def test_infer_on_sialic_acid_example(self):
sgc = sialic_acid_graph.copy()
self.assertFalse(sgc.has_node_with_data(trem2_gene))
self.assertFalse(sgc.has_node_with_data(trem2_rna))
infer_central_dogma(sgc)
self.assertTrue(sgc.has_node_with_data(trem2_gene))
self.assertTrue(sgc.has_node_with_data(trem2_rna))
prune_central_dogma(sgc)
self.assertFalse(sgc.has_node_with_data(trem2_gene))
self.assertFalse(sgc.has_node_with_data(trem2_rna))
def test_add_and_remove_annotation(self):
"""Test adding and removing annotations.
See: :func:`pybel.struct.mutation.add_annotation_value` and
:func:`pybel.struct.mutation.remove_annotation_value` functions.
"""
graph = sialic_acid_graph.copy()
annotation = 'test-annotation'
value = 'test-value'
url = n()
graph.annotation_url[annotation] = url
add_annotation_value(graph, annotation, value)
for u, v, d in graph.edges(data=True):
annotations = d.get(ANNOTATIONS)
if annotations is None:
continue
self.assertIn(annotation, annotations)
self.assertIn(value, annotations[annotation])
remove_annotation_value(graph, annotation, value)
for u, v, d in graph.edges(data=True):
annotations = d.get(ANNOTATIONS)
if annotations is None:
continue
annotation_values = annotations.get(annotation)
if annotation_values is None:
continue
self.assertNotIn(value, annotation_values)
def test_reload(self, mock_get):
"""Test that a graph with the same name and version can't be added twice."""
graph = sialic_acid_graph.copy()
self.assertEqual('1.0.0', graph.version)
to_database(graph, manager=self.manager)
time.sleep(1)
self.assertEqual(1, self.manager.count_networks())
networks = self.manager.list_networks()
self.assertEqual(1, len(networks))
network = networks[0]
self.assertEqual(graph.name, network.name)
self.assertEqual(graph.version, network.version)
self.assertEqual(graph.description, network.description)
reconstituted = self.manager.get_graph_by_name_version(
graph.name, graph.version)
self.assertIsInstance(reconstituted, BELGraph)
self.assertEqual(graph.nodes(data=True),
reconstituted.nodes(data=True))
# self.bel_thorough_reconstituted(reconstituted)
self.assertEqual(1, self.manager.count_networks())
graph_copy = graph.copy()
graph_copy.version = '1.0.1'
network_copy = self.manager.insert_graph(graph_copy)
time.sleep(
1) # Sleep so the first graph always definitely goes in first
self.assertNotEqual(network.id, network_copy.id)
self.assertTrue(
self.manager.has_name_version(graph_copy.name, graph_copy.version))
self.assertFalse(self.manager.has_name_version('wrong name', '0.1.2'))
self.assertFalse(
self.manager.has_name_version(graph_copy.name, '0.1.2'))
self.assertFalse(
self.manager.has_name_version('wrong name', graph_copy.version))
self.assertEqual(2, self.manager.count_networks())
self.assertEqual(
'1.0.1',
self.manager.get_most_recent_network_by_name(graph.name).version)
query_ids = {-1, network.id, network_copy.id}
query_networks_result = self.manager.get_networks_by_ids(query_ids)
self.assertEqual(2, len(query_networks_result))
self.assertEqual({network.id, network_copy.id},
{network.id
for network in query_networks_result})
expected_versions = {'1.0.1', '1.0.0'}
self.assertEqual(expected_versions,
set(self.manager.get_network_versions(graph.name)))
exact_name_version = from_database(graph.name,
graph.version,
manager=self.manager)
self.assertEqual(graph.name, exact_name_version.name)
self.assertEqual(graph.version, exact_name_version.version)
exact_name_version = from_database(graph.name,
'1.0.1',
manager=self.manager)
self.assertEqual(graph.name, exact_name_version.name)
self.assertEqual('1.0.1', exact_name_version.version)
most_recent_version = from_database(graph.name, manager=self.manager)
self.assertEqual(graph.name, most_recent_version.name)
self.assertEqual('1.0.1', exact_name_version.version)
recent_networks = list(self.manager.list_recent_networks()
) # just try it to see if it fails
self.assertIsNotNone(recent_networks)
self.assertEqual([(network.name, '1.0.1')],
[(n.name, n.version) for n in recent_networks])
self.assertEqual('1.0.1', recent_networks[0].version)