Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/boto/services/bs.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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#!/usr/bin/env python # Copyright (c) 2006-2008 Mitch Garnaat http://garnaat.org/ # # 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. from optparse import OptionParser from boto.services.servicedef import ServiceDef from boto.services.submit import Submitter from boto.services.result import ResultProcessor import boto import sys, os from boto.compat import StringIO class BS(object): Usage = "usage: %prog [options] config_file command" Commands = {'reset' : 'Clear input queue and output bucket', 'submit' : 'Submit local files to the service', 'start' : 'Start the service', 'status' : 'Report on the status of the service buckets and queues', 'retrieve' : 'Retrieve output generated by a batch', 'batches' : 'List all batches stored in current output_domain'} def __init__(self): self.service_name = None self.parser = OptionParser(usage=self.Usage) self.parser.add_option("--help-commands", action="store_true", dest="help_commands", help="provides help on the available commands") self.parser.add_option("-a", "--access-key", action="store", type="string", help="your AWS Access Key") self.parser.add_option("-s", "--secret-key", action="store", type="string", help="your AWS Secret Access Key") self.parser.add_option("-p", "--path", action="store", type="string", dest="path", help="the path to local directory for submit and retrieve") self.parser.add_option("-k", "--keypair", action="store", type="string", dest="keypair", help="the SSH keypair used with launched instance(s)") self.parser.add_option("-l", "--leave", action="store_true", dest="leave", help="leave the files (don't retrieve) files during retrieve command") self.parser.set_defaults(leave=False) self.parser.add_option("-n", "--num-instances", action="store", type="string", dest="num_instances", help="the number of launched instance(s)") self.parser.set_defaults(num_instances=1) self.parser.add_option("-i", "--ignore-dirs", action="append", type="string", dest="ignore", help="directories that should be ignored by submit command") self.parser.add_option("-b", "--batch-id", action="store", type="string", dest="batch", help="batch identifier required by the retrieve command") def print_command_help(self): print('\nCommands:') for key in self.Commands.keys(): print(' %s\t\t%s' % (key, self.Commands[key])) def do_reset(self): iq = self.sd.get_obj('input_queue') if iq: print('clearing out input queue') i = 0 m = iq.read() while m: i += 1 iq.delete_message(m) m = iq.read() print('deleted %d messages' % i) ob = self.sd.get_obj('output_bucket') ib = self.sd.get_obj('input_bucket') if ob: if ib and ob.name == ib.name: return print('delete generated files in output bucket') i = 0 for k in ob: i += 1 k.delete() print('deleted %d keys' % i) def do_submit(self): if not self.options.path: self.parser.error('No path provided') if not os.path.exists(self.options.path): self.parser.error('Invalid path (%s)' % self.options.path) s = Submitter(self.sd) t = s.submit_path(self.options.path, None, self.options.ignore, None, None, True, self.options.path) print('A total of %d files were submitted' % t[1]) print('Batch Identifier: %s' % t[0]) def do_start(self): ami_id = self.sd.get('ami_id') instance_type = self.sd.get('instance_type', 'm1.small') security_group = self.sd.get('security_group', 'default') if not ami_id: self.parser.error('ami_id option is required when starting the service') ec2 = boto.connect_ec2() if not self.sd.has_section('Credentials'): self.sd.add_section('Credentials') self.sd.set('Credentials', 'aws_access_key_id', ec2.aws_access_key_id) self.sd.set('Credentials', 'aws_secret_access_key', ec2.aws_secret_access_key) s = StringIO() self.sd.write(s) rs = ec2.get_all_images([ami_id]) img = rs[0] r = img.run(user_data=s.getvalue(), key_name=self.options.keypair, max_count=self.options.num_instances, instance_type=instance_type, security_groups=[security_group]) print('Starting AMI: %s' % ami_id) print('Reservation %s contains the following instances:' % r.id) for i in r.instances: print('\t%s' % i.id) def do_status(self): iq = self.sd.get_obj('input_queue') if iq: print('The input_queue (%s) contains approximately %s messages' % (iq.id, iq.count())) ob = self.sd.get_obj('output_bucket') ib = self.sd.get_obj('input_bucket') if ob: if ib and ob.name == ib.name: return total = 0 for k in ob: total += 1 print('The output_bucket (%s) contains %d keys' % (ob.name, total)) def do_retrieve(self): if not self.options.path: self.parser.error('No path provided') if not os.path.exists(self.options.path): self.parser.error('Invalid path (%s)' % self.options.path) if not self.options.batch: self.parser.error('batch identifier is required for retrieve command') s = ResultProcessor(self.options.batch, self.sd) s.get_results(self.options.path, get_file=(not self.options.leave)) def do_batches(self): d = self.sd.get_obj('output_domain') if d: print('Available Batches:') rs = d.query("['type'='Batch']") for item in rs: print(' %s' % item.name) else: self.parser.error('No output_domain specified for service') def main(self): self.options, self.args = self.parser.parse_args() if self.options.help_commands: self.print_command_help() sys.exit(0) if len(self.args) != 2: self.parser.error("config_file and command are required") self.config_file = self.args[0] self.sd = ServiceDef(self.config_file) self.command = self.args[1] if hasattr(self, 'do_%s' % self.command): method = getattr(self, 'do_%s' % self.command) method() else: self.parser.error('command (%s) not recognized' % self.command) if __name__ == "__main__": bs = BS() bs.main()