No project description provided
Project description
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.
Requires Python 3.6+
Installation
pip3 install cwl-utils
To install from source:
git clone https://github.com/common-workflow-language/cwl-utils.git cd cwl-utils pip3 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.
docker_extract.py DIRECTORY path_to_my_workflow.cwlOr 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.
docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwlUsing the CWL Parsers
from pathlib import Path
from ruamel import yaml
import sys
from cwl_utils.parser import load_document_by_uri, save
# File Input - This is the only thing you will need to adjust or take in as an input to your function:
cwl_file = Path("testdata/md5sum.cwl") # or a plain string works as well
# Import CWL Object
cwl_obj = load_document_by_uri(cwl_file)
# View CWL Object
print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))
# Export CWL Object into a built-in typed object
saved_obj = save(cwl_obj)
print(f"Export of the loaded CWL object: {saved_obj}.")Development
Regenerate parsers
To regenerate install the schema_salad package and run:
cwl_utils/parser/cwl_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/cwl_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/cwl_v1_2.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/CommonWorkflowLanguage.yml
Release
To release CWLUtils, bump the version in cwl_utils/__meta__.py, and tag that commit with the new version. The gh-action-pypi-publish should release that tag.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file cwl-utils-0.15.tar.gz.
File metadata
- Download URL: cwl-utils-0.15.tar.gz
- Upload date:
- Size: 425.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.1 CPython/3.9.13
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 3309ba2854eb272453aae1d63add8885d631035723a901ac5b8f9b30a11d2d57 |
|
| MD5 | d650336e047ebb94f3a7109cc71f9f78 |
|
| BLAKE2b-256 | d3340c0e4c4fa7bdc2888357b14ed613cd3c5dd3abcd84c02b297ba934991466 |
Provenance
File details
Details for the file cwl_utils-0.15-py3-none-any.whl.
File metadata
- Download URL: cwl_utils-0.15-py3-none-any.whl
- Upload date:
- Size: 461.5 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.1 CPython/3.9.13
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 7ccde0c350f0b93c7cc4cc60d2b39f8e453eeceec68708b08f4b10722738577a |
|
| MD5 | d9ec3c86e04c65a0e7dfb5ff8efa4eb4 |
|
| BLAKE2b-256 | 858fa3d0db1aabfd1a733149f90cdba6927299feaa16023f8e8c59b4ed8de104 |
