Merge pull request #216 from hubmapconsortium/test-release

v2.0.15

Author: yuanzhou

VERSION

@@ -1 +1 @@
-2.0.14
+2.0.15

src/app.py

@@ -759,7 +759,7 @@ def get_collections():
 Parameters
 ----------
 entity_type : str
-    One of the target entity types (case-insensitive since will be normalized): Dataset, Donor, Sample
+    One of the target entity types (case-insensitive since will be normalized): Dataset, Donor, Sample, Upload
 
 Returns
 -------
@@ -2420,13 +2420,12 @@ def create_multiple_samples_details(request, normalized_entity_type, user_token,
         samples_dict_list.append(sample_dict)
 
     # Generate property values for the only one Activity node
-    # The resulting list contains only one dict in this case by using the default count = 1
-    activity_data_dict_list = schema_manager.generate_activity_data(normalized_entity_type, user_token, user_info_dict)
+    activity_data_dict = schema_manager.generate_activity_data(normalized_entity_type, user_token, user_info_dict)
 
     # Create new sample nodes and needed relationships as well as activity node in one transaction
     try:
         # No return value
-        app_neo4j_queries.create_multiple_samples(neo4j_driver_instance, samples_dict_list, activity_data_dict_list[0], json_data_dict['direct_ancestor_uuid'])
+        app_neo4j_queries.create_multiple_samples(neo4j_driver_instance, samples_dict_list, activity_data_dict, json_data_dict['direct_ancestor_uuid'])
     except TransactionError:
         msg = "Failed to create multiple samples"
         # Log the full stack trace, prepend a line with our message

src/schema/schema_manager.py

@@ -1389,7 +1389,7 @@ def get_entity_group_name(group_uuid):
 
 
 """
-Generate properties data of one or more Activity nodes
+Generate properties data of the target Activity node
 
 Parameters
 ----------
@@ -1404,30 +1404,25 @@ def get_entity_group_name(group_uuid):
 
 Returns
 -------
-list: A list of gnerated Activity data dicts
+dict: A dict of gnerated Activity data
 """
-def generate_activity_data(normalized_entity_type, user_token, user_info_dict, count = 1):
+def generate_activity_data(normalized_entity_type, user_token, user_info_dict):
     # Activity is not an Entity
     normalized_activity_type = 'Activity'
 
     # Target entity type dict
     # Will be used when calling `set_activity_creation_action()` trigger method
     normalized_entity_type_dict = {'normalized_entity_type': normalized_entity_type}
 
-    # Create new ids for each new Activity node
-    new_ids_dict_list = create_hubmap_ids(normalized_activity_type, json_data_dict = None, user_token = user_token, user_info_dict = None, count = count)
-    
-    activity_data_dict_list = []
-    for new_ids_dict in new_ids_dict_list:
-        data_dict_for_activity = {**user_info_dict, **normalized_entity_type_dict, **new_ids_dict}
-    
-        # Generate property values for Activity node
-        generated_activity_data_dict = generate_triggered_data('before_create_trigger', normalized_activity_type, user_token, {}, data_dict_for_activity)
+    # Create new ids for the Activity node
+    # This resulting list has only one dict
+    new_ids_dict_list = create_hubmap_ids(normalized_activity_type, json_data_dict = None, user_token = user_token, user_info_dict = None)
+    data_dict_for_activity = {**user_info_dict, **normalized_entity_type_dict, **new_ids_dict_list[0]}
 
-        # Add to list
-        activity_data_dict_list.append(generated_activity_data_dict)
-    
-    return activity_data_dict_list
+    # Generate property values for Activity node
+    generated_activity_data_dict = generate_triggered_data('before_create_trigger', normalized_activity_type, user_token, {}, data_dict_for_activity)
+
+    return generated_activity_data_dict
 
 
 """

src/schema/schema_neo4j_queries.py

@@ -70,32 +70,30 @@ def get_dataset_direct_ancestors(neo4j_driver, uuid, property_key = None):
     The uuid of target child entity
 direct_ancestor_uuids : list
     A list of uuids of direct ancestors
-activity_data_dict_list : list
-    A list of activity properties for each activity node to be created
+activity_data_dict : dict
+    A dict of activity properties to be created
 """
-def link_entity_to_direct_ancestors(neo4j_driver, entity_uuid, direct_ancestor_uuids, activity_data_dict_list):
+def link_entity_to_direct_ancestors(neo4j_driver, entity_uuid, direct_ancestor_uuids, activity_data_dict):
     try:
         with neo4j_driver.session() as session:
             tx = session.begin_transaction()
 
-            # First delete all the old linkages between this entity node and its direct ancestors
-            _delete_direct_ancestor_linkages_tx(tx, entity_uuid)
+            # First delete all the old linkages and Activity node between this entity and its direct ancestors
+            _delete_activity_node_and_linkages_tx(tx, entity_uuid)
+
+            # Get the activity uuid
+            activity_uuid = activity_data_dict['uuid']
 
-            # Loop over two lists at the same time using indexes to look up corresponding elements
-            for index, direct_ancestor_uuid in enumerate(direct_ancestor_uuids):
-                # Get the corresponding activity uuid
-                activity_data_dict = activity_data_dict_list[index]
-                activity_uuid = activity_data_dict['uuid']
+            # Create the Acvitity node
+            _create_activity_tx(tx, activity_data_dict)
 
-                # Create the Acvitity node
-                _create_activity_tx(tx, activity_data_dict)
+            # Create relationship from this Activity node to the target entity node
+            _create_relationship_tx(tx, activity_uuid, entity_uuid, 'ACTIVITY_OUTPUT', '->')
 
-                # Create relationship from ancestor entity node to this Activity node
+            # Create relationship from each ancestor entity node to this Activity node
+            for direct_ancestor_uuid in direct_ancestor_uuids:
                 _create_relationship_tx(tx, direct_ancestor_uuid, activity_uuid, 'ACTIVITY_INPUT', '->')
 
-                # Create relationship from this Activity node to the target entity node
-                _create_relationship_tx(tx, activity_uuid, entity_uuid, 'ACTIVITY_OUTPUT', '->')
-
             tx.commit()
     except TransactionError as te:
         msg = "TransactionError from calling link_entity_to_direct_ancestors(): "
@@ -701,7 +699,7 @@ def _create_activity_tx(tx, activity_data_dict):
     return node
 
 """
-Delete thelinkages between an entity and its direct ancestors
+Delete the Activity node and linkages between an entity and its direct ancestors
 
 Parameters
 ----------
@@ -710,13 +708,12 @@ def _create_activity_tx(tx, activity_data_dict):
 uuid : str
     The uuid to target entity (child of those direct ancestors)
 """
-def _delete_direct_ancestor_linkages_tx(tx, uuid):
+def _delete_activity_node_and_linkages_tx(tx, uuid):
     query = (f"MATCH (s:Entity)-[in:ACTIVITY_INPUT]->(a:Activity)-[out:ACTIVITY_OUTPUT]->(t:Entity) "
              f"WHERE t.uuid = '{uuid}' "
-             # Delete the Activity node and in input/output relationships
              f"DELETE in, a, out")
 
-    logger.debug("======_delete_direct_ancestor_linkages_tx() query======")
+    logger.debug("======_delete_activity_node_and_linkages_tx() query======")
     logger.debug(query)
 
     result = tx.run(query)

src/schema/schema_triggers.py

@@ -770,14 +770,12 @@ def link_dataset_to_direct_ancestors(property_key, normalized_type, user_token,
 
     direct_ancestor_uuids = existing_data_dict['direct_ancestor_uuids']
 
-    # Generate property values for each Activity node
-    count = len(direct_ancestor_uuids)
-    activity_data_dict_list = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict, count)
+    # Generate property values for Activity node
+    activity_data_dict = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
 
     try:
-        # Create a linkage (via Activity node) between the dataset node 
-        # and each direct ancestor node in neo4j
-        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict_list)
+        # Create a linkage (via one Activity node) between the dataset node and its direct ancestors in neo4j
+        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict)
     except TransactionError:
         # No need to log
         raise
@@ -1177,14 +1175,13 @@ def link_donor_to_lab(property_key, normalized_type, user_token, existing_data_d
     # Only one uuid in the list in this case
     direct_ancestor_uuids = [existing_data_dict['group_uuid']]
 
-    # Generate property values for Activity
-    # Only one Activity in this case, using the default count = 1
-    activity_data_dict_list = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
+    # Generate property values for Activity node
+    activity_data_dict = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
 
     try:
         # Create a linkage (via Activity node) 
         # between the Donor node and the parent Lab node in neo4j
-        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict_list)
+        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict)
     except TransactionError:
         # No need to log
         raise
@@ -1304,14 +1301,13 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, user_token, ex
     # Only one uuid in the list in this case
     direct_ancestor_uuids = [existing_data_dict['direct_ancestor_uuid']]
 
-    # Generate property values for Activity
-    # Only one Activity in this case, using the default count = 1
-    activity_data_dict_list = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
+    # Generate property values for Activity node
+    activity_data_dict = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
 
     try:
         # Create a linkage (via Activity node) 
         # between the Sample node and the source entity node in neo4j
-        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict_list)
+        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict)
     except TransactionError:
         # No need to log
         raise
@@ -1412,14 +1408,13 @@ def link_upload_to_lab(property_key, normalized_type, user_token, existing_data_
     # Only one uuid in the list in this case
     direct_ancestor_uuids = [existing_data_dict['group_uuid']]
 
-    # Generate property values for Activity
-    # Only one Activity in this case, using the default count = 1
-    activity_data_dict_list = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
+    # Generate property values for Activity node
+    activity_data_dict = schema_manager.generate_activity_data(normalized_type, user_token, existing_data_dict)
 
     try:
         # Create a linkage (via Activity node) 
         # between the Submission node and the parent Lab node in neo4j
-        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict_list)
+        schema_neo4j_queries.link_entity_to_direct_ancestors(schema_manager.get_neo4j_driver_instance(), existing_data_dict['uuid'], direct_ancestor_uuids, activity_data_dict)
     except TransactionError:
         # No need to log
         raise