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Merge pull request #2626 from dannon/backport_hammerthrow

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[16.04] Backport workflow fix
This commit is contained in:
Martin Cech
2016-07-19 11:54:54 -04:00
committed by GitHub
parent 8c59d1c953 f941657332
commit 8a5042d15b
1 changed files with 12 additions and 3 deletions
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lib/galaxy/jobs/actions/post.py
+12 -3
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@@ -427,11 +427,20 @@ class DeleteIntermediatesAction(DefaultJobAction):
else:
log.debug("No job found yet for wfi_step %s, (step %s)" % (wfi_step, wfi_step.workflow_step))
for j2c in jobs_to_check:
creating_jobs = [(x, x.dataset.creating_job) for x in j2c.input_datasets if x.dataset.creating_job]
for (x, creating_job) in creating_jobs:
creating_jobs = []
for input_dataset in j2c.input_datasets:
if not input_dataset.dataset:
log.debug("PJA Async Issue: No dataset attached to input_dataset %s during handling of workflow invocation %s" % (input_dataset.id, wfi))
elif not input_dataset.dataset.creating_job:
log.debug("PJA Async Issue: No creating job attached to dataset %s during handling of workflow invocation %s" % (input_dataset.dataset.id, wfi))
else:
creating_jobs.append((input_dataset, input_dataset.dataset.creating_job))
for (input_dataset, creating_job) in creating_jobs:
sa_session.refresh(creating_job)
sa_session.refresh(x)
sa_session.refresh(input_dataset)
for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step and creating_job.workflow_invocation_step.workflow_invocation == wfi]:
# note that the above input_dataset is a reference to a
# job.input_dataset.dataset at this point
safe_to_delete = True
for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]:
if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]: