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 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(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