Fix RNA uploads/delivery message

[islean]

Description

Closes #4115. The main change is that we filter on the RNA case's collaborators, rather than its samples' but it also merges the logic in the upload flow and the delivery message flow, where different parts of the code was used to link the RNA case to its DNA cases.

Added

Changed

• The RNA uploads to Scout use the query logic found in the ReadHandler
• More robust error raising in the ReadHandler for when there are multiple matching DNA samples or when no subject id is passed.

Fixed

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b fix-rna-uploads -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[Vince-janv]

Oof. At least the we use the same logic now 😅 Well done

[diitaz93]

looks good 👍

[islean]

Upload linking works ✅

[isak.ohlsson@hasta:2025-01-29] [S_base] $ cg upload rna-junctions-to-scout --dry-run sharpbulldog
----------------- UPLOAD -----------------
----------------- UPLOAD RNA JUNCTIONS TO SCOUT -----------------------
Uploading splice junctions bed file for sample ACC5701A14DS800C0M in case alerthawk in Scout.
Uploaded splice junctions bed file for sample ACC5701A14DS800C0M in case alerthawk.
Upload splice junctions bed file finished!
Uploading RNA coverage bigwig file for sample ACC5701A14DS800C0M in case alerthawk in Scout.
Uploaded bigwig coverage file for sample ACC5701A14DS800C0M in case alerthawk.
Upload RNA coverage bigwig file finished!
[isak.ohlsson@hasta:2025-01-29] [S_base] $

[sonarqubecloud]

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 SonarQube Cloud

[islean]

Deployed to Hasta:

Log deploy... done.
cg, version 67.0.15
...
Your branch is behind 'origin/master' by 2 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)
Updating aabb8f7..e0648ab
Fast-forward
 .bumpversion.cfg                                         |   2 +-
 cg/__init__.py                                           |   2 +-
 cg/meta/upload/scout/uploadscoutapi.py                   |  99 ++++++++++++++++++++-------------------------------------------------------------------
 cg/store/api/data_classes.py                             |  11 ++++++++++
 cg/store/crud/read.py                                    | 158 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++----------------------------------------------
 pyproject.toml                                           |   2 +-
 tests/meta/upload/scout/test_meta_upload_scoutapi_rna.py |  52 +++++++++++++++++++++-------------------------
 tests/store/crud/conftest.py                             |  36 +-------------------------------
 tests/store/crud/read/test_read_sample.py                |  65 ---------------------------------------------------------
 9 files changed, 167 insertions(+), 260 deletions(-)
 create mode 100644 cg/store/api/data_classes.py
/home/isak.ohlsson
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.

[islean]

Deployed to the VMs