Fix triple clinvar filter

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Closes Filtering by ClinVar clinsig + CLINSIG Confident + ClinVar hits has a bug #4996

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. Using demo case, go to the SNVs filter and filter using the following criteria:

Check the difference between this branch and main branch!

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]

This is the fix: this filter is removed from the secondary query and set together with the other 2 clinvar-based filters, in the function dedicated to building the clinvar filters

[codecov]

Codecov Report

Attention: Patch coverage is 92.85714% with 2 lines in your changes missing coverage. Please review.

Project coverage is 84.76%. Comparing base (7c68883) to head (8cf42b6).

Files with missing lines	Patch %	Lines
scout/adapter/mongo/query.py	92.59%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #5006   +/-   ##
=======================================
  Coverage   84.76%   84.76%           
=======================================
  Files         320      320           
  Lines       19359    19360    +1     
=======================================
+ Hits        16410    16411    +1     
  Misses       2949     2949           

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[sonarcloud]

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