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from hdmf import Container, Data
from hdmf.build import (BuildManager, TypeMap, GroupBuilder, DatasetBuilder, LinkBuilder, ObjectMapper,
MissingRequiredBuildWarning, IncorrectQuantityBuildWarning)
from hdmf.spec import GroupSpec, DatasetSpec, LinkSpec, SpecCatalog, SpecNamespace, NamespaceCatalog
from hdmf.spec.spec import ZERO_OR_MANY, ONE_OR_MANY, ZERO_OR_ONE, DEF_QUANTITY
from hdmf.testing import TestCase
from hdmf.utils import docval, getargs
from tests.unit.helpers.utils import CORE_NAMESPACE
##########################
# test all crosses:
# {
# untyped, named group with data-type-included groups / data-type-included datasets / links
# nested, type definition
# included groups / included datasets / links
# }
# x
# group/dataset/link with quantity {'*', '+', 1, 2, '?'}
# x
# builder with 2, 1, or 0 instances of the type, or 0 instances of the type with some instances of a mismatched type
class SimpleFoo(Container):
pass
class NotSimpleFoo(Container):
pass
class SimpleQux(Data):
pass
class NotSimpleQux(Data):
pass
class SimpleBucket(Container):
@docval({'name': 'name', 'type': str, 'doc': 'the name of this SimpleBucket'},
{'name': 'foos', 'type': list, 'doc': 'the SimpleFoo objects', 'default': list()},
{'name': 'quxs', 'type': list, 'doc': 'the SimpleQux objects', 'default': list()},
{'name': 'links', 'type': list, 'doc': 'another way to store SimpleFoo objects', 'default': list()})
def __init__(self, **kwargs):
name, foos, quxs, links = getargs('name', 'foos', 'quxs', 'links', kwargs)
super().__init__(name=name)
# note: collections of groups are unordered in HDF5, so make these dictionaries for keyed access
self.foos = {f.name: f for f in foos}
for f in foos:
f.parent = self
self.quxs = {q.name: q for q in quxs}
for q in quxs:
q.parent = self
self.links = {i.name: i for i in links}
for i in links:
i.parent = self
class BasicBucket(Container):
@docval({'name': 'name', 'type': str, 'doc': 'the name of this BasicBucket'},
{'name': 'untyped_dataset', 'type': 'scalar_data',
'doc': 'a scalar dataset within this BasicBucket', 'default': None},
{'name': 'untyped_array_dataset', 'type': ('data', 'array_data'),
'doc': 'an array dataset within this BasicBucket', 'default': None},)
def __init__(self, **kwargs):
name, untyped_dataset, untyped_array_dataset = getargs('name', 'untyped_dataset', 'untyped_array_dataset',
kwargs)
super().__init__(name=name)
self.untyped_dataset = untyped_dataset
self.untyped_array_dataset = untyped_array_dataset
class BuildQuantityMixin:
"""Base test class mixin to set up the BuildManager."""
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 _create_builder(self, container):
"""Helper function to get a basic builder for a container with no subgroups/datasets/links."""
if isinstance(container, Container):
ret = GroupBuilder(
name=container.name,
attributes={'namespace': container.namespace,
'data_type': container.data_type,
'object_id': container.object_id}
)
else:
ret = DatasetBuilder(
name=container.name,
data=container.data,
attributes={'namespace': container.namespace,
'data_type': container.data_type,
'object_id': container.object_id}
)
return ret
class TypeIncUntypedGroupMixin:
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 setUpBucketMapper(self):
class BucketMapper(ObjectMapper):
def __init__(self, spec):
super().__init__(spec)
self.unmap(spec.get_group('foo_holder'))
self.map_spec('foos', spec.get_group('foo_holder').get_data_type('SimpleFoo'))
self.unmap(spec.get_group('qux_holder'))
self.map_spec('quxs', spec.get_group('qux_holder').get_data_type('SimpleQux'))
self.unmap(spec.get_group('link_holder'))
self.map_spec('links', spec.get_group('link_holder').links[0])
return BucketMapper
def get_two_bucket_test(self):
foos = [SimpleFoo('my_foo1'), SimpleFoo('my_foo2')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3]), SimpleQux('my_qux2', data=[4, 5, 6])]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=foos
)
foo1_builder = self._create_builder(bucket.foos['my_foo1'])
foo2_builder = self._create_builder(bucket.foos['my_foo2'])
qux1_builder = self._create_builder(bucket.quxs['my_qux1'])
qux2_builder = self._create_builder(bucket.quxs['my_qux2'])
foo_holder_builder = GroupBuilder(
name='foo_holder',
groups={'my_foo1': foo1_builder,
'my_foo2': foo2_builder}
)
qux_holder_builder = GroupBuilder(
name='qux_holder',
datasets={'my_qux1': qux1_builder,
'my_qux2': qux2_builder}
)
foo1_link_builder = LinkBuilder(builder=foo1_builder)
foo2_link_builder = LinkBuilder(builder=foo2_builder)
link_holder_builder = GroupBuilder(
name='link_holder',
links={'my_foo1': foo1_link_builder,
'my_foo2': foo2_link_builder}
)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'foos': foo_holder_builder,
'quxs': qux_holder_builder,
'links': link_holder_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_one_bucket_test(self):
foos = [SimpleFoo('my_foo1')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3])]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=foos
)
foo1_builder = GroupBuilder(
name='my_foo1',
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleFoo',
'object_id': bucket.foos['my_foo1'].object_id}
)
foo_holder_builder = GroupBuilder(
name='foo_holder',
groups={'my_foo1': foo1_builder}
)
qux1_builder = DatasetBuilder(
name='my_qux1',
data=[1, 2, 3],
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleQux',
'object_id': bucket.quxs['my_qux1'].object_id}
)
qux_holder_builder = GroupBuilder(
name='qux_holder',
datasets={'my_qux1': qux1_builder}
)
foo1_link_builder = LinkBuilder(builder=foo1_builder)
link_holder_builder = GroupBuilder(
name='link_holder',
links={'my_foo1': foo1_link_builder}
)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'foos': foo_holder_builder,
'quxs': qux_holder_builder,
'links': link_holder_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_zero_bucket_test(self):
bucket = SimpleBucket(
name='test_bucket'
)
foo_holder_builder = GroupBuilder(
name='foo_holder',
groups={}
)
qux_holder_builder = GroupBuilder(
name='qux_holder',
datasets={}
)
link_holder_builder = GroupBuilder(
name='link_holder',
links={}
)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'foos': foo_holder_builder,
'quxs': qux_holder_builder,
'links': link_holder_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_mismatch_bucket_test(self):
foos = [NotSimpleFoo('my_foo1'), NotSimpleFoo('my_foo2')]
quxs = [NotSimpleQux('my_qux1', data=[1, 2, 3]), NotSimpleQux('my_qux2', data=[4, 5, 6])]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=foos
)
foo_holder_builder = GroupBuilder(
name='foo_holder',
groups={}
)
qux_holder_builder = GroupBuilder(
name='qux_holder',
datasets={}
)
link_holder_builder = GroupBuilder(
name='link_holder',
links={}
)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'foos': foo_holder_builder,
'quxs': qux_holder_builder,
'links': link_holder_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
class TypeDefMixin:
def create_specs(self, quantity):
# Type SimpleBucket contains:
# - contains [quantity] groups of data_type_def SimpleFoo
# - contains [quantity] datasets of data_type_def SimpleQux
# NOTE: links do not have data_type_def, so leave them out of these tests
# NOTE: nested type definitions are strongly discouraged now
foo_spec = GroupSpec(
doc='the SimpleFoos in this bucket',
data_type_def='SimpleFoo',
quantity=quantity
)
qux_spec = DatasetSpec(
doc='the SimpleQuxs in this bucket',
data_type_def='SimpleQux',
quantity=quantity
)
not_foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='NotSimpleFoo',
)
not_qux_spec = DatasetSpec(
doc='A test group specification with a data type',
data_type_def='NotSimpleQux',
)
bucket_spec = GroupSpec(
doc='A test group specification for a data type containing data type',
name="test_bucket",
data_type_def='SimpleBucket',
groups=[foo_spec],
datasets=[qux_spec]
)
return [foo_spec, not_foo_spec, qux_spec, not_qux_spec, bucket_spec]
def setUpBucketMapper(self):
class BucketMapper(ObjectMapper):
def __init__(self, spec):
super().__init__(spec)
self.map_spec('foos', spec.get_data_type('SimpleFoo'))
self.map_spec('quxs', spec.get_data_type('SimpleQux'))
return BucketMapper
def get_two_bucket_test(self):
foos = [SimpleFoo('my_foo1'), SimpleFoo('my_foo2')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3]), SimpleQux('my_qux2', data=[4, 5, 6])]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
)
foo1_builder = self._create_builder(bucket.foos['my_foo1'])
foo2_builder = self._create_builder(bucket.foos['my_foo2'])
qux1_builder = self._create_builder(bucket.quxs['my_qux1'])
qux2_builder = self._create_builder(bucket.quxs['my_qux2'])
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'my_foo1': foo1_builder,
'my_foo2': foo2_builder},
datasets={'my_qux1': qux1_builder,
'my_qux2': qux2_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_one_bucket_test(self):
foos = [SimpleFoo('my_foo1')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3])]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
)
foo1_builder = self._create_builder(bucket.foos['my_foo1'])
qux1_builder = self._create_builder(bucket.quxs['my_qux1'])
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'my_foo1': foo1_builder},
datasets={'my_qux1': qux1_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_zero_bucket_test(self):
bucket = SimpleBucket(
name='test_bucket'
)
bucket_builder = GroupBuilder(
name='test_bucket',
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_mismatch_bucket_test(self):
foos = [NotSimpleFoo('my_foo1'), NotSimpleFoo('my_foo2')]
quxs = [NotSimpleQux('my_qux1', data=[1, 2, 3]), NotSimpleQux('my_qux2', data=[4, 5, 6])]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
)
bucket_builder = GroupBuilder(
name='test_bucket',
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
class TypeIncMixin:
def create_specs(self, quantity):
# Type SimpleBucket contains:
# - [quantity] groups of data_type_inc SimpleFoo
# - [quantity] datasets of data_type_inc SimpleQux
# - [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
)
qux_inc_spec = DatasetSpec(
doc='the SimpleQuxs in this bucket',
data_type_inc='SimpleQux',
quantity=quantity
)
foo_link_spec = LinkSpec(
doc='the links in this bucket',
target_type='SimpleFoo',
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],
datasets=[qux_inc_spec],
links=[foo_link_spec]
)
return [foo_spec, not_foo_spec, qux_spec, not_qux_spec, bucket_spec]
def setUpBucketMapper(self):
class BucketMapper(ObjectMapper):
def __init__(self, spec):
super().__init__(spec)
self.map_spec('foos', spec.get_data_type('SimpleFoo'))
self.map_spec('quxs', spec.get_data_type('SimpleQux'))
self.map_spec('links', spec.links[0])
return BucketMapper
def get_two_bucket_test(self):
foos = [SimpleFoo('my_foo1'), SimpleFoo('my_foo2')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3]), SimpleQux('my_qux2', data=[4, 5, 6])]
# NOTE: unlike in the other tests, links cannot map to the same foos in bucket because of a name clash
links = [SimpleFoo('my_foo3'), SimpleFoo('my_foo4')]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=links
)
foo1_builder = self._create_builder(bucket.foos['my_foo1'])
foo2_builder = self._create_builder(bucket.foos['my_foo2'])
foo3_builder = self._create_builder(bucket.links['my_foo3'])
foo4_builder = self._create_builder(bucket.links['my_foo4'])
qux1_builder = self._create_builder(bucket.quxs['my_qux1'])
qux2_builder = self._create_builder(bucket.quxs['my_qux2'])
foo3_link_builder = LinkBuilder(builder=foo3_builder)
foo4_link_builder = LinkBuilder(builder=foo4_builder)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'my_foo1': foo1_builder,
'my_foo2': foo2_builder},
datasets={'my_qux1': qux1_builder,
'my_qux2': qux2_builder},
links={'my_foo3': foo3_link_builder,
'my_foo4': foo4_link_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_one_bucket_test(self):
foos = [SimpleFoo('my_foo1')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3])]
# NOTE: unlike in the other tests, links cannot map to the same foos in bucket because of a name clash
links = [SimpleFoo('my_foo3')]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=links
)
foo1_builder = self._create_builder(bucket.foos['my_foo1'])
foo3_builder = self._create_builder(bucket.links['my_foo3'])
qux1_builder = self._create_builder(bucket.quxs['my_qux1'])
foo3_link_builder = LinkBuilder(builder=foo3_builder)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'my_foo1': foo1_builder},
datasets={'my_qux1': qux1_builder},
links={'my_foo1': foo3_link_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_zero_bucket_test(self):
bucket = SimpleBucket(
name='test_bucket'
)
bucket_builder = GroupBuilder(
name='test_bucket',
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def get_mismatch_bucket_test(self):
foos = [NotSimpleFoo('my_foo1'), NotSimpleFoo('my_foo2')]
quxs = [NotSimpleQux('my_qux1', data=[1, 2, 3]), NotSimpleQux('my_qux2', data=[4, 5, 6])]
links = [NotSimpleFoo('my_foo1'), NotSimpleFoo('my_foo2')]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=links
)
bucket_builder = GroupBuilder(
name='test_bucket',
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
class ZeroOrManyMixin:
def setUp(self):
specs = self.create_specs(ZERO_OR_MANY)
self.setUpManager(specs)
def test_build_two(self):
"""Test building a container which contains multiple containers as the spec allows."""
bucket, bucket_builder = self.get_two_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_one(self):
"""Test building a container which contains one container as the spec allows."""
bucket, bucket_builder = self.get_one_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_zero(self):
"""Test building a container which contains no containers as the spec allows."""
bucket, bucket_builder = self.get_zero_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_mismatch(self):
"""Test building a container which contains no containers that match the spec as the spec allows."""
bucket, bucket_builder = self.get_mismatch_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
class OneOrManyMixin:
def setUp(self):
specs = self.create_specs(ONE_OR_MANY)
self.setUpManager(specs)
def test_build_two(self):
"""Test building a container which contains multiple containers as the spec allows."""
bucket, bucket_builder = self.get_two_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_one(self):
"""Test building a container which contains one container as the spec allows."""
bucket, bucket_builder = self.get_one_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_zero(self):
"""Test building a container which contains no containers as the spec allows."""
bucket, bucket_builder = self.get_zero_bucket_test()
msg = r"SimpleBucket 'test_bucket' is missing required value for attribute '.*'\."
with self.assertWarnsRegex(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_mismatch(self):
"""Test building a container which contains no containers that match the spec as the spec allows."""
bucket, bucket_builder = self.get_mismatch_bucket_test()
msg = r"SimpleBucket 'test_bucket' is missing required value for attribute '.*'\."
with self.assertWarnsRegex(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
class OneMixin:
def setUp(self):
specs = self.create_specs(DEF_QUANTITY)
self.setUpManager(specs)
def test_build_two(self):
"""Test building a container which contains multiple containers as the spec allows."""
bucket, bucket_builder = self.get_two_bucket_test()
msg = r"SimpleBucket 'test_bucket' has 2 values for attribute '.*' but spec allows 1\."
with self.assertWarnsRegex(IncorrectQuantityBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_one(self):
"""Test building a container which contains one container as the spec allows."""
bucket, bucket_builder = self.get_one_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_zero(self):
"""Test building a container which contains no containers as the spec allows."""
bucket, bucket_builder = self.get_zero_bucket_test()
msg = r"SimpleBucket 'test_bucket' is missing required value for attribute '.*'\."
with self.assertWarnsRegex(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_mismatch(self):
"""Test building a container which contains no containers that match the spec as the spec allows."""
bucket, bucket_builder = self.get_mismatch_bucket_test()
msg = r"SimpleBucket 'test_bucket' is missing required value for attribute '.*'\."
with self.assertWarnsRegex(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
class TwoMixin:
def setUp(self):
specs = self.create_specs(2)
self.setUpManager(specs)
def test_build_two(self):
"""Test building a container which contains multiple containers as the spec allows."""
bucket, bucket_builder = self.get_two_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_one(self):
"""Test building a container which contains one container as the spec allows."""
bucket, bucket_builder = self.get_one_bucket_test()
msg = r"SimpleBucket 'test_bucket' has 1 values for attribute '.*' but spec allows 2\."
with self.assertWarnsRegex(IncorrectQuantityBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_zero(self):
"""Test building a container which contains no containers as the spec allows."""
bucket, bucket_builder = self.get_zero_bucket_test()
msg = r"SimpleBucket 'test_bucket' is missing required value for attribute '.*'\."
with self.assertWarnsRegex(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_mismatch(self):
"""Test building a container which contains no containers that match the spec as the spec allows."""
bucket, bucket_builder = self.get_mismatch_bucket_test()
msg = r"SimpleBucket 'test_bucket' is missing required value for attribute '.*'\."
with self.assertWarnsRegex(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
class ZeroOrOneMixin:
def setUp(self):
specs = self.create_specs(ZERO_OR_ONE)
self.setUpManager(specs)
def test_build_two(self):
"""Test building a container which contains multiple containers as the spec allows."""
bucket, bucket_builder = self.get_two_bucket_test()
msg = r"SimpleBucket 'test_bucket' has 2 values for attribute '.*' but spec allows '\?'\."
with self.assertWarnsRegex(IncorrectQuantityBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_one(self):
"""Test building a container which contains one container as the spec allows."""
bucket, bucket_builder = self.get_one_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_zero(self):
"""Test building a container which contains no containers as the spec allows."""
bucket, bucket_builder = self.get_zero_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_mismatch(self):
"""Test building a container which contains no containers that match the spec as the spec allows."""
bucket, bucket_builder = self.get_mismatch_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
# Untyped group with included groups / included datasets / links with quantity {'*', '+', 1, 2 '?'}
class TestBuildZeroOrManyTypeIncUntypedGroup(ZeroOrManyMixin, TypeIncUntypedGroupMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has an untyped subgroup with a data type inc subgroup/dataset/link with quantity '*'
"""
pass
class TestBuildOneOrManyTypeIncUntypedGroup(OneOrManyMixin, TypeIncUntypedGroupMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has an untyped subgroup with a data type inc subgroup/dataset/link with quantity '+'
"""
pass
class TestBuildOneTypeIncUntypedGroup(OneMixin, TypeIncUntypedGroupMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has an untyped subgroup with a data type inc subgroup/dataset/link with quantity 1
"""
pass
class TestBuildTwoTypeIncUntypedGroup(TwoMixin, TypeIncUntypedGroupMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has an untyped subgroup with a data type inc subgroup/dataset/link with quantity 2
"""
pass
class TestBuildZeroOrOneTypeIncUntypedGroup(ZeroOrOneMixin, TypeIncUntypedGroupMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has an untyped subgroup with a data type inc subgroup/dataset/link with quantity '?'
"""
pass
# Nested type definition of group/dataset with quantity {'*', '+', 1, 2, '?'}
class TestBuildZeroOrManyTypeDef(ZeroOrManyMixin, TypeDefMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a nested type def with quantity '*'
"""
pass
class TestBuildOneOrManyTypeDef(OneOrManyMixin, TypeDefMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a nested type def with quantity '+'
"""
pass
class TestBuildOneTypeDef(OneMixin, TypeDefMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a nested type def with quantity 1
"""
pass
class TestBuildTwoTypeDef(TwoMixin, TypeDefMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a nested type def with quantity 2
"""
pass
class TestBuildZeroOrOneTypeDef(ZeroOrOneMixin, TypeDefMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a nested type def with quantity '?'
"""
pass
# Included groups / included datasets / links with quantity {'*', '+', 1, 2, '?'}
class TestBuildZeroOrManyTypeInc(ZeroOrManyMixin, TypeIncMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a data type inc subgroup/dataset/link with quantity '*'
"""
pass
class TestBuildOneOrManyTypeInc(OneOrManyMixin, TypeIncMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a data type inc subgroup/dataset/link with quantity '+'
"""
pass
class TestBuildOneTypeInc(OneMixin, TypeIncMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a data type inc subgroup/dataset/link with quantity 1
"""
pass
class TestBuildTwoTypeInc(TwoMixin, TypeIncMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a data type inc subgroup/dataset/link with quantity 2
"""
pass
class TestBuildZeroOrOneTypeInc(ZeroOrOneMixin, TypeIncMixin, BuildQuantityMixin, TestCase):
"""Test building a group that has a data type inc subgroup/dataset/link with quantity '?'
"""
pass
# Untyped group/dataset with quantity {1, '?'}
class UntypedMixin:
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, 'BasicBucket', BasicBucket)
self.manager = BuildManager(type_map)
def create_specs(self, quantity):
# Type BasicBucket contains:
# - [quantity] untyped group
# - [quantity] untyped dataset
# - [quantity] untyped array dataset
# quantity can be only '?' or 1
untyped_group_spec = GroupSpec(
doc='A test group specification with no data type',
name='untyped_group',
quantity=quantity,
)
untyped_dataset_spec = DatasetSpec(
doc='A test dataset specification with no data type',
name='untyped_dataset',
dtype='int',
quantity=quantity,
)
untyped_array_dataset_spec = DatasetSpec(
doc='A test dataset specification with no data type',
name='untyped_array_dataset',
dtype='int',
dims=[None],
shape=[None],
quantity=quantity,
)
basic_bucket_spec = GroupSpec(
doc='A test group specification for a data type containing data type',
name="test_bucket",
data_type_def='BasicBucket',
groups=[untyped_group_spec],
datasets=[untyped_dataset_spec, untyped_array_dataset_spec],
)
return [basic_bucket_spec]
class TestBuildOneUntyped(UntypedMixin, TestCase):
"""Test building a group that has an untyped subgroup/dataset with quantity 1.
"""
def setUp(self):
specs = self.create_specs(DEF_QUANTITY)
self.setUpManager(specs)
def test_build_data(self):
"""Test building a container which contains an untyped empty subgroup and an untyped non-empty dataset."""
bucket = BasicBucket(name='test_bucket', untyped_dataset=3, untyped_array_dataset=[3])
# a required untyped empty group builder will be created by default
untyped_group_builder = GroupBuilder(name='untyped_group')
untyped_dataset_builder = DatasetBuilder(name='untyped_dataset', data=3)
untyped_array_dataset_builder = DatasetBuilder(name='untyped_array_dataset', data=[3])
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'untyped_group': untyped_group_builder},
datasets={'untyped_dataset': untyped_dataset_builder,
'untyped_array_dataset': untyped_array_dataset_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'BasicBucket',
'object_id': bucket.object_id}
)
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_empty_data(self):
"""Test building a container which contains an untyped empty subgroup and an untyped empty dataset."""
bucket = BasicBucket(name='test_bucket')
# a required untyped empty group builder will be created by default
untyped_group_builder = GroupBuilder(name='untyped_group')
# a required untyped empty dataset builder will NOT be created by default
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'untyped_group': untyped_group_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'BasicBucket',
'object_id': bucket.object_id}
)
msg = "BasicBucket 'test_bucket' is missing required value for attribute 'untyped_dataset'."
# also raises "BasicBucket 'test_bucket' is missing required value for attribute 'untyped_array_dataset'."
with self.assertWarnsWith(MissingRequiredBuildWarning, msg):
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
class TestBuildZeroOrOneUntyped(UntypedMixin, TestCase):
"""Test building a group that has an untyped subgroup/dataset with quantity '?'.
"""
def setUp(self):
specs = self.create_specs(ZERO_OR_ONE)
self.setUpManager(specs)
def test_build_data(self):
"""Test building a container which contains an untyped empty subgroup and an untyped non-empty dataset."""
bucket = BasicBucket(name='test_bucket', untyped_dataset=3, untyped_array_dataset=[3])
# an optional untyped empty group builder will NOT be created by default
untyped_dataset_builder = DatasetBuilder(name='untyped_dataset', data=3)
untyped_array_dataset_builder = DatasetBuilder(name='untyped_array_dataset', data=[3])
bucket_builder = GroupBuilder(
name='test_bucket',
datasets={'untyped_dataset': untyped_dataset_builder,
'untyped_array_dataset': untyped_array_dataset_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'BasicBucket',
'object_id': bucket.object_id}
)
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
def test_build_empty_data(self):
"""Test building a container which contains an untyped empty subgroup and an untyped empty dataset."""
bucket = BasicBucket(name='test_bucket')
# an optional untyped empty group builder will NOT be created by default
# an optional untyped empty dataset builder will NOT be created by default
bucket_builder = GroupBuilder(
name='test_bucket',
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'BasicBucket',
'object_id': bucket.object_id}
)
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
# Multiple allowed types
class TestBuildMultiTypeInc(BuildQuantityMixin, TestCase):
"""Test build process when a groupspec allows multiple groups/datasets/links with different data types / targets.
"""
def setUp(self):
specs = self.create_specs(ZERO_OR_MANY)
self.setUpManager(specs)
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 setUpBucketMapper(self):
class BucketMapper(ObjectMapper):
def __init__(self, spec):
super().__init__(spec)
self.map_spec('foos', spec.get_data_type('SimpleFoo'))
self.map_spec('foos', spec.get_data_type('NotSimpleFoo'))
self.map_spec('quxs', spec.get_data_type('SimpleQux'))
self.map_spec('quxs', spec.get_data_type('NotSimpleQux'))
self.map_spec('links', spec.links[0])
self.map_spec('links', spec.links[1])
return BucketMapper
def get_two_bucket_test(self):
foos = [SimpleFoo('my_foo1'), NotSimpleFoo('my_foo2')]
quxs = [SimpleQux('my_qux1', data=[1, 2, 3]), NotSimpleQux('my_qux2', data=[4, 5, 6])]
# NOTE: unlike in the other tests, links cannot map to the same foos in bucket because of a name clash
links = [SimpleFoo('my_foo3'), NotSimpleFoo('my_foo4')]
bucket = SimpleBucket(
name='test_bucket',
foos=foos,
quxs=quxs,
links=links
)
foo1_builder = self._create_builder(bucket.foos['my_foo1'])
foo2_builder = self._create_builder(bucket.foos['my_foo2'])
foo3_builder = self._create_builder(bucket.links['my_foo3'])
foo4_builder = self._create_builder(bucket.links['my_foo4'])
qux1_builder = self._create_builder(bucket.quxs['my_qux1'])
qux2_builder = self._create_builder(bucket.quxs['my_qux2'])
foo3_link_builder = LinkBuilder(builder=foo3_builder)
foo4_link_builder = LinkBuilder(builder=foo4_builder)
bucket_builder = GroupBuilder(
name='test_bucket',
groups={'my_foo1': foo1_builder,
'my_foo2': foo2_builder},
datasets={'my_qux1': qux1_builder,
'my_qux2': qux2_builder},
links={'my_foo3': foo3_link_builder,
'my_foo4': foo4_link_builder},
attributes={'namespace': CORE_NAMESPACE,
'data_type': 'SimpleBucket',
'object_id': bucket.object_id}
)
return bucket, bucket_builder
def test_build_two(self):
"""Test building a container which contains multiple containers of different types as the spec allows."""
bucket, bucket_builder = self.get_two_bucket_test()
builder = self.manager.build(bucket)
self.assertDictEqual(builder, bucket_builder)
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