def test_load_graph_gexf_three_adjacency_matrix(self):
# 0 1 2 3 4 5 6 7 8
result = np.matrix([
[0.00, 0.00, 0.88, 1.00, 0.00, 0.00, 0.00, 0.00, 0.00], # 0
[0.00, 0.00, 0.25, 0.00, 0.00, 0.00, 0.00, 1.00, 0.00], # 1
[0.88, 0.25, 0.00, 0.00, 1.00, 0.00, 0.00, 0.00, 0.00], # 2
[1.00, 0.00, 0.00, 0.00, 1.00, 0.00, 0.00, 0.00, 0.00], # 3
[0.00, 0.00, 1.00, 1.00, 0.00, 0.00, 1.00, 0.00, 1.00], # 4
[0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.52, 0.00], # 5
[0.00, 0.00, 0.00, 0.00, 1.00, 0.00, 0.00, 0.00, 0.52], # 6
[0.00, 1.00, 0.00, 0.00, 0.00, 0.52, 0.00, 0.00, 0.52], # 7
[0.00, 0.00, 0.00, 0.00, 1.00, 0.00, 0.52, 0.52, 0.00]
]) # 8
graph = graphio.load_graph(self.test_three_group_gexf_file,
format='GEXF')
nodes = list(graph.nodes())
adj_matrix = nx.adjacency_matrix(graph).todense()
for i in range(result.shape[0]):
for j in range(result.shape[1]):
result_i = nodes.index(
str(i)) # Order of the nodes is not fixed
result_j = nodes.index(str(j))
self.assertEquals(adj_matrix[i, j], result[result_i, result_j])
def experiment(self, extra_params):
"""
Run the experiment. All config overriding and stuff are performed
in the Experiment class.
"""
self.log.info("Running preprocess xml experiment.")
self.log.info("Parsing from config file.")
required = ['file', 'out', 'precompute']
if self._are_required_parameters_valid(self.config, required):
cfg_params = self._load_parameters(self.params_section)
file = cfg_params['file']
format = cfg_params['format']
labels_as_ids = cfg_params['labels_as_ids']
outfile = cfg_params['out']
cfg_precompute = cfg_params['precompute']
path = cfg_params['data_path']
self.log.info("Reading file format")
graph = graphio.load_graph(file, format=format)
self.log.info("Converting to ProphTools format")
converted = graphio.convert_to_graphdataset(
graph, precompute=cfg_precompute, labels_as_ids=labels_as_ids)
self.log.info("Writing mat file")
converted.write(path, outfile)
self.log.info("Process performed successfully")
return 0
else:
self.log.error("Exiting")
return -1
def test_convert_to_graphdata_zero_matrices_relations_connections(self):
graph = graphio.load_graph(
self.test_three_group_two_relations_gexf_file, format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph)
connections = converted_graph.connections
expected_connections = np.matrix([[-1, 0, -1], [-1, -1, 1],
[-1, -1, -1]])
for i in range(connections.shape[0]):
for j in range(connections.shape[1]):
self.assertEquals(connections[i, j], expected_connections[i,
j])
def test_load_graph_gexf_adjacency_matrix(self):
result = np.matrix([[0, 0.25, 0, 0.88], [0.25, 0, 0.52, 0],
[0, 0.52, 0, 1.00], [0.88, 0, 1.00, 0]])
graph = graphio.load_graph(self.test_file, format='GEXF')
nodes = list(graph.nodes())
adj_matrix = nx.adjacency_matrix(graph).todense()
for i in range(result.shape[0]):
for j in range(result.shape[1]):
result_i = nodes.index(
str(i)) # Order of the nodes is not fixed
result_j = nodes.index(str(j))
self.assertEquals(adj_matrix[i, j], result[result_i, result_j])
def test_convert_to_graphdata_relations_orientation(self):
graph = graphio.load_graph(self.test_three_group_gexf_file,
format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph)
connections = converted_graph.connections
for i in range(connections.shape[0]):
for j in range(connections.shape[1]):
if connections[i, j] != -1:
mat_index = connections[i, j]
relation = converted_graph.relations[mat_index].matrix
src_mat = converted_graph.networks[i].matrix
dst_mat = converted_graph.networks[j].matrix
self.assertEquals(src_mat.shape[0], relation.shape[0])
self.assertEquals(dst_mat.shape[0], relation.shape[1])
def test_txt_file_with_non_unique_ids_raises_exception(self):
with self.assertRaises(ValueError):
graph = graphio.load_graph(self.test_repeated_id_file,
format="TXT")
def test_file_with_missing_group_attributes_raises_exception(self):
with self.assertRaises(ValueError):
graph = graphio.load_graph(self.test_missing_attr_file)
def test_file_with_missing_group_attributes_raises_exception_txt(self):
with self.assertRaises(ValueError):
graph = graphio.load_graph(self.test_txt_missing_group_file,
format='TXT')
def test_load_graph_unknown_format_raises_exception(self):
with self.assertRaises(TypeError):
unknown_format = "unknown"
graphio.load_graph(self.test_file, format=unknown_format)
def test_write_mat_file_load(self):
graph = graphio.load_graph(
self.test_three_group_two_relations_gexf_file, format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph,
precompute=True)
converted_graph.write(self.test_dir, 'test_out.mat')
def test_convert_to_graphdata_one_network_per_group(self):
graph = graphio.load_graph(self.test_three_group_gexf_file,
format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph)
self.assertEquals(len(converted_graph.networks), 3)
def test_convert_to_graphdata_raises_exception_on_repeated_labels(self):
graph = graphio.load_graph(self.test_repeated_label_file,
format='GEXF')
with self.assertRaises(ValueError):
converted_graph = graphio.convert_to_graphdataset(
graph, labels_as_ids=True)
def test_load_graph_txt_undirected_symmetric_adj_matrix(self):
graph = graphio.load_graph(self.test_txt_file, format='TXT')
adj_matrix = nx.adjacency_matrix(graph).todense()
for i in range(adj_matrix.shape[0]):
for j in range(i + 1, adj_matrix.shape[1]):
self.assertEquals(adj_matrix[i, j], adj_matrix[j, i])
def test_load_graph_txt_edge_number(self):
graph = graphio.load_graph(self.test_txt_file, format='TXT')
self.assertEquals(len(graph.edges()), 11)
def test_load_graph_gexf_edge_number(self):
graph = graphio.load_graph(self.test_file, format='GEXF')
self.assertEquals(len(graph.edges()), 4)
def test_load_graph_gexf_valid_format_runs(self):
graphio.load_graph(self.test_file, format='GEXF')
def test_load_graph_txt_valid_format_runs(self):
graphio.load_graph(self.test_txt_file, format='TXT')
def test_convert_to_graphdata_returns_graphdataset_object(self):
graph = graphio.load_graph(self.test_three_group_gexf_file,
format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph)
self.assertTrue(isinstance(converted_graph, GraphDataSet))
def test_node_attributes_txt(self):
graph = graphio.load_graph(self.test_txt_file, format='TXT')
self.assertEquals(graph.node['0']['group'], '0')
self.assertEquals(graph.node['1']['group'], '0')
self.assertEquals(graph.node['2']['group'], '0')
self.assertEquals(graph.node['3']['group'], '1')
def test_convert_to_graphdata_number_of_relations(self):
graph = graphio.load_graph(self.test_three_group_gexf_file,
format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph)
self.assertEquals(len(converted_graph.relations), 3)
def test_labels_txt_are_loaded(self):
graph = graphio.load_graph(self.test_txt_file, format='TXT')
self.assertEquals(graph.node['0']['label'], 'node_0')
self.assertEquals(graph.node['1']['label'], 'node_1')
self.assertEquals(graph.node['2']['label'], 'node_2')
self.assertEquals(graph.node['3']['label'], 'node_3')
def test_convert_to_graphdata_zero_matrices_relations_are_not_added(self):
graph = graphio.load_graph(
self.test_three_group_two_relations_gexf_file, format='GEXF')
converted_graph = graphio.convert_to_graphdataset(graph)
self.assertEquals(len(converted_graph.relations), 2)
def test_labels_gexf_are_loaded(self):
graph = graphio.load_graph(self.test_file, format='GEXF')
self.assertEquals(graph.node['0']['label'], 'Mark Johnson')
self.assertEquals(graph.node['1']['label'], 'Jane Schwartz')
self.assertEquals(graph.node['2']['label'], 'Ed Lopez')
self.assertEquals(graph.node['3']['label'], 'Maria Lopez')
def test_convert_to_graphdata_high_number_of_entity_types(self):
graph = graphio.load_graph(self.test_ten_group_gexf_file,
format='GEXF')
with self.assertRaises(ValueError):
converted_graph = graphio.convert_to_graphdataset(graph)
def test_gexf_file_with_no_label_attr_loads_empty_strings(self):
graph = graphio.load_graph(self.test_no_label_file, format='GEXF')
self.assertEquals(graph.node['0']['label'], '')
self.assertEquals(graph.node['1']['label'], '')
self.assertEquals(graph.node['2']['label'], '')
self.assertEquals(graph.node['3']['label'], '')
def test_file_with_no_group_attribute_assigns_same_to_all_txt(self):
graph = graphio.load_graph(self.test_txt_no_group_file, format='TXT')
self.assertEquals(graph.node['0']['group'], '0')
self.assertEquals(graph.node['1']['group'], '0')
self.assertEquals(graph.node['2']['group'], '0')
self.assertEquals(graph.node['3']['group'], '0')
def test_load_graph_non_existing_file_raises_exception(self):
with self.assertRaises(IOError):
non_existing_filename = '_'
graphio.load_graph(non_existing_filename, format="GEXF")
