Refactor SNV germline ClinVar submissions

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Closes Changes in the ClinVar submission API #5964
• Closes Change clinvarSubmission to germlineSubmission #5986
• Closes New VUS Terms for Germline Classifications on the ClinVar submission form #5987
• Closes Handle the whole ClinVar submission process in scout #5199
• Closes Modify format of non-somatic ClinVar submissions so they look like json API submissions #5197

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

[codecov]

Codecov Report

❌ Patch coverage is 90.60403% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.62%. Comparing base (a49902c) to head (585f21e).

Files with missing lines	Patch %	Lines
scout/server/blueprints/clinvar/controllers.py	90.00%	5 Missing ⚠️
scout/server/blueprints/clinvar/views.py	88.63%	5 Missing ⚠️
scout/adapter/mongo/clinvar.py	83.33%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #5994      +/-   ##
==========================================
- Coverage   83.88%   83.62%   -0.27%     
==========================================
  Files         336      336              
  Lines       21022    20900     -122     
==========================================
- Hits        17635    17478     -157     
- Misses       3387     3422      +35     

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[northwestwitch]

I reasoned that this PR contains enough changes already. This can be fixed shortly after

[northwestwitch]

This works more or less as intended now, so I'm marking it ready for review. I'm aware of its size so I don't expect any quick review on this. I'll just leave it for when we have time

[sonarqubecloud]

Quality Gate failed

Failed conditions
1 Security Hotspot
5.8% Duplication on New Code (required ≤ 3%)

See analysis details on SonarQube Cloud