def test_dynamic_container_constructor_name(self):
# name is specified in spec and cannot be changed
baz_spec = GroupSpec(
'A test extension with no Container class',
data_type_def='Baz',
data_type_inc=self.bar_spec,
name='A fixed name',
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')
with self.assertRaises(TypeError):
inst = cls('My Baz', [1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0)
inst = cls([1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0)
self.assertEqual(inst.name, 'A fixed name')
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 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')
]),
DatasetSpec('an example time dataset',
'isodatetime',
name='time'),
DatasetSpec('an array of times',
'isodatetime',
name='time_array',
dims=('num_times', ),
shape=(None, ))
],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text')
])
return (ret, )
def test_dynamic_container_constructor_name_default_name(self):
# if both name and default_name are specified, name should be used
with self.assertWarns(Warning):
baz_spec = GroupSpec('A test extension with no Container class',
data_type_def='Baz',
data_type_inc=self.bar_spec,
name='A fixed name',
default_name='A default name',
attributes=[
AttributeSpec('attr3',
'a float attribute',
'float'),
AttributeSpec('attr4',
'another float attribute',
'float')
])
self.spec_catalog.register_spec(baz_spec, 'extension.yaml')
cls = self.type_map.get_dt_container_cls('Baz', CORE_NAMESPACE)
inst = cls([1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0)
self.assertEqual(inst.name, 'A fixed name')
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', 'a float attribute',
'float'),
AttributeSpec('attr4',
'another float attribute',
'float')
])
self.spec_catalog.register_spec(baz_spec, 'extension.yaml')
cls = self.type_map.get_dt_container_cls('Baz', CORE_NAMESPACE)
# 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.attr1 = AttributeSpec(name='attr1',
doc='a string attribute',
dtype='text')
self.attr2 = AttributeSpec(name='attr2',
doc='an integer attribute',
dtype='int')
self.attr3 = AttributeSpec(name='attr3',
doc='an integer attribute',
dtype='int')
self.bar_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Bar',
datasets=[
DatasetSpec(doc='a dataset',
dtype='int',
name='data',
attributes=[self.attr2])
],
attributes=[self.attr1])
specs = [self.bar_spec]
containers = {'Bar': Bar}
self.type_map = create_test_type_map(specs, containers)
self.spec_catalog = self.type_map.namespace_catalog.get_namespace(
CORE_NAMESPACE).catalog
self.cls = self.type_map.get_dt_container_cls(self.bar_spec.data_type)
self.bar = self.cls(name='bar', data=[1], attr1='attr1', attr2=1)
obj_mapper_bar = self.type_map.get_map(self.bar)
obj_mapper_bar.map_spec('attr2', spec=self.attr2)
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',
text('an example string attribute'),
'text')
])
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 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 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 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_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 setUpBarSpec(self):
self.bar_spec = GroupSpec(
doc='A test group specification with a data type Bar',
data_type_def='Bar',
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text'),
AttributeSpec('attr2', 'an example integer attribute', 'int')
])
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 setUp(self):
self.catalog = SpecCatalog()
self.attributes = [
AttributeSpec('attribute1', 'my first attribute', 'text'),
AttributeSpec('attribute2', 'my second attribute', 'text')
]
self.spec = DatasetSpec('my first dataset',
'int',
name='dataset1',
dims=(None, None),
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
def test_dynamic_container_composition_missing_type(self):
baz_spec1 = GroupSpec(
'A composition test outside',
data_type_def='Baz1',
data_type_inc=self.bar_spec,
attributes=[
AttributeSpec('attr3', 'a float attribute', 'float'),
AttributeSpec('attr4', 'another float attribute', 'float')
],
groups=[GroupSpec('A composition inside', data_type_inc='Baz2')])
self.spec_catalog.register_spec(baz_spec1, 'extension.yaml')
msg = "No specification for 'Baz2' in namespace 'test_core'"
with self.assertRaisesWith(ValueError, msg):
self.type_map.get_dt_container_cls('Baz1', CORE_NAMESPACE)
def test_update_docval_attr_shape(self):
"""Test that update_docval_args for an attribute with shape sets the type and shape keys."""
spec = GroupSpec(doc='A test group specification with a data type',
data_type_def='Baz',
attributes=[
AttributeSpec(name='attr1',
doc='a string attribute',
dtype='text',
shape=[None])
])
not_inherited_fields = {'attr1': spec.get_attribute('attr1')}
docval_args = list()
CustomClassGenerator.process_field_spec(
classdict={},
docval_args=docval_args,
parent_cls=EmptyBar, # <-- arbitrary class
attr_name='attr1',
not_inherited_fields=not_inherited_fields,
type_map=TypeMap(),
spec=spec)
expected = [{
'name': 'attr1',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [None]
}]
self.assertListEqual(docval_args, expected)
def test_datatype_extension(self):
base = DatasetSpec('my first dataset',
'int',
name='dataset1',
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
attributes = [
AttributeSpec('attribute3', 'my first extending attribute',
'float')
]
ext = DatasetSpec('my first dataset extension',
'int',
name='dataset1',
attributes=attributes,
linkable=False,
data_type_inc=base,
data_type_def='SpikeData')
self.assertDictEqual(ext['attributes'][0], attributes[0])
self.assertDictEqual(ext['attributes'][1], self.attributes[0])
self.assertDictEqual(ext['attributes'][2], self.attributes[1])
ext_attrs = ext.attributes
self.assertIs(ext, ext_attrs[0].parent)
self.assertIs(ext, ext_attrs[1].parent)
self.assertIs(ext, ext_attrs[2].parent)
def setUpBarSpec(self):
attr1_attr = AttributeSpec(
name='attr1',
dtype='text',
doc='an example string attribute',
)
attr2_attr = AttributeSpec(
name='attr2',
dtype='int',
doc='an example int attribute',
)
self.bar_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Bar',
attributes=[attr1_attr, attr2_attr],
)
def test_post_process_fixed_name(self):
"""Test that docval generation for a class with a fixed name does not contain a docval arg for name."""
spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Baz',
name='MyBaz', # <-- fixed name
attributes=[
AttributeSpec(name='attr1',
doc='a string attribute',
dtype='text',
shape=[None])
])
classdict = {}
bases = [Container]
docval_args = [{
'name': 'name',
'type': str,
'doc': 'name'
}, {
'name': 'attr1',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [None]
}]
CustomClassGenerator.post_process(classdict, bases, docval_args, spec)
expected = [{
'name': 'attr1',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [None]
}]
self.assertListEqual(docval_args, expected)
def test_update_docval_default_value_none(self):
"""Test that update_docval_args for an optional field sets default: None."""
spec = GroupSpec(doc='A test group specification with a data type',
data_type_def='Baz',
attributes=[
AttributeSpec(name='attr1',
doc='a string attribute',
dtype='text',
required=False)
])
not_inherited_fields = {'attr1': spec.get_attribute('attr1')}
docval_args = list()
CustomClassGenerator.process_field_spec(
classdict={},
docval_args=docval_args,
parent_cls=EmptyBar, # <-- arbitrary class
attr_name='attr1',
not_inherited_fields=not_inherited_fields,
type_map=TypeMap(),
spec=spec)
expected = [{
'name': 'attr1',
'type': str,
'doc': 'a string attribute',
'default': None
}]
self.assertListEqual(docval_args, expected)
def test_multi_container_spec(self):
multi_spec = GroupSpec(doc='A test extension that contains a multi',
data_type_def='Multi',
groups=[
GroupSpec(data_type_inc=self.bar_spec,
doc='test multi',
quantity='*')
],
attributes=[
AttributeSpec(name='attr3',
doc='a float attribute',
dtype='float')
])
self.spec_catalog.register_spec(multi_spec, 'extension.yaml')
Bar = self.type_map.get_dt_container_cls('Bar', CORE_NAMESPACE)
Multi = self.type_map.get_dt_container_cls('Multi', CORE_NAMESPACE)
assert issubclass(Multi, MultiContainerInterface)
assert Multi.__clsconf__ == [
dict(attr='bars',
type=Bar,
add='add_bars',
get='get_bars',
create='create_bars')
]
multi = Multi(name='my_multi',
bars=[Bar('my_bar', list(range(10)), 'value1', 10)],
attr3=5.)
assert multi.bars['my_bar'] == Bar('my_bar', list(range(10)), 'value1',
10)
assert multi.attr3 == 5.
def test_constructor(self):
spec = AttributeSpec('attribute1', 'my first attribute', 'text')
self.assertEqual(spec['name'], 'attribute1')
self.assertEqual(spec['dtype'], 'text')
self.assertEqual(spec['doc'], 'my first attribute')
self.assertIsNone(spec.parent)
json.dumps(spec) # to ensure there are no circular links
def test_get_namespace_spec(self):
expected = AttributeSpec(
'namespace',
'the namespace for the data type of this object',
'text',
required=False)
self.assertDictEqual(GroupSpec.get_namespace_spec(), expected)
def test_default_value(self):
spec = AttributeSpec('attribute1',
'my first attribute',
'text',
default_value='some text')
self.assertEqual(spec['default_value'], 'some text')
self.assertEqual(spec.default_value, 'some text')
def test_invalid_dtype(self):
with self.assertRaises(ValueError):
AttributeSpec(
name='attribute1',
doc='my first attribute',
dtype='invalid' # <-- Invalid dtype must raise a ValueError
)
def test_dynamic_container_composition_reverse_order(self):
baz_spec2 = GroupSpec('A composition inside',
data_type_def='Baz2',
data_type_inc=self.bar_spec,
attributes=[
AttributeSpec('attr3', 'a float attribute',
'float'),
AttributeSpec('attr4',
'another float attribute',
'float')
])
baz_spec1 = GroupSpec(
'A composition test outside',
data_type_def='Baz1',
data_type_inc=self.bar_spec,
attributes=[
AttributeSpec('attr3', 'a float attribute', 'float'),
AttributeSpec('attr4', 'another float attribute', 'float')
],
groups=[GroupSpec('A composition inside', data_type_inc='Baz2')])
self.spec_catalog.register_spec(baz_spec1, 'extension.yaml')
self.spec_catalog.register_spec(baz_spec2, 'extension.yaml')
Baz1 = self.type_map.get_dt_container_cls('Baz1', CORE_NAMESPACE)
Baz2 = self.type_map.get_dt_container_cls('Baz2', CORE_NAMESPACE)
Baz1('My Baz', [1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0,
baz2=Baz2('My Baz', [1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0))
Bar = self.type_map.get_dt_container_cls('Bar', CORE_NAMESPACE)
bar = Bar('My Bar', [1, 2, 3, 4], 'string attribute', 1000)
with self.assertRaises(TypeError):
Baz1('My Baz', [1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0,
baz2=bar)
def test_shape(self):
shape = [None, 2]
spec = AttributeSpec('attribute1',
'my first attribute',
'text',
shape=shape)
self.assertEqual(spec['shape'], shape)
self.assertEqual(spec.shape, shape)
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 setUpBarSpec(self):
self.bar_spec = GroupSpec(
doc='A test group specification with a data type Bar',
data_type_def='Bar',
attributes=[
AttributeSpec('foo', 'a referenced foo',
RefSpec('Foo', 'object'))
])
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('attr2',
'an example integer attribute',
'int')
])
],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text')
])
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, )
