Version 4.87 - configure RNA build, add igv.js genome aliases

dnil commented 2 months ago

This PR marks a new Scout release. We apply semantic versioning. This is a minor release for reasons.

[4.87]

Added

[x] Option to configure RNA build on case load (default '38')
Changed
[x] Tooltip on RNA alignments now shows RNA genome build version
[x] Updated igv.js to v3.0.4
Fixed
[x] Style of "SNVs" and "SVs" buttons on WTS Outliers page
[x] Chromosome alias files for igv.js
[x] Genes track displayed also when RNA alignments are present without splice junctions track on igv browser
[x] Genes track displayed again when splice junction tracks are present

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 CR
[x] tests executed by DN, CR

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.21%. Comparing base (feb27f5) to head (1d6212d). Report is 1 commits behind head on main.

Files	Patch %	Lines
scout/__version__.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4785 +/- ## ======================================= Coverage 84.21% 84.21% ======================================= Files 318 318 Lines 19178 19178 ======================================= Hits 16151 16151 Misses 3027 3027 ```

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northwestwitch commented 2 months ago

Ok. I've deployed the latest on stage now

northwestwitch commented 2 months ago

Alignment of buttons in the omics variants can be tested here --> https://scout-stage.scilifelab.se/cust002/F0044127/omics_variants/outliers

northwestwitch commented 2 months ago

Do we have an example of a case with TOMTE analysis in build hg19 to load to stage @dnil ?

dnil commented 2 months ago

Lets see, I did manually load one such case (onekoala + dashingdinosaur) - I can dig it up !

northwestwitch commented 2 months ago

Lets see, I did manually load one such case (onekoala + dashingdinosaur) - I can dig it up !

Ok, so it's tested then?

dnil commented 2 months ago

In a way, but let's do it with the release candidate as well. I've set it to test on hasta stage now: Screenshot 2024-08-27 at 14 05 53 Screenshot 2024-08-27 at 14 14 04