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_no_seeding_no_pipeline(self):
graph = egf_graph.copy()
self.add_query(graph)
result = self.run_query()
self.assertEqual(graph.number_of_nodes(), result.number_of_nodes())
self.assertEqual(graph.number_of_edges(), result.number_of_edges())
def test_no_seeding(self):
graph = egf_graph.copy()
seeding = Seeding()
result = seeding.run(graph)
self.assertEqual(graph.number_of_nodes(), result.number_of_nodes())
self.assertEqual(graph.number_of_edges(), result.number_of_edges())
def setUp(self):
self.graph = egf_graph.copy()
self.original_number_nodes = self.graph.number_of_nodes()
self.original_number_edges = self.graph.number_of_edges()
self.manager = MockQueryManager()
self.network_id = self.manager.insert_graph(self.graph).id
build_delete_node_by_hash(self.manager)
build_expand_node_neighborhood_by_hash(self.manager)
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_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):
self.graph = egf_graph.copy()
self.original_number_nodes = self.graph.number_of_nodes()
self.original_number_edges = self.graph.number_of_edges()