return ret
def _get_resources():
# LEGACY: Needed to support legacy implementation.
return __get_resources()
# a global namespace catalog
global __NS_CATALOG
global __TYPE_MAP
__NS_CATALOG = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
hdmf_typemap = hdmf.common.get_type_map()
__NS_CATALOG.merge(hdmf_typemap.namespace_catalog)
__TYPE_MAP = TypeMap(__NS_CATALOG)
__TYPE_MAP.merge(hdmf_typemap)
@docval(
{
'name': 'extensions',
'type': (str, TypeMap, list),
'doc':
'a path to a namespace, a TypeMap, or a list consisting of paths to namespaces and TypeMaps',
'default': None
},
returns="the namespaces loaded from the given file",
rtype=tuple,
class TestCustomSpecClasses(TestCase):
def setUp(self): # noqa: C901
self.ns_catalog = NamespaceCatalog(CustomGroupSpec, CustomDatasetSpec,
CustomSpecNamespace)
hdmf_typemap = get_type_map()
self.ns_catalog.merge(hdmf_typemap.namespace_catalog)
def test_constructor_getters(self):
self.assertEqual(self.ns_catalog.dataset_spec_cls, CustomDatasetSpec)
self.assertEqual(self.ns_catalog.group_spec_cls, CustomGroupSpec)
self.assertEqual(self.ns_catalog.spec_namespace_cls,
CustomSpecNamespace)
def test_load_namespaces(self):
namespace_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'test.namespace.yaml')
namespace_deps = self.ns_catalog.load_namespaces(namespace_path)
# test that the dependencies are correct, including dependencies of the dependencies
expected = set([
'Data', 'Container', 'DynamicTable', 'ElementIdentifiers',
'VectorData'
])
self.assertSetEqual(set(namespace_deps['test']['hdmf-common']),
expected)
# test that the types are loaded
types = self.ns_catalog.get_types('test.base.yaml')
expected = ('TestData', 'TestContainer', 'TestTable')
self.assertTupleEqual(types, expected)
# test that the namespace is correct and the types_key is updated for test ns
test_namespace = self.ns_catalog.get_namespace('test')
expected = {
'doc':
'Test namespace',
'schema': [{
'namespace': 'hdmf-common',
'my_data_types': ['Data', 'DynamicTable', 'Container']
}, {
'doc': 'This source module contains base data types.',
'source': 'test.base.yaml',
'title': 'Base data types'
}],
'name':
'test',
'full_name':
'Test',
'version':
'0.1.0',
'author': ['Test test'],
'contact': ['*****@*****.**']
}
self.assertDictEqual(test_namespace, expected)
# test that the def_key is updated for test ns
test_data_spec = self.ns_catalog.get_spec('test', 'TestData')
self.assertTrue('my_data_type_def' in test_data_spec)
self.assertTrue('my_data_type_inc' in test_data_spec)
# test that the def_key is maintained for hdmf-common
data_spec = self.ns_catalog.get_spec('hdmf-common', 'Data')
self.assertTrue('data_type_def' in data_spec)
def test_load_namespaces_ext(self):
namespace_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'test.namespace.yaml')
self.ns_catalog.load_namespaces(namespace_path)
ext_namespace_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
'test-ext.namespace.yaml')
ext_namespace_deps = self.ns_catalog.load_namespaces(
ext_namespace_path)
# test that the dependencies are correct, including dependencies of the dependencies
expected_deps = set([
'TestData', 'TestContainer', 'TestTable', 'Container', 'Data',
'DynamicTable', 'ElementIdentifiers', 'VectorData'
])
self.assertSetEqual(set(ext_namespace_deps['test-ext']['test']),
expected_deps)
def test_load_namespaces_bad_path(self):
namespace_path = 'test.namespace.yaml'
msg = "namespace file 'test.namespace.yaml' not found"
with self.assertRaisesWith(IOError, msg):
self.ns_catalog.load_namespaces(namespace_path)
def test_load_namespaces_twice(self):
namespace_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'test.namespace.yaml')
namespace_deps1 = self.ns_catalog.load_namespaces(namespace_path)
namespace_deps2 = self.ns_catalog.load_namespaces(namespace_path)
self.assertDictEqual(namespace_deps1, namespace_deps2)
