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[24.0] fix anndata #21079

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[24.0] fix anndata #21079

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27 changes: 19 additions & 8 deletions lib/galaxy/datatypes/binary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1392,6 +1392,8 @@ class Anndata(H5):
True
>>> Anndata().sniff(get_test_fname('adata_unk.h5ad'))
True
>>> Anndata().sniff(get_test_fname('adata_noX.h5ad'))
True
"""

file_ext = "h5ad"
Expand Down Expand Up @@ -1563,14 +1565,23 @@ def _layercountsize(tmp, lennames=0):

# Resolving the problematic shape parameter
if "X" in dataset.metadata.layers_names:
# Shape we determine here due to the non-standard representation of 'X' dimensions
shape = anndata_file["X"].attrs.get("shape")
if shape is not None:
dataset.metadata.shape = tuple(shape)
elif hasattr(anndata_file["X"], "shape"):
dataset.metadata.shape = tuple(anndata_file["X"].shape)

if dataset.metadata.shape is None:

# Check if X is a null/empty matrix (common in fragment-only files of snapatac data for example)
if (
anndata_file["X"].attrs.get("encoding-type") == "null"
or anndata_file["X"].attrs.get("shape") is None
):
# if X matrix is null/empty, derive shape from obs and var sizes
dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size))
else:
# if X matrix has actual data
shape = anndata_file["X"].attrs.get("shape")
if shape is not None:
dataset.metadata.shape = tuple(shape)
elif hasattr(anndata_file["X"], "shape") and anndata_file["X"].shape is not None:
dataset.metadata.shape = tuple(anndata_file["X"].shape)

if dataset.metadata.shape is None or dataset.metadata.shape == (-1, -1):
dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size))

def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
Expand Down
Binary file added lib/galaxy/datatypes/test/adata_noX.h5ad
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