cannot import name 'ConsolidatedMetadataStore' from 'zarr.storage' #1058
Description
Hello,
I don't succeed to export my spatialdata with the function write into a zarr and I've been able to reproduce it with the dataset blob.
from spatialdata.datasets import blobs
test = blobs()
test.write(working_dir + 'test.zarr')Give the following error:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[5], line 4
1 from spatialdata.datasets import blobs
3 test = blobs()
----> 4 test.write(working_dir + 'test.zarr')
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/spatialdata/_utils.py:263, in _deprecation_alias.<locals>.deprecation_decorator.<locals>.wrapper(*args, **kwargs)
261 raise ValueError("version for deprecation must be specified")
262 rename_kwargs(f.__name__, kwargs, alias_copy, class_name, library, version)
--> 263 return f(*args, **kwargs)
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:1177, in SpatialData.write(self, file_path, overwrite, consolidate_metadata, update_sdata_path, sdata_formats)
1174 store.close()
1176 for element_type, element_name, element in self.gen_elements():
-> 1177 self._write_element(
1178 element=element,
1179 zarr_container_path=file_path,
1180 element_type=element_type,
1181 element_name=element_name,
1182 overwrite=False,
1183 parsed_formats=parsed,
1184 )
1186 if self.path != file_path and update_sdata_path:
1187 self.path = file_path
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:1254, in SpatialData._write_element(self, element, zarr_container_path, element_type, element_name, overwrite, parsed_formats)
1248 write_shapes(
1249 shapes=element,
1250 group=element_group,
1251 element_format=parsed_formats["shapes"],
1252 )
1253 elif element_type == "tables":
-> 1254 write_table(
1255 table=element,
1256 group=element_type_group,
1257 name=element_name,
1258 element_format=parsed_formats["tables"],
1259 )
1260 else:
1261 raise ValueError(f"Unknown element type: {element_type}")
File /micromamba/meenvs/sopa/lib/python3.12/site-packages/spatialdata/_io/io_table.py:63, in write_table(table, group, name, group_type, element_format)
60 else:
61 region, region_key, instance_key = (None, None, None)
---> 63 write_adata(group, name, table)
64 tables_group = group[name]
65 tables_group.attrs["spatialdata-encoding-type"] = group_type
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/specs/registry.py:518, in write_elem(store, k, elem, dataset_kwargs)
494 def write_elem(
495 store: GroupStorageType,
496 k: str,
(...) 499 dataset_kwargs: Mapping[str, Any] = MappingProxyType({}),
500 ) -> None:
501 """
502 Write an element to a storage group using anndata encoding.
503
(...) 516 E.g. for zarr this would be `chunks`, `compressor`.
517 """
--> 518 Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/utils.py:272, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
270 raise ValueError(msg)
271 try:
--> 272 return func(*args, **kwargs)
273 except Exception as e:
274 path = _get_display_path(store)
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/specs/registry.py:372, in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
368 if (is_zarr_group and is_zarr_v2()) or (
369 isinstance(store, h5py.Group) and not PurePosixPath(k).is_absolute()
370 ):
371 k = str(PurePosixPath(store.name) / k)
--> 372 is_consolidated = is_group_consolidated(store) if is_zarr_group else False
373 if is_consolidated:
374 msg = "Cannot overwrite/edit a store with consolidated metadata"
File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/zarr.py:167, in is_group_consolidated(group)
165 raise TypeError(msg)
166 if is_zarr_v2():
--> 167 from zarr.storage import ConsolidatedMetadataStore
169 return isinstance(group.store, ConsolidatedMetadataStore)
170 return group.metadata.consolidated_metadata is not None
ImportError: cannot import name 'ConsolidatedMetadataStore' from 'zarr.storage' (/micromamba/me/envs/sopa/lib/python3.12/site-packages/zarr/storage/__init__.py)
Error raised while writing key 'table' of <class 'zarr.core.group.Group'> to /tablesI work with the conda package of spatialdata version 0.6.1
Desktop (optional):
- OS: RedHat 8.7
Thanks for the package !
Lea