Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/boto/services/bs.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 #!/usr/bin/env python
2 # Copyright (c) 2006-2008 Mitch Garnaat http://garnaat.org/
3 #
4 # Permission is hereby granted, free of charge, to any person obtaining a
5 # copy of this software and associated documentation files (the
6 # "Software"), to deal in the Software without restriction, including
7 # without limitation the rights to use, copy, modify, merge, publish, dis-
8 # tribute, sublicense, and/or sell copies of the Software, and to permit
9 # persons to whom the Software is furnished to do so, subject to the fol-
10 # lowing conditions:
11 #
12 # The above copyright notice and this permission notice shall be included
13 # in all copies or substantial portions of the Software.
14 #
15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
21 # IN THE SOFTWARE.
22 from optparse import OptionParser
23 from boto.services.servicedef import ServiceDef
24 from boto.services.submit import Submitter
25 from boto.services.result import ResultProcessor
26 import boto
27 import sys, os
28 from boto.compat import StringIO
29
30 class BS(object):
31
32 Usage = "usage: %prog [options] config_file command"
33
34 Commands = {'reset' : 'Clear input queue and output bucket',
35 'submit' : 'Submit local files to the service',
36 'start' : 'Start the service',
37 'status' : 'Report on the status of the service buckets and queues',
38 'retrieve' : 'Retrieve output generated by a batch',
39 'batches' : 'List all batches stored in current output_domain'}
40
41 def __init__(self):
42 self.service_name = None
43 self.parser = OptionParser(usage=self.Usage)
44 self.parser.add_option("--help-commands", action="store_true", dest="help_commands",
45 help="provides help on the available commands")
46 self.parser.add_option("-a", "--access-key", action="store", type="string",
47 help="your AWS Access Key")
48 self.parser.add_option("-s", "--secret-key", action="store", type="string",
49 help="your AWS Secret Access Key")
50 self.parser.add_option("-p", "--path", action="store", type="string", dest="path",
51 help="the path to local directory for submit and retrieve")
52 self.parser.add_option("-k", "--keypair", action="store", type="string", dest="keypair",
53 help="the SSH keypair used with launched instance(s)")
54 self.parser.add_option("-l", "--leave", action="store_true", dest="leave",
55 help="leave the files (don't retrieve) files during retrieve command")
56 self.parser.set_defaults(leave=False)
57 self.parser.add_option("-n", "--num-instances", action="store", type="string", dest="num_instances",
58 help="the number of launched instance(s)")
59 self.parser.set_defaults(num_instances=1)
60 self.parser.add_option("-i", "--ignore-dirs", action="append", type="string", dest="ignore",
61 help="directories that should be ignored by submit command")
62 self.parser.add_option("-b", "--batch-id", action="store", type="string", dest="batch",
63 help="batch identifier required by the retrieve command")
64
65 def print_command_help(self):
66 print('\nCommands:')
67 for key in self.Commands.keys():
68 print(' %s\t\t%s' % (key, self.Commands[key]))
69
70 def do_reset(self):
71 iq = self.sd.get_obj('input_queue')
72 if iq:
73 print('clearing out input queue')
74 i = 0
75 m = iq.read()
76 while m:
77 i += 1
78 iq.delete_message(m)
79 m = iq.read()
80 print('deleted %d messages' % i)
81 ob = self.sd.get_obj('output_bucket')
82 ib = self.sd.get_obj('input_bucket')
83 if ob:
84 if ib and ob.name == ib.name:
85 return
86 print('delete generated files in output bucket')
87 i = 0
88 for k in ob:
89 i += 1
90 k.delete()
91 print('deleted %d keys' % i)
92
93 def do_submit(self):
94 if not self.options.path:
95 self.parser.error('No path provided')
96 if not os.path.exists(self.options.path):
97 self.parser.error('Invalid path (%s)' % self.options.path)
98 s = Submitter(self.sd)
99 t = s.submit_path(self.options.path, None, self.options.ignore, None,
100 None, True, self.options.path)
101 print('A total of %d files were submitted' % t[1])
102 print('Batch Identifier: %s' % t[0])
103
104 def do_start(self):
105 ami_id = self.sd.get('ami_id')
106 instance_type = self.sd.get('instance_type', 'm1.small')
107 security_group = self.sd.get('security_group', 'default')
108 if not ami_id:
109 self.parser.error('ami_id option is required when starting the service')
110 ec2 = boto.connect_ec2()
111 if not self.sd.has_section('Credentials'):
112 self.sd.add_section('Credentials')
113 self.sd.set('Credentials', 'aws_access_key_id', ec2.aws_access_key_id)
114 self.sd.set('Credentials', 'aws_secret_access_key', ec2.aws_secret_access_key)
115 s = StringIO()
116 self.sd.write(s)
117 rs = ec2.get_all_images([ami_id])
118 img = rs[0]
119 r = img.run(user_data=s.getvalue(), key_name=self.options.keypair,
120 max_count=self.options.num_instances,
121 instance_type=instance_type,
122 security_groups=[security_group])
123 print('Starting AMI: %s' % ami_id)
124 print('Reservation %s contains the following instances:' % r.id)
125 for i in r.instances:
126 print('\t%s' % i.id)
127
128 def do_status(self):
129 iq = self.sd.get_obj('input_queue')
130 if iq:
131 print('The input_queue (%s) contains approximately %s messages' % (iq.id, iq.count()))
132 ob = self.sd.get_obj('output_bucket')
133 ib = self.sd.get_obj('input_bucket')
134 if ob:
135 if ib and ob.name == ib.name:
136 return
137 total = 0
138 for k in ob:
139 total += 1
140 print('The output_bucket (%s) contains %d keys' % (ob.name, total))
141
142 def do_retrieve(self):
143 if not self.options.path:
144 self.parser.error('No path provided')
145 if not os.path.exists(self.options.path):
146 self.parser.error('Invalid path (%s)' % self.options.path)
147 if not self.options.batch:
148 self.parser.error('batch identifier is required for retrieve command')
149 s = ResultProcessor(self.options.batch, self.sd)
150 s.get_results(self.options.path, get_file=(not self.options.leave))
151
152 def do_batches(self):
153 d = self.sd.get_obj('output_domain')
154 if d:
155 print('Available Batches:')
156 rs = d.query("['type'='Batch']")
157 for item in rs:
158 print(' %s' % item.name)
159 else:
160 self.parser.error('No output_domain specified for service')
161
162 def main(self):
163 self.options, self.args = self.parser.parse_args()
164 if self.options.help_commands:
165 self.print_command_help()
166 sys.exit(0)
167 if len(self.args) != 2:
168 self.parser.error("config_file and command are required")
169 self.config_file = self.args[0]
170 self.sd = ServiceDef(self.config_file)
171 self.command = self.args[1]
172 if hasattr(self, 'do_%s' % self.command):
173 method = getattr(self, 'do_%s' % self.command)
174 method()
175 else:
176 self.parser.error('command (%s) not recognized' % self.command)
177
178 if __name__ == "__main__":
179 bs = BS()
180 bs.main()