H5Web App & Providers

H5Web is a collection of React components to visualize and explore data. It consists of two main packages:

• @h5web/lib: visualization components built with react-three-fiber.
• @h5web/app: a stand-alone, web-based viewer to explore HDF5 files (this library).

@h5web/app exposes the HDF5 viewer component App, as well as the following built-in data providers:

• H5GroveProvider for use with server implementations based on H5Grove, like jupyterlab-h5web;
• HsdsProvider for use with HSDS;
• MockProvider for testing purposes.

Prerequisites

The react and react-dom dependencies must be installed in your project. Note that as of version 10, @h5web/app requires React 18.

This package supports TypeScript out of the box without the need to install a separate @types/ package.

Getting started 🚀

npm install @h5web/app

import '@h5web/app/dist/styles.css';

import React from 'react';
import { App, MockProvider } from '@h5web/app';

function MyApp() {
  return (
    <div style={{ height: '100vh' }}>
      <MockProvider>
        <App />
      </MockProvider>
    </div>
  );
}

export default MyApp;

If your bundler supports it (e.g. webpack 5), you may be able to shorten the stylesheet import path as follows:

import '@h5web/app/styles.css';

Examples

The following code sandboxes demonstrate how to set up and use @h5web/app with various front-end development stacks:

• Vite
• Create React App v4
• Create React App v5

Browser support

H5Web works out of the box on Firefox 78 ESR. Support for Firefox 68 ESR is possible by polyfilling the ResizeObserver API. Older versions of Firefox are not supported.

API reference

App

Renders the HDF5 viewer.

For App to work, it must be wrapped in a data provider:

<MockProvider>
  <App />
</MockProvider>

sidebarOpen?: boolean (optional)

Whether the viewer should start with the sidebar open. The sidebar contains the explorer and search panels. Defaults to true. Pass false to hide the sidebar on initial render, thus giving more space to the visualization. This is useful when H5Web is embeded inside another app.

<App sidebarOpen={false} />

This replaces prop explorerOpen, which was deprecated in v7.1.0 and removed in v8.0.0.

initialPath?: string (optional)

The path to select within the file when the viewer is first rendered. Defaults to '/'.

<MockProvider>
  <App initialPath="/nD_datasets/threeD" />
</MockProvider>

getFeedbackURL?: (context: FeedbackContext) => string (optional)

If provided, a "Give feedback" button appears in the breadcrumbs bar, which invokes the function when clicked. The function should return a valid URL, for instance a mailto: URL with a pre-filled subject and body: mailto:[email protected]?subject=Feedback&body=<url-encoded-text>. If the app is publicly available, we recommend returning the URL of a secure online contact form instead.

<App getFeedbackURL={() => 'https://my-feedback-form.com'} />

<App
  getFeedbackURL={(context) => {
    const {
      filePath, // path of current file
      entityPath, // path of currently selected entity
    } = context;

    return `mailto:[email protected]?subject=Feedback&body=${encodeURIComponent(...)}`;
  }}
/>

disableDarkMode?: boolean (optional)

By default, the viewer follows your browser's and/or operating system's dark mode setting. This prop disables this beahviour by forcing the viewer into light mode.

<App disableDarkMode />

propagateErrors?: boolean (optional)

The viewer has a top-level ErrorBoundary that, by default, handles errors thrown outside of the visualization area. These include errors thrown by the data provider when fetching metadata for the explorer. If you prefer to implement your own error boundary, you may choose to let errors through the viewer's top-level boundary:

import { ErrorBoundary } from 'react-error-boundary';

<ErrorBoundary FallbackComponent={MyErrorFallback}>
  <MockProvider>
    <App propagateErrors />
  </MockProvider>
</ErrorBoundary>;

H5GroveProvider

Data provider for H5Grove.

<H5GroveProvider
  url="https://h5grove.server.url"
  filepath="some-file.h5"
  axiosConfig={useMemo(() => ({ params: { file: 'some-file.h5' } }), [])}
>
  <App />
</H5GroveProvider>

url: string (required)

The base URL of the H5Grove server.

filepath: string (required)

The path and/or name of the file to display in the UI.

axiosConfig?: AxiosRequestConfig (optional)

By default, H5GroveProvider does not make any assumption as to how to configure its internal axios client. If you use one of H5Grove's default API implementations, then you'll need to use this prop to pass the file query parameter as shown above.

If your API server requires authentication or is on a different domain, you'll need to pass the necessary request headers and configuration as well.

Remember to memoise or extract your axiosConfig object so the fetching cache does not get cleared if/when your app re-renders.

getExportURL?: (...args) => URL | (() => Promise<URL | Blob>) | undefined (optional)

The DataProvider#getExportURL method is used by the toolbars to generate URLs and controls for exporting the current dataset/slice to various formats. This prop allows providing your own implementation of this method.

getExportURL is called once for every export menu entry. It receives the export format, as well as the current dataset metadata object, selection string, and value array. The export entry behaviour then depends of the return type:

• URL: the URL is set as the href of the export entry's download anchor.
• () => Promise<URL | Blob>: the function is called when the user clicks on the export entry. When the promise resolves, the returned URL or Blob is used to trigger a download.
• undefined: the export entry is not rendered.

Returning an async function enables advanced use cases like generating exports client-side, or server-side but from an authenticated endpoint.

// Client-side CSV export
getExportURL={(format, dataset, selection, value) => {
  if (format === 'csv') {
    // Async function that will be called when the user clicks on a `CSV` export menu entry
    return async () => {
      // Generate CSV string from `value` array
      let csv = '';
      value.forEach((val) => { ... })

      // Return CSV string as Blob so it can be downloaded
      return new Blob([csv]);
    };
  }
}}

// Fetch export data from authenticated endpoint
getExportURL={(format, dataset, selection) => async () => {
  const query = new URLSearchParams({ format, path: dataset.path, selection });
  const response = await fetch(`${AUTH_EXPORT_ENDPOINT}?${query.toString()}`, {
    headers: { /* authentication header */ }
  })

  return response.blob();
}}

// Fetch a one-time export link
getExportURL={(format, dataset, selection) => async () => {
  const query = new URLSearchParams({ format, path: dataset.path, selection });
  const response = await fetch(`${AUTH_TOKEN_ENDPOINT}?${query.toString()}`, {
    headers: { /* authentication header */ }
  })

  // Response body contains temporary, pre-authenticated export URL
  return new URL(await response.body());
}}

You may provide a partial implementation of getExportURL that handles only specific export scenarios. In this case, or if you don't provide a function at all, H5GroveProvider falls back to generating URLs based on the /data endpoint and format query param.

resetKeys?: unknown[] (optional)

You can pass variables in resetKeys that, when changed, will reset the provider's internal fetch cache. You may want to do this, for instance, when the content of the current file changes and you want the viewer to refetch the latest metadata and dataset values.

It is up to you to decide what sort of keys to use and when to update them. For instance:

• Your server could send over a hash of the file via WebSocket.
• You could show a toast notification with a Refresh button when the file changes and simply increment a number when the button is clicked (cf. contrived example below).

function MyApp() {
  const [key, setKey] = useState(0);
  const incrementKey = useCallback(() => setKey((val) => val + 1), []);

  return (
    <>
      <button type="button" onClick={incrementKey}>
        Refresh
      </button>
      <H5GroveProvider resetKeys={[key]} /* ... */>
        <App />
      </H5GroveProvider>
    </>
  );
}

HsdsProvider

Data provider for HSDS.

<HsdsProvider
  url="https://hsds.server.url"
  username="foo"
  password="abc123"
  filepath="/home/reader/some-file.h5"
>
  <App />
</HsdsProvider>

url: string (required)

The base URL of the HSDS server.

username: string; password: string (required)

The credentials to use to authenticate to the HSDS server. Note that this authentication mechanism is not secure; please do not use it to grant access to private data.

filepath: string (required)

The path of the file to request.

getExportURL?: (...args) => URL | (() => Promise<URL | Blob>) | undefined (optional)

See H5GroveProvider#getExportURL.

HsdsProvider does not provide a fallback implementation of getExportURL at this time, so if you don't provide your own, the export menu will remain disabled in the toolbar.

resetKeys?: unknown[] (optional)

See H5GroveProvider#resetKeys.

MockProvider

Data provider for demonstration and testing purposes.

<MockProvider>
  <App />
</MockProvider>

getExportURL?: (...args) => URL | (() => Promise<URL | Blob>) | undefined (optional)

See H5GroveProvider#getExportURL.

MockProvider provides a very basic fallback implementation of getExportURL that can generate only client-side CSV exports of 1D datasets.

Utilities

getFeedbackMailto

Generate a feedback mailto: URL using H5Web's built-in feedback email template.

(context: FeedbackContext, email: string, subject = 'Feedback') => string;

import { getFeedbackMailto } from '@h5web/app';
...
<App getFeedbackURL={(context) => {
  return getFeedbackMailto(context, '[email protected]');
}} />

enableBigIntSerialization

Invoke this function before rendering your application to allow the Raw visualization and metadata inspector to serialize and display big integers:

enableBigIntSerialization();
createRoot(document.querySelector('#root')).render(<MyApp />);

This is recommended if you work with a provider that supports 64-bit integers — i.e. one that may provide dataset and attribute values that include primitive bigint numbers — currently only MockProvider.

The Raw visualization and metadata inspector rely on JSON.stringify() to render dataset and attribute values. By default, JSON.stringify() does not know how to serialize bigint numbers and throws an error if it encounters one. enableBigIntSerialization() teaches JSON.stringify() to convert big integers to strings:

> JSON.stringify(123n);
TypeError: Do not know how to serialize a BigInt

> enableBigIntSerialization();
> JSON.stringify(123n);
"123n"

The n suffix (i.e. the same suffix used for bigint literals as demonstrated above) is added to help distinguish big integer strings from other strings.

If you're application already implements bigint serialization, you don't need to call enableBigIntSerialization(). Doing so would override the existing implementation, which might have unintended effects.

Context

The viewer component App communicates with its wrapping data provider through a React context called DataContext. This context is available via a custom hook called useDataContext. This means you can use the built-in data providers in your own applications:

<MockProvider>
  <MyApp />
</MockProvider>;

function MyApp() {
  const { filename } = useDataContext();
  return <p>{filename}</p>;
}

useDataContext returns the following object:

interface DataContextValue {
  filepath: string;
  filename: string;

  entitiesStore: EntitiesStore;
  valuesStore: ValuesStore;
  attrValuesStore: AttrValuesStore;
}

The three stores are created with the react-suspense-fetch library, which relies on React Suspense. A component that uses one of these stores (e.g. entitiesStore.get('/path/to/entity')) must have a Suspense ancestor to manage the loading state.

<MockProvider>
  <Suspense fallback={<span>Loading...</span>}>
    <MyApp />
  </Suspense>
</MockProvider>;

function MyApp() {
  const { entitiesStore } = useDataContext();
  const group = entitiesStore.get('/resilience/slow_metadata');
  return <pre>{JSON.stringify(group, null, 2)}</pre>;
}