Version 4.89.1 - general case report patches

[dnil]

This PR marks a new Scout release. We apply semantic versioning. This is a patch release for reasons.

It fixes bugs with existing functionality, specifically in the general case report.

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 CR
• [x] tests executed by DN, CR

[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 84.80%. Comparing base (993e0c3) to head (2fb8779). Report is 1 commits behind head on main.

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4900 +/- ## ======================================= Coverage 84.80% 84.80% ======================================= Files 319 319 Lines 19314 19314 ======================================= Hits 16379 16379 Misses 2935 2935 ```

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[dnil]

Testing db update: scout download everything --api-key

scout update genes -f .

scout update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt

scout update diseases -f .

scout update omim --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt

scout update panelapp-green -i cust002 --force

[dnil]

Also did manage to accidentally update prod genes while testing PRs later. No uploads running, so all should be good, but documenting here so there is no confusion later:

There was an upload of Balsamic cases around that time, but as "tur i oturen" would have it we didn't see any errors from that case, quite possibly right in between two loads, or during an insensitive phase.

For an abundance of caution we reupload evolvedmonarch, which has a scout load config older, but case load time later than 16:11 when the genes updated. Thank you @Karl-Svard! 😊