Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/checker/ConfigChecker.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
parents
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import re
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33 import sys
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34 from commons.core.utils.RepetConfigParser import RepetConfigParser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 from commons.core.checker.ConfigValue import ConfigValue
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 from commons.core.checker.IChecker import IChecker
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 from commons.core.checker.RepetException import RepetException
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 from commons.core.utils.FileUtils import FileUtils
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39
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40
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 class Rule(object):
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42
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 def __init__(self, mandatory= False, isPattern=False, type="", set=(), help =""):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 self.mandatory = mandatory
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 self.isPattern = isPattern
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 self.type = type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 self.set = set
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 self.help = help
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49
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 class ConfigRules(object):
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51
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52 def __init__(self, configName = "", configDescription = ""):
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53 self.configName = configName
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 self.configDescription = configDescription
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 self.dRules4Sections={}
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56
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 def _addRule(self, section, option="DEFAULT", mandatory=False, isPattern=False, type="", set=(), help =""):
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58 if not self.dRules4Sections.has_key(section):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 self.dRules4Sections[section] = {}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 self.dRules4Sections[section][option]=Rule(mandatory, isPattern, type.lower(), set)
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61
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62 def addRuleSection(self, section, mandatory=False, isPattern=False, help = ""):
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63 self._addRule(section = section, option = "DEFAULT", mandatory = mandatory, isPattern = isPattern, help = "")
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64
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65 def addRuleOption(self, section, option, mandatory=False, isPattern=False, type="", set=(), help = ""):
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66 self._addRule(section = section, option = option, mandatory = mandatory, isPattern = isPattern, type = type, set=set , help = "")
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67
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68 def isSectionMandatory(self, section):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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69 if self.dRules4Sections.has_key(section):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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70 if self.dRules4Sections[section].has_key("DEFAULT"):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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71 return self.dRules4Sections[section]["DEFAULT"].mandatory
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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72 return False
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73
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74 def isOptionMandatory(self, section, option):
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75 if self.dRules4Sections.has_key(section):
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76 if self.dRules4Sections[section].has_key(option):
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77 return self.dRules4Sections[section][option].mandatory
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78 return False
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79
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80 def getRule(self, section, option):
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81 if self.dRules4Sections.has_key(section):
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82 if self.dRules4Sections[section].has_key(option):
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83 return self.dRules4Sections[section][option]
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84 return None
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85
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86 class ConfigChecker(IChecker):
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87
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88 def __init__ (self, cfgFileName, iCfgRules):
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89 self._configFileName = cfgFileName
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90 self._iConfigRules = iCfgRules
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91 self._iRawConfig = ConfigValue()
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92 self._iExtendedConfigRules = ConfigRules()
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93
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94 def readConfigFile(self):
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95 iConfig = RepetConfigParser()
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96 try:
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97 iConfig.readfp(open(self._configFileName))
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98 return iConfig
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99 # TODO USE OF CONFIG ERROR
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100 # if DuplicateSectionError:
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101 # raise Exception ("Duplicate section exist in config file %s" %(self._configFileName ))
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102 except :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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103 raise RepetException ("Unexpected error: %s" % sys.exc_info()[0])
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104
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105 def setRawConfig(self, iConfig ):
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106 for sectionName in iConfig.sections():
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107 for optionName in iConfig.options(sectionName):
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108 optionValue = iConfig.get(sectionName, optionName)
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109 self._iRawConfig.set(sectionName, optionName, optionValue)
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110
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111 def getOptionValueAccordingRule(self, iConfig, sectionName, optionName):
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112 optionRule = self._iExtendedConfigRules.getRule(sectionName, optionName)
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113 if optionRule == None :
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114 return iConfig.get(sectionName, optionName)
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115
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116 if optionRule.type == "int":
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117 optionValue = iConfig.getint(sectionName, optionName)
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118 elif optionRule.type == "float":
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119 optionValue = iConfig.getfloat(sectionName, optionName)
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120 elif optionRule.type == "bool" or optionRule.type == "boolean":
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121 optionValue = iConfig.getboolean(sectionName, optionName)
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122 else:
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123 optionValue = iConfig.get(sectionName, optionName)
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124 if optionRule.set!=() and not(optionValue in optionRule.set):
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125 #TODO : test and fix
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126 raise RepetException ("value must be in %s " % set.__repr__())
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127
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128 return optionValue
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129
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130 def setConfig(self, iConfig ):
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131 config = ConfigValue()
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132 valueErr = ""
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133 for sectionName in iConfig.sections():
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134 for optionName in iConfig.options(sectionName):
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135 try:
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136 optionValue = self.getOptionValueAccordingRule(iConfig, sectionName, optionName )
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137 config.set(sectionName, optionName, optionValue)
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138 except RepetException, re :
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139 #TODO : test and fix
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140 valueErr += "\n - [%s]: %s %s" % re.getMessage()
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141 if valueErr == "":
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142 self._iRawConfig = config
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143 else:
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144 raise RepetException ("Following errors occurs:%s\n" %valueErr)
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145
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146 def checkIfExistsConfigFile (self):
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147 if not (FileUtils.isRessourceExists(self._configFileName)):
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148 raise RepetException("CONFIG FILE not found - '%s'" % self._configFileName)
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149
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150 def checkMandatorySections (self):
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151 missingSection = ""
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152 for sectionName in self._iExtendedConfigRules.dRules4Sections.keys():
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153 if self._iExtendedConfigRules.isSectionMandatory(sectionName) and not self._iRawConfig.has_section(sectionName):
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154 missingSection += "\n - %s" %(sectionName)
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155 if missingSection != "":
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156 raise RepetException ("Error in configuration file %s, following sections are missing:%s\n" % (self._configFileName, missingSection))
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157
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158 def checkMandatoryOptions (self):
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159 missingOption = ""
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160 for sectionName in self._iExtendedConfigRules.dRules4Sections.keys():
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161 if self._iExtendedConfigRules.isSectionMandatory(sectionName) or self._iRawConfig.has_section(sectionName) :
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162 dRules4OptionsOfThisSection = self._iExtendedConfigRules.dRules4Sections[sectionName]
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163 for optionName in dRules4OptionsOfThisSection.keys():
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164 if optionName != "DEFAULT" and self._iExtendedConfigRules.isOptionMandatory(sectionName, optionName) and not self._iRawConfig.has_option(sectionName, optionName):
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165 missingOption += "\n - [%s]: %s" % (sectionName, optionName)
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166 if missingOption != "":
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167 raise RepetException ("Error in configuration file %s, following options are missing: %s\n" % (self._configFileName, missingOption))
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168
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169 def getSectionNamesAccordingPatternRules (self, sectionWordOrPattern, isPattern):
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170 lSectionsFoundAccordingPatternRules=[]
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171 if isPattern == False:
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172 if self._iRawConfig.has_section(sectionWordOrPattern):
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173 lSectionsFoundAccordingPatternRules.append(sectionWordOrPattern)
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174 else:
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175 for sectionName in self._iRawConfig.sections():
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176 if re.search(sectionWordOrPattern, sectionName, re.IGNORECASE):
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177 lSectionsFoundAccordingPatternRules.append(sectionName)
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178 return lSectionsFoundAccordingPatternRules
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179
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180 def getOptionsNamesAccordingPatternRules(self, sectionName, optionWordOrPattern, isPattern):
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181 lOptionsFoundAccordingPatternRules=[]
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182 if isPattern == False:
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183 if self._iRawConfig.has_option(sectionName, optionWordOrPattern):
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184 lOptionsFoundAccordingPatternRules.append(optionWordOrPattern)
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185 else :
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186 for optionName in self._iRawConfig.options(sectionName):
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187 if re.search(optionWordOrPattern, optionName, re.IGNORECASE)!= None:
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188 lOptionsFoundAccordingPatternRules.append(optionName)
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189 return lOptionsFoundAccordingPatternRules
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190
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191 def extendConfigRulesWithPatternRules(self):
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192 for sectionName in self._iConfigRules.dRules4Sections.keys():
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193 dRules4OptionsOfThisSection = self._iConfigRules.dRules4Sections[sectionName]
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194 lRawSections=[]
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195 if dRules4OptionsOfThisSection.has_key("DEFAULT"):
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196 mandatorySection = dRules4OptionsOfThisSection["DEFAULT"].mandatory
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197 isPatternSection = dRules4OptionsOfThisSection["DEFAULT"].isPattern
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198 lRawSections=self.getSectionNamesAccordingPatternRules(sectionName, isPatternSection)
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199 for rawSectionName in lRawSections:
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200 self._iExtendedConfigRules.addRuleSection(rawSectionName, "DEFAULT", mandatorySection )
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201 if mandatorySection and (len(lRawSections)==0):
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202 self._iExtendedConfigRules.addRuleSection(sectionName, "DEFAULT", mandatorySection )
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203 else:
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204 lRawSections.append(sectionName)
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205 for optionName in dRules4OptionsOfThisSection.keys():
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206 setOption = dRules4OptionsOfThisSection[optionName].set
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207 isPatternOption = dRules4OptionsOfThisSection[optionName].isPattern
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208 mandatoryOption = dRules4OptionsOfThisSection[optionName].mandatory
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209 typeOption = dRules4OptionsOfThisSection[optionName].type
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210 if optionName != "DEFAULT":
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211 for rawSectionName in lRawSections:
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212 lRawOptions=self.getOptionsNamesAccordingPatternRules(rawSectionName, optionName, isPatternOption)
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213 for rawOptionName in lRawOptions:
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214 self._iExtendedConfigRules.addRuleOption(rawSectionName, rawOptionName, mandatoryOption, False, typeOption, setOption)
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215 if mandatoryOption and (len(lRawOptions)==0):
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216 self._iExtendedConfigRules.addRuleOption(rawSectionName, optionName, mandatoryOption, False, typeOption, setOption)
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217
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218 def getConfig(self):
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219 self.checkIfExistsConfigFile()
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220 iConfig = self.readConfigFile()
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221 self.setRawConfig(iConfig)
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222 self.extendConfigRulesWithPatternRules()
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223 self.checkMandatorySections()
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224 self.checkMandatoryOptions()
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225 self.setConfig(iConfig)
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226 return self._iRawConfig