__author__ = 'aarongary'
from nicecxModel.NiceCXNetwork import NiceCXNetwork
niceCx = NiceCXNetwork()
#================================
# Load network from ndex server
#================================
niceCx.create_from_server('public.ndexbio.org', None, None, 'dfba0dfb-6192-11e5-8ac5-06603eb7f303')
#=============================
# convert to pandas dataframe
#=============================
my_pd = niceCx.to_pandas_dataframe()
#=====================
# Export to csv file
#=====================
my_pd.to_csv('CXExport.csv', sep=',')
print('Done')
def test_nice_cx_model(self):
niceCx = NiceCXNetwork()
#main_map = NdexGraph(server='http://dev2.ndexbio.org', username='******', password='******', uuid='7246d8cf-c644-11e6-b48c-0660b7976219')
uuid = '6b968fd2-02a4-11e6-b550-06603eb7f303'
#====================
# NETWORK QUERY
#====================
networkQuery = NetworkQuery()
networkQuery.query_network('40f1def0-3aa4-11e7-b12f-0660b7976219',
'HSPA5,HSPA4')
my_na = NodeAttributesElement(
subnetwork=1,
property_of=11,
name=22,
values=33,
type=ATTRIBUTE_DATA_TYPE.convert_to_data_type('string'))
#====================
# NETWORK ATTRIBUTES
#====================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/nodes'), 'item')
objects = loadAspect('networkAttributes')
obj_items = (o for o in objects)
for network_item in obj_items:
add_this_network_attribute = NetworkAttributesElement(
cx_fragment=network_item)
niceCx.add_network_attribute(add_this_network_attribute)
#===================
# NODES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/nodes'), 'item')
objects = loadAspect('nodes')
obj_items = (o for o in objects)
for node_item in obj_items:
add_this_node = NodeElement(json_obj=node_item)
niceCx.create_node(add_this_node)
#===================
# EDGES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/edges'), 'item')
objects = loadAspect('edges')
obj_items = (o for o in objects)
for edge_item in obj_items:
add_this_edge = EdgeElement(json_obj=edge_item)
niceCx.create_edge(add_this_edge)
#===================
# NODE ATTRIBUTES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/nodeAttributes'), 'item')
objects = loadAspect('nodeAttributes')
obj_items = (o for o in objects)
for att in obj_items:
add_this_node_att = NodeAttributesElement(json_obj=att)
niceCx.add_node_attribute(add_this_node_att)
#===================
# EDGE ATTRIBUTES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/edgeAttributes'), 'item')
objects = loadAspect('edgeAttributes')
obj_items = (o for o in objects)
for att in obj_items:
add_this_edge_att = EdgeAttributesElement(json_obj=att)
niceCx.add_edge_attribute(add_this_edge_att)
#===================
# CITATIONS
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/edgeAttributes'), 'item')
objects = loadAspect('citations')
obj_items = (o for o in objects)
for cit in obj_items:
add_this_citation = CitationElement(cx_fragment=cit)
niceCx.add_citation(add_this_citation)
#===================
# SUPPORTS
#===================
objects = loadAspect('supports')
obj_items = (o for o in objects)
for sup in obj_items:
add_this_supports = SupportElement(cx_fragment=sup)
niceCx.add_support(add_this_supports)
#===================
# NODE CITATIONS
#===================
objects = loadAspect('nodeCitations')
obj_items = (o for o in objects)
for node_cit in obj_items:
niceCx.add_node_citations_from_cx(node_cit)
#===================
# EDGE CITATIONS
#===================
objects = loadAspect('edgeCitations')
obj_items = (o for o in objects)
for edge_cit in obj_items:
niceCx.add_edge_citations_from_cx(edge_cit)
nice_cx_json = niceCx.to_cx()
# serialized = pickle.dumps(niceCx, protocol=0)
# print 'Serialized memory:', sys.getsizeof(serialized)
print('starting to_pandas_dataframe')
niceCx.to_pandas_dataframe()
parser = ijson.parse(
urlopen('http://dev2.ndexbio.org/v2/network/' + uuid +
'/aspect/nodes'))
node_id, node_n, node_r = '', '', ''
edge_id, edge_s, edge_t, edge_i = '', '', '', ''
node_matches = {}
edge_matches = {}
edge_connected = {}
node_found = False
edge_found = False
count = 0
done_searching = False
start_time = time.time()
for prefix, event, value in parser:
if (prefix) == ('item.@id'):
if count % 10000 == 0:
print(count)
count += 1
node_id = value
elif (prefix) == ('item.n'):
node_n = value
node_found = True
elif (prefix) == ('item.r'):
node_r = value
if node_found:
node_matches[node_id] = {'n': node_n, 'r': node_r}
add_this_node = NodeElement(id=node_id,
node_name=node_n,
node_represents=node_r)
niceCx.create_node(add_this_node)
node_found = False
else:
# No represents found
if node_found:
node_matches[node_id] = {'n': node_n}
add_this_node = NodeElement(id=node_id, node_name=node_n)
niceCx.create_node(add_this_node)
node_found = False
print('Response time (Node search): ' + str(time.time() - start_time))
start_time = time.time()
print(edge_matches)
print(node_matches)
parser = ijson.parse(
urlopen('http://dev2.ndexbio.org/v2/network/' + uuid +
'/aspect/edges'))
for prefix, event, value in parser:
if (prefix) == ('item.@id'):
edge_id = value
elif (prefix) == ('item.s'):
edge_s = value
edge_found = True
elif (prefix) == ('item.t'):
edge_t = value
edge_found = True
elif (prefix) == ('item.i'):
edge_i = value
if edge_found:
edge_matches[edge_id] = {
's': edge_s,
't': edge_t,
'i': edge_i
}
add_this_edge = EdgeElement(id=edge_id,
edge_source=edge_s,
edge_target=edge_t,
edge_interaction=edge_i)
niceCx.create_edge(add_this_edge)
edge_connected[edge_s] = 1
edge_connected[edge_t] = 1
edge_found = False
else:
# No interaction found
if edge_found:
edge_matches[edge_id] = {'s': edge_s, 't': edge_t}
add_this_edge = EdgeElement(id=edge_id,
edge_source=edge_s,
edge_target=edge_t)
niceCx.create_edge(add_this_edge)
edge_connected[edge_s] = 1
edge_connected[edge_t] = 1
edge_found = False
print('Response time (Edge search): ' + str(time.time() - start_time))
start_time = time.time()
print(edge_matches)
print(node_matches)
self.assertTrue(niceCx is not None)
