Fix nil @submission in OntologyProcessor when metadata extraction bails#283
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alexskr wants to merge 2 commits into
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Fix nil @submission in OntologyProcessor when metadata extraction bails#283alexskr wants to merge 2 commits into
alexskr wants to merge 2 commits into
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SubmissionMetadataExtractor#extract_metadata used a bare `return` when the submission failed validation, returning nil. OntologyProcessor assigned that nil back over its own @submission, so the ensure-block call to notify_submission_processed raised NoMethodError on nil.archived? -- which its inner rescue logged as the misleading "Email sending failed: undefined method `archived?' for nil:NilClass". - submission_extract_metadata.rb: return @submission on the invalid path so the method has a consistent return value. - submission_processor.rb: stop reassigning @submission from the extract_metadata return value; the extractor mutates the shared instance in place via @submission.save. - submission_processor.rb: guard notify_submission_processed against a nil @submission so a missing submission can't surface as the misleading "Email sending failed" log line. - Add regression test reproducing the full path.
develop already fixed the nil-@submission bug (extract_metadata returns nil on an invalid submission -> processor aborts with a clear StandardError, plus a nil guard in notify_submission_processed). Resolve the conflict by taking develop's processor and extractor verbatim and reverting this branch's superseded `return @submission` change, which would have turned develop's `if @submission.nil?` abort into dead code. Keep this branch's unique contribution -- the regression test -- adapted to develop's abort semantics: it now asserts the processor raises a clean StandardError (not a NoMethodError on nil) and that the misleading "Email sending failed" line never appears.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #283 +/- ##
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+ Coverage 80.74% 80.76% +0.01%
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Files 100 100
Lines 6774 6774
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+ Hits 5470 5471 +1
+ Misses 1304 1303 -1
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Summary
Adds the missing regression test for the misleading log line seen on
ncbo_cron:That error was a symptom — the real failure was upstream in metadata extraction.
Root cause
SubmissionMetadataExtractor#extract_metadatauses a barereturnon theunless @submission.valid?branch, so it returnsnilfor invalid submissions.OntologyProcessor#process_submissiondoes@submission = @submission.extract_metadata(...), overwriting its own submission reference with thatnil.@submission.*calls then failed. In theensureblock,notify_submission_processedinvoked@submission.archived?onnil, and its innerrescuelogged the misleading"Email sending failed: ..."line.Status
The underlying bug was already fixed on
developby f0867418 ("Guard against nil submission after metadata extraction failure"), which merged via #294:process_submissionraises a clearStandardError("Submission processing aborted: extract_metadata returned nil …") instead of silently continuing on anilsubmission.notify_submission_processedguardsreturn if @submission.nil? || @submission.archived?, so a missing submission can no longer surface as the misleading log line.This branch's original code changes are therefore superseded and were dropped during the merge with
develop. What remains — and what this PR now contributes — is the regression test that f086741 did not include.Changes
test/services/test_submission_processor.rbreproducing the exact path. It stubsextract_metadatato returnniland asserts:process_submissionaborts with a cleanStandardError(not aNoMethodErroronnil.archived?), andnotify_submission_processednever logs the misleading"Email sending failed"line.