def test_external_with_successful_hidefdatafile_from_docker(self):
er = cdapsutil.ExternalResultsRunner()
cd = cdapsutil.CommunityDetection(runner=er)
datafile = os.path.join(self.get_data_dir(), 'cdhidef:0.2.2.out')
net_cx = self.get_human_hiv_as_nice_cx()
hier_net = cd.run_community_detection(net_cx=net_cx,
algorithm=datafile)
self.assertEqual(105, len(hier_net.get_nodes()))
self.assertEqual(121, len(hier_net.get_edges()))
self.assertEqual('cdhidef:0.2.2.out_(none)_HIV-human PPI',
hier_net.get_name())
self.assertEqual(
'0',
hier_net.get_network_attribute('__CD_OriginalNetwork')['v'])
def test_apply_style(self):
temp_dir = tempfile.mkdtemp()
try:
net_cx = ndex2.nice_cx_network.NiceCXNetwork()
cd = cdapsutil.CommunityDetection()
cd._apply_style(net_cx)
res = net_cx.get_opaque_aspect('cyVisualProperties')
self.assertEqual('network', res[0]['properties_of'])
net_cx = ndex2.nice_cx_network.NiceCXNetwork()
cd._apply_style(net_cx,
style=os.path.join(self.get_data_dir(),
'hiv_human_ppi.cx'))
altres = net_cx.get_opaque_aspect(('cyVisualProperties'))
self.assertNotEqual(res, altres)
finally:
shutil.rmtree(temp_dir)
def test_run_community_detection_with_all_algorithms(self):
sr = self.get_service_runner()
cd_dict = self.get_algorithms()
algos = []
for algo in cd_dict.keys():
algos.append(algo)
self.assertTrue(len(algos) > 0)
net_cx = self.get_human_hiv_as_nice_cx()
cd = cdapsutil.CommunityDetection(runner=sr)
failures = []
for algo in algos:
try:
hier_net = cd.run_community_detection(net_cx=net_cx,
algorithm=algo)
self.assertTrue(hier_net is not None)
self.assertTrue(len(hier_net.get_nodes()) > 0)
self.assertTrue(algo in hier_net.get_name())
except cdapsutil.CommunityDetectionError as ce:
failures.append(algo + ' failed : ' + str(ce))
self.assertEqual('', ' '.join(failures))
def test_service_with_successful_mock_data(self):
sr = cdapsutil.ServiceRunner(service_endpoint='http://foo',
max_retries=1,
poll_interval=0)
cd = cdapsutil.CommunityDetection(runner=sr)
net_cx = self.get_human_hiv_as_nice_cx()
json_res = self.get_infomap_res_as_dict()
with requests_mock.Mocker() as m:
m.post('http://foo', json={'id': 'taskid'}, status_code=202)
m.get('http://foo/taskid/status',
status_code=200,
json={'progress': 100})
m.get('http://foo/taskid', status_code=200, json=json_res)
hier_net = cd.run_community_detection(net_cx, algorithm='infomap')
self.assertEqual(68, len(hier_net.get_nodes()))
self.assertEqual(67, len(hier_net.get_edges()))
self.assertEqual('infomap_(none)_HIV-human PPI',
hier_net.get_name())
self.assertEqual(
'0',
hier_net.get_network_attribute('__CD_OriginalNetwork')['v'])
def test_run_community_detection_with_all_algorithms_via_docker(self):
cd_dict = self.get_algorithms()
algos = []
for algo in cd_dict.keys():
algos.append(cd_dict[algo]['dockerImage'])
self.assertTrue(len(algos) > 0)
net_cx = self.get_human_hiv_as_nice_cx()
cd = cdapsutil.CommunityDetection(runner=cdapsutil.DockerRunner())
failures = []
for algo in algos:
temp_dir = tempfile.mkdtemp(dir=os.getcwd())
try:
hier_net = cd.run_community_detection(net_cx=net_cx,
algorithm=algo,
temp_dir=temp_dir)
self.assertTrue(hier_net is not None)
self.assertTrue(len(hier_net.get_nodes()) > 0)
self.assertTrue(algo in hier_net.get_name())
except cdapsutil.CommunityDetectionError as ce:
failures.append(algo + ' failed : ' + str(ce))
finally:
shutil.rmtree(temp_dir)
self.assertEqual('', ' '.join(failures))
def test_constructor_none_for_runner(self):
try:
cdapsutil.CommunityDetection(runner=None)
self.fail('Expected CommunityDetectionError')
except cdapsutil.CommunityDetectionError as ce:
self.assertEqual('runner is None', str(ce))
def test_get_node_dictionary(self):
net_cx = self.get_human_hiv_as_nice_cx()
cd = cdapsutil.CommunityDetection()
node_dict = cd._get_node_dictionary(net_cx)
self.assertEqual(471, len(node_dict))
self.assertEqual('REV', node_dict[738])