Mercurial > repos > shellac > guppy_basecaller
view env/bin/glacier @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 26e78fe6e8c4 |
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#!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3 # -*- coding: utf-8 -*- # Copyright (c) 2012 Miguel Olivares http://moliware.com/ # # 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. # """ glacier ~~~~~~~ Amazon Glacier tool built on top of boto. Look at the usage method to see how to use it. Author: Miguel Olivares <miguel@moliware.com> """ import sys from boto.glacier import connect_to_region from getopt import getopt, GetoptError from os.path import isfile, basename COMMANDS = ('vaults', 'jobs', 'upload') def usage(): print(""" glacier <command> [args] Commands vaults - Operations with vaults jobs - Operations with jobs upload - Upload files to a vault. If the vault doesn't exits, it is created Common args: --access_key - Your AWS Access Key ID. If not supplied, boto will use the value of the environment variable AWS_ACCESS_KEY_ID --secret_key - Your AWS Secret Access Key. If not supplied, boto will use the value of the environment variable AWS_SECRET_ACCESS_KEY --region - AWS region to use. Possible values: us-east-1, us-west-1, us-west-2, ap-northeast-1, eu-west-1. Default: us-east-1 Vaults operations: List vaults: glacier vaults Jobs operations: List jobs: glacier jobs <vault name> Uploading files: glacier upload <vault name> <files> Examples : glacier upload pics *.jpg glacier upload pics a.jpg b.jpg """) sys.exit() def connect(region, debug_level=0, access_key=None, secret_key=None): """ Connect to a specific region """ layer2 = connect_to_region(region, aws_access_key_id=access_key, aws_secret_access_key=secret_key, debug=debug_level) if layer2 is None: print('Invalid region (%s)' % region) sys.exit(1) return layer2 def list_vaults(region, access_key=None, secret_key=None): layer2 = connect(region, access_key = access_key, secret_key = secret_key) for vault in layer2.list_vaults(): print(vault.arn) def list_jobs(vault_name, region, access_key=None, secret_key=None): layer2 = connect(region, access_key = access_key, secret_key = secret_key) print(layer2.layer1.list_jobs(vault_name)) def upload_files(vault_name, filenames, region, access_key=None, secret_key=None): layer2 = connect(region, access_key = access_key, secret_key = secret_key) layer2.create_vault(vault_name) glacier_vault = layer2.get_vault(vault_name) for filename in filenames: if isfile(filename): sys.stdout.write('Uploading %s to %s...' % (filename, vault_name)) sys.stdout.flush() archive_id = glacier_vault.upload_archive( filename, description = basename(filename)) print(' done. Vault returned ArchiveID %s' % archive_id) def main(): if len(sys.argv) < 2: usage() command = sys.argv[1] if command not in COMMANDS: usage() argv = sys.argv[2:] options = 'a:s:r:' long_options = ['access_key=', 'secret_key=', 'region='] try: opts, args = getopt(argv, options, long_options) except GetoptError as e: usage() # Parse agument access_key = secret_key = None region = 'us-east-1' for option, value in opts: if option in ('-a', '--access_key'): access_key = value elif option in ('-s', '--secret_key'): secret_key = value elif option in ('-r', '--region'): region = value # handle each command if command == 'vaults': list_vaults(region, access_key, secret_key) elif command == 'jobs': if len(args) != 1: usage() list_jobs(args[0], region, access_key, secret_key) elif command == 'upload': if len(args) < 2: usage() upload_files(args[0], args[1:], region, access_key, secret_key) if __name__ == '__main__': main()