mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-10 00:34:29 +00:00
88 lines
3.5 KiB
Python
88 lines
3.5 KiB
Python
import pdb
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import h5py
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import pytest
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from pathlib import Path
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import numpy as np
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from ..fixtures import tmp_output_dir, set_config_vars, data_dir
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from nwb_linkml.io.hdf5 import HDF5IO
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from nwb_linkml.io.hdf5 import truncate_file
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@pytest.mark.parametrize('dset', ['aibs.nwb'])
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def test_hdf_read(data_dir, dset):
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NWBFILE = data_dir / dset
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io = HDF5IO(path=NWBFILE)
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# the test for now is just whether we can read it lol
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model = io.read()
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def test_truncate_file(tmp_output_dir):
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source = tmp_output_dir / 'truncate_source.hdf5'
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# create a dang ol hdf5 file with a big dataset and some softlinks and make sure
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# we truncate the dataset and preserve softlink
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h5f = h5py.File(str(source), 'w')
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data_group = h5f.create_group('data')
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dataset_contig = h5f.create_dataset(
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'/data/dataset_contig',
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data=np.zeros((1000,30,40), dtype=np.float64),
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compression = "gzip",
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compression_opts = 9
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)
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dataset_chunked = h5f.create_dataset(
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'/data/dataset_chunked',
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data=np.zeros((1000, 40, 50), dtype=np.float64),
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compression="gzip",
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compression_opts=9,
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chunks=True
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)
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dataset_contig.attrs['reference_other'] = dataset_chunked.ref
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dataset_chunked.attrs['reference_other'] = dataset_contig.ref
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dataset_contig.attrs['anattr'] = 1
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link_group = h5f.create_group('link/child')
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link_group.attrs['reference_contig'] = dataset_contig.ref
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link_group.attrs['reference_chunked'] = dataset_chunked.ref
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h5f.flush()
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h5f.close()
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source_size = source.stat().st_size
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# do it without providing target to check that we make filename correctly
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n = 10
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target_output = truncate_file(source, n=n)
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assert target_output == source.parent / (source.stem + '_truncated.hdf5')
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# check that we actually made it smaller
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target_size = target_output.stat().st_size
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# empirically, the source dataset is ~125KB and truncated is ~17KB
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assert target_size < source_size / 5
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# then check that we have what's expected in the file
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target_h5f = h5py.File(target_output, 'r')
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# truncation happened
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assert target_h5f['data']['dataset_contig'].shape == (n, 30, 40)
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assert target_h5f['data']['dataset_chunked'].shape == (n, 40, 50)
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# references still work
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# can't directly assess object identity equality with "is"
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# so this tests if the referenced dereference and that they dereference to the right place
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assert target_h5f[target_h5f['data']['dataset_contig'].attrs['reference_other']].name == target_h5f['data']['dataset_chunked'].name
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assert target_h5f[target_h5f['data']['dataset_chunked'].attrs['reference_other']].name == target_h5f['data']['dataset_contig'].name
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assert target_h5f[target_h5f['link']['child'].attrs['reference_contig']].name == target_h5f['data']['dataset_contig'].name
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assert target_h5f[target_h5f['link']['child'].attrs['reference_chunked']].name == target_h5f['data']['dataset_chunked'].name
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assert target_h5f['data']['dataset_contig'].attrs['anattr'] == 1
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@pytest.mark.skip()
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def test_flatten_hdf():
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from nwb_linkml.io.hdf5 import HDF5IO
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from nwb_linkml.maps.hdf5 import flatten_hdf
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path = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb'
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import h5py
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h5f = h5py.File(path)
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flat = flatten_hdf(h5f)
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assert not any(['specifications' in v.path for v in flat.values()])
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pdb.set_trace()
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raise NotImplementedError('Just a stub for local testing for now, finish me!')
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