Actually deprecate the Chado Query API in favour of Tripal DBX. #2294
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…hado_db_select().
4 new issues
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Diff Coverage: The code coverage on the diff in this pull request is 69.8%. Total Coverage: This PR will decrease coverage by 0.06%. File Coverage Changes
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…ng so in the tests that check old deprecated functions directly.
dsenalik
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Sep 25, 2025
dsenalik
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Sep 25, 2025
dsenalik
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Sep 25, 2025
dsenalik
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Co-authored-by: Douglas Senalik <[email protected]>
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Tripal 4 Core Dev Task
Issue #1341
Description
We need to actually deprecate this very old API as mentioned in tripal/tripal_doc#109. This PR will accomplish this.
More specifically, this PR
IgnoreDeprecationsto API specific tests so that they don't fail due to the deprecations which we expect. This allows us to continue testing these until we remove them in Tripal 4.1.0IgnoreDeprecationsis not available in that version. This seems ok since we will see the deprecations in Drupal 11+NOTE: PHPUnit 11.5 is still configured not to fail on deprecations. I did not fix this in this PR because there are remaining deprecations triggered by this PR that will be fixed in #2297. We should make sure to fix this in that PR to ensure that deprecations triggered in tests outside of those specifically testing the deprecated API get caught and cause failure.
Testing?
I'm not sure how to test this. There are automated tests that check this functionality. Since the importers have not yet been updated in this PR one way to test may be run the importers and make sure they haven't broken in this PR.