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 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)
class TestExternalResourcesGetKey(TestCase):
def setUp(self):
self.er = ExternalResources('terms')
def test_get_key(self):
self.er.add_ref('uuid1', 'field1', 'key1', 'resource1', 'resource_id1', 'url1')
self.er.add_ref('uuid2', 'field2', 'key1', 'resource2', 'resource_id2', 'url2')
keys = self.er.get_key('key1')
self.assertIsInstance(keys, Key)
self.assertEqual(keys.key_name, 'key1')
def test_get_key_w_object_info(self):
self.er.add_ref('uuid1', 'field1', 'key1', 'resource1', 'resource_id1', 'url1')
self.er.add_ref('uuid2', 'field2', 'key1', 'resource2', 'resource_id2', 'url2')
keys = self.er.get_key('key1', 'uuid1', 'field1')
self.assertIsInstance(keys, Key)
self.assertEqual(keys.key_name, 'key1')
def test_get_key_w_bad_object_info(self):
self.er.add_ref('uuid1', 'field1', 'key1', 'resource1', 'resource_id1', 'url1')
self.er.add_ref('uuid2', 'field2', 'key2', 'resource2', 'resource_id2', 'url2')
with self.assertRaisesRegex(ValueError, "No key with name 'key2' for container 'uuid1' and field 'field1'"):
self.er.get_key('key2', 'uuid1', 'field1')
def test_get_key_doesnt_exist(self):
self.er.add_ref('uuid1', 'field1', 'key1', 'resource1', 'resource_id1', 'url1')
self.er.add_ref('uuid2', 'field2', 'key1', 'resource2', 'resource_id2', 'url2')
with self.assertRaisesRegex(ValueError, "key 'bad_key' does not exist"):
self.er.get_key('bad_key')
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', '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')
self.assertIsInstance(keys, list)
self.assertEqual(keys[0].key_name, 'key1')
self.assertEqual(keys[1].key_name, 'key1')
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_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')])
class TestExternalResourcesGetKey(TestCase):
def setUp(self):
self.er = ExternalResources('terms')
def test_get_key(self):
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='key1',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
keys = self.er.get_key('key1', 'uuid2', '')
self.assertIsInstance(keys, Key)
self.assertEqual(keys.idx, 1)
def test_get_key_bad_arg(self):
self.er._add_key('key2')
self.er.add_ref('uuid1',
key='key1',
resource_name='resource1',
resource_uri='resource_uri1',
entity_id="id11",
entity_uri='url11')
with self.assertRaises(ValueError):
self.er.get_key('key2', 'uuid1', '')
@unittest.skip('Outdated do to privatization')
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 test_get_key_w_object_info(self):
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='key1',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
keys = self.er.get_key('key1', 'uuid1', '')
self.assertIsInstance(keys, Key)
self.assertEqual(keys.key, 'key1')
def test_get_key_w_bad_object_info(self):
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='key1',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
with self.assertRaisesRegex(ValueError, "No key 'key2'"):
self.er.get_key('key2', 'uuid1', '')
def test_get_key_doesnt_exist(self):
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='key1',
resource_name='resource2',
resource_uri='resource_uri2',
entity_id="id12",
entity_uri='url21')
with self.assertRaisesRegex(ValueError,
"key 'bad_key' does not exist"):
self.er.get_key('bad_key')
@unittest.skip('Outdated do to privatization')
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', )])