def test_edge_list(self):
ntags, nsinks, iedges = graph.iedge_from_annotations(self.annots)
self.assertEqual(6, ntags)
self.assertEqual(5, nsinks)
edges = set(e for e in iedges)
outgo_edges = [(0, 1),
(0, 3),
(0, 4),
(0, 5),
(1, 3),
(1, 4),
(4, 3)]
#Inverse edges
expected = [] + outgo_edges #Copy
expected.extend((v, k) for k, v in outgo_edges)
#Edges to items
expected.extend([(0, 6),
(0, 8),
(1, 6),
(1, 9),
(1, 10),
(2, 7),
(3, 6),
(4, 6),
(5, 8)])
self.assertEquals(edges, set(expected))
def test_graph(self):
edges = [e for e in graph.iedge_from_annotations(self.annots)[2]]
g = graph.create_nxgraph(edges)
paths = nx.shortest_path_length(g, source=0)
self.assertEquals(paths, {
0: 0,
1: 1,
3: 1,
4: 1,
5: 1,
6: 1,
8: 1,
9: 2,
10: 2
})
def test_edge_list(self):
ntags, nsinks, iedges = graph.iedge_from_annotations(self.annots)
self.assertEqual(6, ntags)
self.assertEqual(5, nsinks)
edges = set(e for e in iedges)
outgo_edges = [(0, 1), (0, 3), (0, 4), (0, 5), (1, 3), (1, 4), (4, 3)]
#Inverse edges
expected = [] + outgo_edges #Copy
expected.extend((v, k) for k, v in outgo_edges)
#Edges to items
expected.extend([(0, 6), (0, 8), (1, 6), (1, 9), (1, 10), (2, 7),
(3, 6), (4, 6), (5, 8)])
self.assertEquals(edges, set(expected))
def create_graph(annotation_it, out_folder):
ntags, nsinks, iedges = \
graph.iedge_from_annotations(annotation_it, 1,
False)
tmp_fname = tempfile.mktemp()
n_edges = 0
with io.open(tmp_fname, 'w') as tmp:
for source, dest in sorted(iedges):
tmp.write(u'%d %d\n' % (source, dest))
n_edges += 1
with io.open(tmp_fname) as tmp:
out_graph = os.path.join(out_folder, 'navi.graph')
with io.open(out_graph, 'w') as out:
out.write(u'#Nodes: %d\n'%ntags)
out.write(u'#Edges: %d\n'%n_edges)
out.write(u'#Directed\n')
for line in tmp:
out.write(line)
def real_main(database, table, out_file, use):
with AnnotReader(database) as reader:
reader.change_table(table)
ntags, nsinks, iedges = \
graph.iedge_from_annotations(reader.iterate(), use)
n_nodes = ntags + nsinks
tmp_fname = tempfile.mktemp()
n_edges = 0
with open(tmp_fname, 'w') as tmp:
for source, dest in sorted(iedges):
print(source, dest, file=tmp)
n_edges += 1
with open(tmp_fname) as tmp:
with open(out_file, 'w') as out:
print('#Nodes: %d'%n_nodes, file=out)
print('#Edges: %d'%n_edges, file=out)
print('#Directed', file=out)
for line in tmp:
print(line[:-1], file=out)
def test_graph(self):
edges = [e for e in graph.iedge_from_annotations(self.annots)[2]]
g = graph.create_nxgraph(edges)
paths = nx.shortest_path_length(g, source = 0)
self.assertEquals(paths, {0: 0, 1: 1, 3: 1, 4: 1, 5: 1, 6: 1, 8: 1, 9: 2, 10: 2})
