Update RegEx patterns for annotation IDs #751
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #751 +/- ##
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Coverage 74.85% 74.85%
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Files 50 50
Lines 2955 2955
Branches 669 669
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Hits 2212 2212
Misses 649 649
Partials 94 94
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carrascomj
requested changes
Sep 22, 2023
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Thanks for the update! Would it be possible to add some identifiers to the tests that did not work before and now pass? Just to track the improvements (at one of met/rxn/gene_each_present fixture builders), it does not have to be exhaustive.
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This fix is related to issue #315, but it is a band-aid solution for the current state of database IDs, not an automatic solution as suggested in the issue.
The Regex patterns which are used to match against annotation IDs in
test_*_annotation_wrong_idstests have gone out of date since they were last updated. This PR replaces out-of-date ID patterns with the latest versions retrieved from https://registry.identifiers.org/registry.I first noticed this problem when evaluating a model which uses a refseq id in the format
WP_*, which is now a valid ID. While updating this pattern, I noticed that others have gone out of date as well and have updated them too.All previous tests in
tests/test_for_support/test_for_annotation.pystill apply and pass, and no additional functionality which would require tests has been introduced.