def test_mock_contents(self):
nfkb_complex_tuple = egf_example.nfkb_complex.as_tuple()
rela_tuple = egf_example.rela.as_tuple()
self.assertIn(nfkb_complex_tuple, self.manager.graphs[0], msg='Graph missing NFKB complex')
self.assertIn(rela_tuple, self.manager.graphs[0], msg='Graph missing RELA')
self.assertIn(nfkb_complex_tuple, self.manager.hash_to_tuple.values(), msg='NFKB is unindexed')
self.assertIn(rela_tuple, self.manager.hash_to_tuple.values(), msg='RELA is unindexed')
self.assertIn(hash_node(nfkb_complex_tuple), self.manager.hash_to_tuple.keys(), msg='NFKB is unindexed')
self.assertIn(hash_node(rela_tuple), self.manager.hash_to_tuple.keys(), msg='RELA is unindexed')
def test_bound_mutation(self):
"""Tests when a node is deleted then re-expanded"""
pipeline = Pipeline(universe=self.graph)
pipeline.append('delete_node_by_hash', hash_node(egf_example.nfkb_complex.as_tuple()))
pipeline.append('expand_node_neighborhood_by_hash', hash_node(egf_example.rela.as_tuple()))
result = pipeline.run(self.graph, in_place=False)
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 test_complex_with_name(self):
"""Tests a what happens with a named complex
.. code-block::
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:HUS1)
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:RAD1)
complex(SCOMP:"9-1-1 Complex") hasComponent p(HGNC:RAD9A)
"""
hus1 = protein(namespace='HGNC', name='HUS1')
rad1 = protein(namespace='HGNC', name='RAD1')
rad9a = protein(namespace='HGNC', name='RAD9A')
members = [hus1, rad1, rad9a]
nine_one_one = complex_abundance(members=members,
namespace='SCOMP',
name='9-1-1 Complex')
node_tuple = (COMPLEX, ) + tuple(member.as_tuple()
for member in members)
self.assertEqual(node_tuple, nine_one_one.as_tuple())
self.assertEqual(hash(node_tuple), hash(nine_one_one))
self.assertEqual(hash_node(node_tuple), nine_one_one.as_sha512())
def test_as_tuple(self):
namespace, name = n(), n()
node_tuple = ABUNDANCE, namespace, name
node = abundance(namespace=namespace, name=name)
self.assertEqual(node_tuple, node.as_tuple())
self.assertEqual(hash(node_tuple), hash(node))
self.assertEqual(hash_node(node_tuple), node.as_sha512())
def insert_graph(self, graph):
"""Inserts a graph
:param pybel.BELGraph graph:
:rtype: Network
"""
network_id = len(self.graphs)
self.graphs.append(graph)
self.id_graph[network_id] = graph
for node in graph:
if not isinstance(node, tuple):
raise TypeError(node)
self.hash_to_tuple[hash_node(node)] = node
return MockNetwork(id=network_id)
def add_identifiers(graph): # FIXME this function shouldn't have to exist.
"""Adds stable node and edge identifiers to the graph, in-place using the PyBEL
node and edge hashes as a hexadecimal str.
:param pybel.BELGraph graph: A BEL Graph
"""
for node, data in graph.iter_node_data_pairs():
if HASH in data:
continue
canonical_node_tuple = node_to_tuple(data)
canonical_node_hash = hash_node(canonical_node_tuple)
graph.node[node][HASH] = canonical_node_hash
for u, v, k, data in graph.edges_iter(keys=True, data=True):
if HASH in data:
continue
graph.edge[u][v][k][HASH] = hash_edge(u, v, data)