Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Add panel indexes and better version check when editing a panel #5068

Closed northwestwitch closed 17 hours ago

northwestwitch commented 17 hours ago

This PR adds a functionality or fixes a bug.

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:

  1. Make sure that the issue can't be reproduced locally, because of missing indexes in the demo DB, see this comment
  2. Switch to this branch and run the commend scout setup demo
  3. At this point the gene panel collection in the database should have 3 indexes.
  4. Try to edit a gene panel again while keeping the same version and see that the panel has actually maintained its version, as intended by the user.

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

Review:

dnil commented 17 hours ago

Ah, oops, I didn't check the tests. Oh well. Onwards!

sonarcloud[bot] commented 17 hours ago

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

codecov[bot] commented 17 hours ago

Codecov Report

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

Project coverage is 84.78%. Comparing base (88cf8e5) to head (e7a2e05). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #5068 +/- ## ======================================= Coverage 84.78% 84.78% ======================================= Files 323 323 Lines 19442 19442 ======================================= Hits 16484 16484 Misses 2958 2958 ```

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