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comparison env/bin/launch_instance @ 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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-1:000000000000 0:26e78fe6e8c4
1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
2 # Copyright (c) 2009 Chris Moyer http://coredumped.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
22 #
23 # Utility to launch an EC2 Instance
24 #
25 VERSION="0.2"
26
27
28 CLOUD_INIT_SCRIPT = """#!/usr/bin/env python
29 f = open("/etc/boto.cfg", "w")
30 f.write(\"\"\"%s\"\"\")
31 f.close()
32 """
33 import boto.pyami.config
34 import boto.utils
35 import re, os
36 from boto.compat import ConfigParser
37
38 class Config(boto.pyami.config.Config):
39 """A special config class that also adds import abilities
40 Directly in the config file. To have a config file import
41 another config file, simply use "#import <path>" where <path>
42 is either a relative path or a full URL to another config
43 """
44
45 def __init__(self):
46 ConfigParser.__init__(self, {'working_dir' : '/mnt/pyami', 'debug' : '0'})
47
48 def add_config(self, file_url):
49 """Add a config file to this configuration
50 :param file_url: URL for the file to add, or a local path
51 :type file_url: str
52 """
53 if not re.match("^([a-zA-Z0-9]*:\/\/)(.*)", file_url):
54 if not file_url.startswith("/"):
55 file_url = os.path.join(os.getcwd(), file_url)
56 file_url = "file://%s" % file_url
57 (base_url, file_name) = file_url.rsplit("/", 1)
58 base_config = boto.utils.fetch_file(file_url)
59 base_config.seek(0)
60 for line in base_config.readlines():
61 match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
62 if match:
63 self.add_config("%s/%s" % (base_url, match.group(1)))
64 base_config.seek(0)
65 self.readfp(base_config)
66
67 def add_creds(self, ec2):
68 """Add the credentials to this config if they don't already exist"""
69 if not self.has_section('Credentials'):
70 self.add_section('Credentials')
71 self.set('Credentials', 'aws_access_key_id', ec2.aws_access_key_id)
72 self.set('Credentials', 'aws_secret_access_key', ec2.aws_secret_access_key)
73
74
75 def __str__(self):
76 """Get config as string"""
77 from StringIO import StringIO
78 s = StringIO()
79 self.write(s)
80 return s.getvalue()
81
82 SCRIPTS = []
83
84 def scripts_callback(option, opt, value, parser):
85 arg = value.split(',')
86 if len(arg) == 1:
87 SCRIPTS.append(arg[0])
88 else:
89 SCRIPTS.extend(arg)
90 setattr(parser.values, option.dest, SCRIPTS)
91
92 def add_script(scr_url):
93 """Read a script and any scripts that are added using #import"""
94 base_url = '/'.join(scr_url.split('/')[:-1]) + '/'
95 script_raw = boto.utils.fetch_file(scr_url)
96 script_content = ''
97 for line in script_raw.readlines():
98 match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
99 #if there is an import
100 if match:
101 #Read the other script and put it in that spot
102 script_content += add_script("%s/%s" % (base_url, match.group(1)))
103 else:
104 #Otherwise, add the line and move on
105 script_content += line
106 return script_content
107
108 if __name__ == "__main__":
109 try:
110 import readline
111 except ImportError:
112 pass
113 import sys
114 import time
115 import boto
116 from boto.ec2 import regions
117 from optparse import OptionParser
118 from boto.mashups.iobject import IObject
119 parser = OptionParser(version=VERSION, usage="%prog [options] config_url")
120 parser.add_option("-c", "--max-count", help="Maximum number of this type of instance to launch", dest="max_count", default="1")
121 parser.add_option("--min-count", help="Minimum number of this type of instance to launch", dest="min_count", default="1")
122 parser.add_option("--cloud-init", help="Indicates that this is an instance that uses 'CloudInit', Ubuntu's cloud bootstrap process. This wraps the config in a shell script command instead of just passing it in directly", dest="cloud_init", default=False, action="store_true")
123 parser.add_option("-g", "--groups", help="Security Groups to add this instance to", action="append", dest="groups")
124 parser.add_option("-a", "--ami", help="AMI to launch", dest="ami_id")
125 parser.add_option("-t", "--type", help="Type of Instance (default m1.small)", dest="type", default="m1.small")
126 parser.add_option("-k", "--key", help="Keypair", dest="key_name")
127 parser.add_option("-z", "--zone", help="Zone (default us-east-1a)", dest="zone", default="us-east-1a")
128 parser.add_option("-r", "--region", help="Region (default us-east-1)", dest="region", default="us-east-1")
129 parser.add_option("-i", "--ip", help="Elastic IP", dest="elastic_ip")
130 parser.add_option("-n", "--no-add-cred", help="Don't add a credentials section", default=False, action="store_true", dest="nocred")
131 parser.add_option("--save-ebs", help="Save the EBS volume on shutdown, instead of deleting it", default=False, action="store_true", dest="save_ebs")
132 parser.add_option("-w", "--wait", help="Wait until instance is running", default=False, action="store_true", dest="wait")
133 parser.add_option("-d", "--dns", help="Returns public and private DNS (implicates --wait)", default=False, action="store_true", dest="dns")
134 parser.add_option("-T", "--tag", help="Set tag", default=None, action="append", dest="tags", metavar="key:value")
135 parser.add_option("-s", "--scripts", help="Pass in a script or a folder containing scripts to be run when the instance starts up, assumes cloud-init. Specify scripts in a list specified by commas. If multiple scripts are specified, they are run lexically (A good way to ensure they run in the order is to prefix filenames with numbers)", type='string', action="callback", callback=scripts_callback)
136 parser.add_option("--role", help="IAM Role to use, this implies --no-add-cred", dest="role")
137
138 (options, args) = parser.parse_args()
139
140 if len(args) < 1:
141 parser.print_help()
142 sys.exit(1)
143 file_url = os.path.expanduser(args[0])
144
145 cfg = Config()
146 cfg.add_config(file_url)
147
148 for r in regions():
149 if r.name == options.region:
150 region = r
151 break
152 else:
153 print("Region %s not found." % options.region)
154 sys.exit(1)
155 ec2 = boto.connect_ec2(region=region)
156 if not options.nocred and not options.role:
157 cfg.add_creds(ec2)
158
159 iobj = IObject()
160 if options.ami_id:
161 ami = ec2.get_image(options.ami_id)
162 else:
163 ami_id = options.ami_id
164 l = [(a, a.id, a.location) for a in ec2.get_all_images()]
165 ami = iobj.choose_from_list(l, prompt='Choose AMI')
166
167 if options.key_name:
168 key_name = options.key_name
169 else:
170 l = [(k, k.name, '') for k in ec2.get_all_key_pairs()]
171 key_name = iobj.choose_from_list(l, prompt='Choose Keypair').name
172
173 if options.groups:
174 groups = options.groups
175 else:
176 groups = []
177 l = [(g, g.name, g.description) for g in ec2.get_all_security_groups()]
178 g = iobj.choose_from_list(l, prompt='Choose Primary Security Group')
179 while g != None:
180 groups.append(g)
181 l.remove((g, g.name, g.description))
182 g = iobj.choose_from_list(l, prompt='Choose Additional Security Group (0 to quit)')
183
184 user_data = str(cfg)
185 # If it's a cloud init AMI,
186 # then we need to wrap the config in our
187 # little wrapper shell script
188
189 if options.cloud_init:
190 user_data = CLOUD_INIT_SCRIPT % user_data
191 scriptuples = []
192 if options.scripts:
193 scripts = options.scripts
194 scriptuples.append(('user_data', user_data))
195 for scr in scripts:
196 scr_url = scr
197 if not re.match("^([a-zA-Z0-9]*:\/\/)(.*)", scr_url):
198 if not scr_url.startswith("/"):
199 scr_url = os.path.join(os.getcwd(), scr_url)
200 try:
201 newfiles = os.listdir(scr_url)
202 for f in newfiles:
203 #put the scripts in the folder in the array such that they run in the correct order
204 scripts.insert(scripts.index(scr) + 1, scr.split("/")[-1] + "/" + f)
205 except OSError:
206 scr_url = "file://%s" % scr_url
207 try:
208 scriptuples.append((scr, add_script(scr_url)))
209 except Exception as e:
210 pass
211
212 user_data = boto.utils.write_mime_multipart(scriptuples, compress=True)
213
214 shutdown_proc = "terminate"
215 if options.save_ebs:
216 shutdown_proc = "save"
217
218 instance_profile_name = None
219 if options.role:
220 instance_profile_name = options.role
221
222 r = ami.run(min_count=int(options.min_count), max_count=int(options.max_count),
223 key_name=key_name, user_data=user_data,
224 security_groups=groups, instance_type=options.type,
225 placement=options.zone, instance_initiated_shutdown_behavior=shutdown_proc,
226 instance_profile_name=instance_profile_name)
227
228 instance = r.instances[0]
229
230 if options.tags:
231 for tag_pair in options.tags:
232 name = tag_pair
233 value = ''
234 if ':' in tag_pair:
235 name, value = tag_pair.split(':', 1)
236 instance.add_tag(name, value)
237
238 if options.dns:
239 options.wait = True
240
241 if not options.wait:
242 sys.exit(0)
243
244 while True:
245 instance.update()
246 if instance.state == 'running':
247 break
248 time.sleep(3)
249
250 if options.dns:
251 print("Public DNS name: %s" % instance.public_dns_name)
252 print("Private DNS name: %s" % instance.private_dns_name)