Gnomad keys

[dnil]

This PR adds a functionality or fixes a bug.

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
• tests executed by DN

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.57%. Comparing base (b5a210f) to head (f3864c7).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4456      +/-   ##
==========================================
- Coverage   84.58%   84.57%   -0.01%     
==========================================
  Files         310      310              
  Lines       18634    18637       +3     
==========================================
+ Hits        15762    15763       +1     
- Misses       2872     2874       +2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[dnil]

I'll leave this like this until we have a good example - I just realised the poorpipe genomes were annotated with 1000g only.

[dnil]

Finally some files passed to annotation again! While perhaps not the finished product, good enough to test this PR:

[northwestwitch]

@dnil just assign me if you think this is ready for a review

[dnil]

@dnil just assign me if you think this is ready for a review

Anytime it's not draft, though things may still change with second or third thought. 😉 I made a small refactor to the parser which was just over the CodeFactor complexity threshold, though not the SonarCloud one yet. I also retested it again on winningchicken, and it seemed to work ok still.

[northwestwitch]

Looks good to me. Only a couple of suggestions.

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud