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1 #!/usr/bin/env python
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2
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3 import user, os, sys, getopt, exceptions, ConfigParser
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4
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5 #-----------------------------------------------------------------------------
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6
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7 def help():
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8
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9 """
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10 Give the list of the command-line options.
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11 """
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12
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13 print
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14 print "usage:",sys.argv[0]," [ options ]"
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15 print "options:"
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16 print " -h: this help"
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17 print " -i: name of the table to export"
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18 print " -o: name of the output file (default=inTable)"
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19 print " -p: extra parameters to add to the SQL query (e.g. 'ORDER BY path')"
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20 print " -k: keep the first line"
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21 print " -C: configuration file from TEdenovo or TEannot pipeline"
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22 print " -H: MySQL host (if no configuration file)"
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23 print " -U: MySQL user (if no configuration file)"
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24 print " -P: MySQL password (if no configuration file)"
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25 print " -D: MySQL database (if no configuration file)"
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26 print " -v: verbose (default=0/1)"
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27 print
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28
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29 #-----------------------------------------------------------------------------
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30
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31 def main():
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32
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33 """
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34 This program exports all the data contained in a MySQL table into a flat file in the current directory.
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35 """
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36
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37 inTable = ""
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38 outFileName = ""
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39 param = ""
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40 keepFirstLine = False
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41 configFileName = ""
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42 host = ""
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43 user = ""
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44 passwd = ""
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45 dbname = ""
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46 verbose = 0
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47
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48 try:
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49 opts, args = getopt.getopt(sys.argv[1:],"hi:o:p:kC:H:U:P:D:v:")
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50 except getopt.GetoptError, err:
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51 print str(err)
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52 help()
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53 sys.exit(1)
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54 for o,a in opts:
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55 if o == "-h":
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56 help()
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57 sys.exit(0)
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58 elif o == "-i":
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59 inTable = a
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60 elif o == "-o":
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61 outFileName = a
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62 elif o == "-p":
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63 param = a
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64 elif o == "-k":
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65 keepFirstLine = True
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66 elif o == "-C":
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67 configFileName = a
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68 elif o == "-H":
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69 host = a
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70 elif o == "-U":
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71 user = a
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72 elif o == "-P":
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73 passwd = a
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74 elif o == "-D":
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75 dbname = a
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76 elif o == "-v":
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77 verbose = int(a)
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78
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79 if inTable == "":
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80 print "*** Error: missing input table name"
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81 help()
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82 sys.exit(1)
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83
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84 if configFileName != "":
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85 config = ConfigParser.ConfigParser()
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86 config.readfp( open(configFileName) )
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87 host = config.get("repet_env","repet_host")
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88 user = config.get("repet_env","repet_user")
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89 passwd = config.get("repet_env","repet_pw")
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90 dbname = config.get("repet_env","repet_db")
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91 if host == "" or user == "" or passwd == "" or dbname == "":
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92 if os.environ.get( "REPET_HOST" ) not in [ "", None ]:
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93 host = os.environ.get( "REPET_HOST" )
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94 if os.environ.get( "REPET_USER" ) not in [ "", None ]:
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95 user = os.environ.get( "REPET_USER" )
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96 if os.environ.get( "REPET_PW" ) not in [ "", None ]:
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97 passwd = os.environ.get( "REPET_PW" )
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98 if os.environ.get( "REPET_DB" ) not in [ "", None ]:
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99 dbname = os.environ.get( "REPET_DB" )
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100 if host == "" or user == "" or passwd == "" or dbname == "":
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101 print "*** Error: missing information about MySQL connection"
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102 sys.exit(1)
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103
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104 if outFileName == "":
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105 outFileName = inTable
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106
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107 prg = "mysql"
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108 cmd = prg
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109 cmd += " -h %s" % ( host )
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110 cmd += " -u %s" % ( user )
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111 cmd += " -p\"%s\"" % ( passwd )
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112 cmd += " --database=%s" % ( dbname )
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113 cmd += " -e\"SELECT * FROM %s" % ( inTable )
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114 if param != "":
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115 cmd += " %s" % ( param )
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116 cmd += ";\""
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117 cmd += " > "
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118 if keepFirstLine == False:
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119 cmd += "%s.tmp" % ( outFileName )
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120 else:
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121 cmd += "%s" % ( outFileName )
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122 if verbose > 0: print cmd; sys.stdout.flush()
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123 log = os.system( cmd )
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124 if log != 0:
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125 print "*** Error: %s returned %i" % ( prg, log )
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126 sys.exit(1)
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127
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128 if keepFirstLine == False:
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129 tmpFileName = "%s.tmp" % ( outFileName )
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130 tmpFile = open( tmpFileName, "r" )
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131 outFile = open( outFileName, "w" )
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132 i = 0
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133 for line in tmpFile:
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134 if i > 0:
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135 outFile.write( line )
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136 i += 1
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137 tmpFile.close()
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138 outFile.close()
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139 os.remove( tmpFileName )
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140
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141 return 0
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142
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143 #----------------------------------------------------------------------------
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144
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145 if __name__ == '__main__':
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146 main()
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