Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/boto/manage/server.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:20:52 -0400 |
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1 # Copyright (c) 2006-2009 Mitch Garnaat http://garnaat.org/ |
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2 # Copyright (c) 2010 Chris Moyer http://coredumped.org/ |
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3 # |
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4 # Permission is hereby granted, free of charge, to any person obtaining a |
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5 # copy of this software and associated documentation files (the |
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6 # "Software"), to deal in the Software without restriction, including |
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7 # without limitation the rights to use, copy, modify, merge, publish, dis- |
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8 # tribute, sublicense, and/or sell copies of the Software, and to permit |
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9 # persons to whom the Software is furnished to do so, subject to the fol- |
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10 # lowing conditions: |
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11 # |
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12 # The above copyright notice and this permission notice shall be included |
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13 # in all copies or substantial portions of the Software. |
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14 # |
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15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS |
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16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- |
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17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT |
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18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, |
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19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS |
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21 # IN THE SOFTWARE. |
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22 """ |
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23 High-level abstraction of an EC2 server |
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24 """ |
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25 |
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26 import boto.ec2 |
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27 from boto.mashups.iobject import IObject |
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28 from boto.pyami.config import BotoConfigPath, Config |
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29 from boto.sdb.db.model import Model |
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30 from boto.sdb.db.property import StringProperty, IntegerProperty, BooleanProperty, CalculatedProperty |
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31 from boto.manage import propget |
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32 from boto.ec2.zone import Zone |
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33 from boto.ec2.keypair import KeyPair |
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34 import os, time |
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35 from contextlib import closing |
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36 from boto.exception import EC2ResponseError |
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37 from boto.compat import six, StringIO |
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38 |
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39 InstanceTypes = ['m1.small', 'm1.large', 'm1.xlarge', |
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40 'c1.medium', 'c1.xlarge', |
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41 'm2.2xlarge', 'm2.4xlarge'] |
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42 |
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43 class Bundler(object): |
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44 |
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45 def __init__(self, server, uname='root'): |
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46 from boto.manage.cmdshell import SSHClient |
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47 self.server = server |
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48 self.uname = uname |
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49 self.ssh_client = SSHClient(server, uname=uname) |
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50 |
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51 def copy_x509(self, key_file, cert_file): |
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52 print('\tcopying cert and pk over to /mnt directory on server') |
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53 self.ssh_client.open_sftp() |
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54 path, name = os.path.split(key_file) |
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55 self.remote_key_file = '/mnt/%s' % name |
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56 self.ssh_client.put_file(key_file, self.remote_key_file) |
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57 path, name = os.path.split(cert_file) |
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58 self.remote_cert_file = '/mnt/%s' % name |
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59 self.ssh_client.put_file(cert_file, self.remote_cert_file) |
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60 print('...complete!') |
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61 |
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62 def bundle_image(self, prefix, size, ssh_key): |
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63 command = "" |
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64 if self.uname != 'root': |
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65 command = "sudo " |
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66 command += 'ec2-bundle-vol ' |
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67 command += '-c %s -k %s ' % (self.remote_cert_file, self.remote_key_file) |
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68 command += '-u %s ' % self.server._reservation.owner_id |
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69 command += '-p %s ' % prefix |
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70 command += '-s %d ' % size |
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71 command += '-d /mnt ' |
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72 if self.server.instance_type == 'm1.small' or self.server.instance_type == 'c1.medium': |
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73 command += '-r i386' |
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74 else: |
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75 command += '-r x86_64' |
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76 return command |
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77 |
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78 def upload_bundle(self, bucket, prefix, ssh_key): |
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79 command = "" |
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80 if self.uname != 'root': |
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81 command = "sudo " |
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82 command += 'ec2-upload-bundle ' |
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83 command += '-m /mnt/%s.manifest.xml ' % prefix |
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84 command += '-b %s ' % bucket |
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85 command += '-a %s ' % self.server.ec2.aws_access_key_id |
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86 command += '-s %s ' % self.server.ec2.aws_secret_access_key |
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87 return command |
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88 |
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89 def bundle(self, bucket=None, prefix=None, key_file=None, cert_file=None, |
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90 size=None, ssh_key=None, fp=None, clear_history=True): |
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91 iobject = IObject() |
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92 if not bucket: |
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93 bucket = iobject.get_string('Name of S3 bucket') |
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94 if not prefix: |
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95 prefix = iobject.get_string('Prefix for AMI file') |
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96 if not key_file: |
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97 key_file = iobject.get_filename('Path to RSA private key file') |
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98 if not cert_file: |
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99 cert_file = iobject.get_filename('Path to RSA public cert file') |
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100 if not size: |
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101 size = iobject.get_int('Size (in MB) of bundled image') |
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102 if not ssh_key: |
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103 ssh_key = self.server.get_ssh_key_file() |
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104 self.copy_x509(key_file, cert_file) |
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105 if not fp: |
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106 fp = StringIO() |
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107 fp.write('sudo mv %s /mnt/boto.cfg; ' % BotoConfigPath) |
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108 fp.write('mv ~/.ssh/authorized_keys /mnt/authorized_keys; ') |
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109 if clear_history: |
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110 fp.write('history -c; ') |
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111 fp.write(self.bundle_image(prefix, size, ssh_key)) |
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112 fp.write('; ') |
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113 fp.write(self.upload_bundle(bucket, prefix, ssh_key)) |
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114 fp.write('; ') |
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115 fp.write('sudo mv /mnt/boto.cfg %s; ' % BotoConfigPath) |
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116 fp.write('mv /mnt/authorized_keys ~/.ssh/authorized_keys') |
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117 command = fp.getvalue() |
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118 print('running the following command on the remote server:') |
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119 print(command) |
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120 t = self.ssh_client.run(command) |
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121 print('\t%s' % t[0]) |
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122 print('\t%s' % t[1]) |
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123 print('...complete!') |
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124 print('registering image...') |
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125 self.image_id = self.server.ec2.register_image(name=prefix, image_location='%s/%s.manifest.xml' % (bucket, prefix)) |
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126 return self.image_id |
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127 |
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128 class CommandLineGetter(object): |
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129 |
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130 def get_ami_list(self): |
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131 my_amis = [] |
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132 for ami in self.ec2.get_all_images(): |
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133 # hack alert, need a better way to do this! |
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134 if ami.location.find('pyami') >= 0: |
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135 my_amis.append((ami.location, ami)) |
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136 return my_amis |
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137 |
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138 def get_region(self, params): |
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139 region = params.get('region', None) |
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140 if isinstance(region, basestring): |
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141 region = boto.ec2.get_region(region) |
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142 params['region'] = region |
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143 if not region: |
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144 prop = self.cls.find_property('region_name') |
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145 params['region'] = propget.get(prop, choices=boto.ec2.regions) |
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146 self.ec2 = params['region'].connect() |
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147 |
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148 def get_name(self, params): |
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149 if not params.get('name', None): |
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150 prop = self.cls.find_property('name') |
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151 params['name'] = propget.get(prop) |
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152 |
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153 def get_description(self, params): |
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154 if not params.get('description', None): |
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155 prop = self.cls.find_property('description') |
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156 params['description'] = propget.get(prop) |
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157 |
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158 def get_instance_type(self, params): |
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159 if not params.get('instance_type', None): |
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160 prop = StringProperty(name='instance_type', verbose_name='Instance Type', |
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161 choices=InstanceTypes) |
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162 params['instance_type'] = propget.get(prop) |
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163 |
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164 def get_quantity(self, params): |
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165 if not params.get('quantity', None): |
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166 prop = IntegerProperty(name='quantity', verbose_name='Number of Instances') |
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167 params['quantity'] = propget.get(prop) |
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168 |
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169 def get_zone(self, params): |
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170 if not params.get('zone', None): |
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171 prop = StringProperty(name='zone', verbose_name='EC2 Availability Zone', |
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172 choices=self.ec2.get_all_zones) |
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173 params['zone'] = propget.get(prop) |
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174 |
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175 def get_ami_id(self, params): |
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176 valid = False |
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177 while not valid: |
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178 ami = params.get('ami', None) |
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179 if not ami: |
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180 prop = StringProperty(name='ami', verbose_name='AMI') |
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181 ami = propget.get(prop) |
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182 try: |
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183 rs = self.ec2.get_all_images([ami]) |
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184 if len(rs) == 1: |
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185 valid = True |
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186 params['ami'] = rs[0] |
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187 except EC2ResponseError: |
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188 pass |
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189 |
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190 def get_group(self, params): |
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191 group = params.get('group', None) |
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192 if isinstance(group, basestring): |
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193 group_list = self.ec2.get_all_security_groups() |
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194 for g in group_list: |
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195 if g.name == group: |
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196 group = g |
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197 params['group'] = g |
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198 if not group: |
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199 prop = StringProperty(name='group', verbose_name='EC2 Security Group', |
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200 choices=self.ec2.get_all_security_groups) |
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201 params['group'] = propget.get(prop) |
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202 |
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203 def get_key(self, params): |
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204 keypair = params.get('keypair', None) |
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205 if isinstance(keypair, basestring): |
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206 key_list = self.ec2.get_all_key_pairs() |
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207 for k in key_list: |
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208 if k.name == keypair: |
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209 keypair = k.name |
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210 params['keypair'] = k.name |
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211 if not keypair: |
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212 prop = StringProperty(name='keypair', verbose_name='EC2 KeyPair', |
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213 choices=self.ec2.get_all_key_pairs) |
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214 params['keypair'] = propget.get(prop).name |
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215 |
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216 def get(self, cls, params): |
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217 self.cls = cls |
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218 self.get_region(params) |
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219 self.ec2 = params['region'].connect() |
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220 self.get_name(params) |
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221 self.get_description(params) |
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222 self.get_instance_type(params) |
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223 self.get_zone(params) |
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224 self.get_quantity(params) |
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225 self.get_ami_id(params) |
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226 self.get_group(params) |
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227 self.get_key(params) |
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228 |
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229 class Server(Model): |
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230 |
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231 # |
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232 # The properties of this object consists of real properties for data that |
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233 # is not already stored in EC2 somewhere (e.g. name, description) plus |
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234 # calculated properties for all of the properties that are already in |
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235 # EC2 (e.g. hostname, security groups, etc.) |
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236 # |
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237 name = StringProperty(unique=True, verbose_name="Name") |
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238 description = StringProperty(verbose_name="Description") |
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239 region_name = StringProperty(verbose_name="EC2 Region Name") |
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240 instance_id = StringProperty(verbose_name="EC2 Instance ID") |
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241 elastic_ip = StringProperty(verbose_name="EC2 Elastic IP Address") |
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242 production = BooleanProperty(verbose_name="Is This Server Production", default=False) |
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243 ami_id = CalculatedProperty(verbose_name="AMI ID", calculated_type=str, use_method=True) |
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244 zone = CalculatedProperty(verbose_name="Availability Zone Name", calculated_type=str, use_method=True) |
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245 hostname = CalculatedProperty(verbose_name="Public DNS Name", calculated_type=str, use_method=True) |
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246 private_hostname = CalculatedProperty(verbose_name="Private DNS Name", calculated_type=str, use_method=True) |
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247 groups = CalculatedProperty(verbose_name="Security Groups", calculated_type=list, use_method=True) |
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248 security_group = CalculatedProperty(verbose_name="Primary Security Group Name", calculated_type=str, use_method=True) |
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249 key_name = CalculatedProperty(verbose_name="Key Name", calculated_type=str, use_method=True) |
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250 instance_type = CalculatedProperty(verbose_name="Instance Type", calculated_type=str, use_method=True) |
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251 status = CalculatedProperty(verbose_name="Current Status", calculated_type=str, use_method=True) |
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252 launch_time = CalculatedProperty(verbose_name="Server Launch Time", calculated_type=str, use_method=True) |
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253 console_output = CalculatedProperty(verbose_name="Console Output", calculated_type=open, use_method=True) |
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254 |
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255 packages = [] |
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256 plugins = [] |
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257 |
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258 @classmethod |
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259 def add_credentials(cls, cfg, aws_access_key_id, aws_secret_access_key): |
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260 if not cfg.has_section('Credentials'): |
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261 cfg.add_section('Credentials') |
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262 cfg.set('Credentials', 'aws_access_key_id', aws_access_key_id) |
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263 cfg.set('Credentials', 'aws_secret_access_key', aws_secret_access_key) |
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264 if not cfg.has_section('DB_Server'): |
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265 cfg.add_section('DB_Server') |
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266 cfg.set('DB_Server', 'db_type', 'SimpleDB') |
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267 cfg.set('DB_Server', 'db_name', cls._manager.domain.name) |
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268 |
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269 @classmethod |
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270 def create(cls, config_file=None, logical_volume = None, cfg = None, **params): |
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271 """ |
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272 Create a new instance based on the specified configuration file or the specified |
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273 configuration and the passed in parameters. |
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274 |
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275 If the config_file argument is not None, the configuration is read from there. |
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276 Otherwise, the cfg argument is used. |
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277 |
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278 The config file may include other config files with a #import reference. The included |
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279 config files must reside in the same directory as the specified file. |
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280 |
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281 The logical_volume argument, if supplied, will be used to get the current physical |
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282 volume ID and use that as an override of the value specified in the config file. This |
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283 may be useful for debugging purposes when you want to debug with a production config |
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284 file but a test Volume. |
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285 |
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286 The dictionary argument may be used to override any EC2 configuration values in the |
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287 config file. |
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288 """ |
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289 if config_file: |
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290 cfg = Config(path=config_file) |
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291 if cfg.has_section('EC2'): |
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292 # include any EC2 configuration values that aren't specified in params: |
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293 for option in cfg.options('EC2'): |
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294 if option not in params: |
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295 params[option] = cfg.get('EC2', option) |
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296 getter = CommandLineGetter() |
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297 getter.get(cls, params) |
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298 region = params.get('region') |
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299 ec2 = region.connect() |
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300 cls.add_credentials(cfg, ec2.aws_access_key_id, ec2.aws_secret_access_key) |
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301 ami = params.get('ami') |
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302 kp = params.get('keypair') |
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303 group = params.get('group') |
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304 zone = params.get('zone') |
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305 # deal with possibly passed in logical volume: |
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306 if logical_volume != None: |
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307 cfg.set('EBS', 'logical_volume_name', logical_volume.name) |
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308 cfg_fp = StringIO() |
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309 cfg.write(cfg_fp) |
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310 # deal with the possibility that zone and/or keypair are strings read from the config file: |
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311 if isinstance(zone, Zone): |
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312 zone = zone.name |
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313 if isinstance(kp, KeyPair): |
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314 kp = kp.name |
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315 reservation = ami.run(min_count=1, |
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316 max_count=params.get('quantity', 1), |
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317 key_name=kp, |
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318 security_groups=[group], |
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319 instance_type=params.get('instance_type'), |
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320 placement = zone, |
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321 user_data = cfg_fp.getvalue()) |
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322 l = [] |
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323 i = 0 |
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324 elastic_ip = params.get('elastic_ip') |
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325 instances = reservation.instances |
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326 if elastic_ip is not None and instances.__len__() > 0: |
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327 instance = instances[0] |
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328 print('Waiting for instance to start so we can set its elastic IP address...') |
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329 # Sometimes we get a message from ec2 that says that the instance does not exist. |
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330 # Hopefully the following delay will giv eec2 enough time to get to a stable state: |
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331 time.sleep(5) |
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332 while instance.update() != 'running': |
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333 time.sleep(1) |
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334 instance.use_ip(elastic_ip) |
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335 print('set the elastic IP of the first instance to %s' % elastic_ip) |
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336 for instance in instances: |
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337 s = cls() |
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338 s.ec2 = ec2 |
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339 s.name = params.get('name') + '' if i==0 else str(i) |
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340 s.description = params.get('description') |
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341 s.region_name = region.name |
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342 s.instance_id = instance.id |
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343 if elastic_ip and i == 0: |
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344 s.elastic_ip = elastic_ip |
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345 s.put() |
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346 l.append(s) |
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347 i += 1 |
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348 return l |
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349 |
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350 @classmethod |
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351 def create_from_instance_id(cls, instance_id, name, description=''): |
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352 regions = boto.ec2.regions() |
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353 for region in regions: |
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354 ec2 = region.connect() |
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355 try: |
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356 rs = ec2.get_all_reservations([instance_id]) |
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357 except: |
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358 rs = [] |
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359 if len(rs) == 1: |
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360 s = cls() |
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361 s.ec2 = ec2 |
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362 s.name = name |
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363 s.description = description |
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364 s.region_name = region.name |
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365 s.instance_id = instance_id |
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366 s._reservation = rs[0] |
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367 for instance in s._reservation.instances: |
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368 if instance.id == instance_id: |
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369 s._instance = instance |
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370 s.put() |
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371 return s |
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372 return None |
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373 |
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374 @classmethod |
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375 def create_from_current_instances(cls): |
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376 servers = [] |
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377 regions = boto.ec2.regions() |
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378 for region in regions: |
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379 ec2 = region.connect() |
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380 rs = ec2.get_all_reservations() |
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381 for reservation in rs: |
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382 for instance in reservation.instances: |
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383 try: |
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384 next(Server.find(instance_id=instance.id)) |
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385 boto.log.info('Server for %s already exists' % instance.id) |
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386 except StopIteration: |
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387 s = cls() |
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388 s.ec2 = ec2 |
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389 s.name = instance.id |
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390 s.region_name = region.name |
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391 s.instance_id = instance.id |
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392 s._reservation = reservation |
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393 s.put() |
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394 servers.append(s) |
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395 return servers |
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396 |
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397 def __init__(self, id=None, **kw): |
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398 super(Server, self).__init__(id, **kw) |
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399 self.ssh_key_file = None |
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400 self.ec2 = None |
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401 self._cmdshell = None |
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402 self._reservation = None |
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403 self._instance = None |
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404 self._setup_ec2() |
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405 |
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406 def _setup_ec2(self): |
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407 if self.ec2 and self._instance and self._reservation: |
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408 return |
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409 if self.id: |
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410 if self.region_name: |
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411 for region in boto.ec2.regions(): |
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412 if region.name == self.region_name: |
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413 self.ec2 = region.connect() |
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414 if self.instance_id and not self._instance: |
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415 try: |
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416 rs = self.ec2.get_all_reservations([self.instance_id]) |
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417 if len(rs) >= 1: |
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418 for instance in rs[0].instances: |
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419 if instance.id == self.instance_id: |
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420 self._reservation = rs[0] |
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421 self._instance = instance |
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422 except EC2ResponseError: |
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423 pass |
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424 |
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425 def _status(self): |
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426 status = '' |
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427 if self._instance: |
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428 self._instance.update() |
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429 status = self._instance.state |
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430 return status |
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431 |
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432 def _hostname(self): |
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433 hostname = '' |
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434 if self._instance: |
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435 hostname = self._instance.public_dns_name |
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436 return hostname |
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437 |
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438 def _private_hostname(self): |
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439 hostname = '' |
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440 if self._instance: |
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441 hostname = self._instance.private_dns_name |
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442 return hostname |
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443 |
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444 def _instance_type(self): |
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445 it = '' |
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446 if self._instance: |
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447 it = self._instance.instance_type |
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448 return it |
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449 |
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450 def _launch_time(self): |
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451 lt = '' |
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452 if self._instance: |
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453 lt = self._instance.launch_time |
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454 return lt |
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455 |
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456 def _console_output(self): |
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457 co = '' |
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458 if self._instance: |
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459 co = self._instance.get_console_output() |
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460 return co |
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461 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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462 def _groups(self): |
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463 gn = [] |
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464 if self._reservation: |
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465 gn = self._reservation.groups |
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466 return gn |
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467 |
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468 def _security_group(self): |
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469 groups = self._groups() |
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470 if len(groups) >= 1: |
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471 return groups[0].id |
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472 return "" |
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473 |
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474 def _zone(self): |
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475 zone = None |
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476 if self._instance: |
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477 zone = self._instance.placement |
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478 return zone |
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479 |
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480 def _key_name(self): |
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481 kn = None |
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482 if self._instance: |
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483 kn = self._instance.key_name |
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484 return kn |
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485 |
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486 def put(self): |
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487 super(Server, self).put() |
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488 self._setup_ec2() |
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489 |
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490 def delete(self): |
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491 if self.production: |
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492 raise ValueError("Can't delete a production server") |
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493 #self.stop() |
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494 super(Server, self).delete() |
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495 |
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496 def stop(self): |
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497 if self.production: |
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498 raise ValueError("Can't delete a production server") |
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499 if self._instance: |
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500 self._instance.stop() |
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501 |
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502 def terminate(self): |
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503 if self.production: |
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504 raise ValueError("Can't delete a production server") |
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505 if self._instance: |
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506 self._instance.terminate() |
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507 |
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508 def reboot(self): |
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509 if self._instance: |
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510 self._instance.reboot() |
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511 |
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512 def wait(self): |
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513 while self.status != 'running': |
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514 time.sleep(5) |
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|
515 |
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516 def get_ssh_key_file(self): |
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517 if not self.ssh_key_file: |
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518 ssh_dir = os.path.expanduser('~/.ssh') |
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519 if os.path.isdir(ssh_dir): |
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520 ssh_file = os.path.join(ssh_dir, '%s.pem' % self.key_name) |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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521 if os.path.isfile(ssh_file): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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522 self.ssh_key_file = ssh_file |
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523 if not self.ssh_key_file: |
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524 iobject = IObject() |
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525 self.ssh_key_file = iobject.get_filename('Path to OpenSSH Key file') |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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526 return self.ssh_key_file |
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parents:
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changeset
|
527 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
528 def get_cmdshell(self): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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529 if not self._cmdshell: |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
530 from boto.manage import cmdshell |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
531 self.get_ssh_key_file() |
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parents:
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532 self._cmdshell = cmdshell.start(self) |
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parents:
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533 return self._cmdshell |
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parents:
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|
534 |
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parents:
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|
535 def reset_cmdshell(self): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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536 self._cmdshell = None |
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parents:
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|
537 |
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parents:
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|
538 def run(self, command): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
539 with closing(self.get_cmdshell()) as cmd: |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
540 status = cmd.run(command) |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
541 return status |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
542 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
543 def get_bundler(self, uname='root'): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
544 self.get_ssh_key_file() |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
545 return Bundler(self, uname) |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
546 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
547 def get_ssh_client(self, uname='root', ssh_pwd=None): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
548 from boto.manage.cmdshell import SSHClient |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
549 self.get_ssh_key_file() |
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parents:
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changeset
|
550 return SSHClient(self, uname=uname, ssh_pwd=ssh_pwd) |
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parents:
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changeset
|
551 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
552 def install(self, pkg): |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
553 return self.run('apt-get -y install %s' % pkg) |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
554 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
555 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
556 |