class CytoscapeClient:
"""This is a wrapper to the py2cytoscape wrapper. The local installation of Py2cytoscape has been modified for it to work"""
def __init__(self, host="localhost", port="1234", version="v1"):
self.cy = CyRestClient(ip=host, port=port, version=version)
def gc(self):
self.cy.gc()
def free_memory(self):
self.cy.gc()
X = self.cy.status()
return max(
X['memoryStatus']['maxMemory'] - X['memoryStatus']['usedMemory'],
X['memoryStatus']['freeMemory'])
def random_id(self, prefix="MY_"):
import random
s = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
return prefix + ''.join(
[s[random.randint(0,
len(s) - 1)] for i in range(10)])
def cynet_from_xgmml(self,
s_file,
name=None,
s_layout="force-directed",
l_bundle=True,
t_xy=None,
l_digraph=False):
"""If t_xy is provided, s_layout is ignored
return CyNetwork"""
import os
if not os.path.exists(s_file):
import util
util.warn_msg('Missing file: %s' % s_file)
return None
if not l_digraph:
net = xgmml.Network(s_file, name=name)
else:
import digraph
net = digraph.Digraph(s_file, name=name)
if t_xy is not None:
net.set_XY(t_xy)
s_layout = None
S = net.T_node.header()
#print "---------------->", S
#S=[x for x in S if x not in ('Gene','Name','Symbol')]
#net.T_node.drop(S, axis=1, inplace=True)
##############################
return self.cynet_from_network(net,
name=name,
s_layout=s_layout,
l_bundle=l_bundle)
def cynet_from_network(self,
net,
name=None,
s_layout="force-directed",
l_bundle=True):
"""Input net: xgmml.Network object
return CyNetwork"""
#print "====>>>>>>>>", net.T_node.header()
data = net.to_json()
if name is None:
name = data['data']['name']
#cynet=self.cy.create(suid=net)
cynet = None
for trial in range(
3): # something Cytoscape errors, try up to three times
try:
if cynet is None:
cynet = self.cy.network.create(name=name, data=data)
except:
cynet = None
print("Fail at trail %d" % (trial + 1))
print("JSON data>", data)
if cynet is None:
import sys
util.warn_msg('Error during plot_go_network(): %s' %
sys.exc_info()[0])
print(traceback.format_exc())
id = cynet.get_id()
if s_layout is not None:
#print "apply layout %s" % s_layout
self.cy.layout.apply(name=s_layout, network=cynet)
if l_bundle:
self.cy.edgebundling.apply(cynet)
#print "apply bundle %s" % s_layout
self.cy.layout.fit(cynet)
return cynet
def delete_cynet(self, cynet=None):
"""None means delete all networks"""
if cynet is None:
self.cy.network.delete_all()
else:
self.cy.network.delete(cynet)
def get_network(self, suid):
"""Get xgmml.Network with X,Y coordinates"""
cynet = self.cy.network.create(suid=suid)
net = xgmml.Network.from_json(cynet.to_json())
net.T_node.drop([
x for x in ['graphics_x', 'graphics_y', 'SUID', 'id_original']
if x in net.T_node.header()
],
axis=1,
inplace=True)
t_xy = self.cynet_get_XY(cynet)
if t_xy is not None:
t_xy.drop('Gene', axis=1, inplace=True)
t_xy.rename2({'x': 'graphics_x', 'y': 'graphics_y'})
net.T_node = net.T_node.merge(t_xy,
left_on='id',
right_on='id',
how='left')
return net
def get_cynet(self, cynet):
"""make sure we return a cynet object"""
if type(cynet) in (str, int):
return self.cy.network.create(suid=int(cynet))
return cynet
def cynet_get_XY(self, cynet):
cynet = self.get_cynet(cynet)
data = cynet.get_first_view()
if data is None: return None # view does not exist
nodes = data['elements']['nodes']
X = []
for node in nodes:
# id is an internal id, Gene is our key
X.append({
'id': str(node['data']['id']),
'x': node['position']['x'],
'y': node['position']['y'],
'Gene': node['data']['Gene']
})
t_xy = pd.DataFrame(X)
return t_xy
def cynet_save(self, cynet, s_file="x.png"):
def save_image(s_file, data):
f = open(s_file, 'wb')
f.write(data)
f.close()
cynet = self.get_cynet(cynet)
s_ext = s_file.upper()
if s_ext.endswith('.PNG'):
save_image(s_file, cynet.get_png())
elif s_ext.endswith('.PDF'):
save_image(s_file, cynet.get_pdf())
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/'
+ 'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
print(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_create_view(self):
print('\n---------- CyNetworkView Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
all_values = view1.get_values()
print(all_values)
def test_view_api(self):
print('\n---------- View API test start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
print(nd)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
self.assertEqual(0, view1.get_x())
view1.set_x(100)
self.assertEqual(100, view1.get_value('NODE_X_LOCATION'))
new_values = {}
for key in nd.keys():
suid = nd[key]
new_values[suid] = 'red'
view.update_node_views('NODE_FILL_COLOR', new_values)
new_values_name = {}
for node_name in new_nodes:
new_values_name[node_name] = 'pink'
print('---------- New Fill colors -----------')
print(new_values_name)
view.update_node_views('NODE_FILL_COLOR', new_values_name, key_type='name')
view.update_network_view('NETWORK_BACKGROUND_PAINT', 'red')
net_view = view.get_network_view_as_dict()
bg_paint = net_view['NETWORK_BACKGROUND_PAINT']
self.assertEqual('#FF0000', bg_paint)
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(
dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'], sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net, name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count, (original_column_count+table_column_count-1))
print('\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/' +
'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
pp(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_create_view(self):
print('\n---------- CyNetworkView Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
all_values = view1.get_values()
print(all_values)
def test_view_api(self):
print('\n---------- View API test start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
print(nd)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
self.assertEqual(0, view1.get_x())
view1.set_x(100)
self.assertEqual(100, view1.get_value('NODE_X_LOCATION'))
new_values = {}
for key in nd.keys():
suid = nd[key]
new_values[suid] = 'red'
view.update_node_views('NODE_FILL_COLOR', new_values)
new_values_name = {}
for node_name in new_nodes:
new_values_name[node_name] = 'pink'
view.update_node_views('NODE_FILL_COLOR',
new_values_name,
key_type='name')
view.update_network_view('NETWORK_BACKGROUND_PAINT', 'red')
net_view = view.get_network_view_as_dict()
bg_paint = net_view['NETWORK_BACKGROUND_PAINT']
self.assertEqual('#FF0000', bg_paint)
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'],
sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net,
name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count,
(original_column_count + table_column_count - 1))
print(
'\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
g.get_adjacency()
type(g.get_adjacency())
g.get_adjacency()._get_data()
type(g.get_adjacency()._get_data())
type(g.get_adjacency().data)
g.get_adjacency().data
g.get_adjacency()._hash_()
g.get_adjacency().__hash__()
g.get_adjacency().__hash__(h)
g.get_adjacency().__hash__(g)
g.get_adjacency().shape
pip install py2cytoscape
import json
from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient()
print(json.dumps(cy.status(), indent=4))
from igraph import *
g = Graph.Read_Adjacency('r_data_science_ch2_fig2.1.txt')
cy.network.create_from_igraph(g)
help(Graph.Read_GML)
from lesmis import *
loadGraphFromGml()
g
from lesmis import LesMis as lm
lm._g
from lesmis import LesMis as lm
lm.getGraph()
from lesmis import LesMis as lm
from lesmis import LesMis
lm = LesMis()
from lesmis import LesMis
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/'
+ 'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
pp(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(
dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'], sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net, name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count, (original_column_count+table_column_count-1))
print('\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/' +
'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
pp(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'],
sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net,
name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count,
(original_column_count + table_column_count - 1))
print(
'\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
