Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Fix #4773 - separate RNA view genome build option #4775

Closed dnil closed 2 months ago

dnil commented 2 months ago

This PR adds a functionality or fixes a bug.

One can now view RNA alns in hg19 by setting rna_human_genome_build: 37 in the load config. Screenshot 2024-08-23 at 14 11 55

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:

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 93.33333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 84.21%. Comparing base (c3b4276) to head (1904df8). Report is 1 commits behind head on main.

Files Patch % Lines
...cout/server/blueprints/alignviewers/controllers.py 83.33% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4775 +/- ## ========================================== - Coverage 84.22% 84.21% -0.01% ========================================== Files 318 318 Lines 19161 19176 +15 ========================================== + Hits 16138 16149 +11 - Misses 3023 3027 +4 ```

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sonarcloud[bot] commented 2 months 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