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.

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

fix(study_locus_valiation): ensure the the transQtlColumn is missing #990

Merged
merged 1 commit into from
Feb 7, 2025

Conversation

project-defiant
Copy link
Contributor

@project-defiant project-defiant commented Feb 7, 2025


✨ Context

The dataproc job for study_locus_valiation step has failed due to the duplicated isTransQtl column.
This can happen when we read the dataset from the parquet file that will automatically align it to existing schema, resulting in the addition of the empty column, which will result in SchemaValidationError when validating the dataset before writing after joining it with the lookup index containing isTransQtl column.

🛠 What does this PR implement

  • Ensure the isTransQtl column is dropped (provided it exists) when running the method StudyLocus.flag_trans_qtls

🙈 Missing

🚦 Before submitting

  • Do these changes cover one single feature (one change at a time)?
  • Did you read the contributor guideline?
  • Did you make sure to update the documentation with your changes?
  • Did you make sure there is no commented out code in this PR?
  • Did you follow conventional commits standards in PR title and commit messages?
  • Did you make sure the branch is up-to-date with the dev branch?
  • Did you write any new necessary tests?
  • Did you make sure the changes pass local tests (make test)?
  • Did you make sure the changes pass pre-commit rules (e.g uv run pre-commit run --all-files)?

* build(deps): update scipy requirementV

---------

Co-authored-by: project-defiant <[email protected]>
@github-actions github-actions bot added bug Something isn't working size-S Dataset labels Feb 7, 2025
Copy link
Contributor

@vivienho vivienho left a comment

Choose a reason for hiding this comment

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

All makes sense!

@vivienho vivienho merged commit 30a6046 into dev Feb 7, 2025
7 checks passed
@vivienho vivienho deleted the szsz-fix-study-locus-validation branch February 7, 2025 12:48
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working Dataset size-S
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants