import pytest from quality_control.parsing import FileType, parse_errors @pytest.mark.slow @pytest.mark.parametrize( "filepath,filetype,seek_pos", (("tests/test_data/average_crlf.tsv", FileType.AVERAGE, 0), ("tests/test_data/average_error_at_end_200MB.tsv", FileType.AVERAGE, 205500004 # Skip first 500K lines ), ("tests/test_data/average.tsv", FileType.AVERAGE, 0), ("tests/test_data/standarderror_1_error_at_end.tsv", FileType.STANDARD_ERROR, 0), ("tests/test_data/standarderror.tsv", FileType.STANDARD_ERROR, 0), ("tests/test_data/duplicated_headers_no_data_errors.tsv", FileType.AVERAGE), )) def test_parse_errors(filepath, filetype, strains, seek_pos): """ Check that only errors are returned, and that certain properties hold for said errors. """ for error in parse_errors(filepath, filetype, strains, seek_pos): assert isinstance(error, dict) assert "filepath" in error assert "filetype" in error assert "position" in error assert "error" in error and isinstance(error["error"], str) assert "message" in error