Minor release 4.83 - Githubissues

northwestwitch commented 3 weeks ago

[4.83]

Added

[x] Edit ACMG classifications from variant page (only for classifications with criteria)
[x] Events for case CLI events (load case, update case, update individual)
[x] Support for loading and displaying local custom IGV tracks
[x] MANE IGV track to be used as a local track for igv.js (see scout demo config file)
[x] Optional separate MT VCFs, for nf-core/raredisease
Changed
[x] Avoid passing verbs from CaseHandler - functions for case sample and individual in CaseEventHandler
[x] Hide mtDNA report and coverage report links on case sidebar for cases with WTS data only
[x] Modified OMIM-AUTO gene panel to include genes in both genome builds
[x] Moved chanjo code into a dedicated extension
[x] Optimise the function that collects "match-safe" genes for an institute by avoiding duplicated genes from different panels
[x] Users must actively select "show matching causatives/managed" on a case page to see matching numbers
[x] Upgraded python version from 3.8 to 3.11 in Docker images
Fixed
[x] Fix several tests that relied on number of events after setup to be 0
[x] Removed unused load case function
[x] Artwork logo sync sketch with png and export svg
[x] Clearer exception handling on chanjo-report setup - fail early and visibly
[x] mtDNA report crashing when one or more samples from a case is not in the chanjo database
[x] Case page crashing on missing phenotype terms
[x] ACMG benign modifiers
[x] Speed up tests by caching python env correctly in Github action and adding two more test groups
[x] Agile issue templates were added globally to the CG-org. Adding custom issue templates to avoid exposing customers
[x] PanelApp panel not saving genes with empty EnsembleGeneIds list
[x] Speed up checking outdated gene panels
[x] Do not load research variants automatically when loading a case

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 DN, CR

codecov[bot] commented 3 weeks ago

Codecov Report

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

Project coverage is 84.49%. Comparing base (86497f3) to head (2e7818d).

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4667 +/- ## ======================================= Coverage 84.49% 84.49% ======================================= Files 310 310 Lines 18798 18798 ======================================= Hits 15884 15884 Misses 2914 2914 ```

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northwestwitch commented 3 weeks ago

Tested updating the OMIM panel: 🆗

Mmm the force update option updates the panel but not the date. This happens because I'm still using the panel files from last time I guess. But still..

northwestwitch commented 3 weeks ago

Tested updating PanelApp green gene panel: 🆗

northwestwitch commented 3 weeks ago

Re-uploaded strongbison, used for testing cli case events and that no research variants were loaded

northwestwitch commented 3 weeks ago

Mane local track can be tested with this variant

Then moving around in the genome: 🆗

dnil commented 3 weeks ago

Benign strength modifiers no longer contribute to the pathogenic side: Screenshot 2024-06-10 at 14 31 44

dnil commented 3 weeks ago

But this is perhaps not super elegant: Screenshot 2024-06-10 at 14 31 09

dnil commented 3 weeks ago

Mmm the force update option updates the panel but not the date. This happens because I'm still using the panel files from last time I guess. But still..

If I recall correctly, that was a somewhat intended or at least accepted feature, but yes, it is not obvious. Perhaps make an issue anyway?

northwestwitch commented 3 weeks ago

If I recall correctly, that was a somewhat intended or at least accepted feature, but yes, it is not obvious. Perhaps make an issue anyway?

Yes I think I will, because when you have the same date and 2 different panels in terms of content it can be confusing

dnil commented 3 weeks ago

Load split out MT VCFs Screenshot 2024-06-10 at 15 07 01 ... 99 MT vars show inserted BUT no MT vars appear when filtering?! Screenshot 2024-06-10 at 15 13 00 Chromosome naming, ranking or load error?