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read is functional again, calling it a night.

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sneakers-the-rat 2023-10-10 00:12:33 -07:00
parent 729da40dfd
commit 2d1fe3ad96
3 changed files with 16 additions and 2 deletions
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5
nwb_linkml/src/nwb_linkml/maps/dtype.py
View file

@ -1,5 +1,6 @@
import numpy as np import numpy as np
from typing import Any from typing import Any
from datetime import datetime
flat_to_linkml = { flat_to_linkml = {
"float" : "float", "float" : "float",
@ -67,6 +68,7 @@ np_to_python = {
np.integer: int, np.integer: int,
np.byte: bytes, np.byte: bytes,
np.bytes_: bytes, np.bytes_: bytes,
np.datetime64: datetime,
**{n:int for n in (np.int8, np.int16, np.int32, np.int64, np.short, np.uint8, np.uint16, np.uint32, np.uint64, np.uint)}, **{n:int for n in (np.int8, np.int16, np.int32, np.int64, np.short, np.uint8, np.uint16, np.uint32, np.uint64, np.uint)},
**{n:float for n in (np.float16, np.float32, np.floating, np.float32, np.float64, np.single, np.double, np.float_)}, **{n:float for n in (np.float16, np.float32, np.floating, np.float32, np.float64, np.single, np.double, np.float_)},
**{n:str for n in (np.character, np.str_, np.string_, np.unicode_)} **{n:str for n in (np.character, np.str_, np.string_, np.unicode_)}
@ -83,7 +85,8 @@ allowed_precisions = {
'float16': ['float16', 'float32', 'float64'], 'float16': ['float16', 'float32', 'float64'],
'float32': ['float32', 'float64'], 'float32': ['float32', 'float64'],
'utf': ['ascii'], 'utf': ['ascii'],
'number': ['short', 'int', 'long', 'int16', 'int32', 'int64', 'uint', 'uint8', 'uint16', 'uint32', 'uint64', 'float', 'float16', 'float32', 'float64'] 'number': ['short', 'int', 'long', 'int16', 'int32', 'int64', 'uint', 'uint8', 'uint16', 'uint32', 'uint64', 'float', 'float16', 'float32', 'float64'],
'datetime64': ['object']
} }
""" """
Following HDMF, it turns out that specifying precision actually specifies minimum precision Following HDMF, it turns out that specifying precision actually specifies minimum precision

12
nwb_linkml/src/nwb_linkml/maps/hdf5.py
View file

@ -9,6 +9,7 @@ import pdb
from abc import abstractmethod from abc import abstractmethod
from pathlib import Path from pathlib import Path
from typing import Literal, List, Dict, Optional, Type, Union, Tuple from typing import Literal, List, Dict, Optional, Type, Union, Tuple
import inspect
import h5py import h5py
from enum import StrEnum from enum import StrEnum
@ -20,6 +21,7 @@ from nwb_linkml.maps import Map
from nwb_linkml.maps.hdmf import dynamictable_to_model from nwb_linkml.maps.hdmf import dynamictable_to_model
from nwb_linkml.types.hdf5 import HDF5_Path from nwb_linkml.types.hdf5 import HDF5_Path
from nwb_linkml.types.ndarray import NDArrayProxy from nwb_linkml.types.ndarray import NDArrayProxy
from nwb_linkml.annotations import unwrap_optional
class ReadPhases(StrEnum): class ReadPhases(StrEnum):
@ -530,6 +532,16 @@ class CompleteModelGroups(HDF5Map):
unpacked_results, errors, completes = resolve_references(src.result, completed) unpacked_results, errors, completes = resolve_references(src.result, completed)
res.update(unpacked_results) res.update(unpacked_results)
# now that we have the model in hand, we can solve any datasets that had an array
# but whose attributes are fixed (and thus should just be an array, rather than a subclass)
for k, v in src.model.model_fields.items():
annotation = unwrap_optional(v.annotation)
if inspect.isclass(annotation) and not issubclass(annotation, BaseModel):
if isinstance(res, dict) and k in res and isinstance(res[k], dict) and 'array' in res[k]:
res[k] = res[k]['array']
instance = src.model(**res) instance = src.model(**res)
return H5ReadResult( return H5ReadResult(
path=src.path, path=src.path,

1
nwb_linkml/tests/test_io/test_io_hdf5.py
View file

@ -10,7 +10,6 @@ from ..fixtures import tmp_output_dir, set_config_vars, data_dir
from nwb_linkml.io.hdf5 import HDF5IO from nwb_linkml.io.hdf5 import HDF5IO
from nwb_linkml.io.hdf5 import truncate_file from nwb_linkml.io.hdf5 import truncate_file
@pytest.mark.skip()
@pytest.mark.parametrize('dset', ['aibs.nwb']) @pytest.mark.parametrize('dset', ['aibs.nwb'])
def test_hdf_read(data_dir, dset): def test_hdf_read(data_dir, dset):
NWBFILE = data_dir / dset NWBFILE = data_dir / dset