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Chanjo2 report available for cases without gene panels #4890

Merged
merged 6 commits into from
Sep 25, 2024
Merged

Chanjo2 report available for cases without gene panels #4890

merged 6 commits into from
Sep 25, 2024

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northwestwitch
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@northwestwitch northwestwitch commented Sep 24, 2024 •
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This PR adds a functionality or fixes a bug.

  • Display coverage report in the side panel of any case with or without associated gene panels - at least one case sample should have a d4 file
  • This PR is used in a combo with this chanjo2 PR
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. Go to this case on scout stage
  2. Check its coverage report
  3. Try adding specific genes to the report, to see if it updates

Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.

Review:

  • code approved by DN
  • tests executed by CR

@northwestwitch northwestwitch marked this pull request as ready for review September 24, 2024 14:02
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codecov bot commented Sep 24, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.81%. Comparing base (8e284bc) to head (f138c5f).
Report is 1 commits behind head on main.

Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #4890   +/-   ##
=======================================
  Coverage   84.81%   84.81%           
=======================================
  Files         319      319           
  Lines       19308    19308           
=======================================
  Hits        16376    16376           
  Misses       2932     2932

☔ View full report in Codecov by Sentry.
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@northwestwitch northwestwitch mentioned this pull request Sep 24, 2024
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dnil
dnil approved these changes Sep 25, 2024
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Cancer cases nowadays should have panels? But really nice to see the coverage code out for d4tools!

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html
@@ -86,7 +86,7 @@
</div>

<!-- If connected to a chanjo or chanjo2 instance, display coverage report -->
{% if case.chanjo2_coverage and case.default_genes %}
{% if case.chanjo2_coverage %}
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🎉

@northwestwitch
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Cancer cases nowadays should have panels?

Ah OK, so perhaps I'll modify the changelog description

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sonarcloud bot commented Sep 25, 2024

Quality Gate Passed 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 northwestwitch merged commit 9170cb9 into main Sep 25, 2024
25 checks passed
dreamweaver-cell pushed a commit to gmc-norr/scout that referenced this pull request Oct 9, 2024
@northwestwitch
Chanjo2 report available for cases without gene panels (Clinical-Geno…
e04351e 
…mics#4890)

* Display chanjo2 coverage report for cases with no gene panels

* Fixed changelog

* fix changelog

* typo

* Modify changelog

---------

Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>
@northwestwitch northwestwitch deleted the chanjo2_report_no_panels branch October 10, 2024 14:32
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