def random_protein_result():
results = list(set([randint(1, 100) for i in range(100)]))
gold_standard = sample(range(1, 101), 10)
evaluator = ProteinEvaluation(doi="test", fn=len(gold_standard))
evaluator.evaluate(results, gold_standard, 0)
return evaluator
class ProteinEvaluationTest(CalculationAssertions):
@patch('biocreative.evaluation.calculation.hits.Hits', spec=True)
def setUp(self, unused):
self.evaluator = ProteinEvaluation()
for attr in C.HITS_ATTRIBUTES:
setattr(self.evaluator.hits, attr, 2)
def test_f_score(self):
self.assert_property("f_score", 0.5)
def test_evaluate_tp_item(self):
self.evaluator.evaluate_item(1, [0,1,2])
self.assert_hits(self.evaluator.hits, tp=3, fp=2, fn=1)
def test_evaluate_fp_item(self):
self.evaluator.evaluate_item(3, [0,1,2])
self.assert_hits(self.evaluator.hits, tp=2, fp=3, fn=2)
def test_evaluate_item_with_illegal_std_items(self):
self.assertRaises(
AssertionError, self.evaluator.evaluate_item, 1, (0,1,2)
)
def test_evaluate(self):
self.evaluator.evaluate_item = Mock()
self.evaluator.store_p_at_current_r = Mock()
gs_set = [0,1,2]
self.evaluator.evaluate([3,4,1,2], gs_set, 3)
self.assertTrue(self.evaluator.store_p_at_current_r.called)
self.assertEqual(self.evaluator.store_p_at_current_r.call_count, 3)
self.assertTrue(self.evaluator.evaluate_item.called)
self.assertEqual(self.evaluator.evaluate_item.call_count, 3)
arg_list = self.evaluator.evaluate_item.call_args_list
exp_list = (((3, gs_set), {}), ((4, gs_set), {}), ((1, gs_set), {}))
for call, args in enumerate(arg_list):
self.assert_values(
"evaluate_item call %i" % (call + 1), exp_list[call], args
)
def test_evaluate_with_illegal_result_items(self):
self.assertRaises(
AssertionError, self.evaluator.evaluate, (1,2,3), set([0,1,2]), 2
)
def set_up_avrg_p_test(self):
for hits in (
{'tp': 1, 'fp': 0, 'fn': 2, 'tn': 0}, # p=1.0, r=0.33
{'tp': 1, 'fp': 1, 'fn': 2, 'tn': 0}, # p=0.5, r=0.33
{'tp': 2, 'fp': 1, 'fn': 1, 'tn': 0}, # p=0.66, r=0.66
{'tp': 2, 'fp': 2, 'fn': 1, 'tn': 0}, # p=0.5, r=0.66
{'tp': 2, 'fp': 3, 'fn': 1, 'tn': 0}, # p=0.4, r=0.66
{'tp': 3, 'fp': 3, 'fn': 0, 'tn': 0}, # p=0.5, r=1.0
):
for attr, value in hits.items():
setattr(self.evaluator.hits, attr, value)
self.evaluator.store_p_at_current_r()
self.p_at_full_r = 0.5
self.avrg_p_values = [(1/1.0, 1/3.0), (2/3.0, 2/3.0), (3/6.0, 3/3.0)]
self.pr_values = (
(1/1.0, 1/3.0), (1/2.0, 1/3.0),
(2/3.0, 2/3.0), (2/5.0, 2/3.0),
(3/6.0, 3/3.0),
)
self.avrg_p = 0.0
last_r = 0.0
for p, r in self.avrg_p_values:
self.avrg_p += p * (r - last_r)
last_r = r
def test_avrg_p_properties(self):
self.set_up_avrg_p_test()
self.assert_property("p_at_full_r", self.p_at_full_r)
self.assert_property("avrg_p", self.avrg_p)
def test_pr_values(self):
self.set_up_avrg_p_test()
pr_values = tuple(self.evaluator.yield_precision_recall_pairs())
self.assertEqual(pr_values, self.pr_values)
