+        val fakeBodyAtoms   = fakeBody.collect { case x: Atom => x }
 
         val index = cqBody.length + 1
         val qc = new QueryCompiler(fakeCQ)
         // TODO self-join?
         val varInBody = (fakeBody.zipWithIndex flatMap {
-          case (x: BodyAtom, i) =>
+          case (x: Atom, i) =>
             if (schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
               // TODO maybe TableAlias can be useful here or we can completely get rid of it?
               Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id\"""")
@@ -508,13 +502,13 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
     // factor function
     val func = {
-      val funcBody = (headAsBody zip stmt.head.terms map { case(x, y) =>
+      val funcBody = (headAsBody zip stmt.head.variables map { case(x, y) =>
         s"""${if (y.isNegated) "!" else ""}${x.name}.R${headAsBody indexOf x}.label"""
       })
 
-      val categoricalVars = stmt.head.terms filter { t => isCategoricalRelation(t.name) }
+      val categoricalVars = stmt.head.variables filter { t => isCategoricalRelation(t.atom.name) }
       val isMultinomialFactor =
-        if (categoricalVars.size == 0 || stmt.head.terms.size == categoricalVars.size)
+        if (categoricalVars.size == 0 || stmt.head.variables.size == categoricalVars.size)
           categoricalVars.size > 0
         else
           sys.error("None or all variables must be categorical")
@@ -561,7 +555,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         "function" -> QuotedString(func),
         "weight" -> QuotedString(weight),
         "input_relations" -> {
-          val relationsInHead = stmt.head.terms map (_.name)
+          val relationsInHead = stmt.head.variables map (_.atom.name)
           val relationsInBody = relationNamesUsedByStatement getOrElse(stmt, List.empty)
           (relationsInHead ++ relationsInBody) distinct
         }
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
index 8d49af363..9cde4a6de 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
@@ -67,7 +67,7 @@ object DeepDiveLogDesugarRewriter {
               headName = relationName,
               q = ConjunctiveQuery(
                 headTerms = schema.a.terms map VarExpr,
-                bodies = List(List(BodyAtom(name = nameUnique, terms = schema.a.terms map VarPattern)))
+                bodies = List(List(Atom(name = nameUnique, terms = schema.a.terms map VarPattern)))
               )
             )
           )
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index fd3636a2e..441caeaf2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -36,7 +36,7 @@ case class ExprPattern(expr: Expr) extends Pattern
 case class PlaceholderPattern() extends Pattern
 
 sealed trait Body
-case class BodyAtom(name : String, terms : List[Pattern]) extends Body
+case class Atom(name : String, terms : List[Pattern]) extends Body
 case class QuantifiedBody(modifier: BodyModifier, bodies: List[Body]) extends Body
 
 sealed trait BodyModifier
@@ -100,8 +100,8 @@ object FactorFunction {
   case class Linear()      extends FactorFunction
   case class Ratio()       extends FactorFunction
 }
-case class HeadAtom(name : String, terms : List[Expr], isNegated: Boolean = false)
-case class InferenceRuleHead(function: FactorFunction.FactorFunction, terms: List[HeadAtom])
+case class HeadAtom(atom: Atom, isNegated: Boolean = false)
+case class InferenceRuleHead(function: FactorFunction.FactorFunction, variables: List[HeadAtom])
 
 
 sealed trait FunctionInputOutputType
@@ -335,9 +335,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
       }
     ) named "pattern"
 
-  def atom = relationName ~ "(" ~ rep1sep(pattern, ",") ~ ")" ^^ {
-    case (r ~ _ ~ patterns ~ _) => BodyAtom(r, patterns)
-  }
+  def atom: Parser[Atom] =
+    relationName ~ ("(" ~> rep1sep(pattern, ",") <~ ")") ^^ {
+      case n ~ ps => Atom(n, ps)
+    }
+
   def quantifiedBody = (opt("!") ~ "EXISTS" | "OPTIONAL" | "ALL") ~ "[" ~ rep1sep(cqBody, ",") ~ "]" ^^ { case (m ~ _ ~ b ~ _) =>
     val modifier = m match {
       case (not ~ "EXISTS") => ExistModifier(not != None)
@@ -394,12 +396,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
     |         headAtom    ~ rep1("=" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.Equal() ,  a +: b) }
     |         headAtom    ~ rep1("^" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.And()   ,  a +: b) }
     |         headAtom    ~ rep1("v" ~> headAtom) ^^ { case (a ~ b) => InferenceRuleHead(FactorFunction.Or()    ,  a +: b) }
-    |         headAtom                            ^^ { case       a => InferenceRuleHead(FactorFunction.IsTrue(), List(a)) }
+    |         headAtom                            ^^ { case  a      => InferenceRuleHead(FactorFunction.IsTrue(), List(a)) }
     )
-  def headAtom =
-    opt("!") ~ relationName ~ conjunctiveQueryHeadTerms ^^ {
-      case (isNegated ~ varName ~ expressions) => HeadAtom(varName, expressions, isNegated isDefined)
-    }
+  def headAtom = opt("!") ~ atom ^^ {
+    case isNegated ~ atom => HeadAtom(atom, isNegated isDefined)
+  }
 
   // rules or schema elements in arbitrary order
   def statement : Parser[Statement] = (
@@ -434,7 +435,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
       rule match {
         case extrRule: ExtractionRule =>
           // turn normal derivation rules to IsTrue factors
-          val headAtom = HeadAtom(name = extrRule.headName, terms = extrRule.q.headTerms, isNegated = false)
+          val headAtom = HeadAtom(Atom(extrRule.headName, extrRule.q.headTerms map {
+            case VarExpr(x) => VarPattern(x)
+            case e => ExprPattern(e)
+          }), isNegated = false)
           InferenceRule(
             head = InferenceRuleHead(FactorFunction.IsTrue(), List(headAtom)),
             q = extrRule.q.copy(headTerms = List.empty),
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
index 6ddcb7e1e..a47b804a2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogPrettyPrinter.scala
@@ -103,7 +103,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
     }
   }
 
-  def print(a: BodyAtom) : String = {
+  def print(a: Atom) : String = {
     val vars = a.terms map print
     s"${a.name}(${vars.mkString(", ")})"
   }
@@ -139,7 +139,7 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(b: Body) : String = b match {
-    case b: BodyAtom => print(b)
+    case b: Atom => print(b)
     case b: Cond => print(b)
     case b: QuantifiedBody => print(b)
   }
@@ -164,21 +164,20 @@ object DeepDiveLogPrettyPrinter extends DeepDiveLogHandler {
   }
 
   def print(a: HeadAtom) : String = {
-    val vars = a.terms map print
-    s"${if (a.isNegated) "!" else ""}${a.name}(${vars.mkString(", ")})"
+    s"${if (a.isNegated) "!" else ""}${print(a.atom)}"
   }
 
   def print(head: InferenceRuleHead) : String = {
-    def printImplyHead = s"""${printHead(head.terms.dropRight(1), ", ")} => ${print(head.terms.last)}"""
+    def printImplyHead = s"""${printHead(head.variables.dropRight(1), ", ")} => ${print(head.variables.last)}"""
     def printHead(a: List[HeadAtom], delim: String) : String = a map print mkString(delim)
     head.function match {
       case FactorFunction.Imply()  => printImplyHead
       case FactorFunction.Linear() => printImplyHead
       case FactorFunction.Ratio()  => printImplyHead
-      case FactorFunction.And()    => printHead(head.terms, " ^ ")
-      case FactorFunction.Or()     => printHead(head.terms, " v ")
-      case FactorFunction.Equal()  => printHead(head.terms, " = ")
-      case FactorFunction.IsTrue() => printHead(head.terms, "")
+      case FactorFunction.And()    => printHead(head.variables, " ^ ")
+      case FactorFunction.Or()     => printHead(head.variables, " v ")
+      case FactorFunction.Equal()  => printHead(head.variables, " = ")
+      case FactorFunction.IsTrue() => printHead(head.variables, "")
     }
   }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 2bcc18993..acbf5fd0c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -45,9 +45,9 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
   }
 
   // iterate over all atoms contained in the body list and apply the checker
-  def checkBodyAtoms(checker: BodyAtom => Unit): List[Body] => Unit = bodies => {
+  def checkBodyAtoms(checker: Atom => Unit): List[Body] => Unit = bodies => {
     bodies foreach {
-      case a: BodyAtom => checker(a)
+      case a: Atom => checker(a)
       case a: QuantifiedBody => checkBodyAtoms(checker)(a.bodies)
       case _ =>
     }
@@ -60,13 +60,13 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
       if (!(namesUsedInHead contains name))
         error(stmt, s"""relation "${name}" is not defined""")
     }
-    def checkAtom(a: BodyAtom) = checkRelation(a.name)
+    def checkAtom(a: Atom) = checkRelation(a.name)
     def check = checkBodyAtoms(checkAtom)
     stmt match {
       case s: ExtractionRule => s.q.bodies foreach check
       case s: InferenceRule => {
         s.q.bodies foreach check
-        s.head.terms map (_.name) foreach checkRelation
+        s.head.variables map (_.atom.name) foreach checkRelation
       }
       case s: FunctionCallRule => s.q.bodies foreach check
       case _ =>
@@ -106,9 +106,9 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
   // check if any factors are defined across categorical and Boolean variables
   def checkMultinomialFactors(stmt: Statement) = stmt match {
     case s: InferenceRule =>
-      val categoricalVars = s.head.terms filter { t =>
-        schemaDeclarationByName get t.name map(_.categoricalColumns nonEmpty) getOrElse(false) }
-      if (! (categoricalVars.isEmpty || s.head.terms.size == categoricalVars.size))
+      val categoricalVars = s.head.variables filter { t =>
+        schemaDeclarationByName get t.atom.name map(_.categoricalColumns nonEmpty) getOrElse(false) }
+      if (! (categoricalVars.isEmpty || s.head.variables.size == categoricalVars.size))
         error(s, "None or all variables must be categorical")
     case _ =>
   }
@@ -120,8 +120,8 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
         (size != schemaDeclarationByName(name).a.terms.size))
         error(stmt, s""""${name}": number of columns in the query does not match number of columns in the schema""")
     }
-    def checkBodyAtom(a: BodyAtom) = check(a.name, a.terms.size)
-    def checkHeadAtom(a: HeadAtom) = check(a.name, a.terms.size)
+    def checkBodyAtom(a: Atom) = check(a.name, a.terms.size)
+    def checkHeadAtom(a: HeadAtom) = checkBodyAtom(a.atom)
     def checkCq(cq: ConjunctiveQuery) {
       cq.bodies foreach checkBodyAtoms(checkBodyAtom)
     }
@@ -135,7 +135,7 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
         checkCq(s.q)
       }
       case s: InferenceRule => {
-        s.head.terms foreach checkHeadAtom
+        s.head.variables foreach checkHeadAtom
         checkCq(s.q)
       }
       case _ =>
@@ -149,13 +149,13 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
         case b: QuantifiedBody => {
           b.modifier match {
             case OuterModifier() =>
-              if ((b.bodies collect { case x: BodyAtom => 1 }).size != 1)
+              if ((b.bodies collect { case x: Atom => 1 }).size != 1)
                 error(stmt, s"One and only one atom should be supplied in OPTIONAL modifier")
             case ExistModifier(_) =>
-              if ((b.bodies collect { case x: BodyAtom => 1 }) isEmpty)
+              if ((b.bodies collect { case x: Atom => 1 }) isEmpty)
                 error(stmt, s"At least one atom should be supplied in EXISTS modifier")
             case AllModifier() =>
-              if ((b.bodies collect { case x: BodyAtom => 1 }) isEmpty)
+              if ((b.bodies collect { case x: Atom => 1 }) isEmpty)
                 error(stmt, s"At least one atom should be supplied in ALL modifier")
           }
         }
@@ -196,7 +196,9 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
     stmt match {
       case s: ExtractionRule => checkCq(s.q)
       case s: SupervisionRule => checkCq(s.q, List(s.supervision) flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet)
-      case s: InferenceRule => checkCq(s.q, s.weights.variables flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet)
+      case s: InferenceRule =>
+        val bodiesWithHeadAtoms = s.q.bodies map (_ ++ (s.head.variables map (_.atom)))
+        checkCq(s.q.copy(bodies = bodiesWithHeadAtoms), s.weights.variables flatMap DeepDiveLogSemanticChecker.collectUsedVars toSet)
       case _ =>
     }
   }
@@ -260,13 +262,13 @@ object DeepDiveLogSemanticChecker extends DeepDiveLogHandler {
   }
 
   def collectUsedVars(body: Body): Set[String] = body match {
-    case a: BodyAtom => a.terms flatMap collectUsedVars toSet
+    case a: Atom => a.terms flatMap collectUsedVars toSet
     case a: QuantifiedBody => a.bodies flatMap collectUsedVars toSet
     case a: Cond => collectUsedVars(a)
   }
 
   def collectDefinedVars(body: Body): Set[String] = body match {
-    case a: BodyAtom => a.terms flatMap collectDefinedVars toSet
+    case a: Atom => a.terms flatMap collectDefinedVars toSet
     case a: QuantifiedBody => a.bodies flatMap collectDefinedVars toSet
     case a: Cond => Set()
   }
diff --git a/test/compile-error-test/unbound_variable_5/compile-error.expected b/test/compile-error-test/unbound_variable_5/compile-error.expected
new file mode 100644
index 000000000..b9953a4fe
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_5/compile-error.expected
@@ -0,0 +1,5 @@
+[error] Variable z must have bindings
+@weight(z)
+b(x) => b(y) :-
+    x < y.
+
diff --git a/test/compile-error-test/unbound_variable_5/input.ddlog b/test/compile-error-test/unbound_variable_5/input.ddlog
new file mode 100644
index 000000000..8518927a2
--- /dev/null
+++ b/test/compile-error-test/unbound_variable_5/input.ddlog
@@ -0,0 +1,12 @@
+a(k int).
+b?(x int).
+
+# these are fine
+b(x) :- a(x).
+
+@weight(y)
+b(x) => b(y) :- x < y.
+
+# but not this
+@weight(z)
+b(x) => b(y) :- x < y.
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
new file mode 100644
index 000000000..0467cc9e5
--- /dev/null
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -0,0 +1,65 @@
+deepdive.schema.variables {
+P.label: Boolean
+Q.label: Boolean
+
+}
+
+deepdive.extraction.extractors.ext_P {
+sql: """SELECT R0.x AS column_0
+FROM data R0
+WHERE R0.y = 1"""
+input_relations: [
+  data
+]
+style: sql_extractor
+output_relation: P
+materialize: false
+
+}
+
+deepdive.extraction.extractors.ext_Q {
+sql: """SELECT R0.x AS column_0
+FROM data R0
+WHERE R0.y = 2"""
+input_relations: [
+  data
+]
+style: sql_extractor
+output_relation: Q
+materialize: false
+
+}
+
+deepdive.inference.factors.inf_imply_P_Q {
+input_query: """SELECT R0.id AS "P.R0.id"
+     , R1.id AS "Q.R1.id"
+FROM P R0
+   , Q R1
+WHERE R1.x = R0.x
+  AND true"""
+function: """Imply(P.R0.label, Q.R1.label)"""
+weight: """1"""
+input_relations: [
+  P
+  Q
+]
+
+}
+
+deepdive.pipeline.run: ${PIPELINE}
+
+deepdive.pipeline.pipelines.extraction: [
+  ext_P
+  ext_Q
+]
+
+deepdive.pipeline.pipelines.inference: [
+  inf_imply_P_Q
+]
+
+deepdive.pipeline.pipelines.endtoend: [
+  ext_P
+  ext_Q
+  inf_imply_P_Q
+]
+
diff --git a/test/expected-output-test/logical_rules/input.ddlog b/test/expected-output-test/logical_rules/input.ddlog
new file mode 100644
index 000000000..45807bdd5
--- /dev/null
+++ b/test/expected-output-test/logical_rules/input.ddlog
@@ -0,0 +1,9 @@
+data(x int, y int).
+P?(x int).
+Q?(x int).
+
+P(x) :- data(x, 1).
+Q(x) :- data(x, 2).
+
+@weight(1)
+P(x) => Q(x) :- TRUE.
diff --git a/test/expected-output-test/logical_rules/print.expected b/test/expected-output-test/logical_rules/print.expected
new file mode 100644
index 000000000..e9b4c0635
--- /dev/null
+++ b/test/expected-output-test/logical_rules/print.expected
@@ -0,0 +1,17 @@
+data(x int,
+     y int).
+
+P?(x int).
+
+Q?(x int).
+
+P(x) :-
+    data(x, 1).
+
+Q(x) :-
+    data(x, 2).
+
+@weight(1)
+P(x) => Q(x) :-
+    true.
+

From 89d0dadd27dd19dec0a3d4a5c800b33be204ca53 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 4 Mar 2016 07:43:01 -0800
Subject: [PATCH 313/347] Cleans up the SQL query code generation

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  49 +++----
 .../arrays/compile.expected                   |  12 +-
 .../chunking_example/compile.expected         |  43 ++++--
 .../expressions/compile.expected              | 138 ++++++++++++------
 .../factor_functions/compile.expected         |  18 ++-
 .../if-then-else/compile.expected             |  18 ++-
 .../logical_rules/compile.expected            |  18 ++-
 .../materialize_annotation/compile.expected   |  24 ++-
 .../compile.expected                          |  88 +++++++----
 .../ocr_example/compile.expected              |  26 +++-
 .../smoke_example/compile.expected            |  24 ++-
 .../spouse_example/compile.expected           |  31 ++--
 .../views/compile.expected                    |  12 +-
 .../weights/compile.expected                  |  32 ++--
 14 files changed, 345 insertions(+), 188 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index bb1730901..58cb7366b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -412,7 +412,9 @@ class QueryCompiler(cq : ConjunctiveQuery) {
       "input_relations" -> (stmts flatMap relationNamesUsedByStatement distinct),
       "output_relation" -> outputRelation,
       "materialize" -> shouldMaterialize,
-      "sql" -> QuotedString(cqs map { q => new QueryCompiler(q).generateSQL() } mkString("\nUNION ALL\n"))
+      "sql" -> QuotedString("\n"+ (
+          cqs map { q => new QueryCompiler(q).generateSQL() } mkString "\nUNION ALL\n"
+        ) +"\n")
     ))
   }
 
@@ -451,7 +453,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
       val blockName = resolveExtractorBlockName(stmt)
       val parallelism = stmt.annotations find (_ named "parallelism") flatMap (_.value) getOrElse("${PARALLELISM}")
       s"deepdive.extraction.extractors.${blockName}" -> (Map(
-        "input" -> QuotedString(new QueryCompiler(stmt.q).generateSQL()),
+        "input" -> QuotedString("\n"+ new QueryCompiler(stmt.q).generateSQL() +"\n"),
         "output_relation" -> stmt.output,
         "input_relations" -> (List(stmt) flatMap relationNamesUsedByStatement distinct),
         "input_batch_size" -> "${INPUT_BATCH_SIZE}",
@@ -463,48 +465,37 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   // generate inference rule part for deepdive
   def compile(stmt: InferenceRule): CompiledBlocks = {
     val headAsBody = stmt.head.variables map (_.atom)
+    val variableIdColumns = headAsBody.zipWithIndex collect {
+      case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
+        // TODO maybe TableAlias can be useful here or we can completely get rid of it?
+        s"""R${headAsBody indexOf x}.id AS "${x.name}.R${headAsBody indexOf x}.id\""""
+    }
 
     val inputQueries =
       stmt.q.bodies map { case cqBody =>
-        // edge query
         // Here we need to select from the bodies atoms as well as the head atoms,
         // which are the variable relations.
         // This is achieved by puting head atoms into the body.
-
         val fakeBody        = headAsBody ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
-        val fakeBodyAtoms   = fakeBody.collect { case x: Atom => x }
-
-        val index = cqBody.length + 1
         val qc = new QueryCompiler(fakeCQ)
-        // TODO self-join?
-        val varInBody = (fakeBody.zipWithIndex flatMap {
-          case (x: Atom, i) =>
-            if (schemaDeclarationByRelationName get(x.name) map(_.isQuery) getOrElse(false))
-              // TODO maybe TableAlias can be useful here or we can completely get rid of it?
-              Some(s"""R${fakeBody indexOf x}.id AS "${x.name}.R${fakeBody indexOf x}.id\"""")
-            else
-              None
-          case _ => None
-        }) mkString("\n     , ")
-
-        // weight string
-        val uwStr = stmt.weights.variables.zipWithIndex.flatMap {
-          case(s: ConstExpr, i) => None
-          case(s: Expr, i) => Some(qc.compileExpr(s) + s""" AS "dd_weight_column_${i}\"""")
-        } mkString("\n     , ")
-
-        val selectStr = List(varInBody, uwStr).filterNot(_.isEmpty).mkString(", ")
+
+        // weight columns
+        val weightColumns = stmt.weights.variables.zipWithIndex collect {
+          case (s: Expr, i) if !s.isInstanceOf[ConstExpr] =>
+            qc.compileExpr(s) + s""" AS "dd_weight_column_${i}\""""
+        }
 
         // factor input query
-        s"""SELECT ${selectStr}\n${qc.generateSQLBody(fakeBody) }"""
+        s"""SELECT ${(variableIdColumns ++ weightColumns) mkString ("\n     , ")
+        }\n${qc.generateSQLBody(fakeBody) }"""
       }
 
     // factor function
     val func = {
-      val funcBody = (headAsBody zip stmt.head.variables map { case(x, y) =>
+      val funcBody = headAsBody zip stmt.head.variables map { case (x, y) =>
         s"""${if (y.isNegated) "!" else ""}${x.name}.R${headAsBody indexOf x}.label"""
-      })
+      }
 
       val categoricalVars = stmt.head.variables filter { t => isCategoricalRelation(t.atom.name) }
       val isMultinomialFactor =
@@ -551,7 +542,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     }
 
     List(s"deepdive.inference.factors.${resolveInferenceBlockName(stmt)}" -> Map(
-        "input_query" -> QuotedString(inputQueries.mkString(" UNION ALL ")),
+        "input_query" -> QuotedString("\n"+inputQueries.mkString(" UNION ALL ")+"\n"),
         "function" -> QuotedString(func),
         "weight" -> QuotedString(weight),
         "input_relations" -> {
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index 545b51c7b..e47d5678e 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -3,12 +3,14 @@ deepdive.schema.variables {
 }
 
 deepdive.extraction.extractors.ext_T {
-sql: """SELECT R0.x[3] AS column_0
+sql: """
+SELECT R0.x[3] AS column_0
      , R1.x AS column_1
 FROM R R0
    , S R1
 WHERE R0.x[1] = R1.y[1]
-  AND R0.x[2] = R1.y[2]"""
+  AND R0.x[2] = R1.y[2]
+"""
 input_relations: [
   R
   S
@@ -20,10 +22,12 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_U {
-sql: """SELECT R1.x AS column_0
+sql: """
+SELECT R1.x AS column_0
 FROM R R0
    , S R1
-WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]"""
+WHERE (R1.x + f(R1.x + 1)[(R1.x + R0.x[1])]) = R1.y[R1.x]
+"""
 input_relations: [
   R
   S
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 0417a607b..8a6cdb9bb 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -7,7 +7,8 @@ tag: Categorical
 }
 
 deepdive.extraction.extractors.ext_chunk {
-sql: """SELECT R0.sent_id AS column_0
+sql: """
+SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R1.tag AS column_2
      , 
@@ -15,7 +16,8 @@ CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS column_3
 FROM words R0
-   , tags R1"""
+   , tags R1
+"""
 input_relations: [
   words
   tags
@@ -27,7 +29,8 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_words {
-sql: """SELECT R0.sent_id AS column_0
+sql: """
+SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R0.word AS column_2
      , R0.pos AS column_3
@@ -39,7 +42,8 @@ CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
      WHEN R0.true_tag = 'O' THEN 'O'
      ELSE NULL
 END AS column_5
-FROM words_raw R0"""
+FROM words_raw R0
+"""
 input_relations: [
   words_raw
 ]
@@ -58,7 +62,8 @@ style: tsv_extractor
 output_relation: word_features
 udf: """udf/ext_features.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sent_id AS column_0
+input: """
+SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R0.word AS column_2
      , R0.pos AS column_3
@@ -68,12 +73,15 @@ FROM words R0
    , words R1
 WHERE R1.sent_id = R0.sent_id
   AND R0.word_id = (R1.word_id + 1)
-  AND R0.word IS NOT NULL"""
+  AND R0.word IS NOT NULL
+"""
 
 }
 
 deepdive.inference.factors.inf_istrue_chunk {
-input_query: """SELECT R0.id AS "chunk.R0.id", R3.feature AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "chunk.R0.id"
+     , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
 FROM chunk R0
    , words R1
@@ -83,7 +91,8 @@ WHERE R1.sent_id = R0.sent_id
   AND R1.word_id = R0.word_id
   AND R2.tag = R0.tag
   AND R3.sent_id = R0.sent_id
-  AND R3.word_id = R0.word_id"""
+  AND R3.word_id = R0.word_id
+"""
 function: """Multinomial(chunk.R0.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
@@ -96,8 +105,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_and_chunk_chunk {
-input_query: """SELECT R0.id AS "chunk.R0.id"
-     , R1.id AS "chunk.R1.id", R0.tag AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "chunk.R0.id"
+     , R1.id AS "chunk.R1.id"
+     , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM chunk R0
    , chunk R1
@@ -112,7 +123,8 @@ WHERE R1.sent_id = R0.sent_id
   AND R3.word_id = R1.word_id
   AND R4.tag = R0.tag
   AND R5.tag = R1.tag
-  AND R1.word_id = (R0.word_id + 1)"""
+  AND R1.word_id = (R0.word_id + 1)
+"""
 function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
@@ -124,8 +136,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf1_and_chunk_chunk {
-input_query: """SELECT R0.id AS "chunk.R0.id"
-     , R1.id AS "chunk.R1.id", R0.tag AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "chunk.R0.id"
+     , R1.id AS "chunk.R1.id"
+     , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM chunk R0
    , chunk R1
@@ -141,7 +155,8 @@ WHERE R1.sent_id = R0.sent_id
   AND R4.tag = R0.tag
   AND R5.tag = R1.tag
   AND R2.tag IS NOT NULL
-  AND R0.word_id < R1.word_id"""
+  AND R0.word_id < R1.word_id
+"""
 function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 595f69334..7addcc6c6 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -3,7 +3,8 @@ deepdive.schema.variables {
 }
 
 deepdive.extraction.extractors.ext_Q {
-sql: """SELECT DISTINCT ('test' :: TEXT) AS column_0
+sql: """
+SELECT DISTINCT ('test' :: TEXT) AS column_0
      , 123 AS column_1
      , R0.k AS column_2
      , unnest(R1.q) AS column_3
@@ -14,7 +15,8 @@ WHERE R1.k = R0.k
   AND R2.s = R1.p || R1.q
   AND R2.n = 10
   AND R2.t = 'foo'
-  AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))"""
+  AND (R1.r > 100 OR (NOT R1.r < 20 AND R1.r < 50))
+"""
 input_relations: [
   a
   b
@@ -27,14 +29,16 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_P {
-sql: """SELECT R1.p AS column_0
+sql: """
+SELECT R1.p AS column_0
      , R1.q AS column_1
      , MAX(R1.r) AS column_2
 FROM a R0
    , b R1
 WHERE R1.k = R0.k
 GROUP BY R1.p
-    , R1.q"""
+    , R1.q
+"""
 input_relations: [
   a
   b
@@ -46,8 +50,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_A {
-sql: """SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
-FROM b R0"""
+sql: """
+SELECT R0.k + (R0.r * (R0.k + R0.r)) AS column_0
+FROM b R0
+"""
 input_relations: [
   b
 ]
@@ -58,8 +64,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_B {
-sql: """SELECT func(R0.k + (R0.r + R0.k)) AS column_0
-FROM b R0"""
+sql: """
+SELECT func(R0.k + (R0.r + R0.k)) AS column_0
+FROM b R0
+"""
 input_relations: [
   b
 ]
@@ -70,8 +78,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_C {
-sql: """SELECT func(func(func(R0.k))) AS column_0
-FROM b R0"""
+sql: """
+SELECT func(func(func(R0.k))) AS column_0
+FROM b R0
+"""
 input_relations: [
   b
 ]
@@ -82,8 +92,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_D {
-sql: """SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
-FROM b R0"""
+sql: """
+SELECT func(R0.k * func2(R0.r + R0.k)) + R0.k AS column_0
+FROM b R0
+"""
 input_relations: [
   b
 ]
@@ -94,8 +106,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_E {
-sql: """SELECT (R0.k :: INT) AS column_0
-FROM b R0"""
+sql: """
+SELECT (R0.k :: INT) AS column_0
+FROM b R0
+"""
 input_relations: [
   b
 ]
@@ -106,8 +120,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_F {
-sql: """SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
-FROM b R0"""
+sql: """
+SELECT (R0.k :: INT) + (R0.r :: INT) AS column_0
+FROM b R0
+"""
 input_relations: [
   b
 ]
@@ -118,9 +134,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_G {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
-WHERE (R0.k + R0.r) = 100"""
+WHERE (R0.k + R0.r) = 100
+"""
 input_relations: [
   b
 ]
@@ -131,10 +149,12 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_H {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
 WHERE (R0.k + R0.r) = 100
-  AND R0.k > 50"""
+  AND R0.k > 50
+"""
 input_relations: [
   b
 ]
@@ -145,9 +165,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_I {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
-WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))"""
+WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
+"""
 input_relations: [
   b
 ]
@@ -158,9 +180,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_J {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
-WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)"""
+WHERE ((R0.k + R0.r) = 100 OR NOT R0.k > 50)
+"""
 input_relations: [
   b
 ]
@@ -171,9 +195,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_K {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
-WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))"""
+WHERE ((R0.k + R0.r) = 100 AND (NOT R0.k > 50 OR R0.k = 40))
+"""
 input_relations: [
   b
 ]
@@ -184,9 +210,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_L {
-sql: """SELECT DISTINCT R0.k AS column_0
+sql: """
+SELECT DISTINCT R0.k AS column_0
 FROM b R0
-LIMIT 100"""
+LIMIT 100
+"""
 input_relations: [
   b
 ]
@@ -197,9 +225,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_M {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
-WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k)"""
+WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k)
+"""
 input_relations: [
   b
   c
@@ -211,10 +241,12 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_N {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
 WHERE EXISTS (SELECT 1 FROM c R1_0 WHERE R1_0.n = R0.k
-  AND R1_0.s > 'a')"""
+  AND R1_0.s > 'a')
+"""
 input_relations: [
   b
   c
@@ -226,11 +258,13 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_O {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
 WHERE EXISTS (SELECT 1 FROM c R1_0
    , a R1_1 WHERE R1_0.n = R0.k
-  AND R1_1.k = R0.k)"""
+  AND R1_1.k = R0.k)
+"""
 input_relations: [
   b
   c
@@ -243,10 +277,12 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_S {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
 LEFT OUTER JOIN c R1_0
-  ON R1_0.n = R0.k"""
+  ON R1_0.n = R0.k
+"""
 input_relations: [
   b
   c
@@ -258,12 +294,14 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_T {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
 LEFT OUTER JOIN c R1_0
   ON R1_0.n = R0.k
   AND R1_0.s > R0.p
-WHERE R1_0.s > R0.p"""
+WHERE R1_0.s > R0.p
+"""
 input_relations: [
   b
   c
@@ -275,11 +313,13 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_U {
-sql: """SELECT R0_0.k AS column_0
+sql: """
+SELECT R0_0.k AS column_0
 FROM b R0_0
   ON 
 FULL OUTER JOIN c R1_0
-  ON R1_0.n = R0_0.k"""
+  ON R1_0.n = R0_0.k
+"""
 input_relations: [
   b
   c
@@ -291,9 +331,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_W {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM a R0
-WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))"""
+WHERE NOT EXISTS (SELECT 1 FROM c R1_0 WHERE NOT (R1_0.n < R0.k))
+"""
 input_relations: [
   a
   c
@@ -305,10 +347,12 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_V {
-sql: """SELECT R0.n AS column_0
+sql: """
+SELECT R0.n AS column_0
 FROM c R0
    , a R1
-WHERE R1.k = R0.n"""
+WHERE R1.k = R0.n
+"""
 input_relations: [
   c
   a
@@ -320,10 +364,12 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_X {
-sql: """SELECT R0.k AS column_0
+sql: """
+SELECT R0.k AS column_0
 FROM b R0
    , c R1
-WHERE R1.n = R0.k"""
+WHERE R1.n = R0.k
+"""
 input_relations: [
   b
   c
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index ef3425b89..5935a7ec9 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -5,13 +5,16 @@ Q.label: Boolean
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
-input_query: """SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id", R1.x AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id"
+     , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
    , R R2
 WHERE R2.a = R0.x
-  AND R2.b = R1.x"""
+  AND R2.b = R1.x
+"""
 function: """Imply(Q.R0.label, Q.R1.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -22,13 +25,16 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_equal_Q_Q {
-input_query: """SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id", R1.x AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id"
+     , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
    , R R2
 WHERE R2.a = R0.x
-  AND R2.b = R1.x"""
+  AND R2.b = R1.x
+"""
 function: """Equal(Q.R0.label, !Q.R1.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 570f9642f..5826599cd 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -4,13 +4,15 @@ q.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_q {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
      , 
 CASE WHEN R0.l > 0 THEN true
      WHEN R0.l < 0 THEN false
      ELSE NULL
 END AS column_1
-FROM labels_resolved R0"""
+FROM labels_resolved R0
+"""
 input_relations: [
   labels_resolved
 ]
@@ -21,7 +23,8 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_p {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
      , 
 CASE WHEN abs(R0.l) > 10 THEN true
      ELSE false
@@ -33,7 +36,8 @@ SELECT R0.x AS column_0
 CASE WHEN (R0.x % 10) = 0 THEN false
      ELSE 
 END AS column_1
-FROM labels R0"""
+FROM labels R0
+"""
 input_relations: [
   labels
 ]
@@ -44,14 +48,16 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_labels_resolved {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
      , SUM(
 CASE WHEN R0.l IS NULL THEN 0
      WHEN R0.l = true THEN 1
      ELSE -1
 END) AS column_1
 FROM labels R0
-GROUP BY R0.x"""
+GROUP BY R0.x
+"""
 input_relations: [
   labels
 ]
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 0467cc9e5..be9e32dcd 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -5,9 +5,11 @@ Q.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_P {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
 FROM data R0
-WHERE R0.y = 1"""
+WHERE R0.y = 1
+"""
 input_relations: [
   data
 ]
@@ -18,9 +20,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_Q {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
 FROM data R0
-WHERE R0.y = 2"""
+WHERE R0.y = 2
+"""
 input_relations: [
   data
 ]
@@ -31,12 +35,14 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_imply_P_Q {
-input_query: """SELECT R0.id AS "P.R0.id"
+input_query: """
+SELECT R0.id AS "P.R0.id"
      , R1.id AS "Q.R1.id"
 FROM P R0
    , Q R1
 WHERE R1.x = R0.x
-  AND true"""
+  AND true
+"""
 function: """Imply(P.R0.label, Q.R1.label)"""
 weight: """1"""
 input_relations: [
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index 80efcfe26..94d24f55e 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -5,8 +5,10 @@ TQ.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_V {
-sql: """SELECT R0.x AS column_0
-FROM D R0"""
+sql: """
+SELECT R0.x AS column_0
+FROM D R0
+"""
 input_relations: [
   D
 ]
@@ -17,9 +19,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_VQ {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
      , true AS column_1
-FROM D R0"""
+FROM D R0
+"""
 input_relations: [
   D
 ]
@@ -30,8 +34,10 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_T {
-sql: """SELECT R0.x AS column_0
-FROM D R0"""
+sql: """
+SELECT R0.x AS column_0
+FROM D R0
+"""
 input_relations: [
   D
 ]
@@ -42,12 +48,14 @@ materialize: true
 }
 
 deepdive.extraction.extractors.ext_TQ {
-sql: """SELECT R0.x AS column_0
+sql: """
+SELECT R0.x AS column_0
      , 
 CASE WHEN length(R0.x) > 5 THEN true
      ELSE NULL
 END AS column_1
-FROM D R0"""
+FROM D R0
+"""
 input_relations: [
   D
 ]
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 33b89e6d6..434557bb1 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -4,7 +4,8 @@ Q.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_S {
-sql: """SELECT R0.a AS column_0
+sql: """
+SELECT R0.a AS column_0
 FROM R R0
    , R R1
 WHERE R1.a = R0.b
@@ -29,7 +30,8 @@ SELECT R0.a AS column_0
 FROM S_1 R0
 UNION ALL
 SELECT R0.a AS column_0
-FROM S_2 R0"""
+FROM S_2 R0
+"""
 input_relations: [
   R
   S_0
@@ -51,15 +53,18 @@ style: tsv_extractor
 output_relation: T___0
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
 FROM R R0
-WHERE R0.a > 1000"""
+WHERE R0.a > 1000
+"""
 
 }
 
 deepdive.extraction.extractors.ext_T {
-sql: """SELECT R0.a AS column_0
+sql: """
+SELECT R0.a AS column_0
 FROM T___0 R0
 UNION ALL
 SELECT R0.a AS column_0
@@ -69,7 +74,8 @@ SELECT R0.a AS column_0
 FROM T___2 R0
 UNION ALL
 SELECT R0.a AS column_0
-FROM T___3 R0"""
+FROM T___3 R0
+"""
 input_relations: [
   T___0
   T___1
@@ -91,11 +97,13 @@ style: tsv_extractor
 output_relation: T___1
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
 FROM R R0
 WHERE 10 < R0.a
-  AND R0.a < 20"""
+  AND R0.a < 20
+"""
 
 }
 
@@ -108,11 +116,13 @@ style: tsv_extractor
 output_relation: T___2
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
 FROM R R0
 WHERE 100 < R0.a
-  AND R0.a < 200"""
+  AND R0.a < 200
+"""
 
 }
 
@@ -125,10 +135,12 @@ style: tsv_extractor
 output_relation: S_0
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
 FROM R R0
-WHERE R0.a < 0"""
+WHERE R0.a < 0
+"""
 
 }
 
@@ -141,10 +153,12 @@ style: tsv_extractor
 output_relation: S_1
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
 FROM R R0
-WHERE R0.a > 0"""
+WHERE R0.a > 0
+"""
 
 }
 
@@ -157,9 +171,11 @@ style: tsv_extractor
 output_relation: T___3
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
-FROM R R0"""
+FROM R R0
+"""
 
 }
 
@@ -172,19 +188,24 @@ style: tsv_extractor
 output_relation: S_2
 udf: """/bin/false"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.a AS column_0
+input: """
+SELECT R0.a AS column_0
      , R0.b AS column_1
 FROM R R0
-WHERE R0.a > 0"""
+WHERE R0.a > 0
+"""
 
 }
 
 deepdive.inference.factors.inf_istrue_Q {
-input_query: """SELECT R0.id AS "Q.R0.id", R0.x AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "Q.R0.id"
+     , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , S R1
 WHERE R1.a = R0.x
-  AND R0.x > 1000"""
+  AND R0.x > 1000
+"""
 function: """Imply(Q.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -195,11 +216,13 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf1_istrue_Q {
-input_query: """SELECT R0.id AS "Q.R0.id"
+input_query: """
+SELECT R0.id AS "Q.R0.id"
 FROM Q R0
    , S R1
 WHERE R1.a = R0.x
-  AND R0.x = 0"""
+  AND R0.x = 0
+"""
 function: """Imply(Q.R0.label)"""
 weight: """1.0"""
 input_relations: [
@@ -210,8 +233,10 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
-input_query: """SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id", R0.x AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "Q.R0.id"
+     , R1.id AS "Q.R1.id"
+     , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
    , S R2
@@ -220,7 +245,8 @@ FROM Q R0
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
-  AND R4.a = R1.x"""
+  AND R4.a = R1.x
+"""
 function: """Imply(Q.R0.label, Q.R1.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -232,7 +258,8 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf1_imply_Q_Q {
-input_query: """SELECT R0.id AS "Q.R0.id"
+input_query: """
+SELECT R0.id AS "Q.R0.id"
      , R1.id AS "Q.R1.id"
 FROM Q R0
    , Q R1
@@ -243,7 +270,8 @@ WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
-  AND (R0.x + R1.x) < 1000"""
+  AND (R0.x + R1.x) < 1000
+"""
 function: """Imply(Q.R0.label, Q.R1.label)"""
 weight: """-10.0"""
 input_relations: [
@@ -255,8 +283,10 @@ input_relations: [
 }
 
 deepdive.extraction.extractors.ext_T__3 {
-sql: """SELECT R0.a AS column_0
-FROM T R0"""
+sql: """
+SELECT R0.a AS column_0
+FROM T R0
+"""
 input_relations: [
   T
 ]
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 377356988..b146831c5 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -5,9 +5,11 @@ q2.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_q1 {
-sql: """SELECT R0.wid AS column_0
+sql: """
+SELECT R0.wid AS column_0
      , R0.val AS column_1
-FROM label1 R0"""
+FROM label1 R0
+"""
 input_relations: [
   label1
 ]
@@ -18,9 +20,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_q2 {
-sql: """SELECT R0.wid AS column_0
+sql: """
+SELECT R0.wid AS column_0
      , R0.val AS column_1
-FROM label2 R0"""
+FROM label2 R0
+"""
 input_relations: [
   label2
 ]
@@ -31,10 +35,13 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_istrue_q1 {
-input_query: """SELECT R0.id AS "q1.R0.id", R1.feature_id AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "q1.R0.id"
+     , R1.feature_id AS "dd_weight_column_0"
 FROM q1 R0
    , features R1
-WHERE R1.word_id = R0.wid"""
+WHERE R1.word_id = R0.wid
+"""
 function: """Imply(q1.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -45,10 +52,13 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_q2 {
-input_query: """SELECT R0.id AS "q2.R0.id", R1.feature_id AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "q2.R0.id"
+     , R1.feature_id AS "dd_weight_column_0"
 FROM q2 R0
    , features R1
-WHERE R1.word_id = R0.wid"""
+WHERE R1.word_id = R0.wid
+"""
 function: """Imply(q2.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 3840faf69..b7933bd6e 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -5,9 +5,11 @@ cancer.label: Boolean
 }
 
 deepdive.extraction.extractors.ext_smoke {
-sql: """SELECT R0.person_id AS column_0
+sql: """
+SELECT R0.person_id AS column_0
      , R0.smokes AS column_1
-FROM person_smokes R0"""
+FROM person_smokes R0
+"""
 input_relations: [
   person_smokes
 ]
@@ -18,9 +20,11 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_cancer {
-sql: """SELECT R0.person_id AS column_0
+sql: """
+SELECT R0.person_id AS column_0
      , R0.has_cancer AS column_1
-FROM person_has_cancer R0"""
+FROM person_has_cancer R0
+"""
 input_relations: [
   person_has_cancer
 ]
@@ -31,13 +35,15 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_imply_smoke_cancer {
-input_query: """SELECT R0.id AS "smoke.R0.id"
+input_query: """
+SELECT R0.id AS "smoke.R0.id"
      , R1.id AS "cancer.R1.id"
 FROM smoke R0
    , cancer R1
    , person_smokes R2
 WHERE R1.person_id = R0.person_id
-  AND R2.person_id = R0.person_id"""
+  AND R2.person_id = R0.person_id
+"""
 function: """Imply(smoke.R0.label, cancer.R1.label)"""
 weight: """0.5"""
 input_relations: [
@@ -49,13 +55,15 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_imply_smoke_smoke {
-input_query: """SELECT R0.id AS "smoke.R0.id"
+input_query: """
+SELECT R0.id AS "smoke.R0.id"
      , R1.id AS "smoke.R1.id"
 FROM smoke R0
    , smoke R1
    , friends R2
 WHERE R2.person_id = R0.person_id
-  AND R2.friend_id = R1.person_id"""
+  AND R2.friend_id = R1.person_id
+"""
 function: """Imply(smoke.R0.label, smoke.R1.label)"""
 weight: """0.4"""
 input_relations: [
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 9a22bc542..9f6f34dc6 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -12,10 +12,12 @@ style: tsv_extractor
 output_relation: people_mentions
 udf: """udf/ext_people.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sentence_id AS column_0
+input: """
+SELECT R0.sentence_id AS column_0
      , ARRAY_TO_STRING(R0.words, '~^~') AS column_1
      , ARRAY_TO_STRING(R0.ner_tags, '~^~') AS column_2
-FROM sentences R0"""
+FROM sentences R0
+"""
 
 }
 
@@ -28,14 +30,16 @@ style: tsv_extractor
 output_relation: has_spouse_candidates
 udf: """udf/ext_has_spouse.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT R0.sentence_id AS column_0
+input: """
+SELECT R0.sentence_id AS column_0
      , R0.mention_id AS column_1
      , R0.text AS column_2
      , R1.mention_id AS column_3
      , R1.text AS column_4
 FROM people_mentions R0
    , people_mentions R1
-WHERE R1.sentence_id = R0.sentence_id"""
+WHERE R1.sentence_id = R0.sentence_id
+"""
 
 }
 
@@ -50,7 +54,8 @@ style: tsv_extractor
 output_relation: has_spouse_features
 udf: """udf/ext_has_spouse_features.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
-input: """SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0
+input: """
+SELECT ARRAY_TO_STRING(R0.words, '~^~') AS column_0
      , R1.relation_id AS column_1
      , R2.start_position AS column_2
      , R2.length AS column_3
@@ -64,14 +69,17 @@ WHERE R1.sentence_id = R0.sentence_id
   AND R2.sentence_id = R0.sentence_id
   AND R2.mention_id = R1.person1_id
   AND R3.sentence_id = R0.sentence_id
-  AND R3.mention_id = R1.person2_id"""
+  AND R3.mention_id = R1.person2_id
+"""
 
 }
 
 deepdive.extraction.extractors.ext_has_spouse {
-sql: """SELECT R0.relation_id AS column_0
+sql: """
+SELECT R0.relation_id AS column_0
      , R0.is_true AS column_1
-FROM has_spouse_candidates R0"""
+FROM has_spouse_candidates R0
+"""
 input_relations: [
   has_spouse_candidates
 ]
@@ -82,12 +90,15 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_istrue_has_spouse {
-input_query: """SELECT R0.id AS "has_spouse.R0.id", R2.feature AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "has_spouse.R0.id"
+     , R2.feature AS "dd_weight_column_0"
 FROM has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
 WHERE R1.relation_id = R0.relation_id
-  AND R2.relation_id = R0.relation_id"""
+  AND R2.relation_id = R0.relation_id
+"""
 function: """Imply(has_spouse.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 5607f956b..541295d7f 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -3,9 +3,11 @@ deepdive.schema.variables {
 }
 
 deepdive.extraction.extractors.ext_A {
-sql: """SELECT R0.a AS column_0
+sql: """
+SELECT R0.a AS column_0
      , R0.a + R0.b AS column_1
-FROM R R0"""
+FROM R R0
+"""
 input_relations: [
   R
 ]
@@ -16,11 +18,13 @@ materialize: false
 }
 
 deepdive.extraction.extractors.ext_B {
-sql: """SELECT R0.column_0 AS column_0
+sql: """
+SELECT R0.column_0 AS column_0
      , R1.b AS column_1
 FROM A R0
    , R R1
-WHERE R1.a = R0.column_1"""
+WHERE R1.a = R0.column_1
+"""
 input_relations: [
   A
   R
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 515326352..e09be42b1 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -8,10 +8,13 @@ f.label: Boolean
 }
 
 deepdive.inference.factors.inf_istrue_a {
-input_query: """SELECT R0.id AS "a.R0.id", R0.k + R1.p AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "a.R0.id"
+     , R0.k + R1.p AS "dd_weight_column_0"
 FROM a R0
    , b R1
-WHERE R1.k = R0.k"""
+WHERE R1.k = R0.k
+"""
 function: """Imply(a.R0.label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
@@ -22,10 +25,12 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_c {
-input_query: """SELECT R0.id AS "c.R0.id"
+input_query: """
+SELECT R0.id AS "c.R0.id"
 FROM c R0
    , b R1
-WHERE R1.k = R0.k"""
+WHERE R1.k = R0.k
+"""
 function: """Imply(c.R0.label)"""
 weight: """?"""
 input_relations: [
@@ -36,11 +41,14 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_d {
-input_query: """SELECT R0.id AS "d.R0.id", R0.k AS "dd_weight_column_0"
+input_query: """
+SELECT R0.id AS "d.R0.id"
+     , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
 FROM d R0
    , b R1
-WHERE R1.k = R0.k"""
+WHERE R1.k = R0.k
+"""
 function: """Imply(d.R0.label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
@@ -51,10 +59,12 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_e {
-input_query: """SELECT R0.id AS "e.R0.id"
+input_query: """
+SELECT R0.id AS "e.R0.id"
 FROM e R0
    , b R1
-WHERE R1.k = R0.k"""
+WHERE R1.k = R0.k
+"""
 function: """Imply(e.R0.label)"""
 weight: """-10"""
 input_relations: [
@@ -65,10 +75,12 @@ input_relations: [
 }
 
 deepdive.inference.factors.inf_istrue_f {
-input_query: """SELECT R0.id AS "f.R0.id"
+input_query: """
+SELECT R0.id AS "f.R0.id"
 FROM f R0
    , b R1
-WHERE R1.k = R0.k"""
+WHERE R1.k = R0.k
+"""
 function: """Imply(f.R0.label)"""
 weight: """-0.3"""
 input_relations: [

From 749ea862a9e436a40a8c4aca6cdc257d153f64a9 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 4 Mar 2016 08:29:31 -0800
Subject: [PATCH 314/347] Factors out compiler constants, id -> dd_id, label ->
 dd_label

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 32 ++++++++++++-------
 .../ddlog/DeepDiveLogSemanticChecker.scala    |  3 +-
 .../compile-error.expected                    |  4 +--
 .../invalid_variable_schema/input.ddlog       |  2 +-
 .../chunking_example/compile.expected         | 16 +++++-----
 .../factor_functions/compile.expected         | 16 +++++-----
 .../if-then-else/compile.expected             |  2 +-
 .../logical_rules/compile.expected            | 10 +++---
 .../materialize_annotation/compile.expected   |  4 +--
 .../compile.expected                          | 22 ++++++-------
 .../ocr_example/compile.expected              | 12 +++----
 .../smoke_example/compile.expected            | 16 +++++-----
 .../spouse_example/compile.expected           |  6 ++--
 .../weights/compile.expected                  | 30 ++++++++---------
 14 files changed, 92 insertions(+), 83 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 58cb7366b..af4b3b005 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -8,9 +8,7 @@ import scala.language.postfixOps
 
 // Compiler that takes parsed program as input and turns into blocks of deepdive.conf
 class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.Config ) {
-  type CompiledBlocks = List[(String, Any)]  // TODO be more specific
-
-  case class QuotedString(value: String)
+  import DeepDiveLogCompiler._
 
   val statements = program
 
@@ -181,9 +179,9 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         val relation = variable.relName
         s""" AS "${relation}.R${index}.${name}\""""
       }
-      case _ => s" AS column_${cq.headTerms indexOf e}"
+      case _ => s" AS ${deepdiveViewOrderedColumnPrefix}${cq.headTerms indexOf e}"
     }
-    case ViewAlias => s" AS column_${cq.headTerms indexOf e}"
+    case ViewAlias => s" AS ${deepdiveViewOrderedColumnPrefix}${cq.headTerms indexOf e}"
     case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}\""""
   }
 
@@ -426,7 +424,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
       stmts map { case stmt => stmt.q.copy(
         headTerms = stmt.q.headTerms :+ stmt.supervision,
         headTermAliases = {
-          stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ :+ Some("label") }
+          stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ :+ Some(deepdiveVariableLabelColumn) }
         },
         isDistinct = false // XXX no need to take DISTINCT here since DeepDive will have to do it anyway
       ) }
@@ -468,7 +466,8 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     val variableIdColumns = headAsBody.zipWithIndex collect {
       case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
         // TODO maybe TableAlias can be useful here or we can completely get rid of it?
-        s"""R${headAsBody indexOf x}.id AS "${x.name}.R${headAsBody indexOf x}.id\""""
+        s"""R${headAsBody indexOf x}.${deepdiveVariableIdColumn
+          } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\""""
     }
 
     val inputQueries =
@@ -483,7 +482,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         // weight columns
         val weightColumns = stmt.weights.variables.zipWithIndex collect {
           case (s: Expr, i) if !s.isInstanceOf[ConstExpr] =>
-            qc.compileExpr(s) + s""" AS "dd_weight_column_${i}\""""
+            s"""${qc.compileExpr(s)} AS "${deepdiveWeightColumnPrefix}${i}\""""
         }
 
         // factor input query
@@ -494,7 +493,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
     // factor function
     val func = {
       val funcBody = headAsBody zip stmt.head.variables map { case (x, y) =>
-        s"""${if (y.isNegated) "!" else ""}${x.name}.R${headAsBody indexOf x}.label"""
+        s"""${if (y.isNegated) "!" else ""}${x.name}.R${headAsBody indexOf x}.${deepdiveVariableLabelColumn}"""
       }
 
       val categoricalVars = stmt.head.variables filter { t => isCategoricalRelation(t.atom.name) }
@@ -534,7 +533,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         case StringConst(value) => "?"
         case _ => {
           val weightVars = stmt.weights.variables.zipWithIndex.flatMap {
-            case(s: Expr, i) => Some(s"dd_weight_column_${i}")
+            case(s: Expr, i) => Some(s"${deepdiveWeightColumnPrefix}${i}")
           } mkString(", ")
           s"?(${weightVars})"
         }
@@ -584,7 +583,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         if (isCategoricalRelation(decl.a.name)) {
           decl.a.name -> (decl.categoricalColumns map (_ -> "Categorical") toMap)
         } else // Boolean variables
-          s"${decl.a.name}.label" -> "Boolean"
+          s"${decl.a.name}.${deepdiveVariableLabelColumn}" -> "Boolean"
       } toMap)
     )
   }
@@ -601,6 +600,15 @@ class QueryCompiler(cq : ConjunctiveQuery) {
 
 object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
+  type CompiledBlocks = List[(String, Any)]  // TODO be more specific
+  case class QuotedString(value: String)
+
+  // some of the reserved names used in compilation
+  val deepdiveViewOrderedColumnPrefix = "column_"
+  val deepdiveWeightColumnPrefix = "dd_weight_column_"
+  val deepdiveVariableIdColumn = "dd_id"
+  val deepdiveVariableLabelColumn = "dd_label"
+
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
     // don't compile if it doesn't pass all semantic checks
@@ -615,7 +623,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
     // codegen HOCON
     def codegenValue(value: Any): String = value match {
-      case compiler.QuotedString(s) => // multi-line string
+      case QuotedString(s) => // multi-line string
         s"""\"\"\"${s replaceAll("\"\"\"", "\\\"\\\"\\\"")}\"\"\""""
       case _ =>
         value.toString
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index acbf5fd0c..081f4f2cc 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -86,7 +86,8 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
 
   // check if the user use reserved column names
   def checkVariableRelationSchema(stmt: Statement) {
-    val reservedSet = Set("label")
+    import DeepDiveLogCompiler._
+    val reservedSet = Set(deepdiveVariableIdColumn, deepdiveVariableLabelColumn)
     stmt match {
       case decl: SchemaDeclaration => {
         if (decl.isQuery) {
diff --git a/test/compile-error-test/invalid_variable_schema/compile-error.expected b/test/compile-error-test/invalid_variable_schema/compile-error.expected
index 09335356f..910fef8d2 100644
--- a/test/compile-error-test/invalid_variable_schema/compile-error.expected
+++ b/test/compile-error-test/invalid_variable_schema/compile-error.expected
@@ -1,5 +1,5 @@
-[error] variable relation contains reserved column "label" 
-c?(label int,
+[error] variable relation contains reserved column "dd_label" 
+c?(dd_label int,
    s text,
    n int,
    t text).
diff --git a/test/compile-error-test/invalid_variable_schema/input.ddlog b/test/compile-error-test/invalid_variable_schema/input.ddlog
index 61f225b66..d2a1ba60c 100644
--- a/test/compile-error-test/invalid_variable_schema/input.ddlog
+++ b/test/compile-error-test/invalid_variable_schema/input.ddlog
@@ -1,5 +1,5 @@
 a(k int).
 b(k int, p text, q text, r int).
-c?(label int, s text, n int, t text).
+c?(dd_label int, s text, n int, t text).
 
 Q(y, z) :- a(x), d(x,y,z,w).
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 8a6cdb9bb..6f022087e 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -80,7 +80,7 @@ WHERE R1.sent_id = R0.sent_id
 
 deepdive.inference.factors.inf_istrue_chunk {
 input_query: """
-SELECT R0.id AS "chunk.R0.id"
+SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
 FROM chunk R0
@@ -93,7 +93,7 @@ WHERE R1.sent_id = R0.sent_id
   AND R3.sent_id = R0.sent_id
   AND R3.word_id = R0.word_id
 """
-function: """Multinomial(chunk.R0.label)"""
+function: """Multinomial(chunk.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
@@ -106,8 +106,8 @@ input_relations: [
 
 deepdive.inference.factors.inf_and_chunk_chunk {
 input_query: """
-SELECT R0.id AS "chunk.R0.id"
-     , R1.id AS "chunk.R1.id"
+SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R1.dd_id AS "chunk.R1.dd_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM chunk R0
@@ -125,7 +125,7 @@ WHERE R1.sent_id = R0.sent_id
   AND R5.tag = R1.tag
   AND R1.word_id = (R0.word_id + 1)
 """
-function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
+function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
@@ -137,8 +137,8 @@ input_relations: [
 
 deepdive.inference.factors.inf1_and_chunk_chunk {
 input_query: """
-SELECT R0.id AS "chunk.R0.id"
-     , R1.id AS "chunk.R1.id"
+SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R1.dd_id AS "chunk.R1.dd_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM chunk R0
@@ -157,7 +157,7 @@ WHERE R1.sent_id = R0.sent_id
   AND R2.tag IS NOT NULL
   AND R0.word_id < R1.word_id
 """
-function: """Multinomial(chunk.R0.label, chunk.R1.label)"""
+function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 5935a7ec9..0424c5524 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -1,13 +1,13 @@
 deepdive.schema.variables {
-S.label: Boolean
-Q.label: Boolean
+S.dd_label: Boolean
+Q.dd_label: Boolean
 
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
-SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
@@ -15,7 +15,7 @@ FROM Q R0
 WHERE R2.a = R0.x
   AND R2.b = R1.x
 """
-function: """Imply(Q.R0.label, Q.R1.label)"""
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
@@ -26,8 +26,8 @@ input_relations: [
 
 deepdive.inference.factors.inf_equal_Q_Q {
 input_query: """
-SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
@@ -35,7 +35,7 @@ FROM Q R0
 WHERE R2.a = R0.x
   AND R2.b = R1.x
 """
-function: """Equal(Q.R0.label, !Q.R1.label)"""
+function: """Equal(Q.R0.dd_label, !Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 5826599cd..ff57611ce 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -1,5 +1,5 @@
 deepdive.schema.variables {
-q.label: Boolean
+q.dd_label: Boolean
 
 }
 
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index be9e32dcd..598a46bab 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -1,6 +1,6 @@
 deepdive.schema.variables {
-P.label: Boolean
-Q.label: Boolean
+P.dd_label: Boolean
+Q.dd_label: Boolean
 
 }
 
@@ -36,14 +36,14 @@ materialize: false
 
 deepdive.inference.factors.inf_imply_P_Q {
 input_query: """
-SELECT R0.id AS "P.R0.id"
-     , R1.id AS "Q.R1.id"
+SELECT R0.dd_id AS "P.R0.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
 FROM P R0
    , Q R1
 WHERE R1.x = R0.x
   AND true
 """
-function: """Imply(P.R0.label, Q.R1.label)"""
+function: """Imply(P.R0.dd_label, Q.R1.dd_label)"""
 weight: """1"""
 input_relations: [
   P
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index 94d24f55e..905f18a95 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -1,6 +1,6 @@
 deepdive.schema.variables {
-VQ.label: Boolean
-TQ.label: Boolean
+VQ.dd_label: Boolean
+TQ.dd_label: Boolean
 
 }
 
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 434557bb1..3525d1c5c 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -1,5 +1,5 @@
 deepdive.schema.variables {
-Q.label: Boolean
+Q.dd_label: Boolean
 
 }
 
@@ -199,14 +199,14 @@ WHERE R0.a > 0
 
 deepdive.inference.factors.inf_istrue_Q {
 input_query: """
-SELECT R0.id AS "Q.R0.id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x > 1000
 """
-function: """Imply(Q.R0.label)"""
+function: """Imply(Q.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
@@ -217,13 +217,13 @@ input_relations: [
 
 deepdive.inference.factors.inf1_istrue_Q {
 input_query: """
-SELECT R0.id AS "Q.R0.id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
 FROM Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x = 0
 """
-function: """Imply(Q.R0.label)"""
+function: """Imply(Q.R0.dd_label)"""
 weight: """1.0"""
 input_relations: [
   Q
@@ -234,8 +234,8 @@ input_relations: [
 
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
-SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
@@ -247,7 +247,7 @@ WHERE R2.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
 """
-function: """Imply(Q.R0.label, Q.R1.label)"""
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
@@ -259,8 +259,8 @@ input_relations: [
 
 deepdive.inference.factors.inf1_imply_Q_Q {
 input_query: """
-SELECT R0.id AS "Q.R0.id"
-     , R1.id AS "Q.R1.id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
 FROM Q R0
    , Q R1
    , S R2
@@ -272,7 +272,7 @@ WHERE R2.a = R0.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) < 1000
 """
-function: """Imply(Q.R0.label, Q.R1.label)"""
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """-10.0"""
 input_relations: [
   Q
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index b146831c5..dc10a1832 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -1,6 +1,6 @@
 deepdive.schema.variables {
-q1.label: Boolean
-q2.label: Boolean
+q1.dd_label: Boolean
+q2.dd_label: Boolean
 
 }
 
@@ -36,13 +36,13 @@ materialize: false
 
 deepdive.inference.factors.inf_istrue_q1 {
 input_query: """
-SELECT R0.id AS "q1.R0.id"
+SELECT R0.dd_id AS "q1.R0.dd_id"
      , R1.feature_id AS "dd_weight_column_0"
 FROM q1 R0
    , features R1
 WHERE R1.word_id = R0.wid
 """
-function: """Imply(q1.R0.label)"""
+function: """Imply(q1.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   q1
@@ -53,13 +53,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_q2 {
 input_query: """
-SELECT R0.id AS "q2.R0.id"
+SELECT R0.dd_id AS "q2.R0.dd_id"
      , R1.feature_id AS "dd_weight_column_0"
 FROM q2 R0
    , features R1
 WHERE R1.word_id = R0.wid
 """
-function: """Imply(q2.R0.label)"""
+function: """Imply(q2.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   q2
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index b7933bd6e..9ab2ad4c5 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -1,6 +1,6 @@
 deepdive.schema.variables {
-smoke.label: Boolean
-cancer.label: Boolean
+smoke.dd_label: Boolean
+cancer.dd_label: Boolean
 
 }
 
@@ -36,15 +36,15 @@ materialize: false
 
 deepdive.inference.factors.inf_imply_smoke_cancer {
 input_query: """
-SELECT R0.id AS "smoke.R0.id"
-     , R1.id AS "cancer.R1.id"
+SELECT R0.dd_id AS "smoke.R0.dd_id"
+     , R1.dd_id AS "cancer.R1.dd_id"
 FROM smoke R0
    , cancer R1
    , person_smokes R2
 WHERE R1.person_id = R0.person_id
   AND R2.person_id = R0.person_id
 """
-function: """Imply(smoke.R0.label, cancer.R1.label)"""
+function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 weight: """0.5"""
 input_relations: [
   smoke
@@ -56,15 +56,15 @@ input_relations: [
 
 deepdive.inference.factors.inf_imply_smoke_smoke {
 input_query: """
-SELECT R0.id AS "smoke.R0.id"
-     , R1.id AS "smoke.R1.id"
+SELECT R0.dd_id AS "smoke.R0.dd_id"
+     , R1.dd_id AS "smoke.R1.dd_id"
 FROM smoke R0
    , smoke R1
    , friends R2
 WHERE R2.person_id = R0.person_id
   AND R2.friend_id = R1.person_id
 """
-function: """Imply(smoke.R0.label, smoke.R1.label)"""
+function: """Imply(smoke.R0.dd_label, smoke.R1.dd_label)"""
 weight: """0.4"""
 input_relations: [
   smoke
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 9f6f34dc6..58cfa80e5 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -1,5 +1,5 @@
 deepdive.schema.variables {
-has_spouse.label: Boolean
+has_spouse.dd_label: Boolean
 
 }
 
@@ -91,7 +91,7 @@ materialize: false
 
 deepdive.inference.factors.inf_istrue_has_spouse {
 input_query: """
-SELECT R0.id AS "has_spouse.R0.id"
+SELECT R0.dd_id AS "has_spouse.R0.dd_id"
      , R2.feature AS "dd_weight_column_0"
 FROM has_spouse R0
    , has_spouse_candidates R1
@@ -99,7 +99,7 @@ FROM has_spouse R0
 WHERE R1.relation_id = R0.relation_id
   AND R2.relation_id = R0.relation_id
 """
-function: """Imply(has_spouse.R0.label)"""
+function: """Imply(has_spouse.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   has_spouse
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index e09be42b1..239e3acc6 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -1,21 +1,21 @@
 deepdive.schema.variables {
-c.label: Boolean
-d.label: Boolean
-a.label: Boolean
-e.label: Boolean
-f.label: Boolean
+f.dd_label: Boolean
+c.dd_label: Boolean
+d.dd_label: Boolean
+a.dd_label: Boolean
+e.dd_label: Boolean
 
 }
 
 deepdive.inference.factors.inf_istrue_a {
 input_query: """
-SELECT R0.id AS "a.R0.id"
+SELECT R0.dd_id AS "a.R0.dd_id"
      , R0.k + R1.p AS "dd_weight_column_0"
 FROM a R0
    , b R1
 WHERE R1.k = R0.k
 """
-function: """Imply(a.R0.label)"""
+function: """Imply(a.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
 input_relations: [
   a
@@ -26,12 +26,12 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_c {
 input_query: """
-SELECT R0.id AS "c.R0.id"
+SELECT R0.dd_id AS "c.R0.dd_id"
 FROM c R0
    , b R1
 WHERE R1.k = R0.k
 """
-function: """Imply(c.R0.label)"""
+function: """Imply(c.R0.dd_label)"""
 weight: """?"""
 input_relations: [
   c
@@ -42,14 +42,14 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_d {
 input_query: """
-SELECT R0.id AS "d.R0.id"
+SELECT R0.dd_id AS "d.R0.dd_id"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
 FROM d R0
    , b R1
 WHERE R1.k = R0.k
 """
-function: """Imply(d.R0.label)"""
+function: """Imply(d.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   d
@@ -60,12 +60,12 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_e {
 input_query: """
-SELECT R0.id AS "e.R0.id"
+SELECT R0.dd_id AS "e.R0.dd_id"
 FROM e R0
    , b R1
 WHERE R1.k = R0.k
 """
-function: """Imply(e.R0.label)"""
+function: """Imply(e.R0.dd_label)"""
 weight: """-10"""
 input_relations: [
   e
@@ -76,12 +76,12 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_f {
 input_query: """
-SELECT R0.id AS "f.R0.id"
+SELECT R0.dd_id AS "f.R0.dd_id"
 FROM f R0
    , b R1
 WHERE R1.k = R0.k
 """
-function: """Imply(f.R0.label)"""
+function: """Imply(f.R0.dd_label)"""
 weight: """-0.3"""
 input_relations: [
   f

From 4485286ddd967ee49b07288344a3f707b8b077c6 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Fri, 4 Mar 2016 08:50:17 -0800
Subject: [PATCH 315/347] Fixes schema.json to use categorical in variable_type

instead of multinomial
---
 .../scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
index 7b3d99f61..a92e9dffd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSchemaExporter.scala
@@ -31,7 +31,7 @@ object DeepDiveLogSchemaExporter extends DeepDiveLogHandler {
     // what type of random variable this relation is
     if (decl.isQuery)
       schema += "variable_type" -> (
-        if (decl.categoricalColumns.size > 0) "multinomial"
+        if (decl.categoricalColumns.size > 0) "categorical"
         else "boolean"
       )
 

From a91e49351dcce79fcb86d5a5041da00bb1372362 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 16 Mar 2016 05:33:50 -0700
Subject: [PATCH 316/347] Compiles inference rules to also project key columns

so DeepDive can eliminate some unnecessary joins
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 17 ++++++++++----
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 23 ++++++++++++-------
 .../chunking_example/compile.expected         | 10 ++++++++
 .../factor_functions/compile.expected         |  4 ++++
 .../logical_rules/compile.expected            |  2 ++
 .../compile.expected                          |  6 +++++
 .../ocr_example/compile.expected              |  2 ++
 .../smoke_example/compile.expected            |  4 ++++
 .../spouse_example/compile.expected           |  1 +
 .../weights/compile.expected                  |  5 ++++
 10 files changed, 62 insertions(+), 12 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index af4b3b005..d801ebc65 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -463,11 +463,20 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   // generate inference rule part for deepdive
   def compile(stmt: InferenceRule): CompiledBlocks = {
     val headAsBody = stmt.head.variables map (_.atom)
-    val variableIdColumns = headAsBody.zipWithIndex collect {
+    val variableIdAndKeyColumns = headAsBody.zipWithIndex flatMap {
       case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
         // TODO maybe TableAlias can be useful here or we can completely get rid of it?
-        s"""R${headAsBody indexOf x}.${deepdiveVariableIdColumn
-          } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\""""
+        // variable id column
+        s"""R${headAsBody indexOf x}.${
+          deepdiveVariableIdColumn
+        } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" :: (
+          // project variable key columns as well (to reduce unnecssary joins)
+          schemaDeclarationByRelationName get x.name map (_.keyColumns map {
+            case term => s"""R${headAsBody indexOf x}.${term
+            } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
+          }) get
+        )
+      case _ => List.empty
     }
 
     val inputQueries =
@@ -486,7 +495,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         }
 
         // factor input query
-        s"""SELECT ${(variableIdColumns ++ weightColumns) mkString ("\n     , ")
+        s"""SELECT ${(variableIdAndKeyColumns ++ weightColumns) mkString ("\n     , ")
         }\n${qc.generateSQLBody(fakeBody) }"""
       }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 441caeaf2..6a391edbe 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -121,15 +121,22 @@ case class SchemaDeclaration(a: Attribute,
                              annotations: List[Annotation] = List.empty
                             ) extends Statement // atom and whether this is a query relation.
 {
-  // infer whether this is a categorical variable based on column annotations
+  // find all columns with @key annotation
+  val keyColumns = {
+    val columnsAnnotatedWithKey = a.terms.zip(a.annotations) collect {
+      case (term, annos) if annos exists (_ named "key") => term
+    }
+    // treat all columns as key if none were annotated
+    if (isQuery && (columnsAnnotatedWithKey isEmpty)) a.terms
+    // otherwise, keys should be explicitly annotated
+    else columnsAnnotatedWithKey
+  }
+  // this is a categorical variable if a strict subset of columns are annotated with @key
   val categoricalColumns =
-    if (isQuery) {
-      val keyColumns = a.terms.zip(a.annotations) collect {
-        case (term, annos) if annos exists (_.name == "key") => term
-      }
-      if (keyColumns isEmpty) List.empty  // treat all columns as key if none were annotated
-      else a.terms diff keyColumns toList  // otherwise, the rest of the columns define categories
-    } else List.empty
+    if (isQuery)
+      a.terms diff keyColumns toList
+    else
+      List.empty
 }
 case class FunctionDeclaration(functionName: String,
                                inputType: FunctionInputOutputType,
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 6f022087e..08d2acb45 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -81,6 +81,8 @@ WHERE R1.sent_id = R0.sent_id
 deepdive.inference.factors.inf_istrue_chunk {
 input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R0.sent_id AS "chunk.R0.sent_id"
+     , R0.word_id AS "chunk.R0.word_id"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
 FROM chunk R0
@@ -107,7 +109,11 @@ input_relations: [
 deepdive.inference.factors.inf_and_chunk_chunk {
 input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R0.sent_id AS "chunk.R0.sent_id"
+     , R0.word_id AS "chunk.R0.word_id"
      , R1.dd_id AS "chunk.R1.dd_id"
+     , R1.sent_id AS "chunk.R1.sent_id"
+     , R1.word_id AS "chunk.R1.word_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM chunk R0
@@ -138,7 +144,11 @@ input_relations: [
 deepdive.inference.factors.inf1_and_chunk_chunk {
 input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R0.sent_id AS "chunk.R0.sent_id"
+     , R0.word_id AS "chunk.R0.word_id"
      , R1.dd_id AS "chunk.R1.dd_id"
+     , R1.sent_id AS "chunk.R1.sent_id"
+     , R1.word_id AS "chunk.R1.word_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM chunk R0
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 0424c5524..96bec9192 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -7,7 +7,9 @@ Q.dd_label: Boolean
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
+     , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
@@ -27,7 +29,9 @@ input_relations: [
 deepdive.inference.factors.inf_equal_Q_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
+     , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 598a46bab..e9a6b2ded 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -37,7 +37,9 @@ materialize: false
 deepdive.inference.factors.inf_imply_P_Q {
 input_query: """
 SELECT R0.dd_id AS "P.R0.dd_id"
+     , R0.x AS "P.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
+     , R1.x AS "Q.R1.x"
 FROM P R0
    , Q R1
 WHERE R1.x = R0.x
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 3525d1c5c..89f4b69c8 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -200,6 +200,7 @@ WHERE R0.a > 0
 deepdive.inference.factors.inf_istrue_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , S R1
@@ -218,6 +219,7 @@ input_relations: [
 deepdive.inference.factors.inf1_istrue_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
 FROM Q R0
    , S R1
 WHERE R1.a = R0.x
@@ -235,7 +237,9 @@ input_relations: [
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
+     , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
@@ -260,7 +264,9 @@ input_relations: [
 deepdive.inference.factors.inf1_imply_Q_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
+     , R1.x AS "Q.R1.x"
 FROM Q R0
    , Q R1
    , S R2
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index dc10a1832..dc484f9ab 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -37,6 +37,7 @@ materialize: false
 deepdive.inference.factors.inf_istrue_q1 {
 input_query: """
 SELECT R0.dd_id AS "q1.R0.dd_id"
+     , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
 FROM q1 R0
    , features R1
@@ -54,6 +55,7 @@ input_relations: [
 deepdive.inference.factors.inf_istrue_q2 {
 input_query: """
 SELECT R0.dd_id AS "q2.R0.dd_id"
+     , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
 FROM q2 R0
    , features R1
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 9ab2ad4c5..22eea5eb3 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -37,7 +37,9 @@ materialize: false
 deepdive.inference.factors.inf_imply_smoke_cancer {
 input_query: """
 SELECT R0.dd_id AS "smoke.R0.dd_id"
+     , R0.person_id AS "smoke.R0.person_id"
      , R1.dd_id AS "cancer.R1.dd_id"
+     , R1.person_id AS "cancer.R1.person_id"
 FROM smoke R0
    , cancer R1
    , person_smokes R2
@@ -57,7 +59,9 @@ input_relations: [
 deepdive.inference.factors.inf_imply_smoke_smoke {
 input_query: """
 SELECT R0.dd_id AS "smoke.R0.dd_id"
+     , R0.person_id AS "smoke.R0.person_id"
      , R1.dd_id AS "smoke.R1.dd_id"
+     , R1.person_id AS "smoke.R1.person_id"
 FROM smoke R0
    , smoke R1
    , friends R2
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 58cfa80e5..9afe3dc1d 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -92,6 +92,7 @@ materialize: false
 deepdive.inference.factors.inf_istrue_has_spouse {
 input_query: """
 SELECT R0.dd_id AS "has_spouse.R0.dd_id"
+     , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
 FROM has_spouse R0
    , has_spouse_candidates R1
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 239e3acc6..98f56e80f 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -10,6 +10,7 @@ e.dd_label: Boolean
 deepdive.inference.factors.inf_istrue_a {
 input_query: """
 SELECT R0.dd_id AS "a.R0.dd_id"
+     , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
 FROM a R0
    , b R1
@@ -27,6 +28,7 @@ input_relations: [
 deepdive.inference.factors.inf_istrue_c {
 input_query: """
 SELECT R0.dd_id AS "c.R0.dd_id"
+     , R0.k AS "c.R0.k"
 FROM c R0
    , b R1
 WHERE R1.k = R0.k
@@ -43,6 +45,7 @@ input_relations: [
 deepdive.inference.factors.inf_istrue_d {
 input_query: """
 SELECT R0.dd_id AS "d.R0.dd_id"
+     , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
 FROM d R0
@@ -61,6 +64,7 @@ input_relations: [
 deepdive.inference.factors.inf_istrue_e {
 input_query: """
 SELECT R0.dd_id AS "e.R0.dd_id"
+     , R0.k AS "e.R0.k"
 FROM e R0
    , b R1
 WHERE R1.k = R0.k
@@ -77,6 +81,7 @@ input_relations: [
 deepdive.inference.factors.inf_istrue_f {
 input_query: """
 SELECT R0.dd_id AS "f.R0.dd_id"
+     , R0.k AS "f.R0.k"
 FROM f R0
    , b R1
 WHERE R1.k = R0.k

From eb3c1e7099603198b1d527ebbcf3cda31e1fcd81 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Wed, 16 Mar 2016 16:14:45 -0700
Subject: [PATCH 317/347] Fixes #86, major bug in inference rule name
 generation

that was mapping different rules into the same name, hence losing all of
them except one.

Related to HazyResearch/deepdive#518
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 20 ++++++-----
 .../factor_functions/compile.expected         |  6 ++--
 .../compile.expected                          | 33 +++++++++++++++++++
 .../desugar.expected                          | 12 +++++++
 .../multiple_rules_for_same_head/input.ddlog  | 10 ++++++
 5 files changed, 70 insertions(+), 11 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 2caf02620..ad4fd8f7a 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -66,18 +66,22 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
 
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
-    val factorFuncName: String = s.head.function.getClass.getSimpleName.toLowerCase
-    val idxInInferenceRulesSharingHead = inferenceRules filter(_.head equals s.head) indexOf(s)
-    s"inf${
-        // XXX This comes right after the prefix to prevent potential collision with user's name
-        optionalIndex(idxInInferenceRulesSharingHead)
-      }_${
+    // how to map a rule to its basename
+    // TODO support @rule("name") annotation to override these generated names
+    def ruleBaseNameFor(s: InferenceRule) = s"${
         // function name
-        factorFuncName
+        s.head.function.getClass.getSimpleName.toLowerCase
       }_${
         // followed by variable names
-        s.head.terms map {_.name} mkString("_")
+        s.head.terms map { case t => s"${if (t.isNegated) "not_" else ""}${t.name}" } mkString("_")
       }"
+    // find this rule's base name and all rules that share it
+    val ruleBaseName = ruleBaseNameFor(s)
+    val allInferenceRulesSharingHead = inferenceRules filter(ruleBaseNameFor(_) equals ruleBaseName)
+    s"inf${
+        // keep an index before the base name to prevent potential collision with user's name
+        optionalIndex(allInferenceRulesSharingHead indexOf s)
+      }_${ruleBaseName}"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index a5631d8f7..4b2b5e009 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -18,7 +18,7 @@ input_relations: [
 
 }
 
-deepdive.inference.factors.inf_equal_Q_Q {
+deepdive.inference.factors.inf_equal_Q_not_Q {
 input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R1.x AS "dd_weight_column_0" 
           FROM Q R0, Q R1, R R2
@@ -36,11 +36,11 @@ deepdive.pipeline.run: ${PIPELINE}
 
 deepdive.pipeline.pipelines.inference: [
   inf_imply_Q_Q
-  inf_equal_Q_Q
+  inf_equal_Q_not_Q
 ]
 
 deepdive.pipeline.pipelines.endtoend: [
   inf_imply_Q_Q
-  inf_equal_Q_Q
+  inf_equal_Q_not_Q
 ]
 
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 1fb8cc7e9..00453f559 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -208,6 +208,20 @@ input_relations: [
 
 }
 
+deepdive.inference.factors.inf_istrue_not_Q {
+input_query: """
+          SELECT R0.id AS "Q.R0.id" 
+          FROM Q R0, S R1
+        WHERE R1.a = R0.x  AND R0.x < 1000"""
+function: """Imply(!Q.R0.label)"""
+weight: """?"""
+input_relations: [
+  Q
+  S
+]
+
+}
+
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
           SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" , R0.x AS "dd_weight_column_0" 
@@ -238,6 +252,21 @@ input_relations: [
 
 }
 
+deepdive.inference.factors.inf2_imply_Q_Q {
+input_query: """
+          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
+          FROM Q R0, Q R1, S R2, R R3, S R4
+        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) > 1000"""
+function: """Imply(Q.R0.label, Q.R1.label)"""
+weight: """10.0"""
+input_relations: [
+  Q
+  S
+  R
+]
+
+}
+
 deepdive.extraction.extractors.ext_T__3 {
 cmd: """
 	deepdive create view T__3 as 'SELECT R0.a AS column_0
@@ -270,8 +299,10 @@ deepdive.pipeline.pipelines.extraction: [
 deepdive.pipeline.pipelines.inference: [
   inf_istrue_Q
   inf1_istrue_Q
+  inf_istrue_not_Q
   inf_imply_Q_Q
   inf1_imply_Q_Q
+  inf2_imply_Q_Q
 ]
 
 deepdive.pipeline.pipelines.endtoend: [
@@ -287,7 +318,9 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_T__3
   inf_istrue_Q
   inf1_istrue_Q
+  inf_istrue_not_Q
   inf_imply_Q_Q
   inf1_imply_Q_Q
+  inf2_imply_Q_Q
 ]
 
diff --git a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
index 873dc7f03..58a65ce19 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
@@ -108,6 +108,11 @@ Q(a) :-
     S(a),
     a = 0.
 
+@weight("?")
+!Q(a) :-
+    S(a),
+    a < 1000.
+
 @weight(a)
 Q(a) => Q(b) :-
     S(a),
@@ -121,6 +126,13 @@ Q(a) => Q(b) :-
     S(b),
     (a + b) < 1000.
 
+@weight(10.0)
+Q(a) => Q(c) :-
+    S(a),
+    R(a, c),
+    S(c),
+    (a + c) > 1000.
+
 T_2(a int).
 
 T__3(x) :-
diff --git a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
index c0dfdfca4..1003b4603 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
+++ b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
@@ -30,11 +30,21 @@ Q(a) :- S(a), a > 1000.
 @weight(1.0)
 Q(a) :- S(a), a = 0.
 
+# compiled rule names should take negation into account
+# See: https://github.com/HazyResearch/ddlog/issues/86
+@weight("?")
+! Q(a) :- S(a), a < 1000.
+
 @weight(a)
 Q(a) => Q(b) :- S(a), R(a, b), S(b).
 @weight(-10.0)
 Q(a) => Q(b) :- S(a), R(a, b), S(b), a + b < 1000.
 
+# compiled rules shouldn't be sensitive to alpha-conversion, i.e., variable name changes
+# See: https://github.com/HazyResearch/deepdive/issues/518
+@weight(10.0)
+Q(a) => Q(c) :- S(a), R(a, c), S(c), a + c > 1000.
+
 # make sure desugars without name clashes
 T_2(a int).
 T__3(x) :- T(x).

From 94e201365de4f93a1d0a0a2386da6b09ae4781c3 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <netj@cs.stanford.edu>
Date: Thu, 24 Mar 2016 00:54:40 -0700
Subject: [PATCH 318/347] Compiles factor queries to use table dd_variables_Q

instead of Q for every variable relation Q in the head, so JOINs
with the internal table holding variable ids can be avoided.
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 13 ++++--
 .../chunking_example/compile.expected         | 10 ++---
 .../factor_functions/compile.expected         |  8 ++--
 .../logical_rules/compile.expected            |  4 +-
 .../compile.expected                          | 44 +++++++++++++------
 .../ocr_example/compile.expected              |  4 +-
 .../smoke_example/compile.expected            |  8 ++--
 .../spouse_example/compile.expected           |  2 +-
 .../weights/compile.expected                  | 10 ++---
 9 files changed, 63 insertions(+), 40 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index d0f75c237..ede863252 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -93,8 +93,14 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   // odd has happened.
   def resolveName( v : Variable ) : String = {
     v match { case Variable(v,relName,i) =>
-      if(attrNameForRelationAndPosition contains (relName,i)) {
-        attrNameForRelationAndPosition(relName,i)
+      val relNameNormalized =
+        // Drop deepdivePrefixForVariablesIdsTable.
+        // XXX This is ugly, but no alternative simpler way for now.  We should soon refactor the resolve*() stuffs as well as the QueryCompiler to make it produce an IR that's easier to manipulate post-hoc.
+        if (relName startsWith deepdivePrefixForVariablesIdsTable)
+          relName.substring(DeepDiveLogCompiler.deepdivePrefixForVariablesIdsTable.length)
+        else relName
+      if(attrNameForRelationAndPosition contains (relNameNormalized,i)) {
+        attrNameForRelationAndPosition(relNameNormalized,i)
       } else {
         // for views, columns names are in the form of "column_index"
         return s"column_${i}"
@@ -488,7 +494,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         // Here we need to select from the bodies atoms as well as the head atoms,
         // which are the variable relations.
         // This is achieved by puting head atoms into the body.
-        val fakeBody        = headAsBody ++ cqBody
+        val fakeBody        = (headAsBody map { h => h.copy(name = s"$deepdivePrefixForVariablesIdsTable${h.name}") }) ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
         val qc = new QueryCompiler(fakeCQ)
 
@@ -621,6 +627,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   val deepdiveWeightColumnPrefix = "dd_weight_column_"
   val deepdiveVariableIdColumn = "dd_id"
   val deepdiveVariableLabelColumn = "dd_label"
+  val deepdivePrefixForVariablesIdsTable = "dd_variables_"
 
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 08d2acb45..cf75b351e 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -85,7 +85,7 @@ SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
-FROM chunk R0
+FROM dd_variables_chunk R0
    , words R1
    , tags R2
    , word_features R3
@@ -116,8 +116,8 @@ SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R1.word_id AS "chunk.R1.word_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
-FROM chunk R0
-   , chunk R1
+FROM dd_variables_chunk R0
+   , dd_variables_chunk R1
    , words R2
    , words R3
    , tags R4
@@ -151,8 +151,8 @@ SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R1.word_id AS "chunk.R1.word_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
-FROM chunk R0
-   , chunk R1
+FROM dd_variables_chunk R0
+   , dd_variables_chunk R1
    , words R2
    , words R3
    , tags R4
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index cd3517d03..349b4acfd 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -11,8 +11,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
-FROM Q R0
-   , Q R1
+FROM dd_variables_Q R0
+   , dd_variables_Q R1
    , R R2
 WHERE R2.a = R0.x
   AND R2.b = R1.x
@@ -33,8 +33,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
-FROM Q R0
-   , Q R1
+FROM dd_variables_Q R0
+   , dd_variables_Q R1
    , R R2
 WHERE R2.a = R0.x
   AND R2.b = R1.x
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index e9a6b2ded..9a758c544 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -40,8 +40,8 @@ SELECT R0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-FROM P R0
-   , Q R1
+FROM dd_variables_P R0
+   , dd_variables_Q R1
 WHERE R1.x = R0.x
   AND true
 """
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 97f8e8f1b..ce07f9d2f 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -202,7 +202,7 @@ input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
-FROM Q R0
+FROM dd_variables_Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x > 1000
@@ -220,7 +220,7 @@ deepdive.inference.factors.inf1_istrue_Q {
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-FROM Q R0
+FROM dd_variables_Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x = 0
@@ -236,10 +236,14 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_not_Q {
 input_query: """
-          SELECT R0.id AS "Q.R0.id" 
-          FROM Q R0, S R1
-        WHERE R1.a = R0.x  AND R0.x < 1000"""
-function: """Imply(!Q.R0.label)"""
+SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+FROM dd_variables_Q R0
+   , S R1
+WHERE R1.a = R0.x
+  AND R0.x < 1000
+"""
+function: """Imply(!Q.R0.dd_label)"""
 weight: """?"""
 input_relations: [
   Q
@@ -255,8 +259,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
-FROM Q R0
-   , Q R1
+FROM dd_variables_Q R0
+   , dd_variables_Q R1
    , S R2
    , R R3
    , S R4
@@ -281,8 +285,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-FROM Q R0
-   , Q R1
+FROM dd_variables_Q R0
+   , dd_variables_Q R1
    , S R2
    , R R3
    , S R4
@@ -304,10 +308,22 @@ input_relations: [
 
 deepdive.inference.factors.inf2_imply_Q_Q {
 input_query: """
-          SELECT R0.id AS "Q.R0.id" , R1.id AS "Q.R1.id" 
-          FROM Q R0, Q R1, S R2, R R3, S R4
-        WHERE R2.a = R0.x  AND R3.a = R0.x  AND R3.b = R1.x  AND R4.a = R1.x  AND (R0.x + R1.x) > 1000"""
-function: """Imply(Q.R0.label, Q.R1.label)"""
+SELECT R0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , R1.dd_id AS "Q.R1.dd_id"
+     , R1.x AS "Q.R1.x"
+FROM dd_variables_Q R0
+   , dd_variables_Q R1
+   , S R2
+   , R R3
+   , S R4
+WHERE R2.a = R0.x
+  AND R3.a = R0.x
+  AND R3.b = R1.x
+  AND R4.a = R1.x
+  AND (R0.x + R1.x) > 1000
+"""
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """10.0"""
 input_relations: [
   Q
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index dc484f9ab..2cd35b659 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -39,7 +39,7 @@ input_query: """
 SELECT R0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
-FROM q1 R0
+FROM dd_variables_q1 R0
    , features R1
 WHERE R1.word_id = R0.wid
 """
@@ -57,7 +57,7 @@ input_query: """
 SELECT R0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
-FROM q2 R0
+FROM dd_variables_q2 R0
    , features R1
 WHERE R1.word_id = R0.wid
 """
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 22eea5eb3..9ddd6cbf9 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -40,8 +40,8 @@ SELECT R0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
      , R1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
-FROM smoke R0
-   , cancer R1
+FROM dd_variables_smoke R0
+   , dd_variables_cancer R1
    , person_smokes R2
 WHERE R1.person_id = R0.person_id
   AND R2.person_id = R0.person_id
@@ -62,8 +62,8 @@ SELECT R0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
      , R1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
-FROM smoke R0
-   , smoke R1
+FROM dd_variables_smoke R0
+   , dd_variables_smoke R1
    , friends R2
 WHERE R2.person_id = R0.person_id
   AND R2.friend_id = R1.person_id
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 9afe3dc1d..6d08931ef 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -94,7 +94,7 @@ input_query: """
 SELECT R0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
-FROM has_spouse R0
+FROM dd_variables_has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
 WHERE R1.relation_id = R0.relation_id
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 98f56e80f..a507d916a 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -12,7 +12,7 @@ input_query: """
 SELECT R0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
-FROM a R0
+FROM dd_variables_a R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -29,7 +29,7 @@ deepdive.inference.factors.inf_istrue_c {
 input_query: """
 SELECT R0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
-FROM c R0
+FROM dd_variables_c R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -48,7 +48,7 @@ SELECT R0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
-FROM d R0
+FROM dd_variables_d R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -65,7 +65,7 @@ deepdive.inference.factors.inf_istrue_e {
 input_query: """
 SELECT R0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
-FROM e R0
+FROM dd_variables_e R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -82,7 +82,7 @@ deepdive.inference.factors.inf_istrue_f {
 input_query: """
 SELECT R0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
-FROM f R0
+FROM dd_variables_f R0
    , b R1
 WHERE R1.k = R0.k
 """

From a544cd946dad4571661187db96f60ea627dddccb Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Sat, 11 Jun 2016 10:51:09 -0700
Subject: [PATCH 319/347] Project category value columns in compiler

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 6 ++++++
 test/expected-output-test/chunking_example/compile.expected | 5 +++++
 2 files changed, 11 insertions(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index ede863252..981a6abbf 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -485,6 +485,12 @@ class QueryCompiler(cq : ConjunctiveQuery) {
             case term => s"""R${headAsBody indexOf x}.${term
             } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
           }) get
+        ) ::: (
+          // project category columns (to pass linking b/w category vals and weights)
+          schemaDeclarationByRelationName get x.name map (_.categoricalColumns map {
+            case term => s"""R${headAsBody indexOf x}.${term
+            } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
+          }) get
         )
       case _ => List.empty
     }
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index cf75b351e..9b66a3271 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -83,6 +83,7 @@ input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
+     , R0.tag AS "chunk.R0.tag"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
 FROM dd_variables_chunk R0
@@ -111,9 +112,11 @@ input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
+     , R0.tag AS "chunk.R0.tag"
      , R1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
+     , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM dd_variables_chunk R0
@@ -146,9 +149,11 @@ input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
+     , R0.tag AS "chunk.R0.tag"
      , R1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
+     , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM dd_variables_chunk R0

From 490b6ff6f482689e84fa1695e447ad5cd107939b Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Sat, 11 Jun 2016 16:14:03 -0700
Subject: [PATCH 320/347] use dd__label instead of term

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala  | 15 ++++++++-------
 .../chunking_example/compile.expected             | 10 +++++-----
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 981a6abbf..cfbaa5d6f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -479,18 +479,18 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         // variable id column
         s"""R${headAsBody indexOf x}.${
           deepdiveVariableIdColumn
-        } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" :: (
+        } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" ::
+        List( isCategoricalRelation(x.name) match {
+          case true => Some(s"""R${headAsBody indexOf x}.${
+            deepdiveVariableInternalLabelColumn
+          } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableInternalLabelColumn}\"""")
+          case false => None
+        }).flatten ::: (
           // project variable key columns as well (to reduce unnecssary joins)
           schemaDeclarationByRelationName get x.name map (_.keyColumns map {
             case term => s"""R${headAsBody indexOf x}.${term
             } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
           }) get
-        ) ::: (
-          // project category columns (to pass linking b/w category vals and weights)
-          schemaDeclarationByRelationName get x.name map (_.categoricalColumns map {
-            case term => s"""R${headAsBody indexOf x}.${term
-            } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
-          }) get
         )
       case _ => List.empty
     }
@@ -633,6 +633,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   val deepdiveWeightColumnPrefix = "dd_weight_column_"
   val deepdiveVariableIdColumn = "dd_id"
   val deepdiveVariableLabelColumn = "dd_label"
+  val deepdiveVariableInternalLabelColumn = "dd__label"
   val deepdivePrefixForVariablesIdsTable = "dd_variables_"
 
   // entry point for compilation
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 9b66a3271..85a9829e4 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -81,9 +81,9 @@ WHERE R1.sent_id = R0.sent_id
 deepdive.inference.factors.inf_istrue_chunk {
 input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R0.dd__label AS "chunk.R0.dd__label"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
-     , R0.tag AS "chunk.R0.tag"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
 FROM dd_variables_chunk R0
@@ -110,13 +110,13 @@ input_relations: [
 deepdive.inference.factors.inf_and_chunk_chunk {
 input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R0.dd__label AS "chunk.R0.dd__label"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
-     , R0.tag AS "chunk.R0.tag"
      , R1.dd_id AS "chunk.R1.dd_id"
+     , R1.dd__label AS "chunk.R1.dd__label"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
-     , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM dd_variables_chunk R0
@@ -147,13 +147,13 @@ input_relations: [
 deepdive.inference.factors.inf1_and_chunk_chunk {
 input_query: """
 SELECT R0.dd_id AS "chunk.R0.dd_id"
+     , R0.dd__label AS "chunk.R0.dd__label"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
-     , R0.tag AS "chunk.R0.tag"
      , R1.dd_id AS "chunk.R1.dd_id"
+     , R1.dd__label AS "chunk.R1.dd__label"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
-     , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
 FROM dd_variables_chunk R0

From d5b50c14e4088c2ccf8a70946918458bb98519c2 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Mon, 13 Jun 2016 21:22:20 -0700
Subject: [PATCH 321/347] Use both var table Q and internal table dd_variable_Q

This reverts commit 94e201365de4f93a1d0a0a2386da6b09ae4781c3.
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 64 +++++++++++--------
 .../chunking_example/compile.expected         | 45 ++++++++-----
 .../factor_functions/compile.expected         | 24 ++++---
 .../logical_rules/compile.expected            | 12 ++--
 .../compile.expected                          | 54 ++++++++++------
 .../ocr_example/compile.expected              | 12 ++--
 .../smoke_example/compile.expected            | 24 ++++---
 .../spouse_example/compile.expected           |  6 +-
 .../weights/compile.expected                  | 30 ++++++---
 9 files changed, 176 insertions(+), 95 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index cfbaa5d6f..53a47a996 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -93,14 +93,8 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   // odd has happened.
   def resolveName( v : Variable ) : String = {
     v match { case Variable(v,relName,i) =>
-      val relNameNormalized =
-        // Drop deepdivePrefixForVariablesIdsTable.
-        // XXX This is ugly, but no alternative simpler way for now.  We should soon refactor the resolve*() stuffs as well as the QueryCompiler to make it produce an IR that's easier to manipulate post-hoc.
-        if (relName startsWith deepdivePrefixForVariablesIdsTable)
-          relName.substring(DeepDiveLogCompiler.deepdivePrefixForVariablesIdsTable.length)
-        else relName
-      if(attrNameForRelationAndPosition contains (relNameNormalized,i)) {
-        attrNameForRelationAndPosition(relNameNormalized,i)
+      if(attrNameForRelationAndPosition contains (relName,i)) {
+        attrNameForRelationAndPosition(relName,i)
       } else {
         // for views, columns names are in the form of "column_index"
         return s"column_${i}"
@@ -132,7 +126,7 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
 
 
   // This is responsible for compiling a single conjunctive query
-class QueryCompiler(cq : ConjunctiveQuery) {
+class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhere: List[String] = Nil) {
   // TODO remove var and make the generate* stuff below side-effect free
   // This is responsible for schema elements within a given query, e.g.,
   // what is the canonical version of x? (i.e., the first time it is
@@ -263,7 +257,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   def generateSQLBody(body: List[Body]) : String = {
     // generate where clause from unification and conditions
     def generateWhereClause(bodies: List[Body], indexPrefix: String) : String = {
-      val conditions = bodies.zipWithIndex.flatMap {
+      val conditions = (bodies.zipWithIndex.flatMap {
         case (Atom(relName, terms), index) => {
           val bodyIndex = s"${indexPrefix}${index}"
           terms.zipWithIndex flatMap { case (pattern, termIndex) =>
@@ -298,15 +292,15 @@ class QueryCompiler(cq : ConjunctiveQuery) {
             case _ => None
           }
         }
-      }
+      }) ::: hackWhere
       conditions.mkString("\n  AND ")
     }
 
     def generateFromClause(bodies: List[Body], indexPrefix: String) : String = {
-      val atoms = bodies.zipWithIndex flatMap {
+      val atoms = (bodies.zipWithIndex flatMap {
         case (x:Atom,i) => Some(s"${x.name} R${indexPrefix}${i}")
         case _ => None
-      }
+      }) ::: hackFrom
       val outers = bodies.zipWithIndex flatMap {
         case (x:QuantifiedBody,i) => {
           val newIndexPrefix = s"${indexPrefix}${i}_"
@@ -473,36 +467,55 @@ class QueryCompiler(cq : ConjunctiveQuery) {
   // generate inference rule part for deepdive
   def compile(stmt: InferenceRule): CompiledBlocks = {
     val headAsBody = stmt.head.variables map (_.atom)
-    val variableIdAndKeyColumns = headAsBody.zipWithIndex flatMap {
+    val variableIdAndColumns = headAsBody.zipWithIndex flatMap {
       case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
         // TODO maybe TableAlias can be useful here or we can completely get rid of it?
         // variable id column
-        s"""R${headAsBody indexOf x}.${
+        s"""R_${headAsBody indexOf x}.${
           deepdiveVariableIdColumn
         } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" ::
-        List( isCategoricalRelation(x.name) match {
-          case true => Some(s"""R${headAsBody indexOf x}.${
-            deepdiveVariableInternalLabelColumn
-          } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableInternalLabelColumn}\"""")
-          case false => None
-        }).flatten ::: (
+        List(
           // project variable key columns as well (to reduce unnecssary joins)
           schemaDeclarationByRelationName get x.name map (_.keyColumns map {
             case term => s"""R${headAsBody indexOf x}.${term
             } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
           }) get
-        )
+        ).flatten ::: List(
+          // project category value columns as well (to reduce unnecssary joins)
+          schemaDeclarationByRelationName get x.name map (_.categoricalColumns map {
+            case term => s"""R${headAsBody indexOf x}.${term
+            } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
+          }) get
+        ).flatten
+
+      case _ => List.empty
+    }
+
+    val internalVarTables = headAsBody.zipWithIndex flatMap {
+      case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
+        List(s"""${deepdivePrefixForVariablesIdsTable}${x.name} AS R_${headAsBody indexOf x}""")
       case _ => List.empty
     }
 
+    val internalVarJoinConds = headAsBody.zipWithIndex flatMap {
+      case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
+        List(
+          // project variable key columns as well (to reduce unnecssary joins)
+          schemaDeclarationByRelationName get x.name map (_.keyColumns map {
+            case term => s"""R${headAsBody indexOf x}.${term} = R_${headAsBody indexOf x}.${term}"""
+          }) get
+        )
+      case _ => List.empty
+    } flatten
+
     val inputQueries =
       stmt.q.bodies map { case cqBody =>
         // Here we need to select from the bodies atoms as well as the head atoms,
         // which are the variable relations.
         // This is achieved by puting head atoms into the body.
-        val fakeBody        = (headAsBody map { h => h.copy(name = s"$deepdivePrefixForVariablesIdsTable${h.name}") }) ++ cqBody
+        val fakeBody        = headAsBody ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
-        val qc = new QueryCompiler(fakeCQ)
+        val qc = new QueryCompiler(fakeCQ, internalVarTables, internalVarJoinConds)
 
         // weight columns
         val weightColumns = stmt.weights.variables.zipWithIndex collect {
@@ -511,7 +524,7 @@ class QueryCompiler(cq : ConjunctiveQuery) {
         }
 
         // factor input query
-        s"""SELECT ${(variableIdAndKeyColumns ++ weightColumns) mkString ("\n     , ")
+        s"""SELECT ${(variableIdAndColumns ++ weightColumns) mkString ("\n     , ")
         }\n${qc.generateSQLBody(fakeBody) }"""
       }
 
@@ -633,7 +646,6 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   val deepdiveWeightColumnPrefix = "dd_weight_column_"
   val deepdiveVariableIdColumn = "dd_id"
   val deepdiveVariableLabelColumn = "dd_label"
-  val deepdiveVariableInternalLabelColumn = "dd__label"
   val deepdivePrefixForVariablesIdsTable = "dd_variables_"
 
   // entry point for compilation
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 85a9829e4..e49e91595 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -80,21 +80,24 @@ WHERE R1.sent_id = R0.sent_id
 
 deepdive.inference.factors.inf_istrue_chunk {
 input_query: """
-SELECT R0.dd_id AS "chunk.R0.dd_id"
-     , R0.dd__label AS "chunk.R0.dd__label"
+SELECT R_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
+     , R0.tag AS "chunk.R0.tag"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
-FROM dd_variables_chunk R0
+FROM chunk R0
    , words R1
    , tags R2
    , word_features R3
+   , dd_variables_chunk AS R_0
 WHERE R1.sent_id = R0.sent_id
   AND R1.word_id = R0.word_id
   AND R2.tag = R0.tag
   AND R3.sent_id = R0.sent_id
   AND R3.word_id = R0.word_id
+  AND R0.sent_id = R_0.sent_id
+  AND R0.word_id = R_0.word_id
 """
 function: """Multinomial(chunk.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
@@ -109,22 +112,24 @@ input_relations: [
 
 deepdive.inference.factors.inf_and_chunk_chunk {
 input_query: """
-SELECT R0.dd_id AS "chunk.R0.dd_id"
-     , R0.dd__label AS "chunk.R0.dd__label"
+SELECT R_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
-     , R1.dd_id AS "chunk.R1.dd_id"
-     , R1.dd__label AS "chunk.R1.dd__label"
+     , R0.tag AS "chunk.R0.tag"
+     , R_1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
+     , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
-FROM dd_variables_chunk R0
-   , dd_variables_chunk R1
+FROM chunk R0
+   , chunk R1
    , words R2
    , words R3
    , tags R4
    , tags R5
+   , dd_variables_chunk AS R_0
+   , dd_variables_chunk AS R_1
 WHERE R1.sent_id = R0.sent_id
   AND R2.sent_id = R0.sent_id
   AND R2.word_id = R0.word_id
@@ -133,6 +138,10 @@ WHERE R1.sent_id = R0.sent_id
   AND R4.tag = R0.tag
   AND R5.tag = R1.tag
   AND R1.word_id = (R0.word_id + 1)
+  AND R0.sent_id = R_0.sent_id
+  AND R0.word_id = R_0.word_id
+  AND R1.sent_id = R_1.sent_id
+  AND R1.word_id = R_1.word_id
 """
 function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
@@ -146,22 +155,24 @@ input_relations: [
 
 deepdive.inference.factors.inf1_and_chunk_chunk {
 input_query: """
-SELECT R0.dd_id AS "chunk.R0.dd_id"
-     , R0.dd__label AS "chunk.R0.dd__label"
+SELECT R_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
-     , R1.dd_id AS "chunk.R1.dd_id"
-     , R1.dd__label AS "chunk.R1.dd__label"
+     , R0.tag AS "chunk.R0.tag"
+     , R_1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
+     , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
-FROM dd_variables_chunk R0
-   , dd_variables_chunk R1
+FROM chunk R0
+   , chunk R1
    , words R2
    , words R3
    , tags R4
    , tags R5
+   , dd_variables_chunk AS R_0
+   , dd_variables_chunk AS R_1
 WHERE R1.sent_id = R0.sent_id
   AND R2.sent_id = R0.sent_id
   AND R2.word_id = R0.word_id
@@ -171,6 +182,10 @@ WHERE R1.sent_id = R0.sent_id
   AND R5.tag = R1.tag
   AND R2.tag IS NOT NULL
   AND R0.word_id < R1.word_id
+  AND R0.sent_id = R_0.sent_id
+  AND R0.word_id = R_0.word_id
+  AND R1.sent_id = R_1.sent_id
+  AND R1.word_id = R_1.word_id
 """
 function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 349b4acfd..06158bb5b 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -6,16 +6,20 @@ Q.dd_label: Boolean
 
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R1.dd_id AS "Q.R1.dd_id"
+     , R_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
-FROM dd_variables_Q R0
-   , dd_variables_Q R1
+FROM Q R0
+   , Q R1
    , R R2
+   , dd_variables_Q AS R_0
+   , dd_variables_Q AS R_1
 WHERE R2.a = R0.x
   AND R2.b = R1.x
+  AND R0.x = R_0.x
+  AND R1.x = R_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -28,16 +32,20 @@ input_relations: [
 
 deepdive.inference.factors.inf_equal_Q_not_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R1.dd_id AS "Q.R1.dd_id"
+     , R_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
-FROM dd_variables_Q R0
-   , dd_variables_Q R1
+FROM Q R0
+   , Q R1
    , R R2
+   , dd_variables_Q AS R_0
+   , dd_variables_Q AS R_1
 WHERE R2.a = R0.x
   AND R2.b = R1.x
+  AND R0.x = R_0.x
+  AND R1.x = R_1.x
 """
 function: """Equal(Q.R0.dd_label, !Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 9a758c544..8c5232c38 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -36,14 +36,18 @@ materialize: false
 
 deepdive.inference.factors.inf_imply_P_Q {
 input_query: """
-SELECT R0.dd_id AS "P.R0.dd_id"
+SELECT R_0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
-     , R1.dd_id AS "Q.R1.dd_id"
+     , R_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-FROM dd_variables_P R0
-   , dd_variables_Q R1
+FROM P R0
+   , Q R1
+   , dd_variables_P AS R_0
+   , dd_variables_Q AS R_1
 WHERE R1.x = R0.x
   AND true
+  AND R0.x = R_0.x
+  AND R1.x = R_1.x
 """
 function: """Imply(P.R0.dd_label, Q.R1.dd_label)"""
 weight: """1"""
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index ce07f9d2f..24b5cc7a7 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -199,13 +199,15 @@ WHERE R0.a > 0
 
 deepdive.inference.factors.inf_istrue_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
-FROM dd_variables_Q R0
+FROM Q R0
    , S R1
+   , dd_variables_Q AS R_0
 WHERE R1.a = R0.x
   AND R0.x > 1000
+  AND R0.x = R_0.x
 """
 function: """Imply(Q.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -218,12 +220,14 @@ input_relations: [
 
 deepdive.inference.factors.inf1_istrue_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-FROM dd_variables_Q R0
+FROM Q R0
    , S R1
+   , dd_variables_Q AS R_0
 WHERE R1.a = R0.x
   AND R0.x = 0
+  AND R0.x = R_0.x
 """
 function: """Imply(Q.R0.dd_label)"""
 weight: """1.0"""
@@ -236,12 +240,14 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_not_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-FROM dd_variables_Q R0
+FROM Q R0
    , S R1
+   , dd_variables_Q AS R_0
 WHERE R1.a = R0.x
   AND R0.x < 1000
+  AND R0.x = R_0.x
 """
 function: """Imply(!Q.R0.dd_label)"""
 weight: """?"""
@@ -254,20 +260,24 @@ input_relations: [
 
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R1.dd_id AS "Q.R1.dd_id"
+     , R_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
-FROM dd_variables_Q R0
-   , dd_variables_Q R1
+FROM Q R0
+   , Q R1
    , S R2
    , R R3
    , S R4
+   , dd_variables_Q AS R_0
+   , dd_variables_Q AS R_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
+  AND R0.x = R_0.x
+  AND R1.x = R_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -281,20 +291,24 @@ input_relations: [
 
 deepdive.inference.factors.inf1_imply_Q_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R1.dd_id AS "Q.R1.dd_id"
+     , R_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-FROM dd_variables_Q R0
-   , dd_variables_Q R1
+FROM Q R0
+   , Q R1
    , S R2
    , R R3
    , S R4
+   , dd_variables_Q AS R_0
+   , dd_variables_Q AS R_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) < 1000
+  AND R0.x = R_0.x
+  AND R1.x = R_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """-10.0"""
@@ -308,20 +322,24 @@ input_relations: [
 
 deepdive.inference.factors.inf2_imply_Q_Q {
 input_query: """
-SELECT R0.dd_id AS "Q.R0.dd_id"
+SELECT R_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R1.dd_id AS "Q.R1.dd_id"
+     , R_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-FROM dd_variables_Q R0
-   , dd_variables_Q R1
+FROM Q R0
+   , Q R1
    , S R2
    , R R3
    , S R4
+   , dd_variables_Q AS R_0
+   , dd_variables_Q AS R_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) > 1000
+  AND R0.x = R_0.x
+  AND R1.x = R_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """10.0"""
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 2cd35b659..430d30cdd 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -36,12 +36,14 @@ materialize: false
 
 deepdive.inference.factors.inf_istrue_q1 {
 input_query: """
-SELECT R0.dd_id AS "q1.R0.dd_id"
+SELECT R_0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
-FROM dd_variables_q1 R0
+FROM q1 R0
    , features R1
+   , dd_variables_q1 AS R_0
 WHERE R1.word_id = R0.wid
+  AND R0.wid = R_0.wid
 """
 function: """Imply(q1.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -54,12 +56,14 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_q2 {
 input_query: """
-SELECT R0.dd_id AS "q2.R0.dd_id"
+SELECT R_0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
-FROM dd_variables_q2 R0
+FROM q2 R0
    , features R1
+   , dd_variables_q2 AS R_0
 WHERE R1.word_id = R0.wid
+  AND R0.wid = R_0.wid
 """
 function: """Imply(q2.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 9ddd6cbf9..be8d3f5d5 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -36,15 +36,19 @@ materialize: false
 
 deepdive.inference.factors.inf_imply_smoke_cancer {
 input_query: """
-SELECT R0.dd_id AS "smoke.R0.dd_id"
+SELECT R_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
-     , R1.dd_id AS "cancer.R1.dd_id"
+     , R_1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
-FROM dd_variables_smoke R0
-   , dd_variables_cancer R1
+FROM smoke R0
+   , cancer R1
    , person_smokes R2
+   , dd_variables_smoke AS R_0
+   , dd_variables_cancer AS R_1
 WHERE R1.person_id = R0.person_id
   AND R2.person_id = R0.person_id
+  AND R0.person_id = R_0.person_id
+  AND R1.person_id = R_1.person_id
 """
 function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 weight: """0.5"""
@@ -58,15 +62,19 @@ input_relations: [
 
 deepdive.inference.factors.inf_imply_smoke_smoke {
 input_query: """
-SELECT R0.dd_id AS "smoke.R0.dd_id"
+SELECT R_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
-     , R1.dd_id AS "smoke.R1.dd_id"
+     , R_1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
-FROM dd_variables_smoke R0
-   , dd_variables_smoke R1
+FROM smoke R0
+   , smoke R1
    , friends R2
+   , dd_variables_smoke AS R_0
+   , dd_variables_smoke AS R_1
 WHERE R2.person_id = R0.person_id
   AND R2.friend_id = R1.person_id
+  AND R0.person_id = R_0.person_id
+  AND R1.person_id = R_1.person_id
 """
 function: """Imply(smoke.R0.dd_label, smoke.R1.dd_label)"""
 weight: """0.4"""
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 6d08931ef..88157e222 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -91,14 +91,16 @@ materialize: false
 
 deepdive.inference.factors.inf_istrue_has_spouse {
 input_query: """
-SELECT R0.dd_id AS "has_spouse.R0.dd_id"
+SELECT R_0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
-FROM dd_variables_has_spouse R0
+FROM has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
+   , dd_variables_has_spouse AS R_0
 WHERE R1.relation_id = R0.relation_id
   AND R2.relation_id = R0.relation_id
+  AND R0.relation_id = R_0.relation_id
 """
 function: """Imply(has_spouse.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index a507d916a..e69e30c2c 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -9,12 +9,14 @@ e.dd_label: Boolean
 
 deepdive.inference.factors.inf_istrue_a {
 input_query: """
-SELECT R0.dd_id AS "a.R0.dd_id"
+SELECT R_0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
-FROM dd_variables_a R0
+FROM a R0
    , b R1
+   , dd_variables_a AS R_0
 WHERE R1.k = R0.k
+  AND R0.k = R_0.k
 """
 function: """Imply(a.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -27,11 +29,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_c {
 input_query: """
-SELECT R0.dd_id AS "c.R0.dd_id"
+SELECT R_0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
-FROM dd_variables_c R0
+FROM c R0
    , b R1
+   , dd_variables_c AS R_0
 WHERE R1.k = R0.k
+  AND R0.k = R_0.k
 """
 function: """Imply(c.R0.dd_label)"""
 weight: """?"""
@@ -44,13 +48,15 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_d {
 input_query: """
-SELECT R0.dd_id AS "d.R0.dd_id"
+SELECT R_0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
-FROM dd_variables_d R0
+FROM d R0
    , b R1
+   , dd_variables_d AS R_0
 WHERE R1.k = R0.k
+  AND R0.k = R_0.k
 """
 function: """Imply(d.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
@@ -63,11 +69,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_e {
 input_query: """
-SELECT R0.dd_id AS "e.R0.dd_id"
+SELECT R_0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
-FROM dd_variables_e R0
+FROM e R0
    , b R1
+   , dd_variables_e AS R_0
 WHERE R1.k = R0.k
+  AND R0.k = R_0.k
 """
 function: """Imply(e.R0.dd_label)"""
 weight: """-10"""
@@ -80,11 +88,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_f {
 input_query: """
-SELECT R0.dd_id AS "f.R0.dd_id"
+SELECT R_0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
-FROM dd_variables_f R0
+FROM f R0
    , b R1
+   , dd_variables_f AS R_0
 WHERE R1.k = R0.k
+  AND R0.k = R_0.k
 """
 function: """Imply(f.R0.dd_label)"""
 weight: """-0.3"""

From df296de64116ec303b3ff17b2c978f57ec392847 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Wed, 15 Jun 2016 15:14:49 -0700
Subject: [PATCH 322/347] rename R_ to dd_id_

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 15 +++---
 .../chunking_example/compile.expected         | 40 +++++++-------
 .../factor_functions/compile.expected         | 24 ++++-----
 .../logical_rules/compile.expected            | 12 ++---
 .../compile.expected                          | 54 +++++++++----------
 .../ocr_example/compile.expected              | 12 ++---
 .../smoke_example/compile.expected            | 24 ++++-----
 .../spouse_example/compile.expected           |  6 +--
 .../weights/compile.expected                  | 30 +++++------
 9 files changed, 109 insertions(+), 108 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 53a47a996..541504559 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -471,29 +471,28 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
       case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
         // TODO maybe TableAlias can be useful here or we can completely get rid of it?
         // variable id column
-        s"""R_${headAsBody indexOf x}.${
+        s"""${deepdiveVariableIdColumn}_${headAsBody indexOf x}.${
           deepdiveVariableIdColumn
-        } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" ::
-        List(
+        } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" :: (
           // project variable key columns as well (to reduce unnecssary joins)
           schemaDeclarationByRelationName get x.name map (_.keyColumns map {
             case term => s"""R${headAsBody indexOf x}.${term
             } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
           }) get
-        ).flatten ::: List(
+        ) ++ (
           // project category value columns as well (to reduce unnecssary joins)
           schemaDeclarationByRelationName get x.name map (_.categoricalColumns map {
             case term => s"""R${headAsBody indexOf x}.${term
             } AS "${x.name}.R${headAsBody indexOf x}.${term}\""""
           }) get
-        ).flatten
+        )
 
       case _ => List.empty
     }
 
     val internalVarTables = headAsBody.zipWithIndex flatMap {
       case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
-        List(s"""${deepdivePrefixForVariablesIdsTable}${x.name} AS R_${headAsBody indexOf x}""")
+        List(s"""${deepdivePrefixForVariablesIdsTable}${x.name} AS ${deepdiveVariableIdColumn}_${headAsBody indexOf x}""")
       case _ => List.empty
     }
 
@@ -502,7 +501,7 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         List(
           // project variable key columns as well (to reduce unnecssary joins)
           schemaDeclarationByRelationName get x.name map (_.keyColumns map {
-            case term => s"""R${headAsBody indexOf x}.${term} = R_${headAsBody indexOf x}.${term}"""
+            case term => s"""R${headAsBody indexOf x}.${term} = ${deepdiveVariableIdColumn}_${headAsBody indexOf x}.${term}"""
           }) get
         )
       case _ => List.empty
@@ -515,6 +514,8 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         // This is achieved by puting head atoms into the body.
         val fakeBody        = headAsBody ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
+
+        // TODO XXX: Fix the `internal` hack below
         val qc = new QueryCompiler(fakeCQ, internalVarTables, internalVarJoinConds)
 
         // weight columns
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index e49e91595..3131317d8 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -80,7 +80,7 @@ WHERE R1.sent_id = R0.sent_id
 
 deepdive.inference.factors.inf_istrue_chunk {
 input_query: """
-SELECT R_0.dd_id AS "chunk.R0.dd_id"
+SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R0.tag AS "chunk.R0.tag"
@@ -90,14 +90,14 @@ FROM chunk R0
    , words R1
    , tags R2
    , word_features R3
-   , dd_variables_chunk AS R_0
+   , dd_variables_chunk AS dd_id_0
 WHERE R1.sent_id = R0.sent_id
   AND R1.word_id = R0.word_id
   AND R2.tag = R0.tag
   AND R3.sent_id = R0.sent_id
   AND R3.word_id = R0.word_id
-  AND R0.sent_id = R_0.sent_id
-  AND R0.word_id = R_0.word_id
+  AND R0.sent_id = dd_id_0.sent_id
+  AND R0.word_id = dd_id_0.word_id
 """
 function: """Multinomial(chunk.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
@@ -112,11 +112,11 @@ input_relations: [
 
 deepdive.inference.factors.inf_and_chunk_chunk {
 input_query: """
-SELECT R_0.dd_id AS "chunk.R0.dd_id"
+SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R0.tag AS "chunk.R0.tag"
-     , R_1.dd_id AS "chunk.R1.dd_id"
+     , dd_id_1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
      , R1.tag AS "chunk.R1.tag"
@@ -128,8 +128,8 @@ FROM chunk R0
    , words R3
    , tags R4
    , tags R5
-   , dd_variables_chunk AS R_0
-   , dd_variables_chunk AS R_1
+   , dd_variables_chunk AS dd_id_0
+   , dd_variables_chunk AS dd_id_1
 WHERE R1.sent_id = R0.sent_id
   AND R2.sent_id = R0.sent_id
   AND R2.word_id = R0.word_id
@@ -138,10 +138,10 @@ WHERE R1.sent_id = R0.sent_id
   AND R4.tag = R0.tag
   AND R5.tag = R1.tag
   AND R1.word_id = (R0.word_id + 1)
-  AND R0.sent_id = R_0.sent_id
-  AND R0.word_id = R_0.word_id
-  AND R1.sent_id = R_1.sent_id
-  AND R1.word_id = R_1.word_id
+  AND R0.sent_id = dd_id_0.sent_id
+  AND R0.word_id = dd_id_0.word_id
+  AND R1.sent_id = dd_id_1.sent_id
+  AND R1.word_id = dd_id_1.word_id
 """
 function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
@@ -155,11 +155,11 @@ input_relations: [
 
 deepdive.inference.factors.inf1_and_chunk_chunk {
 input_query: """
-SELECT R_0.dd_id AS "chunk.R0.dd_id"
+SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R0.tag AS "chunk.R0.tag"
-     , R_1.dd_id AS "chunk.R1.dd_id"
+     , dd_id_1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
      , R1.tag AS "chunk.R1.tag"
@@ -171,8 +171,8 @@ FROM chunk R0
    , words R3
    , tags R4
    , tags R5
-   , dd_variables_chunk AS R_0
-   , dd_variables_chunk AS R_1
+   , dd_variables_chunk AS dd_id_0
+   , dd_variables_chunk AS dd_id_1
 WHERE R1.sent_id = R0.sent_id
   AND R2.sent_id = R0.sent_id
   AND R2.word_id = R0.word_id
@@ -182,10 +182,10 @@ WHERE R1.sent_id = R0.sent_id
   AND R5.tag = R1.tag
   AND R2.tag IS NOT NULL
   AND R0.word_id < R1.word_id
-  AND R0.sent_id = R_0.sent_id
-  AND R0.word_id = R_0.word_id
-  AND R1.sent_id = R_1.sent_id
-  AND R1.word_id = R_1.word_id
+  AND R0.sent_id = dd_id_0.sent_id
+  AND R0.word_id = dd_id_0.word_id
+  AND R1.sent_id = dd_id_1.sent_id
+  AND R1.word_id = dd_id_1.word_id
 """
 function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 06158bb5b..4fc0d9790 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -6,20 +6,20 @@ Q.dd_label: Boolean
 
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R_1.dd_id AS "Q.R1.dd_id"
+     , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
    , R R2
-   , dd_variables_Q AS R_0
-   , dd_variables_Q AS R_1
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R2.b = R1.x
-  AND R0.x = R_0.x
-  AND R1.x = R_1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -32,20 +32,20 @@ input_relations: [
 
 deepdive.inference.factors.inf_equal_Q_not_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R_1.dd_id AS "Q.R1.dd_id"
+     , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
 FROM Q R0
    , Q R1
    , R R2
-   , dd_variables_Q AS R_0
-   , dd_variables_Q AS R_1
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R2.b = R1.x
-  AND R0.x = R_0.x
-  AND R1.x = R_1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
 """
 function: """Equal(Q.R0.dd_label, !Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 8c5232c38..4aa494cc2 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -36,18 +36,18 @@ materialize: false
 
 deepdive.inference.factors.inf_imply_P_Q {
 input_query: """
-SELECT R_0.dd_id AS "P.R0.dd_id"
+SELECT dd_id_0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
-     , R_1.dd_id AS "Q.R1.dd_id"
+     , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
 FROM P R0
    , Q R1
-   , dd_variables_P AS R_0
-   , dd_variables_Q AS R_1
+   , dd_variables_P AS dd_id_0
+   , dd_variables_Q AS dd_id_1
 WHERE R1.x = R0.x
   AND true
-  AND R0.x = R_0.x
-  AND R1.x = R_1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
 """
 function: """Imply(P.R0.dd_label, Q.R1.dd_label)"""
 weight: """1"""
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 24b5cc7a7..47e43d9f0 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -199,15 +199,15 @@ WHERE R0.a > 0
 
 deepdive.inference.factors.inf_istrue_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
 FROM Q R0
    , S R1
-   , dd_variables_Q AS R_0
+   , dd_variables_Q AS dd_id_0
 WHERE R1.a = R0.x
   AND R0.x > 1000
-  AND R0.x = R_0.x
+  AND R0.x = dd_id_0.x
 """
 function: """Imply(Q.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -220,14 +220,14 @@ input_relations: [
 
 deepdive.inference.factors.inf1_istrue_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
 FROM Q R0
    , S R1
-   , dd_variables_Q AS R_0
+   , dd_variables_Q AS dd_id_0
 WHERE R1.a = R0.x
   AND R0.x = 0
-  AND R0.x = R_0.x
+  AND R0.x = dd_id_0.x
 """
 function: """Imply(Q.R0.dd_label)"""
 weight: """1.0"""
@@ -240,14 +240,14 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_not_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
 FROM Q R0
    , S R1
-   , dd_variables_Q AS R_0
+   , dd_variables_Q AS dd_id_0
 WHERE R1.a = R0.x
   AND R0.x < 1000
-  AND R0.x = R_0.x
+  AND R0.x = dd_id_0.x
 """
 function: """Imply(!Q.R0.dd_label)"""
 weight: """?"""
@@ -260,9 +260,9 @@ input_relations: [
 
 deepdive.inference.factors.inf_imply_Q_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R_1.dd_id AS "Q.R1.dd_id"
+     , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
 FROM Q R0
@@ -270,14 +270,14 @@ FROM Q R0
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS R_0
-   , dd_variables_Q AS R_1
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
-  AND R0.x = R_0.x
-  AND R1.x = R_1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -291,24 +291,24 @@ input_relations: [
 
 deepdive.inference.factors.inf1_imply_Q_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R_1.dd_id AS "Q.R1.dd_id"
+     , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
 FROM Q R0
    , Q R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS R_0
-   , dd_variables_Q AS R_1
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) < 1000
-  AND R0.x = R_0.x
-  AND R1.x = R_1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """-10.0"""
@@ -322,24 +322,24 @@ input_relations: [
 
 deepdive.inference.factors.inf2_imply_Q_Q {
 input_query: """
-SELECT R_0.dd_id AS "Q.R0.dd_id"
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , R_1.dd_id AS "Q.R1.dd_id"
+     , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
 FROM Q R0
    , Q R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS R_0
-   , dd_variables_Q AS R_1
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) > 1000
-  AND R0.x = R_0.x
-  AND R1.x = R_1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
 """
 function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 weight: """10.0"""
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 430d30cdd..bd3515c30 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -36,14 +36,14 @@ materialize: false
 
 deepdive.inference.factors.inf_istrue_q1 {
 input_query: """
-SELECT R_0.dd_id AS "q1.R0.dd_id"
+SELECT dd_id_0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
 FROM q1 R0
    , features R1
-   , dd_variables_q1 AS R_0
+   , dd_variables_q1 AS dd_id_0
 WHERE R1.word_id = R0.wid
-  AND R0.wid = R_0.wid
+  AND R0.wid = dd_id_0.wid
 """
 function: """Imply(q1.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -56,14 +56,14 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_q2 {
 input_query: """
-SELECT R_0.dd_id AS "q2.R0.dd_id"
+SELECT dd_id_0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
 FROM q2 R0
    , features R1
-   , dd_variables_q2 AS R_0
+   , dd_variables_q2 AS dd_id_0
 WHERE R1.word_id = R0.wid
-  AND R0.wid = R_0.wid
+  AND R0.wid = dd_id_0.wid
 """
 function: """Imply(q2.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index be8d3f5d5..a12a923d8 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -36,19 +36,19 @@ materialize: false
 
 deepdive.inference.factors.inf_imply_smoke_cancer {
 input_query: """
-SELECT R_0.dd_id AS "smoke.R0.dd_id"
+SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
-     , R_1.dd_id AS "cancer.R1.dd_id"
+     , dd_id_1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
 FROM smoke R0
    , cancer R1
    , person_smokes R2
-   , dd_variables_smoke AS R_0
-   , dd_variables_cancer AS R_1
+   , dd_variables_smoke AS dd_id_0
+   , dd_variables_cancer AS dd_id_1
 WHERE R1.person_id = R0.person_id
   AND R2.person_id = R0.person_id
-  AND R0.person_id = R_0.person_id
-  AND R1.person_id = R_1.person_id
+  AND R0.person_id = dd_id_0.person_id
+  AND R1.person_id = dd_id_1.person_id
 """
 function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 weight: """0.5"""
@@ -62,19 +62,19 @@ input_relations: [
 
 deepdive.inference.factors.inf_imply_smoke_smoke {
 input_query: """
-SELECT R_0.dd_id AS "smoke.R0.dd_id"
+SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
-     , R_1.dd_id AS "smoke.R1.dd_id"
+     , dd_id_1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
 FROM smoke R0
    , smoke R1
    , friends R2
-   , dd_variables_smoke AS R_0
-   , dd_variables_smoke AS R_1
+   , dd_variables_smoke AS dd_id_0
+   , dd_variables_smoke AS dd_id_1
 WHERE R2.person_id = R0.person_id
   AND R2.friend_id = R1.person_id
-  AND R0.person_id = R_0.person_id
-  AND R1.person_id = R_1.person_id
+  AND R0.person_id = dd_id_0.person_id
+  AND R1.person_id = dd_id_1.person_id
 """
 function: """Imply(smoke.R0.dd_label, smoke.R1.dd_label)"""
 weight: """0.4"""
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 88157e222..e89bb3ee2 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -91,16 +91,16 @@ materialize: false
 
 deepdive.inference.factors.inf_istrue_has_spouse {
 input_query: """
-SELECT R_0.dd_id AS "has_spouse.R0.dd_id"
+SELECT dd_id_0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
 FROM has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
-   , dd_variables_has_spouse AS R_0
+   , dd_variables_has_spouse AS dd_id_0
 WHERE R1.relation_id = R0.relation_id
   AND R2.relation_id = R0.relation_id
-  AND R0.relation_id = R_0.relation_id
+  AND R0.relation_id = dd_id_0.relation_id
 """
 function: """Imply(has_spouse.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index e69e30c2c..3a752cd17 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -9,14 +9,14 @@ e.dd_label: Boolean
 
 deepdive.inference.factors.inf_istrue_a {
 input_query: """
-SELECT R_0.dd_id AS "a.R0.dd_id"
+SELECT dd_id_0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
 FROM a R0
    , b R1
-   , dd_variables_a AS R_0
+   , dd_variables_a AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = R_0.k
+  AND R0.k = dd_id_0.k
 """
 function: """Imply(a.R0.dd_label)"""
 weight: """?(dd_weight_column_0)"""
@@ -29,13 +29,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_c {
 input_query: """
-SELECT R_0.dd_id AS "c.R0.dd_id"
+SELECT dd_id_0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
 FROM c R0
    , b R1
-   , dd_variables_c AS R_0
+   , dd_variables_c AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = R_0.k
+  AND R0.k = dd_id_0.k
 """
 function: """Imply(c.R0.dd_label)"""
 weight: """?"""
@@ -48,15 +48,15 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_d {
 input_query: """
-SELECT R_0.dd_id AS "d.R0.dd_id"
+SELECT dd_id_0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
 FROM d R0
    , b R1
-   , dd_variables_d AS R_0
+   , dd_variables_d AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = R_0.k
+  AND R0.k = dd_id_0.k
 """
 function: """Imply(d.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
@@ -69,13 +69,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_e {
 input_query: """
-SELECT R_0.dd_id AS "e.R0.dd_id"
+SELECT dd_id_0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
 FROM e R0
    , b R1
-   , dd_variables_e AS R_0
+   , dd_variables_e AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = R_0.k
+  AND R0.k = dd_id_0.k
 """
 function: """Imply(e.R0.dd_label)"""
 weight: """-10"""
@@ -88,13 +88,13 @@ input_relations: [
 
 deepdive.inference.factors.inf_istrue_f {
 input_query: """
-SELECT R_0.dd_id AS "f.R0.dd_id"
+SELECT dd_id_0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
 FROM f R0
    , b R1
-   , dd_variables_f AS R_0
+   , dd_variables_f AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = R_0.k
+  AND R0.k = dd_id_0.k
 """
 function: """Imply(f.R0.dd_label)"""
 weight: """-0.3"""

From 8c397b2af66c3ab9fe9de29d123672c7d2ceae29 Mon Sep 17 00:00:00 2001
From: alldefector <alldefector@users.noreply.github.com>
Date: Thu, 16 Jun 2016 23:29:40 -0700
Subject: [PATCH 323/347] Make agg func parsing case insensitive (fixes #91)

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 6a391edbe..39f349afb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -300,7 +300,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     | ("TRUE" | "FALSE") ^^ { x => BooleanConst(x.toBoolean) }
     | "NULL" ^^ { _ => NullConst() }
     | functionName ~ "(" ~ rep1sep(expr, ",") ~ ")" ^^ {
-        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, aggregationFunctions contains name)
+        case (name ~ _ ~ args ~ _) => FuncExpr(name, args, aggregationFunctions contains name.toUpperCase)
       }
     | variableName ^^ VarExpr
     | "(" ~> expr <~ ")"

From 14789a1cd64ab2849794c756d60dfb25ac96d883 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Thu, 16 Jun 2016 23:53:24 -0700
Subject: [PATCH 324/347] add agg func test case to expressions

---
 .../expressions/compile.expected               | 18 ++++++++++++++++++
 .../expressions/input.ddlog                    |  5 ++++-
 .../expressions/print.expected                 |  3 +++
 3 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 7addcc6c6..bc1571c4d 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -380,6 +380,22 @@ materialize: false
 
 }
 
+deepdive.extraction.extractors.ext_Y {
+sql: """
+SELECT R0.column_0 AS column_0
+     , Array_Agg(R0.column_1) AS column_1
+FROM C R0
+GROUP BY R0.column_0
+"""
+input_relations: [
+  C
+]
+style: sql_extractor
+output_relation: Y
+materialize: false
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
 
 deepdive.pipeline.pipelines.extraction: [
@@ -406,6 +422,7 @@ deepdive.pipeline.pipelines.extraction: [
   ext_W
   ext_V
   ext_X
+  ext_Y
 ]
 
 deepdive.pipeline.pipelines.endtoend: [
@@ -432,5 +449,6 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_W
   ext_V
   ext_X
+  ext_Y
 ]
 
diff --git a/test/expected-output-test/expressions/input.ddlog b/test/expected-output-test/expressions/input.ddlog
index e167cab4b..5fadd57ea 100644
--- a/test/expected-output-test/expressions/input.ddlog
+++ b/test/expected-output-test/expressions/input.ddlog
@@ -53,4 +53,7 @@ W(x) :- a(x), ALL[c(_,y,_), y < x].
 # placeholder
 V(x) :- c(_,x,_), a(x).
 
-X(x) :- b(x,_,_,z), c(_,x,y).
\ No newline at end of file
+X(x) :- b(x,_,_,z), c(_,x,y).
+
+# agg function name is case insensitive
+Y(a, Array_Agg(b)) :- C(a, b, _).
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 0dfaccc0a..5cef22faf 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -98,3 +98,6 @@ X(x) :-
     b(x, _, _, z),
     c(_, x, y).
 
+Y(a, Array_Agg(b)) :-
+    C(a, b, _).
+

From cc82f76a1089e96c0231610599899fc0154d7b95 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Fri, 17 Jun 2016 21:51:29 -0700
Subject: [PATCH 325/347] Fix ">= and <= comparator not working #90"

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 test/expected-output-test/expressions/compile.expected    | 2 +-
 test/expected-output-test/expressions/input.ddlog         | 2 +-
 test/expected-output-test/expressions/print.expected      | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 39f349afb..34fba2ad7 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -312,7 +312,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
     }
 
   // conditional expressions
-  def compareOperator = ("LIKE" | ">" | "<" | ">=" | "<=" | "!=" | "=" | "IS" ~ "NOT" ^^ { _ => "IS NOT" } | "IS") named "compare operator"
+  def compareOperator = ("LIKE" | ">=" | "<=" | "!=" | ">" | "<" | "=" | "IS" ~ "NOT" ^^ { _ => "IS NOT" } | "IS") named "compare operator"
 
   def cond : Parser[Cond] =
     ( acond ~ ";" ~ cond ^^ { case (lhs ~ op ~ rhs) =>
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index bc1571c4d..31ef5acf6 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -168,7 +168,7 @@ deepdive.extraction.extractors.ext_I {
 sql: """
 SELECT R0.k AS column_0
 FROM b R0
-WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r < 10))
+WHERE ((R0.k + R0.r) = 100 OR (R0.k > 50 AND R0.r <= 10))
 """
 input_relations: [
   b
diff --git a/test/expected-output-test/expressions/input.ddlog b/test/expected-output-test/expressions/input.ddlog
index 5fadd57ea..28e02f0ad 100644
--- a/test/expected-output-test/expressions/input.ddlog
+++ b/test/expected-output-test/expressions/input.ddlog
@@ -26,7 +26,7 @@ G(x) :- b(x,y,z,w), x + w = 100.
 
 H(x) :- b(x,y,z,w), x + w = 100, x > 50.
 
-I(x) :- b(x,y,z,w), [x + w = 100; [x > 50, w < 10]].
+I(x) :- b(x,y,z,w), [x + w = 100; [x > 50, w <= 10]].
 
 J(x) :- b(x,y,z,w), [x + w = 100; !x > 50].
 
diff --git a/test/expected-output-test/expressions/print.expected b/test/expected-output-test/expressions/print.expected
index 5cef22faf..d15076336 100644
--- a/test/expected-output-test/expressions/print.expected
+++ b/test/expected-output-test/expressions/print.expected
@@ -48,7 +48,7 @@ H(x) :-
 
 I(x) :-
     b(x, y, z, w),
-    [(x + w) = 100; [x > 50, w < 10]].
+    [(x + w) = 100; [x > 50, w <= 10]].
 
 J(x) :-
     b(x, y, z, w),

From d996bd150d89f51c92923484b6e78dd1fa7da385 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Fri, 17 Jun 2016 20:02:30 -0700
Subject: [PATCH 326/347] Supports `@materialize` on schema declaration as well

fixes half of #94
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala    |  5 +++--
 .../materialize_annotation/compile.expected     | 17 +++++++++++++++++
 .../materialize_annotation/input.ddlog          |  6 ++++++
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 541504559..544609c0b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -407,8 +407,9 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
   }
 
   def compileExtractorBlock(stmt: Statement, stmts: List[Statement], outputRelation: String, cqs: List[ConjunctiveQuery]): CompiledBlocks = {
-    // look for @materialize annotation on any rule defining the same head
-    val shouldMaterialize = stmts flatMap (_.annotations) exists (_ named "materialize")
+    // look for @materialize annotation on the schema declaration or any rule defining the same head
+    val shouldMaterialize = ((schemaDeclarationByRelationName get outputRelation) ++ stmts
+      ) flatMap (_.annotations) exists (_ named "materialize")
     List(s"deepdive.extraction.extractors.${resolveExtractorBlockName(stmt)}" -> Map(
       "style" -> "sql_extractor",
       "input_relations" -> (stmts flatMap relationNamesUsedByStatement distinct),
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index 905f18a95..ba15f9c7b 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -65,6 +65,21 @@ materialize: true
 
 }
 
+deepdive.extraction.extractors.ext_S {
+sql: """
+SELECT R0.x AS column_0
+FROM D R0
+WHERE R0.x LIKE 'foo%'
+"""
+input_relations: [
+  D
+]
+style: sql_extractor
+output_relation: S
+materialize: true
+
+}
+
 deepdive.pipeline.run: ${PIPELINE}
 
 deepdive.pipeline.pipelines.extraction: [
@@ -72,6 +87,7 @@ deepdive.pipeline.pipelines.extraction: [
   ext_VQ
   ext_T
   ext_TQ
+  ext_S
 ]
 
 deepdive.pipeline.pipelines.endtoend: [
@@ -79,5 +95,6 @@ deepdive.pipeline.pipelines.endtoend: [
   ext_VQ
   ext_T
   ext_TQ
+  ext_S
 ]
 
diff --git a/test/expected-output-test/materialize_annotation/input.ddlog b/test/expected-output-test/materialize_annotation/input.ddlog
index 7a07e1d41..f73f7383a 100644
--- a/test/expected-output-test/materialize_annotation/input.ddlog
+++ b/test/expected-output-test/materialize_annotation/input.ddlog
@@ -20,3 +20,9 @@ TQ?(x text).
 
 # base table
 D(x text).
+
+
+# should recognize @materialize on the schema declaration as well
+@materialize
+S(x text).
+S(x) :- D(x), x LIKE "foo%".

From 1763dc8e829730c9a5165373ddb52ef383c01515 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Sun, 19 Jun 2016 14:08:47 -0700
Subject: [PATCH 327/347] Rename Multinomial to AndCategorical

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala |  6 +++---
 .../deepdive/ddlog/DeepDiveLogSemanticChecker.scala    |  6 +++---
 .../chunking_example/compile.expected                  | 10 +++++-----
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 544609c0b..74cd5cdfb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -537,16 +537,16 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
       }
 
       val categoricalVars = stmt.head.variables filter { t => isCategoricalRelation(t.atom.name) }
-      val isMultinomialFactor =
+      val isCategoricalAndFactor =
         if (categoricalVars.size == 0 || stmt.head.variables.size == categoricalVars.size)
           categoricalVars.size > 0
         else
           sys.error("None or all variables must be categorical")
 
       val function =
-        if (isMultinomialFactor) {
+        if (isCategoricalAndFactor) {
           stmt.head.function match {
-            case FactorFunction.IsTrue() | FactorFunction.And() => "Multinomial"
+            case FactorFunction.IsTrue() | FactorFunction.And() => "AndCategorical"
             case f => sys.error(s"Unsupported factor over categorical variables: ${f}")
           }
         } else { // Boolean
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
index 081f4f2cc..db3222edb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogSemanticChecker.scala
@@ -37,7 +37,7 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
     checkRelationDefined(stmt)
     checkFunctionDefined(stmt)
     checkVariableRelationSchema(stmt)
-    checkMultinomialFactors(stmt)
+    checkCategoricalFactors(stmt)
     checkNumberOfColumns(stmt)
     checkQuantifiedBody(stmt)
     checkWeight(stmt)
@@ -104,8 +104,8 @@ class DeepDiveLogSemanticChecker(program: DeepDiveLog.Program) {
 
   // TODO check if all factors have only isQuery relations in their heads
 
-  // check if any factors are defined across categorical and Boolean variables
-  def checkMultinomialFactors(stmt: Statement) = stmt match {
+  // check if any factors are defined across categorical and Boolean variables (not currently supported)
+  def checkCategoricalFactors(stmt: Statement) = stmt match {
     case s: InferenceRule =>
       val categoricalVars = s.head.variables filter { t =>
         schemaDeclarationByName get t.atom.name map(_.categoricalColumns nonEmpty) getOrElse(false) }
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 3131317d8..ec64f9663 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -11,7 +11,7 @@ sql: """
 SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R1.tag AS column_2
-     , 
+     ,
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS column_3
@@ -35,7 +35,7 @@ SELECT R0.sent_id AS column_0
      , R0.word AS column_2
      , R0.pos AS column_3
      , R0.true_tag AS column_4
-     , 
+     ,
 CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
      WHEN R0.true_tag = 'I-UCP' THEN NULL
      WHEN strpos(R0.true_tag, '-') > 0 THEN split_part(R0.true_tag, '-', 2)
@@ -99,7 +99,7 @@ WHERE R1.sent_id = R0.sent_id
   AND R0.sent_id = dd_id_0.sent_id
   AND R0.word_id = dd_id_0.word_id
 """
-function: """Multinomial(chunk.R0.dd_label)"""
+function: """AndCategorical(chunk.R0.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
@@ -143,7 +143,7 @@ WHERE R1.sent_id = R0.sent_id
   AND R1.sent_id = dd_id_1.sent_id
   AND R1.word_id = dd_id_1.word_id
 """
-function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
+function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
@@ -187,7 +187,7 @@ WHERE R1.sent_id = R0.sent_id
   AND R1.sent_id = dd_id_1.sent_id
   AND R1.word_id = dd_id_1.word_id
 """
-function: """Multinomial(chunk.R0.dd_label, chunk.R1.dd_label)"""
+function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk

From 482efae0c7ba273b93fcceb7c5c1118b4caadbc0 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Mon, 4 Jul 2016 13:36:35 -0700
Subject: [PATCH 328/347] Includes export-schema JSON in compile results

so DeepDive does not have to boot JVM twice during each compilation
---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala    | 8 +++++++-
 test/expected-output-test/arrays/compile.expected         | 2 ++
 .../chunking_example/compile.expected                     | 6 ++++--
 test/expected-output-test/expressions/compile.expected    | 2 ++
 .../factor_functions/compile.expected                     | 2 ++
 test/expected-output-test/if-then-else/compile.expected   | 2 ++
 test/expected-output-test/logical_rules/compile.expected  | 2 ++
 .../materialize_annotation/compile.expected               | 2 ++
 .../multiple_rules_for_same_head/compile.expected         | 2 ++
 test/expected-output-test/ocr_example/compile.expected    | 2 ++
 test/expected-output-test/smoke_example/compile.expected  | 2 ++
 test/expected-output-test/spouse_example/compile.expected | 2 ++
 test/expected-output-test/views/compile.expected          | 2 ++
 test/expected-output-test/weights/compile.expected        | 2 ++
 14 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 74cd5cdfb..115dfbe64 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -662,7 +662,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
     // compile the program into blocks of deepdive.conf
     val blocks = compiler.compile()
 
-    // codegen HOCON
+    // how to codegen HOCON
     def codegenValue(value: Any): String = value match {
       case QuotedString(s) => // multi-line string
         s"""\"\"\"${s replaceAll("\"\"\"", "\\\"\\\"\\\"")}\"\"\""""
@@ -691,6 +691,12 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
 
     }
 
+    // include the schema declarations before the compiled HOCON
+    print("deepdive.schema ")
+    DeepDiveLogSchemaExporter.run(parsedProgram, config)
+    println()
+
+    // codegen HOCON
     blocks foreach { case (key, value) => println(codegen(key, value)) }
   }
 
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index e47d5678e..5d5d1cc8f 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"R" : {"columns" : {"x" : {"type" : "int[]", "index" : 0}}}, "S" : {"columns" : {"x" : {"type" : "int", "index" : 0}, "y" : {"type" : "int[]", "index" : 1}}}, "T" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}, "U" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}}}
+
 deepdive.schema.variables {
 
 }
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index ec64f9663..cd88a412f 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"chunk" : {"columns" : {"sent_id" : {"type" : "bigint", "index" : 0, "annotations" : [{"name" : "key"}]}, "word_id" : {"type" : "bigint", "index" : 1, "annotations" : [{"name" : "key"}]}, "tag" : {"type" : "text", "index" : 2}}, "variable_type" : "categorical"}, "word_features" : {"columns" : {"sent_id" : {"type" : "bigint", "index" : 0}, "word_id" : {"type" : "bigint", "index" : 1}, "feature" : {"type" : "text", "index" : 2}}}, "words_raw" : {"columns" : {"word_id" : {"type" : "bigint", "index" : 1}, "pos" : {"type" : "text", "index" : 3}, "true_tag" : {"type" : "text", "index" : 4}, "sent_id" : {"type" : "bigint", "index" : 0}, "word" : {"type" : "text", "index" : 2}}}, "tags" : {"columns" : {"tag" : {"type" : "text", "index" : 0}}}, "words" : {"columns" : {"tag" : {"type" : "text", "index" : 5}, "word_id" : {"type" : "bigint", "index" : 1}, "pos" : {"type" : "text", "index" : 3}, "true_tag" : {"type" : "text", "index" : 4}, "sent_id" : {"type" : "bigint", "index" : 0}, "word" : {"type" : "text", "index" : 2}}}}}
+
 deepdive.schema.variables {
 chunk {
 tag: Categorical
@@ -11,7 +13,7 @@ sql: """
 SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R1.tag AS column_2
-     ,
+     , 
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS column_3
@@ -35,7 +37,7 @@ SELECT R0.sent_id AS column_0
      , R0.word AS column_2
      , R0.pos AS column_3
      , R0.true_tag AS column_4
-     ,
+     , 
 CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
      WHEN R0.true_tag = 'I-UCP' THEN NULL
      WHEN strpos(R0.true_tag, '-') > 0 THEN split_part(R0.true_tag, '-', 2)
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 31ef5acf6..7a345f6a3 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"E" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "X" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "N" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "T" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "Y" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}, "J" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "U" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "F" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "A" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "a" : {"columns" : {"k" : {"type" : "int", "index" : 0}}}, "M" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "I" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "G" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "V" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "Q" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}, "column_2" : {"type" : "UNKNOWN", "index" : 2}, "column_3" : {"type" : "UNKNOWN", "index" : 3}}}, "L" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "b" : {"columns" : {"k" : {"type" : "int", "index" : 0}, "p" : {"type" : "text", "index" : 1}, "q" : {"type" : "text", "index" : 2}, "r" : {"type" : "int", "index" : 3}}}, "B" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "P" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}, "column_2" : {"type" : "UNKNOWN", "index" : 2}}}, "C" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "H" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "c" : {"columns" : {"s" : {"type" : "text", "index" : 0}, "n" : {"type" : "int", "index" : 1}, "t" : {"type" : "text", "index" : 2}}}, "W" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "K" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "O" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "D" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "S" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}}}
+
 deepdive.schema.variables {
 
 }
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 4fc0d9790..050caa7e4 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"R" : {"columns" : {"a" : {"type" : "int", "index" : 0}, "b" : {"type" : "int", "index" : 1}, "c" : {"type" : "int", "index" : 2}}}, "S" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "Q" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}}}
+
 deepdive.schema.variables {
 S.dd_label: Boolean
 Q.dd_label: Boolean
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index ff57611ce..ee4aa4857 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"labels_resolved" : {"columns" : {"x" : {"type" : "INT", "index" : 0}, "l" : {"type" : "INT", "index" : 1}}}, "q" : {"columns" : {"x" : {"type" : "INT", "index" : 0}}, "variable_type" : "boolean"}, "labels" : {"columns" : {"x" : {"type" : "INT", "index" : 0}, "l" : {"type" : "BOOLEAN", "index" : 1}}}, "p" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}}}
+
 deepdive.schema.variables {
 q.dd_label: Boolean
 
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 4aa494cc2..6578a2638 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"data" : {"columns" : {"x" : {"type" : "int", "index" : 0}, "y" : {"type" : "int", "index" : 1}}}, "P" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "Q" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}}}
+
 deepdive.schema.variables {
 P.dd_label: Boolean
 Q.dd_label: Boolean
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index ba15f9c7b..a7d6580bc 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"T" : {"columns" : {"x" : {"type" : "text", "index" : 0}}}, "TQ" : {"columns" : {"x" : {"type" : "text", "index" : 0}}, "variable_type" : "boolean"}, "V" : {"columns" : {"x" : {"type" : "text", "index" : 0}}}, "VQ" : {"columns" : {"x" : {"type" : "text", "index" : 0}}, "variable_type" : "boolean"}, "D" : {"columns" : {"x" : {"type" : "text", "index" : 0}}}, "S" : {"columns" : {"x" : {"type" : "text", "index" : 0}}, "annotations" : [{"name" : "materialize"}]}}}
+
 deepdive.schema.variables {
 VQ.dd_label: Boolean
 TQ.dd_label: Boolean
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 47e43d9f0..29db11567 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"S_2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T___1" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "S_1" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T_2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T___2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "Q" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "T___3" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "S_0" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T__3" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "T___0" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "R" : {"columns" : {"a" : {"type" : "int", "index" : 0}, "b" : {"type" : "int", "index" : 1}}}, "S" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}}}
+
 deepdive.schema.variables {
 Q.dd_label: Boolean
 
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index bd3515c30..c8e7a8015 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"label1" : {"columns" : {"wid" : {"type" : "INT", "index" : 0}, "val" : {"type" : "BOOLEAN", "index" : 1}}}, "features" : {"columns" : {"id" : {"type" : "BIGSERIAL", "index" : 0}, "word_id" : {"type" : "INT", "index" : 1}, "feature_id" : {"type" : "INT", "index" : 2}, "feature_val" : {"type" : "BOOLEAN", "index" : 3}}}, "label2" : {"columns" : {"wid" : {"type" : "INT", "index" : 0}, "val" : {"type" : "BOOLEAN", "index" : 1}}}, "q1" : {"columns" : {"wid" : {"type" : "INT", "index" : 0}}, "variable_type" : "boolean"}, "q2" : {"columns" : {"wid" : {"type" : "INT", "index" : 0}}, "variable_type" : "boolean"}}}
+
 deepdive.schema.variables {
 q1.dd_label: Boolean
 q2.dd_label: Boolean
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index a12a923d8..18e58706b 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"person_smokes" : {"columns" : {"person_id" : {"type" : "bigint", "index" : 0}, "smokes" : {"type" : "boolean", "index" : 1}}}, "smoke" : {"columns" : {"person_id" : {"type" : "bigint", "index" : 0}}, "variable_type" : "boolean"}, "cancer" : {"columns" : {"person_id" : {"type" : "bigint", "index" : 0}}, "variable_type" : "boolean"}, "friends" : {"columns" : {"person_id" : {"type" : "bigint", "index" : 0}, "friend_id" : {"type" : "bigint", "index" : 1}}}, "person_has_cancer" : {"columns" : {"person_id" : {"type" : "bigint", "index" : 0}, "has_cancer" : {"type" : "boolean", "index" : 1}}}, "person" : {"columns" : {"person_id" : {"type" : "bigint", "index" : 0}, "name" : {"type" : "text", "index" : 1}}}}}
+
 deepdive.schema.variables {
 smoke.dd_label: Boolean
 cancer.dd_label: Boolean
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index e89bb3ee2..a4a0328f5 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"sentences" : {"columns" : {"lemma" : {"type" : "text[]", "index" : 3}, "document_id" : {"type" : "text", "index" : 0}, "sentence_offset" : {"type" : "int", "index" : 7}, "ner_tags" : {"type" : "text[]", "index" : 6}, "words" : {"type" : "text[]", "index" : 2}, "pos_tags" : {"type" : "text[]", "index" : 4}, "dependencies" : {"type" : "text[]", "index" : 5}, "sentence" : {"type" : "text", "index" : 1}, "sentence_id" : {"type" : "text", "index" : 8}}}, "has_spouse_candidates" : {"columns" : {"description" : {"type" : "text", "index" : 3}, "person2_id" : {"type" : "text", "index" : 1}, "person1_id" : {"type" : "text", "index" : 0}, "is_true" : {"type" : "boolean", "index" : 5}, "relation_id" : {"type" : "text", "index" : 4}, "sentence_id" : {"type" : "text", "index" : 2}}}, "has_spouse" : {"columns" : {"relation_id" : {"type" : "text", "index" : 0}}, "variable_type" : "boolean"}, "articles" : {"columns" : {"article_id" : {"type" : "text", "index" : 0}, "text" : {"type" : "text", "index" : 1}}}, "has_spouse_features" : {"columns" : {"relation_id" : {"type" : "text", "index" : 0}, "feature" : {"type" : "text", "index" : 1}}}, "people_mentions" : {"columns" : {"text" : {"type" : "text", "index" : 3}, "length" : {"type" : "int", "index" : 2}, "mention_id" : {"type" : "text", "index" : 4}, "start_position" : {"type" : "int", "index" : 1}, "sentence_id" : {"type" : "text", "index" : 0}}}}}
+
 deepdive.schema.variables {
 has_spouse.dd_label: Boolean
 
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 541295d7f..763e65be3 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"R" : {"columns" : {"a" : {"type" : "int", "index" : 0}, "b" : {"type" : "int", "index" : 1}}}, "A" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}, "B" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}, "column_1" : {"type" : "UNKNOWN", "index" : 1}}}}}
+
 deepdive.schema.variables {
 
 }
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 3a752cd17..4ba471cc0 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -1,3 +1,5 @@
+deepdive.schema {"relations" : {"e" : {"columns" : {"k" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "f" : {"columns" : {"k" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "a" : {"columns" : {"k" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "b" : {"columns" : {"k" : {"type" : "int", "index" : 0}, "p" : {"type" : "int", "index" : 1}, "q" : {"type" : "text", "index" : 2}}}, "c" : {"columns" : {"k" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "d" : {"columns" : {"k" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}}}
+
 deepdive.schema.variables {
 f.dd_label: Boolean
 c.dd_label: Boolean

From 737ebb01912c691f980eb5c531401ffa79cb871e Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Mon, 4 Jul 2016 13:41:06 -0700
Subject: [PATCH 329/347] Removes legacy PIPELINE stuff from compiled HOCON

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 15 -----
 .../arrays/compile.expected                   | 12 ----
 .../chunking_example/compile.expected         | 23 --------
 .../expressions/compile.expected              | 56 -------------------
 .../factor_functions/compile.expected         | 12 ----
 .../if-then-else/compile.expected             | 14 -----
 .../logical_rules/compile.expected            | 17 ------
 .../materialize_annotation/compile.expected   | 18 ------
 .../compile.expected                          | 43 --------------
 .../ocr_example/compile.expected              | 19 -------
 .../smoke_example/compile.expected            | 19 -------
 .../spouse_example/compile.expected           | 21 -------
 .../views/compile.expected                    | 12 ----
 .../weights/compile.expected                  | 18 ------
 14 files changed, 299 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 115dfbe64..e88d59017 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -602,19 +602,6 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
     case _ => sys.error(s"Compiler does not recognize statement: ${stmt}")
   }
 
-  // generate application.conf pipelines
-  def compilePipelines(): CompiledBlocks = {
-    val run = List("deepdive.pipeline.run" -> "${PIPELINE}")
-    val extraction = statements filter(representativeStatements contains _) map resolveExtractorBlockName
-    val extraction_pipeline = if (extraction nonEmpty) List("deepdive.pipeline.pipelines.extraction" -> extraction) else List.empty
-    val inference = inferenceRules map resolveInferenceBlockName
-    val inference_pipeline = if (inference nonEmpty) List("deepdive.pipeline.pipelines.inference" -> inference) else List.empty
-    val endtoend = extraction ++ inference
-    val endtoend_pipeline = if (endtoend nonEmpty) List("deepdive.pipeline.pipelines.endtoend" -> endtoend) else List.empty
-
-    run ++ extraction_pipeline ++ inference_pipeline ++ endtoend_pipeline
-  }
-
   // generate variable schema statements
   def compileVariableSchema(): CompiledBlocks = {
     // generate the statements.
@@ -632,8 +619,6 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
     compileVariableSchema()
     ++
     (statements flatMap compile)
-    ++
-    compilePipelines()
   )
 
 }
diff --git a/test/expected-output-test/arrays/compile.expected b/test/expected-output-test/arrays/compile.expected
index 5d5d1cc8f..93da04246 100644
--- a/test/expected-output-test/arrays/compile.expected
+++ b/test/expected-output-test/arrays/compile.expected
@@ -40,15 +40,3 @@ materialize: false
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_T
-  ext_U
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_T
-  ext_U
-]
-
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index cd88a412f..dee912048 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -199,26 +199,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_chunk
-  ext_words
-  ext_word_features_by_ext_features
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_chunk
-  inf_and_chunk_chunk
-  inf1_and_chunk_chunk
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_chunk
-  ext_words
-  ext_word_features_by_ext_features
-  inf_istrue_chunk
-  inf_and_chunk_chunk
-  inf1_and_chunk_chunk
-]
-
diff --git a/test/expected-output-test/expressions/compile.expected b/test/expected-output-test/expressions/compile.expected
index 7a345f6a3..bc215df9a 100644
--- a/test/expected-output-test/expressions/compile.expected
+++ b/test/expected-output-test/expressions/compile.expected
@@ -398,59 +398,3 @@ materialize: false
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_Q
-  ext_P
-  ext_A
-  ext_B
-  ext_C
-  ext_D
-  ext_E
-  ext_F
-  ext_G
-  ext_H
-  ext_I
-  ext_J
-  ext_K
-  ext_L
-  ext_M
-  ext_N
-  ext_O
-  ext_S
-  ext_T
-  ext_U
-  ext_W
-  ext_V
-  ext_X
-  ext_Y
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_Q
-  ext_P
-  ext_A
-  ext_B
-  ext_C
-  ext_D
-  ext_E
-  ext_F
-  ext_G
-  ext_H
-  ext_I
-  ext_J
-  ext_K
-  ext_L
-  ext_M
-  ext_N
-  ext_O
-  ext_S
-  ext_T
-  ext_U
-  ext_W
-  ext_V
-  ext_X
-  ext_Y
-]
-
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 050caa7e4..66ba605af 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -58,15 +58,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.inference: [
-  inf_imply_Q_Q
-  inf_equal_Q_not_Q
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  inf_imply_Q_Q
-  inf_equal_Q_not_Q
-]
-
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index ee4aa4857..4894ca95e 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -69,17 +69,3 @@ materialize: false
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_q
-  ext_p
-  ext_labels_resolved
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_q
-  ext_p
-  ext_labels_resolved
-]
-
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 6578a2638..56f7f5303 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -60,20 +60,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_P
-  ext_Q
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_imply_P_Q
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_P
-  ext_Q
-  inf_imply_P_Q
-]
-
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index a7d6580bc..8539059be 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -82,21 +82,3 @@ materialize: true
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_V
-  ext_VQ
-  ext_T
-  ext_TQ
-  ext_S
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_V
-  ext_VQ
-  ext_T
-  ext_TQ
-  ext_S
-]
-
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 29db11567..cbd4d5c1c 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -367,46 +367,3 @@ materialize: false
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_S
-  ext_T___0_by_f
-  ext_T
-  ext_T___1_by_f
-  ext_T___2_by_f
-  ext_S_0_by_f
-  ext_S_1_by_f
-  ext_T___3_by_f_1
-  ext_S_2_by_f_1
-  ext_T__3
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_Q
-  inf1_istrue_Q
-  inf_istrue_not_Q
-  inf_imply_Q_Q
-  inf1_imply_Q_Q
-  inf2_imply_Q_Q
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_S
-  ext_T___0_by_f
-  ext_T
-  ext_T___1_by_f
-  ext_T___2_by_f
-  ext_S_0_by_f
-  ext_S_1_by_f
-  ext_T___3_by_f_1
-  ext_S_2_by_f_1
-  ext_T__3
-  inf_istrue_Q
-  inf1_istrue_Q
-  inf_istrue_not_Q
-  inf_imply_Q_Q
-  inf1_imply_Q_Q
-  inf2_imply_Q_Q
-]
-
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index c8e7a8015..1476348c2 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -76,22 +76,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_q1
-  ext_q2
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_q1
-  inf_istrue_q2
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_q1
-  ext_q2
-  inf_istrue_q1
-  inf_istrue_q2
-]
-
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 18e58706b..64ba57018 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -87,22 +87,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_smoke
-  ext_cancer
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_imply_smoke_cancer
-  inf_imply_smoke_smoke
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_smoke
-  ext_cancer
-  inf_imply_smoke_cancer
-  inf_imply_smoke_smoke
-]
-
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index a4a0328f5..42ab1f514 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -114,24 +114,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
-  ext_has_spouse_features_by_ext_has_spouse_features
-  ext_has_spouse
-]
-
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_has_spouse
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_people_mentions_by_ext_people
-  ext_has_spouse_candidates_by_ext_has_spouse
-  ext_has_spouse_features_by_ext_has_spouse_features
-  ext_has_spouse
-  inf_istrue_has_spouse
-]
-
diff --git a/test/expected-output-test/views/compile.expected b/test/expected-output-test/views/compile.expected
index 763e65be3..13f206d9d 100644
--- a/test/expected-output-test/views/compile.expected
+++ b/test/expected-output-test/views/compile.expected
@@ -37,15 +37,3 @@ materialize: false
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.extraction: [
-  ext_A
-  ext_B
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  ext_A
-  ext_B
-]
-
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 4ba471cc0..a17cab4b0 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -107,21 +107,3 @@ input_relations: [
 
 }
 
-deepdive.pipeline.run: ${PIPELINE}
-
-deepdive.pipeline.pipelines.inference: [
-  inf_istrue_a
-  inf_istrue_c
-  inf_istrue_d
-  inf_istrue_e
-  inf_istrue_f
-]
-
-deepdive.pipeline.pipelines.endtoend: [
-  inf_istrue_a
-  inf_istrue_c
-  inf_istrue_d
-  inf_istrue_e
-  inf_istrue_f
-]
-

From 6370c28b6024400263108086ee8653e2a353a4d6 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Thu, 31 Mar 2016 19:43:32 -0700
Subject: [PATCH 330/347] Support for UDF that `handles tsj lines`

drops `plpy`
---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 34fba2ad7..8d7fb916d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -251,12 +251,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
     ) named "function input/output type declaration"
 
   def functionImplementation : Parser[FunctionImplementationDeclaration] =
-    ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsv" | "json") ~ "lines" ^^ {
+    ( "implementation" ~ stringLiteralAsString ~ "handles" ~ ("tsj" | "tsv" | "json") ~ "lines" ^^ {
         case (_ ~ command ~ _ ~ style ~ _) => RowWiseLineHandler(command=command, style=style)
       }
-    | "implementation" ~ stringLiteralAsString ~ "runs" ~ "as" ~ "plpy" ^^ {
-        case (_ ~ command ~ _ ~ _ ~ style) => RowWiseLineHandler(command=command, style=style)
-      }
     ) named "function implementation declaration"
 
   def functionDeclaration : Parser[FunctionDeclaration] =

From 0fa3fd9f071a2d96cdefd28cd99aa878e474b165 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Thu, 7 Jul 2016 12:10:58 -0700
Subject: [PATCH 331/347] Switches some tests to `handles tsj lines`

---
 examples/spouse_example.ddlog                             | 6 +++---
 test/expected-output-test/spouse_example/compile.expected | 6 +++---
 test/expected-output-test/spouse_example/print.expected   | 6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/examples/spouse_example.ddlog b/examples/spouse_example.ddlog
index 014352b9d..67300e6ae 100644
--- a/examples/spouse_example.ddlog
+++ b/examples/spouse_example.ddlog
@@ -36,7 +36,7 @@ has_spouse?(relation_id text).
 
 function ext_people over (sentence_id text, words text, ner_tags text)
                  returns rows like people_mentions
-  implementation "udf/ext_people.py" handles tsv lines.
+  implementation "udf/ext_people.py" handles tsj lines.
 
 people_mentions +=
   ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
@@ -44,7 +44,7 @@ people_mentions +=
 
 function ext_has_spouse over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
                      returns rows like has_spouse_candidates
-  implementation "udf/ext_has_spouse.py" handles tsv lines.
+  implementation "udf/ext_has_spouse.py" handles tsj lines.
 
 has_spouse_candidates +=
   ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
@@ -53,7 +53,7 @@ has_spouse_candidates +=
 
 function ext_has_spouse_features over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
                               returns rows like has_spouse_features
-  implementation "udf/ext_has_spouse_features.py" handles tsv lines.
+  implementation "udf/ext_has_spouse_features.py" handles tsj lines.
 
 has_spouse_features +=
   ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 42ab1f514..9eeae0daa 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -10,7 +10,7 @@ parallelism: ${PARALLELISM}
 input_relations: [
   sentences
 ]
-style: tsv_extractor
+style: tsj_extractor
 output_relation: people_mentions
 udf: """udf/ext_people.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
@@ -28,7 +28,7 @@ parallelism: ${PARALLELISM}
 input_relations: [
   people_mentions
 ]
-style: tsv_extractor
+style: tsj_extractor
 output_relation: has_spouse_candidates
 udf: """udf/ext_has_spouse.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
@@ -52,7 +52,7 @@ input_relations: [
   has_spouse_candidates
   people_mentions
 ]
-style: tsv_extractor
+style: tsj_extractor
 output_relation: has_spouse_features
 udf: """udf/ext_has_spouse_features.py"""
 input_batch_size: ${INPUT_BATCH_SIZE}
diff --git a/test/expected-output-test/spouse_example/print.expected b/test/expected-output-test/spouse_example/print.expected
index 917067752..b7dd4a1b1 100644
--- a/test/expected-output-test/spouse_example/print.expected
+++ b/test/expected-output-test/spouse_example/print.expected
@@ -33,7 +33,7 @@ function ext_people
     over (sentence_id text, words text, ner_tags text)
  returns rows like people_mentions
  implementation "udf/ext_people.py"
-        handles tsv lines.
+        handles tsj lines.
 
 people_mentions += ext_people(s, ARRAY_TO_STRING(words, "~^~"), ARRAY_TO_STRING(ner_tags, "~^~")) :-
     sentences(_, _, words, _, _, _, ner_tags, _, s).
@@ -42,7 +42,7 @@ function ext_has_spouse
     over (sentence_id text, mid1 text, text1 text, mid2 text, text2 text)
  returns rows like has_spouse_candidates
  implementation "udf/ext_has_spouse.py"
-        handles tsv lines.
+        handles tsj lines.
 
 has_spouse_candidates += ext_has_spouse(s, p1_id, p1_text, p2_id, p2_text) :-
     people_mentions(s, _, _, p1_text, p1_id),
@@ -52,7 +52,7 @@ function ext_has_spouse_features
     over (words text, rid text, position1 int, length1 int, position2 int, length2 int)
  returns rows like has_spouse_features
  implementation "udf/ext_has_spouse_features.py"
-        handles tsv lines.
+        handles tsj lines.
 
 has_spouse_features += ext_has_spouse_features(ARRAY_TO_STRING(words, "~^~"), rid, p1idx, p1len, p2idx, p2len) :-
     sentences(_, _, words, _, _, _, _, _, s),

From 23cfcb9ef0b2c9339031bf4577a5fd439c13e7a7 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Mon, 11 Jul 2016 20:43:39 -0700
Subject: [PATCH 332/347] Fix categorical grounding: introduce
 non_category_weight_cols

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 27 +++++++++++-
 .../deepdive/ddlog/DeepDiveLogParser.scala    |  8 ++++
 .../chunking_example/compile.expected         | 21 +++++++---
 .../factor_functions/compile.expected         | 14 +++++--
 .../logical_rules/compile.expected            |  7 +++-
 .../compile.expected                          | 42 +++++++++++++------
 .../ocr_example/compile.expected              | 14 +++++--
 .../smoke_example/compile.expected            | 14 +++++--
 .../spouse_example/compile.expected           |  7 +++-
 .../weights/compile.expected                  | 36 +++++++++++-----
 10 files changed, 145 insertions(+), 45 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index e88d59017..a836baecd 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -4,6 +4,7 @@ package org.deepdive.ddlog
 // See: https://docs.google.com/document/d/1SBIvvki3mnR28Mf0Pkin9w9mWNam5AA0SpIGj1ZN2c4
 
 import scala.collection.immutable.HashMap
+import scala.collection.mutable.HashSet
 import scala.language.postfixOps
 
 // Compiler that takes parsed program as input and turns into blocks of deepdive.conf
@@ -134,6 +135,9 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
   // conditions, select, etc.)
   var query_schema = new HashMap[ String, Tuple2[String,Variable] ]()
 
+  // Set of all symbols ever unified with a categorical column
+  var categorical_val_vars = new HashSet[String]()
+
   // maps each variable name to a canonical version of itself (first occurrence in body in left-to-right order)
   // index is the index of the subgoal/atom this variable is found in the body.
   // variable is the complete Variable type for the found variable.
@@ -142,8 +146,14 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
       a.terms.zipWithIndex.foreach { case (expr, i) =>
         expr match {
           case VarPattern(v) =>
+            schemaDeclarationByRelationName get(a.name) map {
+              case decl =>
+                if (decl.categoricalColumnIndexes contains i)
+                  categorical_val_vars += v
+            }
+
             if (! (query_schema contains v) )
-              query_schema += { v -> (index, Variable(v,a.name,i) ) }
+              query_schema += { v -> (index, Variable(v, a.name, i) ) }
           case _ =>
         }
       }
@@ -189,6 +199,13 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
     case UseVariableAsAlias => s""" AS "${DeepDiveLogPrettyPrinter.print(e)}\""""
   }
 
+  def isCategoricalColumn(e: Expr) : Boolean = {
+    e match {
+      case VarExpr(name) => categorical_val_vars contains name
+      case _ => false
+    }
+  }
+
   // resolve an expression
   def compileExpr(e: Expr) : String = compileExpr(e, 0)
   def compileExpr(e: Expr, level: Int) : String = {
@@ -508,6 +525,8 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
       case _ => List.empty
     } flatten
 
+    var nonCategoryWeightCols = new HashSet[String]()
+
     val inputQueries =
       stmt.q.bodies map { case cqBody =>
         // Here we need to select from the bodies atoms as well as the head atoms,
@@ -519,6 +538,11 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         // TODO XXX: Fix the `internal` hack below
         val qc = new QueryCompiler(fakeCQ, internalVarTables, internalVarJoinConds)
 
+        stmt.weights.variables.zipWithIndex.foreach {case(s: Expr, i) =>
+          if (!qc.isCategoricalColumn(s))
+            nonCategoryWeightCols += s"${deepdiveWeightColumnPrefix}${i}"
+        }
+
         // weight columns
         val weightColumns = stmt.weights.variables.zipWithIndex collect {
           case (s: Expr, i) if !s.isInstanceOf[ConstExpr] =>
@@ -584,6 +608,7 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         "input_query" -> QuotedString("\n"+inputQueries.mkString(" UNION ALL ")+"\n"),
         "function" -> QuotedString(func),
         "weight" -> QuotedString(weight),
+        "non_category_weight_cols" -> nonCategoryWeightCols.toList.sorted,
         "input_relations" -> {
           val relationsInHead = stmt.head.variables map (_.atom.name)
           val relationsInBody = relationNamesUsedByStatement getOrElse(stmt, List.empty)
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 34fba2ad7..c93f296b9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -137,6 +137,14 @@ case class SchemaDeclaration(a: Attribute,
       a.terms diff keyColumns toList
     else
       List.empty
+
+  val categoricalColumnIndexes : Set[Int] =
+    if (isQuery)
+      a.terms.zipWithIndex.filter { case(term, i) =>
+        categoricalColumns contains term
+      } map { _._2} toSet
+    else
+      Set.empty
 }
 case class FunctionDeclaration(functionName: String,
                                inputType: FunctionInputOutputType,
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index dee912048..ffe547f87 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -81,6 +81,10 @@ WHERE R1.sent_id = R0.sent_id
 }
 
 deepdive.inference.factors.inf_istrue_chunk {
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
@@ -101,18 +105,21 @@ WHERE R1.sent_id = R0.sent_id
   AND R0.sent_id = dd_id_0.sent_id
   AND R0.word_id = dd_id_0.word_id
 """
-function: """AndCategorical(chunk.R0.dd_label)"""
-weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
   words
   tags
   word_features
 ]
+function: """AndCategorical(chunk.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_and_chunk_chunk {
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
+non_category_weight_cols: [
+  
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
@@ -145,17 +152,20 @@ WHERE R1.sent_id = R0.sent_id
   AND R1.sent_id = dd_id_1.sent_id
   AND R1.word_id = dd_id_1.word_id
 """
-function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
-weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
   words
   tags
 ]
+function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf1_and_chunk_chunk {
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
+non_category_weight_cols: [
+  
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
@@ -189,13 +199,12 @@ WHERE R1.sent_id = R0.sent_id
   AND R1.sent_id = dd_id_1.sent_id
   AND R1.word_id = dd_id_1.word_id
 """
-function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
-weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   chunk
   words
   tags
 ]
+function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 66ba605af..237f7bb67 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -7,6 +7,10 @@ Q.dd_label: Boolean
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -23,16 +27,19 @@ WHERE R2.a = R0.x
   AND R0.x = dd_id_0.x
   AND R1.x = dd_id_1.x
 """
-function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
   R
 ]
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_equal_Q_not_Q {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -49,12 +56,11 @@ WHERE R2.a = R0.x
   AND R0.x = dd_id_0.x
   AND R1.x = dd_id_1.x
 """
-function: """Equal(Q.R0.dd_label, !Q.R1.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
   R
 ]
+function: """Equal(Q.R0.dd_label, !Q.R1.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 56f7f5303..845f68971 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -37,6 +37,10 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_imply_P_Q {
+weight: """1"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
@@ -51,12 +55,11 @@ WHERE R1.x = R0.x
   AND R0.x = dd_id_0.x
   AND R1.x = dd_id_1.x
 """
-function: """Imply(P.R0.dd_label, Q.R1.dd_label)"""
-weight: """1"""
 input_relations: [
   P
   Q
 ]
+function: """Imply(P.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index cbd4d5c1c..07d579fd2 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -200,6 +200,10 @@ WHERE R0.a > 0
 }
 
 deepdive.inference.factors.inf_istrue_Q {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -211,16 +215,19 @@ WHERE R1.a = R0.x
   AND R0.x > 1000
   AND R0.x = dd_id_0.x
 """
-function: """Imply(Q.R0.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
   S
 ]
+function: """Imply(Q.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf1_istrue_Q {
+weight: """1.0"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -231,16 +238,19 @@ WHERE R1.a = R0.x
   AND R0.x = 0
   AND R0.x = dd_id_0.x
 """
-function: """Imply(Q.R0.dd_label)"""
-weight: """1.0"""
 input_relations: [
   Q
   S
 ]
+function: """Imply(Q.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_istrue_not_Q {
+weight: """?"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -251,16 +261,19 @@ WHERE R1.a = R0.x
   AND R0.x < 1000
   AND R0.x = dd_id_0.x
 """
-function: """Imply(!Q.R0.dd_label)"""
-weight: """?"""
 input_relations: [
   Q
   S
 ]
+function: """Imply(!Q.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_imply_Q_Q {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -281,17 +294,20 @@ WHERE R2.a = R0.x
   AND R0.x = dd_id_0.x
   AND R1.x = dd_id_1.x
 """
-function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   Q
   S
   R
 ]
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf1_imply_Q_Q {
+weight: """-10.0"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -312,17 +328,20 @@ WHERE R2.a = R0.x
   AND R0.x = dd_id_0.x
   AND R1.x = dd_id_1.x
 """
-function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
-weight: """-10.0"""
 input_relations: [
   Q
   S
   R
 ]
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf2_imply_Q_Q {
+weight: """10.0"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
@@ -343,13 +362,12 @@ WHERE R2.a = R0.x
   AND R0.x = dd_id_0.x
   AND R1.x = dd_id_1.x
 """
-function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
-weight: """10.0"""
 input_relations: [
   Q
   S
   R
 ]
+function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 1476348c2..63b3a69c2 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -37,6 +37,10 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_istrue_q1 {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
@@ -47,16 +51,19 @@ FROM q1 R0
 WHERE R1.word_id = R0.wid
   AND R0.wid = dd_id_0.wid
 """
-function: """Imply(q1.R0.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   q1
   features
 ]
+function: """Imply(q1.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_istrue_q2 {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
@@ -67,12 +74,11 @@ FROM q2 R0
 WHERE R1.word_id = R0.wid
   AND R0.wid = dd_id_0.wid
 """
-function: """Imply(q2.R0.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   q2
   features
 ]
+function: """Imply(q2.R0.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 64ba57018..98291fa37 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -37,6 +37,10 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_imply_smoke_cancer {
+weight: """0.5"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
@@ -52,17 +56,20 @@ WHERE R1.person_id = R0.person_id
   AND R0.person_id = dd_id_0.person_id
   AND R1.person_id = dd_id_1.person_id
 """
-function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
-weight: """0.5"""
 input_relations: [
   smoke
   cancer
   person_smokes
 ]
+function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_imply_smoke_smoke {
+weight: """0.4"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
@@ -78,12 +85,11 @@ WHERE R2.person_id = R0.person_id
   AND R0.person_id = dd_id_0.person_id
   AND R1.person_id = dd_id_1.person_id
 """
-function: """Imply(smoke.R0.dd_label, smoke.R1.dd_label)"""
-weight: """0.4"""
 input_relations: [
   smoke
   friends
 ]
+function: """Imply(smoke.R0.dd_label, smoke.R1.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 42ab1f514..549a20193 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -92,6 +92,10 @@ materialize: false
 }
 
 deepdive.inference.factors.inf_istrue_has_spouse {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
@@ -104,13 +108,12 @@ WHERE R1.relation_id = R0.relation_id
   AND R2.relation_id = R0.relation_id
   AND R0.relation_id = dd_id_0.relation_id
 """
-function: """Imply(has_spouse.R0.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   has_spouse
   has_spouse_candidates
   has_spouse_features
 ]
+function: """Imply(has_spouse.R0.dd_label)"""
 
 }
 
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index a17cab4b0..0abb6ecc7 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -10,6 +10,10 @@ e.dd_label: Boolean
 }
 
 deepdive.inference.factors.inf_istrue_a {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
@@ -20,16 +24,19 @@ FROM a R0
 WHERE R1.k = R0.k
   AND R0.k = dd_id_0.k
 """
-function: """Imply(a.R0.dd_label)"""
-weight: """?(dd_weight_column_0)"""
 input_relations: [
   a
   b
 ]
+function: """Imply(a.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_istrue_c {
+weight: """?"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
@@ -39,16 +46,20 @@ FROM c R0
 WHERE R1.k = R0.k
   AND R0.k = dd_id_0.k
 """
-function: """Imply(c.R0.dd_label)"""
-weight: """?"""
 input_relations: [
   c
   b
 ]
+function: """Imply(c.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_istrue_d {
+weight: """?(dd_weight_column_0, dd_weight_column_1)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+  dd_weight_column_1
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
@@ -60,16 +71,19 @@ FROM d R0
 WHERE R1.k = R0.k
   AND R0.k = dd_id_0.k
 """
-function: """Imply(d.R0.dd_label)"""
-weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 input_relations: [
   d
   b
 ]
+function: """Imply(d.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_istrue_e {
+weight: """-10"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
@@ -79,16 +93,19 @@ FROM e R0
 WHERE R1.k = R0.k
   AND R0.k = dd_id_0.k
 """
-function: """Imply(e.R0.dd_label)"""
-weight: """-10"""
 input_relations: [
   e
   b
 ]
+function: """Imply(e.R0.dd_label)"""
 
 }
 
 deepdive.inference.factors.inf_istrue_f {
+weight: """-0.3"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
 input_query: """
 SELECT dd_id_0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
@@ -98,12 +115,11 @@ FROM f R0
 WHERE R1.k = R0.k
   AND R0.k = dd_id_0.k
 """
-function: """Imply(f.R0.dd_label)"""
-weight: """-0.3"""
 input_relations: [
   f
   b
 ]
+function: """Imply(f.R0.dd_label)"""
 
 }
 

From 091296cd6e04fc21e9ec384eba6f2b5de7ec90c6 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Mon, 11 Jul 2016 20:58:00 -0700
Subject: [PATCH 333/347] exclude constant weights

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala      | 11 ++++++-----
 .../logical_rules/compile.expected                    |  2 +-
 .../multiple_rules_for_same_head/compile.expected     |  8 ++++----
 .../smoke_example/compile.expected                    |  4 ++--
 test/expected-output-test/weights/compile.expected    |  6 +++---
 5 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index a836baecd..f3fa30a8d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -538,17 +538,18 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         // TODO XXX: Fix the `internal` hack below
         val qc = new QueryCompiler(fakeCQ, internalVarTables, internalVarJoinConds)
 
-        stmt.weights.variables.zipWithIndex.foreach {case(s: Expr, i) =>
-          if (!qc.isCategoricalColumn(s))
-            nonCategoryWeightCols += s"${deepdiveWeightColumnPrefix}${i}"
-        }
-
         // weight columns
         val weightColumns = stmt.weights.variables.zipWithIndex collect {
           case (s: Expr, i) if !s.isInstanceOf[ConstExpr] =>
             s"""${qc.compileExpr(s)} AS "${deepdiveWeightColumnPrefix}${i}\""""
         }
 
+        // nonCategoryWeightCols
+        stmt.weights.variables.zipWithIndex.foreach {case(s: Expr, i) =>
+          if (!s.isInstanceOf[ConstExpr] && !qc.isCategoricalColumn(s))
+            nonCategoryWeightCols += s"${deepdiveWeightColumnPrefix}${i}"
+        }
+
         // factor input query
         s"""SELECT ${(variableIdAndColumns ++ weightColumns) mkString ("\n     , ")
         }\n${qc.generateSQLBody(fakeBody) }"""
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 845f68971..0f9115ef8 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -39,7 +39,7 @@ materialize: false
 deepdive.inference.factors.inf_imply_P_Q {
 weight: """1"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "P.R0.dd_id"
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index 07d579fd2..cfdb1027a 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -226,7 +226,7 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf1_istrue_Q {
 weight: """1.0"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
@@ -249,7 +249,7 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_not_Q {
 weight: """?"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
@@ -306,7 +306,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf1_imply_Q_Q {
 weight: """-10.0"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
@@ -340,7 +340,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf2_imply_Q_Q {
 weight: """10.0"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 98291fa37..5d13d395e 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -39,7 +39,7 @@ materialize: false
 deepdive.inference.factors.inf_imply_smoke_cancer {
 weight: """0.5"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
@@ -68,7 +68,7 @@ function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_smoke_smoke {
 weight: """0.4"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 0abb6ecc7..ad0612c61 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -35,7 +35,7 @@ function: """Imply(a.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_c {
 weight: """?"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "c.R0.dd_id"
@@ -82,7 +82,7 @@ function: """Imply(d.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_e {
 weight: """-10"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "e.R0.dd_id"
@@ -104,7 +104,7 @@ function: """Imply(e.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_f {
 weight: """-0.3"""
 non_category_weight_cols: [
-  dd_weight_column_0
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "f.R0.dd_id"

From 157b94ddb80005b77c710f71fad06f0f8c3c7660 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Fri, 15 Jul 2016 20:17:05 -0700
Subject: [PATCH 334/347] Add "@value" annotation to support continuous
 features

---
 examples/chunking.ddlog                             |  1 +
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala    |  5 ++++-
 .../org/deepdive/ddlog/DeepDiveLogParser.scala      | 13 +++++++++++--
 .../chunking_example/compile.expected               |  3 +++
 .../factor_functions/compile.expected               |  2 ++
 .../logical_rules/compile.expected                  |  1 +
 .../multiple_rules_for_same_head/compile.expected   |  6 ++++++
 .../ocr_example/compile.expected                    |  2 ++
 .../smoke_example/compile.expected                  |  2 ++
 .../spouse_example/compile.expected                 |  1 +
 test/expected-output-test/weights/compile.expected  |  5 +++++
 11 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index f17d83f26..4f3165e11 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -62,6 +62,7 @@ word_features +=
   word1 IS NOT NULL.
 
 @weight(f, tag)
+@value(f)
 chunk(s, w, tag) :-
                       words(s, w, _, _, _, _), tags(tag), # XXX just to make it compile. remove after fixing https://github.com/HazyResearch/ddlog/issues/72
   word_features(s, w, f).
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index f3fa30a8d..6d647a969 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -550,8 +550,11 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
             nonCategoryWeightCols += s"${deepdiveWeightColumnPrefix}${i}"
         }
 
+        val valueExpr = if (stmt.valueExpr != null) stmt.valueExpr else IntConst(1)
+        val valueColumn = s"""(${qc.compileExpr(valueExpr)})::float AS factor_value"""
+
         // factor input query
-        s"""SELECT ${(variableIdAndColumns ++ weightColumns) mkString ("\n     , ")
+        s"""SELECT ${(variableIdAndColumns ++ weightColumns ++ List(valueColumn)) mkString ("\n     , ")
         }\n${qc.generateSQLBody(fakeBody) }"""
       }
 
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index c93f296b9..0b619d0cf 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -170,6 +170,7 @@ case class SupervisionRule(headName: String,
 case class InferenceRule(head: InferenceRuleHead,
                          q: ConjunctiveQuery,
                          weights: FactorWeight = null,
+                         valueExpr: Expr = null,
                          annotations: List[Annotation] = List.empty
                         ) extends RuleWithConjunctiveQuery
 
@@ -447,6 +448,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       anno => (anno named "weight") && (anno.args isDefined)
     } =>
       val weights = FactorWeight(rule.annotations find (_ named "weight") map (_ exprs) get)
+      val valueExpr = (rule.annotations find (_ named "value") flatMap (_ expr) getOrElse null)
       rule match {
         case extrRule: ExtractionRule =>
           // turn normal derivation rules to IsTrue factors
@@ -458,12 +460,19 @@ class DeepDiveLogParser extends JavaTokenParsers {
             head = InferenceRuleHead(FactorFunction.IsTrue(), List(headAtom)),
             q = extrRule.q.copy(headTerms = List.empty),
             weights = weights,
+            valueExpr = valueExpr,
             annotations = extrRule.annotations
           )
         case infrRule: InferenceRule =>
-          infrRule.copy(weights = weights)
+          var infrRuleUpdated = infrRule.copy(weights = weights)
+          if (valueExpr != null) {
+            infrRuleUpdated.copy(valueExpr = valueExpr)
+          } else {
+            infrRuleUpdated
+          }
         case _ => sys.error(s"Invalid usage of @weight:\n${DeepDiveLogPrettyPrinter.print(rule)}")
       }
+      // DeepDiveLogPrettyPrinter.print(rule)
 
     // treat @label annotation
     case rule: ExtractionRule if rule.annotations exists {
@@ -478,7 +487,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   } ^? {
     // treat @semantics annotation
-    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _) if rule.annotations exists {
+    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _, _) if rule.annotations exists {
       anno => (anno named "semantics") && (anno.exprs.size == 1)
     } =>
       rule.annotations find (_ named "semantics") flatMap (_ value) collect {
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index ffe547f87..6efff0c24 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -92,6 +92,7 @@ SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.tag AS "chunk.R0.tag"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
+     , (R3.feature)::float AS factor_value
 FROM chunk R0
    , words R1
    , tags R2
@@ -131,6 +132,7 @@ SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
+     , (1)::float AS factor_value
 FROM chunk R0
    , chunk R1
    , words R2
@@ -177,6 +179,7 @@ SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
+     , (1)::float AS factor_value
 FROM chunk R0
    , chunk R1
    , words R2
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 237f7bb67..d773df3c5 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -17,6 +17,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM Q R0
    , Q R1
    , R R2
@@ -46,6 +47,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM Q R0
    , Q R1
    , R R2
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 0f9115ef8..36b5bbd7b 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -46,6 +46,7 @@ SELECT dd_id_0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
+     , (1)::float AS factor_value
 FROM P R0
    , Q R1
    , dd_variables_P AS dd_id_0
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index cfdb1027a..dc9e5ee2c 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -208,6 +208,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM Q R0
    , S R1
    , dd_variables_Q AS dd_id_0
@@ -231,6 +232,7 @@ non_category_weight_cols: [
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
+     , (1)::float AS factor_value
 FROM Q R0
    , S R1
    , dd_variables_Q AS dd_id_0
@@ -254,6 +256,7 @@ non_category_weight_cols: [
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
+     , (1)::float AS factor_value
 FROM Q R0
    , S R1
    , dd_variables_Q AS dd_id_0
@@ -280,6 +283,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM Q R0
    , Q R1
    , S R2
@@ -313,6 +317,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
+     , (1)::float AS factor_value
 FROM Q R0
    , Q R1
    , S R2
@@ -347,6 +352,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
+     , (1)::float AS factor_value
 FROM Q R0
    , Q R1
    , S R2
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 63b3a69c2..1e7347bb1 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -45,6 +45,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM q1 R0
    , features R1
    , dd_variables_q1 AS dd_id_0
@@ -68,6 +69,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM q2 R0
    , features R1
    , dd_variables_q2 AS dd_id_0
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 5d13d395e..5f5192def 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -46,6 +46,7 @@ SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
      , dd_id_1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
+     , (1)::float AS factor_value
 FROM smoke R0
    , cancer R1
    , person_smokes R2
@@ -75,6 +76,7 @@ SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
      , dd_id_1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
+     , (1)::float AS factor_value
 FROM smoke R0
    , smoke R1
    , friends R2
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 549a20193..8e3b74a0d 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -100,6 +100,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index ad0612c61..cef75a2e5 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -18,6 +18,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
+     , (1)::float AS factor_value
 FROM a R0
    , b R1
    , dd_variables_a AS dd_id_0
@@ -40,6 +41,7 @@ non_category_weight_cols: [
 input_query: """
 SELECT dd_id_0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
+     , (1)::float AS factor_value
 FROM c R0
    , b R1
    , dd_variables_c AS dd_id_0
@@ -65,6 +67,7 @@ SELECT dd_id_0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
+     , (1)::float AS factor_value
 FROM d R0
    , b R1
    , dd_variables_d AS dd_id_0
@@ -87,6 +90,7 @@ non_category_weight_cols: [
 input_query: """
 SELECT dd_id_0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
+     , (1)::float AS factor_value
 FROM e R0
    , b R1
    , dd_variables_e AS dd_id_0
@@ -109,6 +113,7 @@ non_category_weight_cols: [
 input_query: """
 SELECT dd_id_0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
+     , (1)::float AS factor_value
 FROM f R0
    , b R1
    , dd_variables_f AS dd_id_0

From cf2feab1410d39f02c563745c43887b1d12b0358 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Sat, 16 Jul 2016 16:37:37 -0700
Subject: [PATCH 335/347] cleaner code

---
 .../org/deepdive/ddlog/DeepDiveLogCompiler.scala     |  2 +-
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 12 ++++--------
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 6d647a969..872966600 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -550,7 +550,7 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
             nonCategoryWeightCols += s"${deepdiveWeightColumnPrefix}${i}"
         }
 
-        val valueExpr = if (stmt.valueExpr != null) stmt.valueExpr else IntConst(1)
+        val valueExpr = stmt.valueExpr getOrElse IntConst(1)
         val valueColumn = s"""(${qc.compileExpr(valueExpr)})::float AS factor_value"""
 
         // factor input query
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 0b619d0cf..46b6a327c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -170,7 +170,7 @@ case class SupervisionRule(headName: String,
 case class InferenceRule(head: InferenceRuleHead,
                          q: ConjunctiveQuery,
                          weights: FactorWeight = null,
-                         valueExpr: Expr = null,
+                         valueExpr: Option[Expr] = None,
                          annotations: List[Annotation] = List.empty
                         ) extends RuleWithConjunctiveQuery
 
@@ -448,7 +448,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       anno => (anno named "weight") && (anno.args isDefined)
     } =>
       val weights = FactorWeight(rule.annotations find (_ named "weight") map (_ exprs) get)
-      val valueExpr = (rule.annotations find (_ named "value") flatMap (_ expr) getOrElse null)
+      val valueExpr = (rule.annotations find (_ named "value") flatMap (_ expr))
       rule match {
         case extrRule: ExtractionRule =>
           // turn normal derivation rules to IsTrue factors
@@ -464,12 +464,8 @@ class DeepDiveLogParser extends JavaTokenParsers {
             annotations = extrRule.annotations
           )
         case infrRule: InferenceRule =>
-          var infrRuleUpdated = infrRule.copy(weights = weights)
-          if (valueExpr != null) {
-            infrRuleUpdated.copy(valueExpr = valueExpr)
-          } else {
-            infrRuleUpdated
-          }
+          infrRule.copy(weights = weights, valueExpr = valueExpr)
+
         case _ => sys.error(s"Invalid usage of @weight:\n${DeepDiveLogPrettyPrinter.print(rule)}")
       }
       // DeepDiveLogPrettyPrinter.print(rule)

From f1af91b98bd4ca4bb7a45ead8f4d6b47043ee407 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Mon, 18 Jul 2016 23:30:24 -0700
Subject: [PATCH 336/347] Support @name for inference rules

---
 examples/chunking.ddlog                       |  2 ++
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 34 +++++++++++++------
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 10 ++++--
 .../chunking_example/compile.expected         |  4 +--
 .../compile.expected                          |  6 ++--
 5 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index 4f3165e11..81023172b 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -68,12 +68,14 @@ chunk(s, w, tag) :-
   word_features(s, w, f).
 
 # linear chains ###############################################################
+@name("LINEAR  @   chain")
 @weight(tag1, tag2)
 chunk(s, w1, tag1) ^ chunk(s, w2, tag2) :-
                       words(s, w1, _, _, _, _), words(s, w2, _, _, _, _), tags(tag1), tags(tag2), # XXX just to make it compile. remove after fixing https://github.com/HazyResearch/ddlog/issues/72
   w2 = w1 + 1.
 
 # skip chain ##################################################################
+@name("phony rule")
 @weight(tag1, tag2)
 chunk(s, w1, tag1) ^ chunk(s, w2, tag2) :-
   words(s, w1, _, _, _, tag),
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 872966600..401bbda9d 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -47,6 +47,16 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   val representativeStatements : Set[Statement] =
     statementsByHeadName.values map { _(0) } toSet
 
+  def slugify(input: String): String = {
+    import java.text.Normalizer
+    Normalizer.normalize(input, Normalizer.Form.NFD)
+      .replaceAll("[^\\w\\s-]", "") // Remove all non-word, non-space or non-dash characters
+      .replace('-', ' ')            // Replace dashes with spaces
+      .trim                         // Trim leading/trailing whitespace (including what used to be leading/trailing dashes)
+      .replaceAll("\\s+", "_")      // Replace whitespace (including newlines and repetitions) with underscore
+      .toLowerCase                  // Lowercase the final results
+  }
+
   def optionalIndex(idx: Int) =
     if (idx < 1) "" else s"${idx}"
 
@@ -72,21 +82,25 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   // Given an inference rule, resolve its name for the compiled inference block.
   def resolveInferenceBlockName(s: InferenceRule): String = {
     // how to map a rule to its basename
-    // TODO support @rule("name") annotation to override these generated names
-    def ruleBaseNameFor(s: InferenceRule) = s"${
-        // function name
-        s.head.function.getClass.getSimpleName.toLowerCase
-      }_${
-        // followed by variable names
-        s.head.variables map { case t => s"${if (t.isNegated) "not_" else ""}${t.atom.name}" } mkString("_")
-      }"
+    def ruleBaseNameFor(s: InferenceRule): String =
+      if (!s.ruleName.isEmpty) {
+        slugify(s.ruleName getOrElse "rule")
+      } else {
+        s"inf_${
+          // function name
+          s.head.function.getClass.getSimpleName.toLowerCase
+        }_${
+          // followed by variable names
+          s.head.variables map { case t => s"${if (t.isNegated) "not_" else ""}${t.atom.name}" } mkString("_")
+        }"
+      }
     // find this rule's base name and all rules that share it
     val ruleBaseName = ruleBaseNameFor(s)
     val allInferenceRulesSharingHead = inferenceRules filter(ruleBaseNameFor(_) equals ruleBaseName)
-    s"inf${
+    s"${ruleBaseName}${
         // keep an index before the base name to prevent potential collision with user's name
         optionalIndex(allInferenceRulesSharingHead indexOf s)
-      }_${ruleBaseName}"
+      }"
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 46b6a327c..e98bde5b9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -171,6 +171,7 @@ case class InferenceRule(head: InferenceRuleHead,
                          q: ConjunctiveQuery,
                          weights: FactorWeight = null,
                          valueExpr: Option[Expr] = None,
+                         ruleName: Option[String] = None,
                          annotations: List[Annotation] = List.empty
                         ) extends RuleWithConjunctiveQuery
 
@@ -449,6 +450,11 @@ class DeepDiveLogParser extends JavaTokenParsers {
     } =>
       val weights = FactorWeight(rule.annotations find (_ named "weight") map (_ exprs) get)
       val valueExpr = (rule.annotations find (_ named "value") flatMap (_ expr))
+      val ruleName = (rule.annotations find (_ named "name") flatMap (_ expr) map {
+        case StringConst(x) => x
+        case _ => sys.error(s"Invalid rule name:\n${DeepDiveLogPrettyPrinter.print(rule)}")
+      })
+
       rule match {
         case extrRule: ExtractionRule =>
           // turn normal derivation rules to IsTrue factors
@@ -464,7 +470,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             annotations = extrRule.annotations
           )
         case infrRule: InferenceRule =>
-          infrRule.copy(weights = weights, valueExpr = valueExpr)
+          infrRule.copy(weights = weights, valueExpr = valueExpr, ruleName = ruleName)
 
         case _ => sys.error(s"Invalid usage of @weight:\n${DeepDiveLogPrettyPrinter.print(rule)}")
       }
@@ -483,7 +489,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   } ^? {
     // treat @semantics annotation
-    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _, _) if rule.annotations exists {
+    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _, _, _) if rule.annotations exists {
       anno => (anno named "semantics") && (anno.exprs.size == 1)
     } =>
       rule.annotations find (_ named "semantics") flatMap (_ value) collect {
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 6efff0c24..d3a8d76c4 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -116,7 +116,7 @@ function: """AndCategorical(chunk.R0.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf_and_chunk_chunk {
+deepdive.inference.factors.linear_chain {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
   
@@ -163,7 +163,7 @@ function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf1_and_chunk_chunk {
+deepdive.inference.factors.phony_rule {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
   
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index dc9e5ee2c..b5128acdd 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -224,7 +224,7 @@ function: """Imply(Q.R0.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf1_istrue_Q {
+deepdive.inference.factors.inf_istrue_Q1 {
 weight: """1.0"""
 non_category_weight_cols: [
   
@@ -307,7 +307,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf1_imply_Q_Q {
+deepdive.inference.factors.inf_imply_Q_Q1 {
 weight: """-10.0"""
 non_category_weight_cols: [
   
@@ -342,7 +342,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf2_imply_Q_Q {
+deepdive.inference.factors.inf_imply_Q_Q2 {
 weight: """10.0"""
 non_category_weight_cols: [
   

From d8658acccbe8ad75d44c14571ffe05707904f448 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Mon, 18 Jul 2016 23:33:24 -0700
Subject: [PATCH 337/347] cover alt syntax

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index e98bde5b9..9081315a9 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -467,6 +467,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
             q = extrRule.q.copy(headTerms = List.empty),
             weights = weights,
             valueExpr = valueExpr,
+            ruleName = ruleName,
             annotations = extrRule.annotations
           )
         case infrRule: InferenceRule =>

From c7a8393fcafca365ca1a3b2fc881a3a2543f4dd6 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Tue, 19 Jul 2016 00:29:20 -0700
Subject: [PATCH 338/347] Turns InferenceRule.ruleName into a derived member

instead of an constructor arg
---
 .../deepdive/ddlog/DeepDiveLogParser.scala    | 20 ++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 9081315a9..2cdac34df 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -171,9 +171,16 @@ case class InferenceRule(head: InferenceRuleHead,
                          q: ConjunctiveQuery,
                          weights: FactorWeight = null,
                          valueExpr: Option[Expr] = None,
-                         ruleName: Option[String] = None,
                          annotations: List[Annotation] = List.empty
-                        ) extends RuleWithConjunctiveQuery
+                        ) extends RuleWithConjunctiveQuery {
+
+  val ruleName: Option[String] =
+    annotations find (_ named "name") flatMap (_ expr) map {
+      case StringConst(x) => x
+      case _ => sys.error(s"Invalid rule name:\n${DeepDiveLogPrettyPrinter.print(this)}")
+    }
+
+}
 
 
 
@@ -450,10 +457,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
     } =>
       val weights = FactorWeight(rule.annotations find (_ named "weight") map (_ exprs) get)
       val valueExpr = (rule.annotations find (_ named "value") flatMap (_ expr))
-      val ruleName = (rule.annotations find (_ named "name") flatMap (_ expr) map {
-        case StringConst(x) => x
-        case _ => sys.error(s"Invalid rule name:\n${DeepDiveLogPrettyPrinter.print(rule)}")
-      })
 
       rule match {
         case extrRule: ExtractionRule =>
@@ -467,11 +470,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
             q = extrRule.q.copy(headTerms = List.empty),
             weights = weights,
             valueExpr = valueExpr,
-            ruleName = ruleName,
             annotations = extrRule.annotations
           )
         case infrRule: InferenceRule =>
-          infrRule.copy(weights = weights, valueExpr = valueExpr, ruleName = ruleName)
+          infrRule.copy(weights = weights, valueExpr = valueExpr)
 
         case _ => sys.error(s"Invalid usage of @weight:\n${DeepDiveLogPrettyPrinter.print(rule)}")
       }
@@ -490,7 +492,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   } ^? {
     // treat @semantics annotation
-    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _, _, _) if rule.annotations exists {
+    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _, _) if rule.annotations exists {
       anno => (anno named "semantics") && (anno.exprs.size == 1)
     } =>
       rule.annotations find (_ named "semantics") flatMap (_ value) collect {

From ea9527df03afc12aaa4eaf484fd43f6b7355f2d0 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Tue, 19 Jul 2016 00:39:07 -0700
Subject: [PATCH 339/347] Also turns `InferenceRule.valueExpr` into a derived
 member

---
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala   | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index 2cdac34df..f79b1122f 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -170,7 +170,6 @@ case class SupervisionRule(headName: String,
 case class InferenceRule(head: InferenceRuleHead,
                          q: ConjunctiveQuery,
                          weights: FactorWeight = null,
-                         valueExpr: Option[Expr] = None,
                          annotations: List[Annotation] = List.empty
                         ) extends RuleWithConjunctiveQuery {
 
@@ -180,6 +179,9 @@ case class InferenceRule(head: InferenceRuleHead,
       case _ => sys.error(s"Invalid rule name:\n${DeepDiveLogPrettyPrinter.print(this)}")
     }
 
+  def valueExpr: Option[Expr] =
+    annotations find (_ named "value") flatMap (_ expr)
+
 }
 
 
@@ -456,7 +458,6 @@ class DeepDiveLogParser extends JavaTokenParsers {
       anno => (anno named "weight") && (anno.args isDefined)
     } =>
       val weights = FactorWeight(rule.annotations find (_ named "weight") map (_ exprs) get)
-      val valueExpr = (rule.annotations find (_ named "value") flatMap (_ expr))
 
       rule match {
         case extrRule: ExtractionRule =>
@@ -469,11 +470,10 @@ class DeepDiveLogParser extends JavaTokenParsers {
             head = InferenceRuleHead(FactorFunction.IsTrue(), List(headAtom)),
             q = extrRule.q.copy(headTerms = List.empty),
             weights = weights,
-            valueExpr = valueExpr,
             annotations = extrRule.annotations
           )
         case infrRule: InferenceRule =>
-          infrRule.copy(weights = weights, valueExpr = valueExpr)
+          infrRule.copy(weights = weights)
 
         case _ => sys.error(s"Invalid usage of @weight:\n${DeepDiveLogPrettyPrinter.print(rule)}")
       }
@@ -492,7 +492,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
 
   } ^? {
     // treat @semantics annotation
-    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _, _) if rule.annotations exists {
+    case rule@InferenceRule(InferenceRuleHead(FactorFunction.Imply(), _), _, _, _) if rule.annotations exists {
       anno => (anno named "semantics") && (anno.exprs.size == 1)
     } =>
       rule.annotations find (_ named "semantics") flatMap (_ value) collect {

From ca85bbbc4c877219ee7889e07d69e443acfb3f73 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Tue, 19 Jul 2016 00:51:23 -0700
Subject: [PATCH 340/347] Renames `@value` to `@feature_value`

as per #105
---
 examples/chunking.ddlog                                   | 2 +-
 src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/chunking.ddlog b/examples/chunking.ddlog
index 81023172b..64a0333d5 100644
--- a/examples/chunking.ddlog
+++ b/examples/chunking.ddlog
@@ -62,7 +62,7 @@ word_features +=
   word1 IS NOT NULL.
 
 @weight(f, tag)
-@value(f)
+@feature_value(f)
 chunk(s, w, tag) :-
                       words(s, w, _, _, _, _), tags(tag), # XXX just to make it compile. remove after fixing https://github.com/HazyResearch/ddlog/issues/72
   word_features(s, w, f).
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index f79b1122f..88647cafb 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -180,7 +180,7 @@ case class InferenceRule(head: InferenceRuleHead,
     }
 
   def valueExpr: Option[Expr] =
-    annotations find (_ named "value") flatMap (_ expr)
+    annotations find (_ named "feature_value") flatMap (_ expr)
 
 }
 

From 24198c995b2762dac71764e54c197cb8d0d6efd5 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Tue, 19 Jul 2016 01:22:52 -0700
Subject: [PATCH 341/347] Makes inference rule names always unique again

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  12 +-
 .../ddlog/DeepDiveLogDesugarRewriter.scala    |  15 +-
 .../compile.expected                          | 183 +++++++++++++++++-
 .../desugar.expected                          |  40 ++++
 .../multiple_rules_for_same_head/input.ddlog  |  22 +++
 5 files changed, 257 insertions(+), 15 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 401bbda9d..6341354d2 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -97,10 +97,16 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
     // find this rule's base name and all rules that share it
     val ruleBaseName = ruleBaseNameFor(s)
     val allInferenceRulesSharingHead = inferenceRules filter(ruleBaseNameFor(_) equals ruleBaseName)
-    s"${ruleBaseName}${
-        // keep an index before the base name to prevent potential collision with user's name
-        optionalIndex(allInferenceRulesSharingHead indexOf s)
+    if (allInferenceRulesSharingHead.length == 1) ruleBaseName // no possible name collision
+    else {
+      // keep an index after the base name to prevent collision
+      s"${
+        // TODO finding safe prefix for every inference rule ahead of time will be more efficient
+        DeepDiveLogDesugarRewriter.findSafePrefix(ruleBaseName, inferenceRules map ruleBaseNameFor toSet)
+      }${
+        allInferenceRulesSharingHead indexOf s
       }"
+    }
   }
 
   // Given a variable, resolve it.  TODO: This should give a warning,
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
index 9cde4a6de..f3c9e664e 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogDesugarRewriter.scala
@@ -4,6 +4,14 @@ import scala.language.postfixOps
 
 object DeepDiveLogDesugarRewriter {
 
+  // Finds a safe prefix that starts with given name that is guaranteed to have no collisions with other namesInUse
+  def findSafePrefix(name: String, namesInUse: Set[String], minLength: Int = 1, separator: String = "_"): String =
+    Stream.from(minLength) map { n =>
+      s"${name}${separator * n}"
+    } dropWhile { prefix =>
+      namesInUse exists {_ startsWith prefix}
+    } head
+
   // Rewrite function call rules whose output coincides with normal rules.
   def desugarUnionsImpliedByFunctionCallRules(program: DeepDiveLog.Program) = {
     def indexByFirst[a,b](pairs: Seq[(a,b)]): Map[a,List[b]] =
@@ -35,12 +43,7 @@ object DeepDiveLogDesugarRewriter {
 
     // determine a separator that does not create name clashes with existing heads for each relation to rewrite
     val prefixForRelation: Map[String, String] = relationsToDesugar map { name =>
-      name -> (
-        Stream.from(1) map { n => s"${name}${"_" * n}"
-        } dropWhile { prefix =>
-          relationNamesUsedInProgram exists {_ startsWith prefix}
-        } head
-      )
+      name -> (findSafePrefix(name, relationNamesUsedInProgram))
     } toMap
 
     // how to make names unique
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index b5128acdd..d64672d15 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -1,7 +1,9 @@
-deepdive.schema {"relations" : {"S_2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T___1" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "S_1" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T_2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T___2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "Q" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "T___3" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "S_0" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T__3" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "T___0" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "R" : {"columns" : {"a" : {"type" : "int", "index" : 0}, "b" : {"type" : "int", "index" : 1}}}, "S" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}}}
+deepdive.schema {"relations" : {"Q_1" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "S_2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T___1" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "Q1" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "S_1" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T_2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T___2" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "Q" : {"columns" : {"x" : {"type" : "int", "index" : 0}}, "variable_type" : "boolean"}, "T___3" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "S_0" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "T__3" : {"type" : "view", "columns" : {"column_0" : {"type" : "UNKNOWN", "index" : 0}}}, "T___0" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}, "R" : {"columns" : {"a" : {"type" : "int", "index" : 0}, "b" : {"type" : "int", "index" : 1}}}, "S" : {"columns" : {"a" : {"type" : "int", "index" : 0}}}}}
 
 deepdive.schema.variables {
 Q.dd_label: Boolean
+Q1.dd_label: Boolean
+Q_1.dd_label: Boolean
 
 }
 
@@ -199,7 +201,7 @@ WHERE R0.a > 0
 
 }
 
-deepdive.inference.factors.inf_istrue_Q {
+deepdive.inference.factors.inf_istrue_Q_0 {
 weight: """?(dd_weight_column_0)"""
 non_category_weight_cols: [
   dd_weight_column_0
@@ -224,7 +226,7 @@ function: """Imply(Q.R0.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf_istrue_Q1 {
+deepdive.inference.factors.inf_istrue_Q_1 {
 weight: """1.0"""
 non_category_weight_cols: [
   
@@ -272,7 +274,7 @@ function: """Imply(!Q.R0.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf_imply_Q_Q {
+deepdive.inference.factors.inf_imply_Q_Q__0 {
 weight: """?(dd_weight_column_0)"""
 non_category_weight_cols: [
   dd_weight_column_0
@@ -307,7 +309,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf_imply_Q_Q1 {
+deepdive.inference.factors.inf_imply_Q_Q__1 {
 weight: """-10.0"""
 non_category_weight_cols: [
   
@@ -342,7 +344,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 
 }
 
-deepdive.inference.factors.inf_imply_Q_Q2 {
+deepdive.inference.factors.inf_imply_Q_Q__2 {
 weight: """10.0"""
 non_category_weight_cols: [
   
@@ -391,3 +393,172 @@ materialize: false
 
 }
 
+deepdive.inference.factors.inf_imply_Q_Q1 {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
+input_query: """
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , dd_id_1.dd_id AS "Q1.R1.dd_id"
+     , R1.x AS "Q1.R1.x"
+     , R0.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
+FROM Q R0
+   , Q1 R1
+   , S R2
+   , R R3
+   , S R4
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q1 AS dd_id_1
+WHERE R2.a = R0.x
+  AND R3.a = R0.x
+  AND R3.b = R1.x
+  AND R4.a = R1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
+"""
+input_relations: [
+  Q
+  Q1
+  S
+  R
+]
+function: """Imply(Q.R0.dd_label, Q1.R1.dd_label)"""
+
+}
+
+deepdive.inference.factors.inf_imply_Q_Q_1 {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
+input_query: """
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , dd_id_1.dd_id AS "Q_1.R1.dd_id"
+     , R1.x AS "Q_1.R1.x"
+     , R0.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
+FROM Q R0
+   , Q_1 R1
+   , S R2
+   , R R3
+   , S R4
+   , dd_variables_Q AS dd_id_0
+   , dd_variables_Q_1 AS dd_id_1
+WHERE R2.a = R0.x
+  AND R3.a = R0.x
+  AND R3.b = R1.x
+  AND R4.a = R1.x
+  AND R0.x = dd_id_0.x
+  AND R1.x = dd_id_1.x
+"""
+input_relations: [
+  Q
+  Q_1
+  S
+  R
+]
+function: """Imply(Q.R0.dd_label, Q_1.R1.dd_label)"""
+
+}
+
+deepdive.inference.factors.foo__0 {
+weight: """?(dd_weight_column_0)"""
+non_category_weight_cols: [
+  dd_weight_column_0
+]
+input_query: """
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , R0.x AS "dd_weight_column_0"
+     , (1)::float AS factor_value
+FROM Q R0
+   , S R1
+   , dd_variables_Q AS dd_id_0
+WHERE R1.a = R0.x
+  AND R0.x > 1000
+  AND R0.x = dd_id_0.x
+"""
+input_relations: [
+  Q
+  S
+]
+function: """Imply(Q.R0.dd_label)"""
+
+}
+
+deepdive.inference.factors.foo__1 {
+weight: """1.0"""
+non_category_weight_cols: [
+  
+]
+input_query: """
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , (1)::float AS factor_value
+FROM Q R0
+   , S R1
+   , dd_variables_Q AS dd_id_0
+WHERE R1.a = R0.x
+  AND R0.x = 0
+  AND R0.x = dd_id_0.x
+"""
+input_relations: [
+  Q
+  S
+]
+function: """Imply(Q.R0.dd_label)"""
+
+}
+
+deepdive.inference.factors.foo1 {
+weight: """1.0"""
+non_category_weight_cols: [
+  
+]
+input_query: """
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , (1)::float AS factor_value
+FROM Q R0
+   , S R1
+   , dd_variables_Q AS dd_id_0
+WHERE R1.a = R0.x
+  AND R0.x = 1
+  AND R0.x = dd_id_0.x
+"""
+input_relations: [
+  Q
+  S
+]
+function: """Imply(Q.R0.dd_label)"""
+
+}
+
+deepdive.inference.factors.foo_1 {
+weight: """1.0"""
+non_category_weight_cols: [
+  
+]
+input_query: """
+SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+     , R0.x AS "Q.R0.x"
+     , (1)::float AS factor_value
+FROM Q R0
+   , S R1
+   , dd_variables_Q AS dd_id_0
+WHERE R1.a = R0.x
+  AND R0.x = 2
+  AND R0.x = dd_id_0.x
+"""
+input_relations: [
+  Q
+  S
+]
+function: """Imply(Q.R0.dd_label)"""
+
+}
+
diff --git a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
index 58a65ce19..c26efd3fe 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
@@ -7,6 +7,10 @@ T(a int).
 
 Q?(x int).
 
+Q1?(x int).
+
+Q_1?(x int).
+
 S(a) :-
     R(a, b),
     R(b, _),
@@ -138,3 +142,39 @@ T_2(a int).
 T__3(x) :-
     T(x).
 
+@weight(a)
+Q(a) => Q1(b) :-
+    S(a),
+    R(a, b),
+    S(b).
+
+@weight(a)
+Q(a) => Q_1(b) :-
+    S(a),
+    R(a, b),
+    S(b).
+
+@name("foo")
+@weight(a)
+Q(a) :-
+    S(a),
+    a > 1000.
+
+@name("foo")
+@weight(1.0)
+Q(a) :-
+    S(a),
+    a = 0.
+
+@name("foo1")
+@weight(1.0)
+Q(a) :-
+    S(a),
+    a = 1.
+
+@name("foo_1")
+@weight(1.0)
+Q(a) :-
+    S(a),
+    a = 2.
+
diff --git a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
index 1003b4603..297d034ed 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
+++ b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
@@ -2,6 +2,8 @@ R(a int, b int).
 S(a int).
 T(a int).
 Q?(x int).
+Q1?(x int).
+Q_1?(x int).
 
 # multiple rules for normal extraction rules
 S(a) :- R(a, b), R(b, _), a > 100.
@@ -48,3 +50,23 @@ Q(a) => Q(c) :- S(a), R(a, c), S(c), a + c > 1000.
 # make sure desugars without name clashes
 T_2(a int).
 T__3(x) :- T(x).
+
+# corner cases for unique name generation
+@weight(a)
+Q(a) => Q1(b) :- S(a), R(a, b), S(b).
+@weight(a)
+Q(a) => Q_1(b) :- S(a), R(a, b), S(b).
+
+# gracefully handle repeated @name for inference rules
+@name("foo")
+@weight(a)
+Q(a) :- S(a), a > 1000.
+@name("foo")
+@weight(1.0)
+Q(a) :- S(a), a = 0.
+@name("foo1")
+@weight(1.0)
+Q(a) :- S(a), a = 1.
+@name("foo_1")
+@weight(1.0)
+Q(a) :- S(a), a = 2.

From 96b9aee82e49313672d35d7a6bcccee30e345d27 Mon Sep 17 00:00:00 2001
From: Jaeho Shin <jaeho.shin@lattice.io>
Date: Tue, 19 Jul 2016 01:34:30 -0700
Subject: [PATCH 342/347] Throws compile error when same `@name` gets repeated

for a more deterministic behavior reducing surprise
---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  4 +-
 test/compile-error-test.bats.template         |  4 +-
 .../repated_rule_name/compile-error.expected  |  1 +
 .../repated_rule_name/input.ddlog             | 11 +++
 .../compile.expected                          | 97 -------------------
 .../desugar.expected                          | 24 -----
 .../multiple_rules_for_same_head/input.ddlog  | 14 ---
 7 files changed, 18 insertions(+), 137 deletions(-)
 create mode 100644 test/compile-error-test/repated_rule_name/compile-error.expected
 create mode 100644 test/compile-error-test/repated_rule_name/input.ddlog

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 6341354d2..902fdc2ae 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -83,7 +83,7 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   def resolveInferenceBlockName(s: InferenceRule): String = {
     // how to map a rule to its basename
     def ruleBaseNameFor(s: InferenceRule): String =
-      if (!s.ruleName.isEmpty) {
+      if (s.ruleName nonEmpty) {
         slugify(s.ruleName getOrElse "rule")
       } else {
         s"inf_${
@@ -98,6 +98,8 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
     val ruleBaseName = ruleBaseNameFor(s)
     val allInferenceRulesSharingHead = inferenceRules filter(ruleBaseNameFor(_) equals ruleBaseName)
     if (allInferenceRulesSharingHead.length == 1) ruleBaseName // no possible name collision
+    else if (s.ruleName nonEmpty)
+      sys.error(s"""@name("${s.ruleName get}") repeated ${allInferenceRulesSharingHead.length} times""")
     else {
       // keep an index after the base name to prevent collision
       s"${
diff --git a/test/compile-error-test.bats.template b/test/compile-error-test.bats.template
index 6d289b7e2..422c20cf1 100644
--- a/test/compile-error-test.bats.template
+++ b/test/compile-error-test.bats.template
@@ -15,6 +15,8 @@ setup() {
     expectedError="$TESTDIR"/compile-error.expected
     [ -e "$expectedError" ] || skip
     actualError=${expectedError%.expected}.actual
-    ! ddlog check "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError"
+    ! ddlog check   "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError" ||
+    ! ddlog compile "$TESTDIR"/input.ddlog >/dev/null 2>"$actualError" ||
+    false
     diff "$expectedError" "$actualError"
 }
diff --git a/test/compile-error-test/repated_rule_name/compile-error.expected b/test/compile-error-test/repated_rule_name/compile-error.expected
new file mode 100644
index 000000000..a2493a91b
--- /dev/null
+++ b/test/compile-error-test/repated_rule_name/compile-error.expected
@@ -0,0 +1 @@
+[error] @name("foo") repeated 2 times
diff --git a/test/compile-error-test/repated_rule_name/input.ddlog b/test/compile-error-test/repated_rule_name/input.ddlog
new file mode 100644
index 000000000..a8de875f0
--- /dev/null
+++ b/test/compile-error-test/repated_rule_name/input.ddlog
@@ -0,0 +1,11 @@
+S(a int).
+Q?(x int).
+
+# disallow repeating the same @name for more than one inference rule
+@name("foo")
+@weight(a)
+Q(a) :- S(a), a > 1000.
+
+@name("foo")
+@weight(1.0)
+Q(a) :- S(a), a = 0.
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index d64672d15..a182b2a59 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -465,100 +465,3 @@ function: """Imply(Q.R0.dd_label, Q_1.R1.dd_label)"""
 
 }
 
-deepdive.inference.factors.foo__0 {
-weight: """?(dd_weight_column_0)"""
-non_category_weight_cols: [
-  dd_weight_column_0
-]
-input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
-     , R0.x AS "Q.R0.x"
-     , R0.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
-FROM Q R0
-   , S R1
-   , dd_variables_Q AS dd_id_0
-WHERE R1.a = R0.x
-  AND R0.x > 1000
-  AND R0.x = dd_id_0.x
-"""
-input_relations: [
-  Q
-  S
-]
-function: """Imply(Q.R0.dd_label)"""
-
-}
-
-deepdive.inference.factors.foo__1 {
-weight: """1.0"""
-non_category_weight_cols: [
-  
-]
-input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
-     , R0.x AS "Q.R0.x"
-     , (1)::float AS factor_value
-FROM Q R0
-   , S R1
-   , dd_variables_Q AS dd_id_0
-WHERE R1.a = R0.x
-  AND R0.x = 0
-  AND R0.x = dd_id_0.x
-"""
-input_relations: [
-  Q
-  S
-]
-function: """Imply(Q.R0.dd_label)"""
-
-}
-
-deepdive.inference.factors.foo1 {
-weight: """1.0"""
-non_category_weight_cols: [
-  
-]
-input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
-     , R0.x AS "Q.R0.x"
-     , (1)::float AS factor_value
-FROM Q R0
-   , S R1
-   , dd_variables_Q AS dd_id_0
-WHERE R1.a = R0.x
-  AND R0.x = 1
-  AND R0.x = dd_id_0.x
-"""
-input_relations: [
-  Q
-  S
-]
-function: """Imply(Q.R0.dd_label)"""
-
-}
-
-deepdive.inference.factors.foo_1 {
-weight: """1.0"""
-non_category_weight_cols: [
-  
-]
-input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
-     , R0.x AS "Q.R0.x"
-     , (1)::float AS factor_value
-FROM Q R0
-   , S R1
-   , dd_variables_Q AS dd_id_0
-WHERE R1.a = R0.x
-  AND R0.x = 2
-  AND R0.x = dd_id_0.x
-"""
-input_relations: [
-  Q
-  S
-]
-function: """Imply(Q.R0.dd_label)"""
-
-}
-
diff --git a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
index c26efd3fe..f1a7f7bf5 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/desugar.expected
@@ -154,27 +154,3 @@ Q(a) => Q_1(b) :-
     R(a, b),
     S(b).
 
-@name("foo")
-@weight(a)
-Q(a) :-
-    S(a),
-    a > 1000.
-
-@name("foo")
-@weight(1.0)
-Q(a) :-
-    S(a),
-    a = 0.
-
-@name("foo1")
-@weight(1.0)
-Q(a) :-
-    S(a),
-    a = 1.
-
-@name("foo_1")
-@weight(1.0)
-Q(a) :-
-    S(a),
-    a = 2.
-
diff --git a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
index 297d034ed..c90b88c83 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
+++ b/test/expected-output-test/multiple_rules_for_same_head/input.ddlog
@@ -56,17 +56,3 @@ T__3(x) :- T(x).
 Q(a) => Q1(b) :- S(a), R(a, b), S(b).
 @weight(a)
 Q(a) => Q_1(b) :- S(a), R(a, b), S(b).
-
-# gracefully handle repeated @name for inference rules
-@name("foo")
-@weight(a)
-Q(a) :- S(a), a > 1000.
-@name("foo")
-@weight(1.0)
-Q(a) :- S(a), a = 0.
-@name("foo1")
-@weight(1.0)
-Q(a) :- S(a), a = 1.
-@name("foo_1")
-@weight(1.0)
-Q(a) :- S(a), a = 2.

From 0d0d76b8449db31e043af4eb18895f0e4049a206 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Wed, 20 Jul 2016 22:15:54 -0700
Subject: [PATCH 343/347] factor_value -> feature_value

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  2 +-
 .../chunking_example/compile.expected         | 14 +++++------
 .../factor_functions/compile.expected         |  4 ++--
 .../logical_rules/compile.expected            |  4 ++--
 .../compile.expected                          | 24 +++++++++----------
 .../ocr_example/compile.expected              |  4 ++--
 .../smoke_example/compile.expected            |  8 +++----
 .../spouse_example/compile.expected           |  2 +-
 .../weights/compile.expected                  | 16 ++++++-------
 9 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 902fdc2ae..cb396b942 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -573,7 +573,7 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         }
 
         val valueExpr = stmt.valueExpr getOrElse IntConst(1)
-        val valueColumn = s"""(${qc.compileExpr(valueExpr)})::float AS factor_value"""
+        val valueColumn = s"""(${qc.compileExpr(valueExpr)})::float AS feature_value"""
 
         // factor input query
         s"""SELECT ${(variableIdAndColumns ++ weightColumns ++ List(valueColumn)) mkString ("\n     , ")
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index d3a8d76c4..ec5b3e032 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -13,7 +13,7 @@ sql: """
 SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R1.tag AS column_2
-     , 
+     ,
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS column_3
@@ -37,7 +37,7 @@ SELECT R0.sent_id AS column_0
      , R0.word AS column_2
      , R0.pos AS column_3
      , R0.true_tag AS column_4
-     , 
+     ,
 CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
      WHEN R0.true_tag = 'I-UCP' THEN NULL
      WHEN strpos(R0.true_tag, '-') > 0 THEN split_part(R0.true_tag, '-', 2)
@@ -92,7 +92,7 @@ SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R0.tag AS "chunk.R0.tag"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
-     , (R3.feature)::float AS factor_value
+     , (R3.feature)::float AS feature_value
 FROM chunk R0
    , words R1
    , tags R2
@@ -119,7 +119,7 @@ function: """AndCategorical(chunk.R0.dd_label)"""
 deepdive.inference.factors.linear_chain {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
@@ -132,7 +132,7 @@ SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM chunk R0
    , chunk R1
    , words R2
@@ -166,7 +166,7 @@ function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 deepdive.inference.factors.phony_rule {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
@@ -179,7 +179,7 @@ SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
      , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM chunk R0
    , chunk R1
    , words R2
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index d773df3c5..140a160f0 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -17,7 +17,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q R1
    , R R2
@@ -47,7 +47,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q R1
    , R R2
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 36b5bbd7b..58efd5d4b 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -39,14 +39,14 @@ materialize: false
 deepdive.inference.factors.inf_imply_P_Q {
 weight: """1"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM P R0
    , Q R1
    , dd_variables_P AS dd_id_0
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index a182b2a59..c398fd355 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -210,7 +210,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , S R1
    , dd_variables_Q AS dd_id_0
@@ -229,12 +229,12 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_Q_1 {
 weight: """1.0"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , S R1
    , dd_variables_Q AS dd_id_0
@@ -253,12 +253,12 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_not_Q {
 weight: """?"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , S R1
    , dd_variables_Q AS dd_id_0
@@ -285,7 +285,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q R1
    , S R2
@@ -312,14 +312,14 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_Q_Q__1 {
 weight: """-10.0"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q R1
    , S R2
@@ -347,14 +347,14 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_Q_Q__2 {
 weight: """10.0"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , dd_id_1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q R1
    , S R2
@@ -404,7 +404,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q1.R1.dd_id"
      , R1.x AS "Q1.R1.x"
      , R0.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q1 R1
    , S R2
@@ -440,7 +440,7 @@ SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
      , dd_id_1.dd_id AS "Q_1.R1.dd_id"
      , R1.x AS "Q_1.R1.x"
      , R0.x AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM Q R0
    , Q_1 R1
    , S R2
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 1e7347bb1..4bf018f29 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -45,7 +45,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM q1 R0
    , features R1
    , dd_variables_q1 AS dd_id_0
@@ -69,7 +69,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM q2 R0
    , features R1
    , dd_variables_q2 AS dd_id_0
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 5f5192def..f88d8837e 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -39,14 +39,14 @@ materialize: false
 deepdive.inference.factors.inf_imply_smoke_cancer {
 weight: """0.5"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
      , dd_id_1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM smoke R0
    , cancer R1
    , person_smokes R2
@@ -69,14 +69,14 @@ function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_smoke_smoke {
 weight: """0.4"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
      , dd_id_1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM smoke R0
    , smoke R1
    , friends R2
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 96540ada4..1c3895ece 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -100,7 +100,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index cef75a2e5..6cf94666c 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -18,7 +18,7 @@ input_query: """
 SELECT dd_id_0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM a R0
    , b R1
    , dd_variables_a AS dd_id_0
@@ -36,12 +36,12 @@ function: """Imply(a.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_c {
 weight: """?"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM c R0
    , b R1
    , dd_variables_c AS dd_id_0
@@ -67,7 +67,7 @@ SELECT dd_id_0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM d R0
    , b R1
    , dd_variables_d AS dd_id_0
@@ -85,12 +85,12 @@ function: """Imply(d.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_e {
 weight: """-10"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM e R0
    , b R1
    , dd_variables_e AS dd_id_0
@@ -108,12 +108,12 @@ function: """Imply(e.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_f {
 weight: """-0.3"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
-     , (1)::float AS factor_value
+     , (1)::float AS feature_value
 FROM f R0
    , b R1
    , dd_variables_f AS dd_id_0

From c70e5d29526e8f69776928ef080864ad47b2b83a Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Mon, 26 Sep 2016 19:23:46 -0700
Subject: [PATCH 344/347] Add supervision truthiness and syntax

---
 .../scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala   | 5 +++--
 .../scala/org/deepdive/ddlog/DeepDiveLogParser.scala     | 9 +++++----
 .../chunking_example/compile.expected                    | 9 +++++----
 test/expected-output-test/if-then-else/compile.expected  | 1 +
 .../materialize_annotation/compile.expected              | 2 ++
 test/expected-output-test/ocr_example/compile.expected   | 2 ++
 test/expected-output-test/smoke_example/compile.expected | 6 ++++--
 .../expected-output-test/spouse_example/compile.expected | 1 +
 8 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index cb396b942..0375a6a8c 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -466,9 +466,9 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
 
     compileExtractorBlock(stmt, stmts, stmt.headName,
       stmts map { case stmt => stmt.q.copy(
-        headTerms = stmt.q.headTerms :+ stmt.supervision,
+        headTerms = stmt.q.headTerms :+ stmt.supervision :+ (stmt.truthiness.getOrElse(DoubleConst(1))),
         headTermAliases = {
-          stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ :+ Some(deepdiveVariableLabelColumn) }
+          stmt.q.headTermAliases orElse { Some(stmt.q.headTerms map (_ => None)) } map { _ ::: List(Some(deepdiveVariableLabelColumn), Some(deepdiveVariableLabelTruthinessColumn)) }
         },
         isDistinct = false // XXX no need to take DISTINCT here since DeepDive will have to do it anyway
       ) }
@@ -684,6 +684,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   val deepdiveWeightColumnPrefix = "dd_weight_column_"
   val deepdiveVariableIdColumn = "dd_id"
   val deepdiveVariableLabelColumn = "dd_label"
+  val deepdiveVariableLabelTruthinessColumn = "dd_truthiness"
   val deepdivePrefixForVariablesIdsTable = "dd_variables_"
 
   // entry point for compilation
diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
index e5ad8e41e..eb06adbf0 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogParser.scala
@@ -164,6 +164,7 @@ case class FunctionCallRule(output: String,
                            ) extends RuleWithConjunctiveQuery
 case class SupervisionRule(headName: String,
                            supervision: Expr,
+                           truthiness: Option[Expr],
                            q: ConjunctiveQuery,
                            annotations: List[Annotation] = List.empty
                           ) extends RuleWithConjunctiveQuery
@@ -402,9 +403,9 @@ class DeepDiveLogParser extends JavaTokenParsers {
           InferenceRule(head = head, q = cq)
       }
     | // supervision rule with equal sign
-      relationName ~ conjunctiveQueryHeadTerms ~ ("=" ~> expr) ~ conjunctiveQueryBody() ^^ {
-        case h ~ ts ~ sup ~ cq =>
-          SupervisionRule(headName = h, supervision = sup, q = cq.copy(headTerms = ts))
+      relationName ~ conjunctiveQueryHeadTerms ~ ("=" ~> expr) ~ opt("@" ~> expr) ~ conjunctiveQueryBody() ^^ {
+        case h ~ ts ~ sup ~ truthy ~ cq =>
+          SupervisionRule(headName = h, supervision = sup, truthiness = truthy, q = cq.copy(headTerms = ts))
       }
     | // function call with += sign between head and function call
       relationName ~ ("+=" ~> functionName) ~ conjunctiveQuery ^^ {
@@ -481,7 +482,7 @@ class DeepDiveLogParser extends JavaTokenParsers {
       anno => (anno named "label") && (anno.exprs.size == 1)
     } =>
       val labelExpr = (rule.annotations find (_ named "label") flatMap (_ expr) get)
-      SupervisionRule(headName = rule.headName, supervision = labelExpr, q = rule.q,
+      SupervisionRule(headName = rule.headName, supervision = labelExpr, truthiness = None, q = rule.q,
         annotations = rule.annotations filterNot (_ named "label"))
 
     case rule: ExtractionRule => rule
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index ec5b3e032..3566d830f 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -13,10 +13,11 @@ sql: """
 SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R1.tag AS column_2
-     ,
+     , 
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS column_3
+     , 1.0 AS column_4
 FROM words R0
    , tags R1
 """
@@ -37,7 +38,7 @@ SELECT R0.sent_id AS column_0
      , R0.word AS column_2
      , R0.pos AS column_3
      , R0.true_tag AS column_4
-     ,
+     , 
 CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
      WHEN R0.true_tag = 'I-UCP' THEN NULL
      WHEN strpos(R0.true_tag, '-') > 0 THEN split_part(R0.true_tag, '-', 2)
@@ -119,7 +120,7 @@ function: """AndCategorical(chunk.R0.dd_label)"""
 deepdive.inference.factors.linear_chain {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
@@ -166,7 +167,7 @@ function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 deepdive.inference.factors.phony_rule {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
diff --git a/test/expected-output-test/if-then-else/compile.expected b/test/expected-output-test/if-then-else/compile.expected
index 4894ca95e..33f901d35 100644
--- a/test/expected-output-test/if-then-else/compile.expected
+++ b/test/expected-output-test/if-then-else/compile.expected
@@ -13,6 +13,7 @@ CASE WHEN R0.l > 0 THEN true
      WHEN R0.l < 0 THEN false
      ELSE NULL
 END AS column_1
+     , 1.0 AS column_2
 FROM labels_resolved R0
 """
 input_relations: [
diff --git a/test/expected-output-test/materialize_annotation/compile.expected b/test/expected-output-test/materialize_annotation/compile.expected
index 8539059be..192166e02 100644
--- a/test/expected-output-test/materialize_annotation/compile.expected
+++ b/test/expected-output-test/materialize_annotation/compile.expected
@@ -24,6 +24,7 @@ deepdive.extraction.extractors.ext_VQ {
 sql: """
 SELECT R0.x AS column_0
      , true AS column_1
+     , 1.0 AS column_2
 FROM D R0
 """
 input_relations: [
@@ -56,6 +57,7 @@ SELECT R0.x AS column_0
 CASE WHEN length(R0.x) > 5 THEN true
      ELSE NULL
 END AS column_1
+     , 1.0 AS column_2
 FROM D R0
 """
 input_relations: [
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 4bf018f29..243d73120 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -10,6 +10,7 @@ deepdive.extraction.extractors.ext_q1 {
 sql: """
 SELECT R0.wid AS column_0
      , R0.val AS column_1
+     , 1.0 AS column_2
 FROM label1 R0
 """
 input_relations: [
@@ -25,6 +26,7 @@ deepdive.extraction.extractors.ext_q2 {
 sql: """
 SELECT R0.wid AS column_0
      , R0.val AS column_1
+     , 1.0 AS column_2
 FROM label2 R0
 """
 input_relations: [
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index f88d8837e..6785fa54e 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -10,6 +10,7 @@ deepdive.extraction.extractors.ext_smoke {
 sql: """
 SELECT R0.person_id AS column_0
      , R0.smokes AS column_1
+     , 1.0 AS column_2
 FROM person_smokes R0
 """
 input_relations: [
@@ -25,6 +26,7 @@ deepdive.extraction.extractors.ext_cancer {
 sql: """
 SELECT R0.person_id AS column_0
      , R0.has_cancer AS column_1
+     , 1.0 AS column_2
 FROM person_has_cancer R0
 """
 input_relations: [
@@ -39,7 +41,7 @@ materialize: false
 deepdive.inference.factors.inf_imply_smoke_cancer {
 weight: """0.5"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
@@ -69,7 +71,7 @@ function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_smoke_smoke {
 weight: """0.4"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
 SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 1c3895ece..72978f3fd 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -80,6 +80,7 @@ deepdive.extraction.extractors.ext_has_spouse {
 sql: """
 SELECT R0.relation_id AS column_0
      , R0.is_true AS column_1
+     , 1.0 AS column_2
 FROM has_spouse_candidates R0
 """
 input_relations: [

From 717b100d01607d1a15fbb8f1cbdfa357ef223331 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Wed, 28 Dec 2016 18:04:07 -0800
Subject: [PATCH 345/347] Simplify grounding by removing joins with var ID
 tables

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  | 30 ++-----
 .../chunking_example/compile.expected         | 42 ++++-----
 .../factor_functions/compile.expected         | 24 ++----
 .../logical_rules/compile.expected            | 14 ++-
 .../compile.expected                          | 86 +++++++------------
 .../ocr_example/compile.expected              | 12 +--
 .../smoke_example/compile.expected            | 24 ++----
 .../spouse_example/compile.expected           |  6 +-
 .../weights/compile.expected                  | 36 +++-----
 9 files changed, 94 insertions(+), 180 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 0375a6a8c..bb908214b 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -116,8 +116,9 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   // odd has happened.
   def resolveName( v : Variable ) : String = {
     v match { case Variable(v,relName,i) =>
-      if(attrNameForRelationAndPosition contains (relName,i)) {
-        attrNameForRelationAndPosition(relName,i)
+      val realRel = relName.replaceAll("^" + deepdivePrefixForVariablesWithIdsTable, "")
+      if(attrNameForRelationAndPosition contains (realRel,i)) {
+        attrNameForRelationAndPosition(realRel,i)
       } else {
         // for views, columns names are in the form of "column_index"
         return s"column_${i}"
@@ -511,7 +512,7 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
       case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
         // TODO maybe TableAlias can be useful here or we can completely get rid of it?
         // variable id column
-        s"""${deepdiveVariableIdColumn}_${headAsBody indexOf x}.${
+        s"""R${headAsBody indexOf x}.${
           deepdiveVariableIdColumn
         } AS "${x.name}.R${headAsBody indexOf x}.${deepdiveVariableIdColumn}\"""" :: (
           // project variable key columns as well (to reduce unnecssary joins)
@@ -530,23 +531,10 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
       case _ => List.empty
     }
 
-    val internalVarTables = headAsBody.zipWithIndex flatMap {
-      case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
-        List(s"""${deepdivePrefixForVariablesIdsTable}${x.name} AS ${deepdiveVariableIdColumn}_${headAsBody indexOf x}""")
-      case _ => List.empty
+    val headAsBodyWithIds = headAsBody map {
+      case(x: Atom) => Atom(s"""${deepdivePrefixForVariablesWithIdsTable}${x.name}""", x.terms)
     }
 
-    val internalVarJoinConds = headAsBody.zipWithIndex flatMap {
-      case (x: Atom, i) if schemaDeclarationByRelationName get x.name exists (_.isQuery) =>
-        List(
-          // project variable key columns as well (to reduce unnecssary joins)
-          schemaDeclarationByRelationName get x.name map (_.keyColumns map {
-            case term => s"""R${headAsBody indexOf x}.${term} = ${deepdiveVariableIdColumn}_${headAsBody indexOf x}.${term}"""
-          }) get
-        )
-      case _ => List.empty
-    } flatten
-
     var nonCategoryWeightCols = new HashSet[String]()
 
     val inputQueries =
@@ -554,11 +542,11 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         // Here we need to select from the bodies atoms as well as the head atoms,
         // which are the variable relations.
         // This is achieved by puting head atoms into the body.
-        val fakeBody        = headAsBody ++ cqBody
+        val fakeBody        = headAsBodyWithIds ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
 
         // TODO XXX: Fix the `internal` hack below
-        val qc = new QueryCompiler(fakeCQ, internalVarTables, internalVarJoinConds)
+        val qc = new QueryCompiler(fakeCQ)
 
         // weight columns
         val weightColumns = stmt.weights.variables.zipWithIndex collect {
@@ -685,7 +673,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   val deepdiveVariableIdColumn = "dd_id"
   val deepdiveVariableLabelColumn = "dd_label"
   val deepdiveVariableLabelTruthinessColumn = "dd_truthiness"
-  val deepdivePrefixForVariablesIdsTable = "dd_variables_"
+  val deepdivePrefixForVariablesWithIdsTable = "dd_predicate_"
 
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 3566d830f..86a71b27a 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -85,27 +85,25 @@ deepdive.inference.factors.inf_istrue_chunk {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
   dd_weight_column_0
+  dd_weight_column_1
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
+SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R0.tag AS "chunk.R0.tag"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
      , (R3.feature)::float AS feature_value
-FROM chunk R0
+FROM dd_predicate_chunk R0
    , words R1
    , tags R2
    , word_features R3
-   , dd_variables_chunk AS dd_id_0
 WHERE R1.sent_id = R0.sent_id
   AND R1.word_id = R0.word_id
   AND R2.tag = R0.tag
   AND R3.sent_id = R0.sent_id
   AND R3.word_id = R0.word_id
-  AND R0.sent_id = dd_id_0.sent_id
-  AND R0.word_id = dd_id_0.word_id
 """
 input_relations: [
   chunk
@@ -120,28 +118,27 @@ function: """AndCategorical(chunk.R0.dd_label)"""
 deepdive.inference.factors.linear_chain {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
-  
+  dd_weight_column_0
+  dd_weight_column_1
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
+SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R0.tag AS "chunk.R0.tag"
-     , dd_id_1.dd_id AS "chunk.R1.dd_id"
+     , R1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
      , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
      , (1)::float AS feature_value
-FROM chunk R0
-   , chunk R1
+FROM dd_predicate_chunk R0
+   , dd_predicate_chunk R1
    , words R2
    , words R3
    , tags R4
    , tags R5
-   , dd_variables_chunk AS dd_id_0
-   , dd_variables_chunk AS dd_id_1
 WHERE R1.sent_id = R0.sent_id
   AND R2.sent_id = R0.sent_id
   AND R2.word_id = R0.word_id
@@ -150,10 +147,6 @@ WHERE R1.sent_id = R0.sent_id
   AND R4.tag = R0.tag
   AND R5.tag = R1.tag
   AND R1.word_id = (R0.word_id + 1)
-  AND R0.sent_id = dd_id_0.sent_id
-  AND R0.word_id = dd_id_0.word_id
-  AND R1.sent_id = dd_id_1.sent_id
-  AND R1.word_id = dd_id_1.word_id
 """
 input_relations: [
   chunk
@@ -167,28 +160,27 @@ function: """AndCategorical(chunk.R0.dd_label, chunk.R1.dd_label)"""
 deepdive.inference.factors.phony_rule {
 weight: """?(dd_weight_column_0, dd_weight_column_1)"""
 non_category_weight_cols: [
-  
+  dd_weight_column_0
+  dd_weight_column_1
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "chunk.R0.dd_id"
+SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.sent_id AS "chunk.R0.sent_id"
      , R0.word_id AS "chunk.R0.word_id"
      , R0.tag AS "chunk.R0.tag"
-     , dd_id_1.dd_id AS "chunk.R1.dd_id"
+     , R1.dd_id AS "chunk.R1.dd_id"
      , R1.sent_id AS "chunk.R1.sent_id"
      , R1.word_id AS "chunk.R1.word_id"
      , R1.tag AS "chunk.R1.tag"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
      , (1)::float AS feature_value
-FROM chunk R0
-   , chunk R1
+FROM dd_predicate_chunk R0
+   , dd_predicate_chunk R1
    , words R2
    , words R3
    , tags R4
    , tags R5
-   , dd_variables_chunk AS dd_id_0
-   , dd_variables_chunk AS dd_id_1
 WHERE R1.sent_id = R0.sent_id
   AND R2.sent_id = R0.sent_id
   AND R2.word_id = R0.word_id
@@ -198,10 +190,6 @@ WHERE R1.sent_id = R0.sent_id
   AND R5.tag = R1.tag
   AND R2.tag IS NOT NULL
   AND R0.word_id < R1.word_id
-  AND R0.sent_id = dd_id_0.sent_id
-  AND R0.word_id = dd_id_0.word_id
-  AND R1.sent_id = dd_id_1.sent_id
-  AND R1.word_id = dd_id_1.word_id
 """
 input_relations: [
   chunk
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index 140a160f0..baa306c4a 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -12,21 +12,17 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q.R1.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q R1
    , R R2
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R2.b = R1.x
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
@@ -42,21 +38,17 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q.R1.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q R1
    , R R2
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R2.b = R1.x
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 58efd5d4b..7bdf80583 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -39,22 +39,18 @@ materialize: false
 deepdive.inference.factors.inf_imply_P_Q {
 weight: """1"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "P.R0.dd_id"
+SELECT R0.dd_id AS "P.R0.dd_id"
      , R0.x AS "P.R0.x"
-     , dd_id_1.dd_id AS "Q.R1.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , (1)::float AS feature_value
-FROM P R0
-   , Q R1
-   , dd_variables_P AS dd_id_0
-   , dd_variables_Q AS dd_id_1
+FROM dd_predicate_P R0
+   , dd_predicate_Q R1
 WHERE R1.x = R0.x
   AND true
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   P
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index c398fd355..c85fc533e 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -207,16 +207,14 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM Q R0
+FROM dd_predicate_Q R0
    , S R1
-   , dd_variables_Q AS dd_id_0
 WHERE R1.a = R0.x
   AND R0.x > 1000
-  AND R0.x = dd_id_0.x
 """
 input_relations: [
   Q
@@ -229,18 +227,16 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_Q_1 {
 weight: """1.0"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , (1)::float AS feature_value
-FROM Q R0
+FROM dd_predicate_Q R0
    , S R1
-   , dd_variables_Q AS dd_id_0
 WHERE R1.a = R0.x
   AND R0.x = 0
-  AND R0.x = dd_id_0.x
 """
 input_relations: [
   Q
@@ -253,18 +249,16 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_not_Q {
 weight: """?"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , (1)::float AS feature_value
-FROM Q R0
+FROM dd_predicate_Q R0
    , S R1
-   , dd_variables_Q AS dd_id_0
 WHERE R1.a = R0.x
   AND R0.x < 1000
-  AND R0.x = dd_id_0.x
 """
 input_relations: [
   Q
@@ -280,25 +274,21 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q.R1.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
@@ -312,28 +302,24 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_Q_Q__1 {
 weight: """-10.0"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q.R1.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) < 1000
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
@@ -347,28 +333,24 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_Q_Q__2 {
 weight: """10.0"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q.R1.dd_id"
+     , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
   AND (R0.x + R1.x) > 1000
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
@@ -399,25 +381,21 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q1.R1.dd_id"
+     , R1.dd_id AS "Q1.R1.dd_id"
      , R1.x AS "Q1.R1.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q1 R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q1 R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q1 AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
@@ -435,25 +413,21 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "Q.R0.dd_id"
+SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
-     , dd_id_1.dd_id AS "Q_1.R1.dd_id"
+     , R1.dd_id AS "Q_1.R1.dd_id"
      , R1.x AS "Q_1.R1.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM Q R0
-   , Q_1 R1
+FROM dd_predicate_Q R0
+   , dd_predicate_Q_1 R1
    , S R2
    , R R3
    , S R4
-   , dd_variables_Q AS dd_id_0
-   , dd_variables_Q_1 AS dd_id_1
 WHERE R2.a = R0.x
   AND R3.a = R0.x
   AND R3.b = R1.x
   AND R4.a = R1.x
-  AND R0.x = dd_id_0.x
-  AND R1.x = dd_id_1.x
 """
 input_relations: [
   Q
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 243d73120..68eec8190 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -44,15 +44,13 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "q1.R0.dd_id"
+SELECT R0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM q1 R0
+FROM dd_predicate_q1 R0
    , features R1
-   , dd_variables_q1 AS dd_id_0
 WHERE R1.word_id = R0.wid
-  AND R0.wid = dd_id_0.wid
 """
 input_relations: [
   q1
@@ -68,15 +66,13 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "q2.R0.dd_id"
+SELECT R0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM q2 R0
+FROM dd_predicate_q2 R0
    , features R1
-   , dd_variables_q2 AS dd_id_0
 WHERE R1.word_id = R0.wid
-  AND R0.wid = dd_id_0.wid
 """
 input_relations: [
   q2
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 6785fa54e..8355256fa 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -44,20 +44,16 @@ non_category_weight_cols: [
   
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
+SELECT R0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
-     , dd_id_1.dd_id AS "cancer.R1.dd_id"
+     , R1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
      , (1)::float AS feature_value
-FROM smoke R0
-   , cancer R1
+FROM dd_predicate_smoke R0
+   , dd_predicate_cancer R1
    , person_smokes R2
-   , dd_variables_smoke AS dd_id_0
-   , dd_variables_cancer AS dd_id_1
 WHERE R1.person_id = R0.person_id
   AND R2.person_id = R0.person_id
-  AND R0.person_id = dd_id_0.person_id
-  AND R1.person_id = dd_id_1.person_id
 """
 input_relations: [
   smoke
@@ -74,20 +70,16 @@ non_category_weight_cols: [
   
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "smoke.R0.dd_id"
+SELECT R0.dd_id AS "smoke.R0.dd_id"
      , R0.person_id AS "smoke.R0.person_id"
-     , dd_id_1.dd_id AS "smoke.R1.dd_id"
+     , R1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
      , (1)::float AS feature_value
-FROM smoke R0
-   , smoke R1
+FROM dd_predicate_smoke R0
+   , dd_predicate_smoke R1
    , friends R2
-   , dd_variables_smoke AS dd_id_0
-   , dd_variables_smoke AS dd_id_1
 WHERE R2.person_id = R0.person_id
   AND R2.friend_id = R1.person_id
-  AND R0.person_id = dd_id_0.person_id
-  AND R1.person_id = dd_id_1.person_id
 """
 input_relations: [
   smoke
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index 72978f3fd..a001a6b93 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -98,17 +98,15 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "has_spouse.R0.dd_id"
+SELECT R0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM has_spouse R0
+FROM dd_predicate_has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
-   , dd_variables_has_spouse AS dd_id_0
 WHERE R1.relation_id = R0.relation_id
   AND R2.relation_id = R0.relation_id
-  AND R0.relation_id = dd_id_0.relation_id
 """
 input_relations: [
   has_spouse
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 6cf94666c..221fcf2ae 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -15,15 +15,13 @@ non_category_weight_cols: [
   dd_weight_column_0
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "a.R0.dd_id"
+SELECT R0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM a R0
+FROM dd_predicate_a R0
    , b R1
-   , dd_variables_a AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = dd_id_0.k
 """
 input_relations: [
   a
@@ -36,17 +34,15 @@ function: """Imply(a.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_c {
 weight: """?"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "c.R0.dd_id"
+SELECT R0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
      , (1)::float AS feature_value
-FROM c R0
+FROM dd_predicate_c R0
    , b R1
-   , dd_variables_c AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = dd_id_0.k
 """
 input_relations: [
   c
@@ -63,16 +59,14 @@ non_category_weight_cols: [
   dd_weight_column_1
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "d.R0.dd_id"
+SELECT R0.dd_id AS "d.R0.dd_id"
      , R0.k AS "d.R0.k"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
      , (1)::float AS feature_value
-FROM d R0
+FROM dd_predicate_d R0
    , b R1
-   , dd_variables_d AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = dd_id_0.k
 """
 input_relations: [
   d
@@ -85,17 +79,15 @@ function: """Imply(d.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_e {
 weight: """-10"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "e.R0.dd_id"
+SELECT R0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
      , (1)::float AS feature_value
-FROM e R0
+FROM dd_predicate_e R0
    , b R1
-   , dd_variables_e AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = dd_id_0.k
 """
 input_relations: [
   e
@@ -108,17 +100,15 @@ function: """Imply(e.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_f {
 weight: """-0.3"""
 non_category_weight_cols: [
-
+  
 ]
 input_query: """
-SELECT dd_id_0.dd_id AS "f.R0.dd_id"
+SELECT R0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
      , (1)::float AS feature_value
-FROM f R0
+FROM dd_predicate_f R0
    , b R1
-   , dd_variables_f AS dd_id_0
 WHERE R1.k = R0.k
-  AND R0.k = dd_id_0.k
 """
 input_relations: [
   f

From ea41bc5f3c1d9430f80d05441f719f2cf1b02998 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Wed, 28 Dec 2016 18:40:13 -0800
Subject: [PATCH 346/347] fixes per netj

---
 .../deepdive/ddlog/DeepDiveLogCompiler.scala  |  5 ++-
 .../chunking_example/compile.expected         | 14 ++++----
 .../factor_functions/compile.expected         |  8 ++---
 .../logical_rules/compile.expected            |  6 ++--
 .../compile.expected                          | 34 +++++++++----------
 .../ocr_example/compile.expected              |  4 +--
 .../smoke_example/compile.expected            | 12 +++----
 .../spouse_example/compile.expected           |  2 +-
 .../weights/compile.expected                  | 16 ++++-----
 9 files changed, 50 insertions(+), 51 deletions(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index bb908214b..2ea391d04 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -116,7 +116,7 @@ class DeepDiveLogCompiler( program : DeepDiveLog.Program, config : DeepDiveLog.C
   // odd has happened.
   def resolveName( v : Variable ) : String = {
     v match { case Variable(v,relName,i) =>
-      val realRel = relName.replaceAll("^" + deepdivePrefixForVariablesWithIdsTable, "")
+      val realRel = relName.stripPrefix(deepdivePrefixForVariablesWithIdsTable)
       if(attrNameForRelationAndPosition contains (realRel,i)) {
         attrNameForRelationAndPosition(realRel,i)
       } else {
@@ -545,7 +545,6 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
         val fakeBody        = headAsBodyWithIds ++ cqBody
         val fakeCQ          = stmt.q.copy(bodies = List(fakeBody))
 
-        // TODO XXX: Fix the `internal` hack below
         val qc = new QueryCompiler(fakeCQ)
 
         // weight columns
@@ -673,7 +672,7 @@ object DeepDiveLogCompiler extends DeepDiveLogHandler {
   val deepdiveVariableIdColumn = "dd_id"
   val deepdiveVariableLabelColumn = "dd_label"
   val deepdiveVariableLabelTruthinessColumn = "dd_truthiness"
-  val deepdivePrefixForVariablesWithIdsTable = "dd_predicate_"
+  val deepdivePrefixForVariablesWithIdsTable = "dd_variables_with_id_"
 
   // entry point for compilation
   override def run(parsedProgram: DeepDiveLog.Program, config: DeepDiveLog.Config) = {
diff --git a/test/expected-output-test/chunking_example/compile.expected b/test/expected-output-test/chunking_example/compile.expected
index 86a71b27a..65a4c9cc2 100644
--- a/test/expected-output-test/chunking_example/compile.expected
+++ b/test/expected-output-test/chunking_example/compile.expected
@@ -13,7 +13,7 @@ sql: """
 SELECT R0.sent_id AS column_0
      , R0.word_id AS column_1
      , R1.tag AS column_2
-     , 
+     ,
 CASE WHEN R1.tag = R0.tag THEN true
      ELSE NULL
 END AS column_3
@@ -38,7 +38,7 @@ SELECT R0.sent_id AS column_0
      , R0.word AS column_2
      , R0.pos AS column_3
      , R0.true_tag AS column_4
-     , 
+     ,
 CASE WHEN R0.true_tag = 'B-UCP' THEN NULL
      WHEN R0.true_tag = 'I-UCP' THEN NULL
      WHEN strpos(R0.true_tag, '-') > 0 THEN split_part(R0.true_tag, '-', 2)
@@ -95,7 +95,7 @@ SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R3.feature AS "dd_weight_column_0"
      , R0.tag AS "dd_weight_column_1"
      , (R3.feature)::float AS feature_value
-FROM dd_predicate_chunk R0
+FROM dd_variables_with_id_chunk R0
    , words R1
    , tags R2
    , word_features R3
@@ -133,8 +133,8 @@ SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
      , (1)::float AS feature_value
-FROM dd_predicate_chunk R0
-   , dd_predicate_chunk R1
+FROM dd_variables_with_id_chunk R0
+   , dd_variables_with_id_chunk R1
    , words R2
    , words R3
    , tags R4
@@ -175,8 +175,8 @@ SELECT R0.dd_id AS "chunk.R0.dd_id"
      , R0.tag AS "dd_weight_column_0"
      , R1.tag AS "dd_weight_column_1"
      , (1)::float AS feature_value
-FROM dd_predicate_chunk R0
-   , dd_predicate_chunk R1
+FROM dd_variables_with_id_chunk R0
+   , dd_variables_with_id_chunk R1
    , words R2
    , words R3
    , tags R4
diff --git a/test/expected-output-test/factor_functions/compile.expected b/test/expected-output-test/factor_functions/compile.expected
index baa306c4a..391812d1c 100644
--- a/test/expected-output-test/factor_functions/compile.expected
+++ b/test/expected-output-test/factor_functions/compile.expected
@@ -18,8 +18,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q R1
    , R R2
 WHERE R2.a = R0.x
   AND R2.b = R1.x
@@ -44,8 +44,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.x AS "Q.R1.x"
      , R1.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q R1
    , R R2
 WHERE R2.a = R0.x
   AND R2.b = R1.x
diff --git a/test/expected-output-test/logical_rules/compile.expected b/test/expected-output-test/logical_rules/compile.expected
index 7bdf80583..06699f9a9 100644
--- a/test/expected-output-test/logical_rules/compile.expected
+++ b/test/expected-output-test/logical_rules/compile.expected
@@ -39,7 +39,7 @@ materialize: false
 deepdive.inference.factors.inf_imply_P_Q {
 weight: """1"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "P.R0.dd_id"
@@ -47,8 +47,8 @@ SELECT R0.dd_id AS "P.R0.dd_id"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , (1)::float AS feature_value
-FROM dd_predicate_P R0
-   , dd_predicate_Q R1
+FROM dd_variables_with_id_P R0
+   , dd_variables_with_id_Q R1
 WHERE R1.x = R0.x
   AND true
 """
diff --git a/test/expected-output-test/multiple_rules_for_same_head/compile.expected b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
index c85fc533e..68825ce7e 100644
--- a/test/expected-output-test/multiple_rules_for_same_head/compile.expected
+++ b/test/expected-output-test/multiple_rules_for_same_head/compile.expected
@@ -211,7 +211,7 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
+FROM dd_variables_with_id_Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x > 1000
@@ -227,13 +227,13 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_Q_1 {
 weight: """1.0"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
+FROM dd_variables_with_id_Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x = 0
@@ -249,13 +249,13 @@ function: """Imply(Q.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_not_Q {
 weight: """?"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
      , R0.x AS "Q.R0.x"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
+FROM dd_variables_with_id_Q R0
    , S R1
 WHERE R1.a = R0.x
   AND R0.x < 1000
@@ -280,8 +280,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.x AS "Q.R1.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q R1
    , S R2
    , R R3
    , S R4
@@ -302,7 +302,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_Q_Q__1 {
 weight: """-10.0"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
@@ -310,8 +310,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q R1
    , S R2
    , R R3
    , S R4
@@ -333,7 +333,7 @@ function: """Imply(Q.R0.dd_label, Q.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_Q_Q__2 {
 weight: """10.0"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "Q.R0.dd_id"
@@ -341,8 +341,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.dd_id AS "Q.R1.dd_id"
      , R1.x AS "Q.R1.x"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q R1
    , S R2
    , R R3
    , S R4
@@ -387,8 +387,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.x AS "Q1.R1.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q1 R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q1 R1
    , S R2
    , R R3
    , S R4
@@ -419,8 +419,8 @@ SELECT R0.dd_id AS "Q.R0.dd_id"
      , R1.x AS "Q_1.R1.x"
      , R0.x AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_Q R0
-   , dd_predicate_Q_1 R1
+FROM dd_variables_with_id_Q R0
+   , dd_variables_with_id_Q_1 R1
    , S R2
    , R R3
    , S R4
diff --git a/test/expected-output-test/ocr_example/compile.expected b/test/expected-output-test/ocr_example/compile.expected
index 68eec8190..842da2172 100644
--- a/test/expected-output-test/ocr_example/compile.expected
+++ b/test/expected-output-test/ocr_example/compile.expected
@@ -48,7 +48,7 @@ SELECT R0.dd_id AS "q1.R0.dd_id"
      , R0.wid AS "q1.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_q1 R0
+FROM dd_variables_with_id_q1 R0
    , features R1
 WHERE R1.word_id = R0.wid
 """
@@ -70,7 +70,7 @@ SELECT R0.dd_id AS "q2.R0.dd_id"
      , R0.wid AS "q2.R0.wid"
      , R1.feature_id AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_q2 R0
+FROM dd_variables_with_id_q2 R0
    , features R1
 WHERE R1.word_id = R0.wid
 """
diff --git a/test/expected-output-test/smoke_example/compile.expected b/test/expected-output-test/smoke_example/compile.expected
index 8355256fa..25f1c3c20 100644
--- a/test/expected-output-test/smoke_example/compile.expected
+++ b/test/expected-output-test/smoke_example/compile.expected
@@ -41,7 +41,7 @@ materialize: false
 deepdive.inference.factors.inf_imply_smoke_cancer {
 weight: """0.5"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "smoke.R0.dd_id"
@@ -49,8 +49,8 @@ SELECT R0.dd_id AS "smoke.R0.dd_id"
      , R1.dd_id AS "cancer.R1.dd_id"
      , R1.person_id AS "cancer.R1.person_id"
      , (1)::float AS feature_value
-FROM dd_predicate_smoke R0
-   , dd_predicate_cancer R1
+FROM dd_variables_with_id_smoke R0
+   , dd_variables_with_id_cancer R1
    , person_smokes R2
 WHERE R1.person_id = R0.person_id
   AND R2.person_id = R0.person_id
@@ -67,7 +67,7 @@ function: """Imply(smoke.R0.dd_label, cancer.R1.dd_label)"""
 deepdive.inference.factors.inf_imply_smoke_smoke {
 weight: """0.4"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "smoke.R0.dd_id"
@@ -75,8 +75,8 @@ SELECT R0.dd_id AS "smoke.R0.dd_id"
      , R1.dd_id AS "smoke.R1.dd_id"
      , R1.person_id AS "smoke.R1.person_id"
      , (1)::float AS feature_value
-FROM dd_predicate_smoke R0
-   , dd_predicate_smoke R1
+FROM dd_variables_with_id_smoke R0
+   , dd_variables_with_id_smoke R1
    , friends R2
 WHERE R2.person_id = R0.person_id
   AND R2.friend_id = R1.person_id
diff --git a/test/expected-output-test/spouse_example/compile.expected b/test/expected-output-test/spouse_example/compile.expected
index a001a6b93..64adda9da 100644
--- a/test/expected-output-test/spouse_example/compile.expected
+++ b/test/expected-output-test/spouse_example/compile.expected
@@ -102,7 +102,7 @@ SELECT R0.dd_id AS "has_spouse.R0.dd_id"
      , R0.relation_id AS "has_spouse.R0.relation_id"
      , R2.feature AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_has_spouse R0
+FROM dd_variables_with_id_has_spouse R0
    , has_spouse_candidates R1
    , has_spouse_features R2
 WHERE R1.relation_id = R0.relation_id
diff --git a/test/expected-output-test/weights/compile.expected b/test/expected-output-test/weights/compile.expected
index 221fcf2ae..85452a3db 100644
--- a/test/expected-output-test/weights/compile.expected
+++ b/test/expected-output-test/weights/compile.expected
@@ -19,7 +19,7 @@ SELECT R0.dd_id AS "a.R0.dd_id"
      , R0.k AS "a.R0.k"
      , R0.k + R1.p AS "dd_weight_column_0"
      , (1)::float AS feature_value
-FROM dd_predicate_a R0
+FROM dd_variables_with_id_a R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -34,13 +34,13 @@ function: """Imply(a.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_c {
 weight: """?"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "c.R0.dd_id"
      , R0.k AS "c.R0.k"
      , (1)::float AS feature_value
-FROM dd_predicate_c R0
+FROM dd_variables_with_id_c R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -64,7 +64,7 @@ SELECT R0.dd_id AS "d.R0.dd_id"
      , R0.k AS "dd_weight_column_0"
      , R1.p AS "dd_weight_column_1"
      , (1)::float AS feature_value
-FROM dd_predicate_d R0
+FROM dd_variables_with_id_d R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -79,13 +79,13 @@ function: """Imply(d.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_e {
 weight: """-10"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "e.R0.dd_id"
      , R0.k AS "e.R0.k"
      , (1)::float AS feature_value
-FROM dd_predicate_e R0
+FROM dd_variables_with_id_e R0
    , b R1
 WHERE R1.k = R0.k
 """
@@ -100,13 +100,13 @@ function: """Imply(e.R0.dd_label)"""
 deepdive.inference.factors.inf_istrue_f {
 weight: """-0.3"""
 non_category_weight_cols: [
-  
+
 ]
 input_query: """
 SELECT R0.dd_id AS "f.R0.dd_id"
      , R0.k AS "f.R0.k"
      , (1)::float AS feature_value
-FROM dd_predicate_f R0
+FROM dd_variables_with_id_f R0
    , b R1
 WHERE R1.k = R0.k
 """

From 6305811bd620751e5f1c97665de76bb6f15dbd51 Mon Sep 17 00:00:00 2001
From: alldefector <feng.niu@lattice.io>
Date: Thu, 29 Dec 2016 00:14:59 -0800
Subject: [PATCH 347/347] fix error with complex rules

---
 src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
index 2ea391d04..90ea0e966 100644
--- a/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
+++ b/src/main/scala/org/deepdive/ddlog/DeepDiveLogCompiler.scala
@@ -315,7 +315,8 @@ class QueryCompiler(cq : ConjunctiveQuery, hackFrom: List[String] = Nil, hackWhe
               // expression patterns indicate a filter condition on the column
               case ExprPattern(expr) => {
                 val resolved = compileExpr(expr)
-                val attr = attrNameForRelationAndPosition(relName, termIndex)
+                val realRel = relName.stripPrefix(deepdivePrefixForVariablesWithIdsTable)
+                val attr = attrNameForRelationAndPosition(realRel, termIndex)
                 Some(s"R${bodyIndex}.${attr} = ${resolved}")
               }
             }