Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/services/bs.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 #!/usr/bin/env python
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2 # Copyright (c) 2006-2008 Mitch Garnaat http://garnaat.org/
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3 #
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4 # Permission is hereby granted, free of charge, to any person obtaining a
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5 # copy of this software and associated documentation files (the
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6 # "Software"), to deal in the Software without restriction, including
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7 # without limitation the rights to use, copy, modify, merge, publish, dis-
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8 # tribute, sublicense, and/or sell copies of the Software, and to permit
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9 # persons to whom the Software is furnished to do so, subject to the fol-
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10 # lowing conditions:
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11 #
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12 # The above copyright notice and this permission notice shall be included
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13 # in all copies or substantial portions of the Software.
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14 #
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15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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21 # IN THE SOFTWARE.
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22 from optparse import OptionParser
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23 from boto.services.servicedef import ServiceDef
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24 from boto.services.submit import Submitter
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25 from boto.services.result import ResultProcessor
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26 import boto
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27 import sys, os
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28 from boto.compat import StringIO
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29
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30 class BS(object):
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31
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32 Usage = "usage: %prog [options] config_file command"
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33
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34 Commands = {'reset' : 'Clear input queue and output bucket',
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35 'submit' : 'Submit local files to the service',
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36 'start' : 'Start the service',
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37 'status' : 'Report on the status of the service buckets and queues',
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38 'retrieve' : 'Retrieve output generated by a batch',
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39 'batches' : 'List all batches stored in current output_domain'}
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40
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41 def __init__(self):
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42 self.service_name = None
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43 self.parser = OptionParser(usage=self.Usage)
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44 self.parser.add_option("--help-commands", action="store_true", dest="help_commands",
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45 help="provides help on the available commands")
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46 self.parser.add_option("-a", "--access-key", action="store", type="string",
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47 help="your AWS Access Key")
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48 self.parser.add_option("-s", "--secret-key", action="store", type="string",
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49 help="your AWS Secret Access Key")
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50 self.parser.add_option("-p", "--path", action="store", type="string", dest="path",
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51 help="the path to local directory for submit and retrieve")
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52 self.parser.add_option("-k", "--keypair", action="store", type="string", dest="keypair",
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53 help="the SSH keypair used with launched instance(s)")
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54 self.parser.add_option("-l", "--leave", action="store_true", dest="leave",
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55 help="leave the files (don't retrieve) files during retrieve command")
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56 self.parser.set_defaults(leave=False)
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57 self.parser.add_option("-n", "--num-instances", action="store", type="string", dest="num_instances",
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58 help="the number of launched instance(s)")
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59 self.parser.set_defaults(num_instances=1)
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60 self.parser.add_option("-i", "--ignore-dirs", action="append", type="string", dest="ignore",
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61 help="directories that should be ignored by submit command")
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62 self.parser.add_option("-b", "--batch-id", action="store", type="string", dest="batch",
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63 help="batch identifier required by the retrieve command")
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64
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65 def print_command_help(self):
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66 print('\nCommands:')
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67 for key in self.Commands.keys():
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68 print(' %s\t\t%s' % (key, self.Commands[key]))
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69
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70 def do_reset(self):
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71 iq = self.sd.get_obj('input_queue')
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72 if iq:
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73 print('clearing out input queue')
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74 i = 0
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75 m = iq.read()
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76 while m:
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77 i += 1
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78 iq.delete_message(m)
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79 m = iq.read()
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80 print('deleted %d messages' % i)
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81 ob = self.sd.get_obj('output_bucket')
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82 ib = self.sd.get_obj('input_bucket')
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83 if ob:
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84 if ib and ob.name == ib.name:
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85 return
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86 print('delete generated files in output bucket')
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87 i = 0
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88 for k in ob:
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89 i += 1
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90 k.delete()
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91 print('deleted %d keys' % i)
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92
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93 def do_submit(self):
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94 if not self.options.path:
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95 self.parser.error('No path provided')
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96 if not os.path.exists(self.options.path):
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97 self.parser.error('Invalid path (%s)' % self.options.path)
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98 s = Submitter(self.sd)
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99 t = s.submit_path(self.options.path, None, self.options.ignore, None,
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100 None, True, self.options.path)
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101 print('A total of %d files were submitted' % t[1])
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102 print('Batch Identifier: %s' % t[0])
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103
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104 def do_start(self):
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105 ami_id = self.sd.get('ami_id')
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106 instance_type = self.sd.get('instance_type', 'm1.small')
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107 security_group = self.sd.get('security_group', 'default')
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108 if not ami_id:
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109 self.parser.error('ami_id option is required when starting the service')
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110 ec2 = boto.connect_ec2()
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111 if not self.sd.has_section('Credentials'):
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112 self.sd.add_section('Credentials')
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113 self.sd.set('Credentials', 'aws_access_key_id', ec2.aws_access_key_id)
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114 self.sd.set('Credentials', 'aws_secret_access_key', ec2.aws_secret_access_key)
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115 s = StringIO()
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116 self.sd.write(s)
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117 rs = ec2.get_all_images([ami_id])
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118 img = rs[0]
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119 r = img.run(user_data=s.getvalue(), key_name=self.options.keypair,
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120 max_count=self.options.num_instances,
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121 instance_type=instance_type,
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122 security_groups=[security_group])
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123 print('Starting AMI: %s' % ami_id)
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124 print('Reservation %s contains the following instances:' % r.id)
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125 for i in r.instances:
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126 print('\t%s' % i.id)
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127
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128 def do_status(self):
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129 iq = self.sd.get_obj('input_queue')
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130 if iq:
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131 print('The input_queue (%s) contains approximately %s messages' % (iq.id, iq.count()))
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132 ob = self.sd.get_obj('output_bucket')
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133 ib = self.sd.get_obj('input_bucket')
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134 if ob:
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135 if ib and ob.name == ib.name:
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136 return
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137 total = 0
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138 for k in ob:
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139 total += 1
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140 print('The output_bucket (%s) contains %d keys' % (ob.name, total))
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141
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142 def do_retrieve(self):
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143 if not self.options.path:
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144 self.parser.error('No path provided')
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145 if not os.path.exists(self.options.path):
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146 self.parser.error('Invalid path (%s)' % self.options.path)
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147 if not self.options.batch:
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148 self.parser.error('batch identifier is required for retrieve command')
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149 s = ResultProcessor(self.options.batch, self.sd)
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150 s.get_results(self.options.path, get_file=(not self.options.leave))
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151
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152 def do_batches(self):
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153 d = self.sd.get_obj('output_domain')
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154 if d:
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155 print('Available Batches:')
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156 rs = d.query("['type'='Batch']")
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157 for item in rs:
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158 print(' %s' % item.name)
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159 else:
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160 self.parser.error('No output_domain specified for service')
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161
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162 def main(self):
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163 self.options, self.args = self.parser.parse_args()
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164 if self.options.help_commands:
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165 self.print_command_help()
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166 sys.exit(0)
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167 if len(self.args) != 2:
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168 self.parser.error("config_file and command are required")
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169 self.config_file = self.args[0]
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170 self.sd = ServiceDef(self.config_file)
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171 self.command = self.args[1]
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172 if hasattr(self, 'do_%s' % self.command):
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173 method = getattr(self, 'do_%s' % self.command)
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174 method()
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175 else:
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176 self.parser.error('command (%s) not recognized' % self.command)
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177
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178 if __name__ == "__main__":
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179 bs = BS()
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180 bs.main()