def test_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
fac = DefaultNetworkXFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue(0 in g)
if float(networkx.__version__) >= 2:
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
else:
nodelist = g.nodes(data=True)
edgelist = g.edges(data=True)
self.assertEqual('first', nodelist[0][1]['name'])
self.assertEqual('second', nodelist[1][1]['name'])
self.assertEqual(0, edgelist[0][0])
self.assertEqual(1, edgelist[0][1])
self.assertEqual(None, edgelist[0][2]['interaction'])
def test_add_member_genes(self):
net = NiceCXNetwork()
aid = net.create_node('a')
net.set_node_attribute(aid, NodeMemberUpdator.TYPE, 'proteinfamily')
notinid = net.create_node('x')
net.set_node_attribute(notinid, NodeMemberUpdator.TYPE,
'proteinfamily')
mock = GeneSymbolSearcher(bclient=None)
mock.get_symbol = MagicMock(side_effect=['', None])
updator = NodeMemberUpdator(None, None, genesearcher=mock)
aidnode = net.get_node(aid)
res = updator._add_member_genes(net, aidnode, [])
self.assertEqual(['No proteins obtained for node: ' + str(aidnode)],
res)
notinidnode = net.get_node(notinid)
res = updator._add_member_genes(net, notinidnode, ['x'])
self.assertTrue('For node ' + str(notinidnode) +
' No gene symbol found for x. Skipping.' in res)
self.assertTrue('Not a single gene symbol found. Skipping insertion '
'of member attribute for node ' +
str(notinidnode) in res)
def get_nice_cx_network_from_clusterfile(inputfile):
"""
:param inputfile:
:return:
"""
network = NiceCXNetwork()
network.set_name('clustertocx from ' + str(os.path.basename(os.path.dirname(inputfile))))
with open(inputfile, 'r') as f:
data = f.read()
node_map = {}
protein_map = {}
for line in data.split(';'):
slist = line.split(',')
if len(slist) != 3:
sys.stderr.write(line + ' does not have appropriate number of columns. skipping\n')
continue
if slist[2].startswith('c-c'):
target_is_protein = False
else:
target_is_protein = True
if slist[0] not in node_map:
source_node_id = network.create_node(slist[0])
node_map[slist[0]] = source_node_id
network.add_node_attribute(property_of=source_node_id, name='suid', values=int(slist[0]), type='long')
network.add_node_attribute(property_of=source_node_id, name='type', values='term', type='string')
else:
source_node_id = node_map[slist[0]]
if target_is_protein:
if slist[0] not in protein_map:
protein_map[slist[0]] = set()
protein_map[slist[0]].add(slist[1])
else:
if slist[1] not in protein_map[slist[0]]:
protein_map[slist[0]].add(slist[1])
else:
target_node_id = network.create_node(slist[1])
network.create_edge(source_node_id, target_node_id, 'Child-Parent')
network.add_node_attribute(property_of=target_node_id, name='suid', values=int(slist[1]), type='long')
network.add_node_attribute(property_of=target_node_id, name='type', values='term', type='string')
node_map[slist[1]] = target_node_id
for nodename in protein_map:
genelist = protein_map[nodename]
if len(genelist) > 0:
genesymbol_list = []
for entry in genelist:
genesymbol_list.append(entry)
network.add_node_attribute(property_of=node_map[nodename], name='member', values=genesymbol_list,
type='list_of_string')
network.add_node_attribute(property_of=node_map[nodename], name='type', values='complex', type='string',
overwrite=True)
del node_map
del protein_map
return network
def test_add_edge_to_network_using_src_target_node_ids(self):
net = NiceCXNetwork()
src_node = net.create_node('node1')
target_node = net.create_node('node2')
ne = NetworkEdge(edge_id=1,
source_node_id=src_node,
target_node_id=target_node,
interaction='activates')
self.assertEqual(0, len(net.get_edges()))
edge_id = ne.add_edge_to_network(net_cx=net)
self.assertEqual(1, len(net.get_edges()))
nef = NetworkEdgeFactory()
new_ne = nef.get_network_edge_from_network(net_cx=net, edge_id=edge_id)
self.assertEqual('node1', new_ne.get_source_node_name())
self.assertEqual('node2', new_ne.get_target_node_name())
self.assertEqual(src_node, new_ne.get_source_node_id())
self.assertEqual(target_node, new_ne.get_target_node_id())
self.assertEqual('activates', new_ne.get_interaction())
self.assertEqual([], new_ne.get_attributes())
new_ne.remove_edge_from_network(net_cx=net)
self.assertEqual(0, len(net.get_edges()))
def test_update_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.put(client.DEFAULT_SERVER + '/v2/network/abcd',
request_headers={'Connection': 'close'},
status_code=1,
text=resurl)
net = NiceCXNetwork()
net.create_node('bob')
res = net.update_to('abcd', 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_simple_create(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Food Web")
fox_node = niceCx_creatures.create_node(node_name='Fox')
mouse_node = niceCx_creatures.create_node(node_name='Mouse')
bird_node = niceCx_creatures.create_node(node_name='Bird')
fox_bird_edge = niceCx_creatures.create_edge(
edge_source=fox_node,
edge_target=bird_node,
edge_interaction='interacts-with')
fox_mouse_edge = niceCx_creatures.create_edge(
edge_source=fox_node,
edge_target=mouse_node,
edge_interaction='interacts-with')
niceCx_creatures.add_node_attribute(property_of=fox_node,
name='Color',
values='Red')
niceCx_creatures.add_node_attribute(property_of=mouse_node,
name='Color',
values='Gray')
niceCx_creatures.add_node_attribute(property_of=bird_node,
name='Color',
values='Blue')
niceCx_creatures.add_edge_attribute(property_of=fox_mouse_edge,
name='Hunted',
values='On the ground')
print(niceCx_creatures.get_node_attribute(fox_node, 'Color'))
def test_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
fac = DefaultNetworkXFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue(0 in g)
if NETWORKX_MAJOR_VERSION >= 2:
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
else:
nodelist = g.nodes(data=True)
edgelist = g.edges(data=True)
self.assertEqual('first', nodelist[0][1]['name'])
self.assertEqual('second', nodelist[1][1]['name'])
self.assertEqual(0, edgelist[0][0])
self.assertEqual(1, edgelist[0][1])
self.assertEqual(None, edgelist[0][2]['interaction'])
def test_context(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test")
niceCx_creatures.create_node(node_name="Fox")
try:
self.assertRaises(Exception, niceCx_creatures.set_context("hkjhnk"))
except Exception as e:
print('Bad context exception was caught')
def test_context(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test")
niceCx_creatures.create_node(node_name="Fox")
try:
self.assertRaises(Exception, niceCx_creatures.set_context("hkjhnk"))
except Exception as e:
print('Bad context exception was caught')
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_to_networkx_simple_graph_default_mode(self):
net = NiceCXNetwork(mode='default')
net.set_name('mynetwork')
net.create_node('node0')
net.create_node('node1')
net.create_edge(edge_source=0, edge_target=1)
g = net.to_networkx()
self.assertEqual(g.graph['name'], 'mynetwork')
self.assertEqual(2, len(g))
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__str__(self):
net = NiceCXNetwork()
self.assertEqual('nodes: 0 \n edges: 0', str(net))
net.create_node('foo')
self.assertEqual('nodes: 1 \n edges: 0', str(net))
net.create_node('foo2')
net.create_node('foo3')
self.assertEqual('nodes: 3 \n edges: 0', str(net))
net.create_edge(edge_source=0, edge_target=1)
self.assertEqual('nodes: 3 \n edges: 1', str(net))
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_one_node_no_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue('first' in g)
nodelist = g.nodes(data=True)
self.assertEqual('first', nodelist['first']['represents'])
def test_remove_edge_from_network(self):
net = NiceCXNetwork()
src_node = net.create_node('node1')
target_node = net.create_node('node2')
edge_id = net.create_edge(edge_source=src_node,
edge_target=target_node)
self.assertEqual(1, len(net.get_edges()))
nef = NetworkEdgeFactory()
ne = nef.get_network_edge_from_network(net_cx=net, edge_id=edge_id)
ne.remove_edge_from_network(net_cx=net)
self.assertEqual(0, len(net.get_edges()))
def test_one_node_no_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue('first' in g)
nodelist = g.nodes(data=True)
self.assertEqual('first', nodelist['first']['represents'])
def test_one_node_no_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = DefaultNetworkXFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue(0 in g)
nodelist = g.nodes(data=True)
if NETWORKX_MAJOR_VERSION >= 2:
self.assertEqual('first', nodelist[0]['name'])
else:
self.assertEqual('first', nodelist[0][1]['name'])
def test_one_node_no_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = DefaultNetworkXFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue(0 in g)
nodelist = g.nodes(data=True)
if float(networkx.__version__) >= 2:
self.assertEqual('first', nodelist[0]['name'])
else:
self.assertEqual('first', nodelist[0][1]['name'])
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_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_one_node_no_edge_network_legacytrue(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = DefaultNetworkXFactory(legacymode=True)
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue(0 in g)
if float(networkx.__version__) >= 2:
nodelist = list(g.nodes(data=True))
else:
nodelist = g.nodes(data=True)
self.assertEqual('first', nodelist[0][1]['name'])
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_update_no_nodes_start_with_uniprot(self):
updater = UniProtToGeneSymbolUpdater()
net = NiceCXNetwork()
nodeone = net.create_node(node_name='node1', node_represents='node1')
nodetwo = net.create_node(node_name='node2', node_represents='node2')
res = updater.update(net)
self.assertEqual(0, len(res))
self.assertEqual('node1', net.get_node(nodeone)['n'])
self.assertEqual('node2', net.get_node(nodetwo)['n'])
def test_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue('first' in g)
self.assertTrue('second' in g)
edgelist = list(g.edges(data=True))
self.assertTrue(('first' == edgelist[0][0] and 'second' == edgelist[0][1]) or
('second' == edgelist[0][0] and 'first' == edgelist[0][1]))
self.assertEqual(None, edgelist[0][2]['interaction'])
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_one_node_network(self):
net = NiceCXNetwork()
node_one = net.create_node('first')
net.set_node_attribute(node_one,
'booleanattrib',
'false',
type='boolean')
net.set_node_attribute(node_one, 'integerattrib', '1', type='integer')
net.set_node_attribute(node_one, 'doubleattrib', '2.0', type='double')
net.set_node_attribute(node_one, 'longattrib', '3', type='long')
net.set_node_attribute(node_one,
'stringattrib',
'false',
type='string')
net.set_node_attribute(node_one,
'list_of_booleanattrib', ['True'],
type='list_of_boolean')
net.set_node_attribute(node_one,
'list_of_doubleattrib', ['4.0'],
type='list_of_double')
net.set_node_attribute(node_one,
'list_of_integerattrib', ['5'],
type='list_of_integer')
net.set_node_attribute(node_one,
'list_of_longattrib', ['6'],
type='list_of_long')
net.set_node_attribute(node_one,
'list_of_stringattrib', ['false'],
type='list_of_string')
net.set_name('bob')
fac = DefaultNetworkXFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue(0 in g)
if NETWORKX_MAJOR_VERSION >= 2:
nodelist = list(g.nodes(data=True))
else:
nodelist = g.nodes(data=True)
self.assertEqual('false', nodelist[0][1]['booleanattrib'])
self.assertEqual('1', nodelist[0][1]['integerattrib'])
self.assertEqual('2.0', nodelist[0][1]['doubleattrib'])
self.assertEqual('3', nodelist[0][1]['longattrib'])
self.assertEqual('false', nodelist[0][1]['stringattrib'])
self.assertEqual(['True'], nodelist[0][1]['list_of_booleanattrib'])
self.assertEqual(['4.0'], nodelist[0][1]['list_of_doubleattrib'])
self.assertEqual(['5'], nodelist[0][1]['list_of_integerattrib'])
self.assertEqual(['6'], nodelist[0][1]['list_of_longattrib'])
self.assertEqual(['false'], nodelist[0][1]['list_of_stringattrib'])
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_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue('first' in g)
self.assertTrue('second' in g)
edgelist = list(g.edges(data=True))
self.assertTrue(
('first' == edgelist[0][0] and 'second' == edgelist[0][1])
or ('second' == edgelist[0][0] and 'first' == edgelist[0][1]))
self.assertEqual(None, edgelist[0][2]['interaction'])
def test_apply_cytoscape_layout_networks_not_in_dict(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.layout = 'grid'
p.sifdir = temp_dir
mockpy4 = MagicMock()
mockpy4.import_network_from_file = MagicMock(return_value={})
loader = NDExNciPidLoader(p, py4cyto=mockpy4)
net = NiceCXNetwork()
for x in range(10):
net.create_node('node' + str(x))
try:
loader._apply_cytoscape_layout(net)
self.fail('Expected NDExNciPidLoaderError')
except NDExNciPidLoaderError as e:
self.assertTrue(str(e).startswith('Error network view'))
finally:
shutil.rmtree(temp_dir)
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_upload_network_with_no_network_attributes(self):
"""
So if one uploads a network with NO network attributes
to NDEx and then edits the network (setting name visibility, description)
via [updateNetworkSummary] [/v2/network/6b89b286-e142-11ec-b397-0ac135e8bacf/summary
the CX2 endpoint shows the changed network attributes, but the CX1
is missing the network attributes
:return:
"""
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')
res = client.save_new_network(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?')
self.assertEqual(netid, netsum['externalId'])
self.assertTrue('name' not in netsum, msg=str(netsum))
# okay now we have the network, lets update the name
# and description and then get the network back again
# via cx1 and cx2 endpoints
netname = 'ndex2-client integration test network' + str(
datetime.now())
client.update_network_profile(netid, {'name': netname})
netsum = self.wait_for_network_to_be_ready(client, netid)
self.assertIsNotNone(
netsum, 'Network is still not ready,'
' maybe server is busy?')
cx2_resp = client.get_network_as_cx2_stream(network_id=netid)
cx2_json = json.loads(cx2_resp.content)
net_attrs = None
for aspect in cx2_json:
print(aspect)
if 'networkAttributes' in aspect:
net_attrs = aspect['networkAttributes']
break
self.assertEqual([{'name': netname}], net_attrs)
client_resp = client.get_network_as_cx_stream(network_id=netid)
cx1_net = ndex2.create_nice_cx_from_raw_cx(
json.loads(client_resp.content))
self.assertEqual(netname, cx1_net.get_name(),
'Special test to expose '
'bug in NDEx server')
finally:
client.delete_network(netid)
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_create_edge_with_node_dict_passed_in_for_edge_ids(self):
net = NiceCXNetwork()
nodeone = net.get_node(net.create_node('node1'))
nodetwo = net.get_node(net.create_node('node2'))
edge_id = net.create_edge(edge_source=nodeone,
edge_target=nodetwo)
res = net.get_edge(edge_id)
self.assertEqual(edge_id, res[constants.EDGE_ID])
self.assertEqual(0, res[constants.EDGE_SOURCE])
self.assertEqual(1, res[constants.EDGE_TARGET])
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_attribute_to_node(self):
nef = Attribute(name='foo', value='someval')
net = NiceCXNetwork()
node_one = net.create_node('node1')
nef.add_attribute_to_node(net_cx=net, node_id=node_one)
e_attrs = net.get_node_attributes(node_one)
self.assertEqual(1, len(e_attrs))
self.assertEqual('foo', e_attrs[0]['n'])
self.assertEqual('someval', e_attrs[0]['v'])
def test_simple_create(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Food Web")
fox_node = niceCx_creatures.create_node(node_name='Fox')
mouse_node = niceCx_creatures.create_node(node_name='Mouse')
bird_node = niceCx_creatures.create_node(node_name='Bird')
fox_bird_edge = niceCx_creatures.create_edge(edge_source=fox_node, edge_target=bird_node, edge_interaction='interacts-with')
fox_mouse_edge = niceCx_creatures.create_edge(edge_source=fox_node, edge_target=mouse_node, edge_interaction='interacts-with')
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values='Red')
niceCx_creatures.add_node_attribute(property_of=mouse_node, name='Color', values='Gray')
niceCx_creatures.add_node_attribute(property_of=bird_node, name='Color', values='Blue')
niceCx_creatures.add_edge_attribute(property_of=fox_mouse_edge, name='Hunted', values='On the ground')
print(niceCx_creatures.get_node_attribute(fox_node, 'Color'))
def test_get_node_and_edge_items(self):
net = NiceCXNetwork()
nodeiter, edgeiter = net._get_node_and_edge_items()
nodelist = list(nodeiter)
self.assertEqual(0, len(nodelist))
edgelist = list(edgeiter)
self.assertEqual(0, len(edgelist))
net.create_node('foo')
net.create_edge(edge_source=0, edge_target=1)
nodeiter, edgeiter = net._get_node_and_edge_items()
nodelist = list(nodeiter)
self.assertEqual(1, len(nodelist))
self.assertEqual(nodelist[0], (0, {'@id': 0,
'n': 'foo', 'r': 'foo'}))
edgelist = list(edgeiter)
self.assertEqual(1, len(edgelist))
self.assertEqual(edgelist[0], (0, {'@id': 0, 's': 0, 't': 1}))
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_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_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)
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)