Add flexibility to the parsing of custom archived loqusDB instances

[northwestwitch]

This PR adds a functionality or fixes a bug.

• A partial fix to Refactor how archived loqusdb instances are used on variantS filter #5601
• Removes hard coded archived loqusDB instance names from the parsing module, allowing to define custom keys
• Next step (another PR) would be using these keys from the config file to define custom filters on the variantS pages

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@<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

[northwestwitch]

Is this too complex to have in the config file? Would it be better with a long list of single keys instead?

[dnil]

Hm, yes, it is rather complex isn't it? I like the idea though. Perhaps we could leave the old ones in running code, or as a similar structure from constants, and allow adding only the systematic prefix ones from config?

[northwestwitch]

I like the idea of removing hard coded keys as much as possible. Perhaps we could try to just have a list (no matter how long) of keys (containing prefixes and suffixes). That would be very clear

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.88%. Comparing base (a49902c) to head (eaa8aa4).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #5622      +/-   ##
==========================================
- Coverage   83.88%   83.88%   -0.01%     
==========================================
  Files         336      336              
  Lines       21022    21020       -2     
==========================================
- Hits        17635    17633       -2     
  Misses       3387     3387              

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[northwestwitch]

I want to revise this PR and make sure I access the config values after the config file has been parsed, otherwise I might be skipping the situation where the config is the yaml file used for instance by our cli. Still i progress!

[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