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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
150 stars 46 forks source link

Fix alamut link error #4865

Closed northwestwitch closed 1 week ago

northwestwitch commented 1 week 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. Go to the case general report page of this case

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

Review:

codecov[bot] commented 1 week ago

Codecov Report

Attention: Patch coverage is 50.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 84.77%. Comparing base (c48d621) to head (9c3c43d). Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
scout/server/links.py 50.00% 3 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4865 +/- ## ========================================== - Coverage 84.78% 84.77% -0.02% ========================================== Files 319 319 Lines 19289 19295 +6 ========================================== + Hits 16354 16357 +3 - Misses 2935 2938 +3 ```

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sonarcloud[bot] commented 1 week 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

northwestwitch commented 1 week ago

d, but would hint at an underlying issue (or backwards compatibility I didn't find on a cursory look 😸).

It's weird because some variant gene have the key and some don't. this is an oldish case so perhaps some old bug that now is fixed?