def test_remove_node_from_network_no_edges_no_attrs(self):
net = NiceCXNetwork()
node_id = net.create_node('node1', node_represents='ha')
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(0, len(net.get_nodes()))
def test_get_nodes(self):
net = NiceCXNetwork()
# Verify correct operation on empty network
res = list(net.get_nodes())
self.assertEqual(0, len(res))
# add a node
net.create_node('foo')
res = list(net.get_nodes())
self.assertEqual(1, len(res))
self.assertEqual(res[0], (0, {'@id': 0, 'n': 'foo', 'r': 'foo'}))
# add another node
net.create_node('bar')
res = list(net.get_nodes())
self.assertEqual(2, len(res))
self.assertEqual(res[0], (0, {'@id': 0, 'n': 'foo', 'r': 'foo'}))
self.assertEqual(res[1], (1, {'@id': 1, 'n': 'bar', 'r': 'bar'}))
def test_update_network(self):
client = self.get_ndex2_client()
# create network and add it
net = NiceCXNetwork()
oneid = net.create_node('node1')
twoid = net.create_node('node2')
net.create_edge(oneid, twoid, 'hello')
netname = 'ndex2-client integration test network' + str(datetime.now())
net.set_name(netname)
res = client.save_new_network(net.to_cx(), visibility='PRIVATE')
try:
self.assertTrue('http' in res)
netid = re.sub('^.*/', '', res)
netsum = client.get_network_summary(network_id=netid)
self.assertEqual(netid, netsum['externalId'])
self.assertEqual(netname, netsum['name'])
self.assertEqual('PRIVATE', netsum['visibility'])
self.assertEqual(False, netsum['isReadOnly'])
self.assertEqual(1, netsum['edgeCount'])
self.assertEqual(2, netsum['nodeCount'])
self.assertEqual(False, netsum['isShowcase'])
self.assertEqual('NONE', netsum['indexLevel'])
net.create_node(node_name='hello', node_represents='something')
net.create_node(node_name='hoho', node_represents='heheh')
newnetname = 'update ' + netname
self.assertEqual(4, len(net.get_nodes()))
net.set_name(newnetname)
if sys.version_info.major == 3:
stream = io.BytesIO(json.dumps(net.to_cx(),
cls=DecimalEncoder)
.encode('utf-8'))
else:
stream = io.BytesIO(json.dumps(net.to_cx(),
cls=DecimalEncoder))
newres = client.update_cx_network(stream, netid)
self.assertEqual('', newres)
netsum = client.get_network_summary(network_id=netid)
self.assertEqual(netid, netsum['externalId'])
self.assertEqual(newnetname, netsum['name'])
self.assertEqual('PRIVATE', netsum['visibility'])
self.assertEqual(False, netsum['isReadOnly'])
self.assertEqual(1, netsum['edgeCount'])
self.assertEqual(4, netsum['nodeCount'])
self.assertEqual(False, netsum['isShowcase'])
self.assertEqual('NONE', netsum['indexLevel'])
finally:
client.delete_network(netid)
try:
client.get_network_as_cx_stream(netid)
self.fail('Expected exception')
except HTTPError:
pass
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_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()))
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
#add 10 nodes to the network, each node has 5 attribute with value
for i in range(10):
node_name = "node " + str(i)
node_id = NiceCX_creatures.create_node(node_name)
for j in range(5):
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[ ]:
def test_update_network(self):
client = self.get_ndex2_client()
# create network and add it
net = NiceCXNetwork()
oneid = net.create_node('node1')
twoid = net.create_node('node2')
net.create_edge(oneid, twoid, 'hello')
netname = 'NiceCXNetwork upload_to() test network' + str(
datetime.now())
net.set_name(netname)
creds = self.get_ndex_credentials_as_tuple()
res = net.upload_to(creds['server'],
creds['user'],
creds['password'],
user_agent=creds['user_agent'])
try:
self.assertTrue('http' in res)
netid = re.sub('^.*/', '', res)
netsum = self.wait_for_network_to_be_ready(client, netid)
self.assertIsNotNone(
netsum, 'Network is still not ready,'
' maybe server is busy?')
self.assertEqual(netid, netsum['externalId'])
self.assertTrue('name' in netsum, msg=str(netsum))
self.assertEqual(netname, netsum['name'], str(netsum))
self.assertEqual('PRIVATE', netsum['visibility'])
self.assertEqual(False, netsum['isReadOnly'])
self.assertEqual(1, netsum['edgeCount'])
self.assertEqual(2, netsum['nodeCount'])
self.assertEqual(False, netsum['isShowcase'])
self.assertEqual('NONE', netsum['indexLevel'])
net.create_node(node_name='hello', node_represents='something')
net.create_node(node_name='hoho', node_represents='heheh')
newnetname = 'update via upload_to() ' + netname
self.assertEqual(4, len(net.get_nodes()))
net.set_name(newnetname)
newres = net.update_to(netid,
creds['server'],
creds['user'],
creds['password'],
user_agent=creds['user_agent'])
self.assertEqual('', newres)
netsum = self.wait_for_network_to_be_ready(client,
netid,
num_retries=5,
retry_weight=1)
self.assertIsNotNone(
netsum, 'Network is still not ready,'
' maybe server is busy?')
self.assertEqual(netid, netsum['externalId'])
self.assertEqual(newnetname, netsum['name'])
self.assertEqual('PRIVATE', netsum['visibility'])
self.assertEqual(False, netsum['isReadOnly'])
self.assertEqual(1, netsum['edgeCount'])
self.assertEqual(4, netsum['nodeCount'])
self.assertEqual(False, netsum['isShowcase'])
self.assertEqual('NONE', netsum['indexLevel'])
finally:
client.delete_network(netid)
try:
client.get_network_as_cx_stream(netid)
self.fail('Expected exception')
except HTTPError:
pass