def test_manual_build(self):
print('Testing: Build from empty nice cx')
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
fox_node_id = niceCx.create_node(node_name='Fox')
mouse_node_id = niceCx.create_node(node_name='Mouse')
bird_node_id = niceCx.create_node(node_name='Bird')
fox_bird_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=bird_node_id, edge_interaction='interacts-with')
fox_mouse_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=mouse_node_id, edge_interaction='interacts-with')
niceCx.add_node_attribute(property_of=fox_node_id, name='Color', values='Red')
niceCx.add_node_attribute(property_of=mouse_node_id, name='Color', values='Gray')
niceCx.add_node_attribute(property_of=bird_node_id, name='Color', values='Blue')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
def test_manual_build(self):
print('Testing: Build from empty nice cx')
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
fox_node_id = niceCx.create_node(node_name='Fox')
mouse_node_id = niceCx.create_node(node_name='Mouse')
bird_node_id = niceCx.create_node(node_name='Bird')
fox_bird_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=bird_node_id, edge_interaction='interacts-with')
fox_mouse_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=mouse_node_id, edge_interaction='interacts-with')
niceCx.add_node_attribute(property_of=fox_node_id, name='Color', values='Red')
niceCx.add_node_attribute(property_of=mouse_node_id, name='Color', values='Gray')
niceCx.add_node_attribute(property_of=bird_node_id, name='Color', values='Blue')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
def test_load_edges(self):
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
niceCx.create_node(id=1,
node_name='node%s' % str(1),
node_represents='ABC')
niceCx.create_node(id=2,
node_name='node%s' % str(2),
node_represents='DEF')
niceCx.create_edge(id=1,
edge_source=1,
edge_target=2,
edge_interaction='neighbor')
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
self.assertTrue(upload_message)
def test_load_nodes(self):
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
gene_list = [
'OR2J3', 'AANAT', 'CCDC158', 'PLAC8L1', 'CLK1', 'GLTP', 'PITPNM2',
'TRAPPC8', 'EIF2S2', 'ST14', 'NXF1', 'H3F3B', 'FOSB', 'MTMR4',
'USP46', 'CDH11', 'ENAH', 'CNOT7', 'STK39', 'CAPZA1', 'STIM2',
'DLL4', 'WEE1', 'MYO1D', 'TEAD3'
]
for i in range(1, 10):
niceCx.create_node(id=i,
node_name='node%s' % str(i),
node_represents=gene_list[i])
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
self.assertTrue(upload_message)
def test_pandas_loading(self):
path_to_network = os.path.join(path_this, 'MDA1.txt')
with open(path_to_network, 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,
delimiter='\t',
engine='python',
names=header)
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
for index, row in df.iterrows():
niceCx.create_node(id=row['Bait'],
node_name=row['Bait'],
node_represents=row['Bait'])
niceCx.create_node(id=row['Prey'],
node_name=row['Prey'],
node_represents=row['Prey'])
niceCx.create_edge(id=index,
edge_source=row['Bait'],
edge_target=row['Prey'],
edge_interaction='interacts-with')
niceCx.add_metadata_stub('nodes')
niceCx.add_metadata_stub('edges')
if niceCx.nodeAttributes:
niceCx.add_metadata_stub('nodeAttributes')
if niceCx.edgeAttributes:
niceCx.add_metadata_stub('edgeAttributes')
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
#print(df)
my_df = pd.DataFrame(data=[(4, 14), (5, 15), (6, 16), (7, 17)],
index=range(0, 4),
columns=['A', 'B'])
self.assertIsNotNone(my_df)
def test_data_types_with_special_chars2(self):
self.assertFalse(upload_username == 'username')
niceCx = ndex2.create_empty_nice_cx()
fox_node_id = niceCx.create_node(node_name='A#"')
mouse_node_id = niceCx.create_node(node_name='B!@#$%')
bird_node_id = niceCx.create_node(node_name='*&^%^$')
fox_bird_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=bird_node_id, edge_interaction='&"""""""')
fox_mouse_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=mouse_node_id, edge_interaction='//////\\\\\\')
niceCx.add_node_attribute(property_of=fox_node_id, name='Color', values='Red')
niceCx.add_node_attribute(property_of=mouse_node_id, name='Color', values='Gray')
niceCx.add_node_attribute(property_of=bird_node_id, name='Color', values='Blue')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
spec_char_network_uuid = upload_message.split('\\')[-1]
#niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='fc63173e-df66-11e7-adc1-0ac135e8bacf') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
self.assertTrue(upload_message)
def test_data_types_with_special_chars2(self):
self.assertFalse(upload_username == 'username')
niceCx = ndex2.create_empty_nice_cx()
fox_node_id = niceCx.create_node(node_name='A#"')
mouse_node_id = niceCx.create_node(node_name='B!@#$%')
bird_node_id = niceCx.create_node(node_name='*&^%^$')
fox_bird_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=bird_node_id, edge_interaction='&"""""""')
fox_mouse_edge = niceCx.create_edge(edge_source=fox_node_id, edge_target=mouse_node_id, edge_interaction='//////\\\\\\')
niceCx.add_node_attribute(property_of=fox_node_id, name='Color', values='Red')
niceCx.add_node_attribute(property_of=mouse_node_id, name='Color', values='Gray')
niceCx.add_node_attribute(property_of=bird_node_id, name='Color', values='Blue')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
spec_char_network_uuid = upload_message.split('\\')[-1]
#niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='fc63173e-df66-11e7-adc1-0ac135e8bacf') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
self.assertTrue(upload_message)
def test_manual_build(self):
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
fox_node_id = niceCx.create_node(node_name='Fox')
mouse_node_id = niceCx.create_node(node_name='Mouse')
bird_node_id = niceCx.create_node(node_name='Bird')
fox_bird_edge = niceCx.create_edge(edge_source=fox_node_id,
edge_target=bird_node_id,
edge_interaction='interacts-with')
fox_mouse_edge = niceCx.create_edge(edge_source=fox_node_id,
edge_target=mouse_node_id,
edge_interaction='interacts-with')
niceCx.add_node_attribute(property_of=fox_node_id,
name='Color',
values='Red')
niceCx.add_node_attribute(property_of=mouse_node_id,
name='Color',
values='Gray')
niceCx.add_node_attribute(property_of=bird_node_id,
name='Color',
values='Blue')
def test_create_from_small_cx(self):
my_cx = [{
"numberVerification": [{
"longNumber": 281474976710655
}]
}, {
"metaData": [{
"consistencyGroup": 1,
"elementCount": 2,
"idCounter": 2,
"name": "nodes",
"version": "1.0"
}, {
"consistencyGroup": 1,
"elementCount": 1,
"idCounter": 1,
"name": "edges",
"version": "1.0"
}]
}, {
"nodes": [{
"@id": 1,
"n": "node1",
"r": "ABC"
}, {
"@id": 2,
"n": "node2",
"r": "DEF"
}]
}, {
"edges": [{
"@id": 1,
"s": 1,
"t": 2,
"i": "neighbor"
}]
}, {
"status": [{
"error": "",
"success": True
}]
}]
#niceCx = NiceCXNetwork(cx=my_cx)
#data = [('Source', 'Target', 'interaction', 'EdgeProp'), ('ABC', 'DEF', 'interacts-with', 'Edge property 1'), ('DEF', 'XYZ', 'neighbor-of', 'Edge property 2')]
#df = pd.DataFrame.from_records(data)
#niceCx = NiceCXNetwork(pandas_df=df)
df = pd.DataFrame.from_items([
('Source', ['ABC', 'DEF']), ('Target', ['DEF', 'XYZ']),
('Interaction', ['interacts-with', 'neighbor-of']),
('EdgeProp', ['Edge property 1', 'Edge property 2'])
])
niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
niceCx.create_from_pandas(df,
source_field='Source',
target_field='Target',
edge_attr=['EdgeProp'],
edge_interaction='Interaction')
niceCx = '' #NiceCXNetwork(server='public.ndexbio.org', uuid='f1dd6cc3-0007-11e6-b550-06603eb7f303')
def test_create_empty_nice_cx(self):
net = ndex2.create_empty_nice_cx()
self.assertEqual(None, net.get_name())
self.assertEqual(0, len(net.get_nodes()))
self.assertEqual(0, len(net.get_edges()))