caw 0.0.1rc1

ChRIS Automatic Workflows

ChRIS Automated Workflows

A command-line client for ChRIS supporting execution of pipelines.

Installation

Pip

pip install -U caw

Usage

$ caw [OPTIONS] COMMAND [ARGS]...

Container usage is also supported.

docker run --rm -t -v $PWD/data:/data:ro fnndsc/caw:latest caw upload /data
podman run --rm -t -v $PWD/data:/data:ro fnndsc/caw:latest caw upload /data
singularity exec docker://fnndsc/caw:latest caw upload ./data

Documentation

Options:

• -a, --address TEXT: [env var: CHRIS_URL; default: http://localhost:8000/api/v1/]
• -u, --username TEXT: [env var: CHRIS_USERNAME; default: chris]
• -p, --password TEXT: [env var: CHRIS_PASSWORD; default: chris1234]
• --help: Show this message and exit.

Commands:

• pipeline: Run a pipeline on an existing feed.
• search: Search for pipelines that are saved in ChRIS.
• upload: Upload files into ChRIS storage and then run...
• version: Print version.

caw pipeline

Run a pipeline on an existing feed.

Usage:

$ caw pipeline [OPTIONS] NAME

Arguments:

• NAME: Name of pipeline to run. [required]

Options:

• --target TEXT: Plugin instance ID or URL. [default: ]
• --help: Show this message and exit.

caw search

Search for pipelines that are saved in ChRIS.

Usage:

$ caw search [OPTIONS] [NAME]

Arguments:

• [NAME]: name of pipeline to search for [default: ]

Options:

• --help: Show this message and exit.

caw upload

Upload files into ChRIS storage and then run pl-dircopy, printing the URL for the newly created plugin instance.

Usage:

$ caw upload [OPTIONS] FILES...

Arguments:

• FILES...: Files to upload. Folder upload is supported, but directories are destructured. [required]

Options:

• -t, --threads INTEGER: Number of threads to use for file upload. [default: 4]
• --create-feed / --no-create-feed: Run pl-dircopy on the newly uploaded files. [default: True]
• -n, --name TEXT: Name of the feed. [default: ]
• -d, --description TEXT: Description of the feed. [default: ]
• -p, --pipeline TEXT: Name of pipeline to run on the data. [default: ]
• --help: Show this message and exit.

Development

python -m venv venv
source venv/bin/activate
pip install -e .

Testing

You must set up the ChRIS backend on http://localhost:8000/api/v1/ (say, using miniChRIS) and install the pipeline https://chrisstore.co/api/v1/pipelines/1/

./testing/upload_reconstruction_pipeline.sh

Run all tests using the command

python -m unittest