def test_get_keys_subset(self):
er = ExternalResources('terms')
er.add_ref(container='uuid1',
key='key1',
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
er.add_ref(container='uuid2',
key='key2',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
er.add_ref(container='uuid1',
key=er.get_key(key_name='key1'),
resource_name='resource3',
resource_uri='resource_uri3',
entity_id="id13",
entity_uri='url31')
key = er.keys.row[0]
received = er.get_keys(keys=key)
expected = pd.DataFrame(
data=[['key1', 0, 'id11', 'url11'], ['key1', 2, 'id13', 'url31']],
columns=['key_name', 'resources_idx', 'entity_id', 'entity_uri'])
pd.testing.assert_frame_equal(received, expected)
def test_get_object_resources(self):
er = ExternalResources('terms')
data = Data(name='data_name',
data=np.array([('Mus musculus', 9, 81.0),
('H**o sapien', 3, 27.0)],
dtype=[('species', 'U14'), ('age', 'i4'),
('weight', 'f4')]))
er.add_ref(
container=data,
key='Mus musculus',
resource_name='NCBI_Taxonomy',
resource_uri='https://www.ncbi.nlm.nih.gov/taxonomy',
entity_id='NCBI:txid10090',
entity_uri=
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090'
)
received = er.get_object_resources(data)
expected = pd.DataFrame(data=[[
0, 0, 'NCBI:txid10090',
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090'
]],
columns=[
'keys_idx', 'resource_idx', 'entity_id',
'entity_uri'
])
pd.testing.assert_frame_equal(received, expected)
def test_add_ref(self):
er = ExternalResources('terms')
er.add_ref('uuid1', 'field1', 'key1', 'resource1', 'resource_id1', 'uri1')
self.assertEqual(er.keys.data, [('key1',)])
self.assertEqual(er.resources.data, [(0, 'resource1', 'resource_id1', 'uri1')])
self.assertEqual(er.objects.data, [('uuid1', 'field1')])
def test_get_key_same_keyname_all(self):
self.er = ExternalResources('terms')
key1 = self.er._add_key('key1')
key2 = self.er._add_key('key1')
self.er.add_ref('uuid1',
key=key1,
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
self.er.add_ref('uuid2',
key=key2,
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url12')
self.er.add_ref('uuid1',
key=self.er.get_key('key1', 'uuid1', ''),
resource_name='resource3',
resource_uri='resource_uri3',
entity_id="id13",
entity_uri='url13')
keys = self.er.get_key('key1')
self.assertIsInstance(keys, Key)
self.assertEqual(keys[0].key, 'key1')
self.assertEqual(keys[1].key, 'key1')
def test_get_key_same_keyname_specific(self):
self.er = ExternalResources('terms')
self.er.add_ref('uuid1',
key='key1',
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
self.er.add_ref('uuid2',
key='key2',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url12')
self.er.add_ref('uuid1',
key=self.er.get_key('key1', 'uuid1', ''),
resource_name='resource3',
resource_uri='resource_uri3',
entity_id="id13",
entity_uri='url13')
keys = self.er.get_key('key1', 'uuid1', '')
self.assertIsInstance(keys, Key)
self.assertEqual(keys.key, 'key1')
self.assertEqual(self.er.keys.data, [('key1', ), ('key2', )])
def test_add_ref_deep_nested(self):
er = ExternalResources(name='example', type_map=self.type_map)
er.add_ref(container=self.bar,
attribute='attr2',
key='key1',
resource_name='resource0',
resource_uri='resource0_uri',
entity_id='entity_0',
entity_uri='entity_0_uri')
self.assertEqual(er.objects.data[0][1], 'Bar/data/attr2', '')
def test_add_ref_same_key_diff_objfield(self):
er = ExternalResources('terms')
er.add_ref('uuid1', 'field1', 'key1', 'resource1', 'resource_id1', 'url1')
er.add_ref('uuid2', 'field2', 'key1', 'resource2', 'resource_id2', 'url2')
self.assertEqual(er.keys.data, [('key1',)])
self.assertEqual(er.resources.data,
[(0, 'resource1', 'resource_id1', 'url1'),
(0, 'resource2', 'resource_id2', 'url2')])
self.assertEqual(er.objects.data, [('uuid1', 'field1'),
('uuid2', 'field2')])
def test_get_key_same_keyname_specific(self):
self.er = ExternalResources('terms')
key1 = self.er.add_key('key1')
key2 = self.er.add_key('key1')
self.er.add_ref('uuid1', 'field1', key1, 'resource11', 'resource_id11', 'url11')
self.er.add_ref('uuid2', 'field2', key2, 'resource21', 'resource_id21', 'url21')
self.er.add_ref('uuid1', 'field1', 'key1', 'resource12', 'resource_id12', 'url12')
keys = self.er.get_key('key1', 'uuid1', 'field1')
self.assertIsInstance(keys, Key)
self.assertEqual(keys.key_name, 'key1')
def test_keys_roundtrip(self):
er = ExternalResources('terms')
keys = pd.DataFrame(
data=[['key1', 'resource11', 'resource_id11', 'url11'],
['key1', 'resource12', 'resource_id12', 'url12'],
['key2', 'resource21', 'resource_id21', 'url21']],
columns=['key_name', 'resource_name', 'resource_entity_id', 'resource_entity_uri']
)
er.add_keys(keys)
received = er.get_keys()
pd.testing.assert_frame_equal(received, keys)
def test_add_ref(self):
er = ExternalResources('terms')
data = Data(name="species", data=['H**o sapiens', 'Mus musculus'])
er.add_ref(container=data,
key='key1',
resource_name='resource1',
resource_uri='uri1',
entity_id='entity_id1',
entity_uri='entity1')
self.assertEqual(er.keys.data, [('key1', )])
self.assertEqual(er.resources.data, [('resource1', 'uri1')])
self.assertEqual(er.entities.data, [(0, 0, 'entity_id1', 'entity1')])
self.assertEqual(er.objects.data, [(data.object_id, '', '')])
def test_add_ref_same_keyname(self):
er = ExternalResources('terms')
er.add_ref(container='uuid1',
key='key1',
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
er.add_ref(container='uuid2',
key='key1',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
er.add_ref(container='uuid3',
key='key1',
resource_name='resource3',
resource_uri='resource_uri3',
entity_id="id13",
entity_uri='url31')
self.assertEqual(er.keys.data, [('key1', ), ('key1', ), ('key1', )])
self.assertEqual(er.resources.data, [('resource1', 'resource_uri1'),
('resource2', 'resource_uri2'),
('resource3', 'resource_uri3')])
self.assertEqual(er.entities.data, [(0, 0, 'id11', 'url11'),
(1, 1, 'id12', 'url21'),
(2, 2, 'id13', 'url31')])
self.assertEqual(er.objects.data,
[('uuid1', '', ''), ('uuid2', '', ''),
('uuid3', '', '')])
def test_check_object_field_error(self):
er = ExternalResources('terms')
data = Data(name="species", data=['H**o sapiens', 'Mus musculus'])
er._check_object_field(data, '')
er._add_object(data, '', '')
with self.assertRaises(ValueError):
er._check_object_field(data, '')
def test_add_keys(self):
er = ExternalResources('terms')
keys = pd.DataFrame(
data=[['key1', 'resource11', 'resource_id11', 'url11'],
['key1', 'resource12', 'resource_id12', 'url12'],
['key2', 'resource21', 'resource_id21', 'url21']],
columns=['key_name', 'resource_name', 'resource_entity_id', 'resource_entity_uri']
)
ret = er.add_keys(keys)
self.assertEqual({'key1', 'key2'}, set(ret))
self.assertEqual(er.keys.data, [('key1',), ('key2',)])
self.assertEqual(er.resources.data,
[(0, 'resource11', 'resource_id11', 'url11'),
(0, 'resource12', 'resource_id12', 'url12'),
(1, 'resource21', 'resource_id21', 'url21')])
def test_add_ref_bad_arg(self):
er = ExternalResources('terms')
# The contents of the message are not important. Just make sure an error is raised
with self.assertRaises(ValueError):
er.add_ref('uuid1', 'field1', 'key1', resource_name='resource1', entity_id='resource_id1')
with self.assertRaises(ValueError):
er.add_ref('uuid1', 'field1', 'key1', resource_name='resource1', entity_uri='uri1')
with self.assertRaises(ValueError):
er.add_ref('uuid1', 'field1', 'key1', entity_id='resource_id1', entity_uri='uri1')
def test_object_key_unqiueness(self):
er = ExternalResources('terms')
data = Data(name='data_name',
data=np.array([('Mus musculus', 9, 81.0),
('H**o sapien', 3, 27.0)],
dtype=[('species', 'U14'), ('age', 'i4'),
('weight', 'f4')]))
er.add_ref(
container=data,
key='Mus musculus',
resource_name='NCBI_Taxonomy',
resource_uri='https://www.ncbi.nlm.nih.gov/taxonomy',
entity_id='NCBI:txid10090',
entity_uri=
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090'
)
existing_key = er.get_key('Mus musculus')
er.add_ref(container=data,
key=existing_key,
resource_name='resource2',
resource_uri='resource_uri2',
entity_id='entity2',
entity_uri='entity_uri2')
self.assertEqual(er.object_keys.data, [(0, 0)])
def setUpContainer(self):
er = ExternalResources('terms')
key1 = er.add_key('key1')
key2 = er.add_key('key1')
er.add_ref('uuid1', 'field1', key1, 'resource11', 'resource_id11', 'url11')
er.add_ref('uuid2', 'field2', key2, 'resource21', 'resource_id21', 'url21')
er.add_ref('uuid1', 'field1', 'key1', 'resource12', 'resource_id12', 'url12')
return er
def test_add_ref_nested(self):
table = DynamicTable(name='table', description='table')
table.add_column(name='col1', description="column")
table.add_row(id=0, col1='data')
er = ExternalResources(name='example')
er.add_ref(container=table,
attribute='description',
key='key1',
resource_name='resource0',
resource_uri='resource0_uri',
entity_id='entity_0',
entity_uri='entity_0_uri')
self.assertEqual(er.keys.data, [('key1', )])
self.assertEqual(er.resources.data, [('resource0', 'resource0_uri')])
self.assertEqual(er.entities.data,
[(0, 0, 'entity_0', 'entity_0_uri')])
self.assertEqual(er.objects.data,
[(table.object_id, 'DynamicTable/description', '')])
def test_add_ref_compound_data(self):
er = ExternalResources(name='example')
data = Data(name='data_name',
data=np.array([('Mus musculus', 9, 81.0),
('H**o sapiens', 3, 27.0)],
dtype=[('species', 'U14'), ('age', 'i4'),
('weight', 'f4')]))
er.add_ref(container=data,
field='species',
key='Mus musculus',
resource_name='NCBI_Taxonomy',
resource_uri='resource0_uri',
entity_id='NCBI:txid10090',
entity_uri='entity_0_uri')
self.assertEqual(er.keys.data, [('Mus musculus', )])
self.assertEqual(er.resources.data,
[('NCBI_Taxonomy', 'resource0_uri')])
self.assertEqual(er.entities.data,
[(0, 0, 'NCBI:txid10090', 'entity_0_uri')])
self.assertEqual(er.objects.data, [(data.object_id, '', 'species')])
def test_add_ref_column_as_attribute(self):
# Test to make sure the attribute object is being used for the id
# for the external reference.
table = DynamicTable(name='table', description='table')
table.add_column(name='col1', description="column")
table.add_row(id=0, col1='data')
er = ExternalResources(name='example')
er.add_ref(container=table,
attribute='col1',
key='key1',
resource_name='resource0',
resource_uri='resource0_uri',
entity_id='entity_0',
entity_uri='entity_0_uri')
self.assertEqual(er.keys.data, [('key1', )])
self.assertEqual(er.resources.data, [('resource0', 'resource0_uri')])
self.assertEqual(er.entities.data,
[(0, 0, 'entity_0', 'entity_0_uri')])
self.assertEqual(er.objects.data, [(table['col1'].object_id, '', '')])
def test_check_object_field_add(self):
er = ExternalResources('terms')
data = Data(name="species", data=['H**o sapiens', 'Mus musculus'])
er._check_object_field('uuid1', '')
er._check_object_field(data, '')
self.assertEqual(er.objects.data, [('uuid1', '', ''),
(data.object_id, '', '')])
def test_get_resources(self):
er = ExternalResources('terms')
er.add_ref(container='uuid1',
key='key1',
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
resource = er.get_resource('resource1')
self.assertIsInstance(resource, Resource)
with self.assertRaises(ValueError):
er.get_resource('unknown_resource')
def test_piecewise_add(self):
er = ExternalResources('terms')
# this is the term the user wants to use. They will need to specify this
key = er._add_key('mouse')
resource1 = er._add_resource(resource='resource0', uri='resource_uri0')
# the user will have to supply this info as well. This is the information
# needed to retrieve info about the controled term
er._add_entity(key, resource1, '10090', 'uri')
# The user can also pass in the container or it can be wrapped up under NWBFILE
obj = er._add_object('object', 'species')
# This could also be wrapped up under NWBFile
er._add_object_key(obj, key)
self.assertEqual(er.keys.data, [('mouse', )])
self.assertEqual(er.entities.data, [(0, 0, '10090', 'uri')])
self.assertEqual(er.objects.data, [('object', 'species')])
def test_get_keys_subset(self):
er = ExternalResources('terms')
er.add_ref('uuid1', 'field1', 'key1', 'resource11', 'resource_id11', 'url11')
er.add_ref('uuid2', 'field2', 'key2', 'resource21', 'resource_id21', 'url21')
er.add_ref('uuid1', 'field1', 'key1', 'resource12', 'resource_id12', 'url12')
key = er.keys.row[0]
received = er.get_keys(keys=key)
expected = pd.DataFrame(
data=[['key1', 'resource11', 'resource_id11', 'url11'],
['key1', 'resource12', 'resource_id12', 'url12']],
columns=['key_name', 'resource_name', 'resource_entity_id', 'resource_entity_uri']
)
pd.testing.assert_frame_equal(received, expected)
def test_add_ref_same_keyname(self):
er = ExternalResources('terms')
key1 = er.add_key('key1')
key2 = er.add_key('key1')
er.add_ref('uuid1', 'field1', key1, 'resource11', 'resource_id11', 'url11')
er.add_ref('uuid2', 'field2', key2, 'resource21', 'resource_id21', 'url21')
er.add_ref('uuid1', 'field1', 'key1', 'resource12', 'resource_id12', 'url12')
self.assertEqual(er.keys.data, [('key1',), ('key1',)])
self.assertEqual(er.resources.data,
[(0, 'resource11', 'resource_id11', 'url11'),
(1, 'resource21', 'resource_id21', 'url21'),
(0, 'resource12', 'resource_id12', 'url12')])
self.assertEqual(er.objects.data, [('uuid1', 'field1'),
('uuid2', 'field2')])
def test_piecewise_add(self):
er = ExternalResources('terms')
# this is the term the user wants to use. They will need to specify this
key = er.add_key('mouse')
# the user will have to supply this info as well. This is the information
# needed to retrieve info about the controled term
er.add_resource(key, 'NCBI Taxonomy', '10090',
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10090')
# The user can also pass in the container or it can be wrapped up under NWBFILE
obj = er.add_object('ca885753-e8a3-418a-86f4-7748fc2252a8', 'species')
# This could also be wrapped up under NWBFile
er.add_external_reference(obj, key)
self.assertEqual(er.keys.data, [('mouse',)])
self.assertEqual(er.resources.data,
[(0, 'NCBI Taxonomy', '10090',
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10090')])
self.assertEqual(er.objects.data, [('ca885753-e8a3-418a-86f4-7748fc2252a8', 'species')])
def setUpContainer(self):
er = ExternalResources('terms')
er.add_ref(container='uuid1',
key='key1',
resource_name='resource11',
resource_uri='resource_uri11',
entity_id="id11",
entity_uri='url11')
er.add_ref(container='uuid2',
key='key2',
resource_name='resource21',
resource_uri='resource_uri21',
entity_id="id12",
entity_uri='url21')
return er
def test_add_ref_duplicate_resource(self):
er = ExternalResources('terms')
er.add_ref(container='uuid1',
key='key1',
resource_name='resource0',
resource_uri='uri0',
entity_id='entity_id1',
entity_uri='entity1')
er.add_ref(container='uuid2',
key='key2',
resource_name='resource0',
resource_uri='uri0',
entity_id='entity_id2',
entity_uri='entity2')
resource_list = er.resources.which(resource='resource0')
self.assertEqual(len(resource_list), 1)
def test_add_ref_two_resources(self):
er = ExternalResources('terms')
er.add_ref(container='uuid1',
key='key1',
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
er.add_ref(container='uuid1',
key=er.get_key(key_name='key1'),
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
self.assertEqual(er.keys.data, [('key1', )])
self.assertEqual(er.resources.data, [('resource1', 'resource_uri1'),
('resource2', 'resource_uri2')])
self.assertEqual(er.objects.data, [('uuid1', '', '')])
self.assertEqual(er.entities.data, [(0, 0, 'id11', 'url11'),
(0, 1, 'id12', 'url21')])
def test_get_key_without_container(self):
self.er = ExternalResources('terms')
self.er._add_key('key1')
keys = self.er.get_key('key1')
self.assertIsInstance(keys, Key)
def setUp(self):
self.er = ExternalResources('terms')