def assert_has_edge(
self: unittest.TestCase,
u: BaseEntity,
v: BaseEntity,
graph: BELGraph,
*,
only: bool = False,
permissive: bool = True,
use_identifiers: bool = False,
**expected_edge_data
):
"""A helper function for checking if an edge with the given properties is contained within a graph."""
self.assertIsInstance(u, BaseEntity)
self.assertIsInstance(v, BaseEntity)
self.assertTrue(
graph.has_edge(u, v),
msg='Edge ({}, {}) not in graph. Other edges:\n{}'.format(u, v, '\n'.join(
edge_to_bel(u, v, d, use_identifiers=use_identifiers)
for u, v, d in graph.edges(data=True)
))
)
if not expected_edge_data:
return
if ANNOTATIONS in expected_edge_data:
expected_edge_data[ANNOTATIONS] = graph._clean_annotations(expected_edge_data[ANNOTATIONS])
if only:
_key, actual_edge_data = list(graph[u][v].items())[0]
self.assertEqual(_remove_line(expected_edge_data), _remove_line(actual_edge_data), msg='Only entry not equal')
else:
actual_dicts = {
k: _remove_line(v)
for k, v in graph[u][v].items()
}
if permissive:
matches = any_subdict_matches(actual_dicts, _remove_line(expected_edge_data))
else:
matches = any_dict_matches(actual_dicts, _remove_line(expected_edge_data))
msg = 'No edge ({}, {}) with correct properties. expected:\n {}\nbut got:\n{}'.format(
u,
v,
dumps(expected_edge_data, indent=2, sort_keys=True),
dumps(actual_dicts, indent=2, sort_keys=True),
)
self.assertTrue(matches, msg=msg)
def test_all_filter_dict(self):
graph = BELGraph()
graph.annotation_list['A'] = set('12345')
a, b = Protein(namespace='hgnc', identifier='1', name='A'), Protein(namespace='hgnc', identifier='2', name='B')
graph.add_increases(a, b, citation=n(), evidence=n(), annotations={
'A': {'1', '2', '3'},
})
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({'A': {'1': True}}))))
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({
'A': {'1': True, '2': True}
}))))
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({
'A': {'1': True, '2': True, '3': True}
}))))
self.assertEqual(0, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({
'A': {'1': True, '2': True, '3': True, '4': True}
}))))
self.assertEqual(0, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({
'A': {'4': True}
}))))
def test_all_filter(self):
graph = BELGraph()
graph.annotation_list['A'] = set('12345')
graph.add_increases(Protein(n(), n()), Protein(n(), n()), citation=n(), evidence=n(), annotations={
'A': {'1', '2', '3'},
})
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({'A': {'1'}}))))
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({'A': {'1', '2'}}))))
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({'A': {'1', '2', '3'}}))))
self.assertEqual(0,
count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({'A': {'1', '2', '3', '4'}}))))
self.assertEqual(0, count_passed_edge_filter(graph, build_annotation_dict_all_filter(graph._clean_annotations({'A': {'4'}}))))