Merge pull request #936 from hubmapconsortium/Derek-Furst/avoid-unecessary-linkeages

removed 2 outdated comments about linking to ancestors

Author: yuanzhou

src/schema/provenance_schema.yaml

@@ -462,7 +462,6 @@ ENTITIES:
         exposed: false
         indexed: false
         description: "The uuids of source entities from which this new entity is derived.  Used to pass source entity ids in on POST or PUT calls used to create the linkages."
-        # Note: link_dataset_to_direct_ancestors() will always delete all the old linkages first
         after_create_trigger: link_dataset_to_direct_ancestors
         after_update_trigger: link_dataset_to_direct_ancestors
       direct_ancestors:
@@ -1062,7 +1061,6 @@ ENTITIES:
         exposed: false
         indexed: false
         description: "The uuid of source entity from which this new entity is derived from. Used on creation or edit to create an action and relationship to the ancestor.  The direct ancestor must be a Donor or Sample.  If the direct ancestor is a Donor, the sample must be of type organ."
-        # Note: link_sample_to_direct_ancestor() will always delete all the old linkages first
         after_create_trigger: link_sample_to_direct_ancestor
         after_update_trigger: link_sample_to_direct_ancestor
         before_property_update_validators:

src/schema/schema_triggers.py

@@ -913,18 +913,22 @@ def link_dataset_to_direct_ancestors(property_key, normalized_type, request, use
         activity_uuid = activity_data_dict['uuid']
         create_activity = True
 
-    if new_ancestors:
-        
+    if new_ancestors:    
+        logger.info(f"Linking the following new ancestors: {', '.join(new_ancestors)}")
         try:
             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
 
     if ancestors_to_unlink:
+        logger.info(f"Unlinking the following ancestors: {', '.join(ancestors_to_unlink)}")
         try:
             schema_neo4j_queries.delete_ancestor_linkages_tx(schema_manager.get_neo4j_driver_instance(), dataset_uuid, list(ancestors_to_unlink))
         except TransactionError:
             raise
+    
+    if not(ancestors_to_unlink or new_ancestors):
+        logger.info("No new ancestors linked, nor old ancestors unlinked")
 
 
 """
@@ -1929,13 +1933,19 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_
     create_activity = False
     activity_data_dict = {}
     sample_uuid = existing_data_dict['uuid']
+    new_ancestors = None
+    ancestors_to_unlink = None
 
     # Build a list of direct ancestor uuids
     # Only one uuid in the list in this case
     direct_ancestor_uuids = [new_data_dict['direct_ancestor_uuid']]
     existing_sample_ancestor_uuids = schema_neo4j_queries.get_sample_direct_ancestor(schema_manager.get_neo4j_driver_instance(), sample_uuid, "uuid")
-    new_ancestors = set(direct_ancestor_uuids)-set(existing_sample_ancestor_uuids)
-    ancestors_to_unlink = set(existing_sample_ancestor_uuids)-set(direct_ancestor_uuids)
+    if isinstance(existing_sample_ancestor_uuids, list):
+        existing_sample_ancestor_uuids = existing_sample_ancestor_uuids[0]
+    if existing_sample_ancestor_uuids and existing_sample_ancestor_uuids != direct_ancestor_uuids:
+        new_ancestors = direct_ancestor_uuids
+    if not existing_sample_ancestor_uuids:
+        new_ancestors = 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:
@@ -1944,17 +1954,22 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_
         create_activity = True
 
     if new_ancestors:
-
+        ancestors_to_unlink = existing_sample_ancestor_uuids
+        logger.info(f"Linking the following new ancestors: {new_ancestors}")
         try:
-            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)
+            schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), new_ancestors, activity_uuid, create_activity, activity_data_dict, sample_uuid)
         except TransactionError:
             raise
-    
+
     if ancestors_to_unlink:
+        logger.info(f"Unlinking the following ancestor: {ancestors_to_unlink}")
         try:
-            schema_neo4j_queries.delete_ancestor_linkages_tx(schema_manager.get_neo4j_driver_instance(), sample_uuid, list(ancestors_to_unlink))
+            schema_neo4j_queries.delete_ancestor_linkages_tx(schema_manager.get_neo4j_driver_instance(), sample_uuid, [ancestors_to_unlink])
         except TransactionError:
             raise
+    
+    if not(ancestors_to_unlink or new_ancestors):
+        logger.info("No new ancestors linked, nor old ancestors unlinked")
 
 """
 TriggerTypeEnum.BEFORE_CREATE and TriggerTypeEnum.BEFORE_UPDATE