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read is functional again, calling it a night.

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This commit is contained in:
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
from typing import Any
from datetime import datetime
flat_to_linkml = {
"float" : "float",
@ -67,6 +68,7 @@ np_to_python = {
np.integer: int,
np.byte: 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: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_)}
@ -83,7 +85,8 @@ allowed_precisions = {
'float16': ['float16', 'float32', 'float64'],
'float32': ['float32', 'float64'],
'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

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

@ -9,6 +9,7 @@ import pdb
from abc import abstractmethod
from pathlib import Path
from typing import Literal, List, Dict, Optional, Type, Union, Tuple
import inspect
import h5py
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.types.hdf5 import HDF5_Path
from nwb_linkml.types.ndarray import NDArrayProxy
from nwb_linkml.annotations import unwrap_optional
class ReadPhases(StrEnum):
@ -530,6 +532,16 @@ class CompleteModelGroups(HDF5Map):
unpacked_results, errors, completes = resolve_references(src.result, completed)
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)
return H5ReadResult(
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 truncate_file
@pytest.mark.skip()
@pytest.mark.parametrize('dset', ['aibs.nwb'])
def test_hdf_read(data_dir, dset):
NWBFILE = data_dir / dset