patch(PDC fetching) Except warnings from the dsmc command

[Vince-janv]

Description

The cg.utils.commands.Process.run_command raises an error on all exit codes except 0 (success). This causes problems in the PDC flow since the dsmc command regularly gives warnings, which result in exit code 8. These are non-fatal and should not abort the command.

This PR catches CalledProcessError exceptions checks the return code and does not raise an error if it is 8.

Changed

• Warning exit codes from the dsmc command no longer raise errors

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 fc-fetch-except-warnings

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

• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

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

[seallard]

Looks much cleaner and should handle the exit warnings 👍

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
1 Code Smell

No Coverage information
0.0% Duplication

[Vince-janv]

Retrieval and backup work on stage

[Vince-janv]

Deployed in production