Re-style case HPO terms to have one phenotype per line

northwestwitch commented 2 months ago

This PR adds a functionality or fixes a bug.

Fix #4765

Main branch:

This branch:

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:

[x] code approved by DN
[x] tests executed by CR

codecov[bot] commented 2 months ago

Codecov Report

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

Project coverage is 84.21%. Comparing base (4bfd103) to head (5c778ef). Report is 1 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4766 +/- ## ======================================= Coverage 84.21% 84.21% ======================================= Files 318 318 Lines 19157 19157 ======================================= Hits 16133 16133 Misses 3024 3024 ```

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dnil commented 2 months ago

Did you want to add the "select all", e.g. via the view using all terms if none is selected?

northwestwitch commented 2 months ago

Did you want to add the "select all", e.g. via the view using all terms if none is selected?

I didn't think about it, do you reckon it would be useful?

northwestwitch commented 2 months ago

Did you want to add the "select all", e.g. via the view using all terms if none is selected?

I mean, in terms of creating the HPO panel it is already like this, no?

dnil commented 2 months ago

Did you want to add the "select all", e.g. via the view using all terms if none is selected?

I mean, in terms of creating the HPO panel it is already like this, no?

No? It used to be that we deleted any previously created panel on blank submission, but we dropped that when we added the "remove" function for genes / select all genes.

northwestwitch commented 2 months ago

No? It used to be that we deleted any previously created panel on blank submission, but we dropped that when we added the "remove" function for genes / select all genes.

Ah Ok!

northwestwitch commented 2 months ago

Added the select:

dnil commented 2 months ago

Added the select:

Nice! There is something that bothers me with the text alignment here, especially when there is a lot of empty space. Perhaps moving the toggle down, like just above, or even left of the buttons might work? Or just align the text starts for the toggle and the checkboxes instead? Screenshot 2024-08-21 at 10 41 04