def getSpecs(self):
bar = 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', 'str')
])
foo = GroupSpec('A test group that contains a data type',
data_type_def='Foo',
groups=[
GroupSpec('A Bar group for Foos',
name='my_bar',
data_type_inc='Bar')
],
attributes=[
AttributeSpec(
'foo_attr',
'a string attribute specified as text',
'text',
required=False)
])
return (bar, foo)
def test_set_dataset(self):
spec = GroupSpec('A test group',
name='root_test_set_dataset',
linkable=False,
data_type_def='EphysData')
spec.set_dataset(self.datasets[0])
self.assertIs(spec, self.datasets[0].parent)
def setUpBucketSpec(self):
self.bucket_spec = GroupSpec('A test group specification for a data type containing data type',
name="test_foo_bucket",
data_type_def='FooBucket',
groups=[GroupSpec(
'the Foos in this bucket',
data_type_inc='Foo',
quantity=ZERO_OR_MANY)])
def setUpBarSpec(self):
self.bar_spec = GroupSpec(
'A test group specification with a data type',
data_type_def='Bar',
groups=[GroupSpec('an example group', data_type_def='Foo')],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'str'),
AttributeSpec('attr2', 'an example integer attribute', 'int')
])
def test_set_group(self):
spec = GroupSpec('A test group',
name='root_test_set_group',
linkable=False,
data_type_def='EphysData')
spec.set_group(self.subgroups[0])
spec.set_group(self.subgroups[1])
self.assertListEqual(spec['groups'], self.subgroups)
self.assertIs(spec, self.subgroups[0].parent)
self.assertIs(spec, self.subgroups[1].parent)
json.dumps(spec)
def setUpBucketSpec(self):
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)])
tmp_spec = GroupSpec('A subgroup to hold the subgroup', name='foo_holder_holder', groups=[tmp_spec])
self.bucket_spec = GroupSpec('A test group specification for a data type containing data type',
name="test_foo_bucket",
data_type_def='FooBucket',
groups=[tmp_spec])
def test_update_attribute_spec(self):
spec = GroupSpec('A test group',
name='root_constructor',
attributes=[
AttributeSpec('attribute1', 'my first attribute',
'text'),
])
spec.set_attribute(
AttributeSpec('attribute1', 'my first attribute', 'int', value=5))
res = spec.get_attribute('attribute1')
self.assertEqual(res.value, 5)
self.assertEqual(res.dtype, 'int')
def test_get_subspec_named(self):
child_spec = GroupSpec('A test group specification with a data type',
'my_subgroup')
parent_spec = GroupSpec('Something to hold a Bar',
'my_group',
groups=[child_spec])
sub_builder = GroupBuilder('my_subgroup',
attributes={
'data_type': 'Bar',
'namespace': CORE_NAMESPACE
})
builder = GroupBuilder('my_group', groups={'my_bar':
sub_builder}) # noqa: F841
result = self.type_map.get_subspec(parent_spec, sub_builder)
self.assertIs(result, child_spec)
def test_get_spec_source_file(self):
spikes_spec = GroupSpec('test group', data_type_def='SpikeData')
source_file_path = '/test/myt/test.yaml'
self.catalog.auto_register(spikes_spec, source_file_path)
recorded_source_file_path = self.catalog.get_spec_source_file(
'SpikeData')
self.assertEqual(recorded_source_file_path, source_file_path)
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', 'str')
])
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 getSpecs(self):
ret = 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')])
return (ret,)
def setUp(self):
self.attributes = [
AttributeSpec('attribute1', 'my first attribute', 'text'),
AttributeSpec('attribute2', 'my second attribute', 'text')
]
self.dset1_attributes = [
AttributeSpec('attribute3', 'my third attribute', 'text'),
AttributeSpec('attribute4', 'my fourth attribute', 'text')
]
self.dset2_attributes = [
AttributeSpec('attribute5', 'my fifth attribute', 'text'),
AttributeSpec('attribute6', 'my sixth attribute', 'text')
]
self.datasets = [
DatasetSpec('my first dataset',
'int',
name='dataset1',
attributes=self.dset1_attributes,
linkable=True),
DatasetSpec('my second dataset',
'int',
name='dataset2',
dimension=(None, None),
attributes=self.dset2_attributes,
linkable=True,
namespace='core',
data_type_def='VoltageArray')
]
self.subgroups = [
GroupSpec('A test subgroup', name='subgroup1', linkable=False),
GroupSpec('A test subgroup', name='subgroup2', linkable=False)
]
self.ndt_attr_spec = AttributeSpec('data_type',
'the data type of this object',
'text',
value='EphysData')
self.ns_attr_spec = AttributeSpec(
'namespace',
'the namespace for the data type of this object',
'text',
required=False)
def test_add_attribute(self):
spec = GroupSpec('A test group',
name='root_constructor',
groups=self.subgroups,
datasets=self.datasets,
linkable=False)
for attrspec in self.attributes:
spec.add_attribute(**attrspec)
self.assertListEqual(spec['attributes'], self.attributes)
self.assertListEqual(spec['datasets'], self.datasets)
self.assertNotIn('data_type_def', spec)
self.assertIs(spec, self.subgroups[0].parent)
self.assertIs(spec, self.subgroups[1].parent)
self.assertIs(spec, spec.attributes[0].parent)
self.assertIs(spec, spec.attributes[1].parent)
self.assertIs(spec, self.datasets[0].parent)
self.assertIs(spec, self.datasets[1].parent)
json.dumps(spec)
def setUpBarSpec(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('attr1', 'an example string attribute', 'text'),
AttributeSpec('attr2', 'an example integer attribute', 'int')
])
def setUp(self):
self.bar_spec = GroupSpec(
'A test group specification with a data type', data_type_def='Bar')
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.bar_spec, 'test.yaml')
self.spec_catalog.register_spec(self.foo_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_container_type(CORE_NAMESPACE, 'Foo', Foo)
def test_datatype_extension_groupspec(self):
'''Test to make sure DatasetSpec catches when a GroupSpec used as data_type_inc'''
base = GroupSpec('a fake grop',
data_type_def='EphysData')
with self.assertRaises(TypeError):
ext = DatasetSpec('my first dataset extension', # noqa: F841
'int',
name='dataset1',
data_type_inc=base,
data_type_def='SpikeData')
def test_get_subspec_data_type_noname(self):
parent_spec = GroupSpec('Something to hold a Bar',
'bar_bucket',
groups=[self.bar_spec])
sub_builder = GroupBuilder('my_bar',
attributes={
'data_type': 'Bar',
'namespace': CORE_NAMESPACE
})
builder = GroupBuilder('bar_bucket',
groups={'my_bar': sub_builder}) # noqa: F841
result = self.type_map.get_subspec(parent_spec, sub_builder)
self.assertIs(result, self.bar_spec)
def test_dynamic_container_creation_defaults(self):
baz_spec = GroupSpec(
'A test extension with no Container class',
data_type_def='Baz',
data_type_inc=self.bar_spec,
attributes=[
AttributeSpec('attr3', 'an example float attribute', 'float'),
AttributeSpec('attr4', 'another example float attribute',
'float')
])
self.spec_catalog.register_spec(baz_spec, 'extension.yaml')
cls = self.type_map.get_container_cls(CORE_NAMESPACE, 'Baz')
expected_args = {'name', 'data', 'attr1', 'attr2', 'attr3', 'attr4'}
received_args = set(map(lambda x: x['name'], get_docval(cls.__init__)))
self.assertSetEqual(expected_args, received_args)
self.assertEqual(cls.__name__, 'Baz')
self.assertTrue(issubclass(cls, Bar))
def test_constructor_nwbtype(self):
spec = GroupSpec('A test group',
name='root_constructor_nwbtype',
datasets=self.datasets,
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
self.assertFalse(spec['linkable'])
self.assertListEqual(spec['attributes'], self.attributes)
self.assertListEqual(spec['datasets'], self.datasets)
self.assertEqual(spec['data_type_def'], 'EphysData')
self.assertIs(spec, self.attributes[0].parent)
self.assertIs(spec, self.attributes[1].parent)
self.assertIs(spec, self.datasets[0].parent)
self.assertIs(spec, self.datasets[1].parent)
self.assertEqual(spec.data_type_def, 'EphysData')
self.assertIsNone(spec.data_type_inc)
json.dumps(spec)
def test_dynamic_container_constructor(self):
baz_spec = GroupSpec(
'A test extension with no Container class',
data_type_def='Baz',
data_type_inc=self.bar_spec,
attributes=[
AttributeSpec('attr3', 'an example float attribute', 'float'),
AttributeSpec('attr4', 'another example float attribute',
'float')
])
self.spec_catalog.register_spec(baz_spec, 'extension.yaml')
cls = self.type_map.get_container_cls(CORE_NAMESPACE, 'Baz')
# TODO: test that constructor works!
inst = cls('My Baz', [1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0)
self.assertEqual(inst.name, 'My Baz')
self.assertEqual(inst.data, [1, 2, 3, 4])
self.assertEqual(inst.attr1, 'string attribute')
self.assertEqual(inst.attr2, 1000)
self.assertEqual(inst.attr3, 98.6)
self.assertEqual(inst.attr4, 1.0)
def setUp(self):
self.attributes = [
AttributeSpec('attribute1', 'my first attribute', 'text'),
AttributeSpec('attribute2', 'my second attribute', 'text')
]
self.dset1_attributes = [
AttributeSpec('attribute3', 'my third attribute', 'text'),
AttributeSpec('attribute4', 'my fourth attribute', 'text')
]
self.dset2_attributes = [
AttributeSpec('attribute5', 'my fifth attribute', 'text'),
AttributeSpec('attribute6', 'my sixth attribute', 'text')
]
self.datasets = [
DatasetSpec(
'my first dataset', # noqa: F405
'int',
name='dataset1',
attributes=self.dset1_attributes,
linkable=True),
DatasetSpec(
'my second dataset', # noqa: F405
'int',
name='dataset2',
dimension=(None, None),
attributes=self.dset2_attributes,
linkable=True,
data_type_def='VoltageArray')
]
self.spec = GroupSpec(
'A test group', # noqa: F405
name='root_constructor_nwbtype',
datasets=self.datasets,
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
dset1_attributes_ext = [
AttributeSpec('dset1_extra_attribute',
'an extra attribute for the first dataset', 'text')
]
self.ext_datasets = [
DatasetSpec(
'my first dataset extension', # noqa: F405
'int',
name='dataset1',
attributes=dset1_attributes_ext,
linkable=True),
]
self.ext_attributes = [
AttributeSpec('ext_extra_attribute',
'an extra attribute for the group', 'text'),
]
self.ext_spec = GroupSpec(
'A test group extension', # noqa: F405
name='root_constructor_nwbtype',
datasets=self.ext_datasets,
attributes=self.ext_attributes,
linkable=False,
data_type_inc='EphysData',
data_type_def='SpikeData')
to_dump = {'groups': [self.spec, self.ext_spec]}
self.specs_path = 'test_load_namespace.specs.yaml'
self.namespace_path = 'test_load_namespace.namespace.yaml'
with open(self.specs_path, 'w') as tmp:
yaml.safe_dump(json.loads(json.dumps(to_dump)),
tmp,
default_flow_style=False)
ns_dict = {
'doc': 'a test namespace',
'name': self.NS_NAME,
'schema': [{
'source': self.specs_path
}]
}
self.namespace = SpecNamespace.build_namespace(**ns_dict) # noqa: F405
to_dump = {'namespaces': [self.namespace]}
with open(self.namespace_path, 'w') as tmp:
yaml.safe_dump(json.loads(json.dumps(to_dump)),
tmp,
default_flow_style=False)
self.ns_catalog = NamespaceCatalog() # noqa: F405
def test_type_extension(self):
spec = GroupSpec('A test group',
name='parent_type',
datasets=self.datasets,
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
dset1_attributes_ext = [
AttributeSpec('dset1_extra_attribute',
'an extra attribute for the first dataset', 'text')
]
ext_datasets = [
DatasetSpec('my first dataset extension',
'int',
name='dataset1',
attributes=dset1_attributes_ext,
linkable=True),
]
ext_attributes = [
AttributeSpec('ext_extra_attribute',
'an extra attribute for the group', 'text'),
]
ext = GroupSpec('A test group extension',
name='child_type',
datasets=ext_datasets,
attributes=ext_attributes,
linkable=False,
data_type_inc=spec,
data_type_def='SpikeData')
ext_dset1 = ext.get_dataset('dataset1')
ext_dset1_attrs = ext_dset1.attributes
self.assertDictEqual(ext_dset1_attrs[0], dset1_attributes_ext[0])
self.assertDictEqual(ext_dset1_attrs[1], self.dset1_attributes[0])
self.assertDictEqual(ext_dset1_attrs[2], self.dset1_attributes[1])
self.assertEqual(ext.data_type_def, 'SpikeData')
self.assertEqual(ext.data_type_inc, 'EphysData')
ext_dset2 = ext.get_dataset('dataset2')
self.maxDiff = None
# this will suffice for now, assertDictEqual doesn't do deep equality checks
self.assertEqual(str(ext_dset2), str(self.datasets[1]))
self.assertAttributesEqual(ext_dset2, self.datasets[1])
# self.ns_attr_spec
ndt_attr_spec = AttributeSpec(
'data_type',
'the data type of this object', # noqa: F841
'text',
value='SpikeData')
res_attrs = ext.attributes
self.assertDictEqual(res_attrs[0], ext_attributes[0])
self.assertDictEqual(res_attrs[1], self.attributes[0])
self.assertDictEqual(res_attrs[2], self.attributes[1])
# test that inherited specs are tracked appropriate
for d in self.datasets:
with self.subTest(dataset=d.name):
self.assertTrue(ext.is_inherited_spec(d))
self.assertFalse(spec.is_inherited_spec(d))
json.dumps(spec)
def getSpecs(self):
return (GroupSpec('A test group specification with a data type', data_type_def='Bar'),)
