email_outputs should gracefully handle missing workflow_id
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Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 64/100
Research direction
Start in email_outputs.py at process_workflow around line 367, where the traceback shows the missing workflowId is accessed. Trace how process_submission passes submission data into this entry point, then verify that a submission without workflowId is skipped and processing can continue or retry as intended. Confirm the behavior with the repository's existing tests, if applicable.
Written by the indexing model from the issue text.
Description
Seen returned from Terra, a submission that didn't have a workflowId:
Traceback (most recent call last):
File "/elided/pythonuserbase/lib/python3.12/site-packages/dropseq_terra_utils/email_outputs.py", line 438, in run_with_retries
func()
File "/elided/pythonuserbase/lib/python3.12/site-packages/dropseq_terra_utils/email_outputs.py", line 141, in <lambda>
lambda: send_workspace_emails(system_clients, gcloud_clients_list, email_templates_list, submission_filters),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/elided/pythonuserbase/lib/python3.12/site-packages/dropseq_terra_utils/email_outputs.py", line 306, in send_workspace_emails
process_workspace(system_clients, gcloud_clients, email_templates_list, workspace, submission_filters)
File "/elided/pythonuserbase/lib/python3.12/site-packages/dropseq_terra_utils/email_outputs.py", line 324, in process_workspace
process_submission(system_clients, gcloud_clients, email_templates_list, submission_info)
File "/elided/pythonuserbase/lib/python3.12/site-packages/dropseq_terra_utils/email_outputs.py", line 351, in process_submission
process_workflow(
File "/elided/pythonuserbase/lib/python3.12/site-packages/dropseq_terra_utils/email_outputs.py", line 367, in process_workflow
workflow_id = submission_workflow["workflowId"]
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
KeyError: 'workflowId'
Not sure what other keys might be missing. But at least for this missing workflowId case it's probably ok to just skip this submission and try again later. If we find ourselves infinitely retrying due to perpetually malformed responses we can file another ticket and/or contact Terra support.
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