def test_SetConnection(self):
"""
Tests if the network file is added
to the database.
:return:
"""
test_config = {
'host': 'localhost',
'database': 'test',
'user': '******',
'password': '******'
}
conn = SetConnection()
read_config = conn.config
self.assertTrue(test_config == read_config)
def test_get_union(self):
"""
Tests if the union of the networks is returned.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
union_set = conn_object.get_union(networks=["g1", "g2"])
conn_object.delete_tables()
self.assertTrue(len(union_set.edges), 4)
def test_get_difference(self):
"""
Tests if the difference is returned with edges that have different weights.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
difference_set = conn_object.get_difference(networks=["g1", "g2"])
conn_object.delete_tables()
self.assertEqual(len(difference_set.edges), 3)
def test_aggr_networks(self):
"""
Tests if network names are aggregated to an edge property
named 'source'.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
difference_set = conn_object.get_difference(networks=["g1", "g2"])
conn_object.delete_tables()
self.assertEqual(
difference_set.edges[('GG_OTU_1', 'GG_OTU_2')]['source'], 'g1')
def test_get_intersection_3(self):
"""
Tests if the intersection returns an empty network
when the intersection is too large.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
intersection_set = conn_object.get_intersection(networks=["g1", "g2"],
number=3)
conn_object.delete_tables()
self.assertEqual(len(intersection_set.edges), 0)
def test_get_intersection_weight(self):
"""
Tests if the intersection returns the correct number of edges
when the weight parameter is changed.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
intersection_set = conn_object.get_intersection(networks=["g1", "g2"],
number=2,
weight=False)
conn_object.delete_tables()
self.assertEqual(len(intersection_set.edges), 3)
def test_get_intersection(self):
"""
Tests if the import_network function reads the correct database file,
and imports the network file, by querying the edges table.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
intersection_set = conn_object.get_intersection(networks=["g1", "g2"],
number=2)
conn_object.delete_tables()
self.assertCountEqual(("GG_OTU_2", "GG_OTU_5"),
list(intersection_set.edges)[0])
def test_aggr_weight(self):
"""
Tests if edge weights are aggregated to an edge property
named 'weight'.
:return:
"""
conn_object = BiomConnection()
conn_object.create_tables()
conn_object.add_biom(testbiom, 'test')
conn_object = IoConnection()
conn_object.add_network(network=g1, name='g1', study='test')
conn_object.add_network(network=g2, name='g2', study='test')
conn_object = SetConnection()
intersection_set = conn_object.get_intersection(networks=["g1", "g2"],
number=2,
weight=False)
conn_object.delete_tables()
self.assertEqual(
intersection_set.edges[('GG_OTU_1', 'GG_OTU_2')]['weight'], '1,-1')