class AbstractProteinDataDictTest(unittest.TestCase):
def setUp(self):
self.data = AbstractProteinDataDict()
def test_init_state(self):
pass
def test_map_homonym_orthologs(self):
self.data._mapping_setup = Mock()
self.data.extract_accessions_for = Mock()
self.data._add_ho_gs_mappings_for = Mock()
self.data._map = Mock()
self.data._mapping_logging_and_assertions = Mock()
rc1 = Mock(spec=ResultContainer)
rc1.item = 'a'
rc2 = Mock(spec=ResultContainer)
rc2.item = 'b'
gs = { 1: [rc1, rc2], 2: None, 3: None }
self.data[1] = [rc1, rc2]
self.data[2] = []
self.data.map_homonym_orthologs(sentinel.ho_map, gs)
self.assert_called_once(self.data._mapping_setup, sentinel.ho_map)
self.assert_called_once(self.data._mapping_logging_and_assertions)
self.assert_called_once(self.data._map, 1)
self.assert_called_once(self.data.extract_accessions_for, 1)
self.assert_called_with(
self.data._add_ho_gs_mappings_for, [(('a',), {}), (('b',), {})]
)
def test_mapping_setup(self):
self.data.update( { 1: ['a', 'b'], 2: ['c'], 3: [], 4: ['d'] } )
self.data._mapping_setup(sentinel.ho_map)
self.assertEqual(self.data._ho_map, sentinel.ho_map)
self.assertEqual(self.data._mapped_results, 0)
self.assertEqual(self.data._added_results, 0)
self.assertEqual(self.data._filtered_results, 0)
self.assertEqual(self.data._ho_gs_lists, None)
self.assertEqual(self.data._result_accessions, None)
self.assertEqual(self.data._result_container, None)
self.assertEqual(self.data._replaced_an_entry, False)
self.assertEqual(self.data._old_results_size, 4)
def test_add_ho_gs_mappings_for(self):
self.data._item_in_ho_map = Mock()
self.data._item_in_ho_map.return_value = True
self.data._item_iterator = Mock()
self.data._item_iterator.return_value = [1, 2, 3]
self.data._ho_gs_lists = { 1: [], 2: [], 3: [] }
self.data._gs_items = [1]
self.data._add_ho_gs_mappings_for('a')
self.assert_called_once(self.data._item_in_ho_map, 'a')
self.assert_called_once(self.data._item_iterator, 'a')
self.assertEqual(
self.data._ho_gs_lists, { 1: [], 2: ['a'], 3: ['a'] }
)
def test_map(self):
self.data[1] = ['a', 'b', 'c']
self.data._map_replace = Mock()
def set_flag(result_container):
self.data._replaced_an_entry = True
self.data._map_replace.side_effect = set_flag
self.data._remove_duplicates = Mock()
self.data._remove_duplicates.return_value = sentinel.new_results
self.data._rerank_results = Mock()
result = self.data._map(1)
self.assertEqual(result, sentinel.new_results)
self.assertEqual(self.data._replaced_an_entry, True)
self.assert_called_once(
self.data._map_replace, ['a', 'b', 'c']
)
self.assert_called_once(
self.data._remove_duplicates, ['a', 'b', 'c']
)
self.assert_called_once(
self.data._rerank_results, sentinel.new_results
)
def assert_called_once(self, mock, *args, **kwds):
self.assertEqual(mock.call_count, 1)
self.assert_called_with(mock, [(args, kwds)])
def assert_called_with(self, mock, arg_list):
self.assertEqual(mock.call_args_list, arg_list)
def setUp(self):
self.data = AbstractProteinDataDict()
