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fair-workflows / FAIRWorkflowsExtension

A Jupyterlab extension for searching for Nanopublished computational steps.
BSD 3-Clause "New" or "Revised" License
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FAIRWorkflowsExtension

Github Actions Status DOI fair-software.eu

A Jupyterlab extension for composing and nanopublishing FAIR workflows, with a mixture of manual and computational tasks.

This extension is composed of a Python package named FAIRWorkflowsExtension for the server extension and a NPM package named FAIRWorkflowsExtension for the frontend extension.

Docker setup

It is possible to run the project inside a docker container. Simply run the following command in the project directory:

docker-compose up

Requirements

Install

Note: You will need NodeJS to install the extension.

pip install FAIRWorkflowsExtension
jupyter lab build

(The above should be run from the root of the FAIRWorkflowsExtension repository)

Troubleshoot

If you are seeing the frontend extension but it is not working, check that the server extension is enabled:

jupyter serverextension list

If the server extension is installed and enabled but you are not seeing the frontend, check the frontend is installed:

jupyter labextension list

If it is installed, try:

jupyter lab clean
jupyter lab build

Contributing

Install

The jlpm command is JupyterLab's pinned version of yarn that is installed with JupyterLab. You may use yarn or npm in lieu of jlpm below.

# Clone the repo to your local environment
# Move to FAIRWorkflowsExtension directory

# Install server extension
pip install -e .
# Register server extension
jupyter serverextension enable --py FAIRWorkflowsExtension

# Install dependencies
jlpm
# Build Typescript source
jlpm build
# Link your development version of the extension with JupyterLab
jupyter labextension link .
# Rebuild Typescript source after making changes
jlpm build
# Rebuild JupyterLab after making any changes
jupyter lab build

You can watch the source directory and run JupyterLab in watch mode to watch for changes in the extension's source and automatically rebuild the extension and application.

# Watch the source directory in another terminal tab
jlpm watch
# Run jupyterlab in watch mode in one terminal tab
jupyter lab --watch

Uninstall


pip uninstall FAIRWorkflowsExtension

jupyter labextension uninstall FAIRWorkflowsExtension