Yuanzhou/cache

VERSION

@@ -1 +1 @@
-2.5.6
+2.5.7

src/app.py

@@ -5330,12 +5330,13 @@ def delete_cache(id):
         entity_dict = query_target_entity(id, get_internal_token())
         entity_uuid = entity_dict['uuid']
 
-        # If the target entity is Sample (`direct_ancestor`) or Dataset/Publication (`direct_ancestors`)
-        # Delete the cache of all the direct descendants (children)
-        child_uuids = schema_neo4j_queries.get_children(neo4j_driver_instance, entity_uuid , 'uuid')
+        # Delete the cache of all the descendants
+        descendant_uuids = schema_neo4j_queries.get_descendants(neo4j_driver_instance, entity_uuid , 'uuid')
 
         # If the target entity is Collection, delete the cache for each of its associated 
-        # Datasets and Publications (via [:IN_COLLECTION] relationship) as well as just Publications (via [:USES_DATA] relationship)
+        # Datasets and Publications (via [:IN_COLLECTION]) as well as just Publications (via [:USES_DATA])
+        # NOTE: As of 5/30/2025, the [:USES_DATA] workaround has been deprecated.
+        # Still keep it in the code until further decision - Zhou
         collection_dataset_uuids = schema_neo4j_queries.get_collection_associated_datasets(neo4j_driver_instance, entity_uuid , 'uuid')
 
         # If the target entity is Upload, delete the cache for each of its associated Datasets (via [:IN_UPLOAD] relationship)
@@ -5347,7 +5348,7 @@ def delete_cache(id):
         upload_dict = schema_neo4j_queries.get_dataset_upload(neo4j_driver_instance, entity_uuid)
 
         # We only use uuid in the cache key acorss all the cache types
-        uuids_list = [entity_uuid] + child_uuids + collection_dataset_uuids + upload_dataset_uuids + collection_uuids
+        uuids_list = [entity_uuid] + descendant_uuids + collection_dataset_uuids + upload_dataset_uuids + collection_uuids
 
         # It's possible no linked collection or upload
         if collection_dict:

src/schema/provenance_schema.yaml

@@ -786,6 +786,9 @@ ENTITIES:
         type: string
         indexed: true
         description: 'A DOI pointing to an Organ Mapping Antibody Panel relevant to this publication'
+
+      # NOTE: As of 5/30/2025, the [:USES_DATA] workaround has been deprecated.
+      # Still keep it in the code until further decision - Zhou
       associated_collection:
         type: json_string # dict
         generated: true
@@ -802,6 +805,7 @@ ENTITIES:
         description: "The uuid of the associated collection for a given publication"
         after_create_trigger: link_publication_to_associated_collection
         after_update_trigger: link_publication_to_associated_collection
+
       assigned_to_group_name: null # This assigned_to_group_name is Dataset specific, Publication doesn't have it
       ingest_task: null # This ingest_task is Dataset specific, Publication doesn't have it
       new_associated_multi_assay_uuid: null # Dataset-only attribute of Multi-Assay Dataset relationships

src/schema/schema_neo4j_queries.py

@@ -737,6 +737,8 @@ def link_entity_to_direct_ancestors(neo4j_driver, entity_uuid, direct_ancestor_u
     the uuid of the associated collection
 """
 def link_publication_to_associated_collection(neo4j_driver, entity_uuid, associated_collection_uuid):
+    # NOTE: As of 5/30/2025, the [:USES_DATA] workaround has been deprecated.
+    # Still keep it in the code until further decision - Zhou
     try:
         with neo4j_driver.session() as session:
             tx = session.begin_transaction()
@@ -1008,6 +1010,8 @@ def get_next_revision_uuids(neo4j_driver, uuid):
 def get_collection_associated_datasets(neo4j_driver, uuid, property_key = None):
     results = []
 
+    # NOTE: As of 5/30/2025, the [:USES_DATA] workaround has been deprecated. 
+    # Still keep it in the code until further decision - Zhou
     if property_key:
         query = (f"MATCH (e:Entity)-[:IN_COLLECTION|:USES_DATA]->(c:Collection) "
                  f"WHERE c.uuid = '{uuid}' "
@@ -1099,6 +1103,8 @@ def get_dataset_collections(neo4j_driver, uuid, property_key = None):
 def get_publication_associated_collection(neo4j_driver, uuid):
     result = {}
 
+    # NOTE: As of 5/30/2025, the [:USES_DATA] workaround has been deprecated.
+    # Still keep it in the code until further decision - Zhou
     query = (f"MATCH (p:Publication)-[:USES_DATA]->(c:Collection) "
              f"WHERE p.uuid = '{uuid}' "
              f"RETURN c as {record_field_name}")
@@ -1802,6 +1808,8 @@ def _delete_activity_node_and_linkages_tx(tx, uuid):
     The uuid to target publication
 """
 def _delete_publication_associated_collection_linkages_tx(tx, uuid):
+    # NOTE: As of 5/30/2025, the [:USES_DATA] workaround has been deprecated.
+    # Still keep it in the code until further decision - Zhou
     query = (f"MATCH (p:Publication)-[r:USES_DATA]->(c:Collection) "
              f"WHERE p.uuid = '{uuid}' "
              f"DELETE r")