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")