Consolidated metadata#
Warning
The Consolidated Metadata feature in Zarr-Python is considered experimental for v3 stores. zarr-specs#309 has proposed a formal extension to the v3 specification to support consolidated metadata.
Zarr-Python implements the Consolidated Metadata for v2 and v3 stores. Consolidated metadata can reduce the time needed to load the metadata for an entire hierarchy, especially when the metadata is being served over a network. Consolidated metadata essentially stores all the metadata for a hierarchy in the metadata of the root Group.
Usage#
If consolidated metadata is present in a Zarr Group’s metadata then it is used
by default. The initial read to open the group will need to communicate with
the store (reading from a file for a zarr.storage.LocalStore, making a
network request for a zarr.storage.FsspecStore). After that, any subsequent
metadata reads get child Group or Array nodes will not require reads from the store.
In Python, the consolidated metadata is available on the .consolidated_metadata
attribute of the GroupMetadata object.
>>> import zarr
>>>
>>> store = zarr.storage.MemoryStore()
>>> group = zarr.create_group(store=store)
>>> group.create_array(shape=(1,), name='a', dtype='float64')
<Array memory://.../a shape=(1,) dtype=float64>
>>> group.create_array(shape=(2, 2), name='b', dtype='float64')
<Array memory://.../b shape=(2, 2) dtype=float64>
>>> group.create_array(shape=(3, 3, 3), name='c', dtype='float64')
<Array memory://.../c shape=(3, 3, 3) dtype=float64>
>>> zarr.consolidate_metadata(store)
<Group memory://...>
If we open that group, the Group’s metadata has a zarr.core.group.ConsolidatedMetadata
that can be used.:
>>> consolidated = zarr.open_group(store=store)
>>> consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata
>>> from pprint import pprint
>>> pprint(dict(sorted(consolidated_metadata.items())))
{'a': ArrayV3Metadata(shape=(1,),
data_type=<DataType.float64: 'float64'>,
chunk_grid=RegularChunkGrid(chunk_shape=(1,)),
chunk_key_encoding=DefaultChunkKeyEncoding(name='default',
separator='/'),
fill_value=np.float64(0.0),
codecs=(BytesCodec(endian=<Endian.little: 'little'>),
ZstdCodec(level=0, checksum=False)),
attributes={},
dimension_names=None,
zarr_format=3,
node_type='array',
storage_transformers=()),
'b': ArrayV3Metadata(shape=(2, 2),
data_type=<DataType.float64: 'float64'>,
chunk_grid=RegularChunkGrid(chunk_shape=(2, 2)),
chunk_key_encoding=DefaultChunkKeyEncoding(name='default',
separator='/'),
fill_value=np.float64(0.0),
codecs=(BytesCodec(endian=<Endian.little: 'little'>),
ZstdCodec(level=0, checksum=False)),
attributes={},
dimension_names=None,
zarr_format=3,
node_type='array',
storage_transformers=()),
'c': ArrayV3Metadata(shape=(3, 3, 3),
data_type=<DataType.float64: 'float64'>,
chunk_grid=RegularChunkGrid(chunk_shape=(3, 3, 3)),
chunk_key_encoding=DefaultChunkKeyEncoding(name='default',
separator='/'),
fill_value=np.float64(0.0),
codecs=(BytesCodec(endian=<Endian.little: 'little'>),
ZstdCodec(level=0, checksum=False)),
attributes={},
dimension_names=None,
zarr_format=3,
node_type='array',
storage_transformers=())}
Operations on the group to get children automatically use the consolidated metadata.:
>>> consolidated['a'] # no read / HTTP request to the Store is required
<Array memory://.../a shape=(1,) dtype=float64>
With nested groups, the consolidated metadata is available on the children, recursively.:
>>> child = group.create_group('child', attributes={'kind': 'child'})
>>> grandchild = child.create_group('child', attributes={'kind': 'grandchild'})
>>> consolidated = zarr.consolidate_metadata(store)
>>>
>>> consolidated['child'].metadata.consolidated_metadata
ConsolidatedMetadata(metadata={'child': GroupMetadata(attributes={'kind': 'grandchild'}, zarr_format=3, consolidated_metadata=ConsolidatedMetadata(metadata={}, kind='inline', must_understand=False), node_type='group')}, kind='inline', must_understand=False)
Synchronization and Concurrency#
Consolidated metadata is intended for read-heavy use cases on slowly changing hierarchies. For hierarchies where new nodes are constantly being added, removed, or modified, consolidated metadata may not be desirable.
It will add some overhead to each update operation, since the metadata would need to be re-consolidated to keep it in sync with the store.
Readers using consolidated metadata will regularly see a “past” version of the metadata, at the time they read the root node with its consolidated metadata.
Stores Without Support for Consolidated Metadata#
Some stores may want to opt out of the consolidated metadata mechanism. This may be for several reasons like:
They want to maintain read-write consistency, which is challenging with consolidated metadata.
They have their own consolidated metadata mechanism.
They offer good enough performance without need for consolidation.
This type of store can declare it doesn’t want consolidation by implementing Store.supports_consolidated_metadata and returning False. For stores that don’t support consolidation, Zarr will:
Raise an error on consolidate_metadata calls, maintaining the store in its unconsolidated state.
Raise an error in AsyncGroup.open(…, use_consolidated=True)
Not use consolidated metadata in AsyncGroup.open(…, use_consolidated=None)