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Added check for HDF5 datasets with type = object #46

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Added check for HDF5 datasets with type = object #46

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -124,3 +124,4 @@ dmypy.json
# Pyre type checker
.pyre/

.DS_Store
20 changes: 20 additions & 0 deletions .vscode/launch.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
{
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"name": "Make References",
"type": "python",
"request": "launch",
"program": "${file}",
"console": "integratedTerminal",
"args": [
"-if",
"TEST00USA_R_20203370000_01D_15S_MO.rnx.nc"
],
"cwd": "/Users/metadatagamechanger/data/UNAVCO/rinexData/p226/testData"
}
]
}
13 changes: 10 additions & 3 deletions fsspec_reference_maker/hdf.py
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Expand Up @@ -15,7 +15,6 @@

lggr = logging.getLogger('h5-to-zarr')


class SingleHdf5ToZarr:
"""Translate the content of one HDF5 file into Zarr metadata.

Expand Down Expand Up @@ -147,13 +146,21 @@ def _translator(self, name: str, h5obj: Union[h5py.Dataset, h5py.Group]):
"""
refs = {}
if isinstance(h5obj, h5py.Dataset):
lggr.debug(f'HDF5 dataset: {h5obj.name}')
lggr.debug(f'HDF5 dataset: {h5obj.name} dataType: {h5obj.dtype}')
if h5obj.id.get_create_plist().get_layout() == h5py.h5d.COMPACT:
RuntimeError(
f'Compact HDF5 datasets not yet supported: <{h5obj.name} '
f'{h5obj.shape} {h5obj.dtype} {h5obj.nbytes} bytes>')
return

#
# check for unsupported HDF DataTypes
#
if h5obj.dtype == 'object':
lggr.warning(f'HDF5 variable length strings are not yet supported: <{h5obj.name} ')
lggr.warning(f'shape: {h5obj.shape} type: {h5obj.dtype} bytes: {h5obj.nbytes} bytes>')
RuntimeError(
f'{h5obj.shape} {h5obj.dtype} {h5obj.nbytes} bytes>')
return
#
# check for unsupported HDF encoding/filters
#
Expand Down