Merge pull request #313 from microbiomedata/311-workflow-execution-re…

…cord-in-database-is-missing-ended_at_time

311 workflow execution record in database is missing ended at time

nmdc_automation/workflow_automation/watch_nmdc.py

@@ -264,6 +264,7 @@ def process_successful_job(self, job: WorkflowJob) -> Database:
         logger.info(f"Created workflow execution record for job {job.opid}")
 
         job.done = True
+        job.workflow.state["end"] = workflow_execution.ended_at_time
         self.file_handler.write_metadata_if_not_exists(job)
         self.save_checkpoint()
         return database

nmdc_automation/workflow_automation/wfutils.py

@@ -551,6 +551,7 @@ def make_workflow_execution(self, data_objects: List[DataObject]) -> WorkflowExe
         """
         wf_dict = self.as_workflow_execution_dict
         wf_dict["has_output"] = [dobj.id for dobj in data_objects]
+        wf_dict["ended_at_time"] = self.job.metadata.get("end")
 
         # workflow-specific keys
         logical_names = set()

tests/test_wfutils.py

@@ -284,6 +284,8 @@ def test_workflow_job_data_objects_and_execution_record_mags(site_config, fixtur
     for data_object in data_objects:
         assert isinstance(data_object, DataObject)
     wfe = job.make_workflow_execution(data_objects)
+    assert wfe.started_at_time
+    assert wfe.ended_at_time
     assert isinstance(wfe, MagsAnalysis)
     # attributes from final_stats_json
     assert wfe.mags_list
@@ -305,6 +307,18 @@ def test_workflow_job_data_objects_and_execution_record_mags(site_config, fixtur
     assert isinstance(wfe.binned_contig_num, int)
 
 
+def test_workflow_execution_record_from_workflow_job(site_config, fixtures_dir, tmp_path):
+    job_metadata = json.load(open(fixtures_dir / "mags_job_metadata.json"))
+    workflow_state = json.load(open(fixtures_dir / "mags_workflow_state.json"))
+    # remove 'end' from the workflow state to simulate a job that is still running
+    workflow_state.pop('end')
+    job = WorkflowJob(site_config, workflow_state, job_metadata)
+    data_objects = job.make_data_objects(output_dir=tmp_path)
+
+    wfe = job.make_workflow_execution(data_objects)
+    assert wfe.started_at_time
+    assert wfe.ended_at_time
+
 
 
 def test_workflow_job_from_database_job_record(site_config, fixtures_dir):