Fix automatically loading research variants when loading a case

northwestwitch commented 3 weeks ago

This PR adds a functionality or fixes a bug.

Fix loading also research variants when loading a case (fix #4661 )

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:

Locally, remove all cases from the demo instance
Using main branch install demo case -> scout --demo load case scout/demo/643594.config.yaml
Note the number and type of variants loaded (clinical and research)
Remove case -> scout --demo delete case -i cust000 -c internal_id
Repeat step 2 & 3 using the branch

Expected outcome:

This branch will load only clinical variants

Review:

[x] code approved by DN
[x] tests executed by CR

codecov[bot] commented 3 weeks ago

Codecov Report

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

Project coverage is 84.49%. Comparing base (1779045) to head (9228acc).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4662 +/- ## ======================================= Coverage 84.49% 84.49% ======================================= Files 310 310 Lines 18798 18798 ======================================= Hits 15884 15884 Misses 2914 2914 ```

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northwestwitch commented 3 weeks ago

Loading variants using main branch: