jupyterlab_knowledge_graph

A JupyterLab extension to add a Foam-like knowledge graph to JupyterLab.

This extension is composed of a Python package named jupyterlab_knowledge_graph which bundles the frontend extension and a NPM package named jupyterlab-knowledge-graph for the frontend extension itself.

Code Notes

• RecordManager tracks all known Records with their associated Links to other Records.
• ParserRegistry manages the parsing of JupyterLab documents into Records.
• KnowledgeGraph displays a collection of Records using Cytoscape.js

Future Plans

Currently, only hypertext links between documents are supported. It might be useful / interesting to extend this to other kinds of relations, e.g. visualise the Python notebooks that link to document X and import library Y. To do so, we might wish to move to a graph database.

Requirements

• JupyterLab >= 3.0

Install

To install the extension, execute:

pip install jupyterlab_knowledge_graph

Uninstall

To remove the extension, execute:

pip uninstall jupyterlab_knowledge_graph

Troubleshoot

If you are not seeing the frontend extension, check the frontend extension is installed:

jupyter labextension list

Contributing

Development install

Note: You will need NodeJS to build the extension package.

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
# Change directory to the jupyterlab_knowledge_graph directory
# Install package in development mode
pip install -e .
# Link your development version of the extension with JupyterLab
jupyter labextension develop . --overwrite
# Rebuild extension Typescript source after making changes
jlpm run build

You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.

# Watch the source directory in one terminal, automatically rebuilding when needed
jlpm run watch
# Run JupyterLab in another terminal
jupyter lab

With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).

By default, the jlpm run build command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:

jupyter lab build --minimize=False

Development uninstall

pip uninstall jupyterlab_knowledge_graph

In development mode, you will also need to remove the symlink created by jupyter labextension develop command. To find its location, you can run jupyter labextension list to figure out where the labextensions folder is located. Then you can remove the symlink named jupyterlab-knowledge-graph within that folder.