cwl_utils.cite_extract

Functions

arg_parser()

Construct the argument parser.

run(args)

Extract the software requirements.

main()

Console entry point.

extract_software_reqs(process)

Return an iterator over any SoftwareRequirements found in the given process.

process_software_requirement(req)

Pretty print the software package information.

traverse(process)

Extract the software packages for this process, and any steps.

get_process_from_step(step)

Return the process for this step, loading it if needed.

traverse_workflow(workflow)

Iterate over the given workflow, extracting the software packages.

Module Contents

cwl_utils.cite_extract.arg_parser()

Construct the argument parser.

Return type:

argparse.ArgumentParser

cwl_utils.cite_extract.run(args)

Extract the software requirements.

Parameters:

args (argparse.Namespace) –

Return type:

int

cwl_utils.cite_extract.main()

Console entry point.

Return type:

int

cwl_utils.cite_extract.extract_software_reqs(process)

Return an iterator over any SoftwareRequirements found in the given process.

Parameters:

process (cwl_utils.parser.Process) –

Return type:

Iterator[cwl_utils.parser.SoftwareRequirement]

cwl_utils.cite_extract.process_software_requirement(req)

Pretty print the software package information.

Parameters:

req (cwl_utils.parser.SoftwareRequirement) –

Return type:

None

cwl_utils.cite_extract.traverse(process)

Extract the software packages for this process, and any steps.

Parameters:

process (cwl_utils.parser.Process) –

Return type:

Iterator[cwl_utils.parser.SoftwareRequirement]

cwl_utils.cite_extract.get_process_from_step(step)

Return the process for this step, loading it if needed.

Parameters:

step (cwl_utils.parser.WorkflowStep) –

Return type:

cwl_utils.parser.Process

cwl_utils.cite_extract.traverse_workflow(workflow)

Iterate over the given workflow, extracting the software packages.

Parameters:

workflow (cwl_utils.parser.Workflow) –

Return type:

Iterator[cwl_utils.parser.SoftwareRequirement]