gorule-0000003 and gorule-0000005 dont show up in the reports

[pgaudet]

Hello,

gorule-0000003 and gorule-0000005 dont show up in the reports - for example here:
http://release.geneontology.org/2023-06-11/reports/gorule-report.html

Note that these are the only 2 'legacy' rules (ie implementing owltools code); is this code not being ran anymore?
Would it be more judicious to rewrite these rules in new framework, or should we try to troubleshoot why these are not being displayed?

[pgaudet]

• gorule-0000003 is deprecated (but its status was 'legacy'), gorule-0000003 description is now fixed to indicate it is deprecated, see Update gorule-0000003 #2055
• Note that the owl reports still return errors for gorule-0000003, so we're not sure that it really is deprecated (it seems like it's still implemented)

[pgaudet]

gorule-0000005: we still dont know why the error is not showing up in the reports (probably due to being ran be owl-tools)

@mugitty needs to check with @kltm

[kltm]

owltools output is largely a dead end--those rules need to be re-implemented elsewhere (there are tickets for that).
Otherwise, for non-owltools things missing, one should all check the reports' suppression tags, although that may not be this case.

[mugitty]

@kltm , According to https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000005.md, this is implemented in owltools. Should this be implemented in ontobio?

[kltm]

As a matter of fact, there is no real owltools reporting, although rules may "exist" there. Everything that violates a rule should generate a trace, but that is not where we are at at the moment and I'm not sure this is in scope of any current project.

[pgaudet]

• gorule-0000003 is deprecated >> OK
• gorule-0000005 should be re-implemented at some point.
  I'll create a new ticket but for a future project.

[pgaudet]

Changed status of gorule-0000005 to indicated that its is not implemented (status = approved)
see #2073