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add a positive test for _pubchem_smiles_to_inchikey (#1451)
* Add detailed docstrings and usage examples to Ersilia'a publish module and few update on the utils module (#1448) * Merge sample command with the example command (#1422) * Merge sample command with the example command * Fix example command usage * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Some import cleanup * Few code fixes * Few code fixes * Add detailed docstrings and usage examples to Ersilia'a utils module * Add detailed docstrings and usage examples to Ersilia'a utils module * Merge sample command with the example command (#1422) * Merge sample command with the example command * Fix example command usage * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Some import cleanup --------- Co-authored-by: Dhanshree Arora <[email protected]> * add a positive test for _pubchem_smiles_to_inchikey Signed-off-by: olamidepeterojo <[email protected]> --------- Signed-off-by: olamidepeterojo <[email protected]> Co-authored-by: Abel Legese <[email protected]> Co-authored-by: Dhanshree Arora <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,190 +1,204 @@ | ||
| from ersilia.default import UNPROCESSABLE_INPUT | ||
| import pytest | ||
| from ersilia.utils.identifiers.compound import CompoundIdentifier | ||
| from unittest.mock import patch | ||
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| @pytest.fixture | ||
| def compound_identifier(): | ||
| return CompoundIdentifier() | ||
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| @pytest.mark.parametrize("header", ["smiles", "input", "SMILES", "INPUT"]) | ||
| def test_is_input_header_positive(compound_identifier, header): | ||
| """Test that valid input headers return True.""" | ||
| assert compound_identifier.is_input_header(header) is True | ||
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| @pytest.mark.parametrize("header", ["output", "invalid", "InChI", "inchikey"]) | ||
| def test_is_input_header_negative(compound_identifier, header): | ||
| """Test that invalid input headers return False.""" | ||
| assert compound_identifier.is_input_header(header) is False | ||
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| @pytest.mark.parametrize("header", ["key", "inchiKey", "KEY", "INCHIKEY"]) | ||
| def test_is_key_header_positive(compound_identifier, header): | ||
| """Test that valid key headers return True.""" | ||
| assert compound_identifier.is_key_header(header) is True | ||
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| @pytest.mark.parametrize( | ||
| "header", ["id", "smiles", "inchi", "input", "some_header", "random", "header", ""] | ||
| ) | ||
| def test_is_key_header_negative(compound_identifier, header): | ||
| assert not compound_identifier.is_key_header(header) | ||
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| @pytest.mark.parametrize( | ||
| "inchikey", | ||
| [ | ||
| "BSYNRYMUTXBXSQ-UHFFFAOYSA-N", | ||
| "BQJCRHHNABKAKU-KBQPJGBKSA-N", | ||
| "ZJPODVODJYKFHM-UHFFFAOYSA-N", | ||
| ], | ||
| ) | ||
| def test_is_inchikey_positive(compound_identifier, inchikey): | ||
| """Test that valid InChIKeys return True.""" | ||
| assert compound_identifier._is_inchikey(inchikey) is True | ||
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| @pytest.fixture(params=[True, False], ids=["Chem_None", "Chem_Not_None"]) | ||
| def compound_identifier(request): | ||
| """Fixture that initializes CompoundIdentifier with or without RDKit.""" | ||
| return CompoundIdentifier(local=request.param) | ||
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| @pytest.mark.parametrize("smiles, expected", [("C", True), ("CCO", True)]) | ||
| def test_is_smiles_positive(compound_identifier, smiles, expected): | ||
| """Test _is_smiles returns True for valid SMILES strings.""" | ||
| if compound_identifier.Chem is None: | ||
| assert compound_identifier._is_smiles(smiles) == expected | ||
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| @pytest.mark.parametrize("smiles, expected", [("invalid_smiles", False), ("", False)]) | ||
| def test_is_smiles_negative(compound_identifier, smiles, expected): | ||
| """Test _is_smiles returns False for invalid or empty SMILES strings.""" | ||
| assert compound_identifier._is_smiles(smiles) == expected | ||
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||
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| @pytest.mark.parametrize( | ||
| "inchikey, expected", | ||
| [ | ||
| ("BQJCRHHNABKAKU-KBQPJGBKSA-N", True), | ||
| ], | ||
| ) | ||
| def test_is_inchikey_positive(inchikey, expected): | ||
| """Test _is_inchikey returns True for valid InChIKey.""" | ||
| assert CompoundIdentifier._is_inchikey(inchikey) == expected | ||
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| @pytest.mark.parametrize( | ||
| "inchikey, expected", | ||
| [("invalid_inchikey", False), ("BQJCRHHNABKAKU-KBQPJGBKSA", False)], | ||
| ) | ||
| def test_is_inchikey_negative(inchikey, expected): | ||
| """Test _is_inchikey returns False for invalid InChIKeys.""" | ||
| assert CompoundIdentifier._is_inchikey(inchikey) == expected | ||
|
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||
|
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| @pytest.mark.parametrize( | ||
| "inchikey, expected", | ||
| [ | ||
| ("BQJCRHHNABKAKU-KBQPJGBKSA-N", "inchikey"), | ||
| ("ABCDEFGHIJKLMN-OPQRSTUVWX-Y", "inchikey"), | ||
| ], | ||
| ) | ||
| def test_guess_type_inchikey(compound_identifier, inchikey, expected): | ||
| """Ensure guess_type correctly identifies valid InChIKeys.""" | ||
| result = compound_identifier.guess_type(inchikey) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected 'inchikey', but got '{result}' for input '{inchikey}'" | ||
|
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||
|
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| @pytest.mark.parametrize( | ||
| "smiles, expected", | ||
| [ | ||
| ("C", "smiles"), | ||
| ("CCO", "smiles"), | ||
| ], | ||
| ) | ||
| def test_guess_type_smiles(compound_identifier, smiles, expected): | ||
| """Ensure guess_type correctly identifies valid SMILES strings.""" | ||
| result = compound_identifier.guess_type(smiles) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected 'smiles', but got '{result}' for input '{smiles}'" | ||
|
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||
|
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||
| @pytest.mark.parametrize( | ||
| "input_data, expected", | ||
| [ | ||
| (None, UNPROCESSABLE_INPUT), | ||
| (UNPROCESSABLE_INPUT, UNPROCESSABLE_INPUT), | ||
| ], | ||
| ) | ||
| def test_guess_type_unprocessable(compound_identifier, input_data, expected): | ||
| """Ensure guess_type returns UNPROCESSABLE_INPUT for None or unprocessable inputs.""" | ||
| result = compound_identifier.guess_type(input_data) | ||
| assert result == expected, f"Expected '{UNPROCESSABLE_INPUT}', but got '{result}'" | ||
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|
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| @pytest.mark.parametrize( | ||
| "whitespace_input, expected", | ||
| [ | ||
| ("\n", UNPROCESSABLE_INPUT), | ||
| ("\t", UNPROCESSABLE_INPUT), | ||
| (" ", UNPROCESSABLE_INPUT), | ||
| ], | ||
| ) | ||
| def test_guess_type_whitespace(compound_identifier, whitespace_input, expected): | ||
| """Ensure guess_type returns UNPROCESSABLE_INPUT for whitespace-only input.""" | ||
| result = compound_identifier.guess_type(whitespace_input) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected '{UNPROCESSABLE_INPUT}' for input '{whitespace_input}'" | ||
|
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||
|
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||
| @pytest.mark.parametrize( | ||
| "non_char_input, expected", | ||
| [ | ||
| (12345, UNPROCESSABLE_INPUT), | ||
| (3.14, UNPROCESSABLE_INPUT), | ||
| ("𠜎𠜱𡿺𠬠", UNPROCESSABLE_INPUT), | ||
| ], | ||
| ) | ||
| def test_guess_type_non_character(compound_identifier, non_char_input, expected): | ||
| """Ensure guess_type returns UNPROCESSABLE_INPUT for non-character input.""" | ||
| result = compound_identifier.guess_type(non_char_input) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected '{UNPROCESSABLE_INPUT}' for input '{non_char_input}'" | ||
|
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| # Test with a valid SMILES input | ||
| smiles_string = "CCO" # Ethanol SMILES | ||
| assert compound_identifier._is_smiles(smiles_string) is True | ||
|
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| @patch("requests.get") | ||
| async def test_nci_smiles_to_inchikey_positive(mock_get, compound_identifier): | ||
| """Test _nci_smiles_to_inchikey with a mocked positive response.""" | ||
| mock_response = mock_get.return_value | ||
| mock_response.status_code = 200 | ||
| mock_response.text = "InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N" | ||
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| inchikey = await compound_identifier._nci_smiles_to_inchikey( | ||
| session=None, smiles="CCO" | ||
| ) | ||
| assert inchikey == "BSYNRYMUTXBXSQ-UHFFFAOYSA-N" | ||
|
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| @patch("requests.get") | ||
| async def test_nci_smiles_to_inchikey_negative(mock_get, compound_identifier): | ||
| """Test _nci_smiles_to_inchikey with a mocked negative response.""" | ||
| mock_response = mock_get.return_value | ||
| mock_response.status_code = 404 | ||
|
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| inchikey = await compound_identifier._nci_smiles_to_inchikey( | ||
| session=None, smiles="invalid_smiles" | ||
| ) | ||
| assert inchikey is None | ||
| from ersilia.default import UNPROCESSABLE_INPUT | ||
| import pytest | ||
| from ersilia.utils.identifiers.compound import CompoundIdentifier | ||
| from unittest.mock import patch | ||
|
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||
|
|
||
| @pytest.fixture | ||
| def compound_identifier(): | ||
| return CompoundIdentifier() | ||
|
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|
|
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| @pytest.mark.parametrize("header", ["smiles", "input", "SMILES", "INPUT"]) | ||
| def test_is_input_header_positive(compound_identifier, header): | ||
| """Test that valid input headers return True.""" | ||
| assert compound_identifier.is_input_header(header) is True | ||
|
|
||
|
|
||
| @pytest.mark.parametrize("header", ["output", "invalid", "InChI", "inchikey"]) | ||
| def test_is_input_header_negative(compound_identifier, header): | ||
| """Test that invalid input headers return False.""" | ||
| assert compound_identifier.is_input_header(header) is False | ||
|
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||
|
|
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| @pytest.mark.parametrize("header", ["key", "inchiKey", "KEY", "INCHIKEY"]) | ||
| def test_is_key_header_positive(compound_identifier, header): | ||
| """Test that valid key headers return True.""" | ||
| assert compound_identifier.is_key_header(header) is True | ||
|
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||
|
|
||
| @pytest.mark.parametrize( | ||
| "header", ["id", "smiles", "inchi", "input", "some_header", "random", "header", ""] | ||
| ) | ||
| def test_is_key_header_negative(compound_identifier, header): | ||
| assert not compound_identifier.is_key_header(header) | ||
|
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||
|
|
||
| @pytest.mark.parametrize( | ||
| "inchikey", | ||
| [ | ||
| "BSYNRYMUTXBXSQ-UHFFFAOYSA-N", | ||
| "BQJCRHHNABKAKU-KBQPJGBKSA-N", | ||
| "ZJPODVODJYKFHM-UHFFFAOYSA-N", | ||
| ], | ||
| ) | ||
| def test_is_inchikey_positive(compound_identifier, inchikey): | ||
| """Test that valid InChIKeys return True.""" | ||
| assert compound_identifier._is_inchikey(inchikey) is True | ||
|
|
||
|
|
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| @pytest.fixture(params=[True, False], ids=["Chem_None", "Chem_Not_None"]) | ||
| def compound_identifier(request): | ||
| """Fixture that initializes CompoundIdentifier with or without RDKit.""" | ||
| return CompoundIdentifier(local=request.param) | ||
|
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|
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| @pytest.mark.parametrize("smiles, expected", [("C", True), ("CCO", True)]) | ||
| def test_is_smiles_positive(compound_identifier, smiles, expected): | ||
| """Test _is_smiles returns True for valid SMILES strings.""" | ||
| if compound_identifier.Chem is None: | ||
| assert compound_identifier._is_smiles(smiles) == expected | ||
|
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|
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| @pytest.mark.parametrize("smiles, expected", [("invalid_smiles", False), ("", False)]) | ||
| def test_is_smiles_negative(compound_identifier, smiles, expected): | ||
| """Test _is_smiles returns False for invalid or empty SMILES strings.""" | ||
| assert compound_identifier._is_smiles(smiles) == expected | ||
|
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| @pytest.mark.parametrize( | ||
| "inchikey, expected", | ||
| [ | ||
| ("BQJCRHHNABKAKU-KBQPJGBKSA-N", True), | ||
| ], | ||
| ) | ||
| def test_is_inchikey_positive(inchikey, expected): | ||
| """Test _is_inchikey returns True for valid InChIKey.""" | ||
| assert CompoundIdentifier._is_inchikey(inchikey) == expected | ||
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| @pytest.mark.parametrize( | ||
| "inchikey, expected", | ||
| [("invalid_inchikey", False), ("BQJCRHHNABKAKU-KBQPJGBKSA", False)], | ||
| ) | ||
| def test_is_inchikey_negative(inchikey, expected): | ||
| """Test _is_inchikey returns False for invalid InChIKeys.""" | ||
| assert CompoundIdentifier._is_inchikey(inchikey) == expected | ||
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| @pytest.mark.parametrize( | ||
| "inchikey, expected", | ||
| [ | ||
| ("BQJCRHHNABKAKU-KBQPJGBKSA-N", "inchikey"), | ||
| ("ABCDEFGHIJKLMN-OPQRSTUVWX-Y", "inchikey"), | ||
| ], | ||
| ) | ||
| def test_guess_type_inchikey(compound_identifier, inchikey, expected): | ||
| """Ensure guess_type correctly identifies valid InChIKeys.""" | ||
| result = compound_identifier.guess_type(inchikey) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected 'inchikey', but got '{result}' for input '{inchikey}'" | ||
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| @pytest.mark.parametrize( | ||
| "smiles, expected", | ||
| [ | ||
| ("C", "smiles"), | ||
| ("CCO", "smiles"), | ||
| ], | ||
| ) | ||
| def test_guess_type_smiles(compound_identifier, smiles, expected): | ||
| """Ensure guess_type correctly identifies valid SMILES strings.""" | ||
| result = compound_identifier.guess_type(smiles) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected 'smiles', but got '{result}' for input '{smiles}'" | ||
|
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|
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| @pytest.mark.parametrize( | ||
| "input_data, expected", | ||
| [ | ||
| (None, UNPROCESSABLE_INPUT), | ||
| (UNPROCESSABLE_INPUT, UNPROCESSABLE_INPUT), | ||
| ], | ||
| ) | ||
| def test_guess_type_unprocessable(compound_identifier, input_data, expected): | ||
| """Ensure guess_type returns UNPROCESSABLE_INPUT for None or unprocessable inputs.""" | ||
| result = compound_identifier.guess_type(input_data) | ||
| assert result == expected, f"Expected '{UNPROCESSABLE_INPUT}', but got '{result}'" | ||
|
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|
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| @pytest.mark.parametrize( | ||
| "whitespace_input, expected", | ||
| [ | ||
| ("\n", UNPROCESSABLE_INPUT), | ||
| ("\t", UNPROCESSABLE_INPUT), | ||
| (" ", UNPROCESSABLE_INPUT), | ||
| ], | ||
| ) | ||
| def test_guess_type_whitespace(compound_identifier, whitespace_input, expected): | ||
| """Ensure guess_type returns UNPROCESSABLE_INPUT for whitespace-only input.""" | ||
| result = compound_identifier.guess_type(whitespace_input) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected '{UNPROCESSABLE_INPUT}' for input '{whitespace_input}'" | ||
|
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||
|
|
||
| @pytest.mark.parametrize( | ||
| "non_char_input, expected", | ||
| [ | ||
| (12345, UNPROCESSABLE_INPUT), | ||
| (3.14, UNPROCESSABLE_INPUT), | ||
| ("𠜎𠜱𡿺𠬠", UNPROCESSABLE_INPUT), | ||
| ], | ||
| ) | ||
| def test_guess_type_non_character(compound_identifier, non_char_input, expected): | ||
| """Ensure guess_type returns UNPROCESSABLE_INPUT for non-character input.""" | ||
| result = compound_identifier.guess_type(non_char_input) | ||
| assert ( | ||
| result == expected | ||
| ), f"Expected '{UNPROCESSABLE_INPUT}' for input '{non_char_input}'" | ||
|
|
||
| # Test with a valid SMILES input | ||
| smiles_string = "CCO" # Ethanol SMILES | ||
| assert compound_identifier._is_smiles(smiles_string) is True | ||
|
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||
|
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||
| @patch("requests.get") | ||
| async def test_nci_smiles_to_inchikey_positive(mock_get, compound_identifier): | ||
| """Test _nci_smiles_to_inchikey with a mocked positive response.""" | ||
| mock_response = mock_get.return_value | ||
| mock_response.status_code = 200 | ||
| mock_response.text = "InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N" | ||
|
|
||
| inchikey = await compound_identifier._nci_smiles_to_inchikey( | ||
| session=None, smiles="CCO" | ||
| ) | ||
| assert inchikey == "BSYNRYMUTXBXSQ-UHFFFAOYSA-N" | ||
|
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||
|
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||
| @patch("requests.get") | ||
| async def test_nci_smiles_to_inchikey_negative(mock_get, compound_identifier): | ||
| """Test _nci_smiles_to_inchikey with a mocked negative response.""" | ||
| mock_response = mock_get.return_value | ||
| mock_response.status_code = 404 | ||
|
|
||
| inchikey = await compound_identifier._nci_smiles_to_inchikey( | ||
| session=None, smiles="invalid_smiles" | ||
| ) | ||
| assert inchikey is None | ||
|
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||
|
|
||
| @patch("requests.get") | ||
| async def test_pubchem_smiles_to_inchikey_positive(mock_get, compound_identifier): | ||
| """Test _pubchem_smiles_to_inchikey with a mocked positive response.""" | ||
| mock_response = mock_get.return_value | ||
| mock_response.status_code = 200 | ||
| mock_response.text = "InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N" | ||
|
|
||
| inchikey = await compound_identifier._pubchem_smiles_to_inchikey( | ||
| session=None, smiles="CCO" | ||
| ) | ||
| assert inchikey == "BSYNRYMUTXBXSQ-UHFFFAOYSA-N" | ||
|
|