Unit-test for this edge-case

[hvwaldow]

No description provided.

[JensKrumsieck]

When i understood right the "edge case" was the usage of $(runtime.outdir)? This definitivly would not be something the user needs to type and basically is just an alias for "give me the full working dir as output" or the glob of ..
Added postprocessing to convert "." to the desired magic string.
s4n tool create -o . python create_dir.py creates the following cwl now:

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

requirements:
- class: InitialWorkDirRequirement
  listing:
  - entryname: create_dir.py
    entry:
      $include: ../../create_dir.py

inputs: []
outputs:
- id: output_directory
  type: Directory
  outputBinding:
    glob: $(runtime.outdir)

baseCommand:
- python
- create_dir.py

integration test:

m4.4_sciwin_client/tests/tool_integration_test.rs

Lines 406 to 439 in 40e69c7

	pub fn test_tool_output_complete_dir() {
	let dir = tempdir().unwrap();
	copy_file("tests/test_data/create_dir.py", dir.path().join("create_dir.py").to_str().unwrap()).unwrap();
	let current = env::current_dir().unwrap();
	env::set_current_dir(dir.path()).unwrap();
	init_s4n(None, false).expect("Could not init s4n");
	let name = "create_dir";
	let command = &["python", "create_dir.py"];
	let args = CreateToolArgs {
	name: None,
	container_image: None,
	container_tag: None,
	is_raw: false,
	no_commit: false,
	no_run: false,
	is_clean: false,
	inputs: None,
	outputs: Some(vec![".".into()]), //
	command: command.iter().map(|s| s.to_string()).collect::<Vec<_>>(),
	};
	assert!(create_tool(&args).is_ok());
	let tool = load_tool(format!("workflows/{name}/{name}.cwl")).unwrap();
	assert_eq!(tool.inputs.len(), 0);
	assert_eq!(tool.outputs.len(), 1); //only root folder
	println!("{:#?}", tool.outputs);
	env::set_current_dir(current).unwrap();
	}

This should be a good test to mimic the creation of a cwl file such as https://github.com/fairagro/M4.4_UC6_ARC/blob/main/workflows/simulation/simulation.cwl