def test_simple_create(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Food Web")
fox_node = niceCx_creatures.create_node(node_name='Fox')
mouse_node = niceCx_creatures.create_node(node_name='Mouse')
bird_node = niceCx_creatures.create_node(node_name='Bird')
fox_bird_edge = niceCx_creatures.create_edge(
edge_source=fox_node,
edge_target=bird_node,
edge_interaction='interacts-with')
fox_mouse_edge = niceCx_creatures.create_edge(
edge_source=fox_node,
edge_target=mouse_node,
edge_interaction='interacts-with')
niceCx_creatures.add_node_attribute(property_of=fox_node,
name='Color',
values='Red')
niceCx_creatures.add_node_attribute(property_of=mouse_node,
name='Color',
values='Gray')
niceCx_creatures.add_node_attribute(property_of=bird_node,
name='Color',
values='Blue')
niceCx_creatures.add_edge_attribute(property_of=fox_mouse_edge,
name='Hunted',
values='On the ground')
print(niceCx_creatures.get_node_attribute(fox_node, 'Color'))
def test_update_network_containing_all_types(self):
pfdict = {'a': ['2', '3'], 'SIGNOR-PF10': ['7', '8']}
cdict = {'e': ['5', '6'], 'SIGNOR-C1': ['9', '10']}
net = NiceCXNetwork()
aid = net.create_node('a')
net.set_node_attribute(aid, NodeMemberUpdator.TYPE, 'proteinfamily')
eid = net.create_node('e')
net.set_node_attribute(eid, NodeMemberUpdator.TYPE, 'complex')
oid = net.create_node('c')
o2id = net.create_node('d')
net.set_node_attribute(o2id, NodeMemberUpdator.TYPE, 'protein')
notinid = net.create_node('x')
net.set_node_attribute(notinid, NodeMemberUpdator.TYPE,
'proteinfamily')
notinid2 = net.create_node('y')
net.set_node_attribute(notinid2, NodeMemberUpdator.TYPE, 'complex')
mock = GeneSymbolSearcher(bclient=None)
mock.get_symbol = MagicMock(side_effect=['AA', 'BB', 'CC', 'DD'])
updator = NodeMemberUpdator(pfdict, cdict, genesearcher=mock)
res = updator.update(net)
self.assertTrue(
"No entry in proteinfamily map for node: {'@id': 4, 'n': 'x', 'r': 'x'}"
in res)
self.assertTrue(
"No entry in complexes map for node: {'@id': 5, 'n': 'y', 'r': 'y'}"
in res)
res = net.get_node_attribute(aid, NodeMemberUpdator.MEMBER)
self.assertTrue('hgnc.symbol:AA' in res['v'])
self.assertTrue('hgnc.symbol:BB' in res['v'])
res = net.get_node_attribute(eid, NodeMemberUpdator.MEMBER)
self.assertTrue('hgnc.symbol:CC' in res['v'])
self.assertTrue('hgnc.symbol:DD' in res['v'])
res = net.get_node_attribute(oid, NodeMemberUpdator.MEMBER)
self.assertEqual(None, res)
res = net.get_node_attribute(o2id, NodeMemberUpdator.MEMBER)
self.assertEqual(None, res)
def test_update_network_containing_all_types(self):
updator = UpdatePrefixesForNodeRepresents()
net = NiceCXNetwork()
uni_one = net.create_node('somenode', node_represents='rep1')
net.set_node_attribute(uni_one, 'DATABASE', 'UNIPROT')
uni_two = net.create_node('somenode2', node_represents='uniprot:rep2')
net.set_node_attribute(uni_two, 'DATABASE', 'UNIPROT')
sig_one = net.create_node('somenode3', node_represents='rep3')
net.set_node_attribute(sig_one, 'DATABASE', 'SIGNOR')
sig_two = net.create_node('somenode4', node_represents='signor:rep4')
net.set_node_attribute(sig_two, 'DATABASE', 'SIGNOR')
other = net.create_node('somenode5', node_represents='blah:rep5')
net.set_node_attribute(other, 'DATABASE', 'other')
self.assertEqual([], updator.update(net))
res = net.get_node(uni_one)
self.assertEqual('uniprot:rep1', res['r'])
self.assertEqual(None, net.get_node_attribute(uni_one, 'DATABASE'))
res = net.get_node(uni_two)
self.assertEqual('uniprot:rep2', res['r'])
self.assertEqual(None, net.get_node_attribute(uni_two, 'DATABASE'))
res = net.get_node(sig_one)
self.assertEqual('signor:rep3', res['r'])
self.assertEqual(None, net.get_node_attribute(sig_one, 'DATABASE'))
res = net.get_node(sig_two)
self.assertEqual('signor:rep4', res['r'])
self.assertEqual(None, net.get_node_attribute(sig_two, 'DATABASE'))
res = net.get_node(other)
self.assertEqual('blah:rep5', res['r'])
self.assertEqual(None, net.get_node_attribute(other, 'DATABASE'))
def test_update_network_containing_all_types(self):
updator = NodeLocationUpdator()
net = NiceCXNetwork()
comp_attr = NodeLocationUpdator.LOCATION
no_attr = net.create_node('somenode', node_represents='rep1')
e_attr = net.create_node('somenode2',
node_represents='uniprot:rep2')
net.set_node_attribute(e_attr,
NodeLocationUpdator.LOCATION,
'')
o_attr = net.create_node('somenode2',
node_represents='uniprot:rep2')
net.set_node_attribute(o_attr,
NodeLocationUpdator.LOCATION,
'blah')
ph_attr = net.create_node('anothernode', node_represents='rep3')
net.set_node_attribute(ph_attr,
NodeLocationUpdator.LOCATION,
NodeLocationUpdator.PHENOTYPESLIST)
self.assertEqual([],
updator.update(net))
self.assertEqual(NodeLocationUpdator.CYTOPLASM,
net.get_node_attribute(no_attr, comp_attr)['v'])
self.assertEqual(NodeLocationUpdator.CYTOPLASM,
net.get_node_attribute(e_attr, comp_attr)['v'])
self.assertEqual('blah',
net.get_node_attribute(o_attr, comp_attr)['v'])
self.assertEqual('',
net.get_node_attribute(ph_attr, comp_attr)['v'])
def test_simple_create(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Food Web")
fox_node = niceCx_creatures.create_node(node_name='Fox')
mouse_node = niceCx_creatures.create_node(node_name='Mouse')
bird_node = niceCx_creatures.create_node(node_name='Bird')
fox_bird_edge = niceCx_creatures.create_edge(edge_source=fox_node, edge_target=bird_node, edge_interaction='interacts-with')
fox_mouse_edge = niceCx_creatures.create_edge(edge_source=fox_node, edge_target=mouse_node, edge_interaction='interacts-with')
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values='Red')
niceCx_creatures.add_node_attribute(property_of=mouse_node, name='Color', values='Gray')
niceCx_creatures.add_node_attribute(property_of=bird_node, name='Color', values='Blue')
niceCx_creatures.add_edge_attribute(property_of=fox_mouse_edge, name='Hunted', values='On the ground')
print(niceCx_creatures.get_node_attribute(fox_node, 'Color'))
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
node_id = NiceCX_creatures.create_node("new node")
NiceCX_creatures.add_node_attribute(node_id, "new attribute",
"new attribute value is xxxx")
# #### get_node_attribute(node, attribute_name, subnetwork=None)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
node_id = NiceCX_creatures.create_node("new node")
NiceCX_creatures.set_node_attribute(node_id, "new attribute",
"new attribute value is nnnn")
NiceCX_creatures.get_node_attribute(node_id, "new attribute")
# ##### get_node_attribute_objects(node, attribute_name)
# In[ ]:
#get_node_attribute_objects() is deprecated. Please use get_node_attribute() instead
# #### get_node_attributes(node)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
#create one node
node_id = NiceCX_creatures.create_node("new node")
