Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/mashups/server.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 # Copyright (c) 2006,2007 Mitch Garnaat http://garnaat.org/
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2 #
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3 # Permission is hereby granted, free of charge, to any person obtaining a
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4 # copy of this software and associated documentation files (the
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5 # "Software"), to deal in the Software without restriction, including
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6 # without limitation the rights to use, copy, modify, merge, publish, dis-
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7 # tribute, sublicense, and/or sell copies of the Software, and to permit
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8 # persons to whom the Software is furnished to do so, subject to the fol-
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9 # lowing conditions:
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10 #
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11 # The above copyright notice and this permission notice shall be included
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12 # in all copies or substantial portions of the Software.
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13 #
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14 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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15 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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16 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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17 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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18 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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19 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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20 # IN THE SOFTWARE.
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21 """
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22 High-level abstraction of an EC2 server
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23 """
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24
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25 import boto
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26 import boto.utils
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27 from boto.compat import StringIO
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28 from boto.mashups.iobject import IObject
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29 from boto.pyami.config import Config, BotoConfigPath
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30 from boto.mashups.interactive import interactive_shell
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31 from boto.sdb.db.model import Model
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32 from boto.sdb.db.property import StringProperty
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33 import os
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34
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35
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36 class ServerSet(list):
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37
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38 def __getattr__(self, name):
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39 results = []
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40 is_callable = False
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41 for server in self:
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42 try:
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43 val = getattr(server, name)
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44 if callable(val):
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45 is_callable = True
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46 results.append(val)
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47 except:
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48 results.append(None)
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49 if is_callable:
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50 self.map_list = results
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51 return self.map
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52 return results
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53
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54 def map(self, *args):
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55 results = []
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56 for fn in self.map_list:
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57 results.append(fn(*args))
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58 return results
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59
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60 class Server(Model):
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61
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62 @property
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63 def ec2(self):
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64 if self._ec2 is None:
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65 self._ec2 = boto.connect_ec2()
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66 return self._ec2
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67
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68 @classmethod
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69 def Inventory(cls):
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70 """
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71 Returns a list of Server instances, one for each Server object
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72 persisted in the db
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73 """
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74 l = ServerSet()
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75 rs = cls.find()
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76 for server in rs:
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77 l.append(server)
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78 return l
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79
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80 @classmethod
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81 def Register(cls, name, instance_id, description=''):
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82 s = cls()
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83 s.name = name
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84 s.instance_id = instance_id
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85 s.description = description
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86 s.save()
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87 return s
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88
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89 def __init__(self, id=None, **kw):
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90 super(Server, self).__init__(id, **kw)
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91 self._reservation = None
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92 self._instance = None
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93 self._ssh_client = None
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94 self._pkey = None
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95 self._config = None
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96 self._ec2 = None
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97
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98 name = StringProperty(unique=True, verbose_name="Name")
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99 instance_id = StringProperty(verbose_name="Instance ID")
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100 config_uri = StringProperty()
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101 ami_id = StringProperty(verbose_name="AMI ID")
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102 zone = StringProperty(verbose_name="Availability Zone")
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103 security_group = StringProperty(verbose_name="Security Group", default="default")
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104 key_name = StringProperty(verbose_name="Key Name")
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105 elastic_ip = StringProperty(verbose_name="Elastic IP")
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106 instance_type = StringProperty(verbose_name="Instance Type")
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107 description = StringProperty(verbose_name="Description")
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108 log = StringProperty()
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109
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110 def setReadOnly(self, value):
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111 raise AttributeError
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112
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113 def getInstance(self):
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114 if not self._instance:
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115 if self.instance_id:
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116 try:
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117 rs = self.ec2.get_all_reservations([self.instance_id])
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118 except:
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119 return None
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120 if len(rs) > 0:
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121 self._reservation = rs[0]
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122 self._instance = self._reservation.instances[0]
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123 return self._instance
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124
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125 instance = property(getInstance, setReadOnly, None, 'The Instance for the server')
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126
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127 def getAMI(self):
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128 if self.instance:
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129 return self.instance.image_id
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130
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131 ami = property(getAMI, setReadOnly, None, 'The AMI for the server')
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132
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133 def getStatus(self):
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134 if self.instance:
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135 self.instance.update()
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136 return self.instance.state
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137
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138 status = property(getStatus, setReadOnly, None,
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139 'The status of the server')
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140
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141 def getHostname(self):
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142 if self.instance:
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143 return self.instance.public_dns_name
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144
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145 hostname = property(getHostname, setReadOnly, None,
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146 'The public DNS name of the server')
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147
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148 def getPrivateHostname(self):
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149 if self.instance:
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150 return self.instance.private_dns_name
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151
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152 private_hostname = property(getPrivateHostname, setReadOnly, None,
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153 'The private DNS name of the server')
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154
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155 def getLaunchTime(self):
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156 if self.instance:
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157 return self.instance.launch_time
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158
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159 launch_time = property(getLaunchTime, setReadOnly, None,
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160 'The time the Server was started')
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161
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162 def getConsoleOutput(self):
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163 if self.instance:
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164 return self.instance.get_console_output()
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165
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166 console_output = property(getConsoleOutput, setReadOnly, None,
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167 'Retrieve the console output for server')
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168
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169 def getGroups(self):
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170 if self._reservation:
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171 return self._reservation.groups
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172 else:
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173 return None
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174
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175 groups = property(getGroups, setReadOnly, None,
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176 'The Security Groups controlling access to this server')
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177
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178 def getConfig(self):
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179 if not self._config:
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180 remote_file = BotoConfigPath
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181 local_file = '%s.ini' % self.instance.id
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182 self.get_file(remote_file, local_file)
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183 self._config = Config(local_file)
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184 return self._config
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185
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186 def setConfig(self, config):
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187 local_file = '%s.ini' % self.instance.id
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188 fp = open(local_file)
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189 config.write(fp)
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190 fp.close()
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191 self.put_file(local_file, BotoConfigPath)
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192 self._config = config
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193
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194 config = property(getConfig, setConfig, None,
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195 'The instance data for this server')
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196
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197 def set_config(self, config):
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198 """
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199 Set SDB based config
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200 """
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201 self._config = config
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202 self._config.dump_to_sdb("botoConfigs", self.id)
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203
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204 def load_config(self):
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205 self._config = Config(do_load=False)
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206 self._config.load_from_sdb("botoConfigs", self.id)
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207
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208 def stop(self):
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209 if self.instance:
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210 self.instance.stop()
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211
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212 def start(self):
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213 self.stop()
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214 ec2 = boto.connect_ec2()
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215 ami = ec2.get_all_images(image_ids = [str(self.ami_id)])[0]
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216 groups = ec2.get_all_security_groups(groupnames=[str(self.security_group)])
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217 if not self._config:
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218 self.load_config()
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219 if not self._config.has_section("Credentials"):
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220 self._config.add_section("Credentials")
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221 self._config.set("Credentials", "aws_access_key_id", ec2.aws_access_key_id)
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222 self._config.set("Credentials", "aws_secret_access_key", ec2.aws_secret_access_key)
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223
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224 if not self._config.has_section("Pyami"):
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225 self._config.add_section("Pyami")
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226
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227 if self._manager.domain:
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228 self._config.set('Pyami', 'server_sdb_domain', self._manager.domain.name)
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229 self._config.set("Pyami", 'server_sdb_name', self.name)
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230
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231 cfg = StringIO()
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232 self._config.write(cfg)
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233 cfg = cfg.getvalue()
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234 r = ami.run(min_count=1,
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235 max_count=1,
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236 key_name=self.key_name,
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237 security_groups = groups,
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238 instance_type = self.instance_type,
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239 placement = self.zone,
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240 user_data = cfg)
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241 i = r.instances[0]
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242 self.instance_id = i.id
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243 self.put()
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244 if self.elastic_ip:
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245 ec2.associate_address(self.instance_id, self.elastic_ip)
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246
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247 def reboot(self):
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248 if self.instance:
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249 self.instance.reboot()
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250
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251 def get_ssh_client(self, key_file=None, host_key_file='~/.ssh/known_hosts',
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252 uname='root'):
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253 import paramiko
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254 if not self.instance:
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255 print('No instance yet!')
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256 return
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257 if not self._ssh_client:
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258 if not key_file:
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diff changeset
259 iobject = IObject()
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diff changeset
260 key_file = iobject.get_filename('Path to OpenSSH Key file')
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parents:
diff changeset
261 self._pkey = paramiko.RSAKey.from_private_key_file(key_file)
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diff changeset
262 self._ssh_client = paramiko.SSHClient()
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parents:
diff changeset
263 self._ssh_client.load_system_host_keys()
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parents:
diff changeset
264 self._ssh_client.load_host_keys(os.path.expanduser(host_key_file))
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parents:
diff changeset
265 self._ssh_client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
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diff changeset
266 self._ssh_client.connect(self.instance.public_dns_name,
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parents:
diff changeset
267 username=uname, pkey=self._pkey)
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diff changeset
268 return self._ssh_client
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diff changeset
269
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diff changeset
270 def get_file(self, remotepath, localpath):
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271 ssh_client = self.get_ssh_client()
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272 sftp_client = ssh_client.open_sftp()
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diff changeset
273 sftp_client.get(remotepath, localpath)
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diff changeset
274
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diff changeset
275 def put_file(self, localpath, remotepath):
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diff changeset
276 ssh_client = self.get_ssh_client()
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diff changeset
277 sftp_client = ssh_client.open_sftp()
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diff changeset
278 sftp_client.put(localpath, remotepath)
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279
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diff changeset
280 def listdir(self, remotepath):
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diff changeset
281 ssh_client = self.get_ssh_client()
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diff changeset
282 sftp_client = ssh_client.open_sftp()
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diff changeset
283 return sftp_client.listdir(remotepath)
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diff changeset
284
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diff changeset
285 def shell(self, key_file=None):
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diff changeset
286 ssh_client = self.get_ssh_client(key_file)
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diff changeset
287 channel = ssh_client.invoke_shell()
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diff changeset
288 interactive_shell(channel)
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289
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290 def bundle_image(self, prefix, key_file, cert_file, size):
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diff changeset
291 print('bundling image...')
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diff changeset
292 print('\tcopying cert and pk over to /mnt directory on server')
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diff changeset
293 ssh_client = self.get_ssh_client()
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diff changeset
294 sftp_client = ssh_client.open_sftp()
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diff changeset
295 path, name = os.path.split(key_file)
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diff changeset
296 remote_key_file = '/mnt/%s' % name
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diff changeset
297 self.put_file(key_file, remote_key_file)
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diff changeset
298 path, name = os.path.split(cert_file)
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diff changeset
299 remote_cert_file = '/mnt/%s' % name
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diff changeset
300 self.put_file(cert_file, remote_cert_file)
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diff changeset
301 print('\tdeleting %s' % BotoConfigPath)
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parents:
diff changeset
302 # delete the metadata.ini file if it exists
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parents:
diff changeset
303 try:
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diff changeset
304 sftp_client.remove(BotoConfigPath)
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diff changeset
305 except:
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parents:
diff changeset
306 pass
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diff changeset
307 command = 'sudo ec2-bundle-vol '
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parents:
diff changeset
308 command += '-c %s -k %s ' % (remote_cert_file, remote_key_file)
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parents:
diff changeset
309 command += '-u %s ' % self._reservation.owner_id
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diff changeset
310 command += '-p %s ' % prefix
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diff changeset
311 command += '-s %d ' % size
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diff changeset
312 command += '-d /mnt '
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parents:
diff changeset
313 if self.instance.instance_type == 'm1.small' or self.instance_type == 'c1.medium':
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diff changeset
314 command += '-r i386'
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diff changeset
315 else:
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diff changeset
316 command += '-r x86_64'
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diff changeset
317 print('\t%s' % command)
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diff changeset
318 t = ssh_client.exec_command(command)
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diff changeset
319 response = t[1].read()
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parents:
diff changeset
320 print('\t%s' % response)
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parents:
diff changeset
321 print('\t%s' % t[2].read())
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parents:
diff changeset
322 print('...complete!')
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diff changeset
323
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parents:
diff changeset
324 def upload_bundle(self, bucket, prefix):
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diff changeset
325 print('uploading bundle...')
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parents:
diff changeset
326 command = 'ec2-upload-bundle '
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parents:
diff changeset
327 command += '-m /mnt/%s.manifest.xml ' % prefix
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parents:
diff changeset
328 command += '-b %s ' % bucket
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parents:
diff changeset
329 command += '-a %s ' % self.ec2.aws_access_key_id
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parents:
diff changeset
330 command += '-s %s ' % self.ec2.aws_secret_access_key
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parents:
diff changeset
331 print('\t%s' % command)
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parents:
diff changeset
332 ssh_client = self.get_ssh_client()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
333 t = ssh_client.exec_command(command)
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parents:
diff changeset
334 response = t[1].read()
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parents:
diff changeset
335 print('\t%s' % response)
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parents:
diff changeset
336 print('\t%s' % t[2].read())
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parents:
diff changeset
337 print('...complete!')
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parents:
diff changeset
338
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parents:
diff changeset
339 def create_image(self, bucket=None, prefix=None, key_file=None, cert_file=None, size=None):
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parents:
diff changeset
340 iobject = IObject()
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diff changeset
341 if not bucket:
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parents:
diff changeset
342 bucket = iobject.get_string('Name of S3 bucket')
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parents:
diff changeset
343 if not prefix:
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parents:
diff changeset
344 prefix = iobject.get_string('Prefix for AMI file')
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parents:
diff changeset
345 if not key_file:
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parents:
diff changeset
346 key_file = iobject.get_filename('Path to RSA private key file')
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parents:
diff changeset
347 if not cert_file:
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parents:
diff changeset
348 cert_file = iobject.get_filename('Path to RSA public cert file')
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parents:
diff changeset
349 if not size:
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parents:
diff changeset
350 size = iobject.get_int('Size (in MB) of bundled image')
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parents:
diff changeset
351 self.bundle_image(prefix, key_file, cert_file, size)
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parents:
diff changeset
352 self.upload_bundle(bucket, prefix)
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parents:
diff changeset
353 print('registering image...')
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parents:
diff changeset
354 self.image_id = self.ec2.register_image('%s/%s.manifest.xml' % (bucket, prefix))
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parents:
diff changeset
355 return self.image_id
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parents:
diff changeset
356
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parents:
diff changeset
357 def attach_volume(self, volume, device="/dev/sdp"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
358 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
359 Attach an EBS volume to this server
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
360
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parents:
diff changeset
361 :param volume: EBS Volume to attach
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parents:
diff changeset
362 :type volume: boto.ec2.volume.Volume
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parents:
diff changeset
363
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
364 :param device: Device to attach to (default to /dev/sdp)
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parents:
diff changeset
365 :type device: string
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parents:
diff changeset
366 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
367 if hasattr(volume, "id"):
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parents:
diff changeset
368 volume_id = volume.id
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parents:
diff changeset
369 else:
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parents:
diff changeset
370 volume_id = volume
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parents:
diff changeset
371 return self.ec2.attach_volume(volume_id=volume_id, instance_id=self.instance_id, device=device)
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parents:
diff changeset
372
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parents:
diff changeset
373 def detach_volume(self, volume):
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parents:
diff changeset
374 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
375 Detach an EBS volume from this server
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
376
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
377 :param volume: EBS Volume to detach
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parents:
diff changeset
378 :type volume: boto.ec2.volume.Volume
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parents:
diff changeset
379 """
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parents:
diff changeset
380 if hasattr(volume, "id"):
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parents:
diff changeset
381 volume_id = volume.id
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parents:
diff changeset
382 else:
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parents:
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383 volume_id = volume
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384 return self.ec2.detach_volume(volume_id=volume_id, instance_id=self.instance_id)
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385
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386 def install_package(self, package_name):
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387 print('installing %s...' % package_name)
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388 command = 'yum -y install %s' % package_name
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389 print('\t%s' % command)
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390 ssh_client = self.get_ssh_client()
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391 t = ssh_client.exec_command(command)
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392 response = t[1].read()
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393 print('\t%s' % response)
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394 print('\t%s' % t[2].read())
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395 print('...complete!')