Test any chanjo-report branch

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Test the proposed changes in chanjo and chanjo-report with real data

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
• tests executed by

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.55%. Comparing base (6f6bc89) to head (b98d4ac).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4635   +/-   ##
=======================================
  Coverage   84.55%   84.55%           
=======================================
  Files         309      309           
  Lines       18768    18768           
=======================================
  Hits        15870    15870           
  Misses       2898     2898           

☔ View full report in Codecov by Sentry.
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[northwestwitch]

YESSSSS this works! The branch is deployed on stage and reports are created correctly it seems!

[northwestwitch]

YESSSSS this works! The branch is deployed on stage and reports are created correctly it seems!

Ah! Report works, but overview crashes. Will fix. I knew it was too good the moment I wrote my previous message..

[northwestwitch]

Ok now everything seems to work fine:

Example of a case where to test reports (WES):
https://scout-stage.scilifelab.se/cust000/15026-mip7

Case testable to see if MT report works and contains expected data (WGS):
https://scout-stage.scilifelab.se/cust000/643594-300M

[northwestwitch]

@dnil I don't want to merge this one, just let you know that test with real data is fine now, so I think we can merge the chanjo and chanjo-report PRs

[sonarqubecloud]

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