Rename camel case columns

[dnil]

This PR adds a functionality or fixes a bug.

Fix #4800 - rename DROP TSV columns according to current Tomte status

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
• [x] tests executed by DN

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 85.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 84.20%. Comparing base (a4f46b7) to head (175f5ea). Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
scout/models/omics_variant.py	84.21%	3 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4801 +/- ## ========================================== - Coverage 84.21% 84.20% -0.01% ========================================== Files 318 318 Lines 19179 19187 +8 ========================================== + Hits 16152 16157 +5 - Misses 3027 3030 +3 ```

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[dnil]

Some float values in fraser and outrider tsvs can apparently be empty str as well. Adding a conversion kindly provided from https://github.com/pydantic/pydantic/discussions/2687 to fix that!

[dnil]

[dnil]

I've run a scout setup demo and noticed these fields:

• [ ] Could we rename the geneID to ensembl_gene or something similar
• [ ] sampleID to sample_id
• [ ] meanCorrected to mean_corrected
• [ ] normcounts to norm_counts
• [ ] rawcounts to raw_counts

Nope, should have been done on https://github.com/Clinical-Genomics/scout/pull/4654. 😉 Jk, good call and in time before this went full production. Do we need to support some migration, or should we just mention that these will not work for cases already loaded? The so far only really used one is sampleID which is critical for individual matching, but is only used at load time so we can safely migrate it.

[northwestwitch]

The so far only really used one is sampleID which is critical for individual matching, but is only used at load time so we can safely migrate it.

Sorry I've just noticed. But since we are not in full production perhaps we can manually modify sample ids of the cases already loaded.. Shouldn't be so many

[dnil]

The so far only really used one is sampleID which is critical for individual matching, but is only used at load time so we can safely migrate it.

Sorry I've just noticed. But since we are not in full production perhaps we can manually modify sample ids of the cases already loaded.. Shouldn't be so many

Yes, I think it’s very well timed here - only test cases yet afaik. And it’s so new I doubt many others have implemented yet, but…

[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