def test_apply_simple_spring_layout(self):
net = NiceCXNetwork()
n_one = net.create_node('node1')
n_two = net.create_node('node2')
net.create_edge(n_one, n_two, 'links')
p = MagicMock()
p.datadir = 'datadir'
p.profile = 'foo'
p.organismloadplan = ndexloadbiogrid.get_organism_load_plan()
p.chemicalloadplan = ndexloadbiogrid.get_chemical_load_plan()
p.organismstyle = ndexloadbiogrid.get_organism_style()
p.chemstyle = ndexloadbiogrid.get_chemical_style()
p.biogridversion = '1.0.0'
p.skipdownload = False
loader = NdexBioGRIDLoader(p)
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(2, len(aspect))
# try with 19 nodes
net = NiceCXNetwork()
for x in range(0, 19):
net.create_node(str(x))
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(19, len(aspect))
# try with 99 nodes
net = NiceCXNetwork()
for x in range(0, 99):
net.create_node(str(x))
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(99, len(aspect))
# try with 101 nodes
net = NiceCXNetwork()
for x in range(0, 101):
net.create_node(str(x))
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(101, len(aspect))
def test_apply_simple_spring_layout(self):
net = NiceCXNetwork()
for x in range(2):
net.create_node('node' + str(x))
loader = NDExNciPidLoader(None)
loader._apply_simple_spring_layout(net)
res = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(2, len(res))
self.assertTrue('node' in res[0])
self.assertTrue(res[0]['node'] >= 0)
self.assertTrue('x' in res[0])
self.assertTrue('y' in res[0])
self.assertTrue('node' in res[1])
self.assertTrue(res[1]['node'] >= 1)
self.assertTrue('x' in res[1])
self.assertTrue('y' in res[1])
net = NiceCXNetwork()
for x in range(10):
net.create_node('node' + str(x))
loader._apply_simple_spring_layout(net)
self.assertEqual(10,
len(net.get_opaque_aspect('cartesianLayout')))
net = NiceCXNetwork()
for x in range(20):
net.create_node('node' + str(x))
loader._apply_simple_spring_layout(net)
self.assertEqual(20,
len(net.get_opaque_aspect('cartesianLayout')))
net = NiceCXNetwork()
for x in range(100):
net.create_node('node' + str(x))
loader._apply_simple_spring_layout(net)
self.assertEqual(100,
len(net.get_opaque_aspect('cartesianLayout')))
def test_apply_cytoscape_layout_networks_success(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.layout = 'grid'
p.sifdir = temp_dir
mockpy4 = MagicMock()
imp_res = {'networks': ['netid']}
mockpy4.import_network_from_file = MagicMock(return_value=imp_res)
mockpy4.export_network = MagicMock(return_value='')
loader = NDExNciPidLoader(p, py4cyto=mockpy4)
loader._ndexextra.extract_layout_aspect_from_cx = MagicMock(return_value={'cartesianLayout': []})
net = NiceCXNetwork()
for x in range(10):
net.create_node('node' + str(x))
loader._apply_cytoscape_layout(net)
self.assertEqual([{'cartesianLayout': []}],
net.get_opaque_aspect('cartesianLayout'))
finally:
shutil.rmtree(temp_dir)
def test_apply_template_network(self):
net = NiceCXNetwork()
net.set_name('foo')
creds = self.get_ndex_credentials_as_tuple()
client = self.get_ndex2_client()
template_net = ndex2.create_nice_cx_from_file(
TestNiceCXNetworkIntegration.GLYPICAN2_FILE)
netname = 'ndex2-client integration test network' + str(datetime.now())
template_net.set_name(netname)
res = client.save_new_network(template_net.to_cx(),
visibility='PRIVATE')
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?')
# verify we get the right exception for unauthorized
# call
try:
net.apply_template(creds['server'], netid)
self.fail('Expected NDExUnauthorizedError')
except NDExUnauthorizedError as ne:
self.assertTrue(
'NDEx_Unauthorized_Operation_Exception' in str(ne))
# okay try to apply template on valid network
net.apply_template(creds['server'],
netid,
username=creds['user'],
password=creds['password'])
cyvis = net.get_opaque_aspect(NiceCXNetwork.VISUAL_PROPERTIES)
self.assertEqual(
template_net.get_opaque_aspect(
NiceCXNetwork.CY_VISUAL_PROPERTIES), cyvis)
finally:
# delete network
client.delete_network(netid)
def test_update_network_containing_all_types(self):
updator = SpringLayoutUpdator()
net = NiceCXNetwork()
comp_attr = NodeLocationUpdator.LOCATION
ecnode = net.create_node(node_name='ecnode', node_represents='ecnoder')
net.set_node_attribute(ecnode, comp_attr,
SpringLayoutUpdator.EXTRACELLULAR)
rnode = net.create_node(node_name='rnode', node_represents='rnoder')
net.set_node_attribute(rnode, comp_attr,
SpringLayoutUpdator.RECEPTOR)
cnode = net.create_node(node_name='cnode', node_represents='cnoder')
net.set_node_attribute(cnode, comp_attr,
SpringLayoutUpdator.CYTOPLASM)
fnode = net.create_node(node_name='fnode', node_represents='fnoder')
net.set_node_attribute(fnode, comp_attr,
SpringLayoutUpdator.FACTOR)
pnode = net.create_node(node_name='pnode', node_represents='pnoder')
net.set_node_attribute(pnode, comp_attr,
SpringLayoutUpdator.PHENOTYPESLIST)
xnode = net.create_node(node_name='xnode', node_represents='xnoder')
self.assertEqual([], updator.update(net))
res = net.get_opaque_aspect(SpringLayoutUpdator.CARTESIAN_LAYOUT)
ydict = {}
for entry in res:
ydict[entry['node']] = entry['y']
self.assertTrue(ydict[ecnode] < 0.0)
self.assertTrue(ydict[rnode] < 0.0)
self.assertTrue(ydict[cnode] > -100.0)
self.assertTrue(ydict[fnode] > 0.0)
self.assertTrue(ydict[pnode] > 0.0)
def test_add_opaque_aspect_with_dict(self):
net_cx = NiceCXNetwork()
data = {'hi': 'blah'}
net_cx.add_opaque_aspect('hi', data)
res = net_cx.get_opaque_aspect('hi')
self.assertEqual([data], res)
def test_add_opaque_aspect_success(self):
net_cx = NiceCXNetwork()
data = ['hi']
net_cx.add_opaque_aspect('hi', data)
res = net_cx.get_opaque_aspect('hi')
self.assertEqual(data, res)
