Add Dataset Activity.creation_action to ENTITY.Dataset as creation_ac…

…tion_activity

entity-api-spec.yaml

@@ -807,6 +807,9 @@ components:
         dbgap_study_url:
           type: string
           description: 'A URL linking the dataset to the particular study on dbGap it belongs to'
+        creation_action_activity:
+          type: string
+          description: 'The associated action that represents the creation of that dataset'
     Upload:
       type: object
       properties:

src/app.py

@@ -4669,6 +4669,12 @@ def query_target_entity(id, user_token):
 
             # Make a new query against neo4j
             entity_dict = schema_neo4j_queries.get_entity(neo4j_driver_instance, uuid)
+            # entity_type is found in shared_entity_properties in provenance_schema.yaml
+            if entity_dict.get('entity_type') == 'Dataset':
+                # Entities.Dataset already has a creation_action property which is processed in a different manner
+                # see provenance_schema.yaml and code in this file.
+                entity_dict['creation_action_activity'] =\
+                    schema_neo4j_queries.get_entity_creation_action_activity(neo4j_driver_instance, uuid)
 
             # The uuid exists via uuid-api doesn't mean it also exists in Neo4j
             if not entity_dict:

src/instance/app.cfg.example

@@ -28,6 +28,10 @@ UUID_API_URL = 'http://uuid-api:8080'
 # Works regardless of the trailing slash
 INGEST_API_URL = 'https://ingest-api.dev.hubmapconsortium.org'
 
+# URL for talking to Ontology API (default for DEV)
+# Works regardless of the trailing slash
+ONTOLOGY_API_URL = 'https://ontology-api.dev.hubmapconsortium.org'
+
 # A list of URLs for talking to multiple Search API instances (default value used for docker deployment, no token needed)
 # Works regardless of the trailing slash /
 SEARCH_API_URL_LIST = ['http://search-api:8080']

src/schema/provenance_schema.yaml

@@ -284,6 +284,10 @@ ENTITIES:
         description: "The activity that was performed."
         before_property_create_validators:
           - validate_creation_action
+      creation_action_activity:
+        type: string
+        transient: true
+        description: "The creation action associated with the output activity of the dataset"
       description:
         type: string
         description: "Free text description of the dataset"

src/schema/schema_manager.py

@@ -110,7 +110,7 @@ def load_provenance_schema(valid_yaml_file):
     with open(valid_yaml_file) as file:
         schema_dict = yaml.safe_load(file)
 
-        logger.info("Schema yaml file loaded successfully")
+        logger.info(f"Provenance Schema yaml file loaded successfully from {valid_yaml_file} :)")
 
         return schema_dict
 
@@ -1794,4 +1794,4 @@ def _create_request_headers(user_token):
         auth_header_name: auth_scheme + ' ' + user_token
     }
 
-    return headers_dict
+    return headers_dict

src/schema/schema_neo4j_queries.py

@@ -502,6 +502,20 @@ def get_entity_type(neo4j_driver, entity_uuid: str) -> str:
     return None
 
 
+def get_entity_creation_action_activity(neo4j_driver, entity_uuid: str) -> str:
+    query: str = f"MATCH (ds {{uuid:'{entity_uuid}'}})<-[:ACTIVITY_OUTPUT]-(a:Activity) RETURN a.creation_action"
+
+    logger.info("======get_entity_creation_action() query======")
+    logger.info(query)
+
+    with neo4j_driver.session() as session:
+        record = session.read_transaction(execute_readonly_tx, query)
+        if record and len(record) == 1:
+            return record[0]
+
+    return None
+
+
 """
 Create or recreate one or more linkages (via Activity nodes) 
 between the target entity node and the direct ancestor nodes in neo4j