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Reverting FAIL to OKAY since obsolete terms have no namespace #649

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merged 1 commit into from
Oct 7, 2023

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dustine32
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Change corresponds to geneontology/go-site#2002. Slight correction of initial PR #646.

This fixes a bug introduced with #646 that was failing all obsoleted terms in rule 61 because their ontology node did not have a namespace key:

return TestResult(repair_result(RepairState.FAILED, self.fail_mode), "{}: {}".format(self.message(repair_state), "GO term has no namespace"), annotation)

An example obsoleted term is GO:1902361. The failed GO rule test example is here: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000020.md

I added a test for this (within ontobio!!) under rule 61 and confirmed that the go-site test suite (really just a wrapper around ontobio's validate.py rule command) runs w/o error.

@dustine32 dustine32 requested review from kltm and mugitty October 7, 2023 01:20
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Fix and test.

@kltm kltm merged commit 615de60 into master Oct 7, 2023
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