cancervariants / cancervariants/therapy-normalization

How to specify internal disease normalizer environment?

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#314 1 comment 0 reactions 0 assignees View on GitHub
bug requirement
Dominant language
Python
Stars
15
Forks
3
PR merge metrics
No merged PRs in 30d

Description

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.

Contributor guide

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Research direction

Start with the CLI `_check_disease_normalizer` method and the handling of DISEASE_NORM_DB_URL, DISEASE_NORM_ENV, and THERAPY_NORM_PROD. Clarify the documentation for internal disease-normalizer environments, resolve the condition branches that can raise UnboundLocalError, and ensure the check covers both HemOnc and ChEMBL.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, cli, documentation
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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