For #2093

[mugitty]

No description provided.

[mugitty]

@pgaudet has made some changes to the requirements. I have to made additional changes. I will let you know when it is ready for review.

Thanks

[kltm]

@mugitty The user you want is: @pgaudet, not "Paudet"

[kltm]

@mugitty Updating your comment

[mugitty]

The code is ready for review, I have updated for the new requirements.

[kltm]

For geneontology/go-site#2093 -- to create link

[dustine32]

@mugitty Is this the ontobio change needed to update go-site's Makefile-gaf-reprocess to be used in the GO pipeline's "Temporary post filter" step? Sorry if I'm mixing this up with a slack convo we had last Thurs.

[dustine32]

@mugitty I'm mainly concerned with finding the correct ontobio-parse-assocs.py command that we should be testing for this.

[mugitty]

@dustine32 - You are correct. The update in required for Makefile-gaf-reprocess .

You can review from geneontology/go-site#2127

[dustine32]

Ok, it took me a bit but I realized the "easiest" test of this change was to run Pascale's test GAF through ontobio-parse-assocs.py with the new param:

ontobio-parse-assocs.py -f gorules_test_errors.gaf -F gaf -o gorules_test_errors_valid.gaf -I all.gaferences.json --report-md gorules_test_errors-report.md --report-json gorules_test_errors-report.json -m ~/go/go-site/metadata --allow_paint -l all convert --to gaf -n 2.2

One of the test lines for GORULE:0000030 contains ref GO_REF:0000045, which should now be getting caught and reported (with a WARNING) because it has is_obsolete: True. Indeed, it is warned. Confirmed that master branch doesn't give this WARNING so all good.

@mugitty Feel free to merge whenever.