Partial reading

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables

src/spatialdata/_io/_utils.py

@@ -4,13 +4,16 @@
 import logging
 import os.path
 import re
+import sys
 import tempfile
+import traceback
 import warnings
 from collections.abc import Generator, Mapping, Sequence
 from contextlib import contextmanager
+from enum import Enum
 from functools import singledispatch
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
 import zarr
 from anndata import AnnData
@@ -383,3 +386,59 @@ def save_transformations(sdata: SpatialData) -> None:
  stacklevel=2,
  )
  sdata.write_transformations()
+
+
+class BadFileHandleMethod(Enum):
+ ERROR = "error"
+ WARN = "warn"
+
+
+@contextmanager
+def handle_read_errors(
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+ location: str,
+ exc_types: tuple[type[Exception], ...],
+) -> Generator[None, None, None]:
+ """
+ Handle read errors according to parameter `on_bad_files`.
+
+ Parameters
+ ----------
+ on_bad_files
+ Specifies what to do upon encountering an exception.
+ Allowed values are :
+
+ - 'error', let the exception be raised.
+ - 'warn', convert the exception into a warning if it is one of the expected exception types.
+ location
+ String identifying the function call where the exception happened
+ exc_types
+ A tuple of expected exception classes that should be converted into warnings.
+
+ Raises
+ ------
+ If `on_bad_files="error"`, all encountered exceptions are raised.
+ If `on_bad_files="warn"`, any encountered exceptions not matching the `exc_types` are raised.
+ """
+ on_bad_files = BadFileHandleMethod(on_bad_files) # str to enum
+ if on_bad_files == BadFileHandleMethod.WARN:
+ try:
+ yield
+ except exc_types as e:
+ # Extract the original filename and line number from the exception and
+ # create a warning from it.
+ exc_traceback = sys.exc_info()[-1]
+ last_frame, lineno = list(traceback.walk_tb(exc_traceback))[-1]
+ filename = last_frame.f_code.co_filename
+ # Include the location (element path) in the warning message.
+ message = f"{location}: {e.__class__.__name__}: {e.args[0]}"
+ warnings.warn_explicit(
+ message=message,
+ category=UserWarning,
+ filename=filename,
+ lineno=lineno,
+ )
+ # continue
+ else: # on_bad_files == BadFileHandleMethod.ERROR
+ # Let it raise exceptions
+ yield

src/spatialdata/_io/io_table.py

@@ -1,21 +1,29 @@
 from __future__ import annotations
 
 import os
+from json import JSONDecodeError
+from typing import Literal
 
 import numpy as np
 import zarr
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 from anndata._io.specs import write_elem as write_adata
 from ome_zarr.format import Format
+from zarr.errors import ArrayNotFoundError
 
+from spatialdata._io._utils import BadFileHandleMethod, handle_read_errors
 from spatialdata._io.format import CurrentTablesFormat, TablesFormats, _parse_version
 from spatialdata._logging import logger
 from spatialdata.models import TableModel
 
 
 def _read_table(
- zarr_store_path: str, group: zarr.Group, subgroup: zarr.Group, tables: dict[str, AnnData]
+ zarr_store_path: str,
+ group: zarr.Group,
+ subgroup: zarr.Group,
+ tables: dict[str, AnnData],
+ on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
 ) -> dict[str, AnnData]:
  """
  Read in tables in the tables Zarr.group of a SpatialData Zarr store.
@@ -30,6 +38,8 @@ def _read_table(
  The subgroup containing the tables.
  tables
  A dictionary of tables.
+ on_bad_files
+ Specifies what to do upon encountering a bad file, e.g. corrupted, invalid or missing files.
 
  Returns
  -------
@@ -40,33 +50,38 @@ def _read_table(
  f_elem = subgroup[table_name]
  f_elem_store = os.path.join(zarr_store_path, f_elem.path)
 
- tables[table_name] = read_anndata_zarr(f_elem_store)
+ with handle_read_errors(
+ on_bad_files=on_bad_files,
+ location=f"{subgroup.path}/{table_name}",
+ exc_types=(JSONDecodeError, KeyError, ValueError, ArrayNotFoundError),
+ ):
+ tables[table_name] = read_anndata_zarr(f_elem_store)
 
- f = zarr.open(f_elem_store, mode="r")
- version = _parse_version(f, expect_attrs_key=False)
- assert version is not None
- # since have just one table format, we currently read it but do not use it; if we ever change the format
- # we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
- _ = TablesFormats[version]
- f.store.close()
+f = zarr.open(f_elem_store, mode="r")
+version = _parse_version(f, expect_attrs_key=False)
+assert version is not None
+# since have just one table format, we currently read it but do not use it; if we ever change the format
+# we can rename the two _ to format and implement the per-format read logic (as we do for shapes)
+_ = TablesFormats[version]
+f.store.close()
 
- # # replace with format from above
- # version = "0.1"
- # format = TablesFormats[version]
- if TableModel.ATTRS_KEY in tables[table_name].uns:
- # fill out eventual missing attributes that has been omitted because their value was None
- attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
- if "region" not in attrs:
- attrs["region"] = None
- if "region_key" not in attrs:
- attrs["region_key"] = None
- if "instance_key" not in attrs:
- attrs["instance_key"] = None
- # fix type for region
- if "region" in attrs and isinstance(attrs["region"], np.ndarray):
- attrs["region"] = attrs["region"].tolist()
+# # replace with format from above
+# version = "0.1"
+# format = TablesFormats[version]
+if TableModel.ATTRS_KEY in tables[table_name].uns:
+# fill out eventual missing attributes that has been omitted because their value was None
+attrs = tables[table_name].uns[TableModel.ATTRS_KEY]
+if "region" not in attrs:
+attrs["region"] = None
+if "region_key" not in attrs:
+attrs["region_key"] = None
+if "instance_key" not in attrs:
+attrs["instance_key"] = None
+# fix type for region
+if "region" in attrs and isinstance(attrs["region"], np.ndarray):
+attrs["region"] = attrs["region"].tolist()
 
- count += 1
+count += 1
 
  logger.debug(f"Found {count} elements in {subgroup}")
  return tables