ACMG sandbox

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Closes Empty ACMG classification page #5875

Testing on cg-vm1 server (Clinical Genomics Stockholm)

Prepare for testing

1. Make sure the PR is pushed and available on Docker Hub
2. First 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@<name_of_currently_deployed_branch>
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

[northwestwitch]

Moved to the blank_acmg

[northwestwitch]

Also moved to the blank_acmg

[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 83.88%. Comparing base (a49902c) to head (e012216).

Files with missing lines	Patch %	Lines
scout/server/blueprints/variant/views.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #5983      +/-   ##
==========================================
- Coverage   83.88%   83.88%   -0.01%     
==========================================
  Files         336      336              
  Lines       21022    21026       +4     
==========================================
+ Hits        17635    17638       +3     
- Misses       3387     3388       +1     

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[sonarqubecloud]

Quality Gate failed

Failed conditions
2 Security Hotspots
B Reliability Rating on New Code (required ≥ A)

See analysis details on SonarQube Cloud

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