Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/glacier @ 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 # -*- coding: utf-8 -*-
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3 # Copyright (c) 2012 Miguel Olivares http://moliware.com/
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4 #
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5 # Permission is hereby granted, free of charge, to any person obtaining a
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6 # copy of this software and associated documentation files (the
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7 # "Software"), to deal in the Software without restriction, including
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8 # without limitation the rights to use, copy, modify, merge, publish, dis-
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9 # tribute, sublicense, and/or sell copies of the Software, and to permit
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10 # persons to whom the Software is furnished to do so, subject to the fol-
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11 # lowing conditions:
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12 #
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13 # The above copyright notice and this permission notice shall be included
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14 # in all copies or substantial portions of the Software.
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15 #
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16 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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17 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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18 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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19 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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20 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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21 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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22 # IN THE SOFTWARE.
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23 #
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24 """
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25 glacier
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26 ~~~~~~~
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27
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28 Amazon Glacier tool built on top of boto. Look at the usage method to see
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29 how to use it.
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30
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31 Author: Miguel Olivares <miguel@moliware.com>
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32 """
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33 import sys
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34
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35 from boto.glacier import connect_to_region
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36 from getopt import getopt, GetoptError
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37 from os.path import isfile, basename
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38
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39
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40 COMMANDS = ('vaults', 'jobs', 'upload')
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41
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42
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43 def usage():
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44 print("""
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45 glacier <command> [args]
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46
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47 Commands
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48 vaults - Operations with vaults
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49 jobs - Operations with jobs
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50 upload - Upload files to a vault. If the vault doesn't exits, it is
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51 created
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52
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53 Common args:
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54 --access_key - Your AWS Access Key ID. If not supplied, boto will
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55 use the value of the environment variable
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56 AWS_ACCESS_KEY_ID
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57 --secret_key - Your AWS Secret Access Key. If not supplied, boto
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58 will use the value of the environment variable
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59 AWS_SECRET_ACCESS_KEY
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60 --region - AWS region to use. Possible values: us-east-1, us-west-1,
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61 us-west-2, ap-northeast-1, eu-west-1.
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62 Default: us-east-1
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63
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64 Vaults operations:
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65
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66 List vaults:
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67 glacier vaults
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68
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69 Jobs operations:
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70
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71 List jobs:
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72 glacier jobs <vault name>
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73
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74 Uploading files:
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75
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76 glacier upload <vault name> <files>
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77
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78 Examples :
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79 glacier upload pics *.jpg
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80 glacier upload pics a.jpg b.jpg
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81 """)
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82 sys.exit()
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83
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84
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85 def connect(region, debug_level=0, access_key=None, secret_key=None):
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86 """ Connect to a specific region """
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87 layer2 = connect_to_region(region,
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88 aws_access_key_id=access_key,
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89 aws_secret_access_key=secret_key,
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90 debug=debug_level)
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91 if layer2 is None:
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92 print('Invalid region (%s)' % region)
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93 sys.exit(1)
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94 return layer2
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95
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96
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97 def list_vaults(region, access_key=None, secret_key=None):
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98 layer2 = connect(region, access_key = access_key, secret_key = secret_key)
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99 for vault in layer2.list_vaults():
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100 print(vault.arn)
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101
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102
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103 def list_jobs(vault_name, region, access_key=None, secret_key=None):
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104 layer2 = connect(region, access_key = access_key, secret_key = secret_key)
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105 print(layer2.layer1.list_jobs(vault_name))
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106
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107
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108 def upload_files(vault_name, filenames, region, access_key=None, secret_key=None):
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109 layer2 = connect(region, access_key = access_key, secret_key = secret_key)
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110 layer2.create_vault(vault_name)
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111 glacier_vault = layer2.get_vault(vault_name)
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112 for filename in filenames:
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113 if isfile(filename):
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114 sys.stdout.write('Uploading %s to %s...' % (filename, vault_name))
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115 sys.stdout.flush()
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116 archive_id = glacier_vault.upload_archive(
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117 filename,
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118 description = basename(filename))
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119 print(' done. Vault returned ArchiveID %s' % archive_id)
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120
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121 def main():
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122 if len(sys.argv) < 2:
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123 usage()
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124
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125 command = sys.argv[1]
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126 if command not in COMMANDS:
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127 usage()
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128
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129 argv = sys.argv[2:]
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130 options = 'a:s:r:'
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131 long_options = ['access_key=', 'secret_key=', 'region=']
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132 try:
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133 opts, args = getopt(argv, options, long_options)
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134 except GetoptError as e:
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135 usage()
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136
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137 # Parse agument
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138 access_key = secret_key = None
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139 region = 'us-east-1'
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140 for option, value in opts:
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141 if option in ('-a', '--access_key'):
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142 access_key = value
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143 elif option in ('-s', '--secret_key'):
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144 secret_key = value
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145 elif option in ('-r', '--region'):
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146 region = value
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147 # handle each command
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148 if command == 'vaults':
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149 list_vaults(region, access_key, secret_key)
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150 elif command == 'jobs':
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151 if len(args) != 1:
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152 usage()
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153 list_jobs(args[0], region, access_key, secret_key)
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154 elif command == 'upload':
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155 if len(args) < 2:
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156 usage()
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157 upload_files(args[0], args[1:], region, access_key, secret_key)
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158
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159
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160 if __name__ == '__main__':
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161 main()