def test_pipeline_2(self):
graph = egf_graph.copy()
network = self.manager.insert_graph(graph)
network_id = network.id
query = Query(network_ids=[network_id])
query.append_seeding_neighbors(vcp)
query.append_pipeline(get_subgraph_by_annotation_value, 'Species', '9606')
result = query.run(self.manager)
self.assertIsNotNone(result, msg='Query returned none')
self.assertEqual(3, result.number_of_nodes())
def test_seeding_1(self):
test_network_1 = self.manager.insert_graph(homology_graph.copy())
query = Query(network_ids=[test_network_1.id])
query.append_seeding_neighbors([mouse_csf1_rna, mouse_mapk1_rna])
result = query.run(self.manager)
self.assertIsNotNone(result, msg='Query returned none')
self.assertIsInstance(result, BELGraph)
self.assertIn(mouse_mapk1_rna, result)
self.assertIn(mouse_csf1_rna, result)
self.assertIn(mouse_mapk1_protein, result)
self.assertIn(mouse_csf1_protein, result)
self.assertEqual(6, result.number_of_nodes())
self.assertEqual(4, result.number_of_edges())
def test_seeding_with_pipeline(self):
test_network_1 = self.manager.insert_graph(sialic_acid_graph.copy())
query = Query(network_ids=[test_network_1.id])
query.append_seeding_neighbors([trem2, dap12, shp2])
query.append_pipeline(expand_nodes_neighborhoods, [trem2, dap12, shp2])
result = query.run(self.manager)
self.assertIsNotNone(result, msg='Query returned none')
self.assertIsInstance(result, BELGraph)
self.assertIn(trem2, result)
self.assertIn(dap12, result)
self.assertIn(shp2, result)
self.assertIn(syk, result)
self.assertIn(cd33_phosphorylated, result)
self.assertEqual(5, result.number_of_nodes())
self.assertEqual(4, result.number_of_edges())
def test_query_multiple_networks(self):
sialic_acid_graph_id = self.manager.insert_graph(sialic_acid_graph.copy()).id
egf_graph_id = self.manager.insert_graph(egf_graph.copy()).id
query = Query()
query.append_network(sialic_acid_graph_id)
query.append_network(egf_graph_id)
query.append_seeding_neighbors([syk])
query.append_pipeline(enrich_protein_and_rna_origins)
result = query.run(self.manager)
self.assertIsNotNone(result, msg='Query returned none')
self.assertIn(shp1, result)
self.assertIn(shp2, result)
self.assertIn(trem2, result)
self.assertIn(dap12, result)
self.assertEqual(15, result.number_of_nodes())
self.assertEqual(14, result.number_of_edges())
