Sanger feedback

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Fix Sanger email feedback #4277. Create a way for Sanger recipients to alert other users (those who ordered the verification) that the variant was positively verified

On case page:

---

On caseS page:

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. Deploy on cg-vm1
2. With you user, order sanger sequencing for a variant (your user should be in the list of sanger recipients
3. Go on the case page and mark the variant as verified true positive, note the new modal that allows you to notify the user (yourself in this case) that the variant is a true positive
4. Go to caseS page and note that you have a new blue alert relative to this event
5. Dismiss the alert by clicking on the "x" and make sure it goes away.

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

Review:

• code approved by
• tests executed by CR

[northwestwitch]

Pre-existing code

[northwestwitch]

New code

[codecov]

Codecov Report

Attention: Patch coverage is 89.65517% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 84.74%. Comparing base (948cb0f) to head (987ad80).

Files	Patch %	Lines
scout/server/blueprints/cases/views.py	60.00%	2 Missing ⚠️
scout/adapter/mongo/user.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4345      +/-   ##
==========================================
+ Coverage   84.71%   84.74%   +0.03%     
==========================================
  Files         310      310              
  Lines       18522    18550      +28     
==========================================
+ Hits        15690    15721      +31     
+ Misses       2832     2829       -3     

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[northwestwitch]

I haven't touched this PR in a while because I'd like to simplify it a bit. I'll give it a shot today!

[sonarcloud]

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

[northwestwitch]

Closing this as I've opened a simpler one (#4489)