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fix-logging-warnings (#552)
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. ```python >>> 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'] ```
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src/ga4gh/vrs/extras/translator.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -468,11 +468,11 @@ def _to_spdi(
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alt_length=vo.state.length,
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)
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# Warn if the derived sequence is different from the one in the object
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if vo.state.sequence and vo.state.sequence != alt_seq:
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if vo.state.sequence and vo.state.sequence.root != alt_seq:
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_logger.warning(
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"Derived sequence '%s' is different from provided state.sequence '%s'",
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alt_seq,
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vo.state.sequence,
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vo.state.sequence.root,
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)
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else:
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alt_seq = vo.state.sequence.root

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