hack get root_cres working using Neo4J

application/database/db.py

@@ -5,6 +5,7 @@
     UniqueIdProperty,
     Relationship,
     RelationshipTo,
+    RelationshipFrom,
     ArrayProperty,
     StructuredRel,
     db,
@@ -193,17 +194,24 @@ class NeoDocument(StructuredNode):
     related = Relationship("NeoDocument", "RELATED", model=RelatedRel)
 
     @classmethod
-    def to_cre_def(self, node):
+    def to_cre_def(self, node, parse_links=True):
         raise Exception(f"Shouldn't be parsing a NeoDocument")
 
+    @classmethod
+    def get_links(self, links_dict):
+        links = []
+        for key in links_dict:
+            links.extend([cre_defs.Link(c.to_cre_def(c, parse_links=False), key) for c in links_dict[key]])
+        return links
+
 
 class NeoNode(NeoDocument):
     doctype = StringProperty()
     version = StringProperty(required=True)
     hyperlink = StringProperty()
 
     @classmethod
-    def to_cre_def(self, node):
+    def to_cre_def(self, node, parse_links=True):
         raise Exception(f"Shouldn't be parsing a NeoNode")
 
 
@@ -213,7 +221,7 @@ class NeoStandard(NeoNode):
     section_id = StringProperty()
 
     @classmethod
-    def to_cre_def(self, node) -> cre_defs.Standard:
+    def to_cre_def(self, node, parse_links=True) -> cre_defs.Standard:
         return cre_defs.Standard(
             name=node.name,
             id=node.document_id,
@@ -231,7 +239,7 @@ class NeoTool(NeoStandard):
     tooltype = StringProperty(required=True)
 
     @classmethod
-    def to_cre_def(self, node) -> cre_defs.Tool:
+    def to_cre_def(self, node, parse_links=True) -> cre_defs.Tool:
         return cre_defs.Tool(
             name=node.name,
             id=node.document_id,
@@ -247,7 +255,7 @@ def to_cre_def(self, node) -> cre_defs.Tool:
 
 class NeoCode(NeoNode):
     @classmethod
-    def to_cre_def(self, node) -> cre_defs.Code:
+    def to_cre_def(self, node, parse_links=True) -> cre_defs.Code:
         return cre_defs.Code(
             name=node.name,
             id=node.document_id,
@@ -260,17 +268,24 @@ def to_cre_def(self, node) -> cre_defs.Code:
 
 class NeoCRE(NeoDocument):  # type: ignore
     external_id = StringProperty()
+    contained_in = RelationshipFrom('NeoCRE', 'CONTAINS', model=ContainsRel)
     contains = RelationshipTo("NeoCRE", "CONTAINS", model=ContainsRel)
     linked = RelationshipTo("NeoStandard", "LINKED_TO", model=LinkedToRel)
     same_as = RelationshipTo("NeoStandard", "SAME", model=SameRel)
 
     @classmethod
-    def to_cre_def(self, node) -> cre_defs.CRE:
+    def to_cre_def(self, node, parse_links=True) -> cre_defs.CRE:
         return cre_defs.CRE(
             name=node.name,
             id=node.document_id,
             description=node.description,
             tags=node.tags,
+            links=self.get_links({
+                'Contains': [*node.contains, *node.contained_in],
+                'Linked To': node.linked,
+                'Same as': node.same_as,
+                'Related': node.related
+                }) if parse_links else []
         )
 
 
@@ -464,19 +479,19 @@ def format_segment(seg: StructuredRel, nodes):
             ][0]
 
             return {
-                "start": NEO_DB.parse_node(start_node),
-                "end": NEO_DB.parse_node(end_node),
+                "start": NEO_DB.parse_node_no_links(start_node),
+                "end": NEO_DB.parse_node_no_links(end_node),
                 "relationship": relation_map[type(seg)],
             }
 
         def format_path_record(rec):
             return {
-                "start": NEO_DB.parse_node(rec.start_node),
-                "end": NEO_DB.parse_node(rec.end_node),
+                "start": NEO_DB.parse_node_no_links(rec.start_node),
+                "end": NEO_DB.parse_node_no_links(rec.end_node),
                 "path": [format_segment(seg, rec.nodes) for seg in rec.relationships],
             }
 
-        return [NEO_DB.parse_node(rec) for rec in base_standard], [
+        return [NEO_DB.parse_node_no_links(rec) for rec in base_standard], [
             format_path_record(rec[0]) for rec in (path_records + path_records_all)
         ]
 
@@ -490,6 +505,10 @@ def standards(self) -> List[str]:
     @staticmethod
     def parse_node(node: NeoDocument) -> cre_defs.Document:
         return node.to_cre_def(node)
+
+    @staticmethod
+    def parse_node_no_links(node: NeoDocument) -> cre_defs.Document:
+        return node.to_cre_def(node, parse_links=False)
 
 
 class CRE_Graph:
@@ -1514,30 +1533,8 @@ def text_search(self, text: str) -> List[Optional[cre_defs.Document]]:
 
     def get_root_cres(self):
         """Returns CRES that only have "Contains" links"""
-        linked_groups = aliased(InternalLinks)
-        linked_cres = aliased(InternalLinks)
-        cres = (
-            self.session.query(CRE)
-            .filter(
-                ~CRE.id.in_(
-                    self.session.query(InternalLinks.cre).filter(
-                        InternalLinks.type == cre_defs.LinkTypes.Contains,
-                    )
-                )
-            )
-            .filter(
-                ~CRE.id.in_(
-                    self.session.query(InternalLinks.group).filter(
-                        InternalLinks.type == cre_defs.LinkTypes.PartOf,
-                    )
-                )
-            )
-            .all()
-        )
-        result = []
-        for c in cres:
-            result.extend(self.get_CREs(external_id=c.external_id))
-        return result
+        neo_cres = NeoCRE.nodes.has(contained_in=False)
+        return [c.to_cre_def(c) for c in neo_cres]
 
     def get_embeddings_by_doc_type(self, doc_type: str) -> Dict[str, List[float]]:
         res = {}