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Merge pull request #11886 from pcm32/patch-10

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Handle resubmission before changing job state in CLI runner
This commit is contained in:
Marius van den Beek
2021-04-23 16:46:22 +02:00
committed by GitHub
parent 4fbcb32a8f bc7256cab3
commit 671d52088d
1 changed files with 5 additions and 4 deletions
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lib/galaxy/jobs/runners/cli.py
+5 -4
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@@ -171,15 +171,16 @@ class ShellJobRunner(AsynchronousJobRunner):
job_state = ajs.job_wrapper.get_state()
if state != old_state:
log.debug(f"({id_tag}/{external_job_id}) state change: from {old_state} to {state}")
if not state == model.Job.states.OK:
# No need to change_state when the state is OK, this will be handled by `self.finish_job`
ajs.job_wrapper.change_state(state)
if state == model.Job.states.ERROR and job_state != model.Job.states.STOPPED:
# Try to find out the reason for exiting
# Try to find out the reason for exiting - this needs to happen before change_state
# otherwise jobs depending on resubmission outputs see that job as failed and pause.
self.__handle_out_of_memory(ajs, external_job_id)
self.work_queue.put((self.mark_as_failed, ajs))
# Don't add the job to the watched items once it fails, deals with https://github.com/galaxyproject/galaxy/issues/7820
continue
if not state == model.Job.states.OK:
# No need to change_state when the state is OK, this will be handled by `self.finish_job`
ajs.job_wrapper.change_state(state)
if state == model.Job.states.RUNNING and not ajs.running:
ajs.running = True
ajs.old_state = state