def test_expand_upstream_causal_subgraph(self):
"""Test expanding on the upstream causal subgraph."""
a, b, c, d, e, f = [protein(namespace='test', name=i) for i in string.ascii_lowercase[:6]]
citation, evidence = '', ''
universe = BELGraph()
universe.add_qualified_edge(a, b, INCREASES, citation, evidence)
universe.add_qualified_edge(b, c, INCREASES, citation, evidence)
universe.add_qualified_edge(d, a, ASSOCIATION, citation, evidence)
universe.add_qualified_edge(e, a, INCREASES, citation, evidence)
universe.add_qualified_edge(f, b, DECREASES, citation, evidence)
subgraph = BELGraph()
subgraph.add_qualified_edge(a, b, INCREASES, citation, evidence)
expand_upstream_causal(universe, subgraph)
self.assert_in_graph(a, subgraph)
self.assertIn(FUNCTION, subgraph.node[a.as_tuple()])
self.assertEqual(PROTEIN, subgraph.node[a.as_tuple()][FUNCTION])
self.assert_in_graph(b, subgraph)
self.assert_not_in_graph(c, subgraph)
self.assert_not_in_graph(d, subgraph)
self.assert_in_graph(e, subgraph)
self.assert_in_graph(f, subgraph)
self.assertIn(FUNCTION, subgraph.node[f.as_tuple()])
self.assertEqual(PROTEIN, subgraph.node[f.as_tuple()][FUNCTION])
self.assertEqual(4, subgraph.number_of_nodes())
self.assert_in_edge(e, a, subgraph)
self.assert_in_edge(a, b, subgraph)
self.assert_in_edge(f, b, subgraph)
self.assertEqual(2, len(subgraph[a.as_tuple()][b.as_tuple()]))
self.assertEqual(4, subgraph.number_of_edges(), msg='\n'.join(map(str, subgraph.edges())))
def test_expand_upstream_causal_subgraph(self):
"""Test expanding on the upstream causal subgraph."""
a, b, c, d, e, f = [
protein(namespace='test', name=i)
for i in string.ascii_lowercase[:6]
]
universe = BELGraph()
universe.add_qualified_edge(a, b, INCREASES, n(), n())
universe.add_qualified_edge(b, c, INCREASES, n(), n())
universe.add_qualified_edge(d, a, ASSOCIATION, n(), n())
universe.add_qualified_edge(e, a, INCREASES, n(), n())
universe.add_qualified_edge(f, b, DECREASES, n(), n())
subgraph = BELGraph()
subgraph.add_qualified_edge(a, b, INCREASES, n(), n())
expand_upstream_causal(universe, subgraph)
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertNotIn(c, subgraph)
self.assertNotIn(d, subgraph)
self.assertIn(e, subgraph)
self.assertIn(f, subgraph)
self.assertEqual(4, subgraph.number_of_nodes())
self.assert_in_edge(e, a, subgraph)
self.assert_in_edge(a, b, subgraph)
self.assert_in_edge(f, b, subgraph)
self.assertEqual(2, len(subgraph[a][b]))
self.assertEqual(4,
subgraph.number_of_edges(),
msg='\n'.join(map(str, subgraph.edges())))
def test_expand_upstream_causal_subgraph(self):
"""Test expanding on the upstream causal subgraph."""
a, b, c, d, e, f = [
protein(namespace='test', name=i)
for i in string.ascii_lowercase[:6]
]
universe = BELGraph()
universe.add_increases(a, b, citation=n(), evidence=n())
universe.add_increases(b, c, citation=n(), evidence=n())
universe.add_association(d, a, citation=n(), evidence=n())
universe.add_increases(e, a, citation=n(), evidence=n())
universe.add_decreases(f, b, citation=n(), evidence=n())
subgraph = BELGraph()
subgraph.add_increases(a, b, citation=n(), evidence=n())
expand_upstream_causal(universe, subgraph)
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertNotIn(c, subgraph)
self.assertNotIn(d, subgraph)
self.assertIn(e, subgraph)
self.assertIn(f, subgraph)
self.assertEqual(4, subgraph.number_of_nodes())
self.assert_in_edge(e, a, subgraph)
self.assert_in_edge(a, b, subgraph)
self.assert_in_edge(f, b, subgraph)
self.assertEqual(2, len(subgraph[a][b]))
self.assertEqual(4,
subgraph.number_of_edges(),
msg='\n'.join(map(str, subgraph.edges())))