def _get_network_attributes_from_uuid(self):
response = self._ndex.get_network_as_cx_stream(self._update_uuid)
network = ndex2.create_nice_cx_from_raw_cx(response.json())
names = network.get_network_attribute_names()
network_attributes = []
for name in names:
network_attributes.append(network.get_network_attribute(name))
self._network_attributes = network_attributes
def test_full_core_aspects_cx_file(self):
print('Testing: Full_core_aspects')
path_to_network = os.path.join(path_this, 'network1.cx')
with open(path_to_network, 'r') as ras_cx:
nice_cx = ndex2.create_nice_cx_from_raw_cx(cx=json.load(ras_cx))
upload_message = nice_cx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_upload_network_with_no_network_attributes(self):
"""
So if one uploads a network with NO network attributes
to NDEx and then edits the network (setting name visibility, description)
via [updateNetworkSummary] [/v2/network/6b89b286-e142-11ec-b397-0ac135e8bacf/summary
the CX2 endpoint shows the changed network attributes, but the CX1
is missing the network attributes
:return:
"""
client = self.get_ndex2_client()
# create network and add it
net = NiceCXNetwork()
oneid = net.create_node('node1')
twoid = net.create_node('node2')
net.create_edge(oneid, twoid, 'hello')
res = client.save_new_network(net.to_cx(), visibility='PRIVATE')
try:
self.assertTrue('http' in res)
netid = re.sub('^.*/', '', res)
netsum = self.wait_for_network_to_be_ready(client, netid)
self.assertIsNotNone(
netsum, 'Network is still not ready,'
' maybe server is busy?')
self.assertEqual(netid, netsum['externalId'])
self.assertTrue('name' not in netsum, msg=str(netsum))
# okay now we have the network, lets update the name
# and description and then get the network back again
# via cx1 and cx2 endpoints
netname = 'ndex2-client integration test network' + str(
datetime.now())
client.update_network_profile(netid, {'name': netname})
netsum = self.wait_for_network_to_be_ready(client, netid)
self.assertIsNotNone(
netsum, 'Network is still not ready,'
' maybe server is busy?')
cx2_resp = client.get_network_as_cx2_stream(network_id=netid)
cx2_json = json.loads(cx2_resp.content)
net_attrs = None
for aspect in cx2_json:
print(aspect)
if 'networkAttributes' in aspect:
net_attrs = aspect['networkAttributes']
break
self.assertEqual([{'name': netname}], net_attrs)
client_resp = client.get_network_as_cx_stream(network_id=netid)
cx1_net = ndex2.create_nice_cx_from_raw_cx(
json.loads(client_resp.content))
self.assertEqual(netname, cx1_net.get_name(),
'Special test to expose '
'bug in NDEx server')
finally:
client.delete_network(netid)
def test_cx_file_with_position(self):
print('Testing: network_with_position.cx')
path_to_network = os.path.join(path_this, 'network_with_position.cx')
with open(path_to_network, 'r') as ras_cx:
niceCx = ndex2.create_nice_cx_from_raw_cx(cx=json.load(ras_cx)) #NiceCXNetwork(cx=json.load(ras_cx))
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_export_to_cx_file(self):
print('Testing: MEDIUM_NETWORK.cx')
path_to_network = os.path.join(path_this, 'MEDIUM_NETWORK.cx')
with open(path_to_network, 'r') as ras_cx:
niceCx = ndex2.create_nice_cx_from_raw_cx(cx=json.load(ras_cx)) #NiceCXNetwork(cx=json.load(ras_cx))
niceCx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')
nice_networkx = niceCx.to_networkx()
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_nice_cx_from_raw_cx_with_glypican(self):
with open(TestCreateNiceCXNetworkFromRawCX.GLYPICAN_FILE, 'r') as f:
net_cx = ndex2.create_nice_cx_from_raw_cx(json.load(f))
self.assertEqual('Glypican 2 network', net_cx.get_name())
self.assertEqual(2, len(list(net_cx.get_nodes())))
self.assertEqual(1, len(list(net_cx.get_edges())))
# test for issue #60 make sure node/edge counters are
# properly set
self.assertEqual(2, net_cx.node_int_id_generator)
self.assertEqual(1, net_cx.edge_int_id_generator)
def test_create_nice_cx_from_raw_cx_with_wnt_signaling(self):
with open(TestCreateNiceCXNetworkFromRawCX.WNT_SIGNAL_FILE, 'r') as f:
net_cx = ndex2.create_nice_cx_from_raw_cx(json.load(f))
self.assertEqual('WNT Signaling', net_cx.get_name())
self.assertEqual(32, len(list(net_cx.get_nodes())))
self.assertEqual(74, len(list(net_cx.get_edges())))
# test for issue #60 make sure node/edge counters are
# properly set
self.assertEqual(32, net_cx.node_int_id_generator)
self.assertEqual(74, net_cx.edge_int_id_generator)
def test_create_from_cx_file_with_context(self):
print('Testing: Metabolism_of_RNA_data_types.cx')
path_to_network = os.path.join(path_this, 'Metabolism_of_RNA_data_types.cx')
with open(path_to_network, 'r') as ras_cx:
#====================================
# BUILD NICECX FROM CX OBJECT
#====================================
niceCx = ndex2.create_nice_cx_from_raw_cx(json.load(ras_cx)) #NiceCXNetwork(cx=json.load(ras_cx))
my_cx = niceCx.to_cx()
#print(my_cx)
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_cx_file2(self):
print('Testing: CitationsAndSupports.cx')
path_to_network = os.path.join(path_this, 'CitationsAndSupports.cx')
with open(path_to_network, 'r') as ras_cx:
#====================================
# BUILD NICECX FROM CX OBJECT
#====================================
niceCx = ndex2.create_nice_cx_from_raw_cx(cx=json.load(ras_cx))
my_cx = niceCx.to_cx()
#print(my_cx)
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def generate_viz(self, cx_network):
nice_cx_network = ndex2.create_nice_cx_from_raw_cx(cx_network)
nice_cx_network.print_summary()
# convert nice_cx -> pandas
nice_cx_df = nice_cx_network.to_pandas_dataframe()
nice_cx_df = nice_cx_df.sort_values(
by=([nice_cx_df.columns[0], nice_cx_df.columns[2]]))
# convert pandas -> igraph
edgelist = nice_cx_df.iloc[:, [0, 2]]
tuples = [tuple(x) for x in edgelist.values]
g_original = igraph.Graph.TupleList(tuples, directed=False)
# Pick largest subgraph
subgraphs = g_original.decompose()
tmp = [i.vcount() for i in subgraphs]
largeset_subgraph = subgraphs[tmp.index(max(tmp))]
g_status = graph_status(
largeset_subgraph.simplify(multiple=True, loops=True))
self.__compute_stats(g_status, self.options, self.rest_output)
positions = self.__apply_layout(g_status.graph, g_status, self.options)
# convert igraph -> networkx
G_nx = nx.Graph()
for i in range(g_status.graph.vcount()):
G_nx.add_node(g_status.graph.vs['name'][i])
for i, j in g_status.graph.get_edgelist():
G_nx.add_edge(g_status.graph.vs['name'][i],
g_status.graph.vs['name'][j])
# convert position -> certesian
certesian = [{
'node': i,
'x': list(positions)[i][0],
'y': list(positions)[i][1]
} for i in range(len(positions))]
# convert networkx -> NiceCX
ncx_from_x = ndex2.create_nice_cx_from_networkx(G_nx)
self.__add_ncxattributes(ncx_from_x, g_status, certesian, self.options)
cxobj = ncx_from_x.to_cx()
return cxobj
def test_data_types_with_special_chars(self):
self.assertFalse(upload_username == 'username')
path_to_network = os.path.join(path_this, 'Metabolism_of_RNA_data_types.cx')
with open(path_to_network, 'r') as data_types_cx:
#============================
# BUILD NICECX FROM CX FILE
#============================
niceCx = ndex2.create_nice_cx_from_raw_cx(cx=json.load(data_types_cx))
found_list_of_strings_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'list_of_string':
found_list_of_strings_type = True
self.assertTrue(found_list_of_strings_type)
def test_data_types_with_special_chars(self):
self.assertFalse(upload_username == 'username')
path_to_network = os.path.join(path_this, 'Metabolism_of_RNA_data_types.cx')
with open(path_to_network, 'r') as data_types_cx:
#============================
# BUILD NICECX FROM CX FILE
#============================
niceCx = ndex2.create_nice_cx_from_raw_cx(cx=json.load(data_types_cx))
found_list_of_strings_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'list_of_string':
found_list_of_strings_type = True
self.assertTrue(found_list_of_strings_type)
def test_create_nice_cx_from_raw_cx_with_invalidstr(self):
net_cx = ndex2.create_nice_cx_from_raw_cx('invalid')
self.assertEqual(None, net_cx.get_name())
self.assertEqual(0, len(list(net_cx.get_nodes())))
self.assertEqual(0, len(list(net_cx.get_edges())))
def test_create_nice_cx_from_raw_cx_with_emptystr(self):
try:
ndex2.create_nice_cx_from_raw_cx('')
self.fail('Expected Exception')
except Exception as e:
self.assertEqual('CX is empty', str(e))
# #### *ndex2.create_nice_cx_from_raw_cx(cx)
# In[ ]:
#this method requests to create a NDEx2 Client object
#import ndex2.client as nc
#import json
#my_account="PUT YOUR USER HERE"
#my_password="******"
#my_ndex=nc.Ndex2("http://public.ndexbio.org", my_account, my_password)
#my_ndex.update_status()
#query_result_cx_stream = my_ndex.get_neighborhood_as_cx_stream('c9243cce-2d32-11e8-b939-0ac135e8bacf','XRN1')
#raw_cx = query_result_cx_stream.json()
NiceCX_from_stream = ndex2.create_nice_cx_from_raw_cx(raw_cx)
NiceCX_from_stream.print_summary()
# #### *ndex2.create_nice_cx_from_file(path)
# In[ ]:
nice_cx_from_cx_file = ndex2.create_nice_cx_from_file('SimpleNetwork.cx')
# #### *ndex2.create_nice_cx_from_networkx(networkx)
# In[ ]:
#create an Empty NetworkX
G = nx.Graph()
nice_cx_from_networkx = ndex2.create_nice_cx_from_networkx(G)
def test_get_network_attributes_with_network_with_context_set(self):
p = self.get_dummy_params()
p.description = None
p.name = None
p.t = 'abase'
p.copyattribs = True
loader = TSVLoader(p)
cx = [{
"numberVerification": [{
"longNumber": 281474976710655
}]
}, {
"metaData": [{
"name": "nodes",
"elementCount": 2,
"idCounter": 220,
"version": "1.0",
"properties": []
}, {
"name": "networkAttributes",
"elementCount": 9,
"version": "1.0",
"properties": []
}, {
"name": "edges",
"elementCount": 1,
"idCounter": 221,
"version": "1.0",
"properties": []
}]
}, {
"nodes": [{
"@id": 220,
"n": "alpha"
}, {
"@id": 219,
"n": "omega"
}]
}, {
"networkAttributes": [{
"n": "@context",
"v": "{\"hi\": \"bye\"}"
}, {
"n": "organism",
"v": "z"
}, {
"n": "description",
"v": "hhh"
}, {
"n": "version",
"v": "za"
}, {
"n": "reference",
"v": "z"
}, {
"n": "name",
"v": "small"
}]
}, {
"edges": [{
"@id": 221,
"s": 220,
"t": 219,
"i": "interacts with"
}]
}, {
"status": [{
"error": "",
"success": True
}]
}]
net = ndex2.create_nice_cx_from_raw_cx(cx)
net_attribs = loader._get_network_attributes(net)
self.assertEqual(5, len(net_attribs))
for n_a in net_attribs:
if n_a['n'] == '@context':
self.fail('@context should have been removed, '
'but here it is: ' + str(n_a))
