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geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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GORULE:0000028 fails for GPAD; ensure that GPAD files can make it through QC without failing GAF-specific rules #280

Closed kltm closed 2 years ago

kltm commented 2 years ago

Currently, this means that GORULE:0000028 fails for GPAD with errors like WARNING - Violates GO Rule: GORULE:0000028: Found violation of: Aspect can only be one of C, P, F but was repaired -- MGI MGI:2685011 involved_in GO:0009653 PMID:26258302 ECO:0000315 MGI:MGI:4867020 20160729 MGI part_of(GO:0003183),results_in_morphogenesis_of(UBERON:0007151) contributor=https://orcid.org/0000-0001-7476-6306|model-state=production|noctua-model-id=gomodel:56aac7ad00000038 (http://current.geneontology.org/reports/noctua_mgi-report.html#gorule-0000028)

Aspect checks do not really apply to GPAD.

Tagging @dustine32 See https://github.com/biolink/ontobio/issues/501

kltm commented 2 years ago

@dustine32 This auto-closed (?), so I'm a little unsure about the status. Does this require an ontobio release and pipeline update?

dustine32 commented 2 years ago

@kltm Yes it does! Thanks for the reminder!

I'll do the ontobio release and PR reqs.txt in go-site right away. So this will probably run in snapshot tonight?

kltm commented 2 years ago

@dustine32 Yes, that's correct!

kltm commented 2 years ago

"Testing" in snapshot tonight.

dustine32 commented 2 years ago

Reporting back after the successful snapshot run that GORULE:0000028 no longer is flagged in the GPAD files. Example file noctua_mgi.gpad: http://snapshot.geneontology.org/reports/noctua_mgi.report.md. This gorule-0000028 is not even listed as being tested, which makes sense since the code change skips adding the test result to the parser report object.

Comparing a non-GPAD report (ex for mgi.gaf), I see that gorule-0000028 is listed as tested but there were zero errors. This is consistent with the last release's mgi.report.md results.

@kltm Thinking this is good to close now but no worries if it needs to be reopened.