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)
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 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( 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): spec_catalog = SpecCatalog() for spec in self.getSpecs(): spec_catalog.register_spec(spec, 'test.yaml') self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{ 'source': 'test.yaml' }], catalog=spec_catalog) self.vmap = ValidatorMap(self.namespace)
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 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
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 set_up_spec(self, dtype): spec_catalog = SpecCatalog() spec = GroupSpec( 'A test group specification with a data type', data_type_def='Bar', datasets=[DatasetSpec('an example dataset', dtype, name='data')], attributes=[AttributeSpec('attr1', 'an example attribute', dtype)]) spec_catalog.register_spec(spec, 'test.yaml') self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{ 'source': 'test.yaml' }], version='0.1.0', catalog=spec_catalog) self.vmap = ValidatorMap(self.namespace)
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 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_register_generator(self): """Test TypeMap.register_generator and ClassGenerator.register_generator.""" class MyClassGenerator(CustomClassGenerator): @classmethod def apply_generator_to_field(cls, field_spec, bases, type_map): return True @classmethod def process_field_spec(cls, classdict, docval_args, parent_cls, attr_name, not_inherited_fields, type_map, spec): # append attr_name to classdict['__custom_fields__'] list classdict.setdefault('process_field_spec', list()).append(attr_name) @classmethod def post_process(cls, classdict, bases, docval_args, spec): classdict['post_process'] = True 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') ]) spec_catalog = SpecCatalog() spec_catalog.register_spec(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_generator(MyClassGenerator) cls = type_map.get_dt_container_cls('Baz', CORE_NAMESPACE) self.assertEqual(cls.process_field_spec, ['attr1']) self.assertTrue(cls.post_process)
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 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)