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