Registry / storage / higlass-zarr-datafetchers

higlass-zarr-datafetchers

library0.6.0jsnpmunverified

Plugin data fetchers for loading Zarr-based files in HiGlass, allowing genomic data to be stored in object stores like S3 instead of using higlass-server. Current version 0.6.0 (stable, released 2023). Supports multivec and bar track types. Requires manual registration with higlass-register. Key differentiator: enables serverless HiGlass deployment by fetching data directly from cloud storage.

storage

npm install higlass-zarr-datafetchers

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · HIGLASS-ZARR-DATAF

higlass-zarr-datafetchers

storagejavascriptv0.6.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

ZarrMultivecDataFetcher

✓ import { ZarrMultivecDataFetcher } from 'higlass-zarr-datafetchers'

✗ const ZarrMultivecDataFetcher = require('higlass-zarr-datafetchers')

ESM module; no default export. Must use named import.

ZarrMultivecDataFetcher (CommonJS)

✓ const { ZarrMultivecDataFetcher } = require('higlass-zarr-datafetchers')

✗ const ZarrMultivecDataFetcher = require('higlass-zarr-datafetchers')

CommonJS destructure required; package does not export a default.

✓ import register from 'higlass-register'

✗ const register = require('higlass-register')

higlass-register is a separate package with default export.

import register from 'higlass-register'; import { ZarrMultivecDataFetcher } from 'higlass-zarr-datafetchers'; register( { dataFetcher: ZarrMultivecDataFetcher, config: ZarrMultivecDataFetcher.config }, { pluginType: 'dataFetcher' } ); // Then in your HiGlass view config: const trackConfig = { type: 'horizontal-multivec', uid: 'demo-multivec-track', data: { type: 'zarr-multivec', url: 'https://example.com/path/to/data.zarr', }, };

Debug

Known issues

gotchaPackage does not bundle Zarr library; you must install 'zarr' as a peer dependency

fix

Run: npm install zarr

affects: all

gotchaPlugin must be registered before HiGlass is initialized, otherwise track loading will fail silently

fix

Call register() before new HiGlassComponent()

affects: all

gotchaZarr files must be served with CORS headers when fetched from a different origin

fix

Configure your Zarr storage bucket to allow cross-origin requests

affects: all

gotchaOnly Zarr multivec format is supported; other Zarr arrays (e.g., 2D matrix) may not work

fix

Ensure your Zarr files follow the multivec specification

affects: all

Errors

Common errors & fixes

Error: Cannot find module 'zarr'

Missing peer dependency 'zarr'

fix

npm install zarr

TypeError: ZarrMultivecDataFetcher is not a constructor

Incorrect import (requires destructuring)

fix

Use 'import { ZarrMultivecDataFetcher } from 'higlass-zarr-datafetchers' instead of default import

Error: Track 'zarr-multivec' not registered

Data fetcher not registered before HiGlass initialization

fix

Call register() with the plugin before creating the HiGlass component

Upgrade

Version history

0.6.0latest on npm

Audit

Dependencies

zarrrequiredPeer dependency: Zarr reading primitives

higlass-registeroptionalRequired for plugin registration in HiGlass

Agent activity

21 hits · last 30 days

node

Amazon

Resources

githubhttps://github.com/keller-mark/higlass-zarr-datafetchers ↗

packagehiglass-zarr-datafetchers ↗

homepagehttps://github.com/keller-mark/higlass-zarr-datafetchers#readme ↗