Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix #4624 - show ExHu STR sizes again #4625

Merged
merged 1 commit into from
May 15, 2024
Merged

Fix #4624 - show ExHu STR sizes again #4625

merged 1 commit into from
May 15, 2024

Conversation

dnil
Copy link
Collaborator

@dnil dnil commented May 15, 2024

This PR adds a functionality or fixes a bug.

I was so sure I tested that? Sorry! 😊

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
  • tests executed by

Copy link

sonarcloud bot commented May 15, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

@dnil
Copy link
Collaborator Author

dnil commented May 15, 2024

Before (see issue)
After:
Screenshot 2024-05-15 at 14 49 36

Copy link
Member

@northwestwitch northwestwitch left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice fix! 💯

@@ -6,7 +6,8 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)

## [Unreleased]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Perhaps make it a patch release so we install it right away?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ah no, there is also the other PR merged. We can create a patch branch in another PR, never mind

@dnil dnil marked this pull request as ready for review May 15, 2024 13:00
@dnil
Copy link
Collaborator Author

dnil commented May 15, 2024

Looks ok on stage, both with old ExHu cases and an LRS TRGT case:
Screenshot 2024-05-15 at 15 02 54
Screenshot 2024-05-15 at 15 02 03

Copy link

codecov bot commented May 15, 2024

Codecov Report

Attention: Patch coverage is 50.00000% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 84.52%. Comparing base (3d50453) to head (61917b1).

Files Patch % Lines
scout/server/blueprints/variants/controllers.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##             main    #4625   +/-   ##
=======================================
  Coverage   84.52%   84.52%           
=======================================
  Files         310      310           
  Lines       18747    18747           
=======================================
  Hits        15845    15845           
  Misses       2902     2902           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@dnil dnil merged commit f57bd7d into main May 15, 2024
21 checks passed
@dnil dnil deleted the fix_mc_alt_exhu_cases branch May 15, 2024 13:09
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants