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)
class TestBoundMutation(unittest.TestCase):
"""Random test for mutation functions."""
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 tearDown(self):
"""Remove definitions of the built functions"""
del mapped['expand_node_neighborhood_by_hash']
del mapped['delete_node_by_hash']
def test_functions_registered(self):
self.assertIn('delete_node_by_hash', mapped)
self.assertIn('expand_node_neighborhood_by_hash', mapped)
def check_original_unchanged(self):
self.assertEqual(self.original_number_nodes, self.graph.number_of_nodes(),
msg='original graph nodes should remain unchanged')
self.assertEqual(self.original_number_edges, self.graph.number_of_edges(),
msg='original graph edges should remain unchanged')
def test_mock_contents(self):
self.assertIn(nfkb_complex, self.graph, msg='Graph missing NFKB complex')
self.assertIn(rela, self.graph, msg='Graph missing RELA')
self.assertIn(nfkb_complex.md5, self.manager.hash_to_node, msg='NFKB is unindexed')
self.assertIn(rela.md5, self.manager.hash_to_node, msg='RELA is unindexed')
self.assertIn(nfkb_complex, self.manager.hash_to_node.values(), msg='NFKB is unindexed')
self.assertIn(rela, self.manager.hash_to_node.values(), msg='RELA is unindexed')
def test_bound_mutation(self):
"""Test when a node is deleted then re-expanded."""
pipeline = Pipeline()
pipeline.append('delete_node_by_hash', nfkb_complex.md5)
pipeline.append('expand_node_neighborhood_by_hash', rela.md5)
result = pipeline.run(self.graph)
self.check_original_unchanged()
self.assertEqual(self.original_number_nodes, result.number_of_nodes())
self.assertGreater(self.original_number_edges, result.number_of_edges())
def setUp(self):
"""Set up each test with a mock query manager."""
self.manager = MockQueryManager()
self.query = Query()
def setUp(self):
"""Setup each test with an empty mock query manager."""
self.manager = MockQueryManager()
class QueryTest(unittest.TestCase):
"""Test the query"""
def setUp(self):
"""Setup each test with an empty mock query manager."""
self.manager = MockQueryManager()
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_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 test_get_subgraph_by_annotation_value(self):
graph = homology_graph.copy()
result = get_subgraph_by_annotation_value(graph, 'Species', '10090')
self.assertIsNotNone(result, msg='Query returned none')
self.assertIsInstance(result, BELGraph)
self.assertLess(0, result.number_of_nodes())
self.assertIn(mouse_mapk1_protein,
result,
msg='nodes:\n{}'.format(list(map(repr, graph))))
self.assertIn(mouse_csf1_protein, result)
self.assertEqual(2, result.number_of_nodes())
self.assertEqual(1, result.number_of_edges())
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_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_add_graph(self):
"""Test adding a graph with insert_graph."""
manager = MockQueryManager()
graph = egf_graph.copy()
manager.insert_graph(graph)
self.assertEqual(1, manager.count_networks())
def test_make_with_graph(self):
"""Test counting networks in the mock query manager."""
manager = MockQueryManager(graphs=[egf_graph])
self.assertEqual(1, manager.count_networks())
def test_make(self):
"""Test instantiating the mock query manager."""
manager = MockQueryManager()
self.assertEqual(0, manager.count_networks())