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, tzinfo=tzlocal())
create_date = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
data = np.arange(1000).reshape((100, 10))
timestamps = np.arange(100)
# Create the first file
nwbfile1 = NWBFile(session_description='demonstrate external files',
identifier='NWBE1',
session_start_time=start_time,
file_create_date=create_date)
test_ts1 = TimeSeries(name='test_timeseries',
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 main():
ep = """
use --nspath to validate against an extension. If --ns is not specified,
validate against all namespaces in namespace file.
"""
parser = ArgumentParser(description="Validate an NWB file", epilog=ep)
parser.add_argument("paths", type=str, nargs='+', help="NWB file paths")
parser.add_argument('-p',
'--nspath',
type=str,
help="the path to the namespace YAML file")
parser.add_argument("-n",
"--ns",
type=str,
help="the namespace to validate against")
parser.add_argument("-lns",
"--list-namespaces",
dest="list_namespaces",
action='store_true',
help="List the available namespaces and exit.")
feature_parser = parser.add_mutually_exclusive_group(required=False)
feature_parser.add_argument("--cached-namespace",
dest="cached_namespace",
action='store_true',
help="Use the cached namespace (default).")
feature_parser.add_argument('--no-cached-namespace',
dest="cached_namespace",
action='store_false',
help="Don't use the cached namespace.")
parser.set_defaults(cached_namespace=True)
args = parser.parse_args()
ret = 0
if args.nspath:
if not os.path.isfile(args.nspath):
print("The namespace file {} is not a valid file.".format(
args.nspath),
file=sys.stderr)
sys.exit(1)
if args.cached_namespace:
print(
"Turning off validation against cached namespace information "
"as --nspath was passed.",
file=sys.stderr)
args.cached_namespace = False
for path in args.paths:
if not os.path.isfile(path):
print("The file {} does not exist.".format(path), file=sys.stderr)
ret = 1
continue
if args.cached_namespace:
catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec,
NWBNamespace)
ns_deps = NWBHDF5IO.load_namespaces(catalog, path)
s = set(ns_deps.keys()) # determine which namespaces are the most
for k in ns_deps: # specific (i.e. extensions) and validate
s -= ns_deps[k].keys() # against those
namespaces = list(sorted(s))
if len(namespaces) > 0:
tm = TypeMap(catalog)
manager = BuildManager(tm)
specloc = "cached namespace information"
else:
manager = None
namespaces = [CORE_NAMESPACE]
specloc = "pynwb namespace information"
print("The file {} has no cached namespace information. "
"Falling back to {}.".format(path, specloc),
file=sys.stderr)
elif args.nspath:
catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec,
NWBNamespace)
namespaces = catalog.load_namespaces(args.nspath)
if len(namespaces) == 0:
print("Could not load namespaces from file {}.".format(
args.nspath),
file=sys.stderr)
sys.exit(1)
tm = TypeMap(catalog)
manager = BuildManager(tm)
specloc = "--nspath namespace information"
else:
manager = None
namespaces = [CORE_NAMESPACE]
specloc = "pynwb namespace information"
if args.list_namespaces:
print("\n".join(namespaces))
ret = 0
continue
if args.ns:
if args.ns in namespaces:
namespaces = [args.ns]
else:
print(
"The namespace {} could not be found in {} as only {} is present."
.format(args.ns, specloc, namespaces),
file=sys.stderr)
ret = 1
continue
with NWBHDF5IO(path, mode='r', manager=manager) as io:
for ns in namespaces:
print("Validating {} against {} using namespace {}.".format(
path, specloc, ns))
ret = ret or _validate_helper(io=io, namespace=ns)
sys.exit(ret)
def main(): # noqa: C901
ep = """
If --ns is not specified, validate against all namespaces in the NWB file.
"""
parser = ArgumentParser(description="Validate an NWB file", epilog=ep)
parser.add_argument("paths", type=str, nargs='+', help="NWB file paths")
# parser.add_argument('-p', '--nspath', type=str, help="the path to the namespace YAML file")
parser.add_argument("-n",
"--ns",
type=str,
help="the namespace to validate against")
parser.add_argument("-lns",
"--list-namespaces",
dest="list_namespaces",
action='store_true',
help="List the available namespaces and exit.")
feature_parser = parser.add_mutually_exclusive_group(required=False)
feature_parser.add_argument("--cached-namespace",
dest="cached_namespace",
action='store_true',
help="Use the cached namespace (default).")
feature_parser.add_argument('--no-cached-namespace',
dest="cached_namespace",
action='store_false',
help="Don't use the cached namespace.")
parser.set_defaults(cached_namespace=True)
args = parser.parse_args()
ret = 0
# TODO Validation against a specific namespace file is currently broken. See pynwb#1396
# if args.nspath:
# if not os.path.isfile(args.nspath):
# print("The namespace file {} is not a valid file.".format(args.nspath), file=sys.stderr)
# sys.exit(1)
#
# if args.cached_namespace:
# print("Turning off validation against cached namespace information "
# "as --nspath was passed.", file=sys.stderr)
# args.cached_namespace = False
for path in args.paths:
if not os.path.isfile(path):
print("The file {} does not exist.".format(path), file=sys.stderr)
ret = 1
continue
if args.cached_namespace:
catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec,
NWBNamespace)
ns_deps = NWBHDF5IO.load_namespaces(catalog, path)
s = set(ns_deps.keys()) # determine which namespaces are the most
for k in ns_deps: # specific (i.e. extensions) and validate
s -= ns_deps[k].keys() # against those
# TODO remove this workaround for issue https://github.com/NeurodataWithoutBorders/pynwb/issues/1357
if 'hdmf-experimental' in s:
s.remove('hdmf-experimental'
) # remove validation of hdmf-experimental for now
namespaces = list(sorted(s))
if len(namespaces) > 0:
tm = TypeMap(catalog)
manager = BuildManager(tm)
specloc = "cached namespace information"
else:
manager = None
namespaces = [CORE_NAMESPACE]
specloc = "pynwb namespace information"
print("The file {} has no cached namespace information. "
"Falling back to {}.".format(path, specloc),
file=sys.stderr)
# elif args.nspath:
# catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
# namespaces = catalog.load_namespaces(args.nspath)
#
# if len(namespaces) == 0:
# print("Could not load namespaces from file {}.".format(args.nspath), file=sys.stderr)
# sys.exit(1)
#
# tm = TypeMap(catalog)
# manager = BuildManager(tm)
# specloc = "--nspath namespace information"
else:
manager = None
namespaces = [CORE_NAMESPACE]
specloc = "pynwb namespace information"
if args.list_namespaces:
print("\n".join(namespaces))
ret = 0
continue
if args.ns:
if args.ns in namespaces:
namespaces = [args.ns]
elif args.cached_namespace and args.ns in ns_deps: # validating against a dependency
for k in ns_deps:
if args.ns in ns_deps[k]:
print((
"The namespace '{}' is included by the namespace '{}'. Please validate against "
"that namespace instead.").format(args.ns, k),
file=sys.stderr)
ret = 1
continue
else:
print(
"The namespace '{}' could not be found in {} as only {} is present."
.format(args.ns, specloc, namespaces),
file=sys.stderr)
ret = 1
continue
with NWBHDF5IO(path, mode='r', manager=manager) as io:
for ns in namespaces:
print("Validating {} against {} using namespace '{}'.".format(
path, specloc, ns))
ret = ret or _validate_helper(io=io, namespace=ns)
sys.exit(ret)
