def test_get_pathway_desc(self):
desc = QREx.get_pathway_desc('REACT:R-HSA-70326')
self.assertIsNotNone(desc)
self.assertEqual(
desc,
get_from_test_file('query_desc_test_data.json',
'REACT:R-HSA-70326'))
desc = QREx.get_pathway_desc('REACT:R-HSA-703260')
self.assertEqual(desc, 'None')
def test_update_pathway_entity(self):
f = open('config.json', 'r')
config_data = f.read()
f.close()
config = json.loads(config_data)
conn = Neo4jConnection(config['url'], config['username'], config['password'])
nodes = conn.get_pathway_nodes()
# generate random number array
random_indexes = random_int_list(0, len(nodes)-1, 100)
for i in random_indexes:
# retrieve data from Reactome API
node_id = nodes[i]
extended_info_json_from_api = QueryReactomeExtended.get_pathway_entity(node_id)
# retrieve data from Neo4j
node = conn.get_pathway_node(node_id)
self.assertIsNotNone(node['n']['id'])
self.assertIsNotNone(node['n']['extended_info_json'])
self.assertEqual(node_id, node['n']['id'])
self.maxDiff = None
if node['n']['extended_info_json'] != "UNKNOWN":
self.assertEqual(json.loads(extended_info_json_from_api), json.loads(node['n']['extended_info_json']))
conn.close()
def test_update_pathway_nodes_desc(self):
f = open('config.json', 'r')
config_data = f.read()
f.close()
config = json.loads(config_data)
conn = Neo4jConnection(config['url'], config['username'],
config['password'])
nodes = conn.get_pathway_nodes()
# generate random number array
random_indexes = random_int_list(0, len(nodes) - 1, 100)
for i in random_indexes:
# retrieve data from API
node_id = nodes[i]
desc = QueryReactomeExtended.get_pathway_desc(node_id)
# retrieve data from Neo4j
node = conn.get_pathway_node(node_id)
self.assertIsNotNone(node['n']['id'])
self.assertIsNotNone(node['n']['description'])
self.assertEqual(node_id, node['n']['id'])
self.assertEqual(desc, node['n']['description'])
conn.close()
def update_pathway_nodes_desc():
f = open('config.json', 'r')
config_data = f.read()
f.close()
config = json.loads(config_data)
conn = Neo4jConnection(config['url'], config['username'],
config['password'])
nodes = conn.get_pathway_nodes()
print("the number of pathway: %d" % len(nodes))
from time import time
t = time()
nodes_array = []
for i, node_id in enumerate(nodes):
node = dict()
node['node_id'] = node_id
node['desc'] = QueryReactomeExtended.get_pathway_desc(node_id)
nodes_array.append(node)
print("pathway api pulling time: %f" % (time() - t))
nodes_nums = len(nodes_array)
chunk_size = 10000
group_nums = nodes_nums // chunk_size + 1
for i in range(group_nums):
start = i * chunk_size
end = (i + 1) * chunk_size if (
i + 1) * chunk_size < nodes_nums else nodes_nums
conn.update_pathway_nodes_desc(nodes_array[start:end])
print("pathway total time: %f" % (time() - t))
conn.close()
def test_get_pathway_entity(self):
extended_info_json = QREx.get_pathway_entity('REACT:R-HSA-70326')
self.maxDiff = None
self.assertIsNotNone(extended_info_json)
if extended_info_json != "UNKNOWN":
self.assertEqual(
json.loads(extended_info_json),
json.loads(
get_from_test_file('query_test_data.json',
'REACT:R-HSA-70326')))