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())
class QueryTestEgf(unittest.TestCase):
"""Test querying the EGF subgraph"""
def setUp(self):
"""Set up each test with a mock query manager."""
self.manager = MockQueryManager()
self.query = Query()
def add_query(self, graph):
add(self.query, self.manager, graph)
return self.query
def run_query(self):
return self.query.run(self.manager)
def test_fail_run_with_no_networks(self):
with self.assertRaises(QueryMissingNetworksError):
self.run_query()
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_seed_by_neighbor(self):
graph = BELGraph()
a, b, c, d = (Protein(namespace=n(), name=str(i)) for i in range(4))
graph.add_increases(a, b, n(), n())
graph.add_increases(b, c, n(), n())
graph.add_increases(c, d, n(), n())
self.add_query(graph).append_seeding_neighbors(b)
result = self.run_query()
self.assertIsInstance(result, BELGraph)
# test nodes
self.assertIn(a, result)
self.assertIn(b, result)
self.assertIn(c, result)
self.assertNotIn(d, result)
# test edges
self.assertIn(b, result[a])
self.assertIn(c, result[b])
self.assertNotIn(d, result[c])
def test_seed_by_neighbors(self):
graph = BELGraph()
a, b, c, d, e = (Protein(namespace=n(), name=str(i)) for i in range(5))
graph.add_increases(a, b, n(), n())
graph.add_increases(b, c, n(), n())
graph.add_increases(c, d, n(), n())
graph.add_increases(d, e, n(), n())
self.add_query(graph).append_seeding_neighbors([b, c])
result = self.run_query()
self.assertIsInstance(result, BELGraph)
# test nodes
self.assertIn(a, result)
self.assertIn(b, result)
self.assertIn(c, result)
self.assertIn(d, result)
self.assertNotIn(e, result)
# test edges
self.assertIn(b, result[a])
self.assertIn(c, result[b])
self.assertIn(d, result[c])
self.assertNotIn(e, result[d])
def test_random_sample(self):
"""Test generating multiple random samples and combining them."""
graph = generate_random_graph(50, 1000)
query = self.add_query(graph)
query.append_seeding_sample(number_edges=10)
query.append_seeding_sample(number_edges=10)
result = self.run_query()
# this will fail randomly sometimes, lol
self.assertIn(result.number_of_edges(), {18, 19, 20})
