specs: 'GET /runs/{run_id}' response spec-compliant

Author: uniqueg

requirements.txt

@@ -63,7 +63,7 @@ subprocess32==3.5.2
 swagger-spec-validator==2.3.1
 typed-ast==1.1.0
 typing==3.6.6
-typing-extensions==3.7.4
+typing-extensions==3.6.5
 urllib3==1.24.2
 vine==1.1.4
 Werkzeug==0.15.3

wes_elixir/config/app_config.yaml

@@ -58,6 +58,8 @@ api:
           validate_responses: True
           swagger_ui: True
           swagger_json: True
+    general_params:
+        time_format: "%Y-%m-%dT%H:%M:%SZ"
     endpoint_params:
         default_page_size: 5
         timeout_cancel_run: 60

wes_elixir/database/db_utils.py

@@ -1,6 +1,6 @@
 """Utility functions for MongoDB document insertion, updates and retrieval."""
 
-from typing import (Any, List, Mapping, Optional)
+from typing import (Any, Dict, List, Mapping, Optional)
 
 from bson.objectid import ObjectId
 from pymongo.collection import ReturnDocument
@@ -69,21 +69,34 @@ def update_tes_task_state(
 ) -> Optional[Mapping[Any, Any]]:
     """Updates `state` field in TES task log and returns updated document."""
     return collection.find_one_and_update(
-        {'task_id': task_id, 'api.task_logs': {'$elemMatch': {'id': tes_id}}},
-        {'$set': {'api.task_logs.$.state': state}},
+        {'task_id': task_id, 'internal.tes_logs': {'$elemMatch': {'id': tes_id}}},
+        {'$set': {'internal.tes_logs.$.state': state}},
         return_document=ReturnDocument.AFTER
     )
 
 
 def append_to_tes_task_logs(
     collection: Collection,
     task_id: str,
-    tes_log: str
+    task_log: Dict,
 ) -> Optional[Mapping[Any, Any]]:
     """Appends task log to TES task logs and returns updated document."""
     return collection.find_one_and_update(
         {'task_id': task_id},
-        {'$push': {'api.task_logs': tes_log}},
+        {'$push': {'internal.tes_logs': task_log}},
+        return_document=ReturnDocument.AFTER
+    )
+
+
+def append_to_wes_task_logs(
+    collection: Collection,
+    task_id: str,
+    task_log: Dict,
+) -> Optional[Mapping[Any, Any]]:
+    """Appends task log to WES task logs and returns updated document."""
+    return collection.find_one_and_update(
+        {'task_id': task_id},
+        {'$push': {'api.task_logs': task_log}},
         return_document=ReturnDocument.AFTER
     )
 

wes_elixir/ga4gh/wes/endpoints/run_workflow.py

@@ -363,14 +363,7 @@ def __process_workflow_attachments(data: Dict) -> Dict:
             data['api']['request']['workflow_url']
         )
 
-        # Extract name and extensions of workflow
-        workflow_name_ext = os.path.splitext(
-            os.path.basename(
-                data['internal']['cwl_path']
-            )
-        )
-
-    # Get parameter file
+    # Extract name and extensions of workflow
     workflow_name_ext = os.path.splitext(
         os.path.basename(
             data['internal']['cwl_path']
@@ -431,6 +424,9 @@ def __process_workflow_attachments(data: Dict) -> Dict:
 
         # Strip workflow attachments from data
         del data['api']['request']['workflow_attachment']
+    
+    # Add workflow base name (without extension) to document
+    data['api']['run_log']['name'] = str(workflow_name_ext[0])
 
     # Return form data stripped of workflow attachments
     return data