Mercurial > repos > shellac > sam_consensus_v3

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 #!/Users/cmdms/OneDrive-UOB/Development/Projects/2021/sam-consensus-v3/env/bin/python3
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2 # Copyright (c) 2006,2007,2008 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 #
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23 import getopt
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24 import sys
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25 import os
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26 import boto
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27
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28 from boto.compat import six
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29
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30 try:
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31 # multipart portions copyright Fabian Topfstedt
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32 # https://gist.github.com/924094
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33
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34 import math
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35 import mimetypes
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36 from multiprocessing import Pool
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37 from boto.s3.connection import S3Connection
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38 from filechunkio import FileChunkIO
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39 multipart_capable = True
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40 usage_flag_multipart_capable = """ [--multipart]"""
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41 usage_string_multipart_capable = """
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42 multipart - Upload files as multiple parts. This needs filechunkio.
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43 Requires ListBucket, ListMultipartUploadParts,
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44 ListBucketMultipartUploads and PutObject permissions."""
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45 except ImportError as err:
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46 multipart_capable = False
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47 usage_flag_multipart_capable = ""
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48 if six.PY2:
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49 attribute = 'message'
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50 else:
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51 attribute = 'msg'
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52 usage_string_multipart_capable = '\n\n "' + \
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53 getattr(err, attribute)[len('No module named '):] + \
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54 '" is missing for multipart support '
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55
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56
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57 DEFAULT_REGION = 'us-east-1'
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58
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59 usage_string = """
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60 SYNOPSIS
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61 s3put [-a/--access_key <access_key>] [-s/--secret_key <secret_key>]
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62 -b/--bucket <bucket_name> [-c/--callback <num_cb>]
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63 [-d/--debug <debug_level>] [-i/--ignore <ignore_dirs>]
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64 [-n/--no_op] [-p/--prefix <prefix>] [-k/--key_prefix <key_prefix>]
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65 [-q/--quiet] [-g/--grant grant] [-w/--no_overwrite] [-r/--reduced]
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66 [--header] [--region <name>] [--host <s3_host>]""" + \
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67 usage_flag_multipart_capable + """ path [path...]
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68
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69 Where
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70 access_key - Your AWS Access Key ID. If not supplied, boto will
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71 use the value of the environment variable
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72 AWS_ACCESS_KEY_ID
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73 secret_key - Your AWS Secret Access Key. If not supplied, boto
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74 will use the value of the environment variable
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75 AWS_SECRET_ACCESS_KEY
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76 bucket_name - The name of the S3 bucket the file(s) should be
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77 copied to.
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78 path - A path to a directory or file that represents the items
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79 to be uploaded. If the path points to an individual file,
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80 that file will be uploaded to the specified bucket. If the
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81 path points to a directory, it will recursively traverse
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82 the directory and upload all files to the specified bucket.
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83 debug_level - 0 means no debug output (default), 1 means normal
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84 debug output from boto, and 2 means boto debug output
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85 plus request/response output from httplib
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86 ignore_dirs - a comma-separated list of directory names that will
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87 be ignored and not uploaded to S3.
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88 num_cb - The number of progress callbacks to display. The default
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89 is zero which means no callbacks. If you supplied a value
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90 of "-c 10" for example, the progress callback would be
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91 called 10 times for each file transferred.
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92 prefix - A file path prefix that will be stripped from the full
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93 path of the file when determining the key name in S3.
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94 For example, if the full path of a file is:
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95 /home/foo/bar/fie.baz
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96 and the prefix is specified as "-p /home/foo/" the
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97 resulting key name in S3 will be:
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98 /bar/fie.baz
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99 The prefix must end in a trailing separator and if it
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100 does not then one will be added.
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101 key_prefix - A prefix to be added to the S3 key name, after any
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102 stripping of the file path is done based on the
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103 "-p/--prefix" option.
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104 reduced - Use Reduced Redundancy storage
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105 grant - A canned ACL policy that will be granted on each file
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106 transferred to S3. The value of provided must be one
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107 of the "canned" ACL policies supported by S3:
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108 private|public-read|public-read-write|authenticated-read
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109 no_overwrite - No files will be overwritten on S3, if the file/key
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110 exists on s3 it will be kept. This is useful for
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111 resuming interrupted transfers. Note this is not a
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112 sync, even if the file has been updated locally if
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113 the key exists on s3 the file on s3 will not be
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114 updated.
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115 header - key=value pairs of extra header(s) to pass along in the
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116 request
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117 region - Manually set a region for buckets that are not in the US
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118 classic region. Normally the region is autodetected, but
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119 setting this yourself is more efficient.
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120 host - Hostname override, for using an endpoint other then AWS S3
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121 """ + usage_string_multipart_capable + """
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122
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123
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124 If the -n option is provided, no files will be transferred to S3 but
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125 informational messages will be printed about what would happen.
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126 """
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127
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128
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129 def usage(status=1):
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130 print(usage_string)
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131 sys.exit(status)
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132
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133
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134 def submit_cb(bytes_so_far, total_bytes):
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135 print('%d bytes transferred / %d bytes total' % (bytes_so_far, total_bytes))
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136
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137
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138 def get_key_name(fullpath, prefix, key_prefix):
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139 if fullpath.startswith(prefix):
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140 key_name = fullpath[len(prefix):]
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141 else:
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142 key_name = fullpath
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143 l = key_name.split(os.sep)
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144 return key_prefix + '/'.join(l)
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145
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146
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147 def _upload_part(bucketname, aws_key, aws_secret, multipart_id, part_num,
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148 source_path, offset, bytes, debug, cb, num_cb,
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149 amount_of_retries=10):
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150 """
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151 Uploads a part with retries.
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152 """
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153 if debug == 1:
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154 print("_upload_part(%s, %s, %s)" % (source_path, offset, bytes))
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155
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156 def _upload(retries_left=amount_of_retries):
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157 try:
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158 if debug == 1:
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159 print('Start uploading part #%d ...' % part_num)
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160 conn = S3Connection(aws_key, aws_secret)
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161 conn.debug = debug
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162 bucket = conn.get_bucket(bucketname)
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163 for mp in bucket.get_all_multipart_uploads():
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164 if mp.id == multipart_id:
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165 with FileChunkIO(source_path, 'r', offset=offset,
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166 bytes=bytes) as fp:
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167 mp.upload_part_from_file(fp=fp, part_num=part_num,
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168 cb=cb, num_cb=num_cb)
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169 break
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170 except Exception as exc:
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171 if retries_left:
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172 _upload(retries_left=retries_left - 1)
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173 else:
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174 print('Failed uploading part #%d' % part_num)
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175 raise exc
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176 else:
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177 if debug == 1:
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178 print('... Uploaded part #%d' % part_num)
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179
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180 _upload()
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181
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182 def check_valid_region(conn, region):
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183 if conn is None:
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184 print('Invalid region (%s)' % region)
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185 sys.exit(1)
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186
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187 def multipart_upload(bucketname, aws_key, aws_secret, source_path, keyname,
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188 reduced, debug, cb, num_cb, acl='private', headers={},
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189 guess_mimetype=True, parallel_processes=4,
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190 region=DEFAULT_REGION):
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191 """
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192 Parallel multipart upload.
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193 """
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194 conn = boto.s3.connect_to_region(region, aws_access_key_id=aws_key,
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195 aws_secret_access_key=aws_secret)
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196 check_valid_region(conn, region)
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197 conn.debug = debug
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198 bucket = conn.get_bucket(bucketname)
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199
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200 if guess_mimetype:
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201 mtype = mimetypes.guess_type(keyname)[0] or 'application/octet-stream'
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202 headers.update({'Content-Type': mtype})
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203
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204 mp = bucket.initiate_multipart_upload(keyname, headers=headers,
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205 reduced_redundancy=reduced)
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206
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207 source_size = os.stat(source_path).st_size
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208 bytes_per_chunk = max(int(math.sqrt(5242880) * math.sqrt(source_size)),
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209 5242880)
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210 chunk_amount = int(math.ceil(source_size / float(bytes_per_chunk)))
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211
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212 pool = Pool(processes=parallel_processes)
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213 for i in range(chunk_amount):
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214 offset = i * bytes_per_chunk
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215 remaining_bytes = source_size - offset
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216 bytes = min([bytes_per_chunk, remaining_bytes])
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217 part_num = i + 1
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218 pool.apply_async(_upload_part, [bucketname, aws_key, aws_secret, mp.id,
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219 part_num, source_path, offset, bytes,
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220 debug, cb, num_cb])
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221 pool.close()
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222 pool.join()
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223
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224 if len(mp.get_all_parts()) == chunk_amount:
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225 mp.complete_upload()
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226 key = bucket.get_key(keyname)
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227 key.set_acl(acl)
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228 else:
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229 mp.cancel_upload()
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230
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231
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232 def singlepart_upload(bucket, key_name, fullpath, *kargs, **kwargs):
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233 """
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234 Single upload.
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235 """
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236 k = bucket.new_key(key_name)
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237 k.set_contents_from_filename(fullpath, *kargs, **kwargs)
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238
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239
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240 def expand_path(path):
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241 path = os.path.expanduser(path)
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242 path = os.path.expandvars(path)
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243 return os.path.abspath(path)
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244
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245
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246 def main():
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247
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248 # default values
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249 aws_access_key_id = None
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250 aws_secret_access_key = None
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251 bucket_name = ''
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252 ignore_dirs = []
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253 debug = 0
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254 cb = None
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255 num_cb = 0
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256 quiet = False
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257 no_op = False
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258 prefix = '/'
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259 key_prefix = ''
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260 grant = None
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261 no_overwrite = False
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262 reduced = False
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263 headers = {}
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264 host = None
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265 multipart_requested = False
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266 region = None
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267
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268 try:
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269 opts, args = getopt.getopt(
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270 sys.argv[1:], 'a:b:c::d:g:hi:k:np:qs:wr',
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271 ['access_key=', 'bucket=', 'callback=', 'debug=', 'help', 'grant=',
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272 'ignore=', 'key_prefix=', 'no_op', 'prefix=', 'quiet',
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273 'secret_key=', 'no_overwrite', 'reduced', 'header=', 'multipart',
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274 'host=', 'region='])
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275 except:
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276 usage(1)
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277
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278 # parse opts
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279 for o, a in opts:
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280 if o in ('-h', '--help'):
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281 usage(0)
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282 if o in ('-a', '--access_key'):
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283 aws_access_key_id = a
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284 if o in ('-b', '--bucket'):
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285 bucket_name = a
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286 if o in ('-c', '--callback'):
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287 num_cb = int(a)
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288 cb = submit_cb
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289 if o in ('-d', '--debug'):
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290 debug = int(a)
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291 if o in ('-g', '--grant'):
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292 grant = a
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293 if o in ('-i', '--ignore'):
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294 ignore_dirs = a.split(',')
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295 if o in ('-n', '--no_op'):
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296 no_op = True
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297 if o in ('-w', '--no_overwrite'):
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298 no_overwrite = True
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299 if o in ('-p', '--prefix'):
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300 prefix = a
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301 if prefix[-1] != os.sep:
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302 prefix = prefix + os.sep
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303 prefix = expand_path(prefix)
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304 if o in ('-k', '--key_prefix'):
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305 key_prefix = a
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306 if o in ('-q', '--quiet'):
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307 quiet = True
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308 if o in ('-s', '--secret_key'):
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309 aws_secret_access_key = a
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310 if o in ('-r', '--reduced'):
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311 reduced = True
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312 if o == '--header':
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313 (k, v) = a.split("=", 1)
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314 headers[k] = v
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315 if o == '--host':
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316 host = a
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317 if o == '--multipart':
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318 if multipart_capable:
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319 multipart_requested = True
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320 else:
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321 print("multipart upload requested but not capable")
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322 sys.exit(4)
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323 if o == '--region':
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324 regions = boto.s3.regions()
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325 for region_info in regions:
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326 if region_info.name == a:
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327 region = a
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328 break
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329 else:
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330 raise ValueError('Invalid region %s specified' % a)
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331
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332 if len(args) < 1:
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333 usage(2)
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334
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335 if not bucket_name:
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336 print("bucket name is required!")
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337 usage(3)
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338
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339 connect_args = {
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340 'aws_access_key_id': aws_access_key_id,
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341 'aws_secret_access_key': aws_secret_access_key
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342 }
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343
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344 if host:
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345 connect_args['host'] = host
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346
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347 c = boto.s3.connect_to_region(region or DEFAULT_REGION, **connect_args)
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348 check_valid_region(c, region or DEFAULT_REGION)
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349 c.debug = debug
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350 b = c.get_bucket(bucket_name, validate=False)
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351
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352 # Attempt to determine location and warn if no --host or --region
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353 # arguments were passed. Then try to automagically figure out
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354 # what should have been passed and fix it.
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355 if host is None and region is None:
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parents:
diff changeset
356 try:
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parents:
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357 location = b.get_location()
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358
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359 # Classic region will be '', any other will have a name
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parents:
diff changeset
360 if location:
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361 print('Bucket exists in %s but no host or region given!' % location)
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parents:
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362
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363 # Override for EU, which is really Ireland according to the docs
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parents:
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364 if location == 'EU':
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parents:
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365 location = 'eu-west-1'
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366
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367 print('Automatically setting region to %s' % location)
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parents:
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368
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369 # Here we create a new connection, and then take the existing
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370 # bucket and set it to use the new connection
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371 c = boto.s3.connect_to_region(location, **connect_args)
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372 c.debug = debug
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373 b.connection = c
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374 except Exception as e:
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parents:
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375 if debug > 0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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376 print(e)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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377 print('Could not get bucket region info, skipping...')
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378
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379 existing_keys_to_check_against = []
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parents:
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380 files_to_check_for_upload = []
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381
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382 for path in args:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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383 path = expand_path(path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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384 # upload a directory of files recursively
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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385 if os.path.isdir(path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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386 if no_overwrite:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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387 if not quiet:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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388 print('Getting list of existing keys to check against')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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389 for key in b.list(get_key_name(path, prefix, key_prefix)):
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390 existing_keys_to_check_against.append(key.name)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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391 for root, dirs, files in os.walk(path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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392 for ignore in ignore_dirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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393 if ignore in dirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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394 dirs.remove(ignore)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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395 for path in files:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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396 if path.startswith("."):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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397 continue
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parents:
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398 files_to_check_for_upload.append(os.path.join(root, path))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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399
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shellac
parents:
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400 # upload a single file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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401 elif os.path.isfile(path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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402 fullpath = os.path.abspath(path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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403 key_name = get_key_name(fullpath, prefix, key_prefix)
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shellac
parents:
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404 files_to_check_for_upload.append(fullpath)
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shellac
parents:
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405 existing_keys_to_check_against.append(key_name)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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406
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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407 # we are trying to upload something unknown
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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408 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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409 print("I don't know what %s is, so i can't upload it" % path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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410
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parents:
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411 for fullpath in files_to_check_for_upload:
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parents:
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412 key_name = get_key_name(fullpath, prefix, key_prefix)
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shellac
parents:
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413
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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414 if no_overwrite and key_name in existing_keys_to_check_against:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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415 if b.get_key(key_name):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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416 if not quiet:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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417 print('Skipping %s as it exists in s3' % fullpath)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
418 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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419
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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420 if not quiet:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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421 print('Copying %s to %s/%s' % (fullpath, bucket_name, key_name))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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422
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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423 if not no_op:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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424 # 0-byte files don't work and also don't need multipart upload
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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425 if os.stat(fullpath).st_size != 0 and multipart_capable and \
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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426 multipart_requested:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427 multipart_upload(bucket_name, aws_access_key_id,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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428 aws_secret_access_key, fullpath, key_name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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429 reduced, debug, cb, num_cb,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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430 grant or 'private', headers,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
431 region=region or DEFAULT_REGION)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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432 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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433 singlepart_upload(b, key_name, fullpath, cb=cb, num_cb=num_cb,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
434 policy=grant, reduced_redundancy=reduced,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435 headers=headers)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 if __name__ == "__main__":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438 main()