1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
|
import os
import h5py
import numpy as np
from hdmf import Container, Data
from hdmf.backends.hdf5 import H5DataIO
from hdmf.build import (GroupBuilder, DatasetBuilder, ObjectMapper, BuildManager, TypeMap, ReferenceBuilder,
ReferenceTargetNotBuiltError)
from hdmf.data_utils import DataChunkIterator
from hdmf.spec import (AttributeSpec, DatasetSpec, DtypeSpec, GroupSpec, SpecCatalog, SpecNamespace, NamespaceCatalog,
RefSpec)
from hdmf.spec.spec import ZERO_OR_MANY
from hdmf.testing import TestCase
from hdmf.utils import docval, getargs
from tests.unit.helpers.utils import Foo, CORE_NAMESPACE
class Baz(Data):
@docval({'name': 'name', 'type': str, 'doc': 'the name of this Baz'},
{'name': 'data', 'type': (list, h5py.Dataset, 'data', 'array_data'), 'doc': 'some data'},
{'name': 'baz_attr', 'type': str, 'doc': 'an attribute'})
def __init__(self, **kwargs):
name, data, baz_attr = getargs('name', 'data', 'baz_attr', kwargs)
super().__init__(name=name, data=data)
self.__baz_attr = baz_attr
@property
def baz_attr(self):
return self.__baz_attr
class BazHolder(Container):
@docval({'name': 'name', 'type': str, 'doc': 'the name of this Baz'},
{'name': 'bazs', 'type': list, 'doc': 'some Baz data', 'default': list()})
def __init__(self, **kwargs):
name, bazs = getargs('name', 'bazs', kwargs)
super().__init__(name=name)
self.__bazs = {b.name: b for b in bazs} # note: collections of groups are unordered in HDF5
for b in bazs:
b.parent = self
@property
def bazs(self):
return self.__bazs
class BazSpecMixin:
def setUp(self):
self.setUpBazSpec()
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{'source': 'test.yaml'}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
raise NotImplementedError('Test must implement this method.')
class TestDataMap(BazSpecMixin, TestCase):
def setUp(self):
self.setUpBazSpec()
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{'source': 'test.yaml'}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='an Baz type',
dtype='int',
name='MyBaz',
data_type_def='Baz',
shape=[None],
attributes=[AttributeSpec('baz_attr', 'an example string attribute', 'text')]
)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
container = Baz('MyBaz', list(range(10)), 'abcdefghijklmnopqrstuvwxyz')
builder = self.mapper.build(container, self.manager)
expected = DatasetBuilder('MyBaz', list(range(10)), attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz'})
self.assertBuilderEqual(builder, expected)
def test_build_empty_data(self):
"""Test building of a Data object with empty data."""
baz_inc_spec = DatasetSpec(doc='doc', data_type_inc='Baz', quantity=ZERO_OR_MANY)
baz_holder_spec = GroupSpec(doc='doc', data_type_def='BazHolder', datasets=[baz_inc_spec])
self.spec_catalog.register_spec(baz_holder_spec, 'test.yaml')
self.type_map.register_container_type(CORE_NAMESPACE, 'BazHolder', BazHolder)
self.holder_mapper = ObjectMapper(baz_holder_spec)
baz = Baz('MyBaz', [], 'abcdefghijklmnopqrstuvwxyz')
holder = BazHolder('holder', [baz])
builder = self.holder_mapper.build(holder, self.manager)
expected = GroupBuilder(
name='holder',
datasets=[DatasetBuilder(
name='MyBaz',
data=[],
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz',
'data_type': 'Baz',
'namespace': 'test_core',
'object_id': baz.object_id}
)]
)
self.assertBuilderEqual(builder, expected)
def test_append(self):
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds', data=[1, 2, 3], chunks=True, maxshape=(None,))
container = Baz('MyBaz', test_ds, 'abcdefghijklmnopqrstuvwxyz')
container.append(4)
np.testing.assert_array_equal(container[:], [1, 2, 3, 4])
os.remove('test.h5')
def test_extend(self):
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds', data=[1, 2, 3], chunks=True, maxshape=(None,))
container = Baz('MyBaz', test_ds, 'abcdefghijklmnopqrstuvwxyz')
container.extend([4, 5])
np.testing.assert_array_equal(container[:], [1, 2, 3, 4, 5])
os.remove('test.h5')
class BazScalar(Data):
@docval({'name': 'name', 'type': str, 'doc': 'the name of this BazScalar'},
{'name': 'data', 'type': int, 'doc': 'some data'})
def __init__(self, **kwargs):
super().__init__(**kwargs)
class TestDataMapScalar(TestCase):
def setUp(self):
self.setUpBazSpec()
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{'source': 'test.yaml'}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'BazScalar', BazScalar)
self.type_map.register_map(BazScalar, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a BazScalar type',
dtype='int',
name='MyBaz',
data_type_def='BazScalar'
)
def test_construct_scalar_dataset(self):
"""Test constructing a Data object with an h5py.Dataset with shape (1, ) for scalar spec."""
with h5py.File('test.h5', 'w') as file:
test_ds = file.create_dataset('test_ds', data=[1])
expected = BazScalar(
name='MyBaz',
data=1,
)
builder = DatasetBuilder(
name='MyBaz',
data=test_ds,
attributes={'data_type': 'BazScalar',
'namespace': CORE_NAMESPACE,
'object_id': expected.object_id},
)
container = self.mapper.construct(builder, self.manager)
self.assertTrue(np.issubdtype(type(container.data), np.integer)) # as opposed to h5py.Dataset
self.assertContainerEqual(container, expected)
os.remove('test.h5')
class BazScalarCompound(Data):
@docval({'name': 'name', 'type': str, 'doc': 'the name of this BazScalar'},
{'name': 'data', 'type': 'array_data', 'doc': 'some data'})
def __init__(self, **kwargs):
super().__init__(**kwargs)
class TestDataMapScalarCompound(TestCase):
def setUp(self):
self.setUpBazSpec()
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{'source': 'test.yaml'}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'BazScalarCompound', BazScalarCompound)
self.type_map.register_map(BazScalarCompound, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a BazScalarCompound type',
dtype=[
DtypeSpec(
name='id',
dtype='uint64',
doc='The unique identifier in this table.'
),
DtypeSpec(
name='attr1',
dtype='text',
doc='A text attribute.'
),
],
name='MyBaz',
data_type_def='BazScalarCompound',
)
def test_construct_scalar_compound_dataset(self):
"""Test construct on a compound h5py.Dataset with shape (1, ) for scalar spec does not resolve the data."""
with h5py.File('test.h5', 'w') as file:
comp_type = np.dtype([('id', np.uint64), ('attr1', h5py.special_dtype(vlen=str))])
test_ds = file.create_dataset(
name='test_ds',
data=np.array((1, 'text'), dtype=comp_type),
shape=(1, ),
dtype=comp_type
)
expected = BazScalarCompound(
name='MyBaz',
data=(1, 'text'),
)
builder = DatasetBuilder(
name='MyBaz',
data=test_ds,
attributes={'data_type': 'BazScalarCompound',
'namespace': CORE_NAMESPACE,
'object_id': expected.object_id},
)
container = self.mapper.construct(builder, self.manager)
self.assertEqual(type(container.data), h5py.Dataset)
self.assertContainerEqual(container, expected)
os.remove('test.h5')
class BuildDatasetOfReferencesMixin:
def setUp(self):
self.setUpBazSpec()
self.foo_spec = GroupSpec(
doc='A test group specification with a data type',
data_type_def='Foo',
datasets=[
DatasetSpec(name='my_data', doc='an example dataset', dtype='int')
],
attributes=[
AttributeSpec(name='attr1', doc='an example string attribute', dtype='text'),
AttributeSpec(name='attr2', doc='an example int attribute', dtype='int'),
AttributeSpec(name='attr3', doc='an example float attribute', dtype='float')
]
)
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.spec_catalog.register_spec(self.foo_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{'source': 'test.yaml'}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Baz', Baz)
self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
self.type_map.register_map(Baz, ObjectMapper)
self.type_map.register_map(Foo, ObjectMapper)
self.manager = BuildManager(self.type_map)
class TestBuildUntypedDatasetOfReferences(BuildDatasetOfReferencesMixin, TestCase):
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a list of references to Foo objects',
dtype=None,
name='MyBaz',
shape=[None],
data_type_def='Baz',
attributes=[AttributeSpec('baz_attr', 'an example string attribute', 'text')]
)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
foo = Foo('my_foo1', [1, 2, 3], 'string', 10)
baz = Baz('MyBaz', [foo, None], 'abcdefghijklmnopqrstuvwxyz')
foo_builder = self.manager.build(foo)
baz_builder = self.manager.build(baz, root=True)
expected = DatasetBuilder('MyBaz', [ReferenceBuilder(foo_builder), None],
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz',
'data_type': 'Baz',
'namespace': CORE_NAMESPACE,
'object_id': baz.object_id})
self.assertBuilderEqual(baz_builder, expected)
class TestBuildCompoundDatasetOfReferences(BuildDatasetOfReferencesMixin, TestCase):
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a list of references to Foo objects',
dtype=[
DtypeSpec(
name='id',
dtype='uint64',
doc='The unique identifier in this table.'
),
DtypeSpec(
name='foo',
dtype=RefSpec('Foo', 'object'),
doc='The foo in this table.'
),
],
name='MyBaz',
shape=[None],
data_type_def='Baz',
attributes=[AttributeSpec('baz_attr', 'an example string attribute', 'text')]
)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
foo = Foo('my_foo1', [1, 2, 3], 'string', 10)
baz = Baz('MyBaz', [(1, foo)], 'abcdefghijklmnopqrstuvwxyz')
foo_builder = self.manager.build(foo)
baz_builder = self.manager.build(baz, root=True)
expected = DatasetBuilder('MyBaz', [(1, ReferenceBuilder(foo_builder))],
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz',
'data_type': 'Baz',
'namespace': CORE_NAMESPACE,
'object_id': baz.object_id})
self.assertBuilderEqual(baz_builder, expected)
class TestBuildTypedDatasetOfReferences(BuildDatasetOfReferencesMixin, TestCase):
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a list of references to Foo objects',
dtype=RefSpec('Foo', 'object'),
name='MyBaz',
shape=[None],
data_type_def='Baz',
attributes=[AttributeSpec('baz_attr', 'an example string attribute', 'text')]
)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
foo = Foo('my_foo1', [1, 2, 3], 'string', 10)
baz = Baz('MyBaz', [foo], 'abcdefghijklmnopqrstuvwxyz')
foo_builder = self.manager.build(foo)
baz_builder = self.manager.build(baz, root=True)
expected = DatasetBuilder('MyBaz', [ReferenceBuilder(foo_builder)],
attributes={'baz_attr': 'abcdefghijklmnopqrstuvwxyz',
'data_type': 'Baz',
'namespace': CORE_NAMESPACE,
'object_id': baz.object_id})
self.assertBuilderEqual(baz_builder, expected)
class TestBuildDatasetOfReferencesUnbuiltTarget(BuildDatasetOfReferencesMixin, TestCase):
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='a list of references to Foo objects',
dtype=None,
name='MyBaz',
shape=[None],
data_type_def='Baz',
attributes=[AttributeSpec('baz_attr', 'an example string attribute', 'text')]
)
def test_build(self):
''' Test default mapping functionality when no attributes are nested '''
foo = Foo('my_foo1', [1, 2, 3], 'string', 10)
baz = Baz('MyBaz', [foo], 'abcdefghijklmnopqrstuvwxyz')
msg = "MyBaz (MyBaz): Could not find already-built Builder for Foo 'my_foo1' in BuildManager"
with self.assertRaisesWith(ReferenceTargetNotBuiltError, msg):
self.manager.build(baz, root=True)
class TestDataIOEdgeCases(TestCase):
def setUp(self):
self.setUpBazSpec()
self.spec_catalog = SpecCatalog()
self.spec_catalog.register_spec(self.baz_spec, 'test.yaml')
self.namespace = SpecNamespace('a test namespace', CORE_NAMESPACE, [{'source': 'test.yaml'}],
version='0.1.0',
catalog=self.spec_catalog)
self.namespace_catalog = NamespaceCatalog()
self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
self.type_map = TypeMap(self.namespace_catalog)
self.type_map.register_container_type(CORE_NAMESPACE, 'Baz', Baz)
self.type_map.register_map(Baz, ObjectMapper)
self.manager = BuildManager(self.type_map)
self.mapper = ObjectMapper(self.baz_spec)
def setUpBazSpec(self):
self.baz_spec = DatasetSpec(
doc='an Baz type',
dtype=None,
name='MyBaz',
data_type_def='Baz',
shape=[None],
attributes=[AttributeSpec('baz_attr', 'an example string attribute', 'text')]
)
def test_build_dataio(self):
"""Test building of a dataset with data_type and no dtype with value DataIO."""
container = Baz('my_baz', H5DataIO(['a', 'b', 'c', 'd'], chunks=True), 'value1')
builder = self.type_map.build(container)
self.assertIsInstance(builder.get('data'), H5DataIO)
def test_build_datachunkiterator(self):
"""Test building of a dataset with data_type and no dtype with value DataChunkIterator."""
container = Baz('my_baz', DataChunkIterator(['a', 'b', 'c', 'd']), 'value1')
builder = self.type_map.build(container)
self.assertIsInstance(builder.get('data'), DataChunkIterator)
def test_build_dataio_datachunkiterator(self): # hdmf#512
"""Test building of a dataset with no dtype and no data_type with value DataIO wrapping a DCI."""
container = Baz('my_baz', H5DataIO(DataChunkIterator(['a', 'b', 'c', 'd']), chunks=True), 'value1')
builder = self.type_map.build(container)
self.assertIsInstance(builder.get('data'), H5DataIO)
self.assertIsInstance(builder.get('data').data, DataChunkIterator)
|
