Upload raw data in main upload command

[mogmi]

Description

Closes #4830

Enables raw data cases to be uploaded via the standard cg upload <case_id> command by introducing RawDataUploadAPI.

TODO:

• test in stage

Added

• RawDataUploadAPI — new upload API class following the same pattern as other workflow upload APIs
• deliver_raw_data module (cg/services/deliver_files/deliver_raw_data.py) — shared deliver_analyses function that delivers files and updates upload_started_at in StatusDB

Fixed

• cg upload <case_id> — now routes RAW_DATA workflow cases through RawDataUploadAPI instead of falling through unhandled

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 upload-raw-data-as-others -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 ...

[mogmi]

Started testing in stage and saw that exceptions are handled in a confusing manner, added a TODO for this

[sonarqubecloud]

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 SonarQube Cloud