def test_copy_file_with_external_links(self):
# Setup all the data we need
start_time = datetime(2017, 4, 3, 11, 0, 0)
create_date = datetime(2017, 4, 15, 12, 0, 0)
data = np.arange(1000).reshape((100, 10))
timestamps = np.arange(100)
# Create the first file
nwbfile1 = NWBFile(source='PyNWB tutorial',
session_description='demonstrate external files',
identifier='NWBE1',
session_start_time=start_time,
file_create_date=create_date)
test_ts1 = TimeSeries(name='test_timeseries',
source='PyNWB tutorial',
data=data,
unit='SIunit',
timestamps=timestamps)
nwbfile1.add_acquisition(test_ts1)
# Write the first file
self.io[0].write(nwbfile1)
nwbfile1_read = self.io[0].read()
# Create the second file
nwbfile2 = NWBFile(source='PyNWB tutorial',
session_description='demonstrate external files',
identifier='NWBE1',
session_start_time=start_time,
file_create_date=create_date)
test_ts2 = TimeSeries(name='test_timeseries',
source='PyNWB tutorial',
data=nwbfile1_read.get_acquisition('test_timeseries').data,
unit='SIunit',
timestamps=timestamps)
nwbfile2.add_acquisition(test_ts2)
# Write the second file
self.io[1].write(nwbfile2)
self.io[1].close()
self.io[0].close() # Don't forget to close the first file too
# Copy the file
self.io[2].close()
HDF5IO.copy_file(source_filename=self.test_temp_files[1].name,
dest_filename=self.test_temp_files[2].name,
expand_external=True,
expand_soft=False,
expand_refs=False)
# Test that everything is working as expected
# Confirm that our original data file is correct
f1 = File(self.test_temp_files[0].name)
self.assertTrue(isinstance(f1.get('/acquisition/test_timeseries/data', getlink=True), HardLink))
# Confirm that we successfully created and External Link in our second file
f2 = File(self.test_temp_files[1].name)
self.assertTrue(isinstance(f2.get('/acquisition/test_timeseries/data', getlink=True), ExternalLink))
# Confirm that we successfully resolved the External Link when we copied our second file
f3 = File(self.test_temp_files[2].name)
self.assertTrue(isinstance(f3.get('/acquisition/test_timeseries/data', getlink=True), HardLink))
def test__chunked_iter_fill_numpy_unmatched_buffer_size(
self): # noqa: F811
a = np.arange(30).reshape(5, 2, 3)
dci = DataChunkIterator(data=a.tolist(), buffer_size=3)
my_dset = HDF5IO.__chunked_iter_fill__(self.f, 'test_dataset', dci)
self.assertTrue(np.all(my_dset[:] == a))
self.assertTupleEqual(my_dset.shape, a.shape)
def setUp(self):
self.test_temp_file = tempfile.NamedTemporaryFile()
# On Windows h5py cannot truncate an open file in write mode.
# The temp file will be closed before h5py truncates it
# and will be removed during the tearDown step.
self.test_temp_file.close()
self.io = HDF5IO(self.test_temp_file.name)
self.f = self.io._file
def test__chunked_iter_fill_iterator_unmatched_buffer_size(self):
dci = DataChunkIterator(data=range(10), buffer_size=3)
my_dset = HDF5IO.__chunked_iter_fill__(self.f, 'test_dataset', dci)
self.assertListEqual(my_dset[:].tolist(), list(range(10)))