class TestObjectMapper(with_metaclass(ABCMeta, unittest.TestCase)):
def setUp(self):
self.setUpBarSpec()
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 setUpBarSpec(self):
raise unittest.SkipTest('setUpBarSpec not implemented')
def test_default_mapping(self):
attr_map = self.mapper.get_attr_names(self.bar_spec)
keys = set(attr_map.keys())
for key in keys:
with self.subTest(key=key):
self.assertIs(attr_map[key], self.mapper.get_attr_spec(key))
self.assertIs(attr_map[key], self.mapper.get_carg_spec(key))
class TestBase(unittest.TestCase):
def setUp(self):
self.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')
])
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'
}],
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, ObjectMapper)
self.manager = BuildManager(self.type_map)
def create_test_type_map(specs, container_classes, mappers=None):
"""
Create a TypeMap with the specs registered under a test namespace, and classes and mappers registered to type names.
:param specs: list of specs
:param container_classes: dict of type name to container class
:param mappers: (optional) dict of type name to mapper class
:return: the constructed TypeMap
"""
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)
for type_name, container_cls in container_classes.items():
type_map.register_container_type(CORE_NAMESPACE, type_name,
container_cls)
if mappers:
for type_name, mapper_cls in mappers.items():
container_cls = container_classes[type_name]
type_map.register_map(container_cls, mapper_cls)
return 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)
class ObjectMapperMixin(metaclass=ABCMeta):
def setUp(self):
self.setUpBarSpec()
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'
}],
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, 'Bar', Bar)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.bar_spec)
@abstractmethod
def setUpBarSpec(self):
raise NotImplementedError(
'Cannot run test unless setUpBarSpec is implemented')
def test_default_mapping(self):
attr_map = self.mapper.get_attr_names(self.bar_spec)
keys = set(attr_map.keys())
for key in keys:
with self.subTest(key=key):
self.assertIs(attr_map[key], self.mapper.get_attr_spec(key))
self.assertIs(attr_map[key], self.mapper.get_carg_spec(key))
class TestObjectMapperBadValue(TestCase):
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)
class TestDataIOEdgeCases(TestCase):
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'
}],
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, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='an Baz type',
dtype=None,
name='MyBaz',
data_type_def='Baz',
shape=[None],
attributes=[
AttributeSpec('baz_attr', 'an example string attribute',
'text')
])
def test_build_dataio(self):
"""Test building of a dataset with data_type and no dtype with value DataIO."""
container = Baz('my_baz', H5DataIO(['a', 'b', 'c', 'd'], chunks=True),
'value1')
builder = self.type_map.build(container)
self.assertIsInstance(builder.get('data'), H5DataIO)
def test_build_datachunkiterator(self):
"""Test building of a dataset with data_type and no dtype with value DataChunkIterator."""
container = Baz('my_baz', DataChunkIterator(['a', 'b', 'c', 'd']),
'value1')
builder = self.type_map.build(container)
self.assertIsInstance(builder.get('data'), DataChunkIterator)
def test_build_dataio_datachunkiterator(self): # hdmf#512
"""Test building of a dataset with no dtype and no data_type with value DataIO wrapping a DCI."""
container = Baz(
'my_baz',
H5DataIO(DataChunkIterator(['a', 'b', 'c', 'd']), chunks=True),
'value1')
builder = self.type_map.build(container)
self.assertIsInstance(builder.get('data'), H5DataIO)
self.assertIsInstance(builder.get('data').data, DataChunkIterator)
class TestTypeMap(unittest.TestCase):
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)
# self.build_manager = BuildManager(self.type_map)
def test_get_map_unique_mappers(self):
self.type_map.register_map(Bar, ObjectMapper)
self.type_map.register_map(Foo, ObjectMapper)
bar_inst = Bar('my_bar', list(range(10)), 'value1', 10)
foo_inst = Foo(name='my_foo')
bar_mapper = self.type_map.get_map(bar_inst)
foo_mapper = self.type_map.get_map(foo_inst)
self.assertIsNot(bar_mapper, foo_mapper)
def test_get_map(self):
self.type_map.register_map(Bar, ObjectMapper)
container_inst = Bar('my_bar', list(range(10)), 'value1', 10)
mapper = self.type_map.get_map(container_inst)
self.assertIsInstance(mapper, ObjectMapper)
self.assertIs(mapper.spec, self.bar_spec)
mapper2 = self.type_map.get_map(container_inst)
self.assertIs(mapper, mapper2)
def test_get_map_register(self):
class MyMap(ObjectMapper):
pass
self.type_map.register_map(Bar, MyMap)
container_inst = Bar('my_bar', list(range(10)), 'value1', 10)
mapper = self.type_map.get_map(container_inst)
self.assertIs(mapper.spec, self.bar_spec)
self.assertIsInstance(mapper, MyMap)
def customSetUp(self, bar_spec):
spec_catalog = SpecCatalog()
spec_catalog.register_spec(bar_spec, 'test.yaml')
namespace = SpecNamespace('a test namespace',
CORE_NAMESPACE, [{
'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, 'Bar', Bar)
return type_map
class TestDataMapScalar(TestCase):
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'
}],
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, 'BazScalar',
BazScalar)
self.type_map.register_map(BazScalar, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(doc='a BazScalar type',
dtype='int',
name='MyBaz',
data_type_def='BazScalar')
def test_construct_scalar_dataset(self):
"""Test constructing a Data object with an h5py.Dataset with shape (1, ) for scalar spec."""
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds', data=[1])
expected = BazScalar(
name='MyBaz',
data=1,
)
builder = DatasetBuilder(
name='MyBaz',
data=test_ds,
attributes={
'data_type': 'BazScalar',
'namespace': CORE_NAMESPACE,
'object_id': expected.object_id
},
)
container = self.mapper.construct(builder, self.manager)
self.assertTrue(np.issubdtype(type(
container.data), np.integer)) # as opposed to h5py.Dataset
self.assertContainerEqual(container, expected)
os.remove('test.h5')
class TestGetSubSpec(unittest.TestCase):
def setUp(self):
self.bar_spec = GroupSpec(
'A test group specification with a data type', data_type_def='Bar')
spec_catalog = SpecCatalog()
spec_catalog.register_spec(self.bar_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)
self.type_map = TypeMap(namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Bar', Bar)
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_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)
class BazSpecMixin:
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'
}],
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, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
raise NotImplementedError('Test must implement this method.')
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)
class BuildDatasetOfReferencesMixin:
def setUp(self):
self.setUpBazSpec()
self.foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Foo',
datasets=[
DatasetSpec(name='my_data',
doc='an example dataset',
dtype='int')
],
attributes=[
AttributeSpec(name='attr1',
doc='an example string attribute',
dtype='text'),
AttributeSpec(name='attr2',
doc='an example int attribute',
dtype='int'),
AttributeSpec(name='attr3',
doc='an example float attribute',
dtype='float')
])
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_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, 'Baz', Baz)
self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
self.type_map.register_map(Baz, ObjectMapper)
self.type_map.register_map(Foo, ObjectMapper)
self.manager = BuildManager(self.type_map)
class TestDataMap(unittest.TestCase):
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 setUpBazSpec(self):
self.baz_spec = DatasetSpec(
'an Baz type',
'int',
name='MyBaz',
data_type_def='Baz',
attributes=[
AttributeSpec('baz_attr', 'an example string attribute',
'text')
])
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
container = Baz('my_baz', list(range(10)),
'abcdefghijklmnopqrstuvwxyz')
builder = self.mapper.build(container, self.manager)
expected = DatasetBuilder(
'my_baz',
list(range(10)),
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz'})
self.assertDictEqual(builder, expected)
class TestDataMap(BazSpecMixin, TestCase):
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'
}],
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, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='an Baz type',
dtype='int',
name='MyBaz',
data_type_def='Baz',
shape=[None],
attributes=[
AttributeSpec('baz_attr', 'an example string attribute',
'text')
])
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
container = Baz('MyBaz', list(range(10)), 'abcdefghijklmnopqrstuvwxyz')
builder = self.mapper.build(container, self.manager)
expected = DatasetBuilder(
'MyBaz',
list(range(10)),
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz'})
self.assertBuilderEqual(builder, expected)
def test_build_empty_data(self):
"""Test building of a Data object with empty data."""
baz_inc_spec = DatasetSpec(doc='doc',
data_type_inc='Baz',
quantity=ZERO_OR_MANY)
baz_holder_spec = GroupSpec(doc='doc',
data_type_def='BazHolder',
datasets=[baz_inc_spec])
self.spec_catalog.register_spec(baz_holder_spec, 'test.yaml')
self.type_map.register_container_type(CORE_NAMESPACE, 'BazHolder',
BazHolder)
self.holder_mapper = ObjectMapper(baz_holder_spec)
baz = Baz('MyBaz', [], 'abcdefghijklmnopqrstuvwxyz')
holder = BazHolder('holder', [baz])
builder = self.holder_mapper.build(holder, self.manager)
expected = GroupBuilder(
name='holder',
datasets=[
DatasetBuilder(name='MyBaz',
data=[],
attributes={
'baz_attr': 'abcdefghijklmnopqrstuvwxyz',
'data_type': 'Baz',
'namespace': 'test_core',
'object_id': baz.object_id
})
])
self.assertBuilderEqual(builder, expected)
def test_append(self):
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds',
data=[1, 2, 3],
chunks=True,
maxshape=(None, ))
container = Baz('MyBaz', test_ds, 'abcdefghijklmnopqrstuvwxyz')
container.append(4)
np.testing.assert_array_equal(container[:], [1, 2, 3, 4])
os.remove('test.h5')
def test_extend(self):
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds',
data=[1, 2, 3],
chunks=True,
maxshape=(None, ))
container = Baz('MyBaz', test_ds, 'abcdefghijklmnopqrstuvwxyz')
container.extend([4, 5])
np.testing.assert_array_equal(container[:], [1, 2, 3, 4, 5])
os.remove('test.h5')
class TestDataMapScalarCompound(TestCase):
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'
}],
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,
'BazScalarCompound',
BazScalarCompound)
self.type_map.register_map(BazScalarCompound, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a BazScalarCompound type',
dtype=[
DtypeSpec(name='id',
dtype='uint64',
doc='The unique identifier in this table.'),
DtypeSpec(name='attr1', dtype='text', doc='A text attribute.'),
],
name='MyBaz',
data_type_def='BazScalarCompound',
)
def test_construct_scalar_compound_dataset(self):
"""Test construct on a compound h5py.Dataset with shape (1, ) for scalar spec does not resolve the data."""
with h5py.File('test.h5', 'w') as file:
comp_type = np.dtype([('id', np.uint64),
('attr1', h5py.special_dtype(vlen=str))])
test_ds = file.create_dataset(name='test_ds',
data=np.array((1, 'text'),
dtype=comp_type),
shape=(1, ),
dtype=comp_type)
expected = BazScalarCompound(
name='MyBaz',
data=(1, 'text'),
)
builder = DatasetBuilder(
name='MyBaz',
data=test_ds,
attributes={
'data_type': 'BazScalarCompound',
'namespace': CORE_NAMESPACE,
'object_id': expected.object_id
},
)
container = self.mapper.construct(builder, self.manager)
self.assertEqual(type(container.data), h5py.Dataset)
self.assertContainerEqual(container, expected)
os.remove('test.h5')
class TestDataMap(TestCase):
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'
}],
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, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
'an Baz type',
'int',
name='MyBaz',
data_type_def='Baz',
shape=[None],
attributes=[
AttributeSpec('baz_attr', 'an example string attribute',
'text')
])
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
container = Baz('my_baz', list(range(10)),
'abcdefghijklmnopqrstuvwxyz')
builder = self.mapper.build(container, self.manager)
expected = DatasetBuilder(
'my_baz',
list(range(10)),
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz'})
self.assertDictEqual(builder, expected)
def test_append(self):
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds',
data=[1, 2, 3],
chunks=True,
maxshape=(None, ))
container = Baz('my_baz', test_ds, 'abcdefghijklmnopqrstuvwxyz')
container.append(4)
np.testing.assert_array_equal(container[:], [1, 2, 3, 4])
os.remove('test.h5')
def test_extend(self):
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds',
data=[1, 2, 3],
chunks=True,
maxshape=(None, ))
container = Baz('my_baz', test_ds, 'abcdefghijklmnopqrstuvwxyz')
container.extend([4, 5])
np.testing.assert_array_equal(container[:], [1, 2, 3, 4, 5])
os.remove('test.h5')
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)
class TestLinkedContainer(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',
groups=[self.foo_spec],
datasets=[DatasetSpec('an example dataset', 'int', name='data')],
attributes=[
AttributeSpec('attr1', 'an example string attribute', 'text'),
AttributeSpec('attr2', 'an example integer attribute', 'int')
])
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_child_link(self):
''' Test default mapping functionality when one container contains a child link to another container '''
foo_inst = Foo('my_foo')
bar_inst1 = Bar('my_bar1', list(range(10)), 'value1', 10, foo=foo_inst)
# bar_inst2.foo should link to bar_inst1.foo
bar_inst2 = Bar('my_bar2', list(range(10)), 'value1', 10, foo=foo_inst)
foo_builder = self.foo_mapper.build(foo_inst, self.manager)
bar1_builder = self.bar_mapper.build(bar_inst1, self.manager)
bar2_builder = self.bar_mapper.build(bar_inst2, self.manager)
foo_expected = GroupBuilder('my_foo')
inner_foo_builder = GroupBuilder('my_foo',
attributes={
'data_type': 'Foo',
'namespace': CORE_NAMESPACE,
'object_id': foo_inst.object_id
})
bar1_expected = GroupBuilder(
'my_bar1',
datasets={'data': DatasetBuilder('data', list(range(10)))},
groups={'foo': inner_foo_builder},
attributes={
'attr1': 'value1',
'attr2': 10
})
link_foo_builder = LinkBuilder(builder=inner_foo_builder)
bar2_expected = GroupBuilder(
'my_bar2',
datasets={'data': DatasetBuilder('data', list(range(10)))},
links={'foo': link_foo_builder},
attributes={
'attr1': 'value1',
'attr2': 10
})
self.assertBuilderEqual(foo_builder, foo_expected)
self.assertBuilderEqual(bar1_builder, bar1_expected)
self.assertBuilderEqual(bar2_builder, bar2_expected)
@unittest.expectedFailure
def test_build_broken_link_parent(self):
''' Test that building a container with a broken link that has a parent raises an error. '''
foo_inst = Foo('my_foo')
Bar('my_bar1', list(range(10)), 'value1', 10,
foo=foo_inst) # foo_inst.parent is this bar
# bar_inst2.foo should link to bar_inst1.foo
bar_inst2 = Bar('my_bar2', list(range(10)), 'value1', 10, foo=foo_inst)
# TODO bar_inst.foo.parent exists but is never built - this is a tricky edge case that should raise an error
with self.assertRaises(OrphanContainerBuildError):
self.bar_mapper.build(bar_inst2, self.manager)
def test_build_broken_link_no_parent(self):
''' Test that building a container with a broken link that has no parent raises an error. '''
foo_inst = Foo('my_foo')
bar_inst1 = Bar('my_bar1', list(range(10)), 'value1', 10,
foo=foo_inst) # foo_inst.parent is this bar
# bar_inst2.foo should link to bar_inst1.foo
bar_inst2 = Bar('my_bar2', list(range(10)), 'value1', 10, foo=foo_inst)
bar_inst1.remove_foo()
msg = (
"my_bar2 (my_bar2): Linked Foo 'my_foo' has no parent. Remove the link or ensure the linked container "
"is added properly.")
with self.assertRaisesWith(OrphanContainerBuildError, msg):
self.bar_mapper.build(bar_inst2, self.manager)
class TestBaseProcessFieldSpec(TestCase):
def setUp(self):
self.bar_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='EmptyBar')
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'
}],
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, 'EmptyBar',
EmptyBar)
def test_update_docval(self):
"""Test update_docval_args for a variety of data types and mapping configurations."""
spec = GroupSpec(
doc="A test group specification with a data type",
data_type_def="Baz",
groups=[
GroupSpec(doc="a group",
data_type_inc="EmptyBar",
quantity="?")
],
datasets=[
DatasetSpec(
doc="a dataset",
dtype="int",
name="data",
attributes=[
AttributeSpec(name="attr2",
doc="an integer attribute",
dtype="int")
],
)
],
attributes=[
AttributeSpec(name="attr1",
doc="a string attribute",
dtype="text"),
AttributeSpec(name="attr3",
doc="a numeric attribute",
dtype="numeric"),
AttributeSpec(name="attr4",
doc="a float attribute",
dtype="float"),
],
)
expected = [
{
'name': 'data',
'type': (int, np.int32, np.int64),
'doc': 'a dataset'
},
{
'name': 'attr1',
'type': str,
'doc': 'a string attribute'
},
{
'name': 'attr2',
'type': (int, np.int32, np.int64),
'doc': 'an integer attribute'
},
{
'name':
'attr3',
'doc':
'a numeric attribute',
'type':
(float, np.float32, np.float64, np.int8, np.int16, np.int32,
np.int64, int, np.uint8, np.uint16, np.uint32, np.uint64)
},
{
'name': 'attr4',
'doc': 'a float attribute',
'type': (float, np.float32, np.float64)
},
{
'name': 'bar',
'type': EmptyBar,
'doc': 'a group',
'default': None
},
]
not_inherited_fields = {
'data': spec.get_dataset('data'),
'attr1': spec.get_attribute('attr1'),
'attr2': spec.get_dataset('data').get_attribute('attr2'),
'attr3': spec.get_attribute('attr3'),
'attr4': spec.get_attribute('attr4'),
'bar': spec.groups[0]
}
docval_args = list()
for i, attr_name in enumerate(not_inherited_fields):
with self.subTest(attr_name=attr_name):
CustomClassGenerator.process_field_spec(
classdict={},
docval_args=docval_args,
parent_cls=EmptyBar, # <-- arbitrary class
attr_name=attr_name,
not_inherited_fields=not_inherited_fields,
type_map=self.type_map,
spec=spec)
self.assertListEqual(docval_args, expected[:(
i + 1)]) # compare with the first i elements of expected
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_update_docval_dset_shape(self):
"""Test that update_docval_args for a dataset with shape sets the type and shape keys."""
spec = GroupSpec(doc='A test group specification with a data type',
data_type_def='Baz',
datasets=[
DatasetSpec(name='dset1',
doc='a string dataset',
dtype='text',
shape=[None])
])
not_inherited_fields = {'dset1': spec.get_dataset('dset1')}
docval_args = list()
CustomClassGenerator.process_field_spec(
classdict={},
docval_args=docval_args,
parent_cls=EmptyBar, # <-- arbitrary class
attr_name='dset1',
not_inherited_fields=not_inherited_fields,
type_map=TypeMap(),
spec=spec)
expected = [{
'name': 'dset1',
'type': ('array_data', 'data'),
'doc': 'a string dataset',
'shape': [None]
}]
self.assertListEqual(docval_args, expected)
def test_update_docval_default_value(self):
"""Test that update_docval_args for an optional field with default value sets the default key."""
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,
default_value='value')
])
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': 'value'
}]
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_update_docval_default_value_none_required_parent(self):
"""Test that update_docval_args for an optional field with a required parent sets default: None."""
spec = GroupSpec(doc='A test group specification with a data type',
data_type_def='Baz',
groups=[
GroupSpec(name='group1',
doc='required untyped group',
attributes=[
AttributeSpec(
name='attr1',
doc='a string attribute',
dtype='text',
required=False)
])
])
not_inherited_fields = {
'attr1': spec.get_group('group1').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_update_docval_required_field_optional_parent(self):
"""Test that update_docval_args for a required field with an optional parent sets default: None."""
spec = GroupSpec(doc='A test group specification with a data type',
data_type_def='Baz',
groups=[
GroupSpec(name='group1',
doc='required untyped group',
attributes=[
AttributeSpec(
name='attr1',
doc='a string attribute',
dtype='text')
],
quantity='?')
])
not_inherited_fields = {
'attr1': spec.get_group('group1').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_process_field_spec_overwrite(self):
"""Test that docval generation overwrites previous docval args."""
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 = [
{
'name': 'attr1',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [[None], [None, None]]
}, # this dict will be overwritten below
{
'name': 'attr2',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [[None], [None, None]]
}
]
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]
}, {
'name': 'attr2',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [[None], [None, None]]
}]
self.assertListEqual(docval_args, expected)
def test_process_field_spec_link(self):
"""Test that processing a link spec does not set child=True in __fields__."""
classdict = {}
not_inherited_fields = {
'attr3': LinkSpec(name='attr3',
target_type='EmptyBar',
doc='a link')
}
CustomClassGenerator.process_field_spec(
classdict=classdict,
docval_args=[],
parent_cls=EmptyBar, # <-- arbitrary class
attr_name='attr3',
not_inherited_fields=not_inherited_fields,
type_map=self.type_map,
spec=GroupSpec('dummy', 'doc'))
expected = {'__fields__': [{'name': 'attr3', 'doc': 'a link'}]}
self.assertDictEqual(classdict, expected)
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_post_process_default_name(self):
"""Test that docval generation for a class with a default name has the default value for name set."""
spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Baz',
default_name='MyBaz', # <-- default 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': 'name',
'type': str,
'doc': 'name',
'default': 'MyBaz'
}, {
'name': 'attr1',
'type': ('array_data', 'data'),
'doc': 'a string attribute',
'shape': [None]
}]
self.assertListEqual(docval_args, expected)
class TestDynamicContainer(unittest.TestCase):
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_dynamic_container_creation(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()
for x in get_docval(cls.__init__):
received_args.add(x['name'])
with self.subTest(name=x['name']):
self.assertNotIn('default', x)
self.assertSetEqual(expected_args, received_args)
self.assertEqual(cls.__name__, 'Baz')
self.assertTrue(issubclass(cls, Bar))
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_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 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 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', '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')
inst = cls([1, 2, 3, 4],
'string attribute',
1000,
attr3=98.6,
attr4=1.0)
self.assertEqual(inst.name, 'A fixed name')
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
class TestGetClassSeparateNamespace(TestCase):
def setUp(self):
self.test_dir = tempfile.mkdtemp()
if os.path.exists(self.test_dir): # start clean
self.tearDown()
os.mkdir(self.test_dir)
self.bar_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Bar',
datasets=[DatasetSpec(name='data', doc='a dataset', dtype='int')],
attributes=[
AttributeSpec(name='attr1',
doc='a string attribute',
dtype='text'),
AttributeSpec(name='attr2',
doc='an integer attribute',
dtype='int')
])
self.type_map = TypeMap()
create_load_namespace_yaml(namespace_name=CORE_NAMESPACE,
specs=[self.bar_spec],
output_dir=self.test_dir,
incl_types=dict(),
type_map=self.type_map)
def tearDown(self):
shutil.rmtree(self.test_dir)
def test_get_class_separate_ns(self):
"""Test that get_class correctly sets the name and type hierarchy across namespaces."""
self.type_map.register_container_type(CORE_NAMESPACE, 'Bar', Bar)
baz_spec = GroupSpec(
doc='A test extension',
data_type_def='Baz',
data_type_inc='Bar',
)
create_load_namespace_yaml(namespace_name='ndx-test',
specs=[baz_spec],
output_dir=self.test_dir,
incl_types={CORE_NAMESPACE: ['Bar']},
type_map=self.type_map)
cls = self.type_map.get_dt_container_cls('Baz', 'ndx-test')
self.assertEqual(cls.__name__, 'Baz')
self.assertTrue(issubclass(cls, Bar))
def _build_separate_namespaces(self):
# create an empty extension to test ClassGenerator._get_container_type resolution
# the Bar class has not been mapped yet to the bar spec
qux_spec = DatasetSpec(doc='A test extension', data_type_def='Qux')
spam_spec = DatasetSpec(doc='A test extension', data_type_def='Spam')
create_load_namespace_yaml(namespace_name='ndx-qux',
specs=[qux_spec, spam_spec],
output_dir=self.test_dir,
incl_types={},
type_map=self.type_map)
# resolve Spam first so that ndx-qux is resolved first
self.type_map.get_dt_container_cls('Spam', 'ndx-qux')
baz_spec = GroupSpec(doc='A test extension',
data_type_def='Baz',
data_type_inc='Bar',
groups=[
GroupSpec(data_type_inc='Qux',
doc='a qux',
quantity='?'),
GroupSpec(data_type_inc='Bar',
doc='a bar',
quantity='?')
])
create_load_namespace_yaml(namespace_name='ndx-test',
specs=[baz_spec],
output_dir=self.test_dir,
incl_types={
CORE_NAMESPACE: ['Bar'],
'ndx-qux': ['Qux']
},
type_map=self.type_map)
def _check_classes(self, baz_cls, bar_cls, bar_cls2, qux_cls, qux_cls2):
self.assertEqual(qux_cls.__name__, 'Qux')
self.assertEqual(baz_cls.__name__, 'Baz')
self.assertEqual(bar_cls.__name__, 'Bar')
self.assertIs(bar_cls,
bar_cls2) # same class, two different namespaces
self.assertIs(qux_cls, qux_cls2)
self.assertTrue(issubclass(qux_cls, Data))
self.assertTrue(issubclass(baz_cls, bar_cls))
self.assertTrue(issubclass(bar_cls, Container))
qux_inst = qux_cls(name='qux_name', data=[1])
bar_inst = bar_cls(name='bar_name',
data=100,
attr1='a string',
attr2=10)
baz_inst = baz_cls(name='baz_name',
qux=qux_inst,
bar=bar_inst,
data=100,
attr1='a string',
attr2=10)
self.assertIs(baz_inst.qux, qux_inst)
def test_get_class_include_from_separate_ns_1(self):
"""Test that get_class correctly sets the name and includes types correctly across namespaces.
This is one of multiple tests carried out to ensure that order of which get_dt_container_cls is called
does not impact the results
first use EXTENSION namespace, then use ORIGINAL namespace
"""
self._build_separate_namespaces()
baz_cls = self.type_map.get_dt_container_cls(
'Baz', 'ndx-test') # Qux and Bar are not yet resolved
bar_cls = self.type_map.get_dt_container_cls('Bar', 'ndx-test')
bar_cls2 = self.type_map.get_dt_container_cls('Bar', CORE_NAMESPACE)
qux_cls = self.type_map.get_dt_container_cls('Qux', 'ndx-test')
qux_cls2 = self.type_map.get_dt_container_cls('Qux', 'ndx-qux')
self._check_classes(baz_cls, bar_cls, bar_cls2, qux_cls, qux_cls2)
def test_get_class_include_from_separate_ns_2(self):
"""Test that get_class correctly sets the name and includes types correctly across namespaces.
This is one of multiple tests carried out to ensure that order of which get_dt_container_cls is called
does not impact the results
first use ORIGINAL namespace, then use EXTENSION namespace
"""
self._build_separate_namespaces()
baz_cls = self.type_map.get_dt_container_cls(
'Baz', 'ndx-test') # Qux and Bar are not yet resolved
bar_cls2 = self.type_map.get_dt_container_cls('Bar', CORE_NAMESPACE)
bar_cls = self.type_map.get_dt_container_cls('Bar', 'ndx-test')
qux_cls = self.type_map.get_dt_container_cls('Qux', 'ndx-test')
qux_cls2 = self.type_map.get_dt_container_cls('Qux', 'ndx-qux')
self._check_classes(baz_cls, bar_cls, bar_cls2, qux_cls, qux_cls2)
def test_get_class_include_from_separate_ns_3(self):
"""Test that get_class correctly sets the name and includes types correctly across namespaces.
This is one of multiple tests carried out to ensure that order of which get_dt_container_cls is called
does not impact the results
first use EXTENSION namespace, then use EXTENSION namespace
"""
self._build_separate_namespaces()
baz_cls = self.type_map.get_dt_container_cls(
'Baz', 'ndx-test') # Qux and Bar are not yet resolved
bar_cls = self.type_map.get_dt_container_cls('Bar', 'ndx-test')
bar_cls2 = self.type_map.get_dt_container_cls('Bar', CORE_NAMESPACE)
qux_cls2 = self.type_map.get_dt_container_cls('Qux', 'ndx-qux')
qux_cls = self.type_map.get_dt_container_cls('Qux', 'ndx-test')
self._check_classes(baz_cls, bar_cls, bar_cls2, qux_cls, qux_cls2)
def test_get_class_include_from_separate_ns_4(self):
"""Test that get_class correctly sets the name and includes types correctly across namespaces.
This is one of multiple tests carried out to ensure that order of which get_dt_container_cls is called
does not impact the results
first use ORIGINAL namespace, then use EXTENSION namespace
"""
self._build_separate_namespaces()
baz_cls = self.type_map.get_dt_container_cls(
'Baz', 'ndx-test') # Qux and Bar are not yet resolved
bar_cls2 = self.type_map.get_dt_container_cls('Bar', CORE_NAMESPACE)
bar_cls = self.type_map.get_dt_container_cls('Bar', 'ndx-test')
qux_cls2 = self.type_map.get_dt_container_cls('Qux', 'ndx-qux')
qux_cls = self.type_map.get_dt_container_cls('Qux', 'ndx-test')
self._check_classes(baz_cls, bar_cls, bar_cls2, qux_cls, qux_cls2)
