Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/glacier/concurrent.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 # Copyright (c) 2012 Amazon.com, Inc. or its affiliates. All Rights Reserved
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2 #
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3 # Permission is hereby granted, free of charge, to any person obtaining a
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4 # copy of this software and associated documentation files (the
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5 # "Software"), to deal in the Software without restriction, including
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6 # without limitation the rights to use, copy, modify, merge, publish, dis-
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7 # tribute, sublicense, and/or sell copies of the Software, and to permit
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8 # persons to whom the Software is furnished to do so, subject to the fol-
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9 # lowing conditions:
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10 #
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11 # The above copyright notice and this permission notice shall be included
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12 # in all copies or substantial portions of the Software.
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13 #
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14 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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15 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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16 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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17 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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18 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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19 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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20 # IN THE SOFTWARE.
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21 #
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22 import os
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23 import math
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24 import threading
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25 import hashlib
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26 import time
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27 import logging
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28 from boto.compat import Queue
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29 import binascii
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30
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31 from boto.glacier.utils import DEFAULT_PART_SIZE, minimum_part_size, \
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32 chunk_hashes, tree_hash, bytes_to_hex
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33 from boto.glacier.exceptions import UploadArchiveError, \
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34 DownloadArchiveError, \
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35 TreeHashDoesNotMatchError
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36
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37
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38 _END_SENTINEL = object()
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39 log = logging.getLogger('boto.glacier.concurrent')
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40
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41
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42 class ConcurrentTransferer(object):
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43 def __init__(self, part_size=DEFAULT_PART_SIZE, num_threads=10):
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44 self._part_size = part_size
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45 self._num_threads = num_threads
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46 self._threads = []
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47
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48 def _calculate_required_part_size(self, total_size):
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49 min_part_size_required = minimum_part_size(total_size)
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50 if self._part_size >= min_part_size_required:
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51 part_size = self._part_size
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52 else:
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53 part_size = min_part_size_required
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54 log.debug("The part size specified (%s) is smaller than "
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55 "the minimum required part size. Using a part "
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56 "size of: %s", self._part_size, part_size)
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57 total_parts = int(math.ceil(total_size / float(part_size)))
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58 return total_parts, part_size
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59
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60 def _shutdown_threads(self):
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61 log.debug("Shutting down threads.")
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62 for thread in self._threads:
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63 thread.should_continue = False
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64 for thread in self._threads:
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65 thread.join()
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66 log.debug("Threads have exited.")
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67
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68 def _add_work_items_to_queue(self, total_parts, worker_queue, part_size):
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69 log.debug("Adding work items to queue.")
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70 for i in range(total_parts):
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71 worker_queue.put((i, part_size))
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72 for i in range(self._num_threads):
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73 worker_queue.put(_END_SENTINEL)
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74
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75
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76 class ConcurrentUploader(ConcurrentTransferer):
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77 """Concurrently upload an archive to glacier.
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78
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79 This class uses a thread pool to concurrently upload an archive
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80 to glacier using the multipart upload API.
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81
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82 The threadpool is completely managed by this class and is
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83 transparent to the users of this class.
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84
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85 """
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86 def __init__(self, api, vault_name, part_size=DEFAULT_PART_SIZE,
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87 num_threads=10):
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88 """
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89 :type api: :class:`boto.glacier.layer1.Layer1`
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90 :param api: A layer1 glacier object.
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91
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92 :type vault_name: str
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93 :param vault_name: The name of the vault.
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94
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95 :type part_size: int
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96 :param part_size: The size, in bytes, of the chunks to use when uploading
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97 the archive parts. The part size must be a megabyte multiplied by
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98 a power of two.
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99
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100 :type num_threads: int
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101 :param num_threads: The number of threads to spawn for the thread pool.
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102 The number of threads will control how much parts are being
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103 concurrently uploaded.
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104
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105 """
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106 super(ConcurrentUploader, self).__init__(part_size, num_threads)
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107 self._api = api
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108 self._vault_name = vault_name
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109
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110 def upload(self, filename, description=None):
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111 """Concurrently create an archive.
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112
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113 The part_size value specified when the class was constructed
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114 will be used *unless* it is smaller than the minimum required
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115 part size needed for the size of the given file. In that case,
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116 the part size used will be the minimum part size required
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117 to properly upload the given file.
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118
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119 :type file: str
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120 :param file: The filename to upload
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121
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122 :type description: str
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123 :param description: The description of the archive.
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124
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125 :rtype: str
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126 :return: The archive id of the newly created archive.
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127
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128 """
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129 total_size = os.stat(filename).st_size
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130 total_parts, part_size = self._calculate_required_part_size(total_size)
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131 hash_chunks = [None] * total_parts
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132 worker_queue = Queue()
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133 result_queue = Queue()
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134 response = self._api.initiate_multipart_upload(self._vault_name,
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135 part_size,
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136 description)
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137 upload_id = response['UploadId']
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138 # The basic idea is to add the chunks (the offsets not the actual
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139 # contents) to a work queue, start up a thread pool, let the crank
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140 # through the items in the work queue, and then place their results
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141 # in a result queue which we use to complete the multipart upload.
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142 self._add_work_items_to_queue(total_parts, worker_queue, part_size)
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143 self._start_upload_threads(result_queue, upload_id,
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144 worker_queue, filename)
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145 try:
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146 self._wait_for_upload_threads(hash_chunks, result_queue,
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147 total_parts)
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148 except UploadArchiveError as e:
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149 log.debug("An error occurred while uploading an archive, "
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150 "aborting multipart upload.")
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151 self._api.abort_multipart_upload(self._vault_name, upload_id)
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152 raise e
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153 log.debug("Completing upload.")
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154 response = self._api.complete_multipart_upload(
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155 self._vault_name, upload_id, bytes_to_hex(tree_hash(hash_chunks)),
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156 total_size)
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157 log.debug("Upload finished.")
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158 return response['ArchiveId']
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159
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160 def _wait_for_upload_threads(self, hash_chunks, result_queue, total_parts):
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161 for _ in range(total_parts):
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162 result = result_queue.get()
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163 if isinstance(result, Exception):
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164 log.debug("An error was found in the result queue, terminating "
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165 "threads: %s", result)
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166 self._shutdown_threads()
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167 raise UploadArchiveError("An error occurred while uploading "
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168 "an archive: %s" % result)
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169 # Each unit of work returns the tree hash for the given part
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170 # number, which we use at the end to compute the tree hash of
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171 # the entire archive.
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172 part_number, tree_sha256 = result
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173 hash_chunks[part_number] = tree_sha256
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174 self._shutdown_threads()
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175
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176 def _start_upload_threads(self, result_queue, upload_id, worker_queue,
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177 filename):
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178 log.debug("Starting threads.")
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179 for _ in range(self._num_threads):
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180 thread = UploadWorkerThread(self._api, self._vault_name, filename,
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181 upload_id, worker_queue, result_queue)
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182 time.sleep(0.2)
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183 thread.start()
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184 self._threads.append(thread)
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185
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186
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187 class TransferThread(threading.Thread):
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188 def __init__(self, worker_queue, result_queue):
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189 super(TransferThread, self).__init__()
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190 self._worker_queue = worker_queue
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191 self._result_queue = result_queue
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192 # This value can be set externally by other objects
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193 # to indicate that the thread should be shut down.
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194 self.should_continue = True
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195
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196 def run(self):
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197 while self.should_continue:
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198 try:
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199 work = self._worker_queue.get(timeout=1)
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200 except Empty:
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201 continue
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202 if work is _END_SENTINEL:
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203 self._cleanup()
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204 return
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205 result = self._process_chunk(work)
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206 self._result_queue.put(result)
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207 self._cleanup()
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208
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209 def _process_chunk(self, work):
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210 pass
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211
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212 def _cleanup(self):
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213 pass
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214
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215
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216 class UploadWorkerThread(TransferThread):
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217 def __init__(self, api, vault_name, filename, upload_id,
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218 worker_queue, result_queue, num_retries=5,
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219 time_between_retries=5,
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220 retry_exceptions=Exception):
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221 super(UploadWorkerThread, self).__init__(worker_queue, result_queue)
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222 self._api = api
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223 self._vault_name = vault_name
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224 self._filename = filename
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225 self._fileobj = open(filename, 'rb')
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226 self._upload_id = upload_id
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227 self._num_retries = num_retries
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228 self._time_between_retries = time_between_retries
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229 self._retry_exceptions = retry_exceptions
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230
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231 def _process_chunk(self, work):
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232 result = None
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233 for i in range(self._num_retries + 1):
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234 try:
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235 result = self._upload_chunk(work)
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236 break
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237 except self._retry_exceptions as e:
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238 log.error("Exception caught uploading part number %s for "
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239 "vault %s, attempt: (%s / %s), filename: %s, "
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240 "exception: %s, msg: %s",
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241 work[0], self._vault_name, i + 1, self._num_retries + 1,
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242 self._filename, e.__class__, e)
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243 time.sleep(self._time_between_retries)
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244 result = e
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245 return result
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246
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247 def _upload_chunk(self, work):
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248 part_number, part_size = work
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249 start_byte = part_number * part_size
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250 self._fileobj.seek(start_byte)
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251 contents = self._fileobj.read(part_size)
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252 linear_hash = hashlib.sha256(contents).hexdigest()
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253 tree_hash_bytes = tree_hash(chunk_hashes(contents))
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254 byte_range = (start_byte, start_byte + len(contents) - 1)
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255 log.debug("Uploading chunk %s of size %s", part_number, part_size)
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256 response = self._api.upload_part(self._vault_name, self._upload_id,
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257 linear_hash,
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258 bytes_to_hex(tree_hash_bytes),
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259 byte_range, contents)
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260 # Reading the response allows the connection to be reused.
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261 response.read()
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262 return (part_number, tree_hash_bytes)
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263
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264 def _cleanup(self):
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265 self._fileobj.close()
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266
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267
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268 class ConcurrentDownloader(ConcurrentTransferer):
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269 """
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270 Concurrently download an archive from glacier.
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271
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272 This class uses a thread pool to concurrently download an archive
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273 from glacier.
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274
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275 The threadpool is completely managed by this class and is
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276 transparent to the users of this class.
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277
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278 """
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279 def __init__(self, job, part_size=DEFAULT_PART_SIZE,
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280 num_threads=10):
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281 """
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282 :param job: A layer2 job object for archive retrieval object.
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283
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284 :param part_size: The size, in bytes, of the chunks to use when uploading
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285 the archive parts. The part size must be a megabyte multiplied by
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286 a power of two.
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287
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288 """
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289 super(ConcurrentDownloader, self).__init__(part_size, num_threads)
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290 self._job = job
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291
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292 def download(self, filename):
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293 """
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294 Concurrently download an archive.
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295
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296 :param filename: The filename to download the archive to
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297 :type filename: str
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298
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299 """
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300 total_size = self._job.archive_size
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301 total_parts, part_size = self._calculate_required_part_size(total_size)
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302 worker_queue = Queue()
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303 result_queue = Queue()
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304 self._add_work_items_to_queue(total_parts, worker_queue, part_size)
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305 self._start_download_threads(result_queue, worker_queue)
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306 try:
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307 self._wait_for_download_threads(filename, result_queue, total_parts)
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308 except DownloadArchiveError as e:
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309 log.debug("An error occurred while downloading an archive: %s", e)
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310 raise e
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311 log.debug("Download completed.")
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312
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313 def _wait_for_download_threads(self, filename, result_queue, total_parts):
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314 """
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315 Waits until the result_queue is filled with all the downloaded parts
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316 This indicates that all part downloads have completed
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317
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318 Saves downloaded parts into filename
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319
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320 :param filename:
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321 :param result_queue:
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322 :param total_parts:
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323 """
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324 hash_chunks = [None] * total_parts
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325 with open(filename, "wb") as f:
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326 for _ in range(total_parts):
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327 result = result_queue.get()
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328 if isinstance(result, Exception):
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329 log.debug("An error was found in the result queue, "
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330 "terminating threads: %s", result)
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331 self._shutdown_threads()
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332 raise DownloadArchiveError(
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333 "An error occurred while uploading "
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334 "an archive: %s" % result)
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335 part_number, part_size, actual_hash, data = result
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336 hash_chunks[part_number] = actual_hash
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337 start_byte = part_number * part_size
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338 f.seek(start_byte)
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339 f.write(data)
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340 f.flush()
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341 final_hash = bytes_to_hex(tree_hash(hash_chunks))
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342 log.debug("Verifying final tree hash of archive, expecting: %s, "
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343 "actual: %s", self._job.sha256_treehash, final_hash)
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344 if self._job.sha256_treehash != final_hash:
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345 self._shutdown_threads()
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346 raise TreeHashDoesNotMatchError(
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347 "Tree hash for entire archive does not match, "
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348 "expected: %s, got: %s" % (self._job.sha256_treehash,
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349 final_hash))
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350 self._shutdown_threads()
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351
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352 def _start_download_threads(self, result_queue, worker_queue):
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353 log.debug("Starting threads.")
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354 for _ in range(self._num_threads):
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355 thread = DownloadWorkerThread(self._job, worker_queue, result_queue)
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356 time.sleep(0.2)
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357 thread.start()
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358 self._threads.append(thread)
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359
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360
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361 class DownloadWorkerThread(TransferThread):
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362 def __init__(self, job,
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363 worker_queue, result_queue,
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364 num_retries=5,
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365 time_between_retries=5,
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366 retry_exceptions=Exception):
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367 """
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368 Individual download thread that will download parts of the file from Glacier. Parts
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369 to download stored in work queue.
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370
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371 Parts download to a temp dir with each part a separate file
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372
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373 :param job: Glacier job object
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374 :param work_queue: A queue of tuples which include the part_number and
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375 part_size
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376 :param result_queue: A priority queue of tuples which include the
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377 part_number and the path to the temp file that holds that
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378 part's data.
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379
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380 """
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381 super(DownloadWorkerThread, self).__init__(worker_queue, result_queue)
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382 self._job = job
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383 self._num_retries = num_retries
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384 self._time_between_retries = time_between_retries
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385 self._retry_exceptions = retry_exceptions
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386
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387 def _process_chunk(self, work):
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388 """
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389 Attempt to download a part of the archive from Glacier
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390 Store the result in the result_queue
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391
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392 :param work:
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393 """
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394 result = None
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395 for _ in range(self._num_retries):
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396 try:
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397 result = self._download_chunk(work)
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398 break
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399 except self._retry_exceptions as e:
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400 log.error("Exception caught downloading part number %s for "
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401 "job %s", work[0], self._job,)
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402 time.sleep(self._time_between_retries)
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403 result = e
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404 return result
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405
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406 def _download_chunk(self, work):
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407 """
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408 Downloads a chunk of archive from Glacier. Saves the data to a temp file
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409 Returns the part number and temp file location
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410
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411 :param work:
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412 """
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413 part_number, part_size = work
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414 start_byte = part_number * part_size
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415 byte_range = (start_byte, start_byte + part_size - 1)
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416 log.debug("Downloading chunk %s of size %s", part_number, part_size)
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417 response = self._job.get_output(byte_range)
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418 data = response.read()
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419 actual_hash = bytes_to_hex(tree_hash(chunk_hashes(data)))
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420 if response['TreeHash'] != actual_hash:
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421 raise TreeHashDoesNotMatchError(
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422 "Tree hash for part number %s does not match, "
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shellac
parents:
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423 "expected: %s, got: %s" % (part_number, response['TreeHash'],
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424 actual_hash))
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425 return (part_number, part_size, binascii.unhexlify(actual_hash), data)