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18
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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 import getopt
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6 import ConfigParser
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7
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8 from commons.core.sql.DbMySql import DbMySql
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9
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10
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11 def help():
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12 print
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13 print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
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14 print "options:"
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15 print " -h: this help"
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16 print " -f: name of the input file"
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17 print " -n: name of the MySQL table"
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18 print " -t: table type (fasta|align|path|set|match|map|TEclassif|cluster)"
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19 print " -o: overwrite (default=False)"
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20 print " -c: configuration file from TEdenovo or TEannot pipeline"
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21 print " -H: MySQL host (if no configuration file)"
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22 print " -U: MySQL user (if no configuration file)"
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23 print " -P: MySQL password (if no configuration file)"
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24 print " -D: MySQL database (if no configuration file)"
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25 print " -T: MySQL port (if no configuration file, default=3306)"
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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 def main():
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31 """
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32 This program loads data from a file into a MySQL table.
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33 """
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34 filename = ""
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35 tablename = ""
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36 filetype = ""
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37 overwrite = False
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38 configFileName = ""
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39 host = ""
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40 user = ""
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41 passwd = ""
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42 dbname = ""
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43 port = 0
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44 verbose = 0
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45
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46 try:
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47 opts, args = getopt.getopt( sys.argv[1:], "hf:t:n:oc:H:U:P:D:T:v:" )
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48 except getopt.GetoptError, err:
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49 sys.stderr.write( "%s\n" % str(err) )
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50 help()
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51 sys.exit(1)
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52 for o,a in opts:
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53 if o == "-h":
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54 help()
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55 sys.exit(0)
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56 elif o == "-f":
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57 filename = a
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58 elif o == "-n":
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59 tablename = a
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60 elif o == "-t":
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61 filetype = a
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62 elif o == "-o":
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63 overwrite = True
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64 elif o == "-c":
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65 configFileName = a
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66 elif o == "-H":
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67 host = a
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68 elif o == "-U":
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69 user = a
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70 elif o == "-P":
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71 passwd = a
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72 elif o == "-D":
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73 dbname = a
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74 elif o == "-T":
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75 port = int(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 filename == "" or tablename == "" or filetype == "":
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80 print "ERROR: missing compulsory options"
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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 port = config.get("repet_env","repet_port")
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92
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93 if host == "" and os.environ.get( "REPET_HOST" ) != "":
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94 host = os.environ.get( "REPET_HOST" )
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95 if user == "" and os.environ.get( "REPET_USER" ) != "":
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96 user = os.environ.get( "REPET_USER" )
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97 if passwd == "" and os.environ.get( "REPET_PW" ) != "":
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98 passwd = os.environ.get( "REPET_PW" )
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99 if dbname == "" and os.environ.get( "REPET_DB" ) != "":
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100 dbname = os.environ.get( "REPET_DB" )
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101 if port == 0 and os.environ.get( "REPET_PORT" ) != "":
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102 port = int( os.environ.get( "REPET_PORT" ) )
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103
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104 if host == "":
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105 print "ERROR: missing host"
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106 sys.exit(1)
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107 if user == "":
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108 print "ERROR: missing user"
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109 sys.exit(1)
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110 if passwd == "":
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111 print "ERROR: missing password"
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112 sys.exit(1)
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113 if dbname == "":
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114 print "ERROR: missing db name"
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115 sys.exit(1)
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116 if port == 0:
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117 print "ERROR: missing port"
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118 sys.exit(1)
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119
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120 db = DbMySql(user, host, passwd, dbname, port )
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121
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122 if not os.path.exists( filename ):
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123 print "ERROR: input file '%s' doesn't exist" % ( filename )
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124 sys.exit(1)
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125
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126 db.createTable( tablename, filetype, filename, overwrite)
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127
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128 db.close()
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129
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130 return 0
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131
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132
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133 if __name__ == "__main__":
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134 main()
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