def test_extension_overwrite(self):
link0 = LinkSpec(doc='Link 0',
target_type='TargetType0',
name='MyType0')
link1 = LinkSpec(doc='Link 1',
target_type='TargetType1',
name='MyType1')
# NOTE overwriting unnamed LinkSpec is not allowed
# NOTE overwriting spec with quantity that could be >1 is not allowed
links = [link0, link1]
parent_spec = GroupSpec(doc='A test group',
name='parent',
links=links,
data_type_def='ParentType')
link0_overwrite = LinkSpec(doc='New link 0',
target_type='TargetType0',
name='MyType0')
link1_overwrite = LinkSpec(doc='New link 1',
target_type='TargetType1Child',
name='MyType1')
overwritten_links = [link0_overwrite, link1_overwrite]
child_spec = GroupSpec(doc='A test group',
name='child',
links=overwritten_links,
data_type_inc=parent_spec,
data_type_def='ChildType')
for link in overwritten_links:
with self.subTest(link_target_type=link.target_type):
self.assertTrue(child_spec.is_inherited_spec(link))
self.assertTrue(child_spec.is_overridden_spec(link))
def create_specs(self, quantity):
# Type SimpleBucket contains:
# - [quantity] groups of data_type_inc SimpleFoo and [quantity] group of data_type_inc NotSimpleFoo
# - [quantity] datasets of data_type_inc SimpleQux and [quantity] datasets of data_type_inc NotSimpleQux
# - [quantity] links of target_type SimpleFoo and [quantity] links of target_type NotSimpleFoo
foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='SimpleFoo',
)
not_foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='NotSimpleFoo',
)
qux_spec = DatasetSpec(
doc='A test group specification with a data type',
data_type_def='SimpleQux',
)
not_qux_spec = DatasetSpec(
doc='A test group specification with a data type',
data_type_def='NotSimpleQux',
)
foo_inc_spec = GroupSpec(
doc='the SimpleFoos in this bucket',
data_type_inc='SimpleFoo',
quantity=quantity
)
not_foo_inc_spec = GroupSpec(
doc='the SimpleFoos in this bucket',
data_type_inc='NotSimpleFoo',
quantity=quantity
)
qux_inc_spec = DatasetSpec(
doc='the SimpleQuxs in this bucket',
data_type_inc='SimpleQux',
quantity=quantity
)
not_qux_inc_spec = DatasetSpec(
doc='the SimpleQuxs in this bucket',
data_type_inc='NotSimpleQux',
quantity=quantity
)
foo_link_spec = LinkSpec(
doc='the links in this bucket',
target_type='SimpleFoo',
quantity=quantity
)
not_foo_link_spec = LinkSpec(
doc='the links in this bucket',
target_type='NotSimpleFoo',
quantity=quantity
)
bucket_spec = GroupSpec(
doc='A test group specification for a data type containing data type',
name="test_bucket",
data_type_def='SimpleBucket',
groups=[foo_inc_spec, not_foo_inc_spec],
datasets=[qux_inc_spec, not_qux_inc_spec],
links=[foo_link_spec, not_foo_link_spec]
)
return [foo_spec, not_foo_spec, qux_spec, not_qux_spec, bucket_spec]
def test_constructor(self):
link0 = LinkSpec(doc='Link 0', target_type='TargetType0')
link1 = LinkSpec(doc='Link 1', target_type='TargetType1')
links = [link0, link1]
spec = GroupSpec(doc='A test group', name='root', links=links)
self.assertIs(spec, links[0].parent)
self.assertIs(spec, links[1].parent)
json.dumps(spec)
def test_unnamed_named_link_same_type(self):
"""Test get_target_type when a group contains both an unnamed and named link with type X."""
child0 = LinkSpec(doc='Group 0', target_type='Type0')
child1 = LinkSpec(doc='Group 1', target_type='Type0', name='type1')
parent_spec = GroupSpec(doc='A test group',
name='parent',
links=[child0, child1],
data_type_def='ParentType')
self.assertIs(parent_spec.get_target_type('Type0'), child0)
def test_two_unnamed_links_same_type(self):
"""Test creating a group contains multiple unnamed links with type X."""
child0 = LinkSpec(doc='Group 0', target_type='Type0')
child1 = LinkSpec(doc='Group 1', target_type='Type0')
msg = "Cannot have multiple links with the same target type without specifying name"
with self.assertRaisesWith(ValueError, msg):
GroupSpec(doc='A test group',
name='parent',
links=[child0, child1],
data_type_def='ParentType')
def test_two_named_links_same_type(self):
"""Test get_target_type when a group contains multiple named links with type X."""
child0 = LinkSpec(doc='Group 0', target_type='Type0', name='group0')
child1 = LinkSpec(doc='Group 1', target_type='Type0', name='group1')
parent_spec = GroupSpec(doc='A test group',
name='parent',
links=[child0, child1],
data_type_def='ParentType')
self.assertEqual(parent_spec.get_target_type('Type0'),
[child0, child1])
def test_required_is_many(self):
quantity_opts = ['?', 1, '*', '+']
is_required = [False, True, False, True]
is_many = [False, False, True, True]
for (quantity, req, many) in zip(quantity_opts, is_required, is_many):
with self.subTest(quantity=quantity):
spec = LinkSpec(
doc='A test link',
target_type='Group1',
quantity=quantity,
name='Link1',
)
self.assertEqual(spec.required, req)
self.assertEqual(spec.is_many(), many)
def test_constructor_defaults(self):
spec = LinkSpec(
doc='A test link',
target_type='Group1',
)
self.assertEqual(spec.quantity, 1)
self.assertIsNone(spec.name)
json.dumps(spec)
def test_set_link(self):
group = GroupSpec(doc='A test group', name='root')
link = LinkSpec(doc='A test link',
target_type='LinkTarget',
name='link_name')
group.set_link(link)
self.assertIs(group, link.parent)
self.assertIs(group.get_link('link_name'), link)
def create_specs(self, quantity):
# Type SimpleBucket contains:
# - an untyped group "foo_holder" which contains [quantity] groups of data_type_inc SimpleFoo
# - an untyped group "qux_holder" which contains [quantity] datasets of data_type_inc SimpleQux
# - an untyped group "link_holder" which contains [quantity] links of target_type SimpleFoo
foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='SimpleFoo',
)
not_foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='NotSimpleFoo',
)
qux_spec = DatasetSpec(
doc='A test group specification with a data type',
data_type_def='SimpleQux',
)
not_qux_spec = DatasetSpec(
doc='A test group specification with a data type',
data_type_def='NotSimpleQux',
)
foo_inc_spec = GroupSpec(
doc='the SimpleFoos in this bucket',
data_type_inc='SimpleFoo',
quantity=quantity
)
foo_holder_spec = GroupSpec(
doc='An untyped subgroup for SimpleFoos',
name='foo_holder',
groups=[foo_inc_spec]
)
qux_inc_spec = DatasetSpec(
doc='the SimpleQuxs in this bucket',
data_type_inc='SimpleQux',
quantity=quantity
)
qux_holder_spec = GroupSpec(
doc='An untyped subgroup for SimpleQuxs',
name='qux_holder',
datasets=[qux_inc_spec]
)
foo_link_spec = LinkSpec(
doc='the links in this bucket',
target_type='SimpleFoo',
quantity=quantity
)
link_holder_spec = GroupSpec(
doc='An untyped subgroup for links',
name='link_holder',
links=[foo_link_spec]
)
bucket_spec = GroupSpec(
doc='A test group specification for a data type containing data type',
name="test_bucket",
data_type_def='SimpleBucket',
groups=[foo_holder_spec, qux_holder_spec, link_holder_spec]
)
return [foo_spec, not_foo_spec, qux_spec, not_qux_spec, bucket_spec]
def test_unnamed_dataset_link_same_type(self):
child = DatasetSpec(doc='Dataset 0', data_type_inc='Type0')
link = LinkSpec(doc='Link 0', target_type='Type0')
parent_spec = GroupSpec(doc='A test group',
name='parent',
datasets=[child],
links=[link],
data_type_def='ParentType')
self.assertIs(parent_spec.get_data_type('Type0'), child)
self.assertIs(parent_spec.get_target_type('Type0'), link)
def test_constructor_target_spec_inc(self):
group_spec_inc = GroupSpec(
data_type_inc='Group1',
doc='A test group',
)
msg = "'target_type' must be a string or a GroupSpec or DatasetSpec with a 'data_type_def' key."
with self.assertRaisesWith(ValueError, msg):
LinkSpec(
doc='A test link',
target_type=group_spec_inc,
)
def test_constructor_target_spec_def(self):
group_spec_def = GroupSpec(
data_type_def='Group1',
doc='A test group',
)
spec = LinkSpec(
doc='A test link',
target_type=group_spec_def,
)
self.assertEqual(spec.target_type, 'Group1')
json.dumps(spec)
def test_constructor(self):
spec = LinkSpec(
doc='A test link',
target_type='Group1',
quantity='+',
name='Link1',
)
self.assertEqual(spec.doc, 'A test link')
self.assertEqual(spec.target_type, 'Group1')
self.assertEqual(spec.data_type_inc, 'Group1')
self.assertEqual(spec.quantity, '+')
self.assertEqual(spec.name, 'Link1')
json.dumps(spec)
def test_extension_no_overwrite(self):
link0 = LinkSpec(doc='Link 0',
target_type='TargetType0') # test unnamed
link1 = LinkSpec(doc='Link 1',
target_type='TargetType1',
name='MyType1') # test named
link2 = LinkSpec(doc='Link 2', target_type='TargetType2',
quantity='*') # test named, multiple
links = [link0, link1, link2]
parent_spec = GroupSpec(doc='A test group',
name='parent',
links=links,
data_type_def='ParentType')
child_spec = GroupSpec(doc='A test group',
name='child',
data_type_inc=parent_spec,
data_type_def='ChildType')
for link in links:
with self.subTest(link_target_type=link.target_type):
self.assertTrue(child_spec.is_inherited_spec(link))
self.assertFalse(child_spec.is_overridden_spec(link))
def test_unnamed_link_data_type_inc(self):
"""Test get_subspec on a builder that maps to an unnamed link."""
link_spec = LinkSpec(doc='This Bar', target_type='Bar')
parent_spec = GroupSpec(doc='Something to hold a Bar',
name='bar_bucket',
links=[link_spec])
bar_builder = GroupBuilder(name='my_bar',
attributes={
'data_type': 'Bar',
'namespace': CORE_NAMESPACE,
'object_id': -1
})
sub_builder = LinkBuilder(builder=bar_builder, name='my_link')
GroupBuilder(name='bar_bucket', links={'my_bar': sub_builder})
result = self.type_map.get_subspec(parent_spec, sub_builder)
self.assertIs(result, link_spec)
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 main():
# these arguments were auto-generated from your cookie-cutter inputs
ns_builder = NamespaceBuilder(
doc=
"""Objects for rigorously defining spatial coordinates, object shapes, and transformations""",
name="""ndx-spatial-coordinates""",
version="""0.1.0""",
author=list(map(str.strip, """Ben Dichter""".split(','))),
contact=list(
map(str.strip, """*****@*****.**""".split(','))))
# TODO: specify the neurodata_types that are used by the extension as well
# as in which namespace they are found
# this is similar to specifying the Python modules that need to be imported
# to use your new data types
# as of HDMF 1.6.1, the full ancestry of the neurodata_types that are used by
# the extension should be included, i.e., the neurodata_type and its parent
# type and its parent type and so on. this will be addressed in a future
# release of HDMF.
ns_builder.include_type('Container', namespace='hdmf-common')
# TODO: define your new data types
# see https://pynwb.readthedocs.io/en/latest/extensions.html#extending-nwb
# for more information
Space = GroupSpec(data_type_def='Space',
data_type_inc='Container',
doc='space',
attributes=[
AttributeSpec(name='R',
doc='dimensionality of space',
dtype='int')
])
Spaces = GroupSpec(data_type_def='Spaces',
data_type_inc='Container',
doc='contains spaces',
groups=[
GroupSpec(data_type_inc=Space,
quantity='*',
doc='spaces are stored here')
])
CoordinateSystem = GroupSpec(
data_type_def='CoordinateSystem',
data_type_inc='Container',
doc='coordinate system',
links=[
LinkSpec(doc='link to space', target_type='Space', name='space')
],
attributes=[
AttributeSpec(name='R',
doc='dimensionality of coordinate system',
dtype='int')
])
CoordinateSystems = GroupSpec(
data_type_def='CoordinateSystems',
data_type_inc='Container',
doc='coordinate systems',
groups=[
GroupSpec(data_type_inc=CoordinateSystem,
quantity='*',
doc='coordinate systems are stored here')
],
)
RegistrationProtocol = GroupSpec(data_type_def='RegistrationProtocol',
data_type_inc='Container',
doc='registration protocol')
RegistrationProtocols = GroupSpec(
data_type_def='RegistrationProtocols',
data_type_inc='Container',
doc='registration protocols',
groups=[
GroupSpec(data_type_inc=RegistrationProtocol,
quantity='*',
doc='registration protocols are stored here')
],
)
CoordinateRegistrationProcess = GroupSpec(
data_type_def='CoordinateRegistrationProcess',
data_type_inc='Container',
doc='coordinate registration process',
links=[
LinkSpec(doc='registration protocol',
target_type='RegistrationProtocol',
name='registration_protocol')
])
CoordinateRegistrationProcesses = GroupSpec(
data_type_def='CoordinateRegistrationProcesses',
data_type_inc='Container',
doc='registration process',
groups=[
GroupSpec(data_type_inc=CoordinateRegistrationProcess,
quantity='*',
doc='registration processes are stored here')
],
)
Transform = GroupSpec(
data_type_def='Transform',
data_type_inc='Container',
doc='transform',
links=[
LinkSpec(doc='domain coordinate system',
target_type='CoordinateSystem',
name='domain_coordinate_system'),
LinkSpec(doc='range coordinate system',
target_type='CoordinateSystem',
name='range_coordinate_system')
],
)
AffineTransform = GroupSpec(data_type_def='AffineTransform',
data_type_inc=Transform,
doc='affine transform',
datasets=[
DatasetSpec(doc='affine transform matrix',
dtype='float',
shape=(None, None),
name='M')
])
DeformableTransform = GroupSpec(
data_type_def='DeformableTransform',
data_type_inc=Transform,
doc='deformable transform',
datasets=[DatasetSpec(doc='vector image', dtype='float', name='I')])
Transforms = GroupSpec(
data_type_def='Transforms',
data_type_inc='Container',
doc='transforms',
groups=[
GroupSpec(data_type_inc=Transform,
quantity='*',
doc='transforms are stored here')
],
)
PhysicalObjectType = GroupSpec(data_type_def='PhysicalObjectType',
data_type_inc='Container',
doc='physical object type',
groups=[
GroupSpec(name='geometry',
doc='geometry',
datasets=[
DatasetSpec(name='nodes',
doc='nodes',
dtype='float',
shape=(None,
3)),
DatasetSpec(name='edges',
doc='edges',
dtype='uint',
shape=(None,
3))
])
],
links=[
LinkSpec(name='coordinate_system',
doc='coordinate system',
target_type='CoordinateSystem')
])
ElectrodeType = GroupSpec(data_type_def='ElectrodeType',
data_type_inc=PhysicalObjectType,
doc='electrode type',
attributes=[
AttributeSpec(name='electrode_type',
doc='electrode type',
dtype='text')
])
ElectrodeTypes = GroupSpec(
data_type_def='ElectrodeTypes',
data_type_inc='Container',
doc='electrode types',
groups=[
GroupSpec(data_type_inc=ElectrodeType,
quantity='*',
doc='electrode types are stored here')
],
)
PhysicalObjectWithSubObjectsType = GroupSpec(
data_type_def='PhysicalObjectWithSubObjectsType',
data_type_inc=PhysicalObjectType,
doc='physical object with sub objects',
groups=[
GroupSpec(
name='sites',
doc='sites',
datasets=[
DatasetSpec(
name='sites',
doc='sites',
dtype=[
DtypeSpec(
name='position',
doc='position',
dtype='float',
#shape=(3,)
),
DtypeSpec(
name='normal',
doc='normal',
dtype='float',
#shape=(3,)
),
DtypeSpec(name='object_type',
doc='object type',
dtype=RefSpec(
target_type='PhysicalObjectType',
reftype='object')),
])
])
])
ProbeType = GroupSpec(
data_type_def='ProbeType',
data_type_inc=PhysicalObjectWithSubObjectsType,
doc='probe type',
)
ProbeTypes = GroupSpec(
data_type_def='ProbeTypes',
data_type_inc='Container',
doc='probe types',
groups=[
GroupSpec(data_type_inc=ProbeType,
quantity='*',
doc='probe types are stored here')
],
)
SubjectBrain = GroupSpec(data_type_def='SubjectBrain',
data_type_inc=PhysicalObjectWithSubObjectsType,
doc='subject brain')
SpaceInfo = GroupSpec(
data_type_def='SpaceInfo',
data_type_inc='Container',
doc='all space info goes in here',
groups=[
GroupSpec(data_type_inc=Spaces, doc='spaces'),
GroupSpec(data_type_inc=CoordinateSystems,
doc='coordinate systems'),
GroupSpec(data_type_inc=RegistrationProtocols,
doc='registration protocols'),
GroupSpec(data_type_inc=CoordinateRegistrationProcesses,
doc='registration processes'),
GroupSpec(data_type_inc=Transforms, doc='transforms'),
GroupSpec(data_type_inc=ElectrodeTypes, doc='electrode types'),
GroupSpec(data_type_inc=ProbeTypes, doc='probe types'),
GroupSpec(data_type_inc=SubjectBrain, doc='subject brain')
])
new_data_types = [
Space, Spaces, CoordinateSystem, CoordinateSystems,
RegistrationProtocol, RegistrationProtocols,
CoordinateRegistrationProcess, CoordinateRegistrationProcesses,
Transform, AffineTransform, DeformableTransform, Transforms,
PhysicalObjectType, ElectrodeType, ElectrodeTypes,
PhysicalObjectWithSubObjectsType, ProbeType, ProbeTypes, SubjectBrain,
SpaceInfo
]
# export the spec to yaml files in the spec folder
output_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', '..', 'spec'))
export_spec(ns_builder, new_data_types, output_dir)