galaxyproject / galaxyproject/galaxy
Assertion checking in workflows
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- Dominant language
- Python
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Description
I would like to have the ability to do assertion checking in workflows, and if the assertion fails, stop the workflow. A couple of assert examples that would have helped me:
- I want to check that the values in a particular column are unique. If they aren't stop the workflow.
- Check that a dataset is not empty. If it isn't, stop the workflow.
One of those tests looks at values in the dataset. Another looks at the dataset as a whole. Not sure how best to implement assertions, how complex they can get, and what sorts of things can they test.
It would be nice to have the assertion display user-provided text if an error occurs.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files, tests, or entry points are named. First clarify the assertion model and workflow integration, including dataset-wide and column-level checks and user-provided failure text; done means failed assertions reliably stop workflows and display the requested message.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend, data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100