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Update RegEx patterns for annotation IDs #751

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WalkerKnapp
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  • Does not fix an open issue

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.

  • description of feature/fix

The Regex patterns which are used to match against annotation IDs in test_*_annotation_wrong_ids tests have gone out of date since they were last updated. This PR replaces out-of-date ID patterns with the latest versions retrieved from https://registry.identifiers.org/registry.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 While updating this pattern, I noticed that others have gone out of date as well and have updated them too.

  • tests added/passed

All previous tests in tests/test_for_support/test_for_annotation.py still apply and pass, and no additional functionality which would require tests has been introduced.

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codecov bot commented Sep 22, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (12338a6) 74.85% compared to head (8358d2a) 74.85%.

❗ Current head 8358d2a differs from pull request most recent head 0666f99. Consider uploading reports for the commit 0666f99 to get more accurate results

Additional details and impacted files
@@           Coverage Diff            @@
##           develop     #751   +/-   ##
========================================
  Coverage    74.85%   74.85%           
========================================
  Files           50       50           
  Lines         2955     2955           
  Branches       669      669           
========================================
  Hits          2212     2212           
  Misses         649      649           
  Partials        94       94           
Files Coverage Δ
src/memote/support/annotation.py 100.00% <ø> (ø)

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@carrascomj carrascomj left a comment

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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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2 participants