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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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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 os
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33 import sys
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34 import re
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35 import glob
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36 import ConfigParser
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37 from ConfigParser import NoOptionError
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38 from ConfigParser import NoSectionError
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39 from commons.core.checker.CheckerException import CheckerException
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40
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41
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42 ## A set of static methods used to perform checks.
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43 #
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44 #
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45 class CheckerUtils( object ):
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46
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47 ## Check if blastName param is in ["blastn", "blastp", "blastx", "tblastn", "tblastx"]
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48 #
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49 # @param blastName name to check
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50 # @return True if name is in list False otherwise
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51 #
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52 def isBlastNameNotInBlastValues( blastName ):
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53 blastValuesSet = set( ["blastn", "blastp", "blastx", "tblastn", "tblastx"] )
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54 blastNameSet = set( [ blastName ] )
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55 return not blastNameSet.issubset( blastValuesSet )
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56
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57 isBlastNameNotInBlastValues = staticmethod( isBlastNameNotInBlastValues )
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58
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59
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60 ## Check if param is NOT "TRUE" and NOT false "FALSE"
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61 #
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62 # @param param str to check
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63 # @return True if param is not eq to "TRUE" AND not eq to "FALSE", false otherwise
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64 #
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65 def isNotTRUEisNotFALSE( param ):
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66 return param != "TRUE" and param != "FALSE"
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67
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68 isNotTRUEisNotFALSE = staticmethod( isNotTRUEisNotFALSE )
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69
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70
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71 ## Check if resource (file or dir) do NOT exists
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72 #
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73 # @param resource file or dir to check
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74 # @return True if resource exists False otherwise
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75 #
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76 def isRessourceNotExits( resource ):
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77 return not os.path.exists( resource )
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78
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79 isRessourceNotExits = staticmethod( isRessourceNotExits )
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80
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81
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82 ## Check a specific E-value format: de-dd
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83 #
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84 # @param param E-value to check
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85 # @return True if format is de-dd False otherwise
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86 #
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87 def isNotAeValueWithOneDigit2DecimalsAtLeast( param ):
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88 # \d\d stands for 2 digits and more ???
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89 return not re.match( "\de\-\d\d", param )
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90
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91 isNotAeValueWithOneDigit2DecimalsAtLeast = staticmethod( isNotAeValueWithOneDigit2DecimalsAtLeast )
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92
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93
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94 ## Check a number format
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95 #
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96 # @param param value to check
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97 # @return True if param is a number (d+) False otherwise
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98 #
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99 def isNotANumber( param ):
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100 return not re.match( "\d+", param )
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101
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102 isNotANumber = staticmethod( isNotANumber )
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103
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104
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105 ## Check if an executable is in the user's PATH
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106 #
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107 # @param exeName name of the executable
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108 # @return True if executable in user's PATH, False otherwise
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109 #
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110 def isExecutableInUserPath( exeName ):
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111 dirPathList = os.environ["PATH"].split(":")
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112 for dirPath in dirPathList:
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113 if os.path.isdir( dirPath ):
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114 try:
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115 binPathList = glob.glob( dirPath + "/*" )
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116 except OSError, e:
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117 continue
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118 for binPath in binPathList:
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119 bin = os.path.basename( binPath )
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120 if bin == exeName:
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121 return True
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122 return False
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123
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124 isExecutableInUserPath = staticmethod( isExecutableInUserPath )
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125
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126
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127 ## Return the full path of a given executable
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128 #
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129 def getFullPathFromExecutable( exeName ):
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130 lDirFromUserPath = os.environ["PATH"].split(":")
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131 for dir in lDirFromUserPath:
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132 if os.path.isdir( dir ):
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133 try:
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134 lExecutables = glob.glob( "%s/*" % ( dir ) )
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135 except OSError, e:
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136 continue
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137 for exe in lExecutables:
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138 path, exe = os.path.split( exe )
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139 if exe == exeName:
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140 return path
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141 return ""
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142
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143 getFullPathFromExecutable = staticmethod( getFullPathFromExecutable )
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144
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145
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146 #TODO: to remove ?
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147 ## Check if a queue Name is valid. Warning: Only with the queue manager SGE
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148 #
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149 # @param fullQueueName name of the queue to test (with or without parameters)
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150 # @return True if queue name is valid, False otherwise
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151 #
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152 def isQueueNameValid( fullQueueName ):
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153 queueName = fullQueueName.split()[0]
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154 if queueName == "none":
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155 return True
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156 queueFile = "queueName.txt"
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157 if not CheckerUtils.isExecutableInUserPath( "qconf" ):
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158 msg = "executable 'qconf' can't be found"
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159 sys.stderr.write( "%s\n" % ( msg ) )
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160 return False
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161 cmd = "qconf -sql > " + queueFile
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162 os.system( cmd )
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163 queueFileHandler = open( queueFile, "r" )
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164 lQueueNames = queueFileHandler.readlines()
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165 queueFileHandler.close()
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166 os.remove( queueFile )
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167 queueNameValid = False
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168 for qName in lQueueNames:
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169 qName = qName.strip()
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170 if qName == queueName:
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171 queueNameValid = True
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172 break
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173 return queueNameValid
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174
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175 isQueueNameValid = staticmethod( isQueueNameValid )
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176
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177
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178 ## Check if a string length is lower or equal than 15
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179 #
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180 # @param strName any string
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181 # @return True if string length is <= 15, False otherwise
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182 #
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183 def isMax15Char( strName ):
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184 return (len(strName) <= 15 )
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185
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186 isMax15Char = staticmethod( isMax15Char )
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187
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188
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189 ## Check if a string is made with only alphanumeric or underscore character
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190 #
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191 # @param strName any string
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192 # @return True if string is with alphanumeric or underscore, False otherwise
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193 #
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194 def isCharAlphanumOrUnderscore( strName ):
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195 # authorized ALPHABET [a-z,A-Z,0-9,_]
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196 p = re.compile('\W')
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197 errList=p.findall(strName)
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198 if len( errList ) > 0 :
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199 return False
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200 else:
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201 return True
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202
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203 isCharAlphanumOrUnderscore = staticmethod( isCharAlphanumOrUnderscore )
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204
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205
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206 ## Check if sectionName is in the configuration file
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207 #
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208 # @param config filehandle of configuration file
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209 # @param sectionName string of section name to check
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210 # @exception NoSectionError: if section not found raise a NoSectionError
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211 #
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212 def checkSectionInConfigFile( config, sectionName ):
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213 if not (config.has_section(sectionName)):
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214 raise NoSectionError(sectionName)
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215
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216 checkSectionInConfigFile = staticmethod( checkSectionInConfigFile )
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217
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218
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219 ## Check if an option is in a specified section in the configuration file
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220 #
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221 # @param config filehandle of configuration file
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222 # @param sectionName string of section name
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223 # @param optionName string of option name to check
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224 # @exception NoOptionError: if option not found raise a NoOptionError
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225 #
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226 def checkOptionInSectionInConfigFile( config, sectionName, optionName ):
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227 config.get( sectionName, optionName )
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228
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229 checkOptionInSectionInConfigFile = staticmethod( checkOptionInSectionInConfigFile )
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230
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231
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232 ## Check version number coherency between configFile and CHANGELOG
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233 #
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234 # @param config ConfigParser Instance of configuration file
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235 # @param changeLogFileHandle CHANGELOG file handle
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236 # @exception NoOptionError: if option not found raise a NoOptionError
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237 #
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238 def checkConfigVersion( changeLogFileHandle, config ):
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239 line = changeLogFileHandle.readline()
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240 while not line.startswith("REPET release "):
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241 line = changeLogFileHandle.readline()
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242 numVersionChangeLog = line.split()[2]
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243
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244 numVersionConfig = config.get("repet_env", "repet_version")
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245
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246 if not numVersionChangeLog == numVersionConfig:
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247 message = "*** Error: wrong config file version. Expected version num is " + numVersionChangeLog + " but actual in config file is " + numVersionConfig
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248 raise CheckerException(message)
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249
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250 checkConfigVersion = staticmethod( checkConfigVersion )
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251
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252
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253 ## Get version number from CHANGELOG
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254 #
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255 # @param changeLogFile CHANGELOG file name
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256 #
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257 def getVersionFromChangelogFile(changeLogFileName):
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258 with open(changeLogFileName) as changeLogFileHandle:
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259 line = changeLogFileHandle.readline()
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260 while not line.startswith("REPET release "):
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261 line = changeLogFileHandle.readline()
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262 numVersionChangeLog = line.split()[2]
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263 return numVersionChangeLog
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264
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265
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266 getVersionFromChangelogFile = staticmethod( getVersionFromChangelogFile )
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267
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268
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269 ## Check if headers of an input file contain only alpha numeric characters and "_ : . -"
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270 #
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271 # @param fileHandler file handle
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272 # @exception CheckerException if bad header raise a CheckerException
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273 #
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274 def checkHeaders( fileHandler ):
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275 lHeaders = CheckerUtils._getHeaderFromFastaFile(fileHandler)
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276 p = re.compile('[^a-zA-Z0-9_:\.\-]', re.IGNORECASE)
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277 lWrongHeaders = []
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278 for header in lHeaders:
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279 errList=p.findall(header)
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280 if len( errList ) > 0 :
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281 lWrongHeaders.append(header)
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282 if lWrongHeaders != []:
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283 exception = CheckerException()
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284 exception.setMessages(lWrongHeaders)
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285 raise exception
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286
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287 checkHeaders = staticmethod( checkHeaders )
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288
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289
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290 def _getHeaderFromFastaFile( inFile ):
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291 lHeaders = []
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292 while True:
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293 line = inFile.readline()
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294 if line == "":
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295 break
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296 if line[0] == ">":
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297 lHeaders.append( line[1:-1] )
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298 return lHeaders
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299
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300 _getHeaderFromFastaFile = staticmethod( _getHeaderFromFastaFile )
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301
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302
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303 ## Return True if an option is in a specified section in the configuration file, False otherwise
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304 #
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305 # @param config handler of configuration file
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306 # @param sectionName string of section name
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307 # @param optionName string of option name to check
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308 #
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309 def isOptionInSectionInConfig( configHandler, section, option ):
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310 try:
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311 CheckerUtils.checkOptionInSectionInConfigFile( configHandler, section, option )
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312 except NoOptionError:
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313 return False
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314 return True
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315
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316 isOptionInSectionInConfig = staticmethod( isOptionInSectionInConfig )
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