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Fix re-run with rerun_remap_job_id hiding collection

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Fixes https://github.com/galaxyproject/galaxy/issues/13052
This commit is contained in:
mvdbeek
2022-01-12 20:10:08 +01:00
parent 1e889ad338
commit 855e9f9f2f
2 changed files with 31 additions and 10 deletions
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lib/galaxy/tools/actions/__init__.py
+2 -1
View File
@@ -623,6 +623,8 @@ class DefaultToolAction:
assert old_job.session_id == galaxy_session.id, f'({old_job.id}/{current_job.id}): Old session id ({old_job.session_id}) does not match rerun session id ({galaxy_session.id})'
else:
raise Exception(f'({old_job.id}/{current_job.id}): Remapping via the API is not (yet) supported')
# Start by hiding current job outputs before taking over the old job's (implicit) outputs.
current_job.hide_outputs(flush=False)
# Duplicate PJAs before remap.
for pjaa in old_job.post_job_actions:
current_job.add_post_job_action(pjaa.post_job_action)
@@ -660,7 +662,6 @@ class DefaultToolAction:
job.job_id = current_job.id
for jtoidca in old_job.output_dataset_collections:
jtoidca.dataset_collection.replace_failed_elements(remapped_hdas)
current_job.hide_outputs(flush=False)
except Exception:
log.exception('Cannot remap rerun dependencies.')
lib/galaxy_test/api/test_jobs.py
+29 -9
View File
@@ -269,18 +269,21 @@ steps:
assert_ok=False)
assert dataset['visible']
def _run_map_over_error(self, history_id):
hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("sample1-1", "1 2 3")]).json()
inputs = {
'error_bool': 'true',
'dataset': {
'batch': True,
'values': [{'src': 'hdca', 'id': hdca1['id']}],
}
}
return self._run_detect_errors(history_id=history_id, inputs=inputs)
@skip_without_tool("detect_errors_aggressive")
def test_no_unhide_on_error_if_mapped_over(self):
with self.dataset_populator.test_history() as history_id:
hdca1 = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("sample1-1", "1 2 3")]).json()
inputs = {
'error_bool': 'true',
'dataset': {
'batch': True,
'values': [{'src': 'hdca', 'id': hdca1['id']}],
}
}
run_response = self._run_detect_errors(history_id=history_id, inputs=inputs)
run_response = self._run_map_over_error(history_id)
job_id = run_response['jobs'][0]["id"]
self.dataset_populator.wait_for_job(job_id)
job = self.dataset_populator.get_job_details(job_id).json()
@@ -290,6 +293,23 @@ steps:
assert_ok=False)
assert not dataset['visible']
def test_no_hide_on_rerun(self):
with self.dataset_populator.test_history() as history_id:
run_response = self._run_map_over_error(history_id)
assert run_response['implicit_collections'][0]['visible']
job_id = run_response['jobs'][0]["id"]
rerun_params = self._get(f"jobs/{job_id}/build_for_rerun").json()
inputs = rerun_params['state_inputs']
inputs['rerun_remap_job_id'] = job_id
self._run_detect_errors(history_id=history_id, inputs=inputs)
# Verify source hdca is still visible
hdca = self.dataset_populator.get_history_collection_details(
history_id=history_id,
content_id=run_response['implicit_collections'][0]['id'],
assert_ok=False,
)
assert hdca['visible']
@skip_without_tool('empty_output')
def test_common_problems(self):
with self.dataset_populator.test_history() as history_id: