[20.09] Fix random-ish workflow error with maximum_workflow_jobs_per_scheduling_iteration #11513
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…g max_num_jobs This should recapitulate the error seen when running workflow tests against galaxyproject/iwc#23.
Fixes
```
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 82, in __invoke
outputs = invoker.invoke()
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 190, in invoke
incomplete_or_none = self._invoke_step(workflow_invocation_step)
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 263, in _invoke_step
incomplete_or_none = invocation_step.workflow_step.module.execute(self.trans,
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/modules.py", line 1659, in execute
collection_info = self.compute_collection_info(progress, step, all_inputs)
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/modules.py", line 335, in compute_collection_info
collections_to_match = self._find_collections_to_match(
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/modules.py", line 354, in _find_collections_to_match
data = progress.replacement_for_input(step, input_dict)
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 328, in replacement_for_input
replacement = [self.replacement_for_connection(c) for c in connection]
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 328, in <listcomp>
replacement = [self.replacement_for_connection(c) for c in connection]
File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 358, in replacement_for_connection
raise Exception(message)
Exception: Workflow evaluation problem - failed to find output_name list_output in step_outputs {}
galaxy.workflow.scheduling_manager DEBUG 2021-03-01 19:58:59,493 Workflow invocation [1] scheduled
```
This was referenced Mar 1, 2021
|
This seems easier to believe is a serious issue than the not recording the outputs. Thanks for tracking this down! |
jmchilton
approved these changes
Mar 1, 2021
|
Should we also (or in alternative) replace |
Partially revert commit efa9e0f which broke tools which use `interpreter` and `&&` or environment variables in the `<command />`. xref.: galaxyproject@efa9e0f#r573844945
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If we reach
maximum_workflow_jobs_per_scheduling_iterationin https://github.com/mvdbeek/galaxy/blob/1f82927ace979075dbd1540cad3493700889492a/lib/galaxy/tools/execute.py#L100 without having executed a single job for a new step we write out an empty step_outputs dict, which leads to