def run(self, data):
logging.debug('Worker ID: ' + str(self.id) + ' Building finder '
'=========')
logging.debug(data)
kernel_file_url = data['kernel_url']
network_file_url = data['network_url']
query = data['query']
# Check finder exists or not
if kernel_file_url in self.__finders.keys():
logging.debug('Kernel found. No need to create finder')
finder = self.__finders[kernel_file_url]
else:
logging.debug('Building Finder...')
generator = KernelGenerator()
kernel = generator.create_kernel_from_file(kernel_file_url)
network = util.read_sif(network_file_url)
finder = SubNetworkFinder(kernel=kernel, network=network)
self.__finders[kernel_file_url] = finder
logging.debug('Building Finder... Done!')
# Now find subnet
logging.debug('******** Query: ' + str(query))
subnetwork = finder.get_sub_network(query)
logging.debug('========== Sub Network found: Size = ' +
str(len(subnetwork)))
return subnetwork
def run(self, data):
logging.debug('Worker ID: ' + str(self.id) + ' Building finder '
'=========')
logging.debug(data)
kernel_file_url = data['kernel_url']
network_file_url = data['network_url']
query = data['query']
# Check finder exists or not
if kernel_file_url in self.__finders.keys():
logging.debug('Kernel found. No need to create finder')
finder = self.__finders[kernel_file_url]
else:
logging.debug('Building Finder...')
generator = KernelGenerator()
kernel = generator.create_kernel_from_file(kernel_file_url)
network = util.read_sif(network_file_url)
finder = SubNetworkFinder(kernel=kernel, network=network)
self.__finders[kernel_file_url] = finder
logging.debug('Building Finder... Done!')
# Now find subnet
logging.debug('******** Query: ' + str(query))
subnetwork = finder.get_sub_network(query)
logging.debug('========== Sub Network found: Size = ' + str(len(
subnetwork)))
return subnetwork
def run(self, data):
# Parse input data
sif_url = data['network_url']
generator = KernelGenerator()
kernel = generator.create_kernel(sif_url)
logging.debug('========== Kernel computation finished =========')
req = client.post(KERNEL_FILE_SERVER + 'data',
data=util.get_kernel_as_string(kernel), stream=True)
file_id = req.json()['fileId']
# Register kernel information
kernel_id = str(uuid.uuid4())
kernel_file_url = KERNEL_FILE_SERVER + 'data/' + file_id
self.redis_conn.hset('kernels', kernel_id, kernel_file_url)
self.redis_conn.hset('kernel2network', kernel_id, sif_url)
logging.debug('Kernel File Server response Data = ' + str(req.json()))
result = {
'kernel_id': kernel_id,
'network': sif_url,
'kernel_file': kernel_file_url
}
return result
def run(network):
generator = KernelGenerator()
# First, read network file as table
small_net_df = pd.read_csv(network, sep='\t',
names=['source', 'interaction', 'target'])
print(small_net_df.shape)
sources = small_net_df['source']
targets = small_net_df['target']
merged = sources.append(targets)
print(len(merged.unique()))
# Calculate kernel
small_kernel = generator.create_kernel(network)
# Serialize file
util.write_kernel(small_kernel, 'kernel_out.txt')
# Get kernel as big string
self.assertIsNotNone(small_kernel)
self.assertTrue(isinstance(small_kernel, Kernel))
self.assertIsNotNone(small_kernel.kernel)
self.assertIsNotNone(small_kernel.labels)
df = pd.read_csv('kernel_out.txt', sep='\t', index_col=0)
self.assertIsNotNone(df)
print(df.shape)
def run(network):
generator = KernelGenerator()
# First, read network file as table
small_net_df = pd.read_csv(
network, sep='\t', names=['source', 'interaction', 'target'])
print(small_net_df.shape)
sources = small_net_df['source']
targets = small_net_df['target']
merged = sources.append(targets)
print(len(merged.unique()))
# Calculate kernel
small_kernel = generator.create_kernel(network)
# Serialize file
util.write_kernel(small_kernel, 'kernel_out.txt')
# Get kernel as big string
self.assertIsNotNone(small_kernel)
self.assertTrue(isinstance(small_kernel, Kernel))
self.assertIsNotNone(small_kernel.kernel)
self.assertIsNotNone(small_kernel.labels)
df = pd.read_csv('kernel_out.txt', sep='\t', index_col=0)
self.assertIsNotNone(df)
print(df.shape)
def test_pre_computed_kernel(self):
from hdsubnetfinder.kernel.kernel_generator import KernelGenerator
generator = KernelGenerator()
small_kernel = generator.create_kernel_from_file(pre_computed_kernel_url=SAMPLE_KERNEL_URL)
self.assertIsNotNone(small_kernel)
self.assertIsNotNone(small_kernel.kernel)
self.assertIsNotNone(small_kernel.labels)
self.assertTrue(list, type(small_kernel.labels))
self.assertTrue(list, type(small_kernel.kernel))
def test_pre_computed_kernel(self):
from hdsubnetfinder.kernel.kernel_generator import KernelGenerator
generator = KernelGenerator()
small_kernel = generator.create_kernel_from_file(
pre_computed_kernel_url=SAMPLE_KERNEL_URL)
self.assertIsNotNone(small_kernel)
self.assertIsNotNone(small_kernel.kernel)
self.assertIsNotNone(small_kernel.labels)
self.assertTrue(list, type(small_kernel.labels))
self.assertTrue(list, type(small_kernel.kernel))
def test_find_sub_network2(self):
print('\n---------- Sub Network Finder tests 2 start -----------\n')
from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
import hdsubnetfinder.subnetwork.network_util as util
from hdsubnetfinder.kernel.kernel_generator import KernelGenerator
generator = KernelGenerator()
small_kernel = generator.create_kernel(network_url=NETWORK_URL)
small_sif = util.read_sif(file_url=NETWORK_URL)
finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)
identifiers = ["NRAS", "KRAS", "MAPK1"]
result = finder.get_sub_network(identifiers)
self.assertIsNotNone(result)
print(len(result))
self.assertEqual(list, type(result))
print('\n---------- finder tests2 finished! -----------\n')
def run(self, data):
# Parse input data
sif_url = data["network_url"]
generator = KernelGenerator()
kernel = generator.create_kernel(sif_url)
logging.debug("========== Kernel computation finished =========")
req = client.post(KERNEL_FILE_SERVER + "data", data=util.get_kernel_as_string(kernel), stream=True)
file_id = req.json()["fileId"]
# Register kernel information
kernel_id = str(uuid.uuid4())
kernel_file_url = KERNEL_FILE_SERVER + "data/" + file_id
self.redis_conn.hset("kernels", kernel_id, kernel_file_url)
self.redis_conn.hset("kernel2network", kernel_id, sif_url)
logging.debug("Kernel File Server response Data = " + str(req.json()))
result = {"kernel_id": kernel_id, "network": sif_url, "kernel_file": kernel_file_url}
return result
def test_find_sub_network2(self):
print('\n---------- Sub Network Finder tests 2 start -----------\n')
from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
import hdsubnetfinder.subnetwork.network_util as util
from hdsubnetfinder.kernel.kernel_generator import KernelGenerator
generator = KernelGenerator()
small_kernel = generator.create_kernel(network_url=NETWORK_URL)
small_sif = util.read_sif(file_url=NETWORK_URL)
finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)
identifiers = ["NRAS", "KRAS", "MAPK1"]
result = finder.get_sub_network(identifiers)
self.assertIsNotNone(result)
print(len(result))
self.assertEqual(list, type(result))
print('\n---------- finder tests2 finished! -----------\n')
def test_find_sub_network(self):
print('\n---------- Sub Network Finder tests start -----------\n')
from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
import hdsubnetfinder.subnetwork.network_util as util
# Create kernel from pre-computed kernel file
generator = KernelGenerator()
small_kernel = generator.create_kernel_from_file(
pre_computed_kernel_url=SAMPLE_KERNEL_URL)
small_sif = util.read_sif(file_url=NETWORK_URL)
finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)
identifiers = ["NRAS", "KRAS", "MAPK1"]
result = finder.get_sub_network(identifiers)
self.assertIsNotNone(result)
print(len(result))
self.assertEqual(list, type(result))
print('\n---------- finder tests finished! -----------\n')
def test_find_sub_network(self):
print('\n---------- Sub Network Finder tests start -----------\n')
from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
import hdsubnetfinder.subnetwork.network_util as util
# Create kernel from pre-computed kernel file
generator = KernelGenerator()
small_kernel = generator.create_kernel_from_file(pre_computed_kernel_url=SAMPLE_KERNEL_URL)
small_sif = util.read_sif(file_url=NETWORK_URL)
finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)
identifiers = ["NRAS", "KRAS", "MAPK1"]
result = finder.get_sub_network(identifiers)
self.assertIsNotNone(result)
print(len(result))
self.assertEqual(list, type(result))
print('\n---------- finder tests finished! -----------\n')