Version 4.84 - fix load order, chanjo-report extension load warning, …

[dnil]

…loqus connection flash etc

This PR adds a functionality or fixes a bug.

[4.84]

Changed

• [x] Clearer error message when a loqusdb query fails for an instance that initially connected
• [x] Do not load chanjo-report module if not needed and more visible message when it fails loading
• [x] Converted the HgncGene class into a Pydantic class
• [x] Swap menu open and collapse indicator chevrons - down is now displayed-open, right hidden-closed
• [x] Linters and actions now all use python 3.11

  Fixed

• [x] Safer way to update variant genes and compounds that avoids saving temporary decorators into variants' database documents
• [x] Link to HGNC gene report on gene page
• [x] Case file load priority so that e.g. SNV get loaded before SV, or clinical before research, for consistent variant_id collisions

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:

• [x] code approved by
• [x] tests executed by

[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

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.42%. Comparing base (c3483cc) to head (4e3fbc8).

Files	Patch %	Lines
scout/__version__.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4687 +/- ## ======================================= Coverage 84.42% 84.42% ======================================= Files 311 311 Lines 18756 18756 ======================================= Hits 15835 15835 Misses 2921 2921 ```

:umbrella: View full report in Codecov by Sentry.
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[dnil]

Clearer loqusdb flash: No warning if chanjo is not configured:

Matching collapse arrow causality swapped:

[dnil]

Tested the HGNC gene class change by reloading databases and clicking around for a bit, as per the original PR. Updates were successful:

[dnil]

✅ Deployed to hasta prod:

✅ Updating dbs:

✅ Deployed to cg-services-prod: