Fix nil @submission in OntologyProcessor when metadata extraction bails#283
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Fix nil @submission in OntologyProcessor when metadata extraction bails#283
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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.
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Summary
Fixes the misleading log line observed on
ncbo_cronwhen processing ontologies:That error was a symptom — the real failure was upstream in metadata extraction.
Root cause
SubmissionMetadataExtractor#extract_metadataused a barereturnon theunless @submission.valid?branch, so it returnednilfor invalid submissions.OntologyProcessor#process_submissiondid@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.Changes
submission_extract_metadata.rb:return @submissionon the invalid path so the method has a consistent return value.submission_processor.rb: stop reassigning@submissionfrom theextract_metadatareturn value — the extractor already mutates the shared instance via@submission.save.submission_processor.rb:return if @submission.nil?guard innotify_submission_processed, so a missing submission can't surface as the misleading log line again.test/services/test_submission_processor.rbreproducing the exact path.Test plan
developwithNoMethodError: undefined method 'save' for nil:NilClass(confirmed by reverting the fixes locally).rake test:docker:fs).rake test:docker:fsrun on this branch before merge.