Fix code smell by refactoring add_decompressed_fastq_files_to_housekeeper

[islean]

Description

In #2378 there was a code smell left that this PR handles. It reduces the complexity in add_decompressed_fastq_files_to_housekeeper.

Fixed

• add_decompressed_fastq_files_to_housekeeper is split into smaller methods.

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-code-smell -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 ...

[diitaz93]

This is beautiful 🌷 Maybe add some tests too 👀

[islean]

This is beautiful 🌷 Maybe add some tests too 👀

I definitely could but this is essentially some cutting and pasting work 😅 Does not seem to be any unit tests for this functionality previously though.

[diitaz93]

This is beautiful 🌷 Maybe add some tests too 👀

I definitely could but this is essentially some cutting and pasting work 😅 Does not seem to be any unit tests for this functionality previously though.

Yes, that is what I meant. I think we should try to add tests to functions we touch if they don't have any. But if you feel it is out of scope feel free to disregard

[islean]

@diitaz93 Added some tests now!

[diitaz93]

Good job with the tests 👍

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[islean]

Tests performed successfully:

[islean]

Deployed to production:

Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/isak.ohlsson
done.
Log deploy... done.
cg, version 51.10.4
1d [isak.ohlsson@hasta:~] [P_base] 1m13s $