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Update backend.py
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@rly
rly authored Nov 15, 2024
1 parent a070176 commit 1a5a455
Showing 1 changed file with 5 additions and 39 deletions.
44 changes: 5 additions & 39 deletions src/hdmf_zarr/backend.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@
DatasetBuilder,
LinkBuilder,
BuildManager,
RegionBuilder,
ReferenceBuilder,
TypeMap)
from hdmf.data_utils import AbstractDataChunkIterator
Expand Down Expand Up @@ -634,16 +633,12 @@ def write_attributes(self, **kwargs):
raise TypeError(str(e) + " type=" + str(type(value)) + " data=" + str(value)) from e
# Case 2: References
elif isinstance(value, (Container, Builder, ReferenceBuilder)):
# TODO: Region References are not yet supported
# if isinstance(value, RegionBuilder):
# type_str = 'region'
# refs = self._create_ref(value.builder)
if isinstance(value, (ReferenceBuilder, Container, Builder)):
type_str = 'object'
if isinstance(value, Builder):
refs = self._create_ref(value, export_source)
else:
refs = self._create_ref(value.builder, export_source)
refs = self._create_ref(value.builder, export_source);
tmp = {'zarr_dtype': type_str, 'value': refs}
obj.attrs[key] = tmp
# Case 3: Scalar attributes
Expand Down Expand Up @@ -741,7 +736,7 @@ def __is_ref(self, dtype):
elif isinstance(dtype, np.dtype):
return False
else:
return dtype == DatasetBuilder.OBJECT_REF_TYPE or dtype == DatasetBuilder.REGION_REF_TYPE
return dtype == DatasetBuilder.OBJECT_REF_TYPE

def resolve_ref(self, zarr_ref):
"""
Expand Down Expand Up @@ -792,8 +787,6 @@ def _create_ref(self, ref_object, export_source=None):
:type ref_object: Builder, Container, ReferenceBuilder
:returns: ZarrReference object
"""
if isinstance(ref_object, RegionBuilder): # or region is not None: TODO: Add to support regions
raise NotImplementedError("Region references are currently not supported by ZarrIO")
if isinstance(ref_object, Builder):
if isinstance(ref_object, LinkBuilder):
builder = ref_object.target_builder
Expand All @@ -805,11 +798,6 @@ def _create_ref(self, ref_object, export_source=None):
builder = self.manager.build(ref_object)

path = self.__get_path(builder)
# TODO Add to get region for region references.
# Also add {'name': 'region', 'type': (slice, list, tuple),
# 'doc': 'the region reference indexing object', 'default': None},
# if isinstance(ref_object, RegionBuilder):
# region = ref_object.region

# get the object id if available
object_id = builder.get('object_id', None)
Expand Down Expand Up @@ -1062,10 +1050,7 @@ def write_dataset(self, **kwargs): # noqa: C901
if self.__is_ref(dts['dtype']):
refs.append(i)
ref_tmp = self._create_ref(data[0][i], export_source=export_source)
if isinstance(ref_tmp, ZarrReference):
dts_str = 'object'
else:
dts_str = 'region'
dts_str = 'object'
type_str.append({'name': dts['name'], 'dtype': dts_str})
else:
i = list([dts, ])
Expand Down Expand Up @@ -1122,20 +1107,10 @@ def write_dataset(self, **kwargs): # noqa: C901
dset = self.__list_fill__(parent, name, data, options)
# Write a dataset of references
elif self.__is_ref(options['dtype']):
# TODO Region references are not yet support, but here how the code should look
# if isinstance(data, RegionBuilder):
# shape = (1,)
# type_str = 'region'
# refs = self._create_ref(data.builder, data.region)
if isinstance(data, ReferenceBuilder):
shape = (1,)
type_str = 'object'
refs = self._create_ref(data.builder, export_source=export_source)
# TODO: Region References are not yet supported
# elif options['dtype'] == 'region':
# shape = (len(data), )
# type_str = 'region'
# refs = [self._create_ref(item.builder, item.region) for item in data]
else:
shape = (len(data), )
type_str = 'object'
Expand Down Expand Up @@ -1203,7 +1178,6 @@ def write_dataset(self, **kwargs): # noqa: C901
"ref": ZarrReference,
"reference": ZarrReference,
"object": ZarrReference,
"region": ZarrReference,
}

@classmethod
Expand Down Expand Up @@ -1518,20 +1492,15 @@ def __read_dataset(self, zarr_obj, name):
# Check compound dataset where one of the subsets contains references
has_reference = False
for i, dts in enumerate(dtype):
if dts['dtype'] in ['object', 'region']: # check items for object reference
if dts['dtype'] == 'object': # check items for object reference
has_reference = True
break
retrieved_dtypes = [dtype_dict['dtype'] for dtype_dict in dtype]
if has_reference:
# TODO: BuilderZarrTableDataset does not yet support region reference
data = BuilderZarrTableDataset(zarr_obj, self, retrieved_dtypes)
elif self.__is_ref(dtype):
# Array of references
if dtype == 'object':
data = BuilderZarrReferenceDataset(data, self)
# TODO: Resolution of Region reference not yet supported by BuilderZarrRegionDataset
# elif dtype == 'region':
# data = BuilderZarrRegionDataset(data, self)
data = BuilderZarrReferenceDataset(data, self)

kwargs['data'] = data
if name is None:
Expand All @@ -1554,9 +1523,6 @@ def __read_attrs(self, zarr_obj):
ret[k] = self.__read_group(target_zarr_obj, target_name)
else:
ret[k] = self.__read_dataset(target_zarr_obj, target_name)
# TODO Need to implement region references for attributes
elif v['zarr_dtype'] == 'region':
raise NotImplementedError("Read of region references from attributes not implemented in ZarrIO")
else:
raise NotImplementedError("Unsupported zarr_dtype for attribute " + str(v))
else:
Expand Down

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