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Getting started

Add click2cwl dependency and terradue channel in your environment.yml file, e.g.:

name: my_env
channels:
  - terradue
  - conda-forge
dependencies:
  - python
  - click2cwl

Usage

First import the click2cwl dump function with:

from click2cwl import dump

Then, in the Python application entry point function, update and enrich the Click function decorator with the information for generating the CWL document.

The information defined at the Click function decorator is explained below:

@click.command

The @click.command decorator must:

  • set the allow_extra_args flag to True. This allows using the command line interface to pass the runtime information to generate the CWL.
  • set the short_help to define the CWL Workflow class label
  • set the help to define the CWL Workflow class doc
@click.command(
    short_help="This is Workflow class label",
    help="This is Workflow class doc",
    context_settings=dict(
        ignore_unknown_options=True,
        allow_extra_args=True,
    ),
)

@click.option

The @click.option decorator must:

  • define the option type that can be click.Path for a Directory, a click.File for a File or the default, a String to map as string
  • set the help to define the CWL Workflow class doc and label
  • set the required flag to False if the parameter is optional
@click.option(
    "--input_path",
    "-i",
    "input_path",
    type=click.Path(),
    help="this input path",
    multiple=False,
    required=True,
)

Finally, invoke the dump function in your Click decorated function with:

@click.command ...
@click.option ...
@click.pass_context
def main(ctx, **kwargs):

    dump(ctx)

    print("business as usual")
    print(kwargs)

if __name__ == '__main__':
    main()

Note: See the examples folder to discover typical use cases.

Install your application with:

python setup.py install

When the app help is invoked, it will only show the arguments defined by the click.decorators: 

myapp --help

but it now supports additional args to drive the generation of the CWL document and associated parameters:

The additional args are:

  • --dump cwl|params|clt. Example --dump cwl --dump params will dump the CWL document and the CWL parameters template in YAML. clt will dump the CWl CommandLineTool class only (no Workflow)
  • --requirement with requirement=value where requirement here is one of "coresMin", "coresMax", "ramMin", "ramMax". Example: --requirement ramMax=1 --requirement ramMin=2
  • --docker <docker image> if set, the DockerRequirement hint is set to pull the <docker image>
  • --env sets environment variables in the CWL with env_var=env_var_value. Example --env A=1 --env B=2 where A and B are the environment variables to set in the CWL EnvVarRequirement requirement