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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| import logging | ||
| from absl.testing import parameterized | ||
| from unittest import mock | ||
| from alphapulldown.utils.modelling_setup import parse_fold | ||
|
|
||
| """ | ||
| Test parse_fold function with different scenarios | ||
| """ | ||
|
|
||
| class TestParseFold(parameterized.TestCase): | ||
|
|
||
| def setUp(self) -> None: | ||
| super().setUp() | ||
| # Set logging level to INFO | ||
| logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s') | ||
|
|
||
| @parameterized.named_parameters( | ||
| { | ||
| 'testcase_name': 'single_protein_no_copy', | ||
| 'input': ['protein1'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': True, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| }, | ||
| 'expected_result': [[{'protein1': 'all'}]], | ||
| }, | ||
| { | ||
| 'testcase_name': 'single_protein_with_copy_number', | ||
| 'input': ['protein1:2'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': True, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| }, | ||
| 'expected_result': [[{'protein1': 'all'}, {'protein1': 'all'}]], | ||
| }, | ||
| { | ||
| 'testcase_name': 'single_protein_with_region', | ||
| 'input': ['protein1:1-10'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': True, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| }, | ||
| 'expected_result': [[{'protein1': [(1, 10)]}]], | ||
| }, | ||
| { | ||
| 'testcase_name': 'single_protein_with_copy_and_regions', | ||
| 'input': ['protein1:2:1-10:20-30'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': True, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| }, | ||
| 'expected_result': [[{'protein1': [(1, 10), (20, 30)]}, {'protein1': [(1, 10), (20, 30)]}]], | ||
| }, | ||
| { | ||
| 'testcase_name': 'multiple_proteins', | ||
| 'input': ['protein1:2_protein2:1-50'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': True, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| 'dir1/protein2.pkl': True, | ||
| 'dir1/protein2.pkl.xz': False, | ||
| }, | ||
| 'expected_result': [[{'protein1': 'all'}, {'protein1': 'all'}, {'protein2': [(1, 50)]}]], | ||
| }, | ||
| { | ||
| 'testcase_name': 'missing_features', | ||
| 'input': ['protein1', 'protein2'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': False, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| 'dir1/protein2.pkl': False, | ||
| 'dir1/protein2.pkl.xz': False, | ||
| }, | ||
| 'expected_exception': FileNotFoundError, | ||
| 'expected_exception_message': "['protein1', 'protein2'] not found in ['dir1']", | ||
| }, | ||
| { | ||
| 'testcase_name': 'invalid_format', | ||
| 'input': ['protein1::1-10'], | ||
| 'features_directory': ['dir1'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': {}, | ||
| 'expected_exception': SystemExit, | ||
| }, | ||
| { | ||
| 'testcase_name': 'feature_exists_in_multiple_dirs', | ||
| 'input': ['protein1'], | ||
| 'features_directory': ['dir1', 'dir2'], | ||
| 'protein_delimiter': '_', | ||
| 'mock_side_effect': { | ||
| 'dir1/protein1.pkl': False, | ||
| 'dir1/protein1.pkl.xz': False, | ||
| 'dir2/protein1.pkl': True, | ||
| 'dir2/protein1.pkl.xz': False, | ||
| }, | ||
| 'expected_result': [[{'protein1': 'all'}]], | ||
| }, | ||
| ) | ||
| def test_parse_fold(self, input, features_directory, protein_delimiter, mock_side_effect, | ||
| expected_result=None, expected_exception=None, expected_exception_message=None): | ||
| """Test parse_fold with different input scenarios""" | ||
| with mock.patch('alphapulldown.utils.modelling_setup.exists') as mock_exists, \ | ||
| mock.patch('sys.exit') as mock_exit: | ||
| mock_exists.side_effect = lambda path: mock_side_effect.get(path, False) | ||
| # Mock sys.exit to raise SystemExit exception | ||
| mock_exit.side_effect = SystemExit | ||
| logging.info(f"Testing with input: {input}, features_directory: {features_directory}, " | ||
| f"protein_delimiter: '{protein_delimiter}'") | ||
| logging.info(f"Mock side effects: {mock_side_effect}") | ||
| if expected_exception: | ||
| with self.assertRaises(expected_exception) as context: | ||
| result = parse_fold(input, features_directory, protein_delimiter) | ||
| if expected_exception_message: | ||
| self.assertEqual(str(context.exception), expected_exception_message) | ||
| else: | ||
| result = parse_fold(input, features_directory, protein_delimiter) | ||
| logging.info(f"Result: {result}, Expected: {expected_result}") | ||
| self.assertEqual(result, expected_result) |
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Nice, will test!