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import numpy as np
import os
import shutil
import tempfile
from hdmf.backends.hdf5 import HDF5IO
from hdmf.build import BuildManager, TypeMap
from hdmf.common import get_type_map, DynamicTable, VectorData
from hdmf.spec import GroupSpec, DatasetSpec, SpecCatalog, SpecNamespace, NamespaceCatalog
from hdmf.testing import TestCase
from hdmf.validate import ValidatorMap
from tests.unit.helpers.utils import CORE_NAMESPACE
class TestDynamicDynamicTable(TestCase):
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)
def tearDown(self) -> None:
shutil.rmtree(self.test_dir)
def test_dynamic_table(self):
assert issubclass(self.TestTable, DynamicTable)
assert self.TestTable.__columns__[0] == {
'name': 'my_col',
'description': 'a test column',
'class': VectorData,
'required': True
}
def test_forbids_incorrect_col(self):
test_table = self.TestTable(name='test_table', description='my test table')
with self.assertRaises(ValueError):
test_table.add_row(my_col=3.0, indexed_col=[1.0, 3.0], incorrect_col=5)
def test_dynamic_column(self):
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_column('dynamic_column', 'this is a dynamic column')
test_table.add_row(
my_col=3.0, indexed_col=[1.0, 3.0], dynamic_column=4, optional_col2=.5,
)
test_table.add_row(
my_col=4.0, indexed_col=[2.0, 4.0], dynamic_column=4, optional_col2=.5,
)
np.testing.assert_array_equal(test_table['indexed_col'].target.data, [1., 3., 2., 4.])
np.testing.assert_array_equal(test_table['dynamic_column'].data, [4, 4])
def test_optional_col(self):
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_row(my_col=3.0, indexed_col=[1.0, 3.0], optional_col2=.5)
test_table.add_row(my_col=4.0, indexed_col=[2.0, 4.0], optional_col2=.5)
def test_dynamic_table_region(self):
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_row(my_col=3.0, indexed_col=[1.0, 3.0], optional_col2=.5)
test_table.add_row(my_col=4.0, indexed_col=[2.0, 4.0], optional_col2=.5)
test_dtr_table = self.TestDTRTable(name='test_dtr_table', description='my table',
target_tables={'ref_col': test_table,
'indexed_ref_col': test_table})
self.assertIs(test_dtr_table['ref_col'].table, test_table)
self.assertIs(test_dtr_table['indexed_ref_col'].target.table, test_table)
test_dtr_table.add_row(ref_col=0, indexed_ref_col=[0, 1])
test_dtr_table.add_row(ref_col=0, indexed_ref_col=[0, 1])
np.testing.assert_array_equal(test_dtr_table['indexed_ref_col'].target.data, [0, 1, 0, 1])
np.testing.assert_array_equal(test_dtr_table['ref_col'].data, [0, 0])
def test_dynamic_table_region_optional(self):
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_row(my_col=3.0, indexed_col=[1.0, 3.0], optional_col2=.5)
test_table.add_row(my_col=4.0, indexed_col=[2.0, 4.0], optional_col2=.5)
test_dtr_table = self.TestDTRTable(name='test_dtr_table', description='my table',
target_tables={'optional_ref_col': test_table,
'optional_indexed_ref_col': test_table})
self.assertIs(test_dtr_table['optional_ref_col'].table, test_table)
self.assertIs(test_dtr_table['optional_indexed_ref_col'].target.table, test_table)
test_dtr_table.add_row(ref_col=0, indexed_ref_col=[0, 1],
optional_ref_col=0, optional_indexed_ref_col=[0, 1])
test_dtr_table.add_row(ref_col=0, indexed_ref_col=[0, 1],
optional_ref_col=0, optional_indexed_ref_col=[0, 1])
np.testing.assert_array_equal(test_dtr_table['optional_indexed_ref_col'].target.data, [0, 1, 0, 1])
np.testing.assert_array_equal(test_dtr_table['optional_ref_col'].data, [0, 0])
def test_dynamic_table_region_bad_target_col(self):
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_row(my_col=3.0, indexed_col=[1.0, 3.0], optional_col2=.5)
test_table.add_row(my_col=4.0, indexed_col=[2.0, 4.0], optional_col2=.5)
msg = r"^'bad' is not the name of a predefined column of table .*"
with self.assertRaisesRegex(ValueError, msg):
self.TestDTRTable(name='test_dtr_table', description='my table', target_tables={'bad': test_table})
def test_dynamic_table_region_non_dtr_target(self):
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_row(my_col=3.0, indexed_col=[1.0, 3.0], optional_col2=.5)
test_table.add_row(my_col=4.0, indexed_col=[2.0, 4.0], optional_col2=.5)
msg = "Column 'optional_col3' must be a DynamicTableRegion to have a target table."
with self.assertRaisesWith(ValueError, msg):
self.TestDTRTable(name='test_dtr_table', description='my table',
target_tables={'optional_col3': test_table})
def test_attribute(self):
test_table = self.TestTable(name='test_table', description='my test table')
assert test_table.my_col is not None
assert test_table.indexed_col is not None
assert test_table.my_col is test_table['my_col']
assert test_table.indexed_col is test_table['indexed_col'].target
def test_roundtrip(self):
# NOTE this does not use H5RoundTripMixin because this requires custom validation
test_table = self.TestTable(name='test_table', description='my test table')
test_table.add_column('dynamic_column', 'this is a dynamic column')
test_table.add_row(
my_col=3.0, indexed_col=[1.0, 3.0], dynamic_column=4, optional_col2=.5,
)
self.filename = os.path.join(self.test_dir, 'test_TestTable.h5')
with HDF5IO(self.filename, manager=self.manager, mode='w') as write_io:
write_io.write(test_table, cache_spec=True)
self.reader = HDF5IO(self.filename, manager=self.manager, mode='r')
read_container = self.reader.read()
self.assertIsNotNone(str(test_table)) # added as a test to make sure printing works
self.assertIsNotNone(str(read_container))
# make sure we get a completely new object
self.assertNotEqual(id(test_table), id(read_container))
# the name of the root container of a file is always 'root' (see h5tools.py ROOT_NAME)
# thus, ignore the name of the container when comparing original container vs read container
self.assertContainerEqual(read_container, test_table, ignore_name=True)
builder = self.reader.read_builder()
# TODO fix ValueError: No specification for 'Container' in namespace 'test_core'
validator = ValidatorMap(self.manager.namespace_catalog.get_namespace(name=CORE_NAMESPACE))
errors = validator.validate(builder)
if errors:
for err in errors:
raise Exception(err)
self.reader.close()
|
