def setUp(self):
super().setUp()
self.foo_bucket = FooBucket('test_foo_bucket', [
Foo('my_foo1', list(range(10)), 'value1', 10),
Foo('my_foo2', list(range(10, 20)), 'value2', 20)])
self.foo_builders = {
'my_foo1': GroupBuilder('my_foo1',
datasets={'my_data': DatasetBuilder(
'my_data',
list(range(10)),
attributes={'attr2': 10})},
attributes={'attr1': 'value1', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': self.foo_bucket.foos['my_foo1'].object_id}),
'my_foo2': GroupBuilder('my_foo2', datasets={'my_data':
DatasetBuilder(
'my_data',
list(range(10, 20)),
attributes={'attr2': 20})},
attributes={'attr1': 'value2', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': self.foo_bucket.foos['my_foo2'].object_id})
}
self.setUpBucketBuilder()
self.setUpBucketSpec()
self.spec_catalog.register_spec(self.bucket_spec, 'test.yaml')
self.type_map.register_container_type(CORE_NAMESPACE, 'FooBucket', FooBucket)
self.type_map.register_map(FooBucket, self.setUpBucketMapper())
self.manager = BuildManager(self.type_map)
def setUp(self):
self.foo_spec = GroupSpec(
'A test group specification with data type Foo',
data_type_def='Foo')
self.bar_spec = GroupSpec(
'A test group specification with a data type Bar',
data_type_def='Bar',
datasets=[DatasetSpec('an example dataset', 'int', name='data')],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text'),
AttributeSpec('attr2', 'an example integer attribute', 'int'),
AttributeSpec('foo',
'a referenced foo',
RefSpec('Foo', 'object'),
required=False)
])
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.foo_spec, 'test.yaml')
self.spec_catalog.register_spec(self.bar_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'source': 'test.yaml'
}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
self.type_map.register_container_type(CORE_NAMESPACE, 'Bar', Bar)
self.manager = BuildManager(self.type_map)
self.foo_mapper = ObjectMapper(self.foo_spec)
self.bar_mapper = ObjectMapper(self.bar_spec)
class TestNestedBase(with_metaclass(ABCMeta, TestBase)):
def setUp(self):
super(TestNestedBase, self).setUp()
self.foo_bucket = FooBucket('test_foo_bucket', [
Foo('my_foo1', list(range(10)), 'value1', 10),
Foo('my_foo2', list(range(10, 20)), 'value2', 20)
])
self.foo_builders = {
'my_foo1':
GroupBuilder('my_foo1',
datasets={
'my_data':
DatasetBuilder('my_data',
list(range(10)),
attributes={'attr2': 10})
},
attributes={
'attr1': 'value1',
'namespace': CORE_NAMESPACE,
'data_type': 'Foo'
}),
'my_foo2':
GroupBuilder('my_foo2',
datasets={
'my_data':
DatasetBuilder('my_data',
list(range(10, 20)),
attributes={'attr2': 20})
},
attributes={
'attr1': 'value2',
'namespace': CORE_NAMESPACE,
'data_type': 'Foo'
})
}
self.setUpBucketBuilder()
self.setUpBucketSpec()
self.spec_catalog.register_spec(self.bucket_spec, 'test.yaml')
self.type_map.register_container_type(CORE_NAMESPACE, 'FooBucket',
FooBucket)
self.type_map.register_map(FooBucket, ObjectMapper)
self.manager = BuildManager(self.type_map)
def setUpBucketBuilder(self):
raise unittest.SkipTest('Abstract Base Class')
def setUpBucketSpec(self):
raise unittest.SkipTest('Abstract Base Class')
def test_build(self):
''' Test default mapping for an Container that has an Container as an attribute value '''
builder = self.manager.build(self.foo_bucket)
self.assertDictEqual(builder, self.bucket_builder)
def test_construct(self):
container = self.manager.construct(self.bucket_builder)
self.assertEqual(container, self.foo_bucket)
class NestedBaseMixin(metaclass=ABCMeta):
def setUp(self):
super().setUp()
self.foo_bucket = FooBucket('test_foo_bucket', [
Foo('my_foo1', list(range(10)), 'value1', 10),
Foo('my_foo2', list(range(10, 20)), 'value2', 20)])
self.foo_builders = {
'my_foo1': GroupBuilder('my_foo1',
datasets={'my_data': DatasetBuilder(
'my_data',
list(range(10)),
attributes={'attr2': 10})},
attributes={'attr1': 'value1', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': self.foo_bucket.foos['my_foo1'].object_id}),
'my_foo2': GroupBuilder('my_foo2', datasets={'my_data':
DatasetBuilder(
'my_data',
list(range(10, 20)),
attributes={'attr2': 20})},
attributes={'attr1': 'value2', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': self.foo_bucket.foos['my_foo2'].object_id})
}
self.setUpBucketBuilder()
self.setUpBucketSpec()
self.spec_catalog.register_spec(self.bucket_spec, 'test.yaml')
self.type_map.register_container_type(CORE_NAMESPACE, 'FooBucket', FooBucket)
self.type_map.register_map(FooBucket, self.setUpBucketMapper())
self.manager = BuildManager(self.type_map)
@abstractmethod
def setUpBucketBuilder(self):
raise NotImplementedError('Cannot run test unless setUpBucketBuilder is implemented')
@abstractmethod
def setUpBucketSpec(self):
raise NotImplementedError('Cannot run test unless setUpBucketSpec is implemented')
@abstractmethod
def setUpBucketMapper(self):
raise NotImplementedError('Cannot run test unless setUpBucketMapper is implemented')
def test_build(self):
''' Test default mapping for an Container that has an Container as an attribute value '''
builder = self.manager.build(self.foo_bucket)
self.assertDictEqual(builder, self.bucket_builder)
def test_construct(self):
container = self.manager.construct(self.bucket_builder)
self.assertEqual(container, self.foo_bucket)
def setUp(self):
self.foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Foo',
datasets=[
DatasetSpec(doc='an example dataset',
dtype='int',
name='my_data',
attributes=[
AttributeSpec(
name='attr2',
doc='an example integer attribute',
dtype='int')
])
],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text')
])
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.foo_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'source': 'test.yaml'
}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
self.type_map.register_map(Foo, FooMapper)
self.manager = BuildManager(self.type_map)
def get_manager(**kwargs):
'''
Get a BuildManager to use for I/O using the given extensions. If no extensions are provided,
return a BuildManager that uses the core namespace
'''
type_map = call_docval_func(get_type_map, kwargs)
return BuildManager(type_map)
def setUpManager(self, specs):
spec_catalog = SpecCatalog()
schema_file = 'test.yaml'
for s in specs:
spec_catalog.register_spec(s, schema_file)
namespace = SpecNamespace(doc='a test namespace',
name=CORE_NAMESPACE,
schema=[{
'source': schema_file
}],
version='0.1.0',
catalog=spec_catalog)
namespace_catalog = NamespaceCatalog()
namespace_catalog.add_namespace(CORE_NAMESPACE, namespace)
type_map = TypeMap(namespace_catalog)
type_map.register_container_type(CORE_NAMESPACE, 'SimpleFoo',
SimpleFoo)
type_map.register_container_type(CORE_NAMESPACE, 'NotSimpleFoo',
NotSimpleFoo)
type_map.register_container_type(CORE_NAMESPACE, 'SimpleQux',
SimpleQux)
type_map.register_container_type(CORE_NAMESPACE, 'NotSimpleQux',
NotSimpleQux)
type_map.register_container_type(CORE_NAMESPACE, 'SimpleBucket',
SimpleBucket)
type_map.register_map(SimpleBucket, self.setUpBucketMapper())
self.manager = BuildManager(type_map)
def setUp(self):
self.bar_spec = GroupSpec(
'A test group specification with a data type',
data_type_def='Bar',
datasets=[
DatasetSpec('an example dataset',
'int',
name='data',
attributes=[
AttributeSpec('attr2',
'an example integer attribute',
'int')
])
],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text')
])
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.bar_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'source': 'test.yaml'
}],
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Bar', Bar)
self.type_map.register_map(Bar, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.bar_spec)
def test_bad_value(self):
"""Test that an error is raised if the container attribute value for a spec with a data type is not a container
or collection of containers.
"""
class Qux(Container):
@docval(
{
'name': 'name',
'type': str,
'doc': 'the name of this Qux'
}, {
'name': 'foo',
'type': int,
'doc': 'a group'
})
def __init__(self, **kwargs):
name, foo = getargs('name', 'foo', kwargs)
super().__init__(name=name)
self.__foo = foo
if isinstance(foo, Foo):
self.__foo.parent = self
@property
def foo(self):
return self.__foo
self.qux_spec = GroupSpec(
doc='A test group specification with data type Qux',
data_type_def='Qux',
groups=[GroupSpec('an example dataset', data_type_inc='Foo')])
self.foo_spec = GroupSpec(
'A test group specification with data type Foo',
data_type_def='Foo')
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.qux_spec, 'test.yaml')
self.spec_catalog.register_spec(self.foo_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'source': 'test.yaml'
}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Qux', Qux)
self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.qux_spec)
container = Qux('my_qux', foo=1)
msg = "Qux 'my_qux' attribute 'foo' has unexpected type."
with self.assertRaisesWith(ContainerConfigurationError, msg):
self.mapper.build(container, self.manager)
def setUp(self):
self.setUpBazSpec()
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'source': 'test.yaml'
}],
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def __init__(self, **kwargs):
path, mode, manager, extensions, load_namespaces, file_obj, comm, driver =\
popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces', 'file', 'comm', 'driver', kwargs)
if load_namespaces:
if manager is not None:
warn("loading namespaces from file - ignoring 'manager'")
if extensions is not None:
warn(
"loading namespaces from file - ignoring 'extensions' argument"
)
# namespaces are not loaded when creating an NWBHDF5IO object in write mode
if 'w' in mode or mode == 'x':
raise ValueError(
"cannot load namespaces from file when writing to it")
tm = get_type_map()
super(NWBHDF5IO, self).load_namespaces(tm,
path,
file=file_obj,
driver=driver)
manager = BuildManager(tm)
# XXX: Leaving this here in case we want to revert to this strategy for
# loading cached namespaces
# ns_catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
# super(NWBHDF5IO, self).load_namespaces(ns_catalog, path)
# tm = TypeMap(ns_catalog)
# tm.copy_mappers(get_type_map())
else:
if manager is not None and extensions is not None:
raise ValueError(
"'manager' and 'extensions' cannot be specified together")
elif extensions is not None:
manager = get_manager(extensions=extensions)
elif manager is None:
manager = get_manager()
super(NWBHDF5IO, self).__init__(path,
manager=manager,
mode=mode,
file=file_obj,
comm=comm,
driver=driver)
def setUp(self):
self.set_up_specs()
spec_catalog = SpecCatalog()
spec_catalog.register_spec(self.bar_data_spec, 'test.yaml')
spec_catalog.register_spec(self.bar_data_holder_spec, 'test.yaml')
namespace = SpecNamespace(doc='a test namespace',
name=CORE_NAMESPACE,
schema=[{
'source': 'test.yaml'
}],
version='0.1.0',
catalog=spec_catalog)
namespace_catalog = NamespaceCatalog()
namespace_catalog.add_namespace(CORE_NAMESPACE, namespace)
type_map = TypeMap(namespace_catalog)
type_map.register_container_type(CORE_NAMESPACE, 'BarData', BarData)
type_map.register_container_type(CORE_NAMESPACE, 'BarDataHolder',
BarDataHolder)
type_map.register_map(BarData, ExtBarDataMapper)
type_map.register_map(BarDataHolder, ObjectMapper)
self.manager = BuildManager(type_map)
def __init__(self, **kwargs):
path, mode, manager, extensions, load_namespaces, file_obj, comm =\
popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces', 'file', 'comm', kwargs)
# root group
self.__rgroup = file_obj
chunk_store = getattr(file_obj, 'chunk_store', None)
if chunk_store is not None:
try:
filename = getattr(chunk_store.source, 'path', None)
if filename is None:
filename = chunk_store.source.name
except:
filename = None
if filename is None:
filename = f'{type(file_obj.store).__name__}'
self.__rgroup.filename = filename
file_obj = self.__set_rgroup(file_obj)
self.__built = dict() # keep track of each builder for each dataset/group/link for each file
self.__read = dict() # keep track of which files have been read. Key is the filename value is the builder
self.__file = file_obj
if load_namespaces:
if manager is not None:
warn("loading namespaces from file - ignoring 'manager'")
if extensions is not None:
warn("loading namespaces from file - ignoring 'extensions' argument")
# namespaces are not loaded when creating an NWBZARRHDF5IO object in write mode
if 'w' in mode or mode == 'x':
raise ValueError("cannot load namespaces from file when writing to it")
tm = get_type_map()
self.load_namespaces(tm, path, file=file_obj)
manager = BuildManager(tm)
# XXX: Leaving this here in case we want to revert to this strategy for
# loading cached namespaces
# ns_catalog = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
# super(NWBZARRHDF5IO, self).load_namespaces(ns_catalog, path)
# tm = TypeMap(ns_catalog)
# tm.copy_mappers(get_type_map())
else:
if manager is not None and extensions is not None:
raise ValueError("'manager' and 'extensions' cannot be specified together")
elif extensions is not None:
manager = get_manager(extensions=extensions)
elif manager is None:
manager = get_manager()
self.logger = logging.getLogger('%s.%s' % (self.__class__.__module__, self.__class__.__qualname__))
if file_obj is not None:
if path is None:
path = file_obj.filename
elif os.path.abspath(file_obj.filename) != os.path.abspath(path):
msg = 'You argued %s as this object\'s path, ' % path
msg += 'but supplied a file with filename: %s' % file_obj.filename
raise ValueError(msg)
elif path is None:
TypeError("Must supply either 'path' or 'file' arg to HDF5IO.")
if file_obj is None and not os.path.exists(path) and (mode == 'r' or mode == 'r+'):
msg = "Unable to open file %s in '%s' mode. File does not exist." % (path, mode)
raise UnsupportedOperation(msg)
if file_obj is None and os.path.exists(path) and (mode == 'w-' or mode == 'x'):
msg = "Unable to open file %s in '%s' mode. File already exists." % (path, mode)
raise UnsupportedOperation(msg)
if manager is None:
manager = BuildManager(TypeMap(NamespaceCatalog()))
elif isinstance(manager, TypeMap):
manager = BuildManager(manager)
# TO DO #
self._HDF5IO__comm = comm
self._HDF5IO__mode = mode
self._HDF5IO__path = path
self._HDF5IO__file = file_obj
super(_HDF5IO, self).__init__(manager, source=path)
self._HDF5IO__ref_queue = deque() # a queue of the references that need to be added
self._HDF5IO__dci_queue = deque() # a queue of DataChunkIterators that need to be exhausted
def _get_manager():
foo_spec = GroupSpec('A test group specification with a data type',
data_type_def='Foo',
datasets=[DatasetSpec('an example dataset',
'int',
name='my_data',
attributes=[AttributeSpec('attr2',
'an example integer attribute',
'int')])],
attributes=[AttributeSpec('attr1', 'an example string attribute', 'text')])
tmp_spec = GroupSpec('A subgroup for Foos',
name='foo_holder',
groups=[GroupSpec('the Foos in this bucket', data_type_inc='Foo', quantity=ZERO_OR_MANY)])
bucket_spec = GroupSpec('A test group specification for a data type containing data type',
data_type_def='FooBucket',
groups=[tmp_spec])
class BucketMapper(ObjectMapper):
def __init__(self, spec):
super(BucketMapper, self).__init__(spec)
foo_spec = spec.get_group('foo_holder').get_data_type('Foo')
self.map_spec('foos', foo_spec)
file_spec = GroupSpec("A file of Foos contained in FooBuckets",
name='root',
data_type_def='FooFile',
groups=[GroupSpec('Holds the FooBuckets',
name='buckets',
groups=[GroupSpec("One ore more FooBuckets",
data_type_inc='FooBucket',
quantity=ONE_OR_MANY)])])
class FileMapper(ObjectMapper):
def __init__(self, spec):
super(FileMapper, self).__init__(spec)
bucket_spec = spec.get_group('buckets').get_data_type('FooBucket')
self.map_spec('buckets', bucket_spec)
spec_catalog = SpecCatalog()
spec_catalog.register_spec(foo_spec, 'test.yaml')
spec_catalog.register_spec(bucket_spec, 'test.yaml')
spec_catalog.register_spec(file_spec, 'test.yaml')
namespace = SpecNamespace(
'a test namespace',
CORE_NAMESPACE,
[{'source': 'test.yaml'}],
catalog=spec_catalog)
namespace_catalog = NamespaceCatalog()
namespace_catalog.add_namespace(CORE_NAMESPACE, namespace)
type_map = TypeMap(namespace_catalog)
type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
type_map.register_container_type(CORE_NAMESPACE, 'FooBucket', FooBucket)
type_map.register_container_type(CORE_NAMESPACE, 'FooFile', FooFile)
type_map.register_map(FooBucket, BucketMapper)
type_map.register_map(FooFile, FileMapper)
manager = BuildManager(type_map)
return manager
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)
class TestReference(TestCase):
def setUp(self):
self.foo_spec = GroupSpec(
'A test group specification with data type Foo',
data_type_def='Foo')
self.bar_spec = GroupSpec(
'A test group specification with a data type Bar',
data_type_def='Bar',
datasets=[DatasetSpec('an example dataset', 'int', name='data')],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text'),
AttributeSpec('attr2', 'an example integer attribute', 'int'),
AttributeSpec('foo',
'a referenced foo',
RefSpec('Foo', 'object'),
required=False)
])
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.foo_spec, 'test.yaml')
self.spec_catalog.register_spec(self.bar_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'source': 'test.yaml'
}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
self.type_map.register_container_type(CORE_NAMESPACE, 'Bar', Bar)
self.manager = BuildManager(self.type_map)
self.foo_mapper = ObjectMapper(self.foo_spec)
self.bar_mapper = ObjectMapper(self.bar_spec)
def test_build_attr_ref(self):
''' Test default mapping functionality when one container contains an attribute reference to another container.
'''
foo_inst = Foo('my_foo')
bar_inst1 = Bar('my_bar1', list(range(10)), 'value1', 10, foo=foo_inst)
bar_inst2 = Bar('my_bar2', list(range(10)), 'value1', 10)
foo_builder = self.manager.build(foo_inst, root=True)
bar1_builder = self.manager.build(bar_inst1, root=True) # adds refs
bar2_builder = self.manager.build(bar_inst2, root=True)
foo_expected = GroupBuilder('my_foo',
attributes={
'data_type': 'Foo',
'namespace': CORE_NAMESPACE,
'object_id': foo_inst.object_id
})
bar1_expected = GroupBuilder(
'n/a', # name doesn't matter
datasets={'data': DatasetBuilder('data', list(range(10)))},
attributes={
'attr1': 'value1',
'attr2': 10,
'foo': ReferenceBuilder(foo_expected),
'data_type': 'Bar',
'namespace': CORE_NAMESPACE,
'object_id': bar_inst1.object_id
})
bar2_expected = GroupBuilder(
'n/a', # name doesn't matter
datasets={'data': DatasetBuilder('data', list(range(10)))},
attributes={
'attr1': 'value1',
'attr2': 10,
'data_type': 'Bar',
'namespace': CORE_NAMESPACE,
'object_id': bar_inst2.object_id
})
self.assertDictEqual(foo_builder, foo_expected)
self.assertDictEqual(bar1_builder, bar1_expected)
self.assertDictEqual(bar2_builder, bar2_expected)
def test_build_attr_ref_invalid(self):
''' Test default mapping functionality when one container contains an attribute reference to another container.
'''
bar_inst1 = Bar('my_bar1', list(range(10)), 'value1', 10)
bar_inst1._Bar__foo = object() # make foo object a non-container type
msg = "invalid type for reference 'foo' (<class 'object'>) - must be AbstractContainer"
with self.assertRaisesWith(ValueError, msg):
self.bar_mapper.build(bar_inst1, self.manager)
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
# 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]
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 setUp(self):
self.dt_spec = GroupSpec(
'A test extension that contains a dynamic table',
data_type_def='TestTable',
data_type_inc='DynamicTable',
datasets=[
DatasetSpec(
data_type_inc='VectorData',
name='my_col',
doc='a test column',
dtype='float'
),
DatasetSpec(
data_type_inc='VectorData',
name='indexed_col',
doc='a test column',
dtype='float'
),
DatasetSpec(
data_type_inc='VectorIndex',
name='indexed_col_index',
doc='a test column',
),
DatasetSpec(
data_type_inc='VectorData',
name='optional_col1',
doc='a test column',
dtype='float',
quantity='?',
),
DatasetSpec(
data_type_inc='VectorData',
name='optional_col2',
doc='a test column',
dtype='float',
quantity='?',
)
]
)
self.dt_spec2 = GroupSpec(
'A test extension that contains a dynamic table',
data_type_def='TestDTRTable',
data_type_inc='DynamicTable',
datasets=[
DatasetSpec(
data_type_inc='DynamicTableRegion',
name='ref_col',
doc='a test column',
),
DatasetSpec(
data_type_inc='DynamicTableRegion',
name='indexed_ref_col',
doc='a test column',
),
DatasetSpec(
data_type_inc='VectorIndex',
name='indexed_ref_col_index',
doc='a test column',
),
DatasetSpec(
data_type_inc='DynamicTableRegion',
name='optional_ref_col',
doc='a test column',
quantity='?'
),
DatasetSpec(
data_type_inc='DynamicTableRegion',
name='optional_indexed_ref_col',
doc='a test column',
quantity='?'
),
DatasetSpec(
data_type_inc='VectorIndex',
name='optional_indexed_ref_col_index',
doc='a test column',
quantity='?'
),
DatasetSpec(
data_type_inc='VectorData',
name='optional_col3',
doc='a test column',
dtype='float',
quantity='?',
)
]
)
from hdmf.spec.write import YAMLSpecWriter
writer = YAMLSpecWriter(outdir='.')
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.dt_spec, 'test.yaml')
self.spec_catalog.register_spec(self.dt_spec2, 'test.yaml')
self.namespace = SpecNamespace(
'a test namespace', CORE_NAMESPACE,
[
dict(
namespace='hdmf-common',
),
dict(source='test.yaml'),
],
version='0.1.0',
catalog=self.spec_catalog
)
self.test_dir = tempfile.mkdtemp()
spec_fpath = os.path.join(self.test_dir, 'test.yaml')
namespace_fpath = os.path.join(self.test_dir, 'test-namespace.yaml')
writer.write_spec(dict(groups=[self.dt_spec, self.dt_spec2]), spec_fpath)
writer.write_namespace(self.namespace, namespace_fpath)
self.namespace_catalog = NamespaceCatalog()
hdmf_typemap = get_type_map()
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.merge(hdmf_typemap, ns_catalog=True)
self.type_map.load_namespaces(namespace_fpath)
self.manager = BuildManager(self.type_map)
self.TestTable = self.type_map.get_dt_container_cls('TestTable', CORE_NAMESPACE)
self.TestDTRTable = self.type_map.get_dt_container_cls('TestDTRTable', CORE_NAMESPACE)