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1 #! /usr/bin/env python
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2
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3 # Copyright INRA (Institut National de la Recherche Agronomique)
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4 # http://www.inra.fr
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5 # http://urgi.versailles.inra.fr
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6 #
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7 # This software is governed by the CeCILL license under French law and
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8 # abiding by the rules of distribution of free software. You can use,
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9 # modify and/ or redistribute the software under the terms of the CeCILL
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10 # license as circulated by CEA, CNRS and INRIA at the following URL
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11 # "http://www.cecill.info".
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12 #
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13 # As a counterpart to the access to the source code and rights to copy,
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14 # modify and redistribute granted by the license, users are provided only
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15 # with a limited warranty and the software's author, the holder of the
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16 # economic rights, and the successive licensors have only limited
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17 # liability.
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18 #
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19 # In this respect, the user's attention is drawn to the risks associated
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20 # with loading, using, modifying and/or developing or reproducing the
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21 # software by the user in light of its specific status of free software,
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22 # that may mean that it is complicated to manipulate, and that also
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23 # therefore means that it is reserved for developers and experienced
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24 # professionals having in-depth computer knowledge. Users are therefore
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25 # encouraged to load and test the software's suitability as regards their
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26 # requirements in conditions enabling the security of their systems and/or
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27 # data to be ensured and, more generally, to use and operate it in the
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28 # same conditions as regards security.
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29 #
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30 # The fact that you are presently reading this means that you have had
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31 # knowledge of the CeCILL license and that you accept its terms.
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32
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33 from optparse import OptionParser
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34 from commons.core.sql.DbMySql import DbMySql
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35
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36 class RetrieveInitHeaders(object):
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37
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38 def __init__(self, inTableName = "", linkFileName = "", outTableName = "", isQueryHeaders = True, clean = False, verbose = 0):
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39 self._inTableName = inTableName
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40 self._linkFileName = linkFileName
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41 if outTableName == "":
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42 self._outTableName = self._inTableName
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43 else:
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44 self._outTableName = outTableName
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45 self._isQueryHeaders = isQueryHeaders
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46 self._clean = clean
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47 self._verbose = verbose
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48 self._iDb = None
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49 self._tmpTableName = "%s_tmp" % self._inTableName
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50
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51 #TODO: can handle config file
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52 #TODO: description, help...
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53 def setAttributesFromCmdLine(self):
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54 description = ""
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55 parser = OptionParser(description = description)
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56 parser.add_option("-i", "--input", dest = "inTableName", type = "string", help = "", default = "")
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57 parser.add_option("-l", "--link", dest = "linkFileName", type = "string", help = "", default = "")
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58 parser.add_option("-o", "--output", dest = "outTableName", type = "string", help = "(default = input table name)", default = "")
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59 parser.add_option("-s", "--subject", dest = "isQueryHeaders", action = "store_false", help = "change subject name and not query name", default = True)
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60 parser.add_option("-c", "--clean", dest = "clean", action = "store_true", help = "drop input table", default = False)
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61 parser.add_option("-v", "--verbose", dest = "verbose", type = "int", help = "0 or 1", default = 0)
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62 options, args = parser.parse_args()
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63 self.setAttributesFromOptions(options)
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64
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65 def setAttributesFromOptions(self, options):
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66 self.setInTableName(options.inTableName)
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67 self.setLinkFileName(options.linkFileName)
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68 self.setOutTableName(options.outTableName)
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69 self.setIsQueryHeaders(options.isQueryHeaders)
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70 self.setClean(options.clean)
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71 self.setVerbose(options.verbose)
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72
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73 def setInTableName(self, inTableName):
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74 self._inTableName = inTableName
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75 self._tmpTableName = "%s_tmp" % self._inTableName
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76
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77 def setLinkFileName(self, linkFileName):
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78 self._linkFileName = linkFileName
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79
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80 def setOutTableName(self, outTableName):
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81 if outTableName == "":
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82 self._outTableName = self._inTableName
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83 else:
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84 self._outTableName = outTableName
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85
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86 def setIsQueryHeaders(self, isQueryHeaders):
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87 self._isQueryHeaders = isQueryHeaders
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88
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89 def setClean(self, clean):
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90 self._clean = clean
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91
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92 def setVerbose(self, verbose):
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93 self._verbose = verbose
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94
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95 #TODO: checkOptions
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96 def checkOptions(self):
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97 pass
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98
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99 def run(self):
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100 if self._verbose > 0:
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101 print "START RetrieveInitHeaders.py"
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102 self.checkOptions()
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103
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104 if self._verbose > 0:
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105 print "copy '%s' table to '%s' table" % (self._inTableName, self._tmpTableName)
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106 self._iDb = DbMySql()
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107 self._iDb.copyTable(self._inTableName, self._tmpTableName)
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108
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109 if self._verbose > 0:
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110 print "read '%s' file" % self._linkFileName
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111 f = open(self._linkFileName)
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112 line = f.readline()
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113 count = 0
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114 while line:
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115 oldHeader = line.split()[0]
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116 newHeader = line.split()[1]
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117 if self._isQueryHeaders:
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118 self._updateQueryName(oldHeader, newHeader)
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119 else:
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120 self._updateSubjectName(oldHeader, newHeader)
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121 count += 1
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122 line = f.readline()
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123 f.close()
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124
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125 if self._verbose > 0:
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126 print "nb of relationships: %i" % count
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127 if self._clean:
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128 self._iDb.dropTable(self._inTableName)
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129 if self._verbose > 0:
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130 print "drop '%s' table" % self._inTableName
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131 if self._verbose > 0:
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132 print "rename '%s' table to '%s' table" % (self._tmpTableName, self._outTableName)
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133 self._iDb.renameTable(self._tmpTableName, self._outTableName)
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134 self._iDb.close()
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135 if self._verbose > 0:
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136 print "END RetrieveInitHeaders.py"
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137
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138 #TODO: methods must be in TablePathAdaptator ?
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139 def _updateQueryName(self, oldH, newH):
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140 sqlCmd = "UPDATE %s SET query_name = '%s' WHERE query_name = '%s'" % (self._tmpTableName, newH, oldH)
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141 self._iDb.execute(sqlCmd)
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142
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143 def _updateSubjectName(self, oldH, newH):
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144 sqlCmd = "UPDATE %s SET subject_name = '%s' WHERE subject_name = '%s'" % (self._tmpTableName, newH, oldH)
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145 self._iDb.execute(sqlCmd)
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146
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147 if __name__ == "__main__":
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148 iRIH = RetrieveInitHeaders()
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149 iRIH.setAttributesFromCmdLine()
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150 iRIH.run() |
