cwl-utils

A collection of scripts to demonstrate the use of the new Python classes for loading and parsing CWL v1.0 , CWL v1.1, and CWL v1.2 documents.

Install

Requires Python 3.6+

virtualenv -p python3.6 venv3.6  # Python 3.7, 3.8, or 3.9 would also work
source venv3.6/bin/activate
pip install cwl-utils

or install the latest development version of cwl-utils

git clone https://github.com/common-workflow-language/cwl-utils.git
cd cwl-utils
virtualenv -p python3.6 venv3.6  # Python 3.7, 3.8, or 3.9 would also work
source venv3.6/bin/activate
pip install .

Usage

Pull the all referenced software container images

docker_extract.py is useful to cache or pre-pull all software container images referenced in a CWL CommandLineTool or CWL Workflow (including all referenced CommandLineTools and sub-Workflows and so on).

The default behaviour is to use the Docker engine to download and save the software container images in Docker format.

python docker_extract.py DIRECTORY path_to_my_workflow.cwl

Or you can use the Singularity software container engine to download and save the software container images and convert them to the Singularity format at the same time.

python docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl

Using the CWL Parsers

# Imports
from pathlib import Path
from ruamel import yaml
import sys

# File Input - This is the only thing you will need to adjust or take in as an input to your function:
cwl_file = Path("/path/to/wf.cwl")

# Read in the cwl file from a yaml
with open(cwl_file, "r") as cwl_h:
 yaml_obj = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
    
# Check CWLVersion
if 'cwlVersion' not in list(yaml_obj.keys()):
    print("Error - could not get the cwlVersion")
    sys.exit(1)

# Import parser based on CWL Version    
if yaml_obj['cwlVersion'] == 'v1.0':
    from cwl_utils import parser_v1_0 as parser
elif yaml_obj['cwlVersion'] == 'v1.1':
    from cwl_utils import parser_v1_1 as parser
elif yaml_obj['cwlVersion'] == 'v1.2':
    from cwl_utils import parser_v1_2 as parser
else:
    print("Version error. Did not recognise {} as a CWL version".format(yaml_obj["CWLVersion"]))
    sys.exit(1)

# Import CWL Object
cwl_obj = parser.load_document_by_yaml(yaml_obj, cwl_file.as_uri())

# View CWL Object
print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))

Development

Regenerate parsers

To regenerate install the schema_salad package and run:

cwl_utils/parser_v1_0.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/CommonWorkflowLanguage.yml

cwl_utils/parser_v1_1.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/main/CommonWorkflowLanguage.yml

cwl_utils/parser_v1_2.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/main/CommonWorkflowLanguage.yml

Release

To release CWLUtils, bump the version in cwl_utils/__meta__.py, and tag that commit with the new version. TravisCI should release that tag.