Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Merge `Qual` and `Callers` cell on cancer SNVs page #5045

Closed northwestwitch closed 5 days ago

northwestwitch commented 6 days 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. Check SNV variantS from this case but also other cases, cancer and non-cancer (only SVs in the latter case)

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

Review:

codecov[bot] commented 6 days ago

Codecov Report

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

Project coverage is 84.78%. Comparing base (218cbe6) to head (d5457ea). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #5045 +/- ## ======================================= Coverage 84.78% 84.78% ======================================= Files 323 323 Lines 19432 19432 ======================================= Hits 16475 16475 Misses 2957 2957 ```

:umbrella: View full report in Codecov by Sentry.
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sonarcloud[bot] commented 5 days 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

northwestwitch commented 5 days ago

Demo case:

image

Test case on scout-stage:

image
northwestwitch commented 5 days ago

It gets a little tedious with the redundant PASS and FAIL ones, so checking against that would be an improvement.

You want me to add this check in the PR or it is fine as it is for now? Pehaps we could get some users' feedback afterwards

dnil commented 5 days ago

It gets a little tedious with the redundant PASS and FAIL ones, so checking against that would be an improvement.

You want me to add this check in the PR or it is fine as it is for now? Pehaps we could get some users' feedback afterwards

I think it is tentatively better than main already, so good to merge if you like. If it looks easy and safe to do the check, I'd say do it now while we are thinking about it. But if it gets complicated its fine to leave the extra badges there for a bit.

northwestwitch commented 5 days ago

I think it is tentatively better than main already, so good to merge if you like. If it looks easy and safe to do the check, I'd say do it now while we are thinking about it. But if it gets complicated its fine to leave the extra badges there for a bit.

I'll just merge then. If somebody complains we can fix it