Support h5ad via reference spec

[keller-mark]

Fixes #483

Depends on manzt/zarrita.js#153

Background

Create a reference spec JSON for a local or remote H5AD file using kerchunk:

from kerchunk.hdf import SingleHdf5ToZarr
import json

h5_url = "https://storage.googleapis.com/vitessce-demo-data/habib-2017/habib17.processed.h5ad"
h5chunks = SingleHdf5ToZarr(h5_url, inline_threshold=300)
with open("habib17.reference.json", 'wb') as f:
    f.write(json.dumps(h5chunks.translate()).encode());

(to read back in using Zarr-python):

import fsspec
import zarr

fs = fsspec.filesystem('reference', fo='habib17.reference.json')
m = fs.get_mapper('')

group = zarr.group(store=m)
group['/obs/CellType/categories'][()]

TODO:

• document this feature
• deploy a demo
• clarify what happens if the H5AD is moved (since the remote URL contained in the JSON won't match) (Add options for ReferenceStore manzt/zarrita.js#155)
• clarify what happens if the reference is created locally but then hosted remotely (since the local path contained in the JSON won't match the remote URL) (Add options for ReferenceStore manzt/zarrita.js#155)
• new view config version for obsSets.anndata.zarr and obsFeatureColumns.anndata.zarr options schema changes (array to object) (see comments in packages/schemas/src/file-def-options.ts)
• create utility function in vitessce-python repo for creation of reference spec for local and remote H5AD files

Change List

Checklist

• Ensure PR works with all demos on the dev.vitessce.io homepage
• Open (draft) PR's into vitessce-python and vitessce-r if this is a release PR
• Documentation added or updated

[github-actions]

Size Change: +8.94 kB (0%)

Total Size: 13 MB

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