How to use test_bad_input method in green

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test_BadInput.py

Source:test_BadInput.py

1import unittest2import os3from unittest.mock import patch4import MSParser5from MSOrganiser import no_concatenate_workflow6from MSDataOutput import MSDataOutput_Excel7from MSDataOutput import MSDataOutput_csv8NO_MS_FILE_JSONFILENAME = os.path.join(os.path.dirname(__file__),"testdata", 9                                       "test_bad_input", 'No_MS_File.json')10NO_OUTPUT_DIRECTORY_JSONFILENAME = os.path.join(os.path.dirname(__file__),"testdata", 11                                                "test_bad_input", 'No_Output_Directory.json')12NO_OUTPUT_OPTIONS_JSONFILENAME = os.path.join(os.path.dirname(__file__),"testdata", 13                                              "test_bad_input", 'No_Output_Options.json')14NO_ANNOT_FILE_JSONFILENAME = os.path.join(os.path.dirname(__file__),"testdata", 15                                          "test_bad_input", 'No_Annot_File.json')16INPUT_FOLDERNAME = os.path.join(os.path.dirname(__file__),"testdata", 17                                          "test_bad_input", 'input_folder.csv')18VALID_WIDETABLEFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 19                                            "test_bad_input", 'Valid_WideTableForm.csv')20VALID_COMPOUNDTABLEFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 21                                                "test_bad_input", 'Valid_CompoundTableForm.csv')22NO_DATAFILENAME_WIDETABLEFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 23                                                      "test_bad_input", 'NoDataFileColumn_WideTableForm.csv')24NO_DATAFILENAME_COMPOUNDTABLEFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 25                                                          "test_bad_input", 'NoDataFileColumn_CompoundTableForm.csv')26NO_NAME_COMPOUNDTABLEFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 27                                                  "test_bad_input", 'NoName_CompoundTableForm_Qualifier.csv')28INVALID_AGILENT_DATAFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 29                                                 "test_bad_input", 'Invalid_WideTableForm.csv')30INVALID_AGILENT_DATAFORM_FILENAME2 = os.path.join(os.path.dirname(__file__),"testdata", 31                                                  "test_bad_input", 'Invalid_WideTableForm2.csv')32EMPTY_WIDETABLEFORM_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 33                                            "test_bad_input", 'Empty_WideTableForm.csv')34WRONG_EXTENTION_ANNOTATION_FILENAME = os.path.join(os.path.dirname(__file__),"testdata", 35                                                   "test_bad_input", 'Valid_WideTableForm_Annot.csv')36INPUT_ANNOTATION_FOLDERNAME = os.path.join(os.path.dirname(__file__),"testdata", 37                                           "test_bad_input", 'input_annotation_folder')38class Bad_Input_Json_Test(unittest.TestCase):39    # See https://realpython.com/lessons/mocking-print-unit-tests/40    # for more details on mock41    def test_invalid_json_file(self):42        """Check if the software is able to detect invalid json file43        """44        # Replace the print function in MSParser.py file to a mock45        self.patcher = patch('MSParser.print')46        mock_print = self.patcher.start()47        #Read the parser48        with self.assertRaises(SystemExit) as cm:49            stored_args = MSParser.parse_MSOrganiser_args(args_json_file_path = NO_MS_FILE_JSONFILENAME,50                                                          testing = True)51        # Ensure that the system ends with a -1 to indicate an error52        self.assertEqual(cm.exception.code, -1)53        # Ensure that the error was due to no MS file input54        mock_print.assert_called_with('Please key in at least one input MS file.',55                                      flush = True)56        #Read the parser57        with self.assertRaises(SystemExit) as cm:58            stored_args = MSParser.parse_MSOrganiser_args(args_json_file_path = NO_OUTPUT_DIRECTORY_JSONFILENAME,59                                                          testing = True)60        # Ensure that the system ends with a -1 to indicate an error61        self.assertEqual(cm.exception.code, -1)62        # Ensure that the error was due to no output directory input63        mock_print.assert_called_with('Please key in at least one output directory.',64                                      flush = True)65        #Read the parser66        with self.assertRaises(SystemExit) as cm:67            stored_args = MSParser.parse_MSOrganiser_args(args_json_file_path = NO_OUTPUT_OPTIONS_JSONFILENAME,68                                                          testing = True)69        # Ensure that the system ends with a -1 to indicate an error70        self.assertEqual(cm.exception.code, -1)71        # Ensure that the error was due to no output option input72        mock_print.assert_called_with('Please key in at least one result to output.',73                                      flush = True)74        #Read the parser75        with self.assertRaises(SystemExit) as cm:76            stored_args = MSParser.parse_MSOrganiser_args(args_json_file_path = NO_ANNOT_FILE_JSONFILENAME,77                                                          testing = True)78        # Ensure that the system ends with a -1 to indicate an error79        self.assertEqual(cm.exception.code, -1)80        # Ensure that the error was due to no annotation file input when81        # normArea by ISTD or normConc by ISTD or both are selected 82        # in Output_Options83        mock_print.assert_called_with("Please key in an annotation file when \'normArea by ISTD\' " + 84                                      "or \'normConc by ISTD\' are selected in Output_Options.",85                                      flush = True)86        self.patcher.stop()87class Bad_Input_File_Test(unittest.TestCase):88    # See https://realpython.com/lessons/mocking-print-unit-tests/89    # for more details on mock90    def test_wrong_file_extention(self):91        """Check if the software is able to detect wrong input file extention92        """93        # Replace the print function in MSAnalysis.py file to a mock94        self.patcher = patch('MSAnalysis.print')95        mock_print = self.patcher.start()96        stored_args = {97            'MS_Files': ["wrong_extention"], 98            'MS_FileType': 'Agilent Wide Table in csv', 99            'Output_Directory': 'D:\\MSOrganiser', 100            'Output_Options': ['Area', 'normArea by ISTD', 'normConc by ISTD'], 101            'Annot_File': "", 102            'Output_Format': 'Excel', 103            'Concatenate': 'No Concatenate', 104            'Transpose_Results': False, 105            'Allow_Multiple_ISTD': False, 106            'Long_Table': False, 107            'Long_Table_Annot': False, 108            'Testing': False109        }110        mock_print = self.patcher.start()111        MS_FileType_list = ['Agilent Wide Table in csv', 112                            'Agilent Compound Table in csv',113                            'Multiquant Long Table in txt']114        MS_Files_list = ['no_csv_extention', 115                         'no_csv_extention',116                         'no_txt_extention']117        for i in range(len(MS_FileType_list)):118            stored_args['MS_FileType'] = MS_FileType_list[i]119            stored_args['MS_Files'] = [MS_Files_list[i]]120            right_extention = ""121            if MS_FileType_list[i] in ['Agilent Wide Table in csv', 'Agilent Compound Table in csv']:122                right_extention = ".csv"123            elif MS_FileType_list[i] in ['Multiquant Long Table in txt']:124                right_extention = ".txt"125            with self.assertRaises(SystemExit) as cm:126                [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)127            # Ensure that the system ends with a -1 to indicate an error128            self.assertEqual(cm.exception.code, -1)129            # Ensure that the error was due to wrong file extention130            mock_print.assert_called_with('Input file path ' + 131                                          '\'' + MS_Files_list[i] + '\' ' + 132                                          'must have a '+ right_extention + ' ' + 133                                          'extention.',134                                           flush = True)135        self.patcher.stop()136    def test_input_file_is_a_folder(self):137        """Check if the software is able to detect a folder input when a system138           file input is expected139        """140        # Replace the print function in MSRawData.py file to a mock141        self.patcher = patch('MSRawData.print')142        mock_print = self.patcher.start()143        stored_args = {144            'MS_Files': [INPUT_FOLDERNAME], 145            'MS_FileType': 'Agilent Wide Table in csv', 146            'Output_Directory': 'D:\\MSOrganiser', 147            'Output_Options': ['Area', 'normArea by ISTD', 'normConc by ISTD'], 148            'Annot_File': "", 149            'Output_Format': 'Excel', 150            'Concatenate': 'No Concatenate', 151            'Transpose_Results': False, 152            'Allow_Multiple_ISTD': False, 153            'Long_Table': False, 154            'Long_Table_Annot': False, 155            'Testing': False156        }157        with self.assertRaises(SystemExit) as cm:158            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)159        # Ensure that the system ends with a -1 to indicate an error160        self.assertEqual(cm.exception.code, -1)161        # Ensure that the error was due to input of a folder instead of a file162        mock_print.assert_called_with('Input file path ' + '\'' + INPUT_FOLDERNAME + '\'' +163                                      ' does not lead to a system file. ' + 164                                      'Please check if the input file path is a system file and not a folder.',165                                      flush = True)166        self.patcher.stop()167    def test_input_file_cannot_be_found(self):168        """Check if the software is able to detect if the input file exists.169           If not, gives an error and inform the user about this issue.170        """171        # Replace the print function in MSRawData.py file to a mock172        self.patcher = patch('MSRawData.print')173        mock_print = self.patcher.start()174        stored_args = {175            'MS_Files': ["non_existing_file.csv"], 176            'MS_FileType': 'Agilent Wide Table in csv', 177            'Output_Directory': 'D:\\MSOrganiser', 178            'Output_Options': ['Area', 'normArea by ISTD', 'normConc by ISTD'], 179            'Annot_File': "", 180            'Output_Format': 'Excel', 181            'Concatenate': 'No Concatenate', 182            'Transpose_Results': False, 183            'Allow_Multiple_ISTD': False, 184            'Long_Table': False, 185            'Long_Table_Annot': False, 186            'Testing': False187        }188        with self.assertRaises(SystemExit) as cm:189            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)190        # Ensure that the system ends with a -1 to indicate an error191        self.assertEqual(cm.exception.code, -1)192        # Ensure that the error was due to input of a csv file that does not exists193        mock_print.assert_called_with('Input file path ' + '\'non_existing_file.csv\'' +194                                      ' could not be found. ' +195                                      'Please check if the input file path.',196                                      flush = True)197        self.patcher.stop()198    def test_input_file_empty(self):199        """Check if the software is able to detect if the Agilent input file in200           Wide Table Form is empty and gives an error201        """202        # Replace the print function in MSRawData.py file to a mock203        self.patcher = patch('MSRawData.print')204        mock_print = self.patcher.start()205        stored_args = {206            'MS_Files': [EMPTY_WIDETABLEFORM_FILENAME], 207            'MS_FileType': 'Agilent Wide Table in csv', 208            'Output_Directory': 'D:\\MSOrganiser', 209            'Output_Options': ['Area'], 210            'Annot_File': "", 211            'Output_Format': 'Excel', 212            'Concatenate': 'No Concatenate', 213            'Transpose_Results': False, 214            'Allow_Multiple_ISTD': False, 215            'Long_Table': False, 216            'Long_Table_Annot': False, 217            'Testing': False218        }219        with self.assertRaises(SystemExit) as cm:220            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)221        # Ensure that the system ends with a -1 to indicate an error222        self.assertEqual(cm.exception.code, -1)223        # Ensure that the error was due to empty input data224        mock_print.assert_called_with(EMPTY_WIDETABLEFORM_FILENAME +225                                      ' is an empty file. Please check the input file.',226                                      flush = True)227        self.patcher.stop()228    def test_input_invalid_output_option(self):229        """Check if the software is able to detect if the input output options are valid.230           If not, gives an error and inform the user about this issue.231        """232        # Replace the print function in MSRawData.py file to a mock233        self.patcher = patch('MSRawData.print')234        mock_print = self.patcher.start()235        stored_args = {236            'MS_Files': [VALID_WIDETABLEFORM_FILENAME], 237            'MS_FileType': 'Agilent Wide Table in csv', 238            'Output_Directory': 'D:\\MSOrganiser', 239            'Output_Options': ['Invalid Output Option', 'Area'], 240            'Annot_File': "", 241            'Output_Format': 'Excel', 242            'Concatenate': 'No Concatenate', 243            'Transpose_Results': False, 244            'Allow_Multiple_ISTD': False, 245            'Long_Table': False, 246            'Long_Table_Annot': False, 247            'Testing': False248        }249        with self.assertRaises(SystemExit) as cm:250            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)251        # Ensure that the system ends with a -1 to indicate an error252        self.assertEqual(cm.exception.code, -1)253        # Ensure that the error was due to an invalid output option254        mock_print.assert_called_with('Output option Invalid Output Option ' + 255                                      'is not a valid column in MassHunter or not ' + 256                                      'available as a valid output for this program.',257                                      flush=True)258        stored_args = {259            'MS_Files': [VALID_COMPOUNDTABLEFORM_FILENAME], 260            'MS_FileType': 'Agilent Compound Table in csv', 261            'Output_Directory': 'D:\\MSOrganiser', 262            'Output_Options': ['Invalid Output Option', 'Area'], 263            'Annot_File': "", 264            'Output_Format': 'Excel', 265            'Concatenate': 'No Concatenate', 266            'Transpose_Results': False, 267            'Allow_Multiple_ISTD': False, 268            'Long_Table': False, 269            'Long_Table_Annot': False, 270            'Testing': False271        }272        with self.assertRaises(SystemExit) as cm:273            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)274        # Ensure that the system ends with a -1 to indicate an error275        self.assertEqual(cm.exception.code, -1)276        # Ensure that the error was due to an invalid output option277        mock_print.assert_called_with('Output option Invalid Output Option ' + 278                                      'is not a valid column in MassHunter or not ' + 279                                      'available as a valid output for this program.',280                                      flush=True)281        self.patcher.stop()282    def test_invalid_agilent_dataform(self):283        """Check if the software is able to detect if the Agilent input file is284           neither in Wide Table or Compound Table Form.285        """286        # Replace the print function in MSRawData.py file to a mock287        self.patcher = patch('MSRawData.print')288        mock_print = self.patcher.start()289        stored_args = {290            'MS_Files': [INVALID_AGILENT_DATAFORM_FILENAME], 291            'MS_FileType': 'Agilent Wide Table in csv', 292            'Output_Directory': 'D:\\MSOrganiser', 293            'Output_Options': ['Area'], 294            'Annot_File': "", 295            'Output_Format': 'Excel', 296            'Concatenate': 'No Concatenate', 297            'Transpose_Results': False, 298            'Allow_Multiple_ISTD': False, 299            'Long_Table': False, 300            'Long_Table_Annot': False, 301            'Testing': False302        }303        with self.assertRaises(SystemExit) as cm:304            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)305        # Ensure that the system ends with a -1 to indicate an error306        self.assertEqual(cm.exception.code, -1)307        # Ensure that the error was due to invalid Agilent input file 308        # which is neither in Wide Table or Compound Table Form.309        mock_print.assert_called_with(INVALID_AGILENT_DATAFORM_FILENAME + ' ' +310                                      'is missing \"Sample\" at first row and column in Wide Table form ' + 311                                      'or missing \"Compound Method\" at first row and column in Compound Table form. ' +312                                      'Please check the input file.',313                                      flush=True)314        #self.patcher.stop()315        stored_args = {316            'MS_Files': [INVALID_AGILENT_DATAFORM_FILENAME2], 317            'MS_FileType': 'Agilent Wide Table in csv', 318            'Output_Directory': 'D:\\MSOrganiser', 319            'Output_Options': ['Area'], 320            'Annot_File': "", 321            'Output_Format': 'Excel', 322            'Concatenate': 'No Concatenate', 323            'Transpose_Results': False, 324            'Allow_Multiple_ISTD': False, 325            'Long_Table': False, 326            'Long_Table_Annot': False, 327            'Testing': False328        }329        with self.assertRaises(SystemExit) as cm:330            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)331        # Ensure that the system ends with a -1 to indicate an error332        self.assertEqual(cm.exception.code, -1)333        # Ensure that the error was due to invalid Agilent input file 334        # which is neither in Wide Table or Compound Table Form.335        mock_print.assert_called_with(INVALID_AGILENT_DATAFORM_FILENAME2 + ' ' +336                                      'is missing \"Sample\" at first row and column in Wide Table form ' + 337                                      'or missing \"Compound Method\" at first row and column in Compound Table form. ' +338                                      'Please check the input file.',339                                      flush=True)340        self.patcher.stop()341    342    def test_input_agilent_file_no_data_file(self):343        """Check if the software is able to detect if the Agilent input file in344           Wide Table Form or Compound Table Form have a Data File column 345        """346        # Replace the print function in MSRawData.py file to a mock347        self.patcher = patch('MSRawData.print')348        mock_print = self.patcher.start()349        stored_args = {350            'MS_Files': [NO_DATAFILENAME_WIDETABLEFORM_FILENAME], 351            'MS_FileType': 'Agilent Wide Table in csv', 352            'Output_Directory': 'D:\\MSOrganiser', 353            'Output_Options': ['Area'], 354            'Annot_File': "", 355            'Output_Format': 'Excel', 356            'Concatenate': 'No Concatenate', 357            'Transpose_Results': False, 358            'Allow_Multiple_ISTD': False, 359            'Long_Table': False, 360            'Long_Table_Annot': False, 361            'Testing': False362        }363        with self.assertRaises(SystemExit) as cm:364            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)365        # Ensure that the system ends with a -1 to indicate an error366        self.assertEqual(cm.exception.code, -1)367        # Ensure that the error was due to no Data File column in the Agilent Wide Table Form in csv368        mock_print.assert_called_with('\'' + os.path.basename(NO_DATAFILENAME_WIDETABLEFORM_FILENAME) + '\' ' +369                                      'has no column containing \"Data File\". ' + 370                                      'Please check the input file.',371                                      flush = True)372        stored_args = {373            'MS_Files': [NO_DATAFILENAME_COMPOUNDTABLEFORM_FILENAME], 374            'MS_FileType': 'Agilent Compound Table in csv', 375            'Output_Directory': 'D:\\MSOrganiser', 376            'Output_Options': ['Area'], 377            'Annot_File': "", 378            'Output_Format': 'Excel', 379            'Concatenate': 'No Concatenate', 380            'Transpose_Results': False, 381            'Allow_Multiple_ISTD': False, 382            'Long_Table': False, 383            'Long_Table_Annot': False, 384            'Testing': False385        }386        with self.assertRaises(SystemExit) as cm:387            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)388        # Ensure that the system ends with a -1 to indicate an error389        self.assertEqual(cm.exception.code, -1)390        # Ensure that the error was due to no Data File column in the Agilent Compound Table Form in csv391        mock_print.assert_called_with('\'' + os.path.basename(NO_DATAFILENAME_COMPOUNDTABLEFORM_FILENAME) + '\' ' +392                                      'has no column containing \"Data File\". ' + 393                                      'Please check the input file.',394                                      flush = True)395        self.patcher.stop()396    def test_input_agilent_compound_table_file_no_name(self):397        """Check if the software is able to detect if the Agilent input file in398           Compound Table Form have a Name column 399        """400        stored_args = {401            'MS_Files': [NO_NAME_COMPOUNDTABLEFORM_FILENAME], 402            'MS_FileType': 'Agilent Compound Table in csv', 403            'Output_Directory': 'D:\\MSOrganiser', 404            'Output_Options': ['Area'], 405            'Annot_File': "", 406            'Output_Format': 'Excel', 407            'Concatenate': 'No Concatenate', 408            'Transpose_Results': False, 409            'Allow_Multiple_ISTD': False, 410            'Long_Table': False, 411            'Long_Table_Annot': False, 412            'Testing': False413        }414        # Replace the print function in MSRawData.py file to a mock415        self.patcher = patch('MSRawData.print')416        mock_print = self.patcher.start()417        with self.assertRaises(SystemExit) as cm:418            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)419        # Ensure that the system ends with a -1 to indicate an error420        self.assertEqual(cm.exception.code, -1)421        # Ensure that the error was due to no Name column422        # in Compound Method Table for423        # Agilent Compound Table Form in csv424        mock_print.assert_called_with('\'' + os.path.basename(NO_NAME_COMPOUNDTABLEFORM_FILENAME) + '\' ' +425                                      'has no column contaning \"Name\" in Compound Method Table. ' + 426                                      'Please check the input file.',427                                      flush = True)428        self.patcher.stop()429    def test_input_valid_output_option_agilent_no_data_excel(self):430        """Check if the software is able to detect if the input output option is valid431           but the output option is not found in the input file when creating an excel file432        """433        # Replace the print function in MSDataOutput.py file to a mock434        self.patcher = patch('MSDataOutput.print')435        mock_print = self.patcher.start()436        output_directory = os.path.join(os.path.dirname(__file__),"testdata", "test_bad_input")437        stored_args = {438            'MS_Files': [VALID_WIDETABLEFORM_FILENAME], 439            'MS_FileType': 'Agilent Wide Table in csv', 440            'Output_Directory': output_directory, 441            'Output_Options': ['Area', 'S/N'], 442            'Annot_File': "", 443            'Output_Format': 'Excel', 444            'Concatenate': 'No Concatenate', 445            'Transpose_Results': False, 446            'Allow_Multiple_ISTD': False, 447            'Long_Table': False, 448            'Long_Table_Annot': False, 449            'Testing': False450        }451        [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)452        #print(file_name)453        #print(file_data_list[0][0][1])454        #print(file_data_list[0][0][0])455        DfOutput = MSDataOutput_Excel(stored_args['Output_Directory'], VALID_WIDETABLEFORM_FILENAME, 456                                      result_name = "Results" ,457                                      logger = None, ingui = True)458        DfOutput.start_writer()459        DfOutput.df_to_file("Area",file_data_list[0][0][0],460                            transpose=stored_args['Transpose_Results'],461                            allow_multiple_istd = False)462        DfOutput.df_to_file("S/N",file_data_list[0][0][1],463                            transpose=stored_args['Transpose_Results'],464                            allow_multiple_istd = False)465        DfOutput.end_writer(testing = True)466        # Ensure that the warning was due to no data available for that output option467        mock_print.assert_called_with('S/N has no data. Please check the input file.',468                                      flush=True)469        self.patcher.stop()470    def test_input_valid_output_option_agilent_no_data_csv(self):471        """Check if the software is able to detect if the input output option is valid472           but the output option is not found in the input file when creating a csv file473        """474        # Replace the print function in MSDataOutput.py file to a mock475        self.patcher = patch('MSDataOutput.print')476        mock_print = self.patcher.start()477        output_directory = os.path.join(os.path.dirname(__file__),"testdata", "test_bad_input")478        stored_args = {479            'MS_Files': [VALID_WIDETABLEFORM_FILENAME], 480            'MS_FileType': 'Agilent Wide Table in csv', 481            'Output_Directory': output_directory, 482            'Output_Options': ['S/N'], 483            'Annot_File': "", 484            'Output_Format': 'Excel', 485            'Concatenate': 'No Concatenate', 486            'Transpose_Results': False, 487            'Allow_Multiple_ISTD': False, 488            'Long_Table': True, 489            'Long_Table_Annot': False, 490            'Testing': False491            }492        [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)493        DfOutput = MSDataOutput_csv(stored_args['Output_Directory'], VALID_WIDETABLEFORM_FILENAME, 494                                    result_name = "" , logger = None, ingui = True)495        DfOutput.start_writer()496        DfOutput.df_to_file("S/N",file_data_list[0][0][0],497                            transpose=stored_args['Transpose_Results'],498                            allow_multiple_istd = False)499            500        # Ensure that the warning was due to no data available for that output option501        mock_print.assert_called_with('S/N has no data. Please check the input file.',502                                      flush=True)503        #self.patcher.stop()504        DfLongOutput = MSDataOutput_csv(stored_args['Output_Directory'], VALID_WIDETABLEFORM_FILENAME, 505                                        result_name = "" , logger = None, ingui=True)506        DfLongOutput.start_writer()507        DfLongOutput.df_to_file("Long_Table",file_data_list[0][0][1])508        # Ensure that the warning was due to no data available for that output option509        mock_print.assert_called_with('Long_Table has no data. Please check the input file.',510                                      flush=True)511        self.patcher.stop()512class Bad_Annotation_Test(unittest.TestCase):513    # See https://realpython.com/lessons/mocking-print-unit-tests/514    # for more details on mock515    def test_input_annotation_cannot_be_found(self):516        """Check if the software is able to detect if the input annotation file exists.517           If not, gives an error and inform the user about this issue.518        """519        # Replace the print function in Annotation.py file to a mock520        self.patcher = patch('Annotation.print')521        mock_print = self.patcher.start()522        output_directory = os.path.join(os.path.dirname(__file__),"testdata", "test_bad_input")523        stored_args = {524            'MS_Files': [VALID_WIDETABLEFORM_FILENAME], 525            'MS_FileType': 'Agilent Wide Table in csv', 526            'Output_Directory': output_directory, 527            'Output_Options': ['Area', 'normArea by ISTD'], 528            'Annot_File': "non_existing_annot_file.xlsm", 529            'Output_Format': 'Excel', 530            'Concatenate': 'No Concatenate', 531            'Transpose_Results': False, 532            'Allow_Multiple_ISTD': False, 533            'Long_Table': False, 534            'Long_Table_Annot': False, 535            'Testing': False536        }537        with self.assertRaises(SystemExit) as cm:538            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)539        # Ensure that the system ends with a -1 to indicate an error540        self.assertEqual(cm.exception.code, -1)541        # Ensure that the error was due to no Data File column in the Agilent Wide Table Form in csv542        mock_print.assert_called_with('Input annotation ' + '\'non_existing_annot_file.xlsm\'' +543                                      ' could not be found. ' +544                                      'Please check the input file path.',545                                      flush = True)546        self.patcher.stop()547    def test_input_annotation_wrong_file_extention(self):548        """Check if the software is able to detect if the input annotation file549           has the wrong file extension550        """551        # Replace the print function in Annotation.py file to a mock552        self.patcher = patch('Annotation.print')553        mock_print = self.patcher.start()554        output_directory = os.path.join(os.path.dirname(__file__),"testdata", "test_bad_input")555        stored_args = {556            'MS_Files': [VALID_WIDETABLEFORM_FILENAME], 557            'MS_FileType': 'Agilent Wide Table in csv', 558            'Output_Directory': output_directory, 559            'Output_Options': ['Area', 'normArea by ISTD'], 560            'Annot_File': WRONG_EXTENTION_ANNOTATION_FILENAME, 561            'Output_Format': 'Excel', 562            'Concatenate': 'No Concatenate', 563            'Transpose_Results': False, 564            'Allow_Multiple_ISTD': False, 565            'Long_Table': False, 566            'Long_Table_Annot': False, 567            'Testing': False568        }569        with self.assertRaises(SystemExit) as cm:570            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)571        # Ensure that the system ends with a -1 to indicate an error572        self.assertEqual(cm.exception.code, -1)573        # Ensure that the error was due to no Data File column in the Agilent Wide Table Form in csv574        mock_print.assert_called_with('This program no longer accepts csv file as input for the annotation file. Please use the excel template file given.',575                                      flush = True)576        self.patcher.stop()577    def test_input_annotation_is_a_folder(self):578        """Check if the software is able to detect a folder input when a system579           file input is expected580        """581        # Replace the print function in Annotation.py file to a mock582        self.patcher = patch('Annotation.print')583        mock_print = self.patcher.start()584        stored_args = {585            'MS_Files': [VALID_WIDETABLEFORM_FILENAME],586            'MS_FileType': 'Agilent Wide Table in csv', 587            'Output_Directory': 'D:\\MSOrganiser', 588            'Output_Options': ['Area', 'normArea by ISTD', 'normConc by ISTD'], 589            'Annot_File': INPUT_ANNOTATION_FOLDERNAME, 590            'Output_Format': 'Excel', 591            'Concatenate': 'No Concatenate', 592            'Transpose_Results': False, 593            'Allow_Multiple_ISTD': False, 594            'Long_Table': False, 595            'Long_Table_Annot': False, 596            'Testing': False597        }598        with self.assertRaises(SystemExit) as cm:599            [file_data_list, file_name] = no_concatenate_workflow(stored_args,testing = True)600        # Ensure that the system ends with a -1 to indicate an error601        self.assertEqual(cm.exception.code, -1)602        # Ensure that the error was due to input of a folder instead of a file603        mock_print.assert_called_with('Input file path ' + '\'' + INPUT_ANNOTATION_FOLDERNAME + '\'' +604                                      ' does not lead to a system file. ' + 605                                      'Please check if the input file path is a system file and not a folder.',606                                      flush = True)607        self.patcher.stop()608if __name__ == '__main__':...

test_aging.py

Source:test_aging.py

...79        assert np.sum(80            np.isclose([col_coord[0], col_coord[1], col_coord[2]], [27, 35, 27])) == 3, "color coordinates wrong"81        assert np.sum(82            np.isclose([mag_range[0], mag_range[1], mag_range[2]], [90, 40, 130])) == 3, "magnitude coordinates wrong"83    def test_bad_input(self):84        with pytest.raises(HokiFormatError):85            col_coord, mag_range = au._find_cmd_coordinates(obs_df=bad_hrd_input, mycmd=mycmd)86    def test_bad_input_2(self):87        col_coord, mag_range = au._find_cmd_coordinates(obs_df=bad_cmd_input, mycmd=mycmd)88        #assert np.siz(col_coord[0]), "This should be a nan"89        assert np.isclose(mag_range[0], 90), "This L coordinate is wrong - test_bad_input."90class TestFindHRDCoordinates(object):91    def test_fake_input(self):92        T_coord, L_coord = au._find_hrd_coordinates(obs_df=fake_hrd_input, myhrd=myhrd)93        assert np.sum(94            np.isclose([T_coord[0], T_coord[1], T_coord[2]], [45, 44, 40])) == 3, "Temperature coordinates wrong"95        assert np.sum(96            np.isclose([L_coord[0], L_coord[1], L_coord[2]], [77, 80, 83])) == 3, "Luminosity coordinates wrong"97    def test_bad_input(self):98        with pytest.raises(HokiFormatError):99            __, __ = au._find_hrd_coordinates(obs_df=bad_cmd_input, mycmd=mycmd)100    def test_bad_input(self):101        T_coord, L_coord = au._find_hrd_coordinates(obs_df=bad_hrd_input, myhrd=myhrd)102        #assert np.isnan(T_coord[0]), "This should be a nan"103        assert np.isclose(L_coord[0], 77), "This L coordinate is wrong - test_bad_input."104class TestNormalise1D(object):105    def test_it_runs(self):106        au.normalise_1d(np.array([0, 1, 4, 5, 0, 1, 7, 8]), crop_the_future=False)107    def test_basic(self):108        norm = au.normalise_1d(np.array([0, 0, 1, 0, 0, 0, 0]), crop_the_future=False)109        assert norm[2] == 1, 'Normalisation done wrong'110        assert sum(norm) == 1, "Normalisaton done wrong"111class TestCalculatePDFs(object):112    def test_fake_input(self):113        pdf_df = au.calculate_individual_pdfs(fake_hrd_input, myhrd)114        assert 'star1' in pdf_df.columns, "Column name issue"115        assert int(sum(pdf_df.star1)) == 1, "PDF not calculated correctly"116    def test_input_without_name(self):117        pdf_df = au.calculate_individual_pdfs(no_name_input, myhrd)118        assert 's1' in pdf_df.columns, "Column names not created right"119    def test_bad_input(self):120        pdf_df = au.calculate_individual_pdfs(bad_hrd_input2, myhrd)121        assert not np.isnan(sum(pdf_df.s0)), "somwthing went wrong"122        #assert np.isnan(sum(distributions_df.s1)), "somwthing went wrong"123class TestCalculateSamplePDF(object):124    def test_basic(self):125        distributions = au.calculate_distributions(fake_hrd_input, myhrd)126        combined = au.calculate_sample_pdf(distributions)127        assert np.isclose(combined.pdf[9], 0.2715379752638662), "combined PDF not right"128    def test_drop_bad(self):129        distributions = au.calculate_distributions(fake_hrd_input, myhrd)130        combined = au.calculate_sample_pdf(distributions, not_you=[3])131        assert np.isclose(combined.pdf[9], 0.2715379752638662), "combined PDF not right"132    def test_drop_good(self):133        distributions = au.calculate_distributions(fake_hrd_input, myhrd)...

test_utils.py

Source:test_utils.py

...82        assert np.sum(83            np.isclose([col_coord[0], col_coord[1], col_coord[2]], [27, 35, 27])) == 3, "color coordinates wrong"84        assert np.sum(85            np.isclose([mag_range[0], mag_range[1], mag_range[2]], [90, 40, 130])) == 3, "magnitude coordinates wrong"86    def test_bad_input(self):87        with pytest.raises(HokiFormatError):88            col_coord, mag_range = au._find_cmd_coordinates(obs_df=bad_hrd_input, mycmd=mycmd)89    def test_bad_input_2(self):90        col_coord, mag_range = au._find_cmd_coordinates(obs_df=bad_cmd_input, mycmd=mycmd)91        assert np.isclose(mag_range[0], 90), "This L coordinate is wrong - test_bad_input."92class TestFindHRDCoordinates(object):93    def test_fake_input(self):94        T_coord, L_coord = au._find_hrd_coordinates(obs_df=fake_hrd_input, myhrd=myhrd)95        assert np.sum(96            np.isclose([T_coord[0], T_coord[1], T_coord[2]], [45, 44, 40])) == 3, "Temperature coordinates wrong"97        assert np.sum(98            np.isclose([L_coord[0], L_coord[1], L_coord[2]], [77, 80, 83])) == 3, "Luminosity coordinates wrong"99    def test_bad_input(self):100        with pytest.raises(HokiFormatError):101            __, __ = au._find_hrd_coordinates(obs_df=bad_cmd_input, mycmd=mycmd)102    def test_bad_input(self):103        T_coord, L_coord = au._find_hrd_coordinates(obs_df=bad_hrd_input, myhrd=myhrd)104        #assert np.isnan(T_coord[0]), "This should be a nan"105        assert np.isclose(L_coord[0], 77), "This L coordinate is wrong - test_bad_input."106###############################107# CALCULATING INDIVIDUAL PDFS #108###############################109class TestCalculatePDFs(object):110    def test_fake_input(self):111        pdf_df = au.calculate_individual_pdfs(fake_hrd_input, myhrd)112        assert 'star1' in pdf_df.columns, "Column name issue"113        assert int(sum(pdf_df.star1)) == 1, "PDF not calculated correctly"114    def test_input_without_name(self):115        pdf_df = au.calculate_individual_pdfs(no_name_input, myhrd)116        assert 's1' in pdf_df.columns, "Column names not created right"117    def test_bad_input(self):118        pdf_df = au.calculate_individual_pdfs(bad_hrd_input2, myhrd)119        assert not np.isnan(sum(pdf_df.s0)), "something went wrong"120    def test_symmetric_errors(self):121        pdf_df = au.calculate_individual_pdfs(stars_SYM, myhrd)122        assert not np.isnan(sum(pdf_df['118-4'])), "something went wrong with symmetric errors"123#####################################124# PUTTING PDFS TOGETHER IN SOME WAY #125#####################################126class TestCalculateSamplePDF(object):127    def test_basic(self):128        distributions = au.calculate_distributions(fake_hrd_input, myhrd)129        combined = au.calculate_sample_pdf(distributions)130        assert np.isclose(combined.pdf[9], 0.2715379752638662), "combined PDF not right"131    def test_drop_bad(self):...

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