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How to specify internal disease normalizer environment? #314

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jsstevenson opened this issue Dec 9, 2022 · 1 comment
Open

How to specify internal disease normalizer environment? #314

jsstevenson opened this issue Dec 9, 2022 · 1 comment
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bug Something isn't working requirement Required

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@jsstevenson
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jsstevenson commented Dec 9, 2022

Drug indication data requires a disease normalizer instance, so the CLI currently tries to identify a disease_concepts table location and update it if necessary. However, there are a few condition branches where various values aren't properly set, raising UnboundLocalErrors.

Right now we can use DISEASE_NORM_DB_URL to set a URL, and I think if you define it as a blank string it will push up to prod (and then use the environment set in DISEASE_NORM_ENV). You can also set THERAPY_NORM_PROD to prevent attempts to check/update the disease database. I think we just need to ensure documentation is updated (if only for my sake).

Oh, also, the CLI _check_disease_normalizer method needs to check against ChEMBL too, not just HemOnc.

@jsstevenson jsstevenson added the bug label Dec 9, 2022
@jsstevenson jsstevenson self-assigned this Dec 9, 2022
@jsstevenson jsstevenson added requirement Required bug Something isn't working and removed bug labels Dec 28, 2022
@jsstevenson jsstevenson removed their assignment Aug 27, 2023
@jsstevenson
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Some progress in #378, still cooking

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