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
• Fixes partially submittedAssembly required when providing HGVS in ClinVar submissions #6106

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 89.67742% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.81%. Comparing base (5e26627) to head (b8fc14b).

Files with missing lines	Patch %	Lines
scout/adapter/mongo/clinvar.py	79.31%	6 Missing ⚠️
scout/server/blueprints/clinvar/controllers.py	90.19%	5 Missing ⚠️
scout/server/blueprints/clinvar/views.py	88.63%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #5994      +/-   ##
==========================================
- Coverage   84.08%   83.81%   -0.27%     
==========================================
  Files         347      347              
  Lines       21835    21717     -118     
==========================================
- Hits        18359    18203     -156     
- Misses       3476     3514      +38     

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[northwestwitch]

Summer and holidays start to feel the right period to merge this one. We can perhaps merge it before July so I can work on a couple of other PRs to complement it (include SVs and another one I don't remember now) so we'll be done when everyone is back at the office

[sonarqubecloud]

Quality Gate failed

Failed conditions
D Reliability Rating on New Code (required ≥ A)

See analysis details on SonarQube Cloud

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