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

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

Changed

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

Fixed

• Broken heading anchors in the documentation (admin-guide/login-system.md and admin-guide/setup-scout.md files)
• Avoid open login redirect attacks by always redirecting to cases page upon user login
• Stricter check of ID of gene panels to prevent file downloading vulnerability
• Removed link to the retired SPANR service. SPIDEX scores are still parsed and displayed if available from variant annotation.
• Omics variant view test coverage
• String pattern escape warnings
• Code creating Alamut links for variant genes without canonical_transcript set
• Variant delete button in ClinVar submissions page
• 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
2. Fist book your testing time using the Pax software available at https://pax.scilifelab.se/. The resource you are going to call dibs on is scout-stage and the server is cg-vm1.
3. ssh <USER.NAME>@cg-vm1.scilifelab.se
4. sudo -iu hiseq.clinical
5. ssh localhost
6. (optional) Find out which scout branch is currently deployed on cg-vm1: podman ps
7. Stop the service with current deployed branch: systemctl --user stop scout.target
8. Start the scout service with the branch to test: systemctl --user start scout@<this_branch>
9. Make sure the branch is deployed: systemctl --user status scout.target
10. After testing is done, repeat procedure at 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 <USER.NAME>@hasta.scilifelab.se
2. Book your testing time using the Pax software. us; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.
3. (optional) Find out which scout branch is currently deployed on cg-vm1: conda activate S_scout; pip freeze | grep scout-browser
4. Deploy the branch to test: bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>
5. Make sure the branch is deployed: us; scout --version
6. 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]

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 ⚠️

Additional details and impacted files

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

☔ View full report in Codecov by Sentry.
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[sonarcloud]

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

[northwestwitch]

I think we are good with this one! 👍🏻

[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