galaxyproject / galaxyproject/planemo

planemo test incorrectly passes dataset information instead of text (to text param) when filename matches configured Text value

Open
#1,105 0 comments 0 reactions 0 assignees View on GitHub
bug
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

Open the contributing 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

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