Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/boto/glacier/concurrent.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:20:52 -0400 |
parents | 26e78fe6e8c4 |
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# Copyright (c) 2012 Amazon.com, Inc. or its affiliates. All Rights Reserved # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including # without limitation the rights to use, copy, modify, merge, publish, dis- # tribute, sublicense, and/or sell copies of the Software, and to permit # persons to whom the Software is furnished to do so, subject to the fol- # lowing conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS # IN THE SOFTWARE. # import os import math import threading import hashlib import time import logging from boto.compat import Queue import binascii from boto.glacier.utils import DEFAULT_PART_SIZE, minimum_part_size, \ chunk_hashes, tree_hash, bytes_to_hex from boto.glacier.exceptions import UploadArchiveError, \ DownloadArchiveError, \ TreeHashDoesNotMatchError _END_SENTINEL = object() log = logging.getLogger('boto.glacier.concurrent') class ConcurrentTransferer(object): def __init__(self, part_size=DEFAULT_PART_SIZE, num_threads=10): self._part_size = part_size self._num_threads = num_threads self._threads = [] def _calculate_required_part_size(self, total_size): min_part_size_required = minimum_part_size(total_size) if self._part_size >= min_part_size_required: part_size = self._part_size else: part_size = min_part_size_required log.debug("The part size specified (%s) is smaller than " "the minimum required part size. Using a part " "size of: %s", self._part_size, part_size) total_parts = int(math.ceil(total_size / float(part_size))) return total_parts, part_size def _shutdown_threads(self): log.debug("Shutting down threads.") for thread in self._threads: thread.should_continue = False for thread in self._threads: thread.join() log.debug("Threads have exited.") def _add_work_items_to_queue(self, total_parts, worker_queue, part_size): log.debug("Adding work items to queue.") for i in range(total_parts): worker_queue.put((i, part_size)) for i in range(self._num_threads): worker_queue.put(_END_SENTINEL) class ConcurrentUploader(ConcurrentTransferer): """Concurrently upload an archive to glacier. This class uses a thread pool to concurrently upload an archive to glacier using the multipart upload API. The threadpool is completely managed by this class and is transparent to the users of this class. """ def __init__(self, api, vault_name, part_size=DEFAULT_PART_SIZE, num_threads=10): """ :type api: :class:`boto.glacier.layer1.Layer1` :param api: A layer1 glacier object. :type vault_name: str :param vault_name: The name of the vault. :type part_size: int :param part_size: The size, in bytes, of the chunks to use when uploading the archive parts. The part size must be a megabyte multiplied by a power of two. :type num_threads: int :param num_threads: The number of threads to spawn for the thread pool. The number of threads will control how much parts are being concurrently uploaded. """ super(ConcurrentUploader, self).__init__(part_size, num_threads) self._api = api self._vault_name = vault_name def upload(self, filename, description=None): """Concurrently create an archive. The part_size value specified when the class was constructed will be used *unless* it is smaller than the minimum required part size needed for the size of the given file. In that case, the part size used will be the minimum part size required to properly upload the given file. :type file: str :param file: The filename to upload :type description: str :param description: The description of the archive. :rtype: str :return: The archive id of the newly created archive. """ total_size = os.stat(filename).st_size total_parts, part_size = self._calculate_required_part_size(total_size) hash_chunks = [None] * total_parts worker_queue = Queue() result_queue = Queue() response = self._api.initiate_multipart_upload(self._vault_name, part_size, description) upload_id = response['UploadId'] # The basic idea is to add the chunks (the offsets not the actual # contents) to a work queue, start up a thread pool, let the crank # through the items in the work queue, and then place their results # in a result queue which we use to complete the multipart upload. self._add_work_items_to_queue(total_parts, worker_queue, part_size) self._start_upload_threads(result_queue, upload_id, worker_queue, filename) try: self._wait_for_upload_threads(hash_chunks, result_queue, total_parts) except UploadArchiveError as e: log.debug("An error occurred while uploading an archive, " "aborting multipart upload.") self._api.abort_multipart_upload(self._vault_name, upload_id) raise e log.debug("Completing upload.") response = self._api.complete_multipart_upload( self._vault_name, upload_id, bytes_to_hex(tree_hash(hash_chunks)), total_size) log.debug("Upload finished.") return response['ArchiveId'] def _wait_for_upload_threads(self, hash_chunks, result_queue, total_parts): for _ in range(total_parts): result = result_queue.get() if isinstance(result, Exception): log.debug("An error was found in the result queue, terminating " "threads: %s", result) self._shutdown_threads() raise UploadArchiveError("An error occurred while uploading " "an archive: %s" % result) # Each unit of work returns the tree hash for the given part # number, which we use at the end to compute the tree hash of # the entire archive. part_number, tree_sha256 = result hash_chunks[part_number] = tree_sha256 self._shutdown_threads() def _start_upload_threads(self, result_queue, upload_id, worker_queue, filename): log.debug("Starting threads.") for _ in range(self._num_threads): thread = UploadWorkerThread(self._api, self._vault_name, filename, upload_id, worker_queue, result_queue) time.sleep(0.2) thread.start() self._threads.append(thread) class TransferThread(threading.Thread): def __init__(self, worker_queue, result_queue): super(TransferThread, self).__init__() self._worker_queue = worker_queue self._result_queue = result_queue # This value can be set externally by other objects # to indicate that the thread should be shut down. self.should_continue = True def run(self): while self.should_continue: try: work = self._worker_queue.get(timeout=1) except Empty: continue if work is _END_SENTINEL: self._cleanup() return result = self._process_chunk(work) self._result_queue.put(result) self._cleanup() def _process_chunk(self, work): pass def _cleanup(self): pass class UploadWorkerThread(TransferThread): def __init__(self, api, vault_name, filename, upload_id, worker_queue, result_queue, num_retries=5, time_between_retries=5, retry_exceptions=Exception): super(UploadWorkerThread, self).__init__(worker_queue, result_queue) self._api = api self._vault_name = vault_name self._filename = filename self._fileobj = open(filename, 'rb') self._upload_id = upload_id self._num_retries = num_retries self._time_between_retries = time_between_retries self._retry_exceptions = retry_exceptions def _process_chunk(self, work): result = None for i in range(self._num_retries + 1): try: result = self._upload_chunk(work) break except self._retry_exceptions as e: log.error("Exception caught uploading part number %s for " "vault %s, attempt: (%s / %s), filename: %s, " "exception: %s, msg: %s", work[0], self._vault_name, i + 1, self._num_retries + 1, self._filename, e.__class__, e) time.sleep(self._time_between_retries) result = e return result def _upload_chunk(self, work): part_number, part_size = work start_byte = part_number * part_size self._fileobj.seek(start_byte) contents = self._fileobj.read(part_size) linear_hash = hashlib.sha256(contents).hexdigest() tree_hash_bytes = tree_hash(chunk_hashes(contents)) byte_range = (start_byte, start_byte + len(contents) - 1) log.debug("Uploading chunk %s of size %s", part_number, part_size) response = self._api.upload_part(self._vault_name, self._upload_id, linear_hash, bytes_to_hex(tree_hash_bytes), byte_range, contents) # Reading the response allows the connection to be reused. response.read() return (part_number, tree_hash_bytes) def _cleanup(self): self._fileobj.close() class ConcurrentDownloader(ConcurrentTransferer): """ Concurrently download an archive from glacier. This class uses a thread pool to concurrently download an archive from glacier. The threadpool is completely managed by this class and is transparent to the users of this class. """ def __init__(self, job, part_size=DEFAULT_PART_SIZE, num_threads=10): """ :param job: A layer2 job object for archive retrieval object. :param part_size: The size, in bytes, of the chunks to use when uploading the archive parts. The part size must be a megabyte multiplied by a power of two. """ super(ConcurrentDownloader, self).__init__(part_size, num_threads) self._job = job def download(self, filename): """ Concurrently download an archive. :param filename: The filename to download the archive to :type filename: str """ total_size = self._job.archive_size total_parts, part_size = self._calculate_required_part_size(total_size) worker_queue = Queue() result_queue = Queue() self._add_work_items_to_queue(total_parts, worker_queue, part_size) self._start_download_threads(result_queue, worker_queue) try: self._wait_for_download_threads(filename, result_queue, total_parts) except DownloadArchiveError as e: log.debug("An error occurred while downloading an archive: %s", e) raise e log.debug("Download completed.") def _wait_for_download_threads(self, filename, result_queue, total_parts): """ Waits until the result_queue is filled with all the downloaded parts This indicates that all part downloads have completed Saves downloaded parts into filename :param filename: :param result_queue: :param total_parts: """ hash_chunks = [None] * total_parts with open(filename, "wb") as f: for _ in range(total_parts): result = result_queue.get() if isinstance(result, Exception): log.debug("An error was found in the result queue, " "terminating threads: %s", result) self._shutdown_threads() raise DownloadArchiveError( "An error occurred while uploading " "an archive: %s" % result) part_number, part_size, actual_hash, data = result hash_chunks[part_number] = actual_hash start_byte = part_number * part_size f.seek(start_byte) f.write(data) f.flush() final_hash = bytes_to_hex(tree_hash(hash_chunks)) log.debug("Verifying final tree hash of archive, expecting: %s, " "actual: %s", self._job.sha256_treehash, final_hash) if self._job.sha256_treehash != final_hash: self._shutdown_threads() raise TreeHashDoesNotMatchError( "Tree hash for entire archive does not match, " "expected: %s, got: %s" % (self._job.sha256_treehash, final_hash)) self._shutdown_threads() def _start_download_threads(self, result_queue, worker_queue): log.debug("Starting threads.") for _ in range(self._num_threads): thread = DownloadWorkerThread(self._job, worker_queue, result_queue) time.sleep(0.2) thread.start() self._threads.append(thread) class DownloadWorkerThread(TransferThread): def __init__(self, job, worker_queue, result_queue, num_retries=5, time_between_retries=5, retry_exceptions=Exception): """ Individual download thread that will download parts of the file from Glacier. Parts to download stored in work queue. Parts download to a temp dir with each part a separate file :param job: Glacier job object :param work_queue: A queue of tuples which include the part_number and part_size :param result_queue: A priority queue of tuples which include the part_number and the path to the temp file that holds that part's data. """ super(DownloadWorkerThread, self).__init__(worker_queue, result_queue) self._job = job self._num_retries = num_retries self._time_between_retries = time_between_retries self._retry_exceptions = retry_exceptions def _process_chunk(self, work): """ Attempt to download a part of the archive from Glacier Store the result in the result_queue :param work: """ result = None for _ in range(self._num_retries): try: result = self._download_chunk(work) break except self._retry_exceptions as e: log.error("Exception caught downloading part number %s for " "job %s", work[0], self._job,) time.sleep(self._time_between_retries) result = e return result def _download_chunk(self, work): """ Downloads a chunk of archive from Glacier. Saves the data to a temp file Returns the part number and temp file location :param work: """ part_number, part_size = work start_byte = part_number * part_size byte_range = (start_byte, start_byte + part_size - 1) log.debug("Downloading chunk %s of size %s", part_number, part_size) response = self._job.get_output(byte_range) data = response.read() actual_hash = bytes_to_hex(tree_hash(chunk_hashes(data))) if response['TreeHash'] != actual_hash: raise TreeHashDoesNotMatchError( "Tree hash for part number %s does not match, " "expected: %s, got: %s" % (part_number, response['TreeHash'], actual_hash)) return (part_number, part_size, binascii.unhexlify(actual_hash), data)