def setUp(self):
self.eval = ProteinEvaluator(0)
self.logger_mock = self.eval.logger = Mock()
class ProteinEvaluatorTest(unittest.TestCase):
def setUp(self):
self.eval = ProteinEvaluator(0)
self.logger_mock = self.eval.logger = Mock()
def test_init_state(self):
self.assertEqual(self.eval.gold_standard, None)
self.assertEqual(self.eval.results, None)
self.assertEqual(type(self.eval.logger), Mock)
def test_reset(self):
pass # tested by init state already
@patch('__builtin__.len')
def test_prepare(self, len_mock):
# SETUP
self.eval.primary_eval = Mock(spec=ProteinEvaluation)
self.eval.primary_eval.hits = Mock(spec=Hits)
self.eval.primary_eval.hits.fn = 15
self.eval.primary_eval.hits.fp = 0
self.eval.primary_eval.hits.tp = 0
self.eval.primary_eval.hits.tn = 0
gs_mock = Mock(spec=ProteinDataDict)
results_mock = Mock(spec=ProteinDataDict)
# use distinct return value to make sure things are set up right:
gs_mock.true_items.return_value = 10
self.eval.gold_standard = gs_mock
self.eval.results = results_mock
self.eval._process_micro_scores = Mock()
len_mock.return_value = 5 # again to make sure all as expected
# RUN THE TEST
self.eval._prepare()#results_mock, gs_mock)
# ASSERT RESULTS
self.assertEqual(len_mock.call_count, 2)
self.assertEqual(
len_mock.call_args_list,
[ ( (results_mock,), {} ), ( (gs_mock,), {} ) ]
)
self.assert_called_once_with(gs_mock.true_items)
self.assert_called_once_with(self.eval.primary_eval.set_fn, 10)
self.assert_called_once_with(
self.logger_mock.debug, "INT/IPT evaluation: 15 GS annotations"
)
def test_prepare_raises_error(self):
self.eval.results = {1: None, 2: None}
self.eval.gold_standard = {1: None}
self.assertRaises(AssertionError, self.eval._prepare)
self.eval.results = {}
self.assertRaises(AssertionError, self.eval._prepare)
self.eval.results = {1: None, 2: None}
self.eval.gold_standard = {}
self.assertRaises(AssertionError, self.eval._prepare)
def test_process(self):
# SETUP
self.eval.gold_standard = {'a': [1,2,3], 'b': [1,2,3], 'c': [1,2,3]}
self.eval.results = {'a': [4,5,6], 'b': [4,5,6], 'c': [4,5,6]}
self.eval.cutoff = 2
self.eval._process_doi = Mock()
self.eval.primary_eval.store_p_at_current_r = Mock()
self.eval.secondary_eval.store_p_at_current_r = Mock()
# RUN THE TEST
self.eval._process()
# ASSERT RESULTS
self.assertEqual(self.eval._dois, ['a', 'b', 'c'])
self.assertEqual(self.eval._process_doi.call_count, 6)
result_list = []
for r in (0, 1):
for doi in self.eval._dois:
result_list.append(((doi, r), {}))
self.assertEqual(
self.eval._process_doi.call_args_list, result_list
)
self.assertEqual(
self.eval.primary_eval.store_p_at_current_r.call_count, 2
)
def test_process_doi(self):
self.eval.secondary_eval[1] = ProteinEvaluation(1, 3)
self.eval.primary_eval = Mock(spec=ProteinEvaluation)
self.eval._dois = [1]
self.assertEqual(len(self.eval.secondary_eval), 1)
one = Mock()
one.confidence = None
two = Mock()
two.confidence = None
three = Mock()
three.confidence = None
four = Mock()
four.confidence = None
self.eval.gold_standard = {1: [one,two,three]}
self.eval.results = {1: [one, four]}
self.eval._process_doi(1, 0)
self.eval._process_doi(1, 1)
self.eval._process_doi(1, 2)
protein_eval = self.eval.secondary_eval[1]
self.assertEqual(protein_eval.doi, 1)
self.assertEqual(protein_eval.hits.tp, 1)
self.assertEqual(protein_eval.hits.fp, 1)
self.assertEqual(protein_eval.hits.fn, 2)
def assert_called_once_with(self, mock, *args, **kwds):
self.assertEqual(mock.call_count, 1)
self.assertEqual(mock.call_args, (args, kwds))