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Run fallback external_metadata when finishing job

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That only affects the ShellJobRunner
This commit is contained in:
mvdbeek
2020-01-09 14:40:48 +01:00
parent 1f9dc90f25
commit a7d4d69074
1 changed files with 6 additions and 4 deletions
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lib/galaxy/jobs/runners/cli.py
+6 -4
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@@ -161,10 +161,6 @@ class ShellJobRunner(AsynchronousJobRunner):
if ajs.job_wrapper.get_state() == model.Job.states.DELETED:
continue
external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
if external_metadata:
self._handle_metadata_externally(ajs.job_wrapper, resolve_requirements=True)
log.debug("(%s/%s) job not found in batch state check" % (id_tag, external_job_id))
shell_params, job_params = self.parse_destination_params(ajs.job_destination.params)
shell, job_interface = self.get_cli_plugins(shell_params, job_params)
@@ -187,6 +183,9 @@ class ShellJobRunner(AsynchronousJobRunner):
ajs.running = True
ajs.old_state = state
if state == model.Job.states.OK:
external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB))
if external_metadata:
self.work_queue.put((self.handle_metadata_externally, ajs))
log.debug('(%s/%s) job execution finished, running job wrapper finish method' % (id_tag, external_job_id))
self.work_queue.put((self.finish_job, ajs))
else:
@@ -194,6 +193,9 @@ class ShellJobRunner(AsynchronousJobRunner):
# Replace the watch list with the updated version
self.watched = new_watched
def handle_metadata_externally(self, ajs):
self._handle_metadata_externally(ajs.job_wrapper, resolve_requirements=True)
def __handle_out_of_memory(self, ajs, external_job_id):
shell_params, job_params = self.parse_destination_params(ajs.job_destination.params)
shell, job_interface = self.get_cli_plugins(shell_params, job_params)