Subject id search

[dnil]

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
2. Fist book your testing time using the Pax software available at https://pax.scilifelab.se/. The resource you are going to call dibs on is scout-stage and the server is cg-vm1.
3. ssh <USER.NAME>@cg-vm1.scilifelab.se
4. sudo -iu hiseq.clinical
5. ssh localhost
6. (optional) Find out which scout branch is currently deployed on cg-vm1: podman ps
7. Stop the service with current deployed branch: systemctl --user stop scout.target
8. Start the scout service with the branch to test: systemctl --user start scout@<this_branch>
9. Make sure the branch is deployed: systemctl --user status scout.target
10. After testing is done, repeat procedure at 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 <USER.NAME>@hasta.scilifelab.se
2. Book your testing time using the Pax software. us; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.
3. (optional) Find out which scout branch is currently deployed on cg-vm1: conda activate S_scout; pip freeze | grep scout-browser
4. Deploy the branch to test: bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>
5. Make sure the branch is deployed: us; scout --version
6. 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:

• code approved by CR
• tests executed by DN

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4881   +/-   ##
=======================================
  Coverage   84.77%   84.77%           
=======================================
  Files         319      319           
  Lines       19296    19296           
=======================================
  Hits        16358    16358           
  Misses       2938     2938           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[sonarcloud]

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]

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]

Noticed this one missing in passing.

[dnil]

This is the only change, really.

[northwestwitch]

Looks good! Did you test it?

[dnil]

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

[dnil]

✅

✅