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from hdmf.build import GroupBuilder, DatasetBuilder, LinkBuilder, ReferenceBuilder, RegionBuilder
from hdmf.testing import TestCase
class TestGroupBuilder(TestCase):
def test_constructor(self):
gb1 = GroupBuilder('gb1', source='source')
gb2 = GroupBuilder('gb2', parent=gb1)
self.assertIs(gb1.name, 'gb1')
self.assertIsNone(gb1.parent)
self.assertEqual(gb1.source, 'source')
self.assertIs(gb2.parent, gb1)
def test_repr(self):
gb1 = GroupBuilder('gb1')
expected = "gb1 GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}"
self.assertEqual(gb1.__repr__(), expected)
def test_set_source(self):
"""Test that setting source sets the children builder source."""
gb1 = GroupBuilder('gb1')
db = DatasetBuilder('db', list(range(10)))
lb = LinkBuilder(gb1, 'lb')
gb2 = GroupBuilder('gb1', {'gb1': gb1}, {'db': db}, {}, {'lb': lb})
gb2.source = 'source'
self.assertEqual(gb2.source, 'source')
self.assertEqual(gb1.source, 'source')
self.assertEqual(db.source, 'source')
self.assertEqual(lb.source, 'source')
def test_set_source_no_reset(self):
"""Test that setting source does not set the children builder source if children already have a source."""
gb1 = GroupBuilder('gb1', source='original')
db = DatasetBuilder('db', list(range(10)), source='original')
lb = LinkBuilder(gb1, 'lb', source='original')
gb2 = GroupBuilder('gb1', {'gb1': gb1}, {'db': db}, {}, {'lb': lb})
gb2.source = 'source'
self.assertEqual(gb1.source, 'original')
self.assertEqual(db.source, 'original')
self.assertEqual(lb.source, 'original')
def test_constructor_dset_none(self):
gb1 = GroupBuilder('gb1', datasets={'empty': None})
self.assertEqual(len(gb1.datasets), 0)
def test_set_location(self):
gb1 = GroupBuilder('gb1')
gb1.location = 'location'
self.assertEqual(gb1.location, 'location')
def test_overwrite_location(self):
gb1 = GroupBuilder('gb1')
gb1.location = 'location'
gb1.location = 'new location'
self.assertEqual(gb1.location, 'new location')
class TestGroupBuilderSetters(TestCase):
def test_set_attribute(self):
gb = GroupBuilder('gb')
gb.set_attribute('key', 'value')
self.assertIn('key', gb.obj_type)
self.assertIn('key', gb.attributes)
self.assertEqual(gb['key'], 'value')
def test_set_group(self):
gb1 = GroupBuilder('gb1')
gb2 = GroupBuilder('gb2')
gb1.set_group(gb2)
self.assertIs(gb2.parent, gb1)
self.assertIn('gb2', gb1.obj_type)
self.assertIn('gb2', gb1.groups)
self.assertIs(gb1['gb2'], gb2)
def test_set_dataset(self):
gb = GroupBuilder('gb')
db = DatasetBuilder('db', list(range(10)))
gb.set_dataset(db)
self.assertIs(db.parent, gb)
self.assertIn('db', gb.obj_type)
self.assertIn('db', gb.datasets)
self.assertIs(gb['db'], db)
def test_set_link(self):
gb1 = GroupBuilder('gb1')
gb2 = GroupBuilder('gb2')
lb = LinkBuilder(gb2)
gb1.set_link(lb)
self.assertIs(lb.parent, gb1)
self.assertIn('gb2', gb1.obj_type)
self.assertIn('gb2', gb1.links)
self.assertIs(gb1['gb2'], lb)
def test_setitem_disabled(self):
"""Test __setitem__ is disabled"""
gb = GroupBuilder('gb')
with self.assertRaises(NotImplementedError):
gb['key'] = 'value'
def test_set_exists_wrong_type(self):
gb1 = GroupBuilder('gb1')
gb2 = GroupBuilder('gb2')
db = DatasetBuilder('gb2')
gb1.set_group(gb2)
msg = "'gb2' already exists in gb1.groups, cannot set in datasets."
with self.assertRaisesWith(ValueError, msg):
gb1.set_dataset(db)
class TestGroupBuilderGetters(TestCase):
def setUp(self):
self.subgroup1 = GroupBuilder('subgroup1')
self.dataset1 = DatasetBuilder('dataset1', list(range(10)))
self.link1 = LinkBuilder(self.subgroup1, 'link1')
self.int_attr = 1
self.str_attr = "my_str"
self.group1 = GroupBuilder('group1', {'subgroup1': self.subgroup1})
self.gb = GroupBuilder(
name='gb',
groups={'group1': self.group1},
datasets={'dataset1': self.dataset1},
attributes={'int_attr': self.int_attr,
'str_attr': self.str_attr},
links={'link1': self.link1}
)
def test_path(self):
self.assertEqual(self.subgroup1.path, 'gb/group1/subgroup1')
self.assertEqual(self.dataset1.path, 'gb/dataset1')
self.assertEqual(self.link1.path, 'gb/link1')
self.assertEqual(self.group1.path, 'gb/group1')
self.assertEqual(self.gb.path, 'gb')
def test_getitem_group(self):
"""Test __getitem__ for groups"""
self.assertIs(self.gb['group1'], self.group1)
def test_getitem_group_deeper(self):
"""Test __getitem__ for groups deeper in hierarchy"""
self.assertIs(self.gb['group1/subgroup1'], self.subgroup1)
def test_getitem_dataset(self):
"""Test __getitem__ for datasets"""
self.assertIs(self.gb['dataset1'], self.dataset1)
def test_getitem_attr(self):
"""Test __getitem__ for attributes"""
self.assertEqual(self.gb['int_attr'], self.int_attr)
self.assertEqual(self.gb['str_attr'], self.str_attr)
def test_getitem_invalid_key(self):
"""Test __getitem__ for invalid key"""
with self.assertRaises(KeyError):
self.gb['invalid_key']
def test_getitem_invalid_key_deeper(self):
"""Test __getitem__ for invalid key"""
with self.assertRaises(KeyError):
self.gb['group/invalid_key']
def test_getitem_link(self):
"""Test __getitem__ for links"""
self.assertIs(self.gb['link1'], self.link1)
def test_get_group(self):
"""Test get() for groups"""
self.assertIs(self.gb.get('group1'), self.group1)
def test_get_group_deeper(self):
"""Test get() for groups deeper in hierarchy"""
self.assertIs(self.gb.get('group1/subgroup1'), self.subgroup1)
def test_get_dataset(self):
"""Test get() for datasets"""
self.assertIs(self.gb.get('dataset1'), self.dataset1)
def test_get_attr(self):
"""Test get() for attributes"""
self.assertEqual(self.gb.get('int_attr'), self.int_attr)
self.assertEqual(self.gb.get('str_attr'), self.str_attr)
def test_get_link(self):
"""Test get() for links"""
self.assertIs(self.gb.get('link1'), self.link1)
def test_get_invalid_key(self):
"""Test get() for invalid key"""
self.assertIs(self.gb.get('invalid_key'), None)
def test_items(self):
"""Test items()"""
items = (
('group1', self.group1),
('dataset1', self.dataset1),
('int_attr', self.int_attr),
('str_attr', self.str_attr),
('link1', self.link1),
)
# self.assertSetEqual(items, set(self.gb.items()))
try:
self.assertCountEqual(items, self.gb.items())
except AttributeError:
self.assertItemsEqual(items, self.gb.items())
def test_keys(self):
"""Test keys()"""
keys = (
'group1',
'dataset1',
'int_attr',
'str_attr',
'link1',
)
try:
self.assertCountEqual(keys, self.gb.keys())
except AttributeError:
self.assertItemsEqual(keys, self.gb.keys())
def test_values(self):
"""Test values()"""
values = (
self.group1,
self.dataset1,
self.int_attr,
self.str_attr,
self.link1,
)
try:
self.assertCountEqual(values, self.gb.values())
except AttributeError:
self.assertItemsEqual(values, self.gb.values())
class TestGroupBuilderIsEmpty(TestCase):
def test_is_empty_true(self):
"""Test empty when group has nothing in it"""
gb = GroupBuilder('gb')
self.assertTrue(gb.is_empty())
def test_is_empty_true_group_empty(self):
"""Test is_empty() when group has an empty subgroup"""
gb1 = GroupBuilder('my_subgroup')
gb2 = GroupBuilder('gb', {'my_subgroup': gb1})
self.assertTrue(gb2.is_empty())
def test_is_empty_false_dataset(self):
"""Test is_empty() when group has a dataset"""
gb = GroupBuilder('gb', datasets={'my_dataset': DatasetBuilder('my_dataset')})
self.assertFalse(gb.is_empty())
def test_is_empty_false_group_dataset(self):
"""Test is_empty() when group has a subgroup with a dataset"""
gb1 = GroupBuilder('my_subgroup', datasets={'my_dataset': DatasetBuilder('my_dataset')})
gb2 = GroupBuilder('gb', {'my_subgroup': gb1})
self.assertFalse(gb2.is_empty())
def test_is_empty_false_attribute(self):
"""Test is_empty() when group has an attribute"""
gb = GroupBuilder('gb', attributes={'my_attr': 'attr_value'})
self.assertFalse(gb.is_empty())
def test_is_empty_false_group_attribute(self):
"""Test is_empty() when group has subgroup with an attribute"""
gb1 = GroupBuilder('my_subgroup', attributes={'my_attr': 'attr_value'})
gb2 = GroupBuilder('gb', {'my_subgroup': gb1})
self.assertFalse(gb2.is_empty())
def test_is_empty_false_link(self):
"""Test is_empty() when group has a link"""
gb1 = GroupBuilder('target')
gb2 = GroupBuilder('gb', links={'my_link': LinkBuilder(gb1)})
self.assertFalse(gb2.is_empty())
def test_is_empty_false_group_link(self):
"""Test is_empty() when group has subgroup with a link"""
gb1 = GroupBuilder('target')
gb2 = GroupBuilder('my_subgroup', links={'my_link': LinkBuilder(gb1)})
gb3 = GroupBuilder('gb', {'my_subgroup': gb2})
self.assertFalse(gb3.is_empty())
class TestDatasetBuilder(TestCase):
def test_constructor(self):
gb1 = GroupBuilder('gb1')
db1 = DatasetBuilder(
name='db1',
data=[1, 2, 3],
dtype=int,
attributes={'attr1': 10},
maxshape=10,
chunks=True,
parent=gb1,
source='source',
)
self.assertEqual(db1.name, 'db1')
self.assertListEqual(db1.data, [1, 2, 3])
self.assertEqual(db1.dtype, int)
self.assertDictEqual(db1.attributes, {'attr1': 10})
self.assertEqual(db1.maxshape, 10)
self.assertTrue(db1.chunks)
self.assertIs(db1.parent, gb1)
self.assertEqual(db1.source, 'source')
def test_constructor_data_builder_no_dtype(self):
db1 = DatasetBuilder(name='db1', dtype=int)
db2 = DatasetBuilder(name='db2', data=db1)
self.assertEqual(db2.dtype, DatasetBuilder.OBJECT_REF_TYPE)
def test_constructor_data_builder_dtype(self):
db1 = DatasetBuilder(name='db1', dtype=int)
db2 = DatasetBuilder(name='db2', data=db1, dtype=float)
self.assertEqual(db2.dtype, float)
def test_set_data(self):
db1 = DatasetBuilder(name='db1')
db1.data = [4, 5, 6]
self.assertEqual(db1.data, [4, 5, 6])
def test_set_dtype(self):
db1 = DatasetBuilder(name='db1')
db1.dtype = float
self.assertEqual(db1.dtype, float)
def test_overwrite_data(self):
db1 = DatasetBuilder(name='db1', data=[1, 2, 3])
msg = "Cannot overwrite data."
with self.assertRaisesWith(AttributeError, msg):
db1.data = [4, 5, 6]
def test_overwrite_dtype(self):
db1 = DatasetBuilder(name='db1', data=[1, 2, 3], dtype=int)
msg = "Cannot overwrite dtype."
with self.assertRaisesWith(AttributeError, msg):
db1.dtype = float
def test_overwrite_source(self):
db1 = DatasetBuilder(name='db1', data=[1, 2, 3], source='source')
msg = 'Cannot overwrite source.'
with self.assertRaisesWith(AttributeError, msg):
db1.source = 'new source'
def test_overwrite_parent(self):
gb1 = GroupBuilder('gb1')
db1 = DatasetBuilder(name='db1', data=[1, 2, 3], parent=gb1)
msg = 'Cannot overwrite parent.'
with self.assertRaisesWith(AttributeError, msg):
db1.parent = gb1
def test_repr(self):
gb1 = GroupBuilder('gb1')
db1 = DatasetBuilder(
name='db1',
data=[1, 2, 3],
dtype=int,
attributes={'attr2': 10},
maxshape=10,
chunks=True,
parent=gb1,
source='source',
)
expected = "gb1/db1 DatasetBuilder {'attributes': {'attr2': 10}, 'data': [1, 2, 3]}"
self.assertEqual(db1.__repr__(), expected)
class TestLinkBuilder(TestCase):
def test_constructor(self):
gb = GroupBuilder('gb1')
db = DatasetBuilder('db1', [1, 2, 3])
lb = LinkBuilder(db, 'link_name', gb, 'link_source')
self.assertIs(lb.builder, db)
self.assertEqual(lb.name, 'link_name')
self.assertIs(lb.parent, gb)
self.assertEqual(lb.source, 'link_source')
def test_constructor_no_name(self):
db = DatasetBuilder('db1', [1, 2, 3])
lb = LinkBuilder(db)
self.assertIs(lb.builder, db)
self.assertEqual(lb.name, 'db1')
class TestReferenceBuilder(TestCase):
def test_constructor(self):
db = DatasetBuilder('db1', [1, 2, 3])
rb = ReferenceBuilder(db)
self.assertIs(rb.builder, db)
class TestRegionBuilder(TestCase):
def test_constructor(self):
db = DatasetBuilder('db1', [1, 2, 3])
rb = RegionBuilder(slice(1, 3), db)
self.assertEqual(rb.region, slice(1, 3))
self.assertIs(rb.builder, db)
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