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feat: cleanup job definitions #20

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Merged
merged 3 commits into from
Mar 13, 2025
Merged

feat: cleanup job definitions #20

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c647403
cleanup job definitions
jakevc Mar 12, 2025
48c7553
cleanup after success or failure
jakevc Mar 12, 2025
3b33907
update error info
jakevc Mar 13, 2025
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20 changes: 13 additions & 7 deletions snakemake_executor_plugin_aws_batch/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,13 +185,16 @@ async def check_active_jobs(
for job in active_jobs:
async with self.status_rate_limiter:
status_code, msg = self._get_job_status(job)

if status_code is not None:
if status_code == 0:
self.report_job_success(job)
elif status_code is not None:
else:
message = f"AWS Batch job failed. Code: {status_code}, Msg: {msg}."
self.report_job_error(job, msg=message)
else:
yield job
self.cleanup_job_resources(job)
else:
yield job

def _get_job_status(self, job: SubmittedJobInfo) -> tuple[int, Optional[str]]:
"""
Expand Down Expand Up @@ -240,9 +243,8 @@ def _terminate_job(self, job: SubmittedJobInfo):
reason="terminated by snakemake",
)
except Exception as e:
job_spec = job.aux["job_params"]
self.logger.info(
f"failed to terminate Batch job definition: {job_spec} with error: {e}"
f"failed to terminate Batch job: {job.external_jobid} with error: {e}"
)

def _deregister_job(self, job: SubmittedJobInfo):
Expand All @@ -260,6 +262,11 @@ def _deregister_job(self, job: SubmittedJobInfo):
f"{job_def_arn} with error {e}"
)

def cleanup_job_resources(self, job: SubmittedJobInfo):
"""Terminate and deregister job resources"""
self._terminate_job(job)
self._deregister_job(job)

def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
# Cancel all active jobs.
# This method is called when Snakemake is interrupted.
Expand All @@ -268,5 +275,4 @@ def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
self.logger.info("shutting down...")
# cleanup jobs
for j in active_jobs:
self._terminate_job(j)
self._deregister_job(j)
self.cleanup_job_resources(j)