Mercurial > repos > yufei-luo > s_mart
comparison commons/core/checker/test/Test_F_ConfigChecker.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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| 1 from commons.core.checker.ConfigChecker import ConfigChecker | |
| 2 from commons.core.checker.ConfigChecker import ConfigRules | |
| 3 from commons.core.checker.ConfigValue import ConfigValue | |
| 4 from commons.core.checker.RepetException import RepetException | |
| 5 import unittest | |
| 6 import os | |
| 7 | |
| 8 class Test_F_ConfigChecker(unittest.TestCase): | |
| 9 | |
| 10 #TODO: AJouter test (wrong type, etc..) | |
| 11 def setUp(self): | |
| 12 self._configFileName = "test_conf_checker" | |
| 13 | |
| 14 def tearDown(self): | |
| 15 os.remove(self._configFileName) | |
| 16 | |
| 17 def test_run(self): | |
| 18 iMock = MockConfig() | |
| 19 iMock.write_config(self._configFileName) | |
| 20 | |
| 21 iConfigRules = ConfigRules() | |
| 22 iConfigRules.addRuleSection(section="dir_name", mandatory=True) | |
| 23 iConfigRules.addRuleOption(section="dir_name", option ="work_dir", mandatory=True) | |
| 24 iConfigRules.addRuleSection(section="organism", mandatory=True) | |
| 25 iConfigRules.addRuleOption(section="organism", option ="abbreviation", mandatory=True) | |
| 26 iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True) | |
| 27 iConfigRules.addRuleOption(section="organism", option ="species", mandatory=True) | |
| 28 iConfigRules.addRuleOption(section="organism", option ="common_name", mandatory=True) | |
| 29 iConfigRules.addRuleOption(section="organism", option ="comment") | |
| 30 iConfigRules.addRuleSection(section="analysis", mandatory=True, isPattern=True) | |
| 31 iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True) | |
| 32 iConfigRules.addRuleOption(section="analysis", option ="program", mandatory=True) | |
| 33 iConfigRules.addRuleOption(section="analysis", option ="sourcename", mandatory=True) | |
| 34 iConfigRules.addRuleOption(section="analysis", option ="description") | |
| 35 iConfigRules.addRuleOption(section="analysis", option ="gff_name") | |
| 36 | |
| 37 iConfigChecker = ConfigChecker(self._configFileName,iConfigRules) | |
| 38 | |
| 39 obsValidatedConfig = iConfigChecker.getConfig() | |
| 40 | |
| 41 expValidatedConfig = ConfigValue() | |
| 42 d = {"dir_name" : {"work_dir":"toto"}, | |
| 43 "organism" : {"abbreviation":"T.aestivum", | |
| 44 "genus":"triticum", | |
| 45 "species":"aestivum", | |
| 46 "common_name":"wheat", | |
| 47 "comment":""}, | |
| 48 'analysis1': {'description': '', | |
| 49 'gff_name': 'BLASTX.gff2', | |
| 50 'name': 'BLASTXWheat2', | |
| 51 'program': 'BLASTX2', | |
| 52 'programversion': '3.32', | |
| 53 'sourcename': 'dummyDesc_BLASTX2'} | |
| 54 } | |
| 55 expValidatedConfig.setdOptionsValues4Sections(d) | |
| 56 | |
| 57 self.assertEquals(expValidatedConfig, obsValidatedConfig) | |
| 58 | |
| 59 | |
| 60 def test_run_exception_section_missing(self): | |
| 61 iMock = MockConfig() | |
| 62 iMock.write_config_section_missing(self._configFileName) | |
| 63 | |
| 64 iConfigRules = ConfigRules() | |
| 65 iConfigRules.addRuleSection(section="dir_name", mandatory=True) | |
| 66 iConfigRules.addRuleOption(section="dir_name", option ="work_dir", mandatory=True) | |
| 67 iConfigRules.addRuleSection(section="organism", mandatory=True) | |
| 68 iConfigRules.addRuleOption(section="organism", option ="abbreviation", mandatory=True) | |
| 69 iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True) | |
| 70 iConfigRules.addRuleOption(section="organism", option ="species", mandatory=True) | |
| 71 iConfigRules.addRuleOption(section="organism", option ="common_name", mandatory=True) | |
| 72 iConfigRules.addRuleOption(section="organism", option ="comment") | |
| 73 iConfigRules.addRuleSection(section="analysis", mandatory=True, isPattern=True) | |
| 74 iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True) | |
| 75 iConfigRules.addRuleOption(section="analysis", option ="program", mandatory=True) | |
| 76 iConfigRules.addRuleOption(section="analysis", option ="sourcename", mandatory=True) | |
| 77 iConfigRules.addRuleOption(section="analysis", option ="description") | |
| 78 iConfigRules.addRuleOption(section="analysis", option ="gff_name") | |
| 79 | |
| 80 iConfigChecker = ConfigChecker(self._configFileName,iConfigRules) | |
| 81 | |
| 82 expMessage = "Error in configuration file %s, following sections are missing:\n - organism\n"% self._configFileName | |
| 83 | |
| 84 try : | |
| 85 obsValidatedConfig = iConfigChecker.getConfig() | |
| 86 except RepetException, e: | |
| 87 obsMessage = e.getMessage() | |
| 88 | |
| 89 self.assertEquals(expMessage, obsMessage) | |
| 90 | |
| 91 | |
| 92 def test_run_exception_section_pattern_false(self): | |
| 93 iMock = MockConfig() | |
| 94 iMock.write_config(self._configFileName) | |
| 95 | |
| 96 iConfigRules = ConfigRules() | |
| 97 iConfigRules.addRuleSection(section="dir_name", mandatory=True) | |
| 98 iConfigRules.addRuleOption(section="dir_name", option ="work_dir", mandatory=True) | |
| 99 iConfigRules.addRuleSection(section="organism", mandatory=True) | |
| 100 iConfigRules.addRuleOption(section="organism", option ="abbreviation", mandatory=True) | |
| 101 iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True) | |
| 102 iConfigRules.addRuleOption(section="organism", option ="species", mandatory=True) | |
| 103 iConfigRules.addRuleOption(section="organism", option ="common_name", mandatory=True) | |
| 104 iConfigRules.addRuleOption(section="organism", option ="comment") | |
| 105 iConfigRules.addRuleSection(section="analysis", mandatory=True) | |
| 106 iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True) | |
| 107 iConfigRules.addRuleOption(section="analysis", option ="program", mandatory=True) | |
| 108 iConfigRules.addRuleOption(section="analysis", option ="sourcename", mandatory=True) | |
| 109 iConfigRules.addRuleOption(section="analysis", option ="description") | |
| 110 iConfigRules.addRuleOption(section="analysis", option ="gff_name") | |
| 111 | |
| 112 iConfigChecker = ConfigChecker(self._configFileName,iConfigRules) | |
| 113 | |
| 114 expMessage = "Error in configuration file %s, following sections are missing:\n - analysis\n"% self._configFileName | |
| 115 | |
| 116 try : | |
| 117 obsValidatedConfig = iConfigChecker.getConfig() | |
| 118 except RepetException, e: | |
| 119 obsMessage = e.getMessage() | |
| 120 | |
| 121 self.assertEquals(expMessage, obsMessage) | |
| 122 | |
| 123 | |
| 124 def test_run_exception_option_missing(self): | |
| 125 iMock = MockConfig() | |
| 126 iMock.write_config_option_missing(self._configFileName) | |
| 127 | |
| 128 iConfigRules = ConfigRules() | |
| 129 iConfigRules.addRuleSection(section="dir_name", mandatory=True) | |
| 130 iConfigRules.addRuleOption(section="dir_name", option ="work_dir", mandatory=True) | |
| 131 iConfigRules.addRuleSection(section="organism", mandatory=True) | |
| 132 iConfigRules.addRuleOption(section="organism", option ="abbreviation", mandatory=True) | |
| 133 iConfigRules.addRuleOption(section="organism", option ="genus", mandatory=True) | |
| 134 iConfigRules.addRuleOption(section="organism", option ="species", mandatory=True) | |
| 135 iConfigRules.addRuleOption(section="organism", option ="common_name", mandatory=True) | |
| 136 iConfigRules.addRuleOption(section="organism", option ="comment") | |
| 137 iConfigRules.addRuleSection(section="analysis", mandatory=True, isPattern=True) | |
| 138 iConfigRules.addRuleOption(section="analysis", option ="name", mandatory=True) | |
| 139 iConfigRules.addRuleOption(section="analysis", option ="program", mandatory=True) | |
| 140 iConfigRules.addRuleOption(section="analysis", option ="sourcename", mandatory=True) | |
| 141 iConfigRules.addRuleOption(section="analysis", option ="description") | |
| 142 iConfigRules.addRuleOption(section="analysis", option ="gff_name") | |
| 143 | |
| 144 iConfigChecker = ConfigChecker(self._configFileName,iConfigRules) | |
| 145 | |
| 146 expMessage = "Error in configuration file %s, following options are missing: \n - [organism]: abbreviation\n"% self._configFileName | |
| 147 | |
| 148 try : | |
| 149 obsValidatedConfig = iConfigChecker.getConfig() | |
| 150 except RepetException, e: | |
| 151 obsMessage = e.getMessage() | |
| 152 | |
| 153 self.assertEquals(expMessage, obsMessage) | |
| 154 | |
| 155 class MockConfig (object): | |
| 156 | |
| 157 def write_config(self, configFileName): | |
| 158 configF = open(configFileName, "w" ) | |
| 159 configF.write( "[dir_name]\n") | |
| 160 configF.write( "work_dir : toto \n") | |
| 161 configF.write( "\n") | |
| 162 configF.write( "[organism]\n") | |
| 163 configF.write( "abbreviation: T.aestivum\n") | |
| 164 configF.write( "genus: triticum\n") | |
| 165 configF.write( "species: aestivum\n") | |
| 166 configF.write( "common_name: wheat\n") | |
| 167 configF.write( "comment: \n") | |
| 168 configF.write( "[analysis1]\n") | |
| 169 configF.write( "name: BLASTXWheat2\n") | |
| 170 configF.write( "program: BLASTX2\n") | |
| 171 configF.write( "programversion: 3.32\n") | |
| 172 configF.write( "sourcename: dummyDesc_BLASTX2\n") | |
| 173 configF.write( "description: \n") | |
| 174 configF.write( "gff_name: BLASTX.gff2\n") | |
| 175 configF.write( "\n") | |
| 176 configF.close() | |
| 177 | |
| 178 def write_config_section_missing(self, configFileName): | |
| 179 configF = open(configFileName, "w" ) | |
| 180 configF.write( "[dir_name]\n") | |
| 181 configF.write( "work_dir : toto \n") | |
| 182 configF.write( "\n") | |
| 183 configF.write( "[analysis1]\n") | |
| 184 configF.write( "name: BLASTXWheat2\n") | |
| 185 configF.write( "program: BLASTX2\n") | |
| 186 configF.write( "programversion: 3.32\n") | |
| 187 configF.write( "sourcename: dummyDesc_BLASTX2\n") | |
| 188 configF.write( "description: \n") | |
| 189 configF.write( "gff_name: BLASTX.gff2\n") | |
| 190 configF.write( "\n") | |
| 191 configF.close() | |
| 192 | |
| 193 def write_config_option_missing(self, configFileName): | |
| 194 configF = open(configFileName, "w" ) | |
| 195 configF.write( "[dir_name]\n") | |
| 196 configF.write( "work_dir : toto \n") | |
| 197 configF.write( "\n") | |
| 198 configF.write( "[organism]\n") | |
| 199 configF.write( "genus: triticum\n") | |
| 200 configF.write( "species: aestivum\n") | |
| 201 configF.write( "common_name: wheat\n") | |
| 202 configF.write( "comment: \n") | |
| 203 configF.write( "[analysis1]\n") | |
| 204 configF.write( "name: BLASTXWheat2\n") | |
| 205 configF.write( "program: BLASTX2\n") | |
| 206 configF.write( "programversion: 3.32\n") | |
| 207 configF.write( "sourcename: dummyDesc_BLASTX2\n") | |
| 208 configF.write( "description: \n") | |
| 209 configF.write( "gff_name: BLASTX.gff2\n") | |
| 210 configF.write( "\n") | |
| 211 configF.close() | |
| 212 | |
| 213 if __name__ == "__main__": | |
| 214 unittest.main() |