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feat: implementing ClinVar upload (#99) #270

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merged 44 commits into from
Dec 21, 2023
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WIP

@holtgrewe holtgrewe linked an issue Dec 11, 2023 that may be closed by this pull request
@holtgrewe holtgrewe marked this pull request as draft December 11, 2023 14:33
@holtgrewe holtgrewe force-pushed the main branch 2 times, most recently from 1391c8a to 51c6d4f Compare December 12, 2023 10:50
@holtgrewe holtgrewe force-pushed the 99-implement-clinvar-uploads branch from 4083bf1 to a287715 Compare December 13, 2023 08:10
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codecov bot commented Dec 13, 2023

Codecov Report

Attention: 129 lines in your changes are missing coverage. Please review.

Comparison is base (17eee05) 80.12% compared to head (d26d55a) 84.52%.
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #270      +/-   ##
==========================================
+ Coverage   80.12%   84.52%   +4.40%     
==========================================
  Files         153       53     -100     
  Lines        5192     1577    -3615     
  Branches     1240        0    -1240     
==========================================
- Hits         4160     1333    -2827     
+ Misses        936      244     -692     
+ Partials       96        0      -96     
Files Coverage Δ
backend/app/api/api_v1/api.py 54.16% <100.00%> (+0.97%) ⬆️
backend/app/api/api_v1/endpoints/auth.py 71.42% <100.00%> (-3.58%) ⬇️
backend/app/core/celery_app.py 100.00% <100.00%> (ø)
backend/app/core/config.py 91.76% <100.00%> (+1.35%) ⬆️
backend/app/crud/__init__.py 100.00% <100.00%> (ø)
backend/app/main.py 86.66% <100.00%> (+1.48%) ⬆️
backend/app/models/__init__.py 100.00% <100.00%> (ø)
backend/app/schemas/__init__.py 100.00% <100.00%> (ø)
backend/app/schemas/clinvarsub.py 100.00% <100.00%> (ø)
backend/app/db/session.py 93.75% <92.30%> (-6.25%) ⬇️
... and 6 more

... and 107 files with indirect coverage changes

@holtgrewe holtgrewe marked this pull request as ready for review December 21, 2023 12:46
@holtgrewe holtgrewe enabled auto-merge (squash) December 21, 2023 12:46
@holtgrewe holtgrewe merged commit d4d949e into main Dec 21, 2023
9 checks passed
@holtgrewe holtgrewe deleted the 99-implement-clinvar-uploads branch December 21, 2023 12:49
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Implement ClinVar Uploads
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