Version 4.89

[dnil]

This PR marks a new Scout release. We apply semantic versioning. This is a minor release since it adds new features in a backwards compatible manner.

[4.89]

Added

• [x] Button on SMN CN page to search variants within SMN1 and SMN2 genes
• [x] Options for selectively updating OMICS variants (fraser, outrider) on a case
• [x] Log users' activity to file by specifying USERS_ACTIVITY_LOG_PATH parameter in app config
• [x] Mean MT coverage, Mean chrom 14 coverage and Estimated mtDNA copy number on MT coverage file from chanjo2 if available
• [x] Subject id search from caseS page (supporting multiple sample types e.g.) - adding indexes to speed up caseS queries
• [x] Advanced cases search to narrow down results using more than one search parameter
• [x] Coverage report available for any case with samples containing d4 files, even if case has no associated gene panels
• [x] RNA delivery reports

  Changed

• [x] Documentation for OMICS variants and updating a case
• [x] Include both creation and deletion dates in gene panels pages
• [x] Moved code to collect MT copy number stats for the MT report to the chanjo extension
• [x] On the gene panelS page, show expanded gene panel version list in one column only
• [x] IGV.js WTS loci default to zoom to a region around a variant instead of whole gene
• [x] Refactored logging module
• [x] Case general report no longer shows ORPHA inheritance models. OMIM models are shown colored.
• [x] Chromosome alias tab files used in the igv.js browser, which now contain the alias for chromosome "M" - Tested by collaborators
• [x] Enable Gens CN button also for non-wgs cancer track cases

  Fixed

• [x] Broken heading anchors in the documentation (admin-guide/login-system.md and admin-guide/setup-scout.md files)
• [x] Avoid open login redirect attacks by always redirecting to cases page upon user login
• [x] Stricter check of ID of gene panels to prevent file downloading vulnerability
• [x] Removed link to the retired SPANR service. SPIDEX scores are still parsed and displayed if available from variant annotation.
• [x] Omics variant view test coverage
• [x] String pattern escape warnings
• [x] Code creating Alamut links for variant genes without canonical_transcript set
• [x] Variant delete button in ClinVar submissions page
• [x] Broken search cases by case similarity

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 CR
• [ ] tests executed by DN, CR

[codecov[bot]]

Codecov Report

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

Project coverage is 84.80%. Comparing base (69b622d) to head (37e880d). Report is 1 commits behind head on main.

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4867 +/- ## ======================================= Coverage 84.80% 84.80% ======================================= Files 319 319 Lines 19314 19314 ======================================= Hits 16379 16379 Misses 2935 2935 ```

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[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

[northwestwitch]

Users monitoring is working fine:

We should actually change the settings of scout demo after the testing so it will stop writing on /tmp/tmp_scout_users_activity.log

[northwestwitch]

The alamut link fix also works. Checked using this case

[dnil]

Right, and the log file is disabled by default, and a servers issue for enabling, so we should be all good with this release.

I guess we will ideally want to start the log anyway during deploy to get a feel for how it's working? Do you have a PR on servers already perhaps, since you had the stage one? 😸 Otw no biggie, we can start it whenever later.

[northwestwitch]

Do you have a PR on servers already perhaps, since you had the stage one? 😸 Otw no biggie, we can start it whenever later.

Yes. I closed it. We can reuse that one I guess ---> https://github.com/Clinical-Genomics/servers/pull/1448