def test_add_edge_to_network_using_src_target_node_ids(self):
net = NiceCXNetwork()
src_node = net.create_node('node1')
target_node = net.create_node('node2')
ne = NetworkEdge(edge_id=1,
source_node_id=src_node,
target_node_id=target_node,
interaction='activates')
self.assertEqual(0, len(net.get_edges()))
edge_id = ne.add_edge_to_network(net_cx=net)
self.assertEqual(1, len(net.get_edges()))
nef = NetworkEdgeFactory()
new_ne = nef.get_network_edge_from_network(net_cx=net, edge_id=edge_id)
self.assertEqual('node1', new_ne.get_source_node_name())
self.assertEqual('node2', new_ne.get_target_node_name())
self.assertEqual(src_node, new_ne.get_source_node_id())
self.assertEqual(target_node, new_ne.get_target_node_id())
self.assertEqual('activates', new_ne.get_interaction())
self.assertEqual([], new_ne.get_attributes())
new_ne.remove_edge_from_network(net_cx=net)
self.assertEqual(0, len(net.get_edges()))
def test_get_data_type_for_attributes_two_types(self):
ne = NetworkEdge()
# try various combos of <type> and None
for a in [(None, 'string'), ('string', None), (None, 'list_of_string'),
('list_of_string', None), ('boolean', None),
(None, 'boolean'), ('list_of_integer', None),
(None, 'list_of_double')]:
attrs = [Attribute(data_type=a[0]), Attribute(data_type=a[1])]
self.assertEqual('list_of_string',
ne._get_data_type_for_attributes(attrs))
# try the other types
for a in [('string', 'list_of_string'), ('list_of_string', 'string'),
('boolean', 'list_of_boolean'),
('list_of_boolean', 'boolean'), ('double', 'list_of_double'),
('list_of_double', 'double'), ('integer', 'list_of_integer'),
('list_of_integer', 'integer'), ('long', 'list_of_long'),
('list_of_long', 'long')]:
attrs = [Attribute(data_type=a[0]), Attribute(data_type=a[1])]
if a[0].startswith('list_of'):
checkval = a[0]
else:
checkval = 'list_of_' + a[0]
self.assertEqual(checkval, ne._get_data_type_for_attributes(attrs))
def test_merge_attributes_test_where_dtype_mixed_string_none(self):
ne = NetworkEdge()
attrs = [
Attribute(name='x', value='1', data_type='string'),
Attribute(name='x', value='2')
]
res = ne._merge_attributes(attrs_list=attrs)
self.assertEqual('x', res.get_name())
self.assertEqual(2, len(res.get_value()))
self.assertTrue('1' in res.get_value())
self.assertTrue('2' in res.get_value())
self.assertEqual('list_of_string', res.get_data_type())
def test_merge_attributes_test_with_str_dtype(self):
ne = NetworkEdge()
attrs = [
Attribute(name='x', value=['1'], data_type='list_of_string'),
Attribute(name='x', value='3')
]
res = ne._merge_attributes(attrs_list=attrs)
self.assertEqual('x', res.get_name())
self.assertEqual(2, len(res.get_value()))
self.assertTrue('1' in res.get_value())
self.assertTrue('3' in res.get_value())
self.assertEqual('list_of_string', res.get_data_type())
def test_merge_attributes_test_with_integer_dtype(self):
ne = NetworkEdge()
attrs = [
Attribute(name='x', value=1, data_type='integer'),
Attribute(name='x', value=[2, 3], data_type='list_of_integer')
]
res = ne._merge_attributes(attrs_list=attrs)
self.assertEqual('x', res.get_name())
self.assertEqual(3, len(res.get_value()))
self.assertTrue(1 in res.get_value())
self.assertTrue(2 in res.get_value())
self.assertTrue(3 in res.get_value())
self.assertEqual('list_of_integer', res.get_data_type())
def test_remove_identical_attributes_one_attr(self):
ne = NetworkEdge()
# test where there is 1 attribute
attrs = [Attribute(name='foo', value='bar')]
ne.set_attributes(attrs)
self.assertEqual([], ne.remove_identical_attributes())
self.assertEqual(1, len(ne.get_attributes()))
def test_get_data_type_for_attributes_single_type(self):
ne = NetworkEdge()
# single None
attrs = [Attribute(data_type=None)]
self.assertEqual('list_of_string',
ne._get_data_type_for_attributes(attrs))
# multiple None
attrs = [Attribute(data_type=None), Attribute(data_type=None)]
self.assertEqual('list_of_string',
ne._get_data_type_for_attributes(attrs))
# single other types
for a in ['string', 'boolean', 'double', 'integer', 'long']:
attrs = [Attribute(data_type=a)]
self.assertEqual('list_of_' + a,
ne._get_data_type_for_attributes(attrs))
# multiple of matching types
for a in [
'string', 'boolean', 'double', 'integer', 'long',
'list_of_boolean', 'list_of_double', 'list_of_integer',
'list_of_long', 'list_of_string'
]:
attrs = [
Attribute(data_type=a),
Attribute(data_type=a),
Attribute(data_type=a)
]
if a.startswith('list_of'):
checkval = a
else:
checkval = 'list_of_' + a
self.assertEqual(checkval, ne._get_data_type_for_attributes(attrs))
def test_add_edge_to_network(self):
net = NiceCXNetwork()
src_node = net.create_node('node1')
target_node = net.create_node('node2')
attrs = []
attrs.append(Attribute(name='foo', value='ha'))
attrs.append(Attribute(name='foo2', value='ha2', data_type='string'))
ne = NetworkEdge(edge_id=1, interaction='activates', attributes=attrs)
self.assertEqual(0, len(net.get_edges()))
edge_id = ne.add_edge_to_network(net_cx=net,
source_node_id=src_node,
target_node_id=target_node)
self.assertEqual(1, len(net.get_edges()))
nef = NetworkEdgeFactory()
new_ne = nef.get_network_edge_from_network(net_cx=net, edge_id=edge_id)
self.assertEqual('node1', new_ne.get_source_node_name())
self.assertEqual('node2', new_ne.get_target_node_name())
self.assertEqual(src_node, new_ne.get_source_node_id())
self.assertEqual(target_node, new_ne.get_target_node_id())
self.assertEqual('activates', new_ne.get_interaction())
self.assertEqual(2, len(new_ne.get_attributes()))
a_dict = {}
for attr in new_ne.get_attributes():
a_dict[attr.get_name()] = attr
self.assertEqual('ha', a_dict['foo'].get_value())
self.assertEqual('ha2', a_dict['foo2'].get_value())
new_ne.remove_edge_from_network(net_cx=net)
self.assertEqual(0, len(net.get_edges()))
def test_get_edge_key(self):
ne = NetworkEdge(source_node_id=1, target_node_id=2,
source_node_name='src', target_node_name='target',
interaction='activates')
remover = ProteinFamilyNodeMemberRemover()
# try with no attributes
e_key, d_val = remover._get_edge_key(ne)
self.assertEqual('s=1, t=2, i=activates, directed=False', e_key)
self.assertEqual(False, d_val)
e_key, d_val = remover._get_edge_key(ne, flip_src_target=True)
self.assertEqual('s=2, t=1, i=activates, directed=False', e_key)
self.assertEqual(False, d_val)
# try with attributes but no match
ne.set_attributes([Attribute(name='foo', value='1')])
e_key, d_val = remover._get_edge_key(ne)
self.assertEqual('s=1, t=2, i=activates, directed=False', e_key)
self.assertEqual(False, d_val)
e_key, d_val = remover._get_edge_key(ne, flip_src_target=True)
self.assertEqual('s=2, t=1, i=activates, directed=False', e_key)
self.assertEqual(False, d_val)
# try with directed attribute True
ne.set_attributes([Attribute(name='directed', value=True,
data_type='boolean')])
e_key, d_val = remover._get_edge_key(ne)
self.assertEqual('s=1, t=2, i=activates, directed=True', e_key)
self.assertEqual(True, d_val)
e_key, d_val = remover._get_edge_key(ne, flip_src_target=True)
self.assertEqual('s=2, t=1, i=activates, directed=True', e_key)
self.assertEqual(True, d_val)
# try with directed attribute False
ne.set_attributes([Attribute(name='directed', value=False,
data_type='boolean')])
e_key, d_val = remover._get_edge_key(ne)
self.assertEqual('s=1, t=2, i=activates, directed=False', e_key)
self.assertEqual(False, d_val)
e_key, d_val = remover._get_edge_key(ne, flip_src_target=True)
self.assertEqual('s=2, t=1, i=activates, directed=False', e_key)
self.assertEqual(False, d_val)
def test_remove_identical_attributes_four_attrs_two_same(self):
ne = NetworkEdge()
# test where there is 1 attribute
attrs = [
Attribute(name='foo', value='bar'),
Attribute(name='blah', value='yo'),
Attribute(name='blah', value='yo'),
Attribute(name='ha', value='well')
]
ne.set_attributes(attrs)
merged = ne.remove_identical_attributes()
self.assertEqual(1, len(merged))
self.assertEqual('blah', merged[0].get_name())
self.assertEqual(3, len(ne.get_attributes()))
def test_remove_identical_attributes_five_attrs_two_pair_same(self):
ne = NetworkEdge()
# test where there is 5 attribute
attrs = [
Attribute(name='x', value='xval'),
Attribute(name='a', value='bar'),
Attribute(name='blah', value='yo'),
Attribute(name='a', value='bar'),
Attribute(name='blah', value='yo')
]
ne.set_attributes(attrs)
merged = ne.remove_identical_attributes()
self.assertEqual(2, len(merged))
merged_anames = set(x.get_name() for x in merged)
self.assertTrue('a' in merged_anames)
self.assertTrue('blah' in merged_anames)
self.assertEqual(2, len(merged_anames))
self.assertEqual(3, len(ne.get_attributes()))
def test_get_edge_key(self):
remover = ProteinFamilyNodeMemberRemover()
# try with 1 edge no attributes
ne = NetworkEdge(source_node_id=3, target_node_id=2,
interaction='activates')
res = remover._get_edge_dict([ne])
self.assertEqual(1, len(res))
key = 's=3, t=2, i=activates, directed=False'
self.assertTrue(key in res)
self.assertEqual(1, len(res[key]))
self.assertTrue(ne.get_source_node_id() ==
res[key][0].get_source_node_id())
# try 3 edges where two edges have source/target are flipped and
# directed is same value
ne_one = NetworkEdge(source_node_id=1, target_node_id=2,
interaction='activates',
attributes=[Attribute(name='directed',
value=False,
data_type='boolean')])
ne_two = NetworkEdge(source_node_id=2, target_node_id=1,
interaction='activates',
attributes=[Attribute(name='directed',
value=False,
data_type='boolean')])
res = remover._get_edge_dict([ne_one, ne_two, ne])
self.assertEqual(2, len(res))
self.assertTrue(key in res)
self.assertEqual(1, len(res[key]))
self.assertTrue(ne.get_source_node_id() ==
res[key][0].get_source_node_id())
mkey = 's=1, t=2, i=activates, directed=False'
self.assertTrue(mkey in res)
self.assertEqual(2, len(res[mkey]))
def test_getters_and_setters(self):
ne = NetworkEdge()
ne.set_attributes([])
ne.set_id(1)
ne.set_source_node_id(2)
ne.set_target_node_id(3)
ne.set_source_node_name('src')
ne.set_target_node_name('target')
ne.set_interaction('interaction')
self.assertEqual([], ne.get_attributes())
self.assertEqual(1, ne.get_id())
self.assertEqual(2, ne.get_source_node_id())
self.assertEqual(3, ne.get_target_node_id())
self.assertEqual('interaction', ne.get_interaction())
self.assertEqual('src', ne.get_source_node_name())
self.assertEqual('target', ne.get_target_node_name())
def test_merge(self):
# test against None
ne = NetworkEdge()
ne.merge_edge(None)
# test common scenario
ne_one = NetworkEdge(attributes=[
Attribute(name='directed', value=True, data_type='boolean')
])
ne_two = NetworkEdge(attributes=[
Attribute(name='directed', value=True, data_type='boolean')
])
ne.merge_edge(ne_two)
self.assertTrue(1, len(ne_one.get_attributes()))
self.assertEqual('directed', ne.get_attributes()[0].get_name())
self.assertEqual(True, ne.get_attributes()[0].get_value())
self.assertEqual('boolean', ne.get_attributes()[0].get_data_type())
# test another common scenario
ne_one = NetworkEdge(attributes=[
Attribute(
name='citation', value=['1', '2'], data_type='list_of_string'),
Attribute(name='directed', value=True, data_type='boolean')
])
ne_two = NetworkEdge(attributes=[
Attribute(name='citation',
value=['3', '1', '2'],
data_type='list_of_string'),
Attribute(name='directed', value=True, data_type='boolean')
])
ne.merge_edge(ne_two)
self.assertEqual(2, len(ne.get_attributes()))
a_names = set(x.get_name() for x in ne.get_attributes())
self.assertTrue('citation' in a_names)
self.assertTrue('directed' in a_names)
for x in ne.get_attributes():
if x.get_name() == 'citation':
self.assertEqual(3, len(x.get_value()))
self.assertTrue('1' in x.get_value())
self.assertTrue('2' in x.get_value())
self.assertTrue('3' in x.get_value())
def test_merge_duplicate_attributes(self):
# test merge with None for attributes
ne = NetworkEdge()
ne.merge_duplicate_attributes()
# test merge with only 1 attribute
ne.set_attributes([Attribute(name='foo', value='bar')])
ne.merge_duplicate_attributes()
self.assertEqual(1, len(ne.get_attributes()))
self.assertEqual('foo', ne.get_attributes()[0].get_name())
# test merge with two identical attributes
ne.set_attributes([
Attribute(name='foo', value='bar'),
Attribute(name='foo', value='bar')
])
ne.merge_duplicate_attributes()
self.assertEqual(1, len(ne.get_attributes()))
self.assertEqual('foo', ne.get_attributes()[0].get_name())
# test merge with two identical and 1 different
ne.set_attributes([
Attribute(name='foo', value='bar'),
Attribute(name='foo', value='bar'),
Attribute(name='other', value='yo')
])
ne.merge_duplicate_attributes()
self.assertEqual(2, len(ne.get_attributes()))
a_names = set(x.get_name() for x in ne.get_attributes())
self.assertTrue('foo' in a_names)
self.assertTrue('other' in a_names)
def test_remove_identical_attributes_no_attrs(self):
ne = NetworkEdge()
# test where there are no attributes
self.assertEqual([], ne.remove_identical_attributes())
def test_constructor_and__str__(self):
ne = NetworkEdge()
self.assertEqual(None, ne.get_attributes())
self.assertEqual(None, ne.get_id())
self.assertEqual(None, ne.get_source_node_id())
self.assertEqual(None, ne.get_target_node_id())
self.assertEqual(None, ne.get_interaction())
self.assertEqual(None, ne.get_source_node_name())
self.assertEqual(None, ne.get_target_node_name())
self.assertEqual('po=None, s=None (None), t=None (None), i=None',
str(ne))
# try with values set
ne = NetworkEdge(edge_id=1,
source_node_id=2,
source_node_name='src',
target_node_id=3,
target_node_name='target',
interaction='interaction',
attributes=[])
self.assertEqual([], ne.get_attributes())
self.assertEqual(1, ne.get_id())
self.assertEqual(2, ne.get_source_node_id())
self.assertEqual(3, ne.get_target_node_id())
self.assertEqual('interaction', ne.get_interaction())
self.assertEqual('src', ne.get_source_node_name())
self.assertEqual('target', ne.get_target_node_name())
self.assertEqual('po=1, s=2 (src), t=3 (target), i=interaction',
str(ne))