Open an array in a remote store - #713
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ChangesRemote array access
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: 🟡 Moderate · up to The PR adds remote array reads and is otherwise presented as tested, but the notebook validation status is currently failed. Merge should wait until that failure is resolved or explicitly accepted. Sequence Diagram(s)sequenceDiagram
participant Caller
participant open_array
participant RemoteZarrStore
participant RemoteZarrArray
Caller->>open_array: provide remote store, path, and storage_options
open_array->>RemoteZarrStore: resolve remote array node
open_array->>RemoteZarrArray: create read-only handle
RemoteZarrArray-->>Caller: return metadata or indexed data
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🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 64.71% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 17 functions across 3 files. (1 skipped: 1 unsupported.)
✨ Finishing Touches 💡 1🛠️ Fix failing CI checks 💡
🧪 Generate unit tests (beta)
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| a caller holding a URL had to fall back to another Zarr library for the one | ||
| thing this package could otherwise do end to end. | ||
| """ | ||
| from ngff_zarr import from_ngff_zarr, open_array |
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These newly added tests import and call the legacy from_ngff_zarr alias here and again in test_a_remote_array_refuses_a_region_write. New tests are required to use from_ome_zarr; rename both imports and calls so the tests reinforce the supported public spelling.
AGENTS.md reference: AGENTS.md:L304-L313
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Fixed: both new tests now import and call from_ome_zarr. The pre-existing tests in the same file keep the alias, since the rule is about new code.
| remote = ( | ||
| store | ||
| if isinstance(store, RemoteZarrStore) | ||
| else RemoteZarrStore(str(store), storage_options=storage_options) |
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When store is a remote FsspecStore, _is_remote() returns true by inspecting its filesystem protocol, but str(store) is a representation such as <FsspecStore(...)>, not the underlying URL. Passing that representation to RemoteZarrStore makes obstore.from_url fail before the array can open; extract the wrapper's URL/path and protocol instead, or reject wrapper objects before routing them here.
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Confirmed, and the repository documents the trap two files away: REMOTE_FS_PROTOCOLS exists to "recognize a remote store even after a URL has been wrapped in an FsspecStore, whose str() is "<FsspecStore(...)>" rather than the original URL". I then handed that repr to RemoteZarrStore.
Rejecting the wrapper is the right half of your suggestion, because it is also what the reader does: from_ome_zarr builds a RemoteZarrStore only for isinstance(store, str) and store.startswith(REMOTE_URL_SCHEMES), and hands anything else to _open_root_node. Reconstructing a URL from an FsspecStore would have open_array accept an input the reader does not route that way, on a path with no coverage here.
So the branch is now the reader's own rule, and a store object keeps the path it has today:
if isinstance(store, RemoteZarrStore):
return store
if isinstance(store, str) and store.startswith(REMOTE_URL_SCHEMES):
...
return NonePinned by test_a_store_object_is_not_opened_as_a_url, which asserts both halves: _is_remote_store(store) is true for the wrapper, and _remote_handle returns None for it.
| remote = ( | ||
| store | ||
| if isinstance(store, RemoteZarrStore) | ||
| else RemoteZarrStore(str(store), storage_options=storage_options) |
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For a normal installation without the optional obstore dependency, calling the newly documented open_array() remote path reaches this constructor and raises a raw ModuleNotFoundError. The existing from_ome_zarr remote path first checks remote_read_available() and raises _remote_backend_import_error() with the required pip install "ngff-zarr[remote]" guidance; this entry point should perform the same guard before construction.
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Fixed, with the reader's own guard and its message:
if not remote_read_available():
raise _remote_backend_import_error(store, None)so a URL without the extra names pip install "ngff-zarr[remote]" instead of raising obstore's ModuleNotFoundError. Pinned by test_a_url_without_the_remote_extra_names_the_extra.
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Inline comments:
In `@py/ngff_zarr/_zarrista_utils.py`:
- Line 1108: Update the remote-store branch in open_array so FsspecStore inputs
preserve a valid remote URL by deriving it from the store’s filesystem protocol
and path, or explicitly reject unsupported FsspecStore inputs instead of passing
str(store) to RemoteZarrStore; add a regression test covering this case.
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In `@py/test/test_remote_zarrista.py`:
- Around line 365-369: Update the exception handling around the remote-store
test to skip only documented unavailable-store or network failures, rather than
all exceptions whose modules start with “zarrista” or “obstore”; let metadata,
decoding, indexing, and other remote-read regressions propagate and fail the
test. Preserve the existing OSError handling only if it represents the
documented unavailable-store condition.
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`from_ome_zarr` reads a remote store and `open_array`, the handle regions are read and written through, did not: a caller holding a URL had to fall back to another Zarr library for the one thing this package could otherwise do end to end. The engine was already there -- the remote reader's async adapter is the same `_ZarristaArrayAdapter` the local path uses -- so `RemoteZarrArray` gains the read half of `LocalZarrArray` (`dtype`, `chunks`, `[]`) and `open_array` routes a URL to it. Which inputs that covers is the reader's own rule: a URL string, or a handle already built around one. A store object wrapping a URL is not one -- its `str()` is a repr rather than the URL obstore would be handed -- and `from_ome_zarr` does not route one through the remote engine either, so it keeps the local path it has today. A URL without the `[remote]` extra raises the reader's install hint rather than obstore's ModuleNotFoundError. Writing stays local: a region write on a remote array raises rather than silently doing nothing.
The remote tests build an S3 store and stop there, and the localhost harness serves HTTP, so nothing exercised the S3 path past construction. The bucket is public, so the read needs no credentials; it is opt-in behind NGFF_ZARR_NETWORK_TESTS, like the live read in test_from_ngff_zarr.
from_ome_zarr reached the AIND stores through fsspec, which resolved the bucket's region on its own. The obstore backend that replaced it does not, so the anonymous read went to us-east-1 for a bucket in us-west-2 and failed with a redirect carrying no location. The region is passed explicitly and the notebook is re-executed: the geometry is unchanged, the timings are this machine's.
Ruff 0.15 formats Python blocks inside Markdown and this repository enables preview, so a file nobody touched became unformatted when the prek autoupdate bumped the hook, leaving main red and every PR updated since inheriting it. Refs #707.
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obstore sends the request to us-east-1 when nothing configures a region, and S3 answers for a bucket held elsewhere with a 301 that carries no Location. object_store does not read the region from the header or the body, so the read fails where fsspec's botocore followed the redirect and retried. A store that worked through zarr-python before 0.44 now refuses to open.
The region is resolved from the bucket itself, one unsigned HEAD, cached per bucket, and only when neither storage_options nor AWS_REGION nor AWS_DEFAULT_REGION names one and no endpoint names a service that is not AWS. A bucket that answers nothing is left as it was, so obstore's own error still reaches the caller.
The live test reads a public bucket in us-west-2 with storage_options={'anon': True}, which is the call that regressed.
2 participants
from_ome_zarrreads a remote store;open_array— the handle regions are read and written through — did not. A caller holding a URL had to fall back to another Zarr library for the one thing this package could otherwise do end to end.The engine was already here: the remote reader's async adapter is the same
_ZarristaArrayAdapterthe local path uses, so the change is small.RemoteZarrArraygains the read half ofLocalZarrArray(dtype,chunks,[]), andopen_arrayroutes a URL to it,storage_optionsincluded.Read-only, and it says so: filling a store region by region needs a local directory store, and a silent no-op would leave a producer believing its region landed.
Proven
Windowed and whole reads over the repo's own localhost HTTP harness, with
_forbid_zarr_python()active — so it is zarrista/obstore serving, not zarr-python.A region write is refused;
open_arrayon a group is refused (aRemoteZarrGroupcarries__getitem__for path navigation, so the node's type is what decides, as on the local branch).Full suite: 1462 passed, 3 skipped. Lint clean.
A windowed read from a real S3 bucket,
open_arrayons3://aind-open-data/..., opt-in behindNGFF_ZARR_NETWORK_TESTS. The bucket is public, so it needs no credentials; it closes the gap where the remote tests built an S3 store and stopped there. GCS and Azure stay unexercised.Independent of #708, #709 and #710.
The bucket region an S3 read needs
Separate defect, same surface. obstore sends the request to
us-east-1when nothing configures aregion, and S3 answers for a bucket held elsewhere with a 301 that carries no
Location.object_store reads the region from neither the header nor the body, so the read fails where fsspec's
botocore followed the redirect and retried. A store that opened through zarr-python before 0.44 now
refuses to open: measured on 0.43.0,
from_ome_zarr(uri, storage_options={"anon": True})reads theAIND stores; on 0.45.0 the same call raises
GroupCreateError.The region is resolved from the bucket itself, one unsigned HEAD, cached per bucket, and only when
neither
storage_optionsnorAWS_REGIONnorAWS_DEFAULT_REGIONnames one and noendpointnamesa service that is not AWS. A bucket that answers nothing is left as it was, so obstore's own error
still reaches the caller.
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New Features
Bug Fixes
Documentation