Fix #4862 - ORPHA inheritance patterns hidden

[dnil]

This PR adds a functionality or fixes a bug.

Hide ORPHA inheritance patterns on general report, as they can be misleading. Compare note on variant view. Also added colored badges for the OMIM inheritance models for consistency with the variant page.

Before:

After:

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

[dnil]

Tested on stage. I was kind of expecting to have to split the general css into a colors part and a more formatting oriented one and only have the colors go to the report, but looks like it works, doesn't it? See if you see anything, and I'll give it another go as well with more rested eyes later.

[codecov[bot]]

Codecov Report

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

Project coverage is 84.78%. Comparing base (c48d621) to head (ae1a94f).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4863 +/- ## ======================================= Coverage 84.78% 84.78% ======================================= Files 319 319 Lines 19289 19290 +1 ======================================= + Hits 16354 16355 +1 Misses 2935 2935 ```

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[northwestwitch]

Good that it's a thing that can be fixed without modifying the disease terms code by the way! 😆

[dnil]

This changes the code so it will show inheritance only for OMIM terms.

But check for instance at this variant --> https://scout-stage.scilifelab.se/cust002/17083/161ee740fbbc95136ea4c0ff8cc3a916

I think it is safe enough to show that also the ORPHA inhteritance is AR. We could modify both variant page and the report so that whenever OMIM and ORPHA inheritance matches then it's shown in the ORPHA as well, and then we can show other models that appear on ORPHA but not on OMIM apart. Something like this:

OMIM: AR

ORPHA: AR (AD, XR..)

I considered something like that, but rejected it since I would have to explain that the OMIM data is used to select which of the ORPHA models are not in parenthesis. I do not like this unclear path of information.

I rejected the idea to show them if identical, since it might lead to confusion as to why ORPHA models are missing for other disorders

I also rejected the option to show the ORPHA model if there are no OMIM disorders for the gene, as it is not really clear to me from ORPHA that they then really say the inheritance pattern is for that gene. Not only that cases with that disorder have been seen with that gene, plus another which has this shown inheritance model.

[dnil]

Right, it's a bit of a corollary to https://github.com/Clinical-Genomics/scout/pull/4443. I didn't quite think about the non-specialists reading the report then and was happy with the OMIM and ORPHA being on different lines. Updating the tooltip is a nice suggestion - will do! The reports occasionally live their life on paper, so tooltips there are not always read.

[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