Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Fix #4884 - enable Gens balsamic button #4885

Closed dnil closed 1 month ago

dnil commented 1 month ago

This PR adds a functionality or fixes a bug.

Gens button enabled also on cancer individuals table (if gens integration is enabled).

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. how to test it, possibly with real cases/data

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

Review:

sonarcloud[bot] commented 1 month 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 SonarCloud

codecov[bot] commented 1 month ago

Codecov Report

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

Project coverage is 84.77%. Comparing base (c73ea6b) to head (1803a48).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4885 +/- ## ======================================= Coverage 84.77% 84.77% ======================================= Files 319 319 Lines 19296 19296 ======================================= Hits 16358 16358 Misses 2938 2938 ```

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dnil commented 1 month ago

❌ Before: Screenshot 2024-09-23 at 14 15 23 ✅ After: Screenshot 2024-09-23 at 14 19 17

dnil commented 1 month ago

Ping @mathiasbio - its on stage now, enabled for all cancer track cases as well. Is that as intended?

mathiasbio commented 1 month ago

Sorry for the late reply! Looks like it's working 🙏 Thank you! I don't know how this implementation works, if it will display the button even if GENS results are not uploaded. But either way it should be fine. We're planning to make this release SOON! (I keep saying this but it is true) and if the button is showing and not leading anywhere in the interim time it should be fine!

dnil commented 1 month ago

Good, and quite agree. It will be nice when they are loaded, but reaching a "missing gens data" page in the meantime is no biggie.

There is an old issue on gens to allow api polling for case data. Feel free to work on/nudge that one if you would wish to have the buttons more adaptive.