Adding collections to source and samples

src/app.py

@@ -5604,7 +5604,7 @@ def delete_cache(id):
         upload_dataset_uuids = schema_neo4j_queries.get_upload_datasets(neo4j_driver_instance, entity_uuid , 'uuid')
 
         # If the target entity is Datasets/Publication, delete the associated Collections cache, Upload cache
-        collection_uuids = schema_neo4j_queries.get_dataset_collections(neo4j_driver_instance, entity_uuid , 'uuid')
+        collection_uuids = schema_neo4j_queries.get_entity_collections(neo4j_driver_instance, entity_uuid , 'uuid')
         collection_dict = schema_neo4j_queries.get_publication_associated_collection(neo4j_driver_instance, entity_uuid)
         upload_dict = schema_neo4j_queries.get_dataset_upload(neo4j_driver_instance, entity_uuid)
 

src/schema/provenance_schema.yaml

@@ -444,8 +444,8 @@ ENTITIES:
         transient: true
         generated: true
         description: "A list of collections that this dataset belongs to. Will be returned in response"
-        on_read_trigger: get_dataset_collections
-        on_index_trigger: get_dataset_collections
+        on_read_trigger: get_entity_collections
+        on_index_trigger: get_entity_collections
         # No on_index_trigger to include collections in the OpenSearch document for a Dataset (from HM, we might need this for SN)
       upload:
         type: json_string # dict
@@ -888,6 +888,13 @@ ENTITIES:
         type: string
         required_on_create: true
         description: "A high level description of where this source originates from."
+      collections:
+        type: list
+        transient: true
+        generated: true
+        description: "A list of collections that this source belongs to. Will be returned in response"
+        on_read_trigger: get_entity_collections
+        on_index_trigger: get_entity_collections
 
 
   ############################################# Sample #############################################
@@ -1149,6 +1156,13 @@ ENTITIES:
         immutable: true
         description: "A boolean indicating if the Sample contains any Datasets in its descendants."
         on_index_trigger: get_contains_data
+      collections:
+        type: list
+        transient: true
+        generated: true
+        description: "A list of collections that this sample belongs to. Will be returned in response"
+        on_read_trigger: get_entity_collections
+        on_index_trigger: get_entity_collections
 
   ############################################# Upload #############################################
   # Eventually we might allow folks to bulk register Samples or Sources through the same mechanism.

src/schema/schema_neo4j_queries.py

@@ -662,14 +662,14 @@ def get_next_revision_uuid(neo4j_driver, uuid):
 
 
 """
-Get a list of associated collection uuids for a given dataset
+Get a list of associated collection uuids for a given entity
 
 Parameters
 ----------
 neo4j_driver : neo4j.Driver object
     The neo4j database connection pool
 uuid : str
-    The uuid of dataset
+    The uuid of entity
 property_key : str
     A target property key for result filtering
 
@@ -680,7 +680,7 @@ def get_next_revision_uuid(neo4j_driver, uuid):
 """
 
 
-def get_dataset_collections(neo4j_driver, uuid, property_key=None):
+def get_entity_collections(neo4j_driver, uuid, property_key=None):
     results = []
 
     if property_key:
@@ -692,7 +692,7 @@ def get_dataset_collections(neo4j_driver, uuid, property_key=None):
                  f"WHERE e.uuid = '{uuid}' "
                  f"RETURN apoc.coll.toSet(COLLECT(c)) AS {record_field_name}")
 
-    logger.info("======get_dataset_collections() query======")
+    logger.info("======get_entity_collections() query======")
     logger.info(query)
 
     with neo4j_driver.session() as session:

src/schema/schema_triggers.py

@@ -799,7 +799,7 @@ def set_dataset_status_new(property_key, normalized_type, user_token, existing_d
     return property_key, 'New'
 
 
-def get_dataset_collections(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
+def get_entity_collections(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
     """Trigger event method of getting a list of collections for this new Dataset.
 
     Parameters
@@ -825,15 +825,15 @@ def get_dataset_collections(property_key, normalized_type, user_token, existing_
 
     if 'uuid' not in existing_data_dict:
         msg = create_trigger_error_msg(
-            "Missing 'uuid' key in 'existing_data_dict' during calling 'get_dataset_collections()' trigger method.",
+            "Missing 'uuid' key in 'existing_data_dict' during calling 'get_entity_collections()' trigger method.",
             existing_data_dict, new_data_dict
         )
         raise KeyError(msg)
 
     # No property key needs to filter the result
     # Get back the list of collection dicts
-    collections_list = schema_neo4j_queries.get_dataset_collections(schema_manager.get_neo4j_driver_instance(),
-                                                                    existing_data_dict['uuid'])
+    collections_list = schema_neo4j_queries.get_entity_collections(schema_manager.get_neo4j_driver_instance(),
+                                                                   existing_data_dict['uuid'])
     if collections_list:
         # Exclude datasets from each resulting collection
         # We don't want to show too much nested information