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Do flush when remapping job

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This commit is contained in:
mvdbeek
2021-10-18 11:42:42 +02:00
parent 4352b8c1ac
commit 44c3d8fee0
1 changed files with 8 additions and 3 deletions
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lib/galaxy/tools/actions/__init__.py
+8 -3
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@@ -561,11 +561,16 @@ class DefaultToolAction:
if completed_job:
job.set_copied_from_job_id(completed_job.id)
trans.sa_session.add(job)
# Now that we have a job id, we can remap any outputs if this is a rerun and the user chose to continue dependent jobs
# Remap any outputs if this is a rerun and the user chose to continue dependent jobs
# This functionality requires tracking jobs in the database.
if app.config.track_jobs_in_database and rerun_remap_job_id is not None:
# We need a flush here and get hids in order to rewrite jobs parameter,
# but remapping jobs should only affect single jobs anyway, so this is not too costly.
# Need to flush here so that referencing outputs by id works
session = trans.sa_session()
try:
session.expire_on_commit = False
session.flush()
finally:
session.expire_on_commit = True
self._remap_job_on_rerun(trans=trans,
galaxy_session=galaxy_session,
rerun_remap_job_id=rerun_remap_job_id,