cancervariants / cancervariants/therapy-normalization
How to specify internal disease normalizer environment?
- 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.
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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