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cancervariants / therapy-normalization

Services and guidelines for normalizing drug and other therapy terms
https://normalize.cancervariants.org/therapy/
MIT License
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How to specify internal disease normalizer environment? #314

Open jsstevenson opened 1 year ago

jsstevenson commented 1 year ago

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 commented 10 months ago

Some progress in #378, still cooking