scverse / scverse/spatialdata

Support for private remote object storage

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#441 7 comments 2 reactions 0 assignees View on GitHub

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format
Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

Right now, there is support for local .zarr stores and remote stores publically accessible via HTTP or S3.
Private remote stores are more difficult, as they need certain options or credentials that are not representable by simply a string or Path. One option is to use a zarr.storage.FSStore, which can have storage_options or any fsspec.spec.AbstractFileSystem.

Two pull requests enable this:

  • Support init of ome_zarr_py.io.ZarrLocation with zarr.storage.FSStore (#349)
  • Support remote private storage by consistent use of substore (#442)

Testing is difficult, but this is what I used:

import spatialdata as sd
import zarr
# works now, requires credentials in ~/.aws/credentials
root = zarr.open('s3://BUCKET/spatial-sandbox/visium_associated_xenium_io.zarr', storage_options = {'client_kwargs': {'endpoint_url': MINIO_URL}})
sd.read_zarr(root)
# still works, I think depends on zmetadata?
sd.read_zarr('https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr/')
# still works
sd.read_zarr('~/visium_associated_xenium_io.zarr')

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading PRs #349 and #442, which the issue identifies as enabling support for private remote storage. Reproduce the shown zarr and spatialdata examples with credentials and storage options; done means private remote stores work while the existing HTTP and local store examples continue to work.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cloud, data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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