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fix-logging-warnings #552

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Merged
theferrit32 merged 1 commit into from
Apr 24, 2025
Merged

fix-logging-warnings #552

theferrit32 merged 1 commit into from
Apr 24, 2025

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@ottojolanki
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@ottojolanki ottojolanki commented Apr 24, 2025

This PR stops logging unnecessary warnings like:

Derived sequence '' is different from provided state.sequence 'root='''

Derived sequence 'CCCC' is different from provided state.sequence 'root='CCCC''

An example for reproducing the warning log. Functionality is correct, but the condition for logging has a small bug.

>>> from ga4gh.vrs.extras.translator import AlleleTranslator
>>> from ga4gh.vrs.dataproxy import create_dataproxy
>>> dp = create_dataproxy('seqrepo+file:///usr/local/share/seqrepo/2024-12-20')
>>> translator = AlleleTranslator(data_proxy=dp)
>>> allele = translator.translate_from('21-5030497-C-CACCT', 'gnomad')
>>> translator.translate_to(allele, 'spdi')
Derived sequence 'ACCTACCT' is different from provided state.sequence 'root='ACCTACCT''
['NC_000021.9:5030497:4:ACCTACCT']

@ottojolanki ottojolanki requested review from a team as code owners April 24, 2025 20:36
@theferrit32 theferrit32 merged commit aa49cb1 into ga4gh:main Apr 24, 2025
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@ottojolanki @theferrit32