Merge pull request #933 from hubmapconsortium/Derek-Furst/avoid-unecessary-linkeages

fixed a bug introduced with the new reworked triggers for linking dir…

Author: yuanzhou

src/schema/schema_neo4j_queries.py

@@ -766,11 +766,13 @@ def link_entity_to_direct_ancestors(neo4j_driver, entity_uuid, direct_ancestor_u
 activity_uuid : str
     The uuid of the existing activity node to link to
 """
-def add_new_ancestors_to_existing_activity(neo4j_driver, new_ancestor_uuids, activity_uuid):
+def add_new_ancestors_to_existing_activity(neo4j_driver, new_ancestor_uuids, activity_uuid, create_activity, activity_data_dict, dataset_uuid):
     try:
         with neo4j_driver.session() as session:
             tx = session.begin_transaction()
-
+            if create_activity:
+                create_activity_tx(tx, activity_data_dict)
+                create_relationship_tx(tx, activity_uuid, dataset_uuid, 'ACTIVITY_OUTPUT', '->')
             create_outgoing_activity_relationships_tx(tx=tx
                                                       , source_node_uuids=new_ancestor_uuids
                                                       , activity_node_uuid=activity_uuid)

src/schema/schema_triggers.py

@@ -892,18 +892,25 @@ def link_dataset_to_direct_ancestors(property_key, normalized_type, request, use
 
     if 'direct_ancestor_uuids' not in new_data_dict:
         raise KeyError("Missing 'direct_ancestor_uuids' key in 'new_data_dict' during calling 'link_dataset_to_direct_ancestors()' trigger method.")
-
+    create_activity = False
+    activity_data_dict = {}
     dataset_uuid = existing_data_dict['uuid']
     direct_ancestor_uuids = new_data_dict['direct_ancestor_uuids']
 
     existing_dataset_ancestor_uuids = schema_neo4j_queries.get_dataset_direct_ancestors(schema_manager.get_neo4j_driver_instance(), dataset_uuid, "uuid")
     new_ancestors = set(direct_ancestor_uuids)-set(existing_dataset_ancestor_uuids)
     ancestors_to_unlink = set(existing_dataset_ancestor_uuids)-set(direct_ancestor_uuids)
     activity_uuid = schema_neo4j_queries.get_parent_activity_uuid_from_entity(schema_manager.get_neo4j_driver_instance(), dataset_uuid)
+
+    if not activity_uuid:
+        activity_data_dict = schema_manager.generate_activity_data(normalized_type, request, user_token, existing_data_dict)
+        activity_uuid = activity_data_dict['uuid']
+        create_activity = True
+
     if new_ancestors:
 
         try:
-            schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), list(new_ancestors), activity_uuid)
+            schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), list(new_ancestors), activity_uuid, create_activity, activity_data_dict, dataset_uuid)
         except TransactionError:
             raise
 
@@ -1911,7 +1918,8 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_
 
     if 'direct_ancestor_uuid' not in new_data_dict:
         raise KeyError("Missing 'direct_ancestor_uuid' key in 'new_data_dict' during calling 'link_sample_to_direct_ancestor()' trigger method.")
-
+    create_activity = False
+    activity_data_dict = {}
     sample_uuid = existing_data_dict['uuid']
 
     # Build a list of direct ancestor uuids
@@ -1921,10 +1929,16 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_
     new_ancestors = set(direct_ancestor_uuids)-set(existing_sample_ancestor_uuids)
     ancestors_to_unlink = set(existing_sample_ancestor_uuids)-set(direct_ancestor_uuids)
     activity_uuid = schema_neo4j_queries.get_parent_activity_uuid_from_entity(schema_manager.get_neo4j_driver_instance(), sample_uuid)
+    
+    if not activity_uuid:
+        activity_data_dict = schema_manager.generate_activity_data(normalized_type, request, user_token, existing_data_dict)
+        activity_uuid = activity_data_dict['uuid']
+        create_activity = True
+
     if new_ancestors:
 
         try:
-            schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), list(new_ancestors), activity_uuid)
+            schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), list(new_ancestors), activity_uuid, create_activity, activity_data_dict, sample_uuid)
         except TransactionError:
             raise