search

Clinical-Genomics / scout

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

Minor release 4.88 #4824

Closed northwestwitch closed 2 months ago

northwestwitch commented 2 months ago

[4.88]

Added

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 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.16%. Comparing base (642ecc0) to head (ae5b172). Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
scout/__version__.py 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4824 +/- ## ======================================= Coverage 84.16% 84.16% ======================================= Files 318 318 Lines 19202 19202 ======================================= Hits 16162 16162 Misses 3040 3040 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

northwestwitch commented 2 months ago

Tested loading DROP variants with case orientedsheepdog (scout config present under /home/proj/stage/housekeeper-bundles/orientedsheepdog/2024-08-29)

It works --> https://scout-stage.scilifelab.se/cust003/24045-Tomte

image
northwestwitch commented 2 months ago

The variants have been loaded but I don't get to see them on the WTS outliers page. What I am missing??

image
northwestwitch commented 2 months ago

Whoops, the variants are not visible also on the demo version. It's the GT check that excludes all variants. In fact you see them when you check this checkbox

image
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