Go site 676 gorule 0000022 check for retracted publications

[mugitty]

[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