Fix #4902 - use unambiguos alias if no true hgnc id is known

[dnil]

This PR adds a functionality or fixes a bug.

• Fix OMIM gene missing HGNC id? #4902

Nice with #4903 - thank you, and sorry I didn't see it in time. I think this is a safer solution. Compare how the same data structure is handled in other places e.g. here

scout/scout/adapter/mongo/hgnc.py

Line 436 in 07ad1e2

if not id_info["true"]:

.

We could and should probably refactor it though - seems overly complex, and the generating code is a bit dusty - but if its ok with you I'd prefer not to mess with it since it when it is in use in other places?

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 CR
• tests executed by DN, CR

[dnil]

Did we get the same gene count? 😊

[codecov]

Codecov Report

Attention: Patch coverage is 55.55556% with 4 lines in your changes missing coverage. Please review.

Project coverage is 84.78%. Comparing base (07ad1e2) to head (31a3c0a).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
scout/parse/panel.py	55.55%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4904      +/-   ##
==========================================
- Coverage   84.80%   84.78%   -0.02%     
==========================================
  Files         319      319              
  Lines       19314    19319       +5     
==========================================
+ Hits        16379    16380       +1     
- Misses       2935     2939       +4     

☔ View full report in Codecov by Sentry.
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[northwestwitch]

Looks good! 👍🏻

[northwestwitch]

Did we get the same gene count? 😊

No, I got one more

[sonarcloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[dnil]

Did we get the same gene count? 😊

No, I got one more

Right, but that was from when I updated only the panel, and you had both new genes and panel, right! Or did I miss something? After updating genes I got that dubious ATXN8 gene in, so we both ended up with 4630. Importantly the patch seems to fix the issue with POPDC1 cleanly, and be safe enough by explicitly checking for aliases.