raise a keyerror when multiscales metadata is missing from attributes (…

…#32)

docs/index.md

@@ -38,7 +38,7 @@ import zarr
 url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
 
 # open the Zarr group
-zgroup = zarr.open(url)
+zgroup = zarr.open(url, mode='r')
 
 # group_model is a `GroupSpec`, i.e. a Pydantic model of a Zarr group
 group_model = Group.from_zarr(zgroup)
@@ -113,7 +113,7 @@ print(multi_meta)
 arrays = [zgroup[d.path] for d in multi_meta[0].datasets]
 print(arrays)
 """
-[<zarr.core.Array '/0' (2, 236, 275, 271) uint16>, <zarr.core.Array '/1' (2, 236, 137, 135) uint16>, <zarr.core.Array '/2' (2, 236, 68, 67) uint16>]
+[<zarr.core.Array '/0' (2, 236, 275, 271) uint16 read-only>, <zarr.core.Array '/1' (2, 236, 137, 135) uint16 read-only>, <zarr.core.Array '/2' (2, 236, 68, 67) uint16 read-only>]
 """
 ```
 

src/pydantic_ome_ngff/utils.py

@@ -2,6 +2,7 @@
 
 from collections import Counter
 from typing import TYPE_CHECKING, Protocol, runtime_checkable
+from zarr.storage import BaseStore
 
 import numpy as np
 
@@ -38,3 +39,14 @@ def listify_numpy(data: Any) -> Any:
     if isinstance(data, np.ndarray):
         return data.tolist()
     return data
+
+
+def get_path(store: BaseStore) -> str:
+    """
+    Get a path from a zarr store
+    """
+    if hasattr(store, "path"):
+        return store.path
+
+    else:
+        return ""

src/pydantic_ome_ngff/v04/multiscale.py

@@ -25,6 +25,7 @@
     ArrayLike,
     ChunkedArrayLike,
     duplicates,
+    get_path,
 )
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 from pydantic_ome_ngff.v04.base import version
@@ -296,16 +297,17 @@ def from_zarr(cls, node: zarr.Group) -> Group:
             A model of the Zarr group.
         """
         # on unlistable storage backends, the members of this group will be {}
-        guess = GroupSpec.from_zarr(node)
+        guess = GroupSpec.from_zarr(node, depth=0)
 
         try:
             multi_meta_maybe = guess.attributes["multiscales"]
         except KeyError as e:
+            store_path = get_path(node.store)
             msg = (
                 "Failed to find mandatory `multiscales` key in the attributes of the Zarr group at "
-                f"{node.store}://{node.path}."
+                f"{node.store}://{store_path}://{node.path}."
             )
-            raise ValueError(msg) from e
+            raise KeyError(msg) from e
 
         multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
         members_tree_flat = {}
@@ -331,7 +333,7 @@ def from_zarr(cls, node: zarr.Group) -> Group:
         members_normalized = GroupSpec.from_flat(members_tree_flat)
 
         guess_inferred_members = guess.model_copy(
-            update={"members": {**guess.members, **members_normalized.members}}
+            update={"members": members_normalized.members}
         )
         return cls(**guess_inferred_members.model_dump())
 
@@ -347,7 +349,9 @@ def from_arrays(
         name: str | None = None,
         type: str | None = None,
         metadata: dict[str, Any] | None = None,
-        chunks: tuple[int, ...] | tuple[tuple[int, ...]] | Literal["auto"] = "auto",
+        chunks: tuple[int, ...]
+        | tuple[tuple[int, ...], ...]
+        | Literal["auto"] = "auto",
         compressor: Codec = DEFAULT_COMPRESSOR,
         fill_value: Any = 0,
         order: Literal["C", "F", "auto"] = "auto",

tests/v04/test_multiscales.py

@@ -377,7 +377,7 @@ def test_from_arrays(
         axes = all_axes[:ndim]
     else:
         axes = tuple([*all_axes[4:], *all_axes[:3]])
-
+    chunks_arg: tuple[tuple[int, ...], ...] | tuple[int, ...] | Literal["auto"]
     if chunks == "auto":
         chunks_arg = chunks
         chunks_expected = (
@@ -441,7 +441,12 @@ def test_from_zarr_missing_metadata(
     )
     group_model = GroupSpec()
     group = group_model.to_zarr(store, path="test")
-    with pytest.raises(ValueError):
+    store_path = store.path if hasattr(store, "path") else ""
+    match = (
+        "Failed to find mandatory `multiscales` key in the attributes of the Zarr group at "
+        f"{store}://{store_path}://{group.path}."
+    )
+    with pytest.raises(KeyError, match=match):
         Group.from_zarr(group)