added MDX and Units plugins

pom.xml

@@ -3,7 +3,49 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>gov.nist.healthcare.pcd.pcdtool</groupId>
 	<artifactId>pcdtool-message-validation</artifactId>
-	<version>0.0.1-SNAPSHOT</version>
+	<version>1.0.0-SNAPSHOT</version>
+
+
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.codehaus.mojo</groupId>
+					<artifactId>properties-maven-plugin</artifactId>
+					<version>1.0-alpha-2</version>
+					<executions>
+						<execution>
+							<phase>initialize</phase>
+							<goals>
+								<goal>read-project-properties</goal>
+							</goals>
+							<configuration>
+								<files>
+									<file>pom.properties</file>
+								</files>
+							</configuration>
+						</execution>
+					</executions>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-compiler-plugin</artifactId>
+					<configuration>
+						<source>1.8</source>
+						<target>1.8</target>
+					</configuration>
+				</plugin>
+				<plugin>
+					<artifactId>maven-release-plugin</artifactId>
+					<version>2.0</version>
+					<configuration>
+						<autoVersionSubmodules>true</autoVersionSubmodules>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+
+	</build>
 
 	<dependencies>
 		<dependency>

src/main/java/gov/nist/hit/pcd/custom/OBX_3.java

@@ -0,0 +1,66 @@
+package gov.nist.hit.pcd.custom;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import hl7.v2.instance.Element;
+import hl7.v2.instance.Query;
+import hl7.v2.instance.Simple;
+import scala.collection.Iterator;
+import scala.collection.immutable.List;
+
+public class OBX_3 {
+
+
+    /*
+     * OBX-3: If OBX-3.3 is MDC, check if code/refid is valid .
+     */
+
+    /**
+     * @param e
+     *        OBX context
+     * @return true if OBX-3.3 not MDC, true if OBX-3.2 and OBX-3.1 are valid, false otherwise
+     */
+
+	public boolean assertion(hl7.v2.instance.Element e) {
+        List<Element> OBXList = Query.query(e, "3[1]").get();
+        if (OBXList == null || OBXList.size() == 0) {
+            // OBR-3 is not present
+            return true;
+        }
+
+        Iterator<Element> it = OBXList.iterator();
+        while (it.hasNext()) {
+            Element next = it.next();
+            List<Simple> OBX3_1List = Query.queryAsSimple(next, "1[1]").get();
+            List<Simple> OBX3_2List = Query.queryAsSimple(next, "2[1]").get();
+            List<Simple> OBX3_3List = Query.queryAsSimple(next, "3[1]").get();
+
+            String OBX3_1 = OBX3_1List.size() > 0 ? OBX3_1List.apply(0).value().raw()   : "";
+            String OBX3_2 = OBX3_2List.size() > 0 ? OBX3_2List.apply(0).value().raw()   : "";
+            String OBX3_3 = OBX3_3List.size() > 0 ? OBX3_3List.apply(0).value().raw()   : "";
+
+            // ignore 0 code terms or MDCX terms 
+            if (OBX3_1.equals("0") || OBX3_2.startsWith("MDCX_")) {
+            		return true;
+            }
+
+
+            if (OBX3_3.equals("MDC")) {
+            	ResourceHandler rh = new ResourceHandler();
+            	if (rh.dupletIsValid(OBX3_1, OBX3_2)) {
+            		return true;
+            	}else {
+            		return false;
+            	}
+
+            }else {
+            		return true;
+            }
+
+        }
+
+        return true;
+    }	
+}

src/main/java/gov/nist/hit/pcd/custom/OBX_UnitCheck.java

@@ -0,0 +1,95 @@
+package gov.nist.hit.pcd.custom;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import hl7.v2.instance.Element;
+import hl7.v2.instance.Query;
+import hl7.v2.instance.Simple;
+import scala.collection.Iterator;
+import scala.collection.immutable.List;
+
+public class OBX_UnitCheck {
+
+
+    /*
+     * OBX-3: If OBX-3.3 is MDC, check if code/refid is valid .
+     */
+
+    /**
+     * @param e
+     *        OBX context
+     * @return true if OBX-3.3 not MDC, true if OBX-3.2 and OBX-3.1 are valid, false otherwise
+     */
+
+	public boolean assertion(hl7.v2.instance.Element e) {
+        List<Element> OBX3List = Query.query(e, "3[1]").get();
+        if (OBX3List == null || OBX3List.size() == 0) {
+            // OBX-3 is not present
+            return true;
+        }
+
+        List<Element> OBX6List = Query.query(e, "6[1]").get();
+        if (OBX6List == null || OBX6List.size() == 0) {
+            // OBX-6 is not present
+            return true;
+        }
+
+        Iterator<Element> it = OBX3List.iterator();
+        while (it.hasNext()) {
+            Element next = it.next();
+            List<Simple> OBX3_1List = Query.queryAsSimple(next, "1[1]").get();
+            List<Simple> OBX3_2List = Query.queryAsSimple(next, "2[1]").get();
+            List<Simple> OBX3_3List = Query.queryAsSimple(next, "3[1]").get();
+
+            String OBX3_1 = OBX3_1List.size() > 0 ? OBX3_1List.apply(0).value().raw()   : "";
+            String OBX3_2 = OBX3_2List.size() > 0 ? OBX3_2List.apply(0).value().raw()   : "";
+            String OBX3_3 = OBX3_3List.size() > 0 ? OBX3_3List.apply(0).value().raw()   : "";
+
+            // ignore 0 code terms or MDCX terms 
+            if (OBX3_1.equals("0") || OBX3_2.startsWith("MDCX_")) {
+            		return true;
+            }
+
+
+            if (OBX3_3.equals("MDC")) {
+
+
+            	 Iterator<Element> it6 = OBX6List.iterator();
+            	 while (it6.hasNext()) {
+                     Element next6 = it6.next();
+
+
+                     //primary 
+                     List<Simple> OBX6_2List = Query.queryAsSimple(next6, "2[1]").get();
+                     String OBX6_2 = OBX6_2List.size() > 0 ? OBX6_2List.apply(0).value().raw()   : "";
+
+                     //alternate
+                     List<Simple> OBX6_5List = Query.queryAsSimple(next6, "5[1]").get();
+                     String OBX6_5 = OBX6_5List.size() > 0 ? OBX6_5List.apply(0).value().raw()   : "";
+
+
+                     ResourceHandler rh = new ResourceHandler();
+
+
+		            	if (rh.unitIsValid(OBX3_2, OBX6_2) && rh.unitIsValid(OBX3_2, OBX6_5)) {
+		            		return true;
+		            	}else {
+
+		            		return false;
+		            	}
+            	 }
+
+
+
+
+	            }else {
+	            		return true;
+            }
+
+        }
+
+        return true;
+    }	
+}

src/main/java/gov/nist/hit/pcd/custom/ResourceHandler.java

@@ -0,0 +1,99 @@
+package gov.nist.hit.pcd.custom;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import gov.nist.hit.pcd.custom.model.MDCUnitsterm;
+import gov.nist.hit.pcd.custom.model.MDCterm;
+
+public class ResourceHandler {
+
+	private static List<MDCterm> mdcValues;
+	private static List<MDCUnitsterm> mdcUnitsTerms;
+
+
+	public ResourceHandler() {
+		if (mdcValues == null) {
+			mdcValues = loadMDC();
+		}
+
+		if (mdcUnitsTerms == null) {
+			mdcUnitsTerms = loadMdcUnitsTerms(); 
+		}
+
+
+	}
+
+	public List<MDCterm> loadMDC(){
+
+		List<MDCterm> values = new ArrayList<>();
+		try(BufferedReader br= new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream("/" + "mdccodes.csv")))) {
+		    values = br.lines().map(line -> {return new MDCterm(line.split(",")[0],line.split(",")[1]);}).collect(Collectors.toList());
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		return values;
+	}
+
+	public List<MDCUnitsterm> loadMdcUnitsTerms(){
+
+		List<MDCUnitsterm> values = new ArrayList<>();
+		try(BufferedReader br= new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream("/" + "units.csv")))) {
+		    values = br.lines().map(line -> {return new MDCUnitsterm(line.split(",")); }).collect(Collectors.toList());
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		return values;
+	}
+
+
+
+
+
+
+	public boolean codeExists(String code) {
+		for (MDCterm mdc : mdcValues) {
+			if (mdc.getTermcode().equals(code)) {
+				return true;
+			}
+		}
+		return false;
+	}
+
+
+	public boolean dupletIsValid (String code, String refid) {
+		for (MDCterm mdc : mdcValues) {
+			if (mdc.getRefid().equals(refid)) {
+				if (mdc.getTermcode().equals(code)) {
+					return true;
+				}else {
+					return false;
+				}
+			}
+		}
+		return false;
+	}
+
+
+	public boolean unitIsValid (String refid, String unit) {
+		for (MDCUnitsterm mdc : mdcUnitsTerms) {
+			if (mdc.getRefid().equals(refid)) {
+				if (mdc.getUnits().contains(unit)) {
+					return true;
+				}else {
+					return false;
+				}
+			}
+		}
+		//couldn't find refid, no errors
+		return true;
+	}
+
+
+
+}

src/main/java/gov/nist/hit/pcd/custom/model/MDCUnitsterm.java

@@ -0,0 +1,52 @@
+package gov.nist.hit.pcd.custom.model;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class MDCUnitsterm {
+
+	private List<String> units;
+	private String refid;
+
+
+
+	public MDCUnitsterm(String[] refAndunits) {
+		refid = refAndunits[0];
+		units = new ArrayList<>(Arrays.asList(refAndunits));
+		units.remove(0);
+	}
+
+
+	public MDCUnitsterm(String refid,List<String>  units) {
+		super();
+		this.units = units;
+		this.refid = refid;
+	}
+
+
+	public List<String>  getUnits() {
+		return units;
+	}
+
+
+	public void setUnits(List<String>  units) {
+		this.units = units;
+	}
+
+
+	public String getRefid() {
+		return refid;
+	}
+
+
+	public void setRefid(String refid) {
+		this.refid = refid;
+	}
+
+
+
+
+
+
+}