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[Internal] [Bug] Mistake in metadata validation not allowing valid strings #241

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jessicarowell opened this issue Jan 3, 2025 · 2 comments · Fixed by #244
Closed

[Internal] [Bug] Mistake in metadata validation not allowing valid strings #241

jessicarowell opened this issue Jan 3, 2025 · 2 comments · Fixed by #244
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@jessicarowell
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Need to modify populate_fields() function assert statement to allow valid strings and not only "" or "Not Provided"

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Command to replicate the error:
nextflow run main.nf -profile test,singularity --species bacteria --output_dir test_bact --submission_config ~/02.scratch/submission_config.yaml --bakta_db_path /scicomp/reference/bakta/db

Any Additional Context or Information?
This mistake got missed with viral test data because all the terms_2_replace were missing. In bacteria test data, isolation_source = "Clinical," which is a valid string that was getting caught in the incorrect assert statement.

@jessicarowell jessicarowell added the bug Something isn't working label Jan 3, 2025
@jessicarowell jessicarowell added this to the v4.1.0 milestone Jan 3, 2025
@jessicarowell jessicarowell self-assigned this Jan 3, 2025
@jessicarowell
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This is completed and will be closed with the next PR

@jessicarowell jessicarowell linked a pull request Jan 6, 2025 that will close this issue
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@jessicarowell
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Fixed on ick4-dev-patch

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