Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/manage/cmdshell.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 # Copyright (c) 2006-2009 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 The cmdshell module uses the paramiko package to create SSH connections
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23 to the servers that are represented by instance objects. The module has
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24 functions for running commands, managing files, and opening interactive
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25 shell sessions over those connections.
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26 """
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27 from boto.mashups.interactive import interactive_shell
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28 import boto
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29 import os
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30 import time
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31 import shutil
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32 import paramiko
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33 import socket
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34 import subprocess
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35
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36 from boto.compat import StringIO
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37
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38 class SSHClient(object):
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39 """
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40 This class creates a paramiko.SSHClient() object that represents
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41 a session with an SSH server. You can use the SSHClient object to send
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42 commands to the remote host and manipulate files on the remote host.
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43
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44 :ivar server: A Server object or FakeServer object.
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45 :ivar host_key_file: The path to the user's .ssh key files.
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46 :ivar uname: The username for the SSH connection. Default = 'root'.
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47 :ivar timeout: The optional timeout variable for the TCP connection.
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48 :ivar ssh_pwd: An optional password to use for authentication or for
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49 unlocking the private key.
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50 """
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51 def __init__(self, server,
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52 host_key_file='~/.ssh/known_hosts',
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53 uname='root', timeout=None, ssh_pwd=None):
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54 self.server = server
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55 self.host_key_file = host_key_file
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56 self.uname = uname
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57 self._timeout = timeout
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58 self._pkey = paramiko.RSAKey.from_private_key_file(server.ssh_key_file,
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59 password=ssh_pwd)
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60 self._ssh_client = paramiko.SSHClient()
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61 self._ssh_client.load_system_host_keys()
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62 self._ssh_client.load_host_keys(os.path.expanduser(host_key_file))
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63 self._ssh_client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
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64 self.connect()
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65
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66 def connect(self, num_retries=5):
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67 """
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68 Connect to an SSH server and authenticate with it.
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69
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70 :type num_retries: int
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71 :param num_retries: The maximum number of connection attempts.
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72 """
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73 retry = 0
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74 while retry < num_retries:
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75 try:
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76 self._ssh_client.connect(self.server.hostname,
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77 username=self.uname,
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78 pkey=self._pkey,
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79 timeout=self._timeout)
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80 return
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81 except socket.error as xxx_todo_changeme:
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82 (value, message) = xxx_todo_changeme.args
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83 if value in (51, 61, 111):
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84 print('SSH Connection refused, will retry in 5 seconds')
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85 time.sleep(5)
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86 retry += 1
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87 else:
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88 raise
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89 except paramiko.BadHostKeyException:
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90 print("%s has an entry in ~/.ssh/known_hosts and it doesn't match" % self.server.hostname)
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91 print('Edit that file to remove the entry and then hit return to try again')
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92 raw_input('Hit Enter when ready')
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93 retry += 1
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94 except EOFError:
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95 print('Unexpected Error from SSH Connection, retry in 5 seconds')
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96 time.sleep(5)
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97 retry += 1
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98 print('Could not establish SSH connection')
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99
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100 def open_sftp(self):
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101 """
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102 Open an SFTP session on the SSH server.
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103
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104 :rtype: :class:`paramiko.sftp_client.SFTPClient`
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105 :return: An SFTP client object.
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106 """
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107 return self._ssh_client.open_sftp()
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108
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109 def get_file(self, src, dst):
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110 """
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111 Open an SFTP session on the remote host, and copy a file from
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112 the remote host to the specified path on the local host.
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113
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114 :type src: string
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115 :param src: The path to the target file on the remote host.
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116
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117 :type dst: string
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118 :param dst: The path on your local host where you want to
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119 store the file.
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120 """
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121 sftp_client = self.open_sftp()
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122 sftp_client.get(src, dst)
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123
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124 def put_file(self, src, dst):
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125 """
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126 Open an SFTP session on the remote host, and copy a file from
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127 the local host to the specified path on the remote host.
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128
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129 :type src: string
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130 :param src: The path to the target file on your local host.
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131
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132 :type dst: string
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133 :param dst: The path on the remote host where you want to store
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134 the file.
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135 """
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136 sftp_client = self.open_sftp()
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137 sftp_client.put(src, dst)
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138
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139 def open(self, filename, mode='r', bufsize=-1):
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140 """
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141 Open an SFTP session to the remote host, and open a file on
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142 that host.
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143
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144 :type filename: string
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145 :param filename: The path to the file on the remote host.
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146
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147 :type mode: string
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148 :param mode: The file interaction mode.
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149
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150 :type bufsize: integer
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151 :param bufsize: The file buffer size.
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152
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153 :rtype: :class:`paramiko.sftp_file.SFTPFile`
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154 :return: A paramiko proxy object for a file on the remote server.
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155 """
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156 sftp_client = self.open_sftp()
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157 return sftp_client.open(filename, mode, bufsize)
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158
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159 def listdir(self, path):
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160 """
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161 List all of the files and subdirectories at the specified path
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162 on the remote host.
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163
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164 :type path: string
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165 :param path: The base path from which to obtain the list.
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166
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167 :rtype: list
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168 :return: A list of files and subdirectories at the specified path.
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169 """
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170 sftp_client = self.open_sftp()
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171 return sftp_client.listdir(path)
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172
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173 def isdir(self, path):
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174 """
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175 Check the specified path on the remote host to determine if
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176 it is a directory.
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177
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178 :type path: string
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179 :param path: The path to the directory that you want to check.
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180
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181 :rtype: integer
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182 :return: If the path is a directory, the function returns 1.
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183 If the path is a file or an invalid path, the function
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184 returns 0.
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185 """
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186 status = self.run('[ -d %s ] || echo "FALSE"' % path)
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187 if status[1].startswith('FALSE'):
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188 return 0
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189 return 1
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190
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191 def exists(self, path):
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192 """
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193 Check the remote host for the specified path, or a file
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194 at the specified path. This function returns 1 if the
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195 path or the file exist on the remote host, and returns 0 if
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196 the path or the file does not exist on the remote host.
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197
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198 :type path: string
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199 :param path: The path to the directory or file that you want to check.
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200
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201 :rtype: integer
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202 :return: If the path or the file exist, the function returns 1.
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203 If the path or the file do not exist on the remote host,
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204 the function returns 0.
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205 """
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206
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207 status = self.run('[ -a %s ] || echo "FALSE"' % path)
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208 if status[1].startswith('FALSE'):
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209 return 0
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210 return 1
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211
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212 def shell(self):
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213 """
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214 Start an interactive shell session with the remote host.
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215 """
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216 channel = self._ssh_client.invoke_shell()
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217 interactive_shell(channel)
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218
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219 def run(self, command):
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220 """
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221 Run a command on the remote host.
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222
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223 :type command: string
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224 :param command: The command that you want to send to the remote host.
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225
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226 :rtype: tuple
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227 :return: This function returns a tuple that contains an integer status,
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228 the stdout from the command, and the stderr from the command.
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229
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230 """
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231 boto.log.debug('running:%s on %s' % (command, self.server.instance_id))
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232 status = 0
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233 try:
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234 t = self._ssh_client.exec_command(command)
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235 except paramiko.SSHException:
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236 status = 1
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237 std_out = t[1].read()
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238 std_err = t[2].read()
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239 t[0].close()
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240 t[1].close()
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241 t[2].close()
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242 boto.log.debug('stdout: %s' % std_out)
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243 boto.log.debug('stderr: %s' % std_err)
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244 return (status, std_out, std_err)
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245
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246 def run_pty(self, command):
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247 """
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248 Request a pseudo-terminal from a server, and execute a command on that
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249 server.
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250
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251 :type command: string
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252 :param command: The command that you want to run on the remote host.
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253
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254 :rtype: :class:`paramiko.channel.Channel`
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255 :return: An open channel object.
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256 """
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257 boto.log.debug('running:%s on %s' % (command, self.server.instance_id))
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258 channel = self._ssh_client.get_transport().open_session()
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259 channel.get_pty()
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260 channel.exec_command(command)
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261 return channel
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262
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263 def close(self):
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264 """
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265 Close an SSH session and any open channels that are tied to it.
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266 """
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267 transport = self._ssh_client.get_transport()
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268 transport.close()
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269 self.server.reset_cmdshell()
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270
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271 class LocalClient(object):
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272 """
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273 :ivar server: A Server object or FakeServer object.
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274 :ivar host_key_file: The path to the user's .ssh key files.
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275 :ivar uname: The username for the SSH connection. Default = 'root'.
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276 """
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277 def __init__(self, server, host_key_file=None, uname='root'):
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278 self.server = server
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279 self.host_key_file = host_key_file
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280 self.uname = uname
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281
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282 def get_file(self, src, dst):
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283 """
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284 Copy a file from one directory to another.
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285 """
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286 shutil.copyfile(src, dst)
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287
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288 def put_file(self, src, dst):
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289 """
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290 Copy a file from one directory to another.
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291 """
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292 shutil.copyfile(src, dst)
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293
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294 def listdir(self, path):
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295 """
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296 List all of the files and subdirectories at the specified path.
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297
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298 :rtype: list
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299 :return: Return a list containing the names of the entries
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300 in the directory given by path.
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301 """
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302 return os.listdir(path)
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303
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304 def isdir(self, path):
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305 """
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306 Check the specified path to determine if it is a directory.
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307
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308 :rtype: boolean
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309 :return: Returns True if the path is an existing directory.
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310 """
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311 return os.path.isdir(path)
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312
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313 def exists(self, path):
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314 """
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315 Check for the specified path, or check a file at the specified path.
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316
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317 :rtype: boolean
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318 :return: If the path or the file exist, the function returns True.
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319 """
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320 return os.path.exists(path)
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321
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322 def shell(self):
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323 raise NotImplementedError('shell not supported with LocalClient')
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324
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325 def run(self):
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326 """
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327 Open a subprocess and run a command on the local host.
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328
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329 :rtype: tuple
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330 :return: This function returns a tuple that contains an integer status
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331 and a string with the combined stdout and stderr output.
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332 """
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333 boto.log.info('running:%s' % self.command)
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334 log_fp = StringIO()
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335 process = subprocess.Popen(self.command, shell=True, stdin=subprocess.PIPE,
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336 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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337 while process.poll() is None:
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338 time.sleep(1)
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339 t = process.communicate()
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340 log_fp.write(t[0])
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341 log_fp.write(t[1])
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342 boto.log.info(log_fp.getvalue())
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343 boto.log.info('output: %s' % log_fp.getvalue())
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344 return (process.returncode, log_fp.getvalue())
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345
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346 def close(self):
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347 pass
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348
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349 class FakeServer(object):
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350 """
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351 This object has a subset of the variables that are normally in a
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352 :class:`boto.manage.server.Server` object. You can use this FakeServer
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353 object to create a :class:`boto.manage.SSHClient` object if you
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354 don't have a real Server object.
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355
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356 :ivar instance: A boto Instance object.
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357 :ivar ssh_key_file: The path to the SSH key file.
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358 """
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359 def __init__(self, instance, ssh_key_file):
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360 self.instance = instance
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361 self.ssh_key_file = ssh_key_file
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362 self.hostname = instance.dns_name
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363 self.instance_id = self.instance.id
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364
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365 def start(server):
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366 """
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367 Connect to the specified server.
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368
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369 :return: If the server is local, the function returns a
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370 :class:`boto.manage.cmdshell.LocalClient` object.
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371 If the server is remote, the function returns a
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372 :class:`boto.manage.cmdshell.SSHClient` object.
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373 """
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374 instance_id = boto.config.get('Instance', 'instance-id', None)
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375 if instance_id == server.instance_id:
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376 return LocalClient(server)
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377 else:
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378 return SSHClient(server)
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379
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380 def sshclient_from_instance(instance, ssh_key_file,
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381 host_key_file='~/.ssh/known_hosts',
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382 user_name='root', ssh_pwd=None):
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383 """
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384 Create and return an SSHClient object given an
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385 instance object.
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386
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387 :type instance: :class`boto.ec2.instance.Instance` object
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388 :param instance: The instance object.
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389
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390 :type ssh_key_file: string
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391 :param ssh_key_file: A path to the private key file that is
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392 used to log into the instance.
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393
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394 :type host_key_file: string
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395 :param host_key_file: A path to the known_hosts file used
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396 by the SSH client.
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397 Defaults to ~/.ssh/known_hosts
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398 :type user_name: string
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399 :param user_name: The username to use when logging into
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400 the instance. Defaults to root.
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401
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402 :type ssh_pwd: string
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403 :param ssh_pwd: The passphrase, if any, associated with
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404 private key.
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405 """
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406 s = FakeServer(instance, ssh_key_file)
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407 return SSHClient(s, host_key_file, user_name, ssh_pwd)