Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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A small projection on panels, and use sets instead of explicit loops #4657

Closed dnil closed 3 weeks ago

dnil commented 3 weeks ago

This PR speeds up a slow controller, partially addressing #4655.

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 3 weeks ago

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

codecov[bot] commented 3 weeks ago

Codecov Report

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

Project coverage is 84.62%. Comparing base (b663681) to head (a40ac87).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4657 +/- ## ======================================= Coverage 84.62% 84.62% ======================================= Files 310 310 Lines 18788 18789 +1 ======================================= + Hits 15899 15900 +1 Misses 2889 2889 ```

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dnil commented 3 weeks ago

Ive tested, in as much as it is just supposed to pass tests and do what the previous things did, but not really timed. I can merge it into the timing branch perhaps and see what we get?

northwestwitch commented 3 weeks ago

Ive tested, in as much as it is just supposed to pass tests and do what the previous things did, but not really timed. I can merge it into the timing branch perhaps and see what we get?

Yes, let's do it!

dnil commented 3 weeks ago

I think it shaves a decent slice; looks like the panels are stably below matching causatives now on the case controller timing branch with this merged in: Screenshot 2024-06-04 at 10 40 17