def test_pipeline(self): graph = egf_graph.copy() enrich_protein_and_rna_origins(graph) self.assertEqual( 32, # 10 protein nodes already there + complex + bp + 2*10 (genes and rnas) graph.number_of_nodes() ) # 6 already there + 5 complex hasComponent edges + new 2*10 edges self.assertEqual(31, graph.number_of_edges()) network = self.manager.insert_graph(graph) pipeline = Pipeline() pipeline.append(collapse_to_genes) query = Query( network_ids=[network.id], pipeline=pipeline ) result_graph = query.run(self.manager) self.assertEqual(12, result_graph.number_of_nodes()) # same number of nodes than there were self.assertEqual(11, result_graph.number_of_edges()) # same number of edges than there were
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_query_multiple_networks_with_api(self): test_network_1 = self.manager.insert_graph(homology_graph.copy()) pipeline = Pipeline() pipeline.append(expand_node_neighborhood, mouse_mapk1_protein) query = Query(network_ids=[test_network_1.id], pipeline=pipeline) query.append_seeding_annotation('Species', {'10090'}) result = query.run(self.manager) self.assertIsNotNone(result, msg='Query returned none') self.assertEqual(3, result.number_of_nodes()) self.assertIn(mouse_mapk1_protein, result) self.assertIn(mouse_csf1_protein, result) self.assertEqual(2, 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())
def setUp(self): """Set up each test with a mock query manager.""" self.manager = MockQueryManager() self.query = Query()
def test_pipeline(self): query = Query(pipeline=Pipeline()) self.assertEqual(0, len(query.pipeline))
def test_seeding(self): query = Query(seeding=Seeding()) self.assertEqual(0, len(query.seeding))
def test_network_ids_type_error(self): with self.assertRaises(TypeError): Query(network_ids='a')
def test_network_ids_multiple(self): query = Query(network_ids=[1, 2, 3]) self.assertIsInstance(query.network_ids, list) self.assertEqual(3, len(query.network_ids))
def test_network_ids_single(self): query = Query(network_ids=1) self.assertIsInstance(query.network_ids, list) self.assertEqual(1, len(query.network_ids))
def test_network_ids_none(self): query = Query() self.assertIsInstance(query.network_ids, list) self.assertIsInstance(query.seeding, Seeding) self.assertIsInstance(query.pipeline, Pipeline) self.assertEqual(0, len(query.network_ids))