def test_update_network_with_empty_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'])
newnet = NiceCXNetwork()
newres = newnet.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('PRIVATE', netsum['visibility'])
self.assertEqual(False, netsum['isReadOnly'])
self.assertEqual(0, netsum['edgeCount'])
self.assertEqual(0, 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_upload_to_success(self):
with requests_mock.mock() as m:
resurl = client.DEFAULT_SERVER + '/v2/network/asdf'
m.get(self.get_rest_admin_status_url(),
json=self.get_rest_admin_status_dict("2.4.0"))
m.post(client.DEFAULT_SERVER + '/v2/network',
request_headers={'Connection': 'close'},
status_code=1,
text=resurl)
net = NiceCXNetwork()
net.create_node('bob')
res = net.upload_to(client.DEFAULT_SERVER, 'bob', 'warnerbrandis',
user_agent='jeez')
self.assertEqual(res, resurl)
decode_txt = m.last_request.text.read().decode('UTF-8')
self.assertEqual(m.last_request.headers['User-Agent'],
client.userAgent + ' jeez')
self.assertTrue('Content-Disposition: form-data; name='
'"CXNetworkStream"; filename='
'"filename"' in decode_txt)
self.assertTrue('Content-Type: application/'
'octet-stream' in decode_txt)
self.assertTrue('{"nodes": [{' in decode_txt)
self.assertTrue('"@id": 0' in decode_txt)
self.assertTrue('"n": "bob"' in decode_txt)
self.assertTrue('"r": "bob"' in decode_txt)
self.assertTrue('{"status": [{"' in decode_txt)
self.assertTrue('"error": ""' in decode_txt)
self.assertTrue('"success": true' in decode_txt)
def test_bad_nodes_add_edge(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
node1_id = niceCx_creatures.create_node(node_name=324)
node2_id = niceCx_creatures.create_node(node_name=453)
niceCx_creatures.create_edge(edge_source=node1_id, edge_target=node2_id, edge_interaction=['inte'])
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_node_attr(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
fox_node = niceCx_creatures.create_node(node_name=453)
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values=['Red',"tree"])
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_nodes_add_edge(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
node1_id = niceCx_creatures.create_node(node_name=324)
node2_id = niceCx_creatures.create_node(node_name=453)
niceCx_creatures.create_edge(edge_source=node1_id, edge_target=node2_id, edge_interaction=['inte'])
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_node_attr(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
fox_node = niceCx_creatures.create_node(node_name=453)
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values=['Red',"tree"])
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_add_bad_net_attrs(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test")
niceCx_creatures.create_node(node_name="Fox")
niceCx_creatures.set_network_attribute(name="version", values="1.0")
print(niceCx_creatures)
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_add_bad_net_attrs(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test")
niceCx_creatures.create_node(node_name="Fox")
niceCx_creatures.set_network_attribute(name="version", values="1.0")
print(niceCx_creatures)
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_edge_attr(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
node1_id = niceCx_creatures.create_node(node_name=324)
node2_id = niceCx_creatures.create_node(node_name=453)
edge = niceCx_creatures.create_edge(edge_source=node1_id, edge_target=node2_id, edge_interaction='inte')
niceCx_creatures.add_edge_attribute(property_of=edge, name= "djks", values= "jfkl")
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_edge_attr(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
node1_id = niceCx_creatures.create_node(node_name=324)
node2_id = niceCx_creatures.create_node(node_name=453)
edge = niceCx_creatures.create_edge(edge_source=node1_id, edge_target=node2_id, edge_interaction='inte')
niceCx_creatures.add_edge_attribute(property_of=edge, name= "djks", values= "jfkl")
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_add_int_attr(self):
niceCx = NiceCXNetwork()
int_node = niceCx.create_node(node_name="testint")
niceCx.add_node_attribute(property_of=int_node, name='Size', values=1, type="integer")
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', uuid=UUID, username=upload_username, password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "integer")
def test_add_lst_flt(self):
niceCx = NiceCXNetwork()
list_float_node = niceCx.create_node(node_name="testlstflt")
niceCx.add_node_attribute(property_of=list_float_node, name='Too many scores', values=[15.3,43.6,-34.0,43.3], type="list_of_float")
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', uuid=UUID, username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "list_of_double")
def test_add_flt(self):
niceCx = NiceCXNetwork()
float_node = niceCx.create_node(node_name="testflt")
niceCx.add_node_attribute(property_of=float_node,
name='Score',
values=1.0,
type="float")
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(
server='dev.ndexbio.org',
uuid=UUID,
username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "double")
def test_load_edges(self):
self.assertFalse(upload_username == 'username')
nice_cx = NiceCXNetwork()
node_id_1 = nice_cx.create_node(node_name='node%s' % str(1), node_represents='ABC')
node_id_2 = nice_cx.create_node(node_name='node%s' % str(2), node_represents='DEF')
edge_id_1 = nice_cx.create_edge(edge_source=node_id_1, edge_target=node_id_2, edge_interaction='neighbor')
citation1 = nice_cx.add_citation(id=0, title='Hi 1', identifier='pmid:28947956')
nice_cx.add_edge_citations(edge_id_1, citation1.get('@id'))
supports1 = nice_cx.add_support(id=0, text='Hi supports 1')
nice_cx.add_edge_supports(edge_id_1, supports1.get('@id'))
nice_cx.set_name('Citation testing')
upload_message = nice_cx.upload_to(upload_server, upload_username, upload_password)
print(upload_message)
def test_add_lst_int(self):
niceCx = NiceCXNetwork()
list_int_node = niceCx.create_node(node_name="testlstint")
niceCx.add_node_attribute(property_of=list_int_node,
name='Too many sizes',
values=[1, 2, 3, 4, 5],
type="list_of_integer")
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(
server='dev.ndexbio.org',
uuid=UUID,
username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "list_of_integer")
def test_load_edges(self):
self.assertFalse(upload_username == 'username')
nice_cx = NiceCXNetwork()
node_id_1 = nice_cx.create_node(node_name='node%s' % str(1), node_represents='ABC')
node_id_2 = nice_cx.create_node(node_name='node%s' % str(2), node_represents='DEF')
edge_id_1 = nice_cx.create_edge(edge_source=node_id_1, edge_target=node_id_2, edge_interaction='neighbor')
citation1 = nice_cx.add_citation(id=0, title='Hi 1', identifier='pmid:28947956')
nice_cx.add_edge_citations(edge_id_1, citation1.get('@id'))
supports1 = nice_cx.add_support(id=0, text='Hi supports 1')
nice_cx.add_edge_supports(edge_id_1, supports1.get('@id'))
nice_cx.set_name('Citation testing')
upload_message = nice_cx.upload_to(upload_server, upload_username, upload_password)
print(upload_message)
def test_bad_name_add_node(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
node1_id = niceCx_creatures.create_node(node_name=54, node_represents="Tree")
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_name_add_node(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
node1_id = niceCx_creatures.create_node(node_name=54, node_represents="Tree")
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_set_name(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name(43)
niceCx_creatures.create_node(node_name="tree")
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
# #### to_networkx()
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
networkx_network = NiceCX_creatures.to_networkx()
# #### to_pandas_dataframe()
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
pandas_network = NiceCX_creatures.to_pandas_dataframe()
# #### upload(ndex_server, username, password, update_uuid=None)
# In[ ]:
upload_message = NiceCX_creatures.upload_to("http://public.ndexbio.org",
"ENTER YOUR USER",
"ENTER YOUR PASSWORD")
uuid = upload_message.rpartition('/')[-1]
# ##### apply_template(server, username, password, uuid)
# ##### addNode(json_obj=None)
# ##### add_edge_element(json_obj=None, edge)
# ##### addNetworkAttribute(json_obj=None)
def test_set_name(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name(43)
niceCx_creatures.create_node(node_name="tree")
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
