galaxyproject / galaxyproject/planemo

Understanding output of planemo workflow_lint

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Dominant language
Python
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110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
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Description

It seems that workflow linting currently always warns about at least one `output without a label` for any workflow generated through the GUI editor.
This is because from the GUI you can set a label for input datasets, but not for the contained "output" the properties of which are inaccessible via the GUI. To make that warning disappear you have to open a text editor and add a label in the workflow outputs section of the input dataset step like so:

```
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "my input"
}
],
"label": "my input as set in the GUI editor",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 227.3125,
"top": 469.5
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "c33af17b-8945-46f5-bdb2-10911d038db8",
"workflow_outputs": [
{
"label": "this output label can only be added through a text editor",
"output_name": "output",
"uuid": "b5f19eb0-775c-4a02-802a-ef715ce8fcc6"
}
]
```

I'm not sure what to think of this:
- why does an input dataset even define workflow outputs (when the dataset is not produced by the WF)? Is this for technical/formal reasons?
- is it a bug in the graphical editor that it does not let you set an important output label?
- or is it a bug in the workflow_lint subcommand that it warns about an unimportant technical detail?

Any guidance what's best practice here?

Contributor guide

Open the contributing guide

Research direction

Start with the planemo workflow_lint subcommand and the GUI-generated workflow example in the report. Determine whether the missing output label belongs in the graphical editor or whether lint should ignore it; done means the expected behavior is agreed and verified for generated workflows.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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