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

Subject id search #4881

Closed dnil closed 1 week ago

dnil 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. 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 1 week ago

Codecov Report

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

Project coverage is 84.77%. Comparing base (cc4f98b) to head (bba815e). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4881 +/- ## ======================================= Coverage 84.77% 84.77% ======================================= Files 319 319 Lines 19296 19296 ======================================= Hits 16358 16358 Misses 2938 2938 ```

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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

dnil commented 1 week ago

Unfortunately we can't quite index this fully as it is: the name query is for all collaborators, and for all individuals and we can't index on both arrays simultaneously. Fortunately the collection is pretty small and the individuals array is short so this should work out anyway.

dnil commented 1 week ago

Yep, tested both indexes and subject_id search locally. Will take it to stage for a spin as well before merging.

Screenshot 2024-09-19 at 15 02 04

dnil commented 1 week ago

Screenshot 2024-09-19 at 15 49 02

Screenshot 2024-09-19 at 15 55 46