def test_nice_cx_from_networkx_using_graph_from_jupyternotebook(self):
g = nx.Graph()
g.add_node('ABC')
g.add_node('DEF')
g.add_node('GHI')
g.add_node('JKL')
g.add_node('MNO')
g.add_node('PQR')
g.add_node('XYZ')
g.add_edges_from([('ABC', 'DEF'), ('DEF', 'GHI'), ('GHI', 'JKL'),
('DEF', 'JKL'), ('JKL', 'MNO'), ('DEF', 'MNO'),
('MNO', 'XYZ'), ('DEF', 'PQR')])
short_path = nx.shortest_path(g, source='ABC', target="MNO")
path_subgraph = g.subgraph(short_path)
g.name = 'Created from NetworkX (full)'
nice_cx_full = ndex2.create_nice_cx_from_networkx(g)
self.assertEqual(7, len(nice_cx_full.get_nodes()))
self.assertEqual(8, len(nice_cx_full.get_edges()))
self.assertEqual(g.name, nice_cx_full.get_name())
g.name = 'Created from NetworkX (shortest path)'
nice_cx_short = ndex2.create_nice_cx_from_networkx(path_subgraph)
self.assertEqual(3, len(nice_cx_short.get_nodes()))
self.assertEqual(2, len(nice_cx_short.get_edges()))
self.assertEqual(g.name, nice_cx_short.get_name())
def test_netx_plot(self):
my_ndex = ndex2.client.Ndex2('http://test.ndexbio.org', 'scratch',
'scratch')
my_ndex.update_status()
test1 = my_ndex.get_network_ids_for_user('scratch')
nx_my_graph = nx.read_edgelist("edge_list_network_adrian.txt",
nodetype=str)
cx_my_graph = NdexGraph(networkx_G=nx_my_graph)
cx_my_graph.upload_to('http://dev.ndexbio.org', 'scratch', 'scratch')
G = nx.Graph()
G.add_node('ABC')
G.add_node('DEF')
G.add_node('GHI')
G.add_node('JKL')
G.add_node('MNO')
G.add_node('PQR')
G.add_node('XYZ')
G.add_edges_from([('ABC', 'DEF'), ('DEF', 'GHI'), ('GHI', 'JKL'),
('DEF', 'JKL'), ('JKL', 'MNO'), ('DEF', 'MNO'),
('MNO', 'XYZ'), ('DEF', 'PQR')])
niceCx_full = ndex2.create_nice_cx_from_networkx(G)
niceCx_full_networkx = niceCx_full.to_networkx()
names = nx.get_node_attributes(niceCx_full_networkx, 'name')
for n in niceCx_full_networkx.nodes():
print(n)
print(niceCx_full_networkx.nodes)
print(names)
def test_create_from_networkx(self):
path_to_network = os.path.join(path_this, 'SIMPLE3.txt')
with open(path_to_network, 'rU') as tsvfile:
reader = csv.DictReader(filter(lambda row: row[0] != '#', tsvfile),
dialect='excel-tab',
fieldnames=['s', 't', 'e'])
#===========================
# BUILD NETWORKX GRAPH
#===========================
G = nx.Graph(name='loaded from Simple3.txt')
for row in reader:
G.add_node(row.get('s'), test1='test1_s', test2='test2_s')
G.add_node(row.get('t'), test1='test1_t', test2='test2_t')
G.add_edge(row.get('s'), row.get('t'), {
'interaction': 'controls-production-of',
'test3': 'test3'
})
#====================================
# BUILD NICECX FROM NETWORKX GRAPH
#====================================
niceCx = ndex2.create_nice_cx_from_networkx(
G) #NiceCXNetwork(networkx_G=G)
niceCx.apply_template('public.ndexbio.org',
'72ef5c3a-caff-11e7-ad58-0ac135e8bacf')
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
self.assertTrue(upload_message)
def test_create_from_tsv_manipulate_and_save(self):
path_to_network = os.path.join(path_this, 'mgdb_mutations.txt')
with open(path_to_network, 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='CDS Mutation', target_field='Gene Symbol', source_node_attr=['Primary Tissue', 'Histology', 'Genomic Locus'], target_node_attr=['Gene ID'], edge_interaction='variant-gene-relationship') #NiceCXNetwork()
nice_networkx = niceCx.to_networkx()
nice_pandas = niceCx.to_pandas_dataframe()
my_csv = nice_pandas.to_csv(sep='\t')
with open("pandas_to_cx_to_tsv_results.txt", "w") as text_file:
text_file.write(my_csv)
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '72ef5c3a-caff-11e7-ad58-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_nice_cx_from_networkx_roundtrip_no_attrs(self):
net = ndex2.nice_cx_network.NiceCXNetwork()
node_one = net.create_node('Node 1')
node_two = net.create_node('Node 2')
net.create_edge(edge_source=node_one, edge_target=node_two)
netx_net = net.to_networkx(mode='default')
net_roundtrip = ndex2.create_nice_cx_from_networkx(netx_net)
self.assertEqual(
'created from networkx by '
'ndex2.create_nice_cx_networkx()', net_roundtrip.get_name())
self.assertEqual(1, len(net_roundtrip.get_edges()))
self.assertEqual(2, len(net_roundtrip.get_nodes()))
self.assertEqual((0, {
'@id': 0,
's': 0,
't': 1,
'i': 'neighbor-of'
}),
list(net_roundtrip.get_edges())[0])
for node_id, node_obj in net_roundtrip.get_nodes():
if node_id == 0:
self.assertEqual({
'@id': 0,
'n': 'Node 1',
'r': 'Node 1'
}, node_obj)
elif node_id == 1:
self.assertEqual({
'@id': 1,
'n': 'Node 2',
'r': 'Node 2'
}, node_obj)
else:
self.fail('Invalid node: ' + str(node_obj))
def test_create_from_tsv_manipulate_and_save(self):
print('Testing: mgdb_mutations.txt')
path_to_network = os.path.join(path_this, 'mgdb_mutations.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='CDS Mutation', target_field='Gene Symbol', source_node_attr=['Primary Tissue', 'Histology', 'Genomic Locus'], target_node_attr=['Gene ID'], edge_interaction='variant-gene-relationship') #NiceCXNetwork()
nice_networkx = niceCx.to_networkx()
nice_pandas = niceCx.to_pandas_dataframe()
my_csv = nice_pandas.to_csv(sep='\t')
with open("pandas_to_cx_to_tsv_results.txt", "w") as text_file:
text_file.write(my_csv)
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('ndexbio.org', '2e8f9bdc-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_netx_plot(self):
print('Testing: Get user networks (user: scratch) and networkx building')
my_ndex=ndex2.client.Ndex2('http://test.ndexbio.org', 'scratch', 'scratch')
my_ndex.update_status()
test1 = my_ndex.get_network_ids_for_user('scratch')
#nx_my_graph = nx.read_edgelist("edge_list_network_adrian.txt", nodetype=str)
G = nx.Graph()
G.add_node('ABC')
G.add_node('DEF')
G.add_node('GHI')
G.add_node('JKL')
G.add_node('MNO')
G.add_node('PQR')
G.add_node('XYZ')
G.add_edges_from([('ABC','DEF'), ('DEF', 'GHI'),('GHI', 'JKL'),
('DEF', 'JKL'), ('JKL', 'MNO'), ('DEF', 'MNO'),
('MNO', 'XYZ'), ('DEF', 'PQR')])
niceCx_full = ndex2.create_nice_cx_from_networkx(G)
niceCx_full_networkx = niceCx_full.to_networkx()
names = nx.get_node_attributes(niceCx_full_networkx, 'name')
for n in niceCx_full_networkx.nodes():
print(n)
print(niceCx_full_networkx.nodes)
niceCx_full.upload_to(upload_server, upload_username, upload_password)
print(names)
def to_ndex(self,
name="subgraph",
server="http://test.ndexbio.org",
username="******",
password="******"):
"""Uploads graph to NDEx
Parameters
----------
name : str
The key in self.graphs that contains the graph
server: str
The NDEx server hyperlink
username : str
Username of the NDEx account
password : str
Password of the NDEx account
"""
try:
g = ndex2.create_nice_cx_from_networkx(self.network)
except KeyError:
raise KeyError("%s is not in self.graphs dictionary!" % name)
uuid = g.upload_to(server=server, username=username, password=password)
return uuid
def publish(self, name, graph):
""" Save a networkx graph to NDEx. """
assert name, "A name for the network is required."
""" Serialize node and edge python objects. """
g = nx.MultiDiGraph()
print(f"{json.dumps (graph, indent=2)}")
jsonpath_query = parse("$.[*].node_list.[*].[*]")
nodes = [match.value for match in jsonpath_query.find(graph)]
print(f"{json.dumps(nodes, indent=2)}")
jsonpath_query = parse("$.[*].edge_list.[*].[*]")
edges = [match.value for match in jsonpath_query.find(graph)]
print(f"{json.dumps(edges, indent=2)}")
for n in nodes:
g.add_node(n['id'], attr_dict=n)
for e in edges:
print(f" s: {json.dumps(e,indent=2)}")
g.add_edge(e['source_id'], e['target_id'], attr_dict=e)
""" Convert to CX network. """
nice_cx = create_nice_cx_from_networkx(g)
nice_cx.set_name(name)
print(f" connected: edges: {len(g.edges())} nodes: {len(g.nodes())}")
print(nice_cx)
""" Upload to NDEx. """
upload_message = nice_cx.upload_to(self.uri, self.account,
self.password)
def _publish(self, name, graph):
""" Save a graph to NDEx. First, validate input. """
assert name, "Missing required network name."
assert graph, "Graph must be non null. "
assert len(graph) > 0, "Graph may not be empty."
""" TODO: Use graph tools to_nx instead. """
""" Select pieces of interest. """
""" May require different handling if this needs to run as a workflow step as opposed to a CLI argument. """
nodes = graph['nodes'] if 'nodes' in graph\
else self.jsonkit.select (query="$.[*].node_list.[*].[*]",
graph=graph)
edges = graph['edges'] if 'edges' in graph \
else self.jsonkit.select (query="$.[*].edge_list.[*].[*]",
graph=graph)
""" Create the NetworkX graph. """
g = nx.MultiDiGraph()
for n in nodes:
g.add_node(n['id'], attr_dict=n)
for e in edges:
g.add_edge(e['source_id'], e['target_id'], attr_dict=e)
assert len(g.nodes()) > 0, "Cannot save empty graph."
logger.debug(
f" connected: edges: {len(g.edges())} nodes: {len(g.nodes())}")
""" Convert to CX network. """
nice_cx = create_nice_cx_from_networkx(g)
nice_cx.set_name(name)
""" Upload to NDEx. """
upload_message = nice_cx.upload_to(self.uri, self.account,
self.password)
logger.debug("Upload to NDEx complete.")
logger.debug(f"upload message {upload_message}")
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_create_from_server_manipulate_and_save2(self):
print('public network')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='21106ea7-cbba-11e7-ad58-0ac135e8bacf')
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '72ef5c3a-caff-11e7-ad58-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_cx_file_with_position(self):
path_to_network = os.path.join(path_this, 'network_with_position.cx')
with open(path_to_network, 'rU') as ras_cx:
#====================================
# BUILD NICECX FROM PANDAS DATAFRAME
#====================================
niceCx = ndex2.create_nice_cx_from_cx(cx=json.load(ras_cx)) #NiceCXNetwork(cx=json.load(ras_cx))
nice_networkx = niceCx.to_networkx()
#my_cx = niceCx.to_cx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
#print(nice_networkx)
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_server_manipulate_and_save(self):
print('Testing: Create from server and manupulate (uuid:51247435-1e5f-11e8-b939-0ac135e8bacf)')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='51247435-1e5f-11e8-b939-0ac135e8bacf')
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.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_create_from_server_manipulate_and_save2(self):
print('Testing: Create from server and generate networkx (uuid:51247435-1e5f-11e8-b939-0ac135e8bacf)')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='51247435-1e5f-11e8-b939-0ac135e8bacf')
#serialized = pickle.dumps(niceCx.to_cx(), protocol=0)
#print('Serialized memory:', sys.getsizeof(serialized))
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
print(niceCx_from_netx)
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def save_nx_graph(self, name, graph):
""" Save a networkx graph to NDEx. """
assert name, "A name for the network is required."
""" Serialize node and edge python objects. """
g = nx.MultiDiGraph()
nodes = {n.id: i for i, n in enumerate(graph.nodes())}
for n in graph.nodes():
g.add_node(n.id, attr_dict=n.n2json())
for e in graph.edges(data=True):
edge = e[2]['object']
g.add_edge(edge.source_id,
edge.target_id,
attr_dict=e[2]['object'].e2json())
""" Convert to CX network. """
nice_cx = create_nice_cx_from_networkx(g)
nice_cx.set_name(name)
print(
f" connected: {nx.is_connected(graph.to_undirected())} edges: {len(graph.edges())} nodes: {len(graph.nodes())}"
)
print(nice_cx)
""" Upload to NDEx. """
upload_message = nice_cx.upload_to(self.uri, self.account,
self.password)
def test_create_from_networkx(self):
print('Testing: SIMPLE3.txt with DictReader')
path_to_network = os.path.join(path_this, 'SIMPLE3.txt')
with open(path_to_network, 'r') as tsvfile:
reader = csv.DictReader(filter(lambda row: row[0] != '#', tsvfile), dialect='excel-tab', fieldnames=['s','t','e'])
#===========================
# BUILD NETWORKX GRAPH
#===========================
G = nx.Graph(name='loaded from Simple3.txt')
for row in reader:
G.add_node(row.get('s'), test1='test1_s', test2='test2_s')
G.add_node(row.get('t'), test1='test1_t', test2='test2_t')
G.add_edges_from([(row.get('s'), row.get('t'), {'interaction': 'controls-production-of', 'test3': 'test3',
'non-number': np.nan})])
#====================================
# BUILD NICECX FROM NETWORKX GRAPH
#====================================
niceCx = ndex2.create_nice_cx_from_networkx(G) #NiceCXNetwork(networkx_G=G)
niceCx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_data_types_from_networkx(self):
self.assertFalse(upload_username == 'username')
G = nx.Graph()
G.add_node('ABC')
G.add_node('DEF')
G.add_node('GHI')
G.add_node('JKL')
G.add_node('MNO')
G.add_node('PQR')
G.add_node('XYZ')
G.add_edges_from([('ABC', 'DEF'), ('DEF', 'GHI'), ('GHI', 'JKL'),
('DEF', 'JKL'), ('JKL', 'MNO'), ('DEF', 'MNO'),
('MNO', 'XYZ'), ('DEF', 'PQR')])
G['ABC']['DEF']['ABC'] = 1
G['DEF']['GHI']['DEF'] = 2
G['GHI']['JKL']['GHI'] = 3
G['MNO']['XYZ']['JKL'] = 4
G['MNO']['XYZ']['MNO'] = 5
G['ABC']['DEF']['weight'] = 0.321
G['DEF']['GHI']['weight'] = 0.434
G['GHI']['JKL']['weight'] = 0.555
G['MNO']['XYZ']['weight'] = 0.987
G.nodes['ABC']['attr1'] = 1
G.nodes['DEF']['attr1'] = 1
G.nodes['GHI']['attr1'] = 1
G.nodes['JKL']['attr1'] = 1
G.nodes['MNO']['attr1'] = 1
G.nodes['PQR']['attr1'] = 1
G.nodes['XYZ']['attr1'] = 1
G.nodes['ABC']['attr2'] = 0.1
G.nodes['DEF']['attr2'] = 0.1
G.nodes['GHI']['attr2'] = 0.1
G.nodes['JKL']['attr2'] = 0.1
G.nodes['MNO']['attr2'] = 0.1
G.nodes['PQR']['attr2'] = 0.1
G.nodes['XYZ']['attr2'] = 0.1
niceCx_full = ndex2.create_nice_cx_from_networkx(G)
abc_node_attrs = niceCx_full.get_node_attributes(0)
found_int_type = False
found_float_type = False
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'integer':
found_int_type = True
if node_attr.get('d') == 'double':
found_float_type = True
found_edge_float_type = False
for id, edge in niceCx_full.get_edges():
edge_attrs = niceCx_full.get_edge_attributes(edge)
if edge_attrs is not None:
for edge_attr in edge_attrs:
if edge_attr.get('d') == 'double':
found_edge_float_type = True
self.assertTrue(found_int_type)
self.assertTrue(found_float_type)
self.assertTrue(found_edge_float_type)
def process(node_list, edge_list, load_plan, network_name, username, password,
server):
try:
here = path.abspath(path.dirname(__file__))
with open(path.join(here, load_plan), 'r') as lp:
load_plan = json.load(lp)
with open(path.join(here, 'loading_plan_schema.json')) as schema_file:
plan_schema = json.load(schema_file)
validate(load_plan, plan_schema)
node_id = load_plan.get('source_plan').get('rep_column')
node_name = load_plan.get('source_plan').get('node_name_column')
edge_source = load_plan.get('edge_plan').get('edge_source')
edge_target = load_plan.get('edge_plan').get('edge_target')
predicate_id_column = load_plan.get('edge_plan').get(
'predicate_id_column')
default_edge_interaction = load_plan.get('edge_plan').get(
'default_predicate')
except jsonschema.ValidationError as e1:
print("Failed to parse the loading plan: " + e1.message)
print('at path: ' + str(e1.absolute_path))
print("in block: ")
print(e1.instance)
except Exception as ex1:
print("Failed to parse the loading plan: ")
G = nx.Graph(name=network_name)
# ==============================
# ADD NODES TO NETWORKX GRAPH
# ==============================
node_label_id_map = {}
for n in node_list:
n_attrs = {}
node_label_id_map[n.get(node_id)] = n.get(node_name)
for k, v in n.items():
if k != node_id and k != node_name:
n_attrs[k] = v
G.add_node(n.get(node_id), n_attrs)
# ==============================
# ADD EDGES TO NETWORKX GRAPH
# ==============================
for e in edge_list:
e_attrs = {}
interaction_found = False
for k, v in e.items():
if k != edge_source and k != edge_target and k != 'id':
e_attrs[k] = v
if predicate_id_column is not None and k == predicate_id_column:
interaction_found = True
set_edge_interaction_map(e.get(edge_source),
e.get(edge_target),
e.get(predicate_id_column))
#if edge_interaction_map.get(e.get(edge_source)) is None:
# edge_interaction_map[e.get(edge_source)] = {e.get(edge_target): e.get(predicate_id_column)}
#else:
# edge_interaction_map[e.get(edge_source)][e.get(edge_target)] = e.get(predicate_id_column)
#if edge_interaction_map.get(e.get(edge_target)) is None:
# edge_interaction_map[e.get(edge_target)] = {e.get(edge_source): e.get(predicate_id_column)}
#else:
# edge_interaction_map[e.get(edge_target)][e.get(edge_source)] = e.get(predicate_id_column)
if not interaction_found and default_edge_interaction is not None:
set_edge_interaction_map(e.get(edge_source), e.get(edge_target),
default_edge_interaction)
G.add_edge(e.get(edge_source), e.get(edge_target), e_attrs)
# ======================
# RUN NETWORKX LAYOUT
# ======================
G.pos = nx.drawing.spring_layout(G, iterations=20, weight='weight')
# =========================
# CREATE CX FROM NETWORKX
# =========================
niceCx = ndex2.create_nice_cx_from_networkx(G)
niceCx.apply_template('public.ndexbio.org',
'84d64a82-23bc-11e8-b939-0ac135e8bacf')
# =========================
# POST-PROCESS NODES
# SET NODE NAME TO LABEL
# =========================
for k, v in niceCx.nodes.items():
v.set_node_represents(v.get_name())
v.set_node_name(node_label_id_map.get(v.get_name()))
for k, v in niceCx.edges.items():
if predicate_id_column is None:
v.set_interaction(default_edge_interaction)
else:
v.set_interaction(
edge_interaction_map.get(v.get_source()).get(v.get_target()))
# =======================
# UPLOAD TO NDEX SERVER
# =======================
if username is not None and password is not None and server is not None:
message = niceCx.upload_to(server, username, password)
if 'error' not in message:
network_uuid = message.split('/')[-1]
my_ndex = nc.Ndex2(server, username, password)
my_ndex._make_network_public_indexed(network_uuid)
return message
return None
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)
# #### *ndex2.create_nice_cx_from_pandas(dataframe)
# In[ ]:
#create an Empty Pandas Dataframe
df = pd.DataFrame()
nice_cx_from_pandas = ndex2.create_nice_cx_from_pandas(df)
# #### *ndex2.create_nice_cx_from_server(server, username=None, password=None, uuid=None)
# In[ ]:
uuid = "1c69beff-1229-11e6-a039-06603eb7f303"
nice_cx_from_server = ndex2.create_nice_cx_from_server(
def test_data_types_from_networkx(self):
self.assertFalse(upload_username == 'username')
G = nx.Graph()
G.add_node('ABC')
G.add_node('DEF')
G.add_node('GHI')
G.add_node('JKL')
G.add_node('MNO')
G.add_node('PQR')
G.add_node('XYZ')
G.add_edges_from([('ABC','DEF'), ('DEF', 'GHI'),('GHI', 'JKL'),
('DEF', 'JKL'), ('JKL', 'MNO'), ('DEF', 'MNO'),
('MNO', 'XYZ'), ('DEF', 'PQR')])
G['ABC']['DEF']['ABC'] = 1
G['DEF']['GHI']['DEF'] = 2
G['GHI']['JKL']['GHI'] = 3
G['MNO']['XYZ']['JKL'] = 4
G['MNO']['XYZ']['MNO'] = 5
G['ABC']['DEF']['weight'] = 0.321
G['DEF']['GHI']['weight'] = 0.434
G['GHI']['JKL']['weight'] = 0.555
G['MNO']['XYZ']['weight'] = 0.987
G.nodes['ABC']['attr1'] = 1
G.nodes['DEF']['attr1'] = 1
G.nodes['GHI']['attr1'] = 1
G.nodes['JKL']['attr1'] = 1
G.nodes['MNO']['attr1'] = 1
G.nodes['PQR']['attr1'] = 1
G.nodes['XYZ']['attr1'] = 1
G.nodes['ABC']['attr2'] = 0.1
G.nodes['DEF']['attr2'] = 0.1
G.nodes['GHI']['attr2'] = 0.1
G.nodes['JKL']['attr2'] = 0.1
G.nodes['MNO']['attr2'] = 0.1
G.nodes['PQR']['attr2'] = 0.1
G.nodes['XYZ']['attr2'] = 0.1
niceCx_full = ndex2.create_nice_cx_from_networkx(G)
abc_node_attrs = niceCx_full.get_node_attributes(0)
found_int_type = False
found_float_type = False
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'integer':
found_int_type = True
if node_attr.get('d') == 'double':
found_float_type = True
found_edge_float_type = False
for id, edge in niceCx_full.get_edges():
edge_attrs = niceCx_full.get_edge_attributes(edge)
if edge_attrs is not None:
for edge_attr in edge_attrs:
if edge_attr.get('d') == 'double':
found_edge_float_type = True
self.assertTrue(found_int_type)
self.assertTrue(found_float_type)
self.assertTrue(found_edge_float_type)
def test_create_nice_cx_from_networkx_roundtrip_glypican(self):
net = ndex2.create_nice_cx_from_file(
TestCreateNiceCXNetworkFromNetworkX.GLYPICAN_FILE)
netx_net = net.to_networkx(mode='default')
net_roundtrip = ndex2.create_nice_cx_from_networkx(netx_net)
self.assertEqual(2, len(net_roundtrip.get_nodes()))
self.assertEqual(1, len(net_roundtrip.get_edges()))
self.assertEqual('Glypican 2 network', net_roundtrip.get_name())
edge = net_roundtrip.get_edge(0)
self.assertEqual({
'@id': 0,
's': 1,
't': 0,
'i': 'in-complex-with'
}, edge)
e_a = net_roundtrip.get_edge_attribute(edge['@id'], 'directed')
# currently DefaultNetworkXFactory blindly
# migrates the value from NiceCXNetwork to
# networkx, since values are strings that is
# what the value is set to so during roundtrip
# a string is set as the datatype
self.assertEqual(
{
'po': 0,
'n': 'directed',
'v': 'false',
'd': 'string'
}, e_a)
n_a = net_roundtrip.get_node_attribute(0, 'type')
self.assertEqual({
'po': 0,
'n': 'type',
'v': 'Protein',
'd': 'string'
}, n_a)
n_a = net_roundtrip.get_node_attribute(1, 'type')
self.assertEqual({
'po': 1,
'n': 'type',
'v': 'Protein',
'd': 'string'
}, n_a)
n_a = net_roundtrip.get_node_attribute(0, 'alias')
self.assertEqual(
{
"po":
0,
"n":
"alias",
"v": [
"uniprot knowledgebase:Q2LEK4",
"uniprot knowledgebase:Q9UCC7"
],
"d":
"list_of_string"
}, n_a)
n_a = net_roundtrip.get_node_attribute(1, 'alias')
self.assertEqual(
{
"po": 1,
"n": "alias",
"v": ["uniprot knowledgebase:Q8N158"],
"d": "list_of_string"
}, n_a)
cart = net_roundtrip.get_opaque_aspect(
ndex2.constants.CARTESIAN_LAYOUT_ASPECT)
self.assertEqual(2, len(cart))
self.assertEqual(0, cart[0]['node'])
self.assertEqual(-398.3511334928659, cart[0]['x'])
self.assertEqual(70.71067799518471, cart[0]['y'])
self.assertEqual(1, cart[1]['node'])
self.assertEqual(-353.49370090105185, cart[1]['x'])
self.assertEqual(70.71067822788493, cart[1]['y'])
def test_create_nice_cx_from_networkx_with_none(self):
try:
ndex2.create_nice_cx_from_networkx(None)
self.fail('Expected Exception')
except Exception as e:
self.assertEqual('Networkx input is empty', str(e))
def test_create_nice_cx_from_networkx_with_invalidstr(self):
try:
ndex2.create_nice_cx_from_networkx('invalid')
self.fail('Expected Exception')
except AttributeError as e:
self.assertTrue('object has no' in str(e))
def process_rtx(rtx_json, network_name, username, password, server):
G = nx.Graph(name=network_name)
# ===========================
# CHECK FOR REQUIRED FIELDS
# ===========================
result_graph = rtx_json.get('result_graph')
if result_graph is not None:
n_data = result_graph.get('node_list')
e_data = result_graph.get('edge_list')
else:
raise Exception('ERROR: No result_graph found in input file')
# ==============================
# ADD NODES TO NETWORKX GRAPH
# ==============================
node_type_dict = {}
node_label_id_map = {}
edge_interaction_map = {}
layout_nlist = []
layout_level1_nlist = []
layout_level2_nlist = []
layout_other_nlist = []
for nds in n_data:
if nds.get('id') is not None and nds.get('type') is not None:
node_type_dict[nds.get('id')] = nds.get('type')
for n in n_data:
n_attrs = {}
node_label_id_map[n.get('id')] = n.get('name')
for k, v in n.items():
if k != 'id' and k != 'name':
n_attrs[k] = v
G.add_node(n.get('id'), n_attrs)
# Shell layout setup
if len(layout_level1_nlist) < 25:
layout_level1_nlist.append(n.get('id'))
elif len(layout_level2_nlist) < 50:
layout_level2_nlist.append(n.get('id'))
else:
layout_other_nlist.append(n.get('id'))
layout_nlist.append(layout_level1_nlist)
layout_nlist.append(layout_level2_nlist)
layout_nlist.append(layout_other_nlist)
# ==============================
# ADD EDGES TO NETWORKX GRAPH
# ==============================
edge_type_dict = {}
if e_data is not None:
for eds in e_data:
if eds.get('name') is not None and eds.get('type') is not None:
edge_type_dict[eds.get('name')] = eds.get('type')
for e in e_data:
#print(e)
e_attrs = {}
for k, v in e.items():
if k != 'source_id' and k != 'target_id' and k != 'id':
e_attrs[k] = v
if k == 'type':
if edge_interaction_map.get(e.get('source_id')) is None:
edge_interaction_map[e.get('source_id')] = {
e.get('target_id'): e.get('type')
}
else:
edge_interaction_map[e.get('source_id')][e.get(
'target_id')] = e.get('type')
if edge_interaction_map.get(e.get('target_id')) is None:
edge_interaction_map[e.get('target_id')] = {
e.get('source_id'): e.get('type')
}
else:
edge_interaction_map[e.get('target_id')][e.get(
'source_id')] = e.get('type')
G.add_edge(e.get('source_id'), e.get('target_id'), e_attrs)
else:
n1 = G.nodes()[0]
G.add_edge(n1, n1, {})
edge_interaction_map[n1] = {n1: 'self-ref'}
# ======================
# RUN NETWORKX LAYOUT
# ======================
init_pos = nx.drawing.circular_layout(G)
G.pos = nx.drawing.spring_layout(G,
iterations=20,
pos=init_pos,
weight='weight')
# G.pos = nx.drawing.shell_layout(G, nlist=layout_nlist)
# G.pos = nx.drawing.spring_layout(G, weight='weight')
# =========================
# CREATE CX FROM NETWORKX
# =========================
niceCx = ndex2.create_nice_cx_from_networkx(G)
niceCx.apply_template('public.ndexbio.org',
'84d64a82-23bc-11e8-b939-0ac135e8bacf')
# =========================
# SET NODE NAME TO LABEL
# =========================
for k, v in niceCx.nodes.items():
v.set_node_represents(v.get_name())
v.set_node_name(node_label_id_map.get(v.get_name()))
for k, v in niceCx.edges.items():
v.set_interaction(
edge_interaction_map.get(v.get_source()).get(v.get_target()))
# =======================
# UPLOAD TO NDEX SERVER
# =======================
if username is not None and password is not None and server is not None:
message = niceCx.upload_to(server, username, password)
network_uuid = message.split('/')[-1]
my_ndex = nc.Ndex2(server, username, password)
if 'error' not in message:
my_ndex._make_network_public_indexed(network_uuid)
return message
return None
def test_create_nice_cx_from_networkx_roundtrip_with_attrs(self):
net = ndex2.nice_cx_network.NiceCXNetwork()
node_one = net.create_node('Node 1')
node_two = net.create_node('Node 2')
net.set_node_attribute(node_one, 'somestrfield', 'hi')
edge_one = net.create_edge(edge_source=node_one,
edge_target=node_two,
edge_interaction='breaks')
net.set_edge_attribute(edge_one, 'somestrfield', 'bye')
net.set_opaque_aspect(ndex2.constants.CARTESIAN_LAYOUT_ASPECT,
[{
'node': node_one,
'x': 1.0,
'y': 2.0
}, {
'node': node_two,
'x': 3.0,
'y': 4.0
}])
net.set_name('mynetwork')
netx_net = net.to_networkx(mode='default')
net_roundtrip = ndex2.create_nice_cx_from_networkx(netx_net)
self.assertEqual(netx_net.pos[0], (1.0, -2.0))
self.assertEqual(netx_net.pos[1], (3.0, -4.0))
self.assertEqual('mynetwork', net_roundtrip.get_name())
self.assertEqual(1, len(net_roundtrip.get_edges()))
self.assertEqual(2, len(net_roundtrip.get_nodes()))
self.assertEqual((0, {
'@id': 0,
's': 0,
't': 1,
'i': 'breaks'
}),
list(net_roundtrip.get_edges())[0])
for node_id, node_obj in net_roundtrip.get_nodes():
if node_id == 0:
self.assertEqual({
'@id': 0,
'n': 'Node 1',
'r': 'Node 1'
}, node_obj)
elif node_id == 1:
self.assertEqual({
'@id': 1,
'n': 'Node 2',
'r': 'Node 2'
}, node_obj)
else:
self.fail('Invalid node: ' + str(node_obj))
n_a = net_roundtrip.get_node_attribute(node_one, 'somestrfield')
self.assertEqual(
{
'po': 0,
'n': 'somestrfield',
'v': 'hi',
'd': 'string'
}, n_a)
n_a = net_roundtrip.get_edge_attribute(node_one, 'somestrfield')
self.assertEqual(
{
'po': 0,
'n': 'somestrfield',
'v': 'bye',
'd': 'string'
}, n_a)
def process_tcpa(file_name):
tcpa_file_path = path.join(current_directory, file_name)
if path.isfile(tcpa_file_path):
with open(tcpa_file_path, 'r') as tfp:
tcpa_json = json.load(tfp)
G = nx.Graph(name=file_name.replace('.json', ''))
#===========================
# CHECK FOR REQUIRED FIELDS
#===========================
data_schema = tcpa_json.get('dataSchema')
if data_schema is not None:
n_data_schema = data_schema.get('nodes')
e_data_schema = data_schema.get('edges')
else:
raise Exception('ERROR: No data schema found in input file')
data = tcpa_json.get('data')
if data is None:
raise Exception('ERROR: No data found in input file')
#==============================
# ADD NODES TO NETWORKX GRAPH
#==============================
node_type_dict = {}
node_label_id_map = {}
layout_nlist = []
layout_level1_nlist = []
layout_level2_nlist = []
layout_level3_nlist = []
layout_other_nlist = []
for nds in n_data_schema:
if nds.get('name') is not None and nds.get('type') is not None:
node_type_dict[nds.get('name')] = nds.get('type')
for n in data.get('nodes'):
print(n)
n_attrs = {}
node_label_id_map[n.get('id')] = n.get('label')
for k, v in n.items():
if k != 'id':
n_attrs[k] = v
G.add_node(n.get('id'), n_attrs)
# Shell layout setup
if len(layout_level1_nlist) < 25:
layout_level1_nlist.append(n.get('id'))
elif len(layout_level2_nlist) < 50:
layout_level2_nlist.append(n.get('id'))
else:
layout_other_nlist.append(n.get('id'))
layout_nlist.append(layout_level1_nlist)
layout_nlist.append(layout_level2_nlist)
layout_nlist.append(layout_other_nlist)
#==============================
# ADD EDGES TO NETWORKX GRAPH
#==============================
edge_type_dict = {}
for eds in e_data_schema:
if eds.get('name') is not None and eds.get('type') is not None:
edge_type_dict[eds.get('name')] = eds.get('type')
for e in data.get('edges'):
print(e)
e_attrs = {}
for k, v in e.items():
if k != 'source' and k != 'target' and k != 'id':
e_attrs[k] = v
G.add_edge(e.get('source'), e.get('target'), e_attrs)
#======================
# RUN NETWORKX LAYOUT
#======================
init_pos = nx.drawing.circular_layout(G)
G.pos = nx.drawing.spring_layout(G,
iterations=20,
pos=init_pos,
weight='weight')
G.pos = nx.drawing.shell_layout(G, nlist=layout_nlist)
#G.pos = nx.drawing.spring_layout(G, weight='weight')
#=========================
# CREATE CX FROM NETWORKX
#=========================
niceCx = ndex2.create_nice_cx_from_networkx(G)
niceCx.apply_template('public.ndexbio.org',
'84d64a82-23bc-11e8-b939-0ac135e8bacf')
#=========================
# SET NODE NAME TO LABEL
#=========================
for k, v in niceCx.nodes.items():
v.set_node_name(node_label_id_map.get(v.get_name()))
#=======================
# UPLOAD TO NDEX SERVER
#=======================
if upload_username is not None and upload_password is not None and upload_server is not None:
niceCx.upload_to(upload_server, upload_username,
upload_password)
with open(data_file.replace('.json', '.cx'), 'w') as outfile:
json.dump(niceCx.to_cx(), outfile)
else:
raise Exception('ERROR: File does not exist ' + data_file)
def test_data_types_from_networkx(self):
G = nx.Graph()
G.add_node('ABC')
G.add_node('DEF')
G.add_node('GHI')
G.add_node('JKL')
G.add_node('MNO')
G.add_node('PQR')
G.add_node('XYZ')
G.add_edges_from([('ABC', 'DEF'), ('DEF', 'GHI'), ('GHI', 'JKL'),
('DEF', 'JKL'), ('JKL', 'MNO'), ('DEF', 'MNO'),
('MNO', 'XYZ'), ('DEF', 'PQR')])
attribute_floats = {
'ABC': 1.234,
'DEF': 1.345,
'GHI': 1.456,
'JKL': 1.567,
'MNO': 1.678
}
attribute_integers = {'ABC': 1, 'DEF': 2, 'GHI': 3, 'JKL': 4, 'MNO': 5}
nx.set_node_attributes(G, 'floatLabels', attribute_floats)
nx.set_node_attributes(G, 'integerLabels', attribute_integers)
G['ABC']['DEF']['weight'] = 0.321
G['DEF']['GHI']['weight'] = 0.434
G['GHI']['JKL']['weight'] = 0.555
G['MNO']['XYZ']['weight'] = 0.987
niceCx_full = ndex2.create_nice_cx_from_networkx(G)
context = [{
'ncbigene': 'http://identifiers.org/ncbigene/',
'hgnc.symbol': 'http://identifiers.org/hgnc.symbol/',
'uniprot': 'http://identifiers.org/uniprot/'
}]
niceCx_full.set_context(context)
#print(niceCx_full.__str__())
abc_node_attrs = niceCx_full.get_node_attributes('ABC')
found_int_type = False
found_float_type = False
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get_data_type() == ATTRIBUTE_DATA_TYPE.INTEGER:
found_int_type = True
if node_attr.get_data_type() == ATTRIBUTE_DATA_TYPE.FLOAT:
found_float_type = True
found_edge_float_type = False
for id, edge in niceCx_full.get_edges():
edge_attrs = niceCx_full.get_edge_attributes(edge)
if edge_attrs is not None:
for edge_attr in edge_attrs:
if edge_attr.get_data_type() == ATTRIBUTE_DATA_TYPE.FLOAT:
found_edge_float_type = True
self.assertTrue(found_int_type)
self.assertTrue(found_float_type)
self.assertTrue(found_edge_float_type)
