Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/sdbadmin @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
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2 # Copyright (c) 2009 Chris Moyer http://kopertop.blogspot.com/
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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
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22 #
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23 # Tools to dump and recover an SDB domain
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24 #
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25 VERSION = "%prog version 1.0"
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26 import boto
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27 import time
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28 from boto import sdb
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29 from boto.compat import json
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30
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31 def choice_input(options, default=None, title=None):
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32 """
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33 Choice input
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34 """
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35 if title == None:
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36 title = "Please choose"
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37 print title
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38 objects = []
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39 for n, obj in enumerate(options):
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40 print "%s: %s" % (n, obj)
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41 objects.append(obj)
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42 choice = int(raw_input(">>> "))
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43 try:
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44 choice = objects[choice]
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45 except:
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46 choice = default
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47 return choice
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48
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49 def confirm(message="Are you sure?"):
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50 choice = raw_input("%s [yN] " % message)
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51 return choice and len(choice) > 0 and choice[0].lower() == "y"
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52
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53
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54 def dump_db(domain, file_name, use_json=False, sort_attributes=False):
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55 """
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56 Dump SDB domain to file
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57 """
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58 f = open(file_name, "w")
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59 if use_json:
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60 for item in domain:
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61 data = {"name": item.name, "attributes": item}
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62 print >> f, json.dumps(data, sort_keys=sort_attributes)
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63 else:
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64 doc = domain.to_xml(f)
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65
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66 def empty_db(domain):
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67 """
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68 Remove all entries from domain
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69 """
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70 for item in domain:
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71 item.delete()
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72
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73 def load_db(domain, file, use_json=False):
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74 """
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75 Load a domain from a file, this doesn't overwrite any existing
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76 data in the file so if you want to do a full recovery and restore
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77 you need to call empty_db before calling this
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78
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79 :param domain: The SDB Domain object to load to
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80 :param file: The File to load the DB from
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81 """
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82 if use_json:
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83 for line in file.readlines():
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84 if line:
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85 data = json.loads(line)
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86 item = domain.new_item(data['name'])
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87 item.update(data['attributes'])
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88 item.save()
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89
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90 else:
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91 domain.from_xml(file)
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92
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93 def check_valid_region(conn, region):
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94 if conn is None:
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95 print 'Invalid region (%s)' % region
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96 sys.exit(1)
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97
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98 def create_db(domain_name, region_name):
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99 """Create a new DB
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100
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101 :param domain: Name of the domain to create
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102 :type domain: str
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103 """
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104 sdb = boto.sdb.connect_to_region(region_name)
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105 check_valid_region(sdb, region_name)
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106 return sdb.create_domain(domain_name)
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107
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108 if __name__ == "__main__":
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109 from optparse import OptionParser
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110 parser = OptionParser(version=VERSION, usage="Usage: %prog [--dump|--load|--empty|--list|-l] [options]")
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111
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112 # Commands
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113 parser.add_option("--dump", help="Dump domain to file", dest="dump", default=False, action="store_true")
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114 parser.add_option("--load", help="Load domain contents from file", dest="load", default=False, action="store_true")
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115 parser.add_option("--empty", help="Empty all contents of domain", dest="empty", default=False, action="store_true")
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116 parser.add_option("-l", "--list", help="List All domains", dest="list", default=False, action="store_true")
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117 parser.add_option("-c", "--create", help="Create domain", dest="create", default=False, action="store_true")
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118
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119 parser.add_option("-a", "--all-domains", help="Operate on all domains", action="store_true", default=False, dest="all_domains")
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120 if json:
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121 parser.add_option("-j", "--use-json", help="Load/Store as JSON instead of XML", action="store_true", default=False, dest="json")
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122 parser.add_option("-s", "--sort-attibutes", help="Sort the element attributes", action="store_true", default=False, dest="sort_attributes")
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123 parser.add_option("-d", "--domain", help="Do functions on domain (may be more then one)", action="append", dest="domains")
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124 parser.add_option("-f", "--file", help="Input/Output file we're operating on", dest="file_name")
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125 parser.add_option("-r", "--region", help="Region (e.g. us-east-1[default] or eu-west-1)", default="us-east-1", dest="region_name")
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126 (options, args) = parser.parse_args()
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127
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128 if options.create:
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129 for domain_name in options.domains:
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130 create_db(domain_name, options.region_name)
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131 exit()
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132
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133 sdb = boto.sdb.connect_to_region(options.region_name)
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134 check_valid_region(sdb, options.region_name)
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135 if options.list:
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136 for db in sdb.get_all_domains():
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137 print db
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138 exit()
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139
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140 if not options.dump and not options.load and not options.empty:
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141 parser.print_help()
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142 exit()
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143
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144
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145
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146
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147 #
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148 # Setup
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149 #
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150 if options.domains:
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151 domains = []
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152 for domain_name in options.domains:
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153 domains.append(sdb.get_domain(domain_name))
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154 elif options.all_domains:
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155 domains = sdb.get_all_domains()
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156 else:
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157 domains = [choice_input(options=sdb.get_all_domains(), title="No domain specified, please choose one")]
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158
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159
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160 #
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161 # Execute the commands
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162 #
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163 stime = time.time()
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164 if options.empty:
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165 if confirm("WARNING!!! Are you sure you want to empty the following domains?: %s" % domains):
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166 stime = time.time()
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167 for domain in domains:
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168 print "--------> Emptying %s <--------" % domain.name
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169 empty_db(domain)
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170 else:
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171 print "Canceling operations"
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172 exit()
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173
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174 if options.dump:
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175 for domain in domains:
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176 print "--------> Dumping %s <---------" % domain.name
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177 if options.file_name:
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178 file_name = options.file_name
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179 else:
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180 file_name = "%s.db" % domain.name
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181 dump_db(domain, file_name, options.json, options.sort_attributes)
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182
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183 if options.load:
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184 for domain in domains:
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185 print "---------> Loading %s <----------" % domain.name
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186 if options.file_name:
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187 file_name = options.file_name
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188 else:
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189 file_name = "%s.db" % domain.name
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190 load_db(domain, open(file_name, "rb"), options.json)
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191
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192
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193 total_time = round(time.time() - stime, 2)
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194 print "--------> Finished in %s <--------" % total_time