don't serialize consolidated metadata if it's None (#3535)

* don't serialize consolidated metadata if it's unset (for zarr v3 groups)

* changelog

Author: d-v-b

changes/3535.bugfix.md

@@ -0,0 +1,2 @@
+Fixed a bug where the `"consolidated_metadata"` key was written to metadata documents even when
+consolidated metadata was not used, resulting in invalid metadata documents.

src/zarr/core/group.py

@@ -432,8 +432,11 @@ def from_dict(cls, data: dict[str, Any]) -> GroupMetadata:
 
     def to_dict(self) -> dict[str, Any]:
         result = asdict(replace(self, consolidated_metadata=None))
-        if self.consolidated_metadata:
+        if self.consolidated_metadata is not None:
             result["consolidated_metadata"] = self.consolidated_metadata.to_dict()
+        else:
+            # Leave consolidated metadata unset if it's None
+            result.pop("consolidated_metadata")
         return result
 
 

tests/test_metadata/test_v3.py

@@ -7,6 +7,7 @@
 import numpy as np
 import pytest
 
+from zarr import consolidate_metadata, create_group
 from zarr.codecs.bytes import BytesCodec
 from zarr.core.buffer import default_buffer_prototype
 from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding, V2ChunkKeyEncoding
@@ -21,7 +22,12 @@
     parse_dimension_names,
     parse_zarr_format,
 )
-from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError
+from zarr.errors import (
+    MetadataValidationError,
+    NodeTypeValidationError,
+    UnknownCodecError,
+    ZarrUserWarning,
+)
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -338,3 +344,52 @@ def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> N
     codecs = [{"name": "unknown"}]
     with pytest.raises(UnknownCodecError):
         parse_codecs(codecs)
+
+
+@pytest.mark.parametrize("use_consolidated", [True, False])
+@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
+def test_group_to_dict(use_consolidated: bool, attributes: None | dict[str, Any]) -> None:
+    """
+    Test that the output of GroupMetadata.to_dict() is what we expect
+    """
+    store: dict[str, object] = {}
+    if attributes is None:
+        expect_attributes = {}
+    else:
+        expect_attributes = attributes
+
+    group = create_group(store, attributes=attributes, zarr_format=3)
+    group.create_group("foo")
+    if use_consolidated:
+        with pytest.warns(
+            ZarrUserWarning,
+            match="Consolidated metadata is currently not part in the Zarr format 3 specification.",
+        ):
+            group = consolidate_metadata(store)
+        meta = group.metadata
+        expect = {
+            "node_type": "group",
+            "zarr_format": 3,
+            "consolidated_metadata": {
+                "kind": "inline",
+                "must_understand": False,
+                "metadata": {
+                    "foo": {
+                        "attributes": {},
+                        "zarr_format": 3,
+                        "node_type": "group",
+                        "consolidated_metadata": {
+                            "kind": "inline",
+                            "metadata": {},
+                            "must_understand": False,
+                        },
+                    }
+                },
+            },
+            "attributes": expect_attributes,
+        }
+    else:
+        meta = group.metadata
+        expect = {"node_type": "group", "zarr_format": 3, "attributes": expect_attributes}
+
+    assert meta.to_dict() == expect