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_remove_edge_from_network(self):
net = NiceCXNetwork()
src_node = net.create_node('node1')
target_node = net.create_node('node2')
edge_id = net.create_edge(edge_source=src_node,
edge_target=target_node)
self.assertEqual(1, len(net.get_edges()))
nef = NetworkEdgeFactory()
ne = nef.get_network_edge_from_network(net_cx=net, edge_id=edge_id)
ne.remove_edge_from_network(net_cx=net)
self.assertEqual(0, len(net.get_edges()))
def test_get_edges(self):
net = NiceCXNetwork()
# Verify correct operation on empty network
res = list(net.get_edges())
self.assertEqual(0, len(res))
# add an edge
net.create_edge(edge_source=0, edge_target=1)
res = list(net.get_edges())
self.assertEqual(1, len(res))
self.assertEqual(res[0], (0, {'@id': 0, 's': 0, 't': 1}))
# add another edge
net.create_edge(edge_source=1, edge_target=2)
res = list(net.get_edges())
self.assertEqual(2, len(res))
self.assertEqual(res[0], (0, {'@id': 0, 's': 0, 't': 1}))
self.assertEqual(res[1], (1, {'@id': 1, 's': 1, 't': 2}))
def test_update_no_family_members(self):
net = NiceCXNetwork()
node1 = net.create_node('node1')
node2 = net.create_node('node2')
net.create_edge(edge_source=node1, edge_target=node2,
edge_interaction='activates')
remover = ProteinFamilyNodeMemberRemover()
remover.update(net)
self.assertEqual(2, len(net.get_nodes()))
self.assertEqual(1, len(net.get_edges()))
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_basic_network_where_neighbor_of_citations_merges_enabled(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
edge_map = {}
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
net.set_edge_attribute(nid,
RedundantEdgeAdjudicator.CITATION, ['pubmed:5'],
type='list_of_string')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
net.set_edge_attribute(cid,
RedundantEdgeAdjudicator.CITATION, ['pubmed:6'],
type='list_of_string')
neighbor_of_map = {}
controls_state_change_map = {}
other_edge_exists = {}
for k, v in net.get_edges():
s = v['s']
t = v['t']
i = v['i']
if i == 'neighbor-of':
if not s in neighbor_of_map:
neighbor_of_map[s] = {}
if not t in neighbor_of_map:
neighbor_of_map[t] = {}
neighbor_of_map[s][t] = k
neighbor_of_map[t][s] = k
elif i == 'controls-state-change-of':
adjud._add_to_edge_map(controls_state_change_map, k, s, t)
else:
adjud._add_to_edge_map(other_edge_exists, k, s, t)
adjud.remove_and_merge_neighbor_of(net, neighbor_of_map, edge_map)
net.print_summary()
def test_remove_node_from_network_with_edges_and_attrs(self):
net = NiceCXNetwork()
node_id = net.create_node('node1', node_represents='ha')
other_node_id = net.create_node('node2', node_represents='ha')
edge_id = net.create_edge(edge_source=node_id,
edge_target=other_node_id,
edge_interaction='activates')
net.set_node_attribute(node_id, 'nodeattr', values='foo')
net.set_node_attribute(node_id, 'nodeattr2', values='foo2')
net.set_edge_attribute(edge_id, 'edgeattr', values='hello')
net.set_edge_attribute(edge_id, 'edgeattr2', values='hello2')
nef = NetworkNodeFactory()
nn = nef.get_network_node_from_network(net_cx=net, node_id=node_id)
nn.remove_node_from_network(net_cx=net)
self.assertEqual(1, len(net.get_nodes()))
self.assertEqual(0, len(net.get_edges()))
NiceCX_creatures.set_edge_attribute(edge_id, attr_name, attr_value)
#print(NiceCX_creatures.get_edge_attribute(edge_id, attr_name))
NiceCX_creatures.get_edge_attributes(edge_id)
# #### get_edges()
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
#add 3 edges to the network
edge_1 = NiceCX_creatures.create_edge("A", "B")
edge_2 = NiceCX_creatures.create_edge("C", "D")
edge_3 = NiceCX_creatures.create_edge("B", "C")
NiceCX_creatures.get_edges()
# ##### get_name()
# #### set_name(network name)
# In[ ]:
#create/initial an empty niceCX network before setting the network name
NiceCX_creatures = NiceCXNetwork()
NiceCX_creatures.set_name("new web")
# ##### getSummary()
# ##### set_network_attribute(name=None, values=None, type=None, subnetwork_id=None)