def test_add_member_genes(self):
net = NiceCXNetwork()
aid = net.create_node('a')
net.set_node_attribute(aid, NodeMemberUpdator.TYPE, 'proteinfamily')
notinid = net.create_node('x')
net.set_node_attribute(notinid, NodeMemberUpdator.TYPE,
'proteinfamily')
mock = GeneSymbolSearcher(bclient=None)
mock.get_symbol = MagicMock(side_effect=['', None])
updator = NodeMemberUpdator(None, None, genesearcher=mock)
aidnode = net.get_node(aid)
res = updator._add_member_genes(net, aidnode, [])
self.assertEqual(['No proteins obtained for node: ' + str(aidnode)],
res)
notinidnode = net.get_node(notinid)
res = updator._add_member_genes(net, notinidnode, ['x'])
self.assertTrue('For node ' + str(notinidnode) +
' No gene symbol found for x. Skipping.' in res)
self.assertTrue('Not a single gene symbol found. Skipping insertion '
'of member attribute for node ' +
str(notinidnode) in res)
def test_update_one_node_to_update_symbol_not_none(self):
mock = MagicMock()
mock.get_symbol = MagicMock(return_value='SMILE')
updater = UniProtToGeneSymbolUpdater(searcher=mock)
net = NiceCXNetwork()
nodeone = net.create_node(node_name='Q1', node_represents='uniprot:q1')
res = updater.update(net)
self.assertEqual(0, len(res))
self.assertEqual('SMILE', net.get_node(nodeone)['n'])
self.assertEqual('uniprot:q1', net.get_node(nodeone)['r'])
mock.get_symbol.assert_called_with('Q1')
def test_update_one_node_to_update_symbol_is_none(self):
mock = MagicMock()
mock.get_symbol = MagicMock(return_value=None)
updater = UniProtToGeneSymbolUpdater(searcher=mock)
net = NiceCXNetwork()
nodeone = net.create_node(node_name='bob',
node_represents='uniprot:bob')
res = updater.update(net)
self.assertEqual(1, len(res))
self.assertTrue('No symbol found to replace' in res[0])
self.assertEqual('bob', net.get_node(nodeone)['n'])
self.assertEqual('uniprot:bob', net.get_node(nodeone)['r'])
mock.get_symbol.assert_called_with('bob')
def test_update_no_nodes_start_with_uniprot(self):
updater = UniProtToGeneSymbolUpdater()
net = NiceCXNetwork()
nodeone = net.create_node(node_name='node1', node_represents='node1')
nodetwo = net.create_node(node_name='node2', node_represents='node2')
res = updater.update(net)
self.assertEqual(0, len(res))
self.assertEqual('node1', net.get_node(nodeone)['n'])
self.assertEqual('node2', net.get_node(nodetwo)['n'])
def test_create_edge_with_node_dict_passed_in_for_edge_ids(self):
net = NiceCXNetwork()
nodeone = net.get_node(net.create_node('node1'))
nodetwo = net.get_node(net.create_node('node2'))
edge_id = net.create_edge(edge_source=nodeone,
edge_target=nodetwo)
res = net.get_edge(edge_id)
self.assertEqual(edge_id, res[constants.EDGE_ID])
self.assertEqual(0, res[constants.EDGE_SOURCE])
self.assertEqual(1, res[constants.EDGE_TARGET])
def test_set_node_attribute_passing_node_object(self):
# try int
net = NiceCXNetwork()
node_id = net.create_node(node_name='foo')
node = net.get_node(node_id)
net.set_node_attribute(node, 'attrname', 5)
res = net.get_node_attributes(node_id)
self.assertEqual(len(res), 1)
self.assertEqual(res[0][constants.NODE_ATTR_PROPERTYOF], node_id)
self.assertEqual(res[0][constants.NODE_ATTR_NAME], 'attrname')
self.assertEqual(res[0][constants.NODE_ATTR_VALUE], 5)
self.assertEqual(res[0][constants.NODE_ATTR_DATATYPE], 'integer')
def test_update_no_represents_in_nodes(self):
updater = UniProtToGeneSymbolUpdater()
net = NiceCXNetwork()
nodeone = net.create_node(node_name='node1', node_represents=None)
nodetwo = net.create_node(node_name='node2', node_represents=None)
# so in NDEx2 python client 3.2.0 and earlier if you
# pass node_represents=None the represents field is set
# to the values set in node_name which doesn't seem like
# correct behavior...
firstnode = net.get_node(nodeone)
del firstnode['r']
secondnode = net.get_node(nodetwo)
del secondnode['r']
res = updater.update(net)
self.assertEqual(2, len(res))
self.assertTrue('(0) and name (node1) no represents' in res[0])
self.assertTrue('(1) and name (node2) no represents' in res[1])
self.assertEqual('node1', net.get_node(nodeone)['n'])
self.assertEqual('node2', net.get_node(nodetwo)['n'])
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'))
attr_name = "attribute " + str(i) + str(j)
attr_value = "attribute value is " + str(i) + str(j)
NiceCX_creatures.set_node_attribute(node_id, attr_name, attr_value)
print("\n", NiceCX_creatures.get_node_attribute(node_id, attr_name))
NiceCX_creatures.get_nodes()
# #### *get_node(node)
# 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(node_id)
# #### create_edge(source, target, interaction)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
#create_edge() method returns the new edge id. IDs are always assigned in an ascending order.
print(NiceCX_creatures.create_edge("A", "B"))
print(NiceCX_creatures.create_edge("C", "D"))
print(NiceCX_creatures.create_edge("B", "C"))
# #### add_edge(edge)
# In[ ]:
