Fix #4773 - separate RNA view genome build option

[dnil]

This PR adds a functionality or fixes a bug.

One can now view RNA alns in hg19 by setting rna_human_genome_build: 37 in the load config.

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. 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 CR
• tests executed by DN

[codecov]

Codecov Report

Attention: Patch coverage is 93.33333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 84.21%. Comparing base (c3b4276) to head (1904df8).
Report is 1 commits behind head on main.

Files	Patch %	Lines
...cout/server/blueprints/alignviewers/controllers.py	83.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4775      +/-   ##
==========================================
- Coverage   84.22%   84.21%   -0.01%     
==========================================
  Files         318      318              
  Lines       19161    19176      +15     
==========================================
+ Hits        16138    16149      +11     
- Misses       3023     3027       +4     

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[northwestwitch]

Looks good, just those pydantic checks that should at least swap names

[northwestwitch]

Shouldn't this be named format_rna_build and the function down (line 516) format_build?

[northwestwitch]

Also these 2 functions have some common code. Couldn't they be unified somehow?

[dnil]

Sure, one way would be to break out the genome string check to a separate helper..

[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 SonarCloud