Mercurial > repos > yufei-luo > s_mart
view commons/core/checker/test/Test_ConfigChecker.py @ 8:4dded8b1fbc4
Deleted selected files
author | m-zytnicki |
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date | Fri, 18 Jan 2013 09:01:47 -0500 |
parents | 769e306b7933 |
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from commons.core.checker.ConfigChecker import ConfigChecker from commons.core.checker.ConfigChecker import ConfigRules from commons.core.checker.RepetException import RepetException import os import unittest class Test_ConfigChecker(unittest.TestCase): def setUp(self): self._configFileName = "testConfigChecker.cfg" self._iMock = MockConfig() def test_checkIfExistsConfigFile_file_exist(self): f=open(self._configFileName, "w") f.close() doesFileExists = True iConfigRules = ConfigRules() try: iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfigChecker.checkIfExistsConfigFile() except RepetException: doesFileExists = False os.remove(self._configFileName) self.assertTrue(doesFileExists) def test_checkIfExistsConfigFile_file_not_exist(self): iConfigRules = ConfigRules() expMsg ="CONFIG FILE not found - '%s'" %self._configFileName doesFileExists = True try: iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfigChecker.checkIfExistsConfigFile() except RepetException, re: doesFileExists = False self.assertFalse(doesFileExists) self.assertEqual(expMsg, re.getMessage()) def test_readConfigFile(self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() expDictRawConfigValues = {"dir_name" : {"work_dir":"toto"}, "organism" : {"abbreviation":"T.aestivum", "genus":"triticum", "species":"aestivum", "common_name":"wheat", "comment":""}, 'analysis1': {'description': '', 'gff_name': 'BLASTX.gff2', 'name': 'BLASTXWheat2', 'program': 'BLASTX2', 'programversion': '3.32', 'sourcename': 'dummyDesc_BLASTX2'} } isNoExceptionRaised = True try: iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections except RepetException: isNoExceptionRaised = False os.remove(self._configFileName) self.assertTrue(isNoExceptionRaised) self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues) def test_readConfigFile_section_define_twice(self): self._iMock.write_case_section_define_twice(self._configFileName) iConfigRules = ConfigRules() expMsg = "Duplicate section exist in config file %s" %self._configFileName expDictRawConfigValues = {"dir_name": {"work_dir":"toto"}, "analysis1" : {"name": "BLASTXWheat2", "program" : "BLASTX2", "programversion" : "3.32", "sourcename" :"dummyDesc_BLASTX2", "description" : "", "gff_name" :"BLASTX.gff2"} } doesNoExceptionRaised = True try: iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections except RepetException, re: doesNoExceptionRaised = False os.remove(self._configFileName) # self.assertFalse(doesNoExceptionRaised) # self.assertEqual(expMsg, re.getMessage()) # self.assertTrue(doesNoExceptionRaised) self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues) def test_readConfigFile_option_define_twice(self): self._iMock.write_case_option_define_twice(self._configFileName) iConfigRules = ConfigRules() doesNoExceptionRaised = True expDictRawConfigValues = {"dir_name": {"work_dir":"toto"}, "analysis1" : {"name": "BLASTXWheat", "program" : "BLASTX2", "programversion" : "3.3", "sourcename" :"dummyDesc_BLASTX", "description" : "", "gff_name" :"BLASTX.gff"} } try: iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) obsDictRawConfigValues = iConfigChecker._iRawConfig.dOptionsValues4Sections except RepetException, re: doesNoExceptionRaised = False os.remove(self._configFileName) ## self.assertFalse(doesNoExceptionRaised) ## self.assertEqual(expMsg, re.getMessage()) self.assertTrue(doesNoExceptionRaised) self.assertEquals(obsDictRawConfigValues, expDictRawConfigValues) def test_checkMandatorySections(self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="dir_name", mandatory=True) iConfigRules.addRuleSection(section="organism", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatorySectionsFound = True try: iConfigChecker.checkMandatorySections() except RepetException: areAllMandatorySectionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatorySectionsFound) def test_checkMandatorySections_one_missing (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="dir_name", mandatory=True) iConfigRules.addRuleSection(section="target", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() expMsg = "Error in configuration file %s, following sections are missing:\n - target\n"% self._configFileName areAllMandatorySectionsFound = True try: iConfigChecker.checkMandatorySections() except RepetException, re: areAllMandatorySectionsFound = False os.remove(self._configFileName) self.assertFalse(areAllMandatorySectionsFound) self.assertEquals(expMsg, re.getMessage()) def test_checkMandatorySections_mandatory_section_with_pattern_section_is_missing (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="dir_name", mandatory=True) iConfigRules.addRuleSection(section="mandatorySection", mandatory=True, isPattern = True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() expMsg = "Error in configuration file %s, following sections are missing:\n - mandatorySection\n"% self._configFileName areAllMandatorySectionsFound = True try: iConfigChecker.checkMandatorySections() except RepetException, re: areAllMandatorySectionsFound = False os.remove(self._configFileName) self.assertFalse(areAllMandatorySectionsFound) self.assertEquals(expMsg, re.getMessage()) def test_checkMandatorySections_mandatory_section_is_pattern (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="dir_name", mandatory=True) iConfigRules.addRuleSection(section="analysis[0-9]*", mandatory=True, isPattern = True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatorySectionsFound = True try: iConfigChecker.checkMandatorySections() except RepetException: areAllMandatorySectionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatorySectionsFound) def test_checkMandatoryOptions_in_mandatory_section (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="organism", mandatory=True) iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_in_mandatory_section_option_is_missing (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="organism", mandatory=True) iConfigRules.addRuleOption(section="organism", option ="MissingOption", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() expMsg = "Error in configuration file %s, following options are missing: \n - [organism]: MissingOption\n" % self._configFileName areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException, re: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertFalse(areAllMandatoryOptionsFound) self.assertEquals(expMsg, re.getMessage()) def test_checkMandatoryOptions_in_non_mandatory_section_and_section_and_option_exist (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_in_non_mandatory_section_and_section_exist_option_is_missing (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleOption(section="organism", option ="MissingOption", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() expMsg = "Error in configuration file %s, following options are missing: \n - [organism]: MissingOption\n" % self._configFileName areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException, re: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertFalse(areAllMandatoryOptionsFound) self.assertEquals(expMsg,re.getMessage()) def test_checkMandatoryOptions_in_non_mandatory_section_and_section_does_not_exist (self): self._iMock.write_config(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleOption(section="NonExistingAndNonMandatorySection", option ="genus", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_with_Pattern_rules_in_section (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="analysis", isPattern=True) iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_with_pattern_rules_in_option_section_is_mandatory (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="section_with_option_pattern", mandatory=True) iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_with_pattern_rules_in_option_in_mandatory_section_option_is_missing (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="section_with_option_pattern", mandatory=True) iConfigRules.addRuleOption(section="section_with_option_pattern", option ="MissingOption", isPattern= True, mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() expMsg = "Error in configuration file %s, following options are missing: \n - [section_with_option_pattern]: MissingOption\n" % self._configFileName areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException, re: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertFalse(areAllMandatoryOptionsFound) self.assertEquals(expMsg, re.getMessage()) def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_and_option_exist (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_exist_option_is_missing (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleOption(section="section_with_option_pattern", option ="MissingOption", isPattern= True, mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() expMsg = "Error in configuration file %s, following options are missing: \n - [section_with_option_pattern]: MissingOption\n" % self._configFileName areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException, re: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertFalse(areAllMandatoryOptionsFound) self.assertEquals(expMsg,re.getMessage()) def test_checkMandatoryOptions_with_pattern_rules_in_non_mandatory_section_and_section_does_not_exist (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleOption(section="non_mandatory_section", option ="MissingOption", isPattern= True, mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_with_pattern_rules_for_both_section_and_option (self): self._iMock.write_case_pattern_rule(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection(section="section_with_option_pattern", isPattern=True) iConfigRules.addRuleOption(section="section_with_option_pattern", option ="option", isPattern= True, mandatory=True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatoryOptionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatoryOptionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatoryOptionsFound) def test_checkMandatoryOptions_case(self): self._iMock.write_config_case(self._configFileName) iConfigRules = ConfigRules() iConfigRules.addRuleSection("dir_name", True) iConfigRules.addRuleSection("organism", True) iConfigRules.addRuleOption("organism", "min_SSR_coverage", True) iConfigChecker = ConfigChecker(self._configFileName, iConfigRules) iConfig = iConfigChecker.readConfigFile() iConfigChecker.setRawConfig(iConfig) iConfigChecker.extendConfigRulesWithPatternRules() areAllMandatorySectionsFound = True try: iConfigChecker.checkMandatoryOptions() except RepetException: areAllMandatorySectionsFound = False os.remove(self._configFileName) self.assertTrue(areAllMandatorySectionsFound) #TODO Test de extendConfigRulesWithPatternRules et de applyRuleToRawValue # option avec une liste de valeurs possibles dans un ensemble # option type=string type="num" type="date"???. #option define twice and options use in other class MockConfig (object): def write_config(self, configFileName): configF = open(configFileName, "w" ) configF.write( "[dir_name]\n") configF.write( "work_dir : toto \n") configF.write( "\n") configF.write( "[organism]\n") configF.write( "abbreviation: T.aestivum\n") configF.write( "genus: triticum\n") configF.write( "species: aestivum\n") configF.write( "common_name: wheat\n") configF.write( "comment: \n") configF.write( "[analysis1]\n") configF.write( "name: BLASTXWheat2\n") configF.write( "program: BLASTX2\n") configF.write( "programversion: 3.32\n") configF.write( "sourcename: dummyDesc_BLASTX2\n") configF.write( "description: \n") configF.write( "gff_name: BLASTX.gff2\n") configF.write( "\n") configF.close() def write_case_section_define_twice(self, configFileName): configF = open(configFileName, "w" ) configF.write( "[dir_name]\n") configF.write( "work_dir : toto \n") configF.write( "\n") configF.write( "[analysis1]\n") configF.write( "name: BLASTXWheat\n") configF.write( "program: BLASTX\n") configF.write( "programversion: 3.3\n") configF.write( "sourcename: dummyDesc_BLASTX\n") configF.write( "description: \n") configF.write( "gff_name: BLASTX.gff\n") configF.write( "\n") configF.write( "[analysis1]\n") configF.write( "name: BLASTXWheat2\n") configF.write( "program: BLASTX2\n") configF.write( "programversion: 3.32\n") configF.write( "sourcename: dummyDesc_BLASTX2\n") configF.write( "description: \n") configF.write( "gff_name: BLASTX.gff2\n") configF.write( "\n") configF.close() def write_case_option_define_twice(self, configFileName): configF = open(configFileName, "w" ) configF.write( "[dir_name]\n") configF.write( "work_dir : toto \n") configF.write( "\n") configF.write( "[analysis1]\n") configF.write( "name: BLASTXWheat\n") configF.write( "program: BLASTX\n") configF.write( "programversion: 3.3\n") configF.write( "sourcename: dummyDesc_BLASTX\n") configF.write( "program: BLASTX2\n") configF.write( "description: \n") configF.write( "gff_name: BLASTX.gff\n") configF.write( "\n") configF.write( "\n") configF.close() #configuration file with section with option depends on presence of other options def write_with_one_option_depends_of_an_other_one(self, configFileName ): configF = open(configFileName, "w" ) configF.write( "[dir_name]\n") configF.write( "work_dir : toto\n") configF.write( "\n") configF.write( "[organism]\n") configF.write( "abbreviation: T.aestivum\n") configF.write( "genus: Triticum\n") configF.write( "species: aestivum\n") configF.write( "common_name: wheat\n") configF.write( "comment: \n") configF.write( "\n") configF.write( "[analysis1]\n") configF.write( "name: BLASTXWheat\n") configF.write( "program: BLASTX\n") configF.write( "programversion: 3.3\n") configF.write( "sourcename: src_BLASTX\n") configF.write( "description: \n") configF.write( "gff_name: BLASTX.gff\n") configF.write( "\n") configF.write( "[analysis2]\n") configF.write( "name: GMHMMWheat\n") configF.write( "program: GMHMM\n") configF.write( "programversion: 4.3\n") configF.write( "sourcename: src_GMHMM\n") configF.write( "description: \n") configF.write( "gff_name: GMHMM.gff\n") configF.write( "\n") configF.write( "[target]\n") configF.write( "target_used: yes\n") configF.write( "target_used_list: target.lst\n") configF.close() def write_case_pattern_rule(self, configFileName ): configF = open(configFileName, "w" ) configF.write( "[dir_name]\n") configF.write( "work_dir : toto\n" ) configF.write( "\n") configF.write( "[organism]\n") configF.write( "abbreviation: T.aestivum\n") configF.write( "genus: Triticum\n") configF.write( "species: aestivum\n") configF.write( "common_name: wheat\n") configF.write( "comment: \n") configF.write( "\n") configF.write( "[analysis1]\n") configF.write( "name: BLASTXWheat\n") configF.write( "program: BLASTX\n") configF.write( "programversion: 3.3\n") configF.write( "sourcename: src_BLASTX\n") configF.write( "description: \n") configF.write( "gff_name: BLASTX.gff\n") configF.write( "\n") configF.write( "[analysis2]\n") configF.write( "name: GMHMMWheat\n") configF.write( "program: GMHMM\n") configF.write( "programversion: 4.3\n") configF.write( "sourcename: src_GMHMM\n") configF.write( "description: \n") configF.write( "gff_name: GMHMM.gff\n") configF.write( "\n") configF.write( "[target]\n") configF.write( "target_used: yes\n") configF.write( "target_used_list: target.lst\n") configF.write( "\n") configF.write( "[section_with_option_pattern]\n") configF.write( "option1: value1\n") configF.write( "option2: value2\n") configF.write( "[second_section_with_option_pattern]\n") configF.write( "option1: value1\n") configF.write( "option2: value2\n") configF.close() def write_config_case(self, configFileName): configF = open(configFileName, "w" ) configF.write( "[dir_name]\n") configF.write( "work_dir : toto \n") configF.write( "\n") configF.write( "[organism]\n") configF.write( "min_SSR_coverage: 0.50\n") configF.write( "\n") configF.close() if __name__ == "__main__": unittest.main()