Refactor cancer SNVs code to use shared routines

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Refactor and simplify cancer SNVs code

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 CR

[northwestwitch]

Removed this test which is testing an impossible condition, as the form now has enforced a HTML5 check, so you can't enter a string - it just accepts numbers

NOTE that the test would have failed with
assert 200 == 302

This is because cancer variant form is currently validated.

Validation is lost with the refactoring - it's complicated to have a common function and just validate cancer variants forms on POST request. Would be much easier to start working on a common validation code for each variant type at a later stage.

[codecov]

Codecov Report

❌ Patch coverage is 79.16667% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.88%. Comparing base (4602f73) to head (02abcef).

Files with missing lines	Patch %	Lines
scout/server/blueprints/variants/controllers.py	70.58%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #6128      +/-   ##
==========================================
- Coverage   83.93%   83.88%   -0.06%     
==========================================
  Files         343      343              
  Lines       21174    21126      -48     
==========================================
- Hits        17773    17722      -51     
- Misses       3401     3404       +3     

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[northwestwitch]

This is not a typo: cancer_variants expects the WTF itself, not the request form

[sonarqubecloud]

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 SonarQube Cloud