Load/parse cwl in python

Question

[johnegarza]

Hello,

I have been working with cwl a lot recently, and found myself needing to parse cwl documents within python for various tasks. Is there an existing simple library or tool to load cwl into a format that can be easily manipulated within python (ideally a dictionary or dictionary-like structure), rather than writing code to parse it myself each time? I'm generally only working with one file at a time, just trying to grab a list of inputs, outputs + metadata, etc. I know there are implementations like cwltool in python, but these are large and complicated, and lacking in documentation for tasks as simple as mine.

Answer 1

[bogdan.gavrilovic]

You can use pyyaml.
Install with pip install pyyaml

Load a CWL (which can be in JSON or YAML format) using

with open(cwl_file_path, 'r') as cwl_file:  
    cwl_dict = yaml.safe_load(cwl_file)

This will return a python dict with all the fields.

Answer 2

[Michael R. Crusoe]

There's a new Python 3.6/3.7 method of accessing CWL documents, but you get full objects (with doc strings copied from the spec), not dictionaries: https://github.com/common-workflow-language/cwl-utils