Load genes missing Ensembl ID using cytoband coordinates

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Closes #4505

Testing on cg-vm1 server (Clinical Genomics Stockholm)

**Prepare for testing** 1. Make sure the PR is pushed and available on [Docker Hub](https://hub.docker.com/repository/docker/clinicalgenomics/scout-server-stage) 1. Fist book your testing time using the Pax software available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). The resource you are going to call dibs on is `scout-stage` and the server is `cg-vm1`. 1. `ssh @cg-vm1.scilifelab.se` 1. `sudo -iu hiseq.clinical` 1. `ssh localhost` 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps` 1. Stop the service with current deployed branch: `systemctl --user stop scout.target` 1. Start the scout service with the branch to test: `systemctl --user start scout@` 1. Make sure the branch is deployed: `systemctl --user status scout.target` 1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](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 @hasta.scilifelab.se` 1. Book your testing time using the Pax software. `us; paxa -u -s hasta -r scout-stage`. You can also use the WSGI Pax app available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `conda activate S_scout; pip freeze | grep scout-browser` 1. Deploy the branch to test: `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b ` 1. Make sure the branch is deployed: `us; scout --version` 1. 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

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 93.75000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 84.44%. Comparing base (4d00d74) to head (9c066b4).

Files	Patch %	Lines
scout/load/hgnc_gene.py	89.47%	2 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4677 +/- ## ========================================== + Coverage 84.43% 84.44% +0.01% ========================================== Files 311 311 Lines 18761 18783 +22 ========================================== + Hits 15840 15861 +21 - Misses 2921 2922 +1 ```

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[northwestwitch]

Marking this PR as ready for review. It doesn't solve the fact that fusion variant with gene IGH@ gets assigned a valid gene (yet) but opens up to a fix involving genes aliases.

Genes using this branch were loaded on hasta stage.

[northwestwitch]

In the spirit of summer, I'm approving, and fairly safely assuming you are right about all ensembl genes having coords.

That's how it worked so far. Also, now we have a pydantic check before saving genes in the database and the genes loading would fail in the eventuality that coordinates are missing.

[sonarcloud[bot]]

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