galaxyproject / galaxyproject/planemo
planemo test incorrectly passes dataset information instead of text (to text param) when filename matches configured Text value
- Dominant language
- Python
- Stars
- 110
- Forks
- 102
- Avg merge
- 4d 21h
- Merged PRs (30d)
- 13
Description
Issue found by @nvk747
This issue popped up when testing several tools at a time -- when the tests were run individually on the tools, they passed. I did not check to see if the issue can be replicated on a single tool (although it seems likely).
Tools being tested are from here: https://github.com/nvk747/papaa in galaxy directory
One tool test uploads files named 'GBM' and uses them. The next tool has a text parameter, with text set to 'GBM':
```
grep '
Contributor guide
Research direction
Start with the planemo test entry point and reproduce the order-dependent case using the Galaxy tools in the papaa repository, especially pancancer_classifier.xml and within_disease_analysis.xml. Compare runs where tools execute individually and together, and verify that a text parameter set to literal GBM is not replaced by dataset information.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, testing-qa
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100