def test_write_cache_spec(self):
'''
Round-trip test for writing spec and reading it back in
'''
with File(self.path) as fil:
with HDF5IO(self.path, manager=self.manager, file=fil,
mode='a') as io:
io.write(self.container)
with File(self.path) as f:
self.assertIn('specifications', f)
ns_catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec,
NWBNamespace)
HDF5IO.load_namespaces(ns_catalog, self.path, namespaces=['core'])
original_ns = self.manager.namespace_catalog.get_namespace('core')
cached_ns = ns_catalog.get_namespace('core')
self.maxDiff = None
for key in ('author', 'contact', 'doc', 'full_name', 'name'):
with self.subTest(namespace_field=key):
self.assertEqual(original_ns[key], cached_ns[key])
for dt in original_ns.get_registered_types():
with self.subTest(neurodata_type=dt):
original_spec = original_ns.get_spec(dt)
cached_spec = cached_ns.get_spec(dt)
with self.subTest(test='data_type spec read back in'):
self.assertIsNotNone(cached_spec)
with self.subTest(test='cached spec preserved original spec'):
self.assertDictEqual(original_spec, cached_spec)
def _check_spec(self):
ns_catalog = NamespaceCatalog()
HDF5IO.load_namespaces(ns_catalog, self.path)
self.maxDiff = None
for namespace in self.manager.namespace_catalog.namespaces:
with self.subTest(namespace=namespace):
original_ns = self.manager.namespace_catalog.get_namespace(namespace)
cached_ns = ns_catalog.get_namespace(namespace)
ns_fields_to_check = list(original_ns.keys())
ns_fields_to_check.remove('schema') # schema fields will not match, so reset
for ns_field in ns_fields_to_check:
with self.subTest(namespace_field=ns_field):
self.assertEqual(original_ns[ns_field], cached_ns[ns_field])
for dt in original_ns.get_registered_types():
with self.subTest(data_type=dt):
original_spec = original_ns.get_spec(dt)
cached_spec = cached_ns.get_spec(dt)
with self.subTest('Data type spec is read back in'):
self.assertIsNotNone(cached_spec)
with self.subTest('Cached spec matches original spec'):
self.assertDictEqual(original_spec, cached_spec)
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")
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)
namespaces = HDF5IO.load_namespaces(catalog, path).keys()
if len(namespaces) > 0:
tm = TypeMap(catalog)
manager = BuildManager(tm)
specloc = "cached namespace information"
else:
manager = None
namespaces = available_namespaces()
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 = available_namespaces()
specloc = "pynwb namespace information"
if args.ns:
if args.ns in namespaces:
namespaces = [args.ns]
else:
print("The namespace {} could not be found in {}.".format(
args.ns, specloc),
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)