Export schema wrongly fails on gene names starting with 'nuc' due to lookahead #1433
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corneliusroemer
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Mar 7, 2024
…ong as not equal to `nuc` Fixes #1433
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corneliusroemer
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Mar 14, 2024
…ong as not equal to `nuc` (#1434) * fix(export): In export schema, allow cds name with `nuc` prefix, as long as not equal to `nuc` Fixes #1433 * chore(CHANGES): Add changelog entry * fix(export): use correct schema for meta.genome_annotations Co-authored-by: james hadfield <hadfield.james@gmail.com> --------- Co-authored-by: james hadfield <hadfield.james@gmail.com>
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Current Behavior
Augur export fails at validation when a gene name for which mutations are included starts with 'nuc', for example if there's a gene named 'nucleocapsid'.
Expected behavior
Gene names can start with 'nuc'
How to reproduce
Look at the export schema:
augur/augur/data/schema-export-v2.json
Line 313 in b0c5010
The regex for additional patterns was rewritten and a negative lookahead (?!nuc) was added 6 months ago:
8209dad
Possible solution
Include a $ at the end of the lookahead to only match exactly, not just a prefix of nuc.
Your environment: if running Nextstrain locally
auspice 2.7.0): augur 24.2.3Additional context
Discovered together with @corneliusroemer
It would have made debugging easier if #1426 was implemented! So plus 1 on that issue!
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