def test_parse_pajet_mat(self):
data = """*Vertices 3\n1 "one"\n2 "two"\n3 "three"\n*Matrix\n1 1 0\n0 1 0\n0 1 0\n"""
G = nx.parse_pajek(data)
assert set(G.nodes()) == {'one', 'two', 'three'}
assert G.nodes['two'] == {'id': '2'}
assert_edges_equal(set(G.edges()), {('one', 'one'), ('two', 'one'),
('two', 'two'), ('two', 'three')})
def test_noname(self):
# Make sure we can parse a line such as: *network
# Issue #952
line = "*network\n"
other_lines = self.data.split('\n')[1:]
data = line + '\n'.join(other_lines)
G = nx.parse_pajek(data)
def pajek_to_files(name, url, pajek_lines, dir_name):
if pajek_lines:
try:
G = nx.parse_pajek(pajek_lines)
if not nx.is_empty(G):
old_attributes = list(G.nodes)
G = nx.convert_node_labels_to_integers(G)
id_mapping = []
node_list = list(G.nodes)
for i in range(len(node_list)):
id_mapping.append([old_attributes[i], str(node_list[i])])
mapping_file = open('..' + dir_name +
'/node_id_mappings/mapping_' +
url.split('/')[-1] + '.csv',
'w',
newline='')
mapping_file_writer = csv.writer(mapping_file)
mapping_file_writer.writerow(['id', 'name'])
for tup in id_mapping:
mapping_file_writer.writerow(list(tup))
nx.write_edgelist(G,
'..' + dir_name + '/edge_lists/' +
url.split('/')[-1] + '.csv',
delimiter=',')
insert_into_db(
name, url,
dir_name + '/edge_lists/' + url.split('/')[-1] + '.csv',
dir_name + '/node_id_mappings/mapping_' +
url.split('/')[-1] + '.csv', G.is_directed(),
G.is_multigraph(), int(G.number_of_nodes()),
int(nx.number_of_selfloops(G)))
except Exception as e:
traceback.print_exc()
print(e)
print("Couldn't parse " + url)
def test_read_pajek(self):
G = nx.parse_pajek(self.data)
Gin = nx.read_pajek(self.fname)
assert sorted(G.nodes()) == sorted(Gin.nodes())
assert_edges_equal(G.edges(), Gin.edges())
assert self.G.graph == Gin.graph
for n in G:
assert G.nodes[n] == Gin.nodes[n]
def test_write_pajek(self):
import io
G = nx.parse_pajek(self.data)
fh = io.BytesIO()
nx.write_pajek(G, fh)
fh.seek(0)
H = nx.read_pajek(fh)
assert_nodes_equal(list(G), list(H))
assert_edges_equal(list(G.edges()), list(H.edges()))
def test_parse_pajet_mat(self):
data = """*Vertices 3\n1 "one"\n2 "two"\n3 "three"\n*Matrix\n1 1 0\n0 1 0\n0 1 0\n"""
G = nx.parse_pajek(data)
assert set(G.nodes()) == {"one", "two", "three"}
assert G.nodes["two"] == {"id": "2"}
assert_edges_equal(
set(G.edges()),
{("one", "one"), ("two", "one"), ("two", "two"), ("two", "three")},
)
def test_parse_pajek(self):
G = nx.parse_pajek(self.data)
assert sorted(G.nodes()) == ["A1", "Bb", "C", "D2"]
assert_edges_equal(
G.edges(),
[
("A1", "A1"),
("A1", "Bb"),
("A1", "C"),
("Bb", "A1"),
("C", "C"),
("C", "D2"),
("D2", "Bb"),
],
)
def graphs_visualize_visjs(request, input_dict, output_dict, widget):
import networkx as nx
def prepare_visjs_data(g):
nodes = []
for node in g.nodes_iter():
new = {'id': str(node),
'label': str(g.node[node]['label']) if 'label' in g.node[node] else str(node),
'shape': 'box'
}
nodes.append(new)
edges = []
for fromnode, tonode, etype in g.edges_iter(keys=True):
if 'label' in g[fromnode][tonode][etype]:
label = str(g[fromnode][tonode][etype]['label'])
elif 'weight' in g[fromnode][tonode][etype]:
label = str(g[fromnode][tonode][etype]['weight'])
else:
#label = str(etype)
label = ''
new = {'from': str(fromnode),
'to': str(tonode),
'label': label,
'color': {'color': 'black', 'highlight': 'blue', 'hover': 'blue'},
}
if nx.is_directed(g):
new['arrows'] = 'to'
edges.append(new)
return {'nodes': nodes,
'edges': edges}
# end
g = input_dict['graph']
gtext = input_dict['gtext']
if not g:
g = nx.parse_pajek(gtext)
data = prepare_visjs_data(g)
return render(request, 'visualizations/graphs_visualize_visjs.html',
{'widget': widget,
'nodes': data['nodes'],
'edges': data['edges']
})
def pajek_to_files(name, url, pajek_lines):
if pajek_lines:
try:
check_matrix = pajek_lines.find('*matrix')
if check_matrix != -1:
pajek_lines = pajek_lines[check_matrix + 6:].strip(' ').strip('\r').strip('\n')
matrix_lines = pajek_lines.split('\r')
numbers_exp = re.compile(r'[0-9]')
append = ";"
for i in range(len(matrix_lines)):
if numbers_exp.search(matrix_lines[i]):
matrix_lines[i] = matrix_lines[i].strip('\n') + append
else:
matrix_lines[i] = ''
matrix_lines = list(filter(lambda x: x is not '', matrix_lines))
adj_matrix = " ".join(matrix_lines)
adj_matrix = adj_matrix[:len(adj_matrix) - 1]
# print(np.matrix(adj_matrix))
G = nx.from_numpy_array(np.matrix(adj_matrix))
else:
G = nx.parse_pajek(pajek_lines)
if not nx.is_empty(G):
old_attributes = list(G.nodes)
G = nx.convert_node_labels_to_integers(G)
id_mapping = []
node_list = list(G.nodes)
for i in range(len(node_list)):
id_mapping.append([old_attributes[i], str(node_list[i])])
mapping_file = open('../pajek_networks/node_id_mappings/mapping_' + url.split('/')[-1] + '.csv', 'w',
newline='')
mapping_file_writer = csv.writer(mapping_file)
mapping_file_writer.writerow(['id', 'name'])
for tup in id_mapping:
mapping_file_writer.writerow(list(tup))
nx.write_edgelist(G, '../pajek_networks/edge_lists/' + url.split('/')[-1] + '.csv',
delimiter=',')
utils.insert_into_db(name, url, '/pajek_networks/edge_lists/' + url.split('/')[-1] + '.csv',
'/pajek_networks/node_id_mappings/mapping_' + url.split('/')[-1] + '.csv',
G.is_directed(),
G.is_multigraph(), int(G.number_of_nodes()), int(nx.number_of_selfloops(G)))
except Exception as e:
traceback.print_exc()
print(e)
print("Couldn't parse " + url)
def test_parse_pajek(self):
G = nx.parse_pajek(self.data)
assert sorted(G.nodes()) == ['A1', 'Bb', 'C', 'D2']
assert_edges_equal(G.edges(), [('A1', 'A1'), ('A1', 'Bb'), ('A1', 'C'),
('Bb', 'A1'), ('C', 'C'), ('C', 'D2'),
('D2', 'Bb')])
def test_parse_pajek_simple(self):
# Example without node positions or shape
data = """*Vertices 2\n1 "1"\n2 "2"\n*Edges\n1 2\n2 1"""
G = nx.parse_pajek(data)
assert sorted(G.nodes()) == ['1', '2']
assert_edges_equal(G.edges(), [('1', '2'), ('1', '2')])
