Re-raise infrastructure errors during output collection#467
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ksuderman wants to merge 2 commits into
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Surface ImportError, MemoryError, SystemError and infrastructure OSErrors
(e.g. disk full, I/O errors) during output collection instead of silently
downgrading them to warnings, so they fail the job rather than producing a
job that 'succeeds' with empty outputs.
Two exceptions are deliberately NOT treated as infrastructure failures and
keep flowing through the normal _allow_collect_failure handling:
* FileNotFoundError — a missing output file is expected and recoverable
(e.g. a from_work_dir output the tool legitimately did not produce, which
Galaxy represents as an empty dataset).
* HTTP 403 — Galaxy authoritatively refused the upload (dataset purged mid
job); checked before the OSError test because requests.HTTPError is itself
an OSError subclass.
jmchilton
reviewed
Jul 3, 2026
| getattr(action, "url", None) or getattr(action, "path", action), | ||
| ) | ||
| return False | ||
| if isinstance(e, OSError) and not isinstance(e, FileNotFoundError): |
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Can you move this logic into allow_collect_failure? It looks like there is an abstraction esbalished for this. You'll have to add the exception to the method interface. I think that is fine.
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Part of #465.
Split out of #466
What this does
_collect_outputdowngraded all collection exceptions to warnings foroutput_workdiroutputs (via_allow_collect_failure). That is correct for a missingoutput, but it also swallowed genuine infrastructure failures — a disk-full or
out-of-memory during collection would surface as a "successful" job with empty outputs.
ImportError,MemoryError,SystemError, and infrastructureOSErrors(disk full, I/O errors) so they fail the job.
_allow_collect_failurehandling:FileNotFoundError— a missing output file is expected (e.g. afrom_work_diroutput a tool legitimately did not produce, which Galaxy represents as an empty
dataset).
checked before the
OSErrortest becauserequests.HTTPErroris itself anOSErrorsubclass.Branch is based on current
master.