Fix ZarrParser when zarr store is nested inside object store root

ZarrParser.__call__ was discarding the store-relative path from
registry.resolve(), causing two bugs with nested stores:
1. open_group_async couldn't find the zarr group within the store
2. Chunk manifest paths were doubled (e.g. subdir/data.zarr/subdir/data.zarr/temp/0.0)

Now correctly uses the store-relative path for group opening and the
store root URI for chunk path construction.

Note: also requires zarr-developers/zarr-python#3657 (on zarr main,
not yet released) which fixes ObjectStore.list_dir corrupting directory
names.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: TomNicholas

virtualizarr/parsers/zarr.py

@@ -517,13 +517,21 @@ def __call__(
         virtualizarr.open_virtual_dataset : High-level interface for virtual datasets.
         virtualizarr.manifests.ManifestStore : The returned virtual store object.
         """
-        path = validate_and_normalize_path_to_uri(url, fs_root=Path.cwd().as_uri())
-        object_store, _ = registry.resolve(path)
+        uri = validate_and_normalize_path_to_uri(url, fs_root=Path.cwd().as_uri())
+        object_store, store_relative_path = registry.resolve(uri)
         zarr_store = ObjectStore(store=object_store)  # type: ignore[type-var]
+        # Compute the store root URI by stripping the relative path from the full URI
+        rel_path = str(store_relative_path)
+        store_root_uri = uri.removesuffix(rel_path).rstrip("/") if rel_path else uri
+        # Combine the store-relative path with optional group to get the full
+        # path within the object store to the zarr group
+        group_path = rel_path
+        if self.group:
+            group_path = f"{group_path}/{self.group}" if group_path else self.group
         coro = _construct_manifest_group(
             store=zarr_store,
-            path=url,
-            group=self.group,
+            path=store_root_uri,
+            group=group_path or None,
             skip_variables=self.skip_variables,
         )
         manifest_group = _run_async(coro)

virtualizarr/tests/test_parsers/test_zarr.py

@@ -495,6 +495,32 @@ async def run_parser_in_loop():
             xr.testing.assert_identical(actual, expected)
 
 
+@zarr_versions()
+def test_parser_with_nested_store_path(tmpdir, zarr_format):
+    """Regression test for https://github.com/zarr-developers/VirtualiZarr/issues/912."""
+    parent_dir = f"{tmpdir}/bucket_root"
+    filepath = f"{parent_dir}/subdir/data.zarr"
+
+    ds = xr.Dataset(
+        {"temp": (("x", "y"), np.arange(12, dtype="float32").reshape(3, 4))},
+    )
+    ds.to_zarr(filepath, consolidated=False, zarr_format=zarr_format)
+
+    store = LocalStore(prefix=parent_dir)
+    registry = ObjectStoreRegistry({f"file://{parent_dir}": store})
+    parser = ZarrParser()
+
+    manifeststore = parser(url=filepath, registry=registry)
+
+    with xr.open_dataset(
+        filepath, engine="zarr", consolidated=False, zarr_format=zarr_format
+    ) as expected:
+        with xr.open_dataset(
+            manifeststore, engine="zarr", consolidated=False, zarr_format=3
+        ) as actual:
+            xr.testing.assert_identical(actual, expected)
+
+
 def test_sharded_array_raises_error(tmpdir):
     """Test that attempting to virtualize a sharded Zarr V3 array raises NotImplementedError."""
     filepath = f"{tmpdir}/test_sharded.zarr"