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Fix #4442 - do not bring in ORPHA inheritance model to OMIM specific … #4443

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merged 18 commits into from
Feb 20, 2024
Merged

Fix #4442 - do not bring in ORPHA inheritance model to OMIM specific … #4443

merged 18 commits into from
Feb 20, 2024

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dnil
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@dnil dnil commented Feb 20, 2024 •
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…fields

This PR adds a functionality or fixes a bug.

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

@dnil dnil marked this pull request as draft February 20, 2024 06:59
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codecov bot commented Feb 20, 2024 •
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Codecov Report

Attention: 7 lines in your changes are missing coverage. Please review.

Comparison is base (371f8c1) 84.64% compared to head (1f79444) 84.64%.

Files Patch % Lines
scout/server/blueprints/variant/utils.py 80.55% 7 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #4443      +/-   ##
==========================================
- Coverage   84.64%   84.64%   -0.01%     
==========================================
  Files         310      310              
  Lines       18439    18448       +9     
==========================================
+ Hits        15608    15615       +7     
- Misses       2831     2833       +2

☔ View full report in Codecov by Sentry.
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@dnil dnil marked this pull request as ready for review February 20, 2024 07:18
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dnil commented Feb 20, 2024

✅ Test on stage

Before
Screenshot 2024-02-20 at 08 57 10

After
Screenshot 2024-02-20 at 09 24 59

northwestwitch
northwestwitch approved these changes Feb 20, 2024
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Great fix! 💯

scout/server/blueprints/variant/controllers.py Show resolved Hide resolved
scout/server/blueprints/variant/templates/variant/gene_disease_relations.html Outdated Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Outdated Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Outdated Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Outdated Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Outdated Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Show resolved Hide resolved
scout/server/blueprints/variant/utils.py Outdated Show resolved Hide resolved
dnil and others added 6 commits February 20, 2024 09:55
@dnil @northwestwitch
Update scout/server/blueprints/variant/utils.py
0ffc42a 
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
@dnil @northwestwitch
Update scout/server/blueprints/variant/utils.py
5eaba0a 
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
@dnil @northwestwitch
Update scout/server/blueprints/variant/utils.py
5c6fe81 
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
@dnil
Clarify tooltip - thanks!
a17ab87
@dnil @northwestwitch
Update scout/server/blueprints/variant/utils.py
e9bc2b6 
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
@dnil @northwestwitch
Update scout/server/blueprints/variant/utils.py
1f79444 
Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
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sonarcloud bot commented Feb 20, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues

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

See analysis details on SonarCloud

@dnil dnil merged commit 0fc1afc into main Feb 20, 2024
20 checks passed
@northwestwitch northwestwitch deleted the orpha_omim_inheritance_sep branch March 14, 2024 11:59
This was referenced Sep 18, 2024
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@northwestwitch northwestwitch northwestwitch approved these changes

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@dnil @northwestwitch