def test_load_large_sim_matrix(self):
#==========================================
# Create 2d array with 10,000,000 elements
#==========================================
n = 25000000
X = np.c_[np.random.randint(1,11,(n))].reshape(5000, 5000)
print('Array created')
X_cols = ['Col' + str(col) for col in range(0,5000)]
X_rows = ['Node' + str(x) for x in range(0, 5000)]
print('Labels created')
#==========================================
# Generate and upload network to NDEx
#==========================================
new_network_url = ndex2.load_matrix_to_ndex(X, X_cols, X_rows, self.params['ndex_server'], self.params['ndex_user'], self.params['ndex_pass'], 'matrix test')
uuid = new_network_url.split('/')[-1]
print('Upload complete')
#==========================================
# Get network from NDEx in np.array format
#==========================================
time.sleep(2)
try:
new_network, x_cols, y_rows = ndex2.get_matrix_from_ndex(self.params['ndex_server'], self.params['ndex_user'], self.params['ndex_pass'], uuid)
except Exception as e:
time.sleep(5)
new_network, x_cols, y_rows = ndex2.get_matrix_from_ndex(self.params['ndex_server'], self.params['ndex_user'], self.params['ndex_pass'], uuid)
print(new_network)
print('Download complete')
self.assertTrue(isinstance(new_network, np.ndarray))
def test_load_small_matrix(self):
X = np.array([[1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0],
[0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1]])
X_cols = [
'ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2',
'DEF2', 'GHI2', 'XYZ2', 'ABC3', 'DEF3', 'GHI3'
]
X_rows = [
'ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2',
'DEF2', 'GHI2', 'XYZ2', 'ABC3', 'DEF3', 'GHI3'
]
array_data_type = X.dtype.name
as_bytes = X.tobytes()
array_shape = X.shape
serialized = base64.b64encode(as_bytes)
deserialized = base64.b64decode(serialized)
print(
np.frombuffer(deserialized,
dtype=array_data_type).reshape(array_shape))
new_network_url = ndex2.load_matrix_to_ndex(X, X_cols, X_rows,
self.params['ndex_server'],
self.params['ndex_user'],
self.params['ndex_pass'],
'matrix test')
uuid = new_network_url.split('/')[-1]
time.sleep(2)
new_network, x_cols, y_rows = ndex2.get_matrix_from_ndex(
self.params['ndex_server'], self.params['ndex_user'],
self.params['ndex_pass'], uuid)
print(new_network)
self.assertTrue(new_network.shape == (15, 15))
def test_load_small_matrix(self):
X = np.array(
[[1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0],
[0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1]]
)
X_cols = ['ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2', 'DEF2', 'GHI2', 'XYZ2', 'ABC3',
'DEF3', 'GHI3']
X_rows = ['ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2', 'DEF2', 'GHI2', 'XYZ2', 'ABC3',
'DEF3', 'GHI3']
array_data_type = X.dtype.name
as_bytes = X.tobytes()
array_shape = X.shape
serialized = base64.b64encode(as_bytes)
deserialized = base64.b64decode(serialized)
print(np.frombuffer(deserialized, dtype=array_data_type).reshape(array_shape))
new_network_url = ndex2.load_matrix_to_ndex(X, X_cols, X_rows, self.params['ndex_server'], self.params['ndex_user'],
self.params['ndex_pass'], 'matrix test')
uuid = new_network_url.split('/')[-1]
time.sleep(2)
new_network, x_cols, y_rows = ndex2.get_matrix_from_ndex(self.params['ndex_server'], self.params['ndex_user'],
self.params['ndex_pass'], uuid)
print(new_network)
self.assertTrue(new_network.shape == (15, 15))
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1]])
X_cols = [
'ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2', 'DEF2',
'GHI2', 'XYZ2', 'ABC3', 'DEF3', 'GHI3'
]
X_rows = [
'ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2', 'DEF2',
'GHI2', 'XYZ2', 'ABC3', 'DEF3', 'GHI3'
]
if params['ndex_user'] == 'username':
print('************** WARNING!!!!! **************')
raise Exception(
'Please set the username and password before running this test')
new_network_url = ndex2.load_matrix_to_ndex(X, X_cols, X_rows,
params['ndex_server'],
params['ndex_user'],
params['ndex_pass'], 'matrix test')
uuid = new_network_url.split('/')[-1]
time.sleep(2)
new_network, x_cols, y_rows = ndex2.get_matrix_from_ndex(
params['ndex_server'], params['ndex_user'], params['ndex_pass'], uuid)
print(new_network)
[0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1]]
)
X_cols = ['ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2', 'DEF2',
'GHI2', 'XYZ2', 'ABC3', 'DEF3', 'GHI3']
X_rows = ['ABC', 'DEF', 'GHI', 'XYZ', 'ABC1', 'DEF1', 'GHI1', 'XYZ1', 'ABC2', 'DEF2',
'GHI2', 'XYZ2', 'ABC3', 'DEF3', 'GHI3']
if params['ndex_user'] == 'username':
print('************** WARNING!!!!! **************')
raise Exception('Please set the username and password before running this test')
new_network_url = ndex2.load_matrix_to_ndex(X, X_cols, X_rows, params['ndex_server'], params['ndex_user'],
params['ndex_pass'], 'matrix test')
uuid = new_network_url.split('/')[-1]
time.sleep(2)
new_network, x_cols, y_rows = ndex2.get_matrix_from_ndex(params['ndex_server'], params['ndex_user'],
params['ndex_pass'], uuid)
print(new_network)