def test_set_ontology(self):
ontology = OntologyFactory().create()
for i in range(4):
ontology.add_node(i, 'node' + str(i))
ontology.add_parent(1, 0)
ontology.add_parent(2, 0)
ontology.add_parent(3, 0)
self.df.set_ontology(ontology_type=DataType.GO, ontology=ontology, config=self.conf_parser)
self.assertTrue(list(self.df.go_ontology.nodes()) == list(ontology.nodes()))
def test_set_covering_with_ontology(self):
# 0 ic(0) = 0
# /| |\
# / | | \
# 1 2 3 4 ic(1) = 0.693147181, ic(2) = 0.470003629, ic(3) = 0.980829253
# /\ /\/ \/
# / 5 6 7 ic(5) = 0.980829253, ic(6) = 1.16315081, ic(7) = 1.16315081
# / /\ \/
# / 8 9 10 ic(8) = 1.049822124, ic(10) = 1.252762968
# \ / \/ \
# 11 12 13 ic(11) = 1.386294361, ic(12) = 1.386294361, ic(13) = 1.386294361
ontology = OntologyFactory().create()
for i in range(14):
ontology.add_node(i, 'node' + str(i))
ontology.add_parent(1, 0)
ontology.add_parent(2, 0)
ontology.add_parent(3, 0)
ontology.add_parent(4, 0)
ontology.add_parent(5, 1)
ontology.add_parent(5, 2)
ontology.add_parent(6, 2)
ontology.add_parent(6, 3)
ontology.add_parent(7, 3)
ontology.add_parent(7, 4)
ontology.add_parent(8, 5)
ontology.add_parent(9, 5)
ontology.add_parent(10, 6)
ontology.add_parent(10, 7)
ontology.add_parent(11, 1)
ontology.add_parent(11, 8)
ontology.add_parent(12, 8)
ontology.add_parent(12, 9)
ontology.add_parent(13, 10)
subsets = [
CommonAncestor(node_id=1,
node_label="1",
covered_starting_nodes={"11", "12"}),
CommonAncestor(node_id=2,
node_label="2",
covered_starting_nodes={"11", "12", "13"}),
CommonAncestor(node_id=3,
node_label="3",
covered_starting_nodes={"13"}),
CommonAncestor(node_id=4,
node_label="4",
covered_starting_nodes={"13"}),
CommonAncestor(node_id=5,
node_label="2",
covered_starting_nodes={"11", "12"}),
CommonAncestor(node_id=6,
node_label="6",
covered_starting_nodes={"13"}),
CommonAncestor(node_id=7,
node_label="7",
covered_starting_nodes={"13"}),
CommonAncestor(node_id=8,
node_label="8",
covered_starting_nodes={"11", "12"}),
CommonAncestor(node_id=9,
node_label="9",
covered_starting_nodes={"12"}),
CommonAncestor(node_id=10,
node_label="10",
covered_starting_nodes={"13"}),
CommonAncestor(node_id=11,
node_label="11",
covered_starting_nodes={"11"}),
CommonAncestor(node_id=12,
node_label="12",
covered_starting_nodes={"12"}),
CommonAncestor(node_id=13,
node_label="13",
covered_starting_nodes={"13"})
]
values = [1, 1, 1, 1, 1, 1, 1, 20, 1, 1, 100, 1, 1]
res = find_set_covering(subsets=subsets,
ontology=ontology,
value=values,
max_num_subsets=2)
self.assertTrue(all([sub[0] != 11 for sub in res]))