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Fix _search_for_backing_files_recursively() to support multifile parquet #1127

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Merged
LucaMarconato merged 1 commit into from
May 13, 2026
+40 −11
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Fix _search_for_backing_files_recursively() to support multifile parquet #1127

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51 changes: 40 additions & 11 deletions src/spatialdata/_io/_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@

from spatialdata._core.spatialdata import SpatialData
from spatialdata._io.format import RasterFormatType, RasterFormatV01, RasterFormatV02, RasterFormatV03
from spatialdata._logging import logger
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
MappingToCoordinateSystem_t,
Expand Down Expand Up @@ -357,17 +358,45 @@ def _search_for_backing_files_recursively(subgraph: Any, files: list[str]) -> No
# This occurs when for example points and images are mixed, the main task still starts with
# read_parquet, but the execution happens through a subgraph which we iterate over to get the
# actual read_parquet task.
for task in v.args[0].values():
# Recursively go through tasks, this is required because differences between dask versions.
piece_dict = _find_piece_dict(task)
if isinstance(piece_dict, dict) and "piece" in piece_dict:
parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
if not parquet_file.endswith(".parquet") or check0 is not None or check1 is not None:
raise ValueError(
f"Unable to parse the parquet file from the dask subgraph {subgraph}. Please "
f"report this bug."
)
files.append(os.path.realpath(parquet_file))
#
# v.args[0] has two known shapes:
# dict – keys are task keys, values are Task objects (classic subgraph case)
# list – list of piece dicts produced when aggregate_files=True aggregates multiple
# parquet files into one partition; check0/check1 are row-group selectors
# ([0], []) rather than None, so only the file extension is validated.
args0 = v.args[0]
if isinstance(args0, dict):
for task in args0.values():
# Recursively go through tasks, this is required because differences between dask
# versions.
piece_dict = _find_piece_dict(task)
if isinstance(piece_dict, dict) and "piece" in piece_dict:
parquet_file, check0, check1 = piece_dict["piece"] # type: ignore[misc]
if (
not parquet_file.endswith(".parquet")
or check0 is not None
or check1 is not None
):
raise ValueError(
f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
f"Please report this bug."
)
files.append(os.path.realpath(parquet_file))
elif isinstance(args0, list):
for item in args0:
if isinstance(item, dict) and "piece" in item:
parquet_file = item["piece"][0]
if not parquet_file.endswith(".parquet"):
raise ValueError(
f"Unable to parse the parquet file from the dask subgraph {subgraph}. "
f"Please report this bug."
)
files.append(os.path.realpath(parquet_file))
else:
logger.warning(
f"Unexpected type {type(args0)} for v.args[0] in the read_parquet task graph. "
f"Backing files may not be detected correctly. Please report this as a bug."
)


def _backed_elements_contained_in_path(path: Path, object: SpatialData | SpatialElement | AnnData) -> list[bool]:
Expand Down
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