Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Raredisease configurator - Create services for file creation #4260

Merged
merged 44 commits into from
Mar 10, 2025
Merged

Raredisease configurator - Create services for file creation #4260

merged 44 commits into from
Mar 10, 2025

Conversation

diitaz93
Copy link
Contributor

@diitaz93 diitaz93 commented Mar 3, 2025 •
edited
Loading

Description

Alternate version of #4255

Need to solve: The Nextflow configurators need to create the following files:

  1. Sample sheet
  2. Config file
  3. Params file

Some pipelines need to create more files.

The process of file creation follows a common structure:

  1. Define a Path
  2. Create content
  3. Write content to a file in the path

The content creation is specific for each pipeline and for each file type.

The file creation process was defined in the 3 steps mentioned above. In its abstract form, content creation (step 2) requires a class called FileContentCreator, which is implemented for every pipeline and file type.

Added

Changed

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 [THIS-BRANCH-NAME] -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 diitaz93 mentioned this pull request Mar 3, 2025
Draft
15 tasks
islean
islean reviewed Mar 5, 2025
View reviewed changes
Copy link
Contributor

@islean islean left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I will continue looking after lunch!

islean
islean approved these changes Mar 7, 2025
View reviewed changes
Copy link
Contributor

@islean islean left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Super nice works with the tests!

@sonarqubecloud SonarQubeCloud
Copy link

Quality Gate Passed 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 islean merged commit a78b608 into dev-start-pipelines Mar 10, 2025
8 checks passed
@islean islean deleted the config-separate-services branch March 10, 2025 12:04
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ChrOertlin ChrOertlin ChrOertlin left review comments

@islean islean islean approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@diitaz93 @ChrOertlin @islean