def test_build_pmid_inclusion_filter(self):
"""Test getting a sub-graph by a single PubMed identifier."""
a, b, c, d = [protein(namespace='test', name=n()) for _ in range(4)]
p1, p2, p3, p4 = n(), n(), n(), n()
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
graph.add_increases(a, b, n(), citation=p1)
graph.add_increases(a, b, n(), citation=p2)
graph.add_increases(b, c, n(), citation=p1)
graph.add_increases(b, c, n(), citation=p3)
graph.add_increases(c, d, n(), citation=p3)
subgraph = get_subgraph_by_pubmed(graph, p1)
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(c, subgraph)
self.assertNotIn(d, subgraph)
empty_subgraph = get_subgraph_by_pubmed(graph, p4)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertEqual(0, empty_subgraph.number_of_nodes())
def test_build_pmid_set_inclusion_filter(self):
"""Test getting a sub-graph by a set of PubMed identifiers."""
a, b, c, d, e, f = [protein(namespace='test', name=n()) for _ in range(6)]
p1, p2, p3, p4, p5, p6 = n(), n(), n(), n(), n(), n()
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
graph.add_increases(a, b, n(), citation=p1)
graph.add_increases(a, b, n(), citation=p2)
graph.add_increases(b, c, n(), citation=p1)
graph.add_increases(b, c, n(), citation=p3)
graph.add_increases(c, d, n(), citation=p3)
graph.add_increases(e, f, n(), citation=p4)
subgraph = get_subgraph_by_pubmed(graph, [p1, p4])
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assert_in_graph(a, subgraph)
self.assert_in_graph(b, subgraph)
self.assert_in_graph(c, subgraph)
self.assert_not_in_graph(d, subgraph)
self.assert_in_graph(e, subgraph)
self.assert_in_graph(f, subgraph)
empty_subgraph = get_subgraph_by_pubmed(graph, [p5, p6])
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertEqual(0, empty_subgraph.number_of_nodes())
