SMN search buttons on SMN CN page

Jakob37 commented 3 weeks ago

This PR adds a functionality or fixes a bug.

Closes #4822

As recommended, I used the buttons on the transcript outliers page as a guide, replacing the HGNC IDs with "SMN1, SMN2".

In the demo instance, the search did not find the "SMN1" and "SMN2" IDs. It did work for a real case with a variant in SMN1 though when trying it out in our test environment. I guess not all HGNC IDs just aren't loaded in the demo.

A minor detail is the [''] appearing up to the right. This is the same for the transcript outliers page.

Any feedback is warmly welcome!

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:

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
[ ] tests executed by

codecov[bot] commented 3 weeks ago

Codecov Report

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

Project coverage is 84.17%. Comparing base (6d70817) to head (3e245ce). Report is 10 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4832 +/- ## ======================================= Coverage 84.16% 84.17% ======================================= Files 318 318 Lines 19202 19202 ======================================= + Hits 16162 16163 +1 + Misses 3040 3039 -1 ```

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dnil commented 3 weeks ago

Good point with the empty panels indicator. It is not super consistent. But when e.g. searching a case without a set of default panels it will go to "All" which kind of makes sense, but then not revert to none when searching only explicitly a few genes. That is not perfect, and has been the case for a long time. Let's make an issue for it and fix on a quality-of-life prio.

dnil commented 3 weeks ago

Feel very free to add the SMN genes to the demo gene set - might be a good exercise. But it is expected so not a problem really.

Jakob37 commented 3 weeks ago

Feel very free to add the SMN genes to the demo gene set - might be a good exercise. But it is expected so not a problem really.

I'll give it a go 👌

Jakob37 commented 3 weeks ago

OK, I have added the SMN gene to the resources. It was indeed an informative journey through the Scout resources. Now the demo instance does not complain neither about missing terms nor about not being present in panels.