Merge pull request #256 from hubmapconsortium/test-release

v2.0.20 release

Author: yuanzhou

VERSION

@@ -1 +1 @@
-2.0.19
+2.0.20

src/app.py

@@ -2146,6 +2146,59 @@ def get_revisions_list(id):
 
     return jsonify(results)
 
+"""
+Get all organs associated with a given dataset
+
+The gateway treats this endpoint as public accessible
+
+Parameters
+----------
+id : str
+    The HuBMAP ID (e.g. HBM123.ABCD.456) or UUID of given entity
+
+Returns
+-------
+json
+    a list of all the organs associated with the target dataset
+"""
+@app.route('/datasets/<id>/organs', methods=['GET'])
+def get_associated_organs_from_dataset(id):
+    # Token is not required, but if an invalid token provided,
+    # we need to tell the client with a 401 error
+    validate_token_if_auth_header_exists(request)
+
+    # Use the internal token to query the target entity
+    # since public entities don't require user token
+    token = get_internal_token()
+
+    # Query target entity against uuid-api and neo4j and return as a dict if exists
+    entity_dict = query_target_entity(id, token)
+    normalized_entity_type = entity_dict['entity_type']
+
+    # Only for Dataset
+    if normalized_entity_type != 'Dataset':
+        bad_request_error("The entity of given id is not a Dataset")
+
+    # published/public datasets don't require token
+    if entity_dict['status'].lower() != DATASET_STATUS_PUBLISHED:
+        # Token is required and the user must belong to HuBMAP-READ group
+        token = get_user_token(request, non_public_access_required=True)
+
+    # By now, either the entity is public accessible or
+    # the user token has the correct access level
+    associated_organs = app_neo4j_queries.get_associated_organs_from_dataset(neo4j_driver_instance, entity_dict['uuid'])
+
+    # If there are zero items in the list associated organs, then there are no associated
+    # Organs and a 404 will be returned.
+    if len(associated_organs) < 1:
+        not_found_error("the dataset does not have any associated organs")
+
+    complete_entities_list = schema_manager.get_complete_entities_list(token, associated_organs)
+
+    # Final result after normalization
+    final_result = schema_manager.normalize_entities_list_for_response(complete_entities_list)
+
+    return jsonify(final_result)
 
 ####################################################################################################
 ## Internal Functions

src/app_neo4j_queries.py

@@ -891,6 +891,32 @@ def get_dataset_revision_number(neo4j_driver, uuid):
     return revision_number
 
 
+"""
+Retrieve the list of uuids for organs associated with a given dataset
+
+Parameters
+----------
+neo4j_driver : neo4j.Driver object
+    The neo4j database connection pool
+uuid : str
+    The uuid of the target entity: Dataset
+"""
+def get_associated_organs_from_dataset(neo4j_driver, dataset_uuid):
+    results = []
+    query = (f"MATCH (ds:Dataset)<-[*]-(organ:Sample {{specimen_type:'organ'}}) "
+             f"WHERE ds.uuid='{dataset_uuid}'"
+             f"RETURN apoc.coll.toSet(COLLECT(organ)) AS {record_field_name}")
+    logger.debug("======get_associated_organs_from_dataset() query======")
+    logger.debug(query)
+
+    with neo4j_driver.session() as session:
+        record = session.read_transaction(_execute_readonly_tx, query)
+
+        if record and record[record_field_name]:
+            results = _nodes_to_dicts(record[record_field_name])
+
+    return results
+
 ####################################################################################################
 ## Internal Functions
 ####################################################################################################