Go site 676 gorule 0000022 check for retracted publications

[mugitty]

No description provided.

[kltm]

@mugitty These changes generally make sense to me.
Looking at this, one thing we had discussed was making the use of retracted publications completely optional--i.e. adding a new option to the path and only executing if available. It looks like this just depends on the go-site metadata directory? We would like to be able to turn these on/off, switch targets, etc.; it looks like it errors out on file not existing now?

[kltm]

@mugitty It looks like the test error:

==================================== ERRORS ====================================
_______________ ERROR collecting tests/test_validation_rules.py ________________
tests/test_validation_rules.py:1: in <module>
    from ontobio.validation import rules
ontobio/validation/rules.py:11: in <module>
    from ontobio.validation import metadata
ontobio/validation/metadata.py:188: in <module>
    def retracted_pub_set(metadata)->set[str]:
E   TypeError: 'type' object is not subscriptable
=============================== warnings summary ===============================

is related to the handling of go-site metadata as mentioned above.

[mugitty]

@kltm , I did not realized that we wanted a flag to determine if the test should be run. So, it would only be in ontobio-parse-assocs.py as a parameter?

For the error, is it expecting set[] instead of set[str] due to version of python?

[kltm]

@mugitty For me, I just want to make sure that the file is optional, and ideally be able to specify it in different contexts. The exact mechanism isn't too too important.

[dustine32]

Linking to issue geneontology/go-site#676

Updated as requested

[kltm]

Examining code, it looks like:

• if file given, rule run
• if file found at assumed location, rule run
• otherwise, rule skipped

I believe this is in line with what we discussed; if so, please merge at your convenience