def setUp(self):
super().setUp()
self.foo_bucket = FooBucket('test_foo_bucket', [
Foo('my_foo1', list(range(10)), 'value1', 10),
Foo('my_foo2', list(range(10, 20)), 'value2', 20)])
self.foo_builders = {
'my_foo1': GroupBuilder('my_foo1',
datasets={'my_data': DatasetBuilder(
'my_data',
list(range(10)),
attributes={'attr2': 10})},
attributes={'attr1': 'value1', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': self.foo_bucket.foos['my_foo1'].object_id}),
'my_foo2': GroupBuilder('my_foo2', datasets={'my_data':
DatasetBuilder(
'my_data',
list(range(10, 20)),
attributes={'attr2': 20})},
attributes={'attr1': 'value2', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': self.foo_bucket.foos['my_foo2'].object_id})
}
self.setUpBucketBuilder()
self.setUpBucketSpec()
self.spec_catalog.register_spec(self.bucket_spec, 'test.yaml')
self.type_map.register_container_type(CORE_NAMESPACE, 'FooBucket', FooBucket)
self.type_map.register_map(FooBucket, self.setUpBucketMapper())
self.manager = BuildManager(self.type_map)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
foo = Foo('my_foo1', [1, 2, 3], 'string', 10)
baz = Baz('MyBaz', [foo], 'abcdefghijklmnopqrstuvwxyz')
msg = "MyBaz (MyBaz): Could not find already-built Builder for Foo 'my_foo1' in BuildManager"
with self.assertRaisesWith(ReferenceTargetNotBuiltError, msg):
self.manager.build(baz, root=True)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
foo = Foo('my_foo1', [1, 2, 3], 'string', 10)
baz = Baz('MyBaz', [foo], 'abcdefghijklmnopqrstuvwxyz')
foo_builder = self.manager.build(foo)
baz_builder = self.manager.build(baz, root=True)
expected = DatasetBuilder('MyBaz', [ReferenceBuilder(foo_builder)],
attributes={
'baz_attr': 'abcdefghijklmnopqrstuvwxyz',
'data_type': 'Baz',
'namespace': CORE_NAMESPACE,
'object_id': baz.object_id
})
self.assertBuilderEqual(baz_builder, expected)
def test_build(self):
container_inst = Foo('my_foo', list(range(10)), 'value1', 10)
expected = GroupBuilder(
'my_foo',
datasets={
'my_data':
DatasetBuilder(
'my_data',
list(range(10)),
attributes={'attr2': 10})},
attributes={'attr1': 'value1', 'namespace': CORE_NAMESPACE, 'data_type': 'Foo',
'object_id': container_inst.object_id})
builder1 = self.manager.build(container_inst)
self.assertDictEqual(builder1, expected)
def test_build(self):
"""Test that an error is raised when a spec is mapped to a non-existent container attribute."""
class Unmapper(ObjectMapper):
def __init__(self, spec):
super().__init__(spec)
self.map_spec("unknown", self.spec.get_dataset('my_data'))
self.type_map.register_map(Foo, Unmapper) # override
container_inst = Foo('my_foo', list(range(10)), 'value1', 10)
msg = ("Foo 'my_foo' does not have attribute 'unknown' for mapping to spec: %s"
% self.foo_spec.get_dataset('my_data'))
with self.assertRaisesWith(ContainerConfigurationError, msg):
self.manager.build(container_inst)
def test_append_1_0_5(self):
'''Test whether we can append to files made by hdmf version 1.0.5'''
foo = Foo('foo3', [10, 20, 30, 40, 50], "I am foo3", 17, 3.14)
foobucket = FooBucket('foobucket2', [foo])
with HDF5IO(self.path_1_0_5, manager=self.manager, mode='a') as io:
read_foofile = io.read()
read_foofile.add_bucket(foobucket)
io.write(read_foofile)
with HDF5IO(self.path_1_0_5, manager=self.manager, mode='r') as io:
read_foofile = io.read()
self.assertListEqual(
read_foofile.buckets['foobucket2'].foos['foo3'].my_data[:].
tolist(), foo.my_data)
def test_append_1_0_5(self):
'''Test whether we can append to files made by hdmf version 1.0.5'''
foo = Foo('foo3', [10, 20, 30, 40, 50], "I am foo3", 17, 3.14)
foobucket = FooBucket('foobucket2', [foo])
with HDF5IO(self.path_1_0_5, manager=self.manager, mode='a') as io:
read_foofile = io.read()
read_foofile.buckets.append(foobucket)
foobucket.parent = read_foofile
io.write(read_foofile)
with HDF5IO(self.path_1_0_5, manager=self.manager, mode='r') as io:
read_foofile = io.read()
# workaround for the fact that order of buckets is not maintained
for bucket in read_foofile.buckets:
if bucket.name == 'foobucket2':
self.assertListEqual(bucket.foos[0].my_data[:].tolist(), foo.my_data)
def test_build(self):
"""Test that an error is raised when a spec is not mapped to a container attribute."""
class Unmapper(ObjectMapper):
def __init__(self, spec):
super().__init__(spec)
self.unmap(
self.spec.get_dataset('my_data')
) # remove mapping from this spec to container attribute
self.type_map.register_map(Foo, Unmapper) # override
container_inst = Foo('my_foo', list(range(10)), 'value1', 10)
msg = (
r"<class '.*Unmapper'> has no container attribute mapped to spec: %s"
% re.escape(str(self.foo_spec.get_dataset('my_data'))))
with self.assertRaisesRegex(ContainerConfigurationError, msg):
self.manager.build(container_inst)
def setUp(self):
self.manager = _get_manager()
self.path = "test_io_hdf5.h5"
self.foo_builder = GroupBuilder('foo1',
attributes={'data_type': 'Foo',
'namespace': 'test_core',
'attr1': "bar",
'object_id': -1},
datasets={'my_data': DatasetBuilder('my_data', list(range(100, 200, 10)),
attributes={'attr2': 17})})
self.foo = Foo('foo1', list(range(100, 200, 10)), attr1="bar", attr2=17, attr3=3.14)
self.manager.prebuilt(self.foo, self.foo_builder)
self.builder = GroupBuilder(
'root',
source=self.path,
groups={'test_bucket':
GroupBuilder('test_bucket',
groups={'foo_holder':
GroupBuilder('foo_holder',
groups={'foo1': self.foo_builder})})},
attributes={'data_type': 'FooFile'})