def test_cache_spec(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 = NWBHDF5IO(self.test_temp_file.name)
# 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.write(nwbfile1, cache_spec=True)
self.io.close()
ns_catalog = NamespaceCatalog(group_spec_cls=NWBGroupSpec,
dataset_spec_cls=NWBDatasetSpec,
spec_namespace_cls=NWBNamespace)
NWBHDF5IO.load_namespaces(ns_catalog, self.test_temp_file.name)
self.assertEqual(ns_catalog.namespaces, ('core', ))
source_types = self.__get_types(self.io.manager.namespace_catalog)
read_types = self.__get_types(ns_catalog)
self.assertSetEqual(source_types, read_types)
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))