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())