nbtx: Jupyter Notebook Transformation Library


Transform Jupyter notebook JSON files (*.ipynb) to and from more compact data structures for use in web applications or other contexts where loading component parts (e.g. images, data, etc.) is preferred. For example, in pulling apart a notebook in a publishing workflow the images, interactive charts or other outputs are required either on-disk or through a specific web-request.

Driving Use Cases

1. Optimize a notebook for a viewing context, so that initial network payload is small (no images, html, data), allowing large components to be loaded lazily.
2. Identify and extract known output images, html and other data for other formats (e.g. JATS, LaTeX, Word), where the images and outputs are required to be accessed independently.
3. Allow for additional, post-processed mimetypes to be added to the transformed notebook (e.g. WebP, thumbnail images) while maintaining a transformation path back to original notebook.

Scope

The scope of this library is currently isolated to "minifying" large notebook cell outputs, including stream, error, and mimetype outputs (update_display_data, display_data, execute_result). Large outputs are extracted from the notebook JSON, moved to a cache data structure, and referenced in the notebook by their hash and content_type. This library also provides a function to restore notebook outputs to their original state, given minifed outputs and the cached output content.

This library uses existing notebook types defined in nbformat (see docs); the only new types defined in nbtx are for "minified" outputs. However, there are no functions for handling entire notebooks; outputs must be isolated prior to invoking nbtx functions. This choice allows the library to be used in non-notebook contexts (e.g. MyST Markdown), which include output mime-bundles, but does not conform to the full notebook specification.

Goals

- Stay as close as possible to the nbformat for defining outputs.
- Identify and transforming outputs; nbtx does not write files to disk or fetch pieces of a notebook.
- Identify and extract large stream and error outputs, the length can be customized depending on use case.

Installation

Install using npm or yarn

``
npm install nbtx
`

Usage

The following example loads a notebook, then iterates through each cell and, if outputs are present, mutates the cells to include minified output objects that reference a separate outputCache:

`typescript
import fs from 'fs';
import type { MinifiedContentCache, MinifyOptions } from 'nbtx';
import { minifyCellOutput } from 'nbtx';

const notebook = JSON.parse(fs.readFileSync('my-notebook.ipynb'));
const outputCache: MinifiedContentCache = {};
// Options for minification, see note on hashing below
const opts: Partial = { computeHash };

notebook.cells.forEach((cell) => {
if (!cell.outputs?.length) return;
cell.outputs = minifyCellOutput(cell.outputs, outputCache);
});
`

You may then handle the outputCache however you want. For example, writing each large output to its own file and updating the cell outputs to point to those files (in this example by adding the path field):

`typescript
import { extFromMimeType, walkOutputs } from 'nbtx';

notebook.cells.forEach((cell) => {
if (!cell.outputs?.length) return;
walkOutputs(cell.outputs, (output) => {
if (!output.hash || !outputCache[output.hash]) return;
const [content, { contentType, encoding }] = outputCache[hash];
const filename = ${hash}${extFromMimeType(contentType)};
fs.writeFileSync(filename, content, { encoding: encoding as BufferEncoding });
// The path can be used, for example in a web-context
output.path = filename;
});
});
`

You may also rehydrate the original notebook from an outputCache:

`typescript
import { convertToIOutputs } from 'nbtx';

notebook.cells.forEach((cell) => {
if (!cell.outputs?.length) return;
cell.outputs = convertToIOutputs(cell.outputs, outputCache);
});
`

> Note
> Minifying and restoring notebook outputs may change the structure of output text from a string list to a single,
> new-line-delimited string. Both of these formats are acceptable in the notebook types defined by nbformat.

Hashing function

To be able to have no dependencies and also run easily in the browser, nbtx does not bundle a hashing library.
To create the computeHash function, choose an algorithm, for example, md5 and digest the content. If you are in the browser, consider using crypto-js or some other random function.

`typescript
import { createHash } from 'crypto';

function computeHash(content: string): string {
return createHash('md5').update(content).digest('hex');
}
`

By default nbtx will create a random string for the hash and raise a warning.

Data transformation example

Starting with an ipynb JSON document, the following example shows the output transformation for an execute_result with three outputs (html, image, text):

`json
{
...,
"cells": [
{
"cell_type": "code",
...,
"outputs": {
"output_type": "execute_result",
...,
"data": {
"text/html": ["...veryLargeString\n", "on many lines\n"],
"image/png": "base64-encoded-data-without-a-header",
"text/plain": ["alt.VConcatChart(...)"],
}
}
}
],
...
}
`

After minifyCellOutput is called and an optional pass to write to disk and add a path (as in the above example), the JSON structure would be:

`json
{
...,
"cells": [
{
"cell_type": "code",
...,
"outputs": {
"output_type": "execute_result",
...,
"data": {
"text/html": {
"content_type": "text/html",
"hash": "29cb113f927eb3abba1b303571caa653",
// The path isn't added by nbtx, but is a common place to put a URL
"path": "/static/29cb113f927eb3abba1b303571caa653.html"
},
"image/png": {
"content_type": "image/png",
"hash": "W5Zulz9J5PLlOkjN2RWMa6CRgJdjxq2r",
// Known output types are given sensible extensions through extFromMimeType
"path": "/static/W5Zulz9J5PLlOkjN2RWMa6CRgJdjxq2r.png"
},
"text/plain": {
// Small strings are by default not extracted, this can be modified in options
"content": "alt.VConcatChart(...)",
"content_type": "text/plain"
}
}
}
}
],
...
}
`

Viewing and "rehydration" applications can choose to walkOutputs and download the various parts of a notebook, and/or add additional mimetypes` to the bundle. For example, adding transformations to take screenshots of outputs for long-term preservation or add web-optimized images (e.g. WebP) that were not created in the execution process.

This can be done asyncronously from the first request of notebook content payload, improving pageload speed and leaving it up to the consuming application which of the mime-bundles to fetch.

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As of v0.4.0 this package is ESM only.

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Continuous Science Foundation