JupyterLite + Galaxy Integration

This project integrates JupyterLite with the Pyodide kernel and custom extensions such as jl-galaxy.

The jl-galaxy extension enables Jupyter users to interact seamlessly with their Galaxy history — including loading and saving notebooks — through a fully integrated browser-based interface.

⚙️ Requirements

• Python 3.10.17+
• Node.js 20.19.1+
• npm 10.8.2+

📦 Setup Instructions

1. Create and activate a virtual environment

python -m venv .venv
source .venv/bin/activate

2. Install Python dependencies

pip install -r requirements.txt

This installs jupyterlite, jupyterlite-pyodide-kernel, and the gxy utility module for Galaxy integration.

3. Install Node.js dependencies

npm install

This installs JavaScript dependencies listed in package.json, including custom JupyterLite extensions.

🔨 Build

Run the full build to generate a standalone JupyterLite distribution:

npm run build

This will:

• Run jupyter lite build
• Include the Pyodide kernel
• Bundle federated extensions like jl-galaxy
• Output the final static site to: ./static/dist/_output

🚀 Serve

To serve the JupyterLite site locally:

npm run serve

Then open http://localhost:3000 in your browser.

🧰 Galaxy Integration Utilities (gxy)

The gxy module provides Python functions to interact with the Galaxy API directly from JupyterLite.

✅ api(endpoint, method="GET", data=None)

Makes an HTTP request to a Galaxy API endpoint and returns the parsed JSON response.

await api("/api/histories")
await api("/api/histories", method="POST", data={"name": "New History"})

✅ get(datasets_identifiers, identifier_type="hid", retrieve_datatype=False)

Downloads dataset(s) by HID, ID, or regex pattern. Saves them to Pyodide's virtual filesystem.

await get(3)                          # by HID
await get("some_id", "id")
await get("myfile.*", "regex")
await get("mytag", "tag")

✅ put(name, output=None, ext="auto", dbkey="?", history_id=None)

Uploads a file from the virtual filesystem to the current Galaxy history.

await put("mydata.txt", "newname.txt", ext="txt")

✅ get_history(history_id=None)

Returns metadata for all visible datasets in the current history.

await get_history()

✅ get_history_id()

Returns the current history ID based on the dataset context.

await get_history_id()

✅ get_environment()

Returns the Galaxy environment injected into the session via __gxy__.

get_environment()

✅ _find_matching_ids(history_datasets, list_of_regex_patterns, identifier_type='hid')

Used internally to resolve regex patterns to dataset identifiers.

📎 Notes

• The jl-galaxy extension allows users to browse and manage Galaxy histories directly from the Jupyter UI.
• All files must be placed within static/dist/_output; writing outside this directory breaks the build.
• The upload helper uses XMLHttpRequest to work around Pyodide's limitations with fetch.