moved code around to fix error

VectorDatabase.py

@@ -1,5 +1,39 @@
 import psycopg2
-from database_entities import Fragment, Publication
+
+
+# Class to represent a publication with attributes id, title, pmc, pubmed, and doi
+class Publication:
+    id = ""
+    title = ""
+    pmc = ""
+    pubmed = ""
+    doi = ""
+
+    def __init__(self, id, title, pmc, pubmed, doi):
+        self.id = id  # (DOI) Unique identifier for the publication
+        self.title = title  # Title of the publication
+        self.pmc = pmc  # PubMed Central (PMC) Link
+        self.pubmed = pubmed  # PubMed Link
+        self.doi = doi  # Digital Object Identifier (DOI) Link for the publication
+
+
+# Class to represent a fragment of a publication with attributes id, header, content, and vector
+class Fragment:
+    # Class variables to store default values for attributes
+    id = ""
+    header = ""
+    content = ""
+    vector = ""
+
+    def __init__(self, id, header, content, vector):
+        # Constructor to initialize the attributes of the Fragment object
+
+        # Set the attributes of the object with the values provided during instantiation
+        self.id = id  # (DOI) Unique identifier for the fragment
+        self.header = header  # Header or title of the fragment
+        self.content = content  # Content or text of the fragment
+        self.vector = vector  # Vector representation of the fragment
+
 
 # Lantern class that exposes functionality of database to application
 class Lantern:
@@ -249,7 +283,7 @@ def getUnreadPublications(self, delete_unread_entries=True):
 
         if delete_unread_entries:
             cursor.execute('DELETE FROM unread;')
-            
+
         conn.commit()
         cursor.close()
 
@@ -292,49 +326,15 @@ def publicationExists(self, id):
         - [(text, embedding)] content of a publication's embeddings
     Notes:
     """
+
     def get_embeddings_for_pub(self, id):
         texts = []
         embeddings = []
         if not self.publicationExists(id):
-            return 
+            return
         fragments = self.getAllFragmentsOfPublication(id)
         for fragment in fragments:
             texts.append(fragment.content)
             embeddings.append(fragment.vector)
         text_embeddings = list(zip(texts, embeddings))
         return text_embeddings
-
-# Class to represent a publication with attributes id, title, pmc, pubmed, and doi
-class Publication:
-
-    id = ""
-    title = ""
-    pmc = ""
-    pubmed = ""
-    doi = ""
-
-    def __init__(self, id, title, pmc, pubmed, doi):
-        self.id = id # (DOI) Unique identifier for the publication
-        self.title = title    # Title of the publication
-        self.pmc = pmc        # PubMed Central (PMC) Link
-        self.pubmed = pubmed  # PubMed Link
-        self.doi = doi # Digital Object Identifier (DOI) Link for the publication
-
-# Class to represent a fragment of a publication with attributes id, header, content, and vector
-class Fragment:
-
-
-    # Class variables to store default values for attributes
-    id = ""        
-    header = ""    
-    content = ""   
-    vector = ""    
-
-    def __init__(self, id, header, content, vector):
-        # Constructor to initialize the attributes of the Fragment object
-
-        # Set the attributes of the object with the values provided during instantiation
-        self.id = id          # (DOI) Unique identifier for the fragment
-        self.header = header  # Header or title of the fragment
-        self.content = content # Content or text of the fragment
-        self.vector = vector  # Vector representation of the fragment