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phenopolis / phenopolis_genomics_browser

Python API and React frontend for the Phenopolis Genomics Browser
https://dev-live.phenopolis.org
MIT License
31 stars 2 forks source link

Simplifying tests and coverage #235

Closed alanwilter closed 3 years ago

alanwilter commented 3 years ago

I essentially simplified tests in order to improve coverage. I did some simple code organisation as well. Doing GH workflow after each commit to find out what's the culprit.

Fixed the issue that was failing GH tests

alanwilter commented 3 years ago

It's now opened for reviews.

And to anticipate a question, for test_get_genotypes_exception in test_variants.py, the idea is that the exception in def _get_genotypes(chrom, pos): should never ever happen because if it does something really flawed has happened and S3 VCF file is out of sync with variant table in DB.

Think of updating the DB or the VCF file but forgetting to reconcile the counterpart. In principle it should be only the VCF file being updated (not often) and then deriving the changes to the DB.

alanwilter commented 3 years ago

I definitely need to update this PR. I will close it and create a new one.