gorule-0000057 is not implemented but showing up in reports

[pgaudet]

Hi @mugitty

According to @dustine32 , gorule-0000057 was never implemented (see #1553), but it's showing up in reports, see

http://current.geneontology.org/reports/assigned-by-gorule-report.html

Can you please remove it from the pipeline?

Thanks, Pascale

[kltm]

There is a report filter list in the pipeline (variable) to deal with things like this.

[mugitty]

@kltm, If the rule is valid, then we need to ensure it is implemented correctly and @pgaudet will add tests. When I discussed with @dustine32, he indicated that the rule was no longer necessary and I was going to remove

[dustine32]

@mugitty As @kltm mentioned (different list, sorry), there is a list of GoRules here:
https://github.com/biolink/ontobio/blob/57adf9c2bcdc9385c45116b58535e446f6b30bd0/ontobio/io/qc.py#L950
You can try removing GoRule57 from this list and running the validation to see if the rule row is removed from the assigned-by-gorule-report.html.

[dustine32]

@kltm Is this GORULE_TAGS_TO_SUPPRESS the rule filter variable you were referring to?
https://github.com/geneontology/pipeline/blob/5990c634683d2e5fc51f6c1baa4db8e8cc67b96b/Jenkinsfile#L135C4-L135C27

[mugitty]

I know how to remove the rule so that it does not appear in the reports.
@pgaudet has deprecated the rule, however @kltm may want to keep it. I am not sure how to proceed. There are config parameters that can be passed to filter out the annotations.

[kltm]

There are two approaches: one is not running the rule (internal variable); one is filtering the rule (pipeline variable). Both are viable. It may be worth considering on what timeline the activity of the is being considered. If it is not planned and has no code, it may be worth excising from ontobio altogether as it may be more confusing for future developers figuring out what is going on. I'm happy with any decision made here by the two of you.

[kltm]

@mugitty If the rule is deprecated, I would consider excising unnecessary code and commenting as such in the rule implementation notes in the rule metadata itself.

[mugitty]

#biolink/ontobio#667

[pgaudet]

Not shown in go-rules reports, so this is OK for me -

@kltm Do you want a 'cleaner' solution to this?

[kltm]

@pgaudet I'm okay with whatever is practical, but I just wanted to make sure we're all on the same page about expectations.

[pgaudet]

Working as needed for curators. We can revisit the system if needed.