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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Make ACMG BA1 fully Stand Alone #4924

Closed dnil closed 1 month ago

dnil commented 1 month ago

This PR adds a functionality or fixes a bug.

On re-reading Richards 2015, while not explicitly clear from figures, the wording on "Stand Alone" benign, in combination with the efforts to exclude the handful of clearly pathogenic variants at the original "ba1" frequency level (https://www.clinicalgenome.org/site/assets/files/3460/ba1_exception_list_07_30_2018.pdf) it seems rather clear that this should really be Stand Alone.

Testing on cg-vm1 server (Clinical Genomics Stockholm) **Prepare for testing** 1. Make sure the PR is pushed and available on [Docker Hub](https://hub.docker.com/repository/docker/clinicalgenomics/scout-server-stage) 1. Fist book your testing time using the Pax software available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). The resource you are going to call dibs on is `scout-stage` and the server is `cg-vm1`. 1. `ssh @cg-vm1.scilifelab.se` 1. `sudo -iu hiseq.clinical` 1. `ssh localhost` 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps` 1. Stop the service with current deployed branch: `systemctl --user stop scout.target` 1. Start the scout service with the branch to test: `systemctl --user start scout@` 1. Make sure the branch is deployed: `systemctl --user status scout.target` 1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](https://pax.scilifelab.se), which will release the allocated resource (`scout-stage`) to be used for testing by other users.
Testing on hasta server (Clinical Genomics Stockholm) **Prepare for testing** 1. `ssh @hasta.scilifelab.se` 1. Book your testing time using the Pax software. `us; paxa -u -s hasta -r scout-stage`. You can also use the WSGI Pax app available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `conda activate S_scout; pip freeze | grep scout-browser` 1. Deploy the branch to test: `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b ` 1. Make sure the branch is deployed: `us; scout --version` 1. After testing is done, repeat the `paxa` procedure, which will release the allocated resource (`scout-stage`) to be used for testing by other users.

How to test: e.g. replicate the BA1 test on the ACMG page:

  1. fill BA1,
  2. fill two additional strong benign criteria
  3. note how the prediction goes to from Benign to Likely benign
  4. with patch, stays Benign

Expected outcome: The functionality should be working Take a screenshot and attach or copy/paste the output.

Review:

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.79%. Comparing base (eb06f57) to head (9a93f3c). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4924 +/- ## ========================================== + Coverage 84.78% 84.79% +0.01% ========================================== Files 319 319 Lines 19326 19328 +2 ========================================== + Hits 16385 16390 +5 + Misses 2941 2938 -3 ```

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