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EVA-4231 - Add error handling for missing validation outputs - #173

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tcezard merged 8 commits into
EBIvariation:mainfrom
tcezard:parsing_crashes
Aug 3, 2026
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EVA-4231 - Add error handling for missing validation outputs#173
tcezard merged 8 commits into
EBIvariation:mainfrom
tcezard:parsing_crashes

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@tcezard

@tcezard tcezard commented Jul 24, 2026

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  • run_status per check now has 3 type (success / crashed / did not run) to replaces the old ad-hoc boolean
  • Validation parsers now either find all files missing (crashed) or some missing (dummy validation error)
  • The HTML/text report templates have a new report_crashed_task() banner and the VCF section is split into independent "Assembly check" / "VCF check" subsections

Comment thread eva_sub_cli/validators/validator.py Outdated
Comment thread tests/test_validator.py Outdated
Comment thread eva_sub_cli/validators/validator.py
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tcezard requested a review from apriltuesday July 29, 2026 16:38

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I think it's also worth updating any eva-sub-cli results files used in eva-submission tests, e.g. here -- I don't think the result_status value is actually used by eva-submission but it would be good to be sure. Presumably the integration tests will also show if there are any issues.

Comment thread eva_sub_cli/jinja_templates/html/report.html Outdated
Comment thread eva_sub_cli/jinja_templates/text/report.txt Outdated
Comment thread eva_sub_cli/validators/validator.py
Comment thread eva_sub_cli/validators/validator.py
tcezard and others added 2 commits July 30, 2026 13:44
@tcezard
tcezard requested a review from apriltuesday July 30, 2026 15:54
tcezard added 2 commits July 31, 2026 12:54
… some files missing some present (report dummy validation errors)

Split the VCF and assembly check validation report

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This looks great! Just a tiny nitpick for the report format but otherwise all looks good to me.

Comment thread eva_sub_cli/jinja_templates/text/report.txt Outdated
Comment thread eva_sub_cli/jinja_templates/text/report.txt Outdated
Co-authored-by: April Shen <april.tuesday@gmail.com>
@tcezard
tcezard merged commit e8bd788 into EBIvariation:main Aug 3, 2026
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2 participants