Fix setup database command

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Fix #4802

After the fix:

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 DN
• [x] tests executed by CR

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.21%. Comparing base (80df00a) to head (e44c44b). Report is 1 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4806 +/- ## ======================================= Coverage 84.21% 84.21% ======================================= Files 318 318 Lines 19178 19179 +1 ======================================= + Hits 16151 16152 +1 Misses 3027 3027 ```

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[northwestwitch]

This should fix the issue at hand. Are there other downstream problems from the same issue to consider? I noted a few other direct geneish["ensembl_id"] uses, but have not looked carefully at them!

I'll check if they are an issue

[northwestwitch]

I found just another situation in the code which might pose a risk --> https://github.com/Clinical-Genomics/scout/blob/80df00ac3e1dd93d462cfecca697aeea1dc7661f/scout/build/variant/gene.py#L57

Fixed in this PR!

[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