nwb-linkml/nwb_linkml/tests/test_io/test_io_hdf5.py

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import pdb
import h5py
import pytest
from pathlib import Path
import numpy as np
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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
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@pytest.mark.parametrize('dset', ['aibs.nwb'])
def test_hdf_read(data_dir, dset):
NWBFILE = data_dir / dset
io = HDF5IO(path=NWBFILE)
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# the test for now is just whether we can read it lol
model = io.read()
@pytest.mark.skip()
def test_truncate_file(tmp_output_dir):
source = tmp_output_dir / 'truncate_source.hdf5'
# create a dang ol hdf5 file with a big dataset and some softlinks and make sure
# we truncate the dataset and preserve softlink
h5f = h5py.File(str(source), 'w')
data_group = h5f.create_group('data')
dataset_contig = h5f.create_dataset(
'/data/dataset_contig',
data=np.zeros((1000,30,40), dtype=np.float64),
compression = "gzip",
compression_opts = 9
)
dataset_chunked = h5f.create_dataset(
'/data/dataset_chunked',
data=np.zeros((1000, 40, 50), dtype=np.float64),
compression="gzip",
compression_opts=9,
chunks=True
)
dataset_contig.attrs['reference_other'] = dataset_chunked.ref
dataset_chunked.attrs['reference_other'] = dataset_contig.ref
dataset_contig.attrs['anattr'] = 1
link_group = h5f.create_group('link/child')
link_group.attrs['reference_contig'] = dataset_contig.ref
link_group.attrs['reference_chunked'] = dataset_chunked.ref
h5f.flush()
h5f.close()
source_size = source.stat().st_size
# do it without providing target to check that we make filename correctly
n = 10
target_output = truncate_file(source, n=n)
assert target_output == source.parent / (source.stem + '_truncated.hdf5')
# check that we actually made it smaller
target_size = target_output.stat().st_size
# empirically, the source dataset is ~125KB and truncated is ~17KB
assert target_size < source_size / 5
# then check that we have what's expected in the file
target_h5f = h5py.File(target_output, 'r')
# truncation happened
assert target_h5f['data']['dataset_contig'].shape == (n, 30, 40)
assert target_h5f['data']['dataset_chunked'].shape == (n, 40, 50)
# references still work
# can't directly assess object identity equality with "is"
# so this tests if the referenced dereference and that they dereference to the right place
assert target_h5f[target_h5f['data']['dataset_contig'].attrs['reference_other']].name == target_h5f['data']['dataset_chunked'].name
assert target_h5f[target_h5f['data']['dataset_chunked'].attrs['reference_other']].name == target_h5f['data']['dataset_contig'].name
assert target_h5f[target_h5f['link']['child'].attrs['reference_contig']].name == target_h5f['data']['dataset_contig'].name
assert target_h5f[target_h5f['link']['child'].attrs['reference_chunked']].name == target_h5f['data']['dataset_chunked'].name
assert target_h5f['data']['dataset_contig'].attrs['anattr'] == 1
@pytest.mark.skip()
def test_flatten_hdf():
from nwb_linkml.io.hdf5 import HDF5IO
from nwb_linkml.maps.hdf5 import flatten_hdf
path = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb'
import h5py
h5f = h5py.File(path)
flat = flatten_hdf(h5f)
assert not any(['specifications' in v.path for v in flat.values()])
pdb.set_trace()
raise NotImplementedError('Just a stub for local testing for now, finish me!')