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[20.01] Run email post job action only once per implicit collection jobs #9277

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[20.01] Run email post job action only once per implicit collection jobs #9277

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5ceee49
Run email post job action only once per implicit collection jobs
mvdbeek Jan 29, 2020
de1f38e
Update lib/galaxy/jobs/actions/post.py
mvdbeek Jan 29, 2020
c68e1e8
Fix execute action for PJAs.
dannon Jan 29, 2020
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12 changes: 12 additions & 0 deletions lib/galaxy/jobs/actions/post.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@

from markupsafe import escape

from galaxy.managers.jobs import summarize_jobs_to_dict
from galaxy.util import (
send_mail,
unicodify,
Expand Down Expand Up @@ -470,6 +471,8 @@ class ActionBox(object):
# being scheduled and jobs created.
immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction',
'TagDatasetAction', 'RemoveTagDatasetAction']
# Actions that should happen only once per set of jobs
run_once = ['EmailAction']
# Actions that will be applied to implicit mapped over collection outputs and not
# just individual outputs when steps include mapped over tools and implicit collection outputs.
mapped_over_output_actions = ['RenameDatasetAction', 'HideDatasetAction',
Expand Down Expand Up @@ -511,5 +514,14 @@ def execute_on_mapped_over(cls, trans, sa_session, pja, step_inputs, step_output

@classmethod
def execute(cls, app, sa_session, pja, job, replacement_dict=None):
execute_action = True
if pja.action_type in ActionBox.actions:
if pja.action_type in ActionBox.run_once:
implicit_collection_jobs_association = job.implicit_collection_jobs_association
if implicit_collection_jobs_association:
summary = summarize_jobs_to_dict(sa_session, implicit_collection_jobs_association.implicit_collection_jobs)
# PJA get's executed prior to changing the job state,
# so the one running job should be this one.
execute_action = summary['states'].get('running', 1) == 1
if execute_action:
ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict)