class SpecCatalogTest(TestCase):
def setUp(self):
self.catalog = SpecCatalog()
self.attributes = [
AttributeSpec('attribute1', 'my first attribute', 'text'),
AttributeSpec('attribute2', 'my second attribute', 'text')
]
self.spec = DatasetSpec('my first dataset',
'int',
name='dataset1',
dims=(None, None),
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
def test_register_spec(self):
self.catalog.register_spec(self.spec, 'test.yaml')
result = self.catalog.get_spec('EphysData')
self.assertIs(result, self.spec)
def test_hierarchy(self):
spikes_spec = DatasetSpec('my extending dataset',
'int',
data_type_inc='EphysData',
data_type_def='SpikeData')
lfp_spec = DatasetSpec('my second extending dataset',
'int',
data_type_inc='EphysData',
data_type_def='LFPData')
self.catalog.register_spec(self.spec, 'test.yaml')
self.catalog.register_spec(spikes_spec, 'test.yaml')
self.catalog.register_spec(lfp_spec, 'test.yaml')
spike_hierarchy = self.catalog.get_hierarchy('SpikeData')
lfp_hierarchy = self.catalog.get_hierarchy('LFPData')
ephys_hierarchy = self.catalog.get_hierarchy('EphysData')
self.assertTupleEqual(spike_hierarchy, ('SpikeData', 'EphysData'))
self.assertTupleEqual(lfp_hierarchy, ('LFPData', 'EphysData'))
self.assertTupleEqual(ephys_hierarchy, ('EphysData', ))
def test_subtypes(self):
"""
-BaseContainer--+-->AContainer--->ADContainer
|
+-->BContainer
"""
base_spec = GroupSpec(doc='Base container',
data_type_def='BaseContainer')
acontainer = GroupSpec(doc='AContainer',
data_type_inc='BaseContainer',
data_type_def='AContainer')
adcontainer = GroupSpec(doc='ADContainer',
data_type_inc='AContainer',
data_type_def='ADContainer')
bcontainer = GroupSpec(doc='BContainer',
data_type_inc='BaseContainer',
data_type_def='BContainer')
self.catalog.register_spec(base_spec, 'test.yaml')
self.catalog.register_spec(acontainer, 'test.yaml')
self.catalog.register_spec(adcontainer, 'test.yaml')
self.catalog.register_spec(bcontainer, 'test.yaml')
base_spec_subtypes = self.catalog.get_subtypes('BaseContainer')
base_spec_subtypes = tuple(
sorted(base_spec_subtypes
)) # Sort so we have a guaranteed order for comparison
acontainer_subtypes = self.catalog.get_subtypes('AContainer')
bcontainer_substypes = self.catalog.get_subtypes('BContainer')
adcontainer_subtypes = self.catalog.get_subtypes('ADContainer')
self.assertTupleEqual(adcontainer_subtypes, ())
self.assertTupleEqual(bcontainer_substypes, ())
self.assertTupleEqual(acontainer_subtypes, ('ADContainer', ))
self.assertTupleEqual(base_spec_subtypes,
('AContainer', 'ADContainer', 'BContainer'))
def test_subtypes_norecursion(self):
"""
-BaseContainer--+-->AContainer--->ADContainer
|
+-->BContainer
"""
base_spec = GroupSpec(doc='Base container',
data_type_def='BaseContainer')
acontainer = GroupSpec(doc='AContainer',
data_type_inc='BaseContainer',
data_type_def='AContainer')
adcontainer = GroupSpec(doc='ADContainer',
data_type_inc='AContainer',
data_type_def='ADContainer')
bcontainer = GroupSpec(doc='BContainer',
data_type_inc='BaseContainer',
data_type_def='BContainer')
self.catalog.register_spec(base_spec, 'test.yaml')
self.catalog.register_spec(acontainer, 'test.yaml')
self.catalog.register_spec(adcontainer, 'test.yaml')
self.catalog.register_spec(bcontainer, 'test.yaml')
base_spec_subtypes = self.catalog.get_subtypes('BaseContainer',
recursive=False)
base_spec_subtypes = tuple(
sorted(base_spec_subtypes
)) # Sort so we have a guaranteed order for comparison
acontainer_subtypes = self.catalog.get_subtypes('AContainer',
recursive=False)
bcontainer_substypes = self.catalog.get_subtypes('BContainer',
recursive=False)
adcontainer_subtypes = self.catalog.get_subtypes('ADContainer',
recursive=False)
self.assertTupleEqual(adcontainer_subtypes, ())
self.assertTupleEqual(bcontainer_substypes, ())
self.assertTupleEqual(acontainer_subtypes, ('ADContainer', ))
self.assertTupleEqual(base_spec_subtypes, ('AContainer', 'BContainer'))
def test_subtypes_unknown_type(self):
subtypes_of_bad_type = self.catalog.get_subtypes('UnknownType')
self.assertTupleEqual(subtypes_of_bad_type, ())
def test_get_spec_source_file(self):
spikes_spec = GroupSpec('test group', data_type_def='SpikeData')
source_file_path = '/test/myt/test.yaml'
self.catalog.auto_register(spikes_spec, source_file_path)
recorded_source_file_path = self.catalog.get_spec_source_file(
'SpikeData')
self.assertEqual(recorded_source_file_path, source_file_path)
def test_get_full_hierarchy(self):
"""
BaseContainer--+-->AContainer--->ADContainer
|
+-->BContainer
Expected output:
>> print(json.dumps(full_hierarchy, indent=4))
>> {
>> "BaseContainer": {
>> "AContainer": {
>> "ADContainer": {}
>> },
>> "BContainer": {}
>> }
"""
base_spec = GroupSpec(doc='Base container',
data_type_def='BaseContainer')
acontainer = GroupSpec(doc='AContainer',
data_type_inc='BaseContainer',
data_type_def='AContainer')
adcontainer = GroupSpec(doc='ADContainer',
data_type_inc='AContainer',
data_type_def='ADContainer')
bcontainer = GroupSpec(doc='BContainer',
data_type_inc='BaseContainer',
data_type_def='BContainer')
self.catalog.register_spec(base_spec, 'test.yaml')
self.catalog.register_spec(acontainer, 'test.yaml')
self.catalog.register_spec(adcontainer, 'test.yaml')
self.catalog.register_spec(bcontainer, 'test.yaml')
full_hierarchy = self.catalog.get_full_hierarchy()
expected_hierarchy = {
"BaseContainer": {
"AContainer": {
"ADContainer": {}
},
"BContainer": {}
}
}
self.assertDictEqual(full_hierarchy, expected_hierarchy)
def test_copy_spec_catalog(self):
# Register the spec first
self.catalog.register_spec(self.spec, 'test.yaml')
result = self.catalog.get_spec('EphysData')
self.assertIs(result, self.spec)
# Now test the copy
re = copy.copy(self.catalog)
self.assertTupleEqual(self.catalog.get_registered_types(),
re.get_registered_types())
def test_deepcopy_spec_catalog(self):
# Register the spec first
self.catalog.register_spec(self.spec, 'test.yaml')
result = self.catalog.get_spec('EphysData')
self.assertIs(result, self.spec)
# Now test the copy
re = copy.deepcopy(self.catalog)
self.assertTupleEqual(self.catalog.get_registered_types(),
re.get_registered_types())
def test_catch_duplicate_spec_nested(self):
spec1 = GroupSpec(
data_type_def='Group1',
doc='This is my new group 1',
)
spec2 = GroupSpec(
data_type_def='Group2',
doc='This is my new group 2',
groups=[spec1], # nested definition
)
source = 'test_extension.yaml'
self.catalog.register_spec(spec1, source)
self.catalog.register_spec(
spec2, source) # this is OK because Group1 is the same spec
ret = self.catalog.get_spec('Group1')
self.assertIs(ret, spec1)
def test_catch_duplicate_spec_different(self):
spec1 = GroupSpec(
data_type_def='Group1',
doc='This is my new group 1',
)
spec2 = GroupSpec(
data_type_def='Group1',
doc='This is my other group 1',
)
source = 'test_extension.yaml'
self.catalog.register_spec(spec1, source)
msg = "'Group1' - cannot overwrite existing specification"
with self.assertRaisesWith(ValueError, msg):
self.catalog.register_spec(spec2, source)
def test_catch_duplicate_spec_different_source(self):
spec1 = GroupSpec(
data_type_def='Group1',
doc='This is my new group 1',
)
spec2 = GroupSpec(
data_type_def='Group1',
doc='This is my new group 1',
)
source1 = 'test_extension1.yaml'
source2 = 'test_extension2.yaml'
self.catalog.register_spec(spec1, source1)
msg = "'Group1' - cannot overwrite existing specification"
with self.assertRaisesWith(ValueError, msg):
self.catalog.register_spec(spec2, source2)
class SpecCatalogTest(unittest.TestCase):
def setUp(self):
self.catalog = SpecCatalog()
self.attributes = [
AttributeSpec('attribute1', 'my first attribute', 'text'),
AttributeSpec('attribute2', 'my second attribute', 'text')
]
self.spec = DatasetSpec('my first dataset',
'int',
name='dataset1',
dims=(None, None),
attributes=self.attributes,
linkable=False,
data_type_def='EphysData')
def test_register_spec(self):
self.catalog.register_spec(self.spec, 'test.yaml')
result = self.catalog.get_spec('EphysData')
self.assertIs(result, self.spec)
def test_hierarchy(self):
spikes_spec = DatasetSpec('my extending dataset',
'int',
data_type_inc='EphysData',
data_type_def='SpikeData')
lfp_spec = DatasetSpec('my second extending dataset',
'int',
data_type_inc='EphysData',
data_type_def='LFPData')
self.catalog.register_spec(self.spec, 'test.yaml')
self.catalog.register_spec(spikes_spec, 'test.yaml')
self.catalog.register_spec(lfp_spec, 'test.yaml')
spike_hierarchy = self.catalog.get_hierarchy('SpikeData')
lfp_hierarchy = self.catalog.get_hierarchy('LFPData')
ephys_hierarchy = self.catalog.get_hierarchy('EphysData')
self.assertTupleEqual(spike_hierarchy, ('SpikeData', 'EphysData'))
self.assertTupleEqual(lfp_hierarchy, ('LFPData', 'EphysData'))
self.assertTupleEqual(ephys_hierarchy, ('EphysData', ))
def test_subtypes(self):
"""
-BaseContainer--+-->AContainer--->ADContainer
|
+-->BContainer
"""
base_spec = GroupSpec(doc='Base container',
data_type_def='BaseContainer')
acontainer = GroupSpec(doc='AContainer',
data_type_inc='BaseContainer',
data_type_def='AContainer')
adcontainer = GroupSpec(doc='ADContainer',
data_type_inc='AContainer',
data_type_def='ADContainer')
bcontainer = GroupSpec(doc='BContainer',
data_type_inc='BaseContainer',
data_type_def='BContainer')
self.catalog.register_spec(base_spec, 'test.yaml')
self.catalog.register_spec(acontainer, 'test.yaml')
self.catalog.register_spec(adcontainer, 'test.yaml')
self.catalog.register_spec(bcontainer, 'test.yaml')
base_spec_subtypes = self.catalog.get_subtypes('BaseContainer')
base_spec_subtypes = tuple(
sorted(base_spec_subtypes
)) # Sort so we have a guaranteed order for comparison
acontainer_subtypes = self.catalog.get_subtypes('AContainer')
bcontainer_substypes = self.catalog.get_subtypes('BContainer')
adcontainer_subtypes = self.catalog.get_subtypes('ADContainer')
self.assertTupleEqual(adcontainer_subtypes, ())
self.assertTupleEqual(bcontainer_substypes, ())
self.assertTupleEqual(acontainer_subtypes, ('ADContainer', ))
self.assertTupleEqual(base_spec_subtypes,
('AContainer', 'ADContainer', 'BContainer'))
def test_subtypes_norecursion(self):
"""
-BaseContainer--+-->AContainer--->ADContainer
|
+-->BContainer
"""
base_spec = GroupSpec(doc='Base container',
data_type_def='BaseContainer')
acontainer = GroupSpec(doc='AContainer',
data_type_inc='BaseContainer',
data_type_def='AContainer')
adcontainer = GroupSpec(doc='ADContainer',
data_type_inc='AContainer',
data_type_def='ADContainer')
bcontainer = GroupSpec(doc='BContainer',
data_type_inc='BaseContainer',
data_type_def='BContainer')
self.catalog.register_spec(base_spec, 'test.yaml')
self.catalog.register_spec(acontainer, 'test.yaml')
self.catalog.register_spec(adcontainer, 'test.yaml')
self.catalog.register_spec(bcontainer, 'test.yaml')
base_spec_subtypes = self.catalog.get_subtypes('BaseContainer',
recursive=False)
base_spec_subtypes = tuple(
sorted(base_spec_subtypes
)) # Sort so we have a guaranteed order for comparison
acontainer_subtypes = self.catalog.get_subtypes('AContainer',
recursive=False)
bcontainer_substypes = self.catalog.get_subtypes('BContainer',
recursive=False)
adcontainer_subtypes = self.catalog.get_subtypes('ADContainer',
recursive=False)
self.assertTupleEqual(adcontainer_subtypes, ())
self.assertTupleEqual(bcontainer_substypes, ())
self.assertTupleEqual(acontainer_subtypes, ('ADContainer', ))
self.assertTupleEqual(base_spec_subtypes, ('AContainer', 'BContainer'))
def test_subtypes_unknown_type(self):
subtypes_of_bad_type = self.catalog.get_subtypes('UnknownType')
self.assertTupleEqual(subtypes_of_bad_type, ())
def test_get_spec_source_file(self):
spikes_spec = GroupSpec('test group', data_type_def='SpikeData')
source_file_path = '/test/myt/test.yaml'
self.catalog.auto_register(spikes_spec, source_file_path)
recorded_source_file_path = self.catalog.get_spec_source_file(
'SpikeData')
self.assertEqual(recorded_source_file_path, source_file_path)
def test_get_full_hierarchy(self):
"""
BaseContainer--+-->AContainer--->ADContainer
|
+-->BContainer
Expected output:
>> print(json.dumps(full_hierarchy, indent=4))
>> {
>> "BaseContainer": {
>> "AContainer": {
>> "ADContainer": {}
>> },
>> "BContainer": {}
>> }
"""
base_spec = GroupSpec(doc='Base container',
data_type_def='BaseContainer')
acontainer = GroupSpec(doc='AContainer',
data_type_inc='BaseContainer',
data_type_def='AContainer')
adcontainer = GroupSpec(doc='ADContainer',
data_type_inc='AContainer',
data_type_def='ADContainer')
bcontainer = GroupSpec(doc='BContainer',
data_type_inc='BaseContainer',
data_type_def='BContainer')
self.catalog.register_spec(base_spec, 'test.yaml')
self.catalog.register_spec(acontainer, 'test.yaml')
self.catalog.register_spec(adcontainer, 'test.yaml')
self.catalog.register_spec(bcontainer, 'test.yaml')
full_hierarchy = self.catalog.get_full_hierarchy()
expected_hierarchy = {
"BaseContainer": {
"AContainer": {
"ADContainer": {}
},
"BContainer": {}
}
}
self.assertDictEqual(full_hierarchy, expected_hierarchy)
def test_copy_spec_catalog(self):
# Register the spec first
self.catalog.register_spec(self.spec, 'test.yaml')
result = self.catalog.get_spec('EphysData')
self.assertIs(result, self.spec)
# Now test the copy
re = copy.copy(self.catalog)
self.assertTupleEqual(self.catalog.get_registered_types(),
re.get_registered_types())
def test_deepcopy_spec_catalog(self):
# Register the spec first
self.catalog.register_spec(self.spec, 'test.yaml')
result = self.catalog.get_spec('EphysData')
self.assertIs(result, self.spec)
# Now test the copy
re = copy.deepcopy(self.catalog)
self.assertTupleEqual(self.catalog.get_registered_types(),
re.get_registered_types())
