Version 4.111.0 release candidate

[dnil]

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

[4.111.0]

Added

• Custom MT Saltshaker HTML report loading (Fix #6241 - add Saltshaker html case report #6242)
• Command to download all PanelApp panels to file (Download command to pre-download all PanelApp panels to file #6239)
• Alternatively load and update PANELAPP-GREEN panel from a pre-downloaded file (Parse panelapp green panel from pre-downloaded file #6244)
• Command to remove loaded rank models (Fix #6154 - add CLI command to delete rank model from db #6262)

Changed

• Default gnomAD linkout for hg38 to non_uk_biobank subset (Fix #6243 - hg38 variants default gnomAD link to non-UK-biobank #6250)
• Handle conflicts and duplicates when uploading managed variants (Fix duplicated managed variants from same causatives #6256, Fix merging managed variants on None institute #6258, Small fix on managed variant upsert #6259)
• On caseS page, dynamically hide empty categories of cases (Hide empty categories of cases on caseS page #6260)
• scout download everything command downloads Ensembl data last, so that if the Ensembl download fails, it does not prevent the other files from being downloaded (Dowload Ensembl data last when running "scout downloading everything" #6269)

Fixed

• Saltshaker report update command (Fix missing commits on Saltshaker report #6246)
• Managed variants counter, wrongly defaulting to build 37 (Fix managed variants counter #6252)
• Managed variants matching follows build on case page (Build sens match managed #6254)
• Updated docs on load case images (Fix #6266 - Update docs on case config custom images #6267)
• Blog posts for 4.111 and 4.110 releases, removed obsolete expected_coverage key from documentation (Old expected_coverage option removed from docs, blog post, some layout and typos #6270)

Testing on cg-vm1 server (Clinical Genomics Stockholm)

Prepare for testing

1. Make sure the PR is pushed and available on Docker Hub
2. First 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@<name_of_currently_deployed_branch>
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
• tests executed by

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.88%. Comparing base (90e564f) to head (91e95d2).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #6264   +/-   ##
=======================================
  Coverage   83.88%   83.88%           
=======================================
  Files         346      346           
  Lines       21539    21539           
=======================================
  Hits        18067    18067           
  Misses       3472     3472           

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[northwestwitch]

PanelApp download OK:

[northwestwitch]

Updating PanelApp panel from pre-downloaded file is also OK:

[dnil]

Scout 38 instance rank models:

✅ Delete one:

✅ Reloaded when visiting a variant that demands it:

[dnil]

✅ Saltshaker loading

And fwiw also the image:

[dnil]

Note that deployment to hasta now needs an initial, one-off init for blue-green deployment, per https://github.com/Clinical-Genomics/servers/pull/1855.

✅ Done and working well on stage, but should be applied for

• prod as well when there is a short deployment window.

[northwestwitch]

Nice! 👍

[northwestwitch]

Update of database

Tested on stage (37)

Download all files

Done with difficulty given that Ensembl data downloaded apart using a branch of Schug which takes care of the many errors occurring on the Ensembl server . Files saved under /home/proj/development/rare-disease/scout/scout_update_260507

Update HPO terms

scout update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt

Updating diseases

scout update diseases -f .

Updating genes

scout update genes -f .

Update the OMIM AUTO panel

scout update omim --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt

Update the PanelApp green genes panel

scout update panelapp-green -i cust002 --downloads_folder . --force

[sonarqubecloud]

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 SonarQube Cloud