def test_all_filter(self):
graph = BELGraph()
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({'A': {'1'}})))
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'1', '2'}})))
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'1', '2',
'3'}})))
self.assertEqual(
0,
count_passed_edge_filter(
graph,
build_annotation_dict_all_filter({'A': {'1', '2', '3', '4'}})))
self.assertEqual(
0,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'4'}})))
def test_all_filter(self):
graph = BELGraph()
graph.add_edge(1, 2, annotations={'A': {'1', '2', '3'}})
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'1'}})))
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'1', '2'}})))
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'1', '2',
'3'}})))
self.assertEqual(
0,
count_passed_edge_filter(
graph,
build_annotation_dict_all_filter({'A': {'1', '2', '3', '4'}})))
self.assertEqual(
0,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'4'}})))
def test_any_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_any_filter(graph._clean_annotations({'A': {'1'}}))))
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_any_filter(graph._clean_annotations({'A': {'1', '2'}}))))
self.assertEqual(1, count_passed_edge_filter(graph, build_annotation_dict_any_filter(graph._clean_annotations({'A': {'1', '2', '3'}}))))
def test_all_filter_no_annotations(self):
graph = BELGraph()
graph.add_increases(protein(n(), n()), protein(n(), n()), n(), n())
self.assertEqual(
0,
count_passed_edge_filter(
graph, build_annotation_dict_all_filter({'A': {'1'}})))
def summarize_edge_filter(graph: BELGraph,
edge_predicates: EdgePredicates) -> None:
"""Print a summary of the number of edges passing a given set of filters."""
passed = count_passed_edge_filter(graph, edge_predicates)
e = (', '.join(edge_filter.__name__ for edge_filter in edge_predicates) if
isinstance(edge_predicates, Iterable) else edge_predicates.__name__)
print(f'{passed}/{graph.number_of_edges()} edges passed {e}')
def test_all_filter_no_query(self):
"""Test that the all filter returns true when there's no argument"""
graph = BELGraph()
graph.add_increases(protein(n(), n()), protein(n(), n()), n(), n())
self.assertEqual(
1,
count_passed_edge_filter(graph,
build_annotation_dict_all_filter({})))
def test_any_filter(self):
graph = BELGraph()
graph.add_increases(protein(n(), n()),
protein(n(), n()),
n(),
n(),
annotations={'A': {'1', '2', '3'}})
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_any_filter({'A': {'1'}})))
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_any_filter({'A': {'1', '2'}})))
self.assertEqual(
1,
count_passed_edge_filter(
graph, build_annotation_dict_any_filter({'A': {'1', '2',
'3'}})))
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 summarize_edge_filter(graph, edge_filters):
"""Prints a summary of the number of edges passing a given set of filters
:param pybel.BELGraph graph: A BEL graph
:param edge_filters: A filter or list of filters
:type edge_filters: (pybel.BELGraph, tuple, tuple, int) -> bool or iter[(pybel.BELGraph, tuple, tuple, int) -> bool]
"""
passed = count_passed_edge_filter(graph, edge_filters)
print('{}/{} edges passed {}'.format(
passed, graph.number_of_edges(),
(', '.join(edge_filter.__name__ for edge_filter in edge_filters)
if isinstance(edge_filters, Iterable) else edge_filters.__name__)))
def test_concatenate_multiple_edge_filter(self):
def has_odd_source(graph, u, v, k):
return u % 2 != 0
def has_even_target(graph, u, v, k):
return v % 2 == 0
edges = make_edge_iterator_set(filter_edges(self.universe, [has_odd_source, has_even_target]))
self.assertEqual({(1, 2), (1, 4), (5, 6)}, edges)
self.assertEqual(3, count_passed_edge_filter(self.universe, [has_odd_source, has_even_target]))
has_even_source = invert_edge_predicate(has_odd_source)
edges = make_edge_iterator_set(filter_edges(self.universe, has_even_source))
self.assertEqual({(2, 3), (8, 2)}, edges)
