Mercurial > repos > shellac > guppy_basecaller
comparison env/lib/python3.7/site-packages/boto/manage/cmdshell.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
| author | shellac |
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| date | Thu, 14 May 2020 14:56:58 -0400 |
| parents | 26e78fe6e8c4 |
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| 1:75ca89e9b81c | 2:6af9afd405e9 |
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| 1 # Copyright (c) 2006-2009 Mitch Garnaat http://garnaat.org/ | |
| 2 # | |
| 3 # Permission is hereby granted, free of charge, to any person obtaining a | |
| 4 # copy of this software and associated documentation files (the | |
| 5 # "Software"), to deal in the Software without restriction, including | |
| 6 # without limitation the rights to use, copy, modify, merge, publish, dis- | |
| 7 # tribute, sublicense, and/or sell copies of the Software, and to permit | |
| 8 # persons to whom the Software is furnished to do so, subject to the fol- | |
| 9 # lowing conditions: | |
| 10 # | |
| 11 # The above copyright notice and this permission notice shall be included | |
| 12 # in all copies or substantial portions of the Software. | |
| 13 # | |
| 14 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS | |
| 15 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- | |
| 16 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT | |
| 17 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, | |
| 18 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 19 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS | |
| 20 # IN THE SOFTWARE. | |
| 21 """ | |
| 22 The cmdshell module uses the paramiko package to create SSH connections | |
| 23 to the servers that are represented by instance objects. The module has | |
| 24 functions for running commands, managing files, and opening interactive | |
| 25 shell sessions over those connections. | |
| 26 """ | |
| 27 from boto.mashups.interactive import interactive_shell | |
| 28 import boto | |
| 29 import os | |
| 30 import time | |
| 31 import shutil | |
| 32 import paramiko | |
| 33 import socket | |
| 34 import subprocess | |
| 35 | |
| 36 from boto.compat import StringIO | |
| 37 | |
| 38 class SSHClient(object): | |
| 39 """ | |
| 40 This class creates a paramiko.SSHClient() object that represents | |
| 41 a session with an SSH server. You can use the SSHClient object to send | |
| 42 commands to the remote host and manipulate files on the remote host. | |
| 43 | |
| 44 :ivar server: A Server object or FakeServer object. | |
| 45 :ivar host_key_file: The path to the user's .ssh key files. | |
| 46 :ivar uname: The username for the SSH connection. Default = 'root'. | |
| 47 :ivar timeout: The optional timeout variable for the TCP connection. | |
| 48 :ivar ssh_pwd: An optional password to use for authentication or for | |
| 49 unlocking the private key. | |
| 50 """ | |
| 51 def __init__(self, server, | |
| 52 host_key_file='~/.ssh/known_hosts', | |
| 53 uname='root', timeout=None, ssh_pwd=None): | |
| 54 self.server = server | |
| 55 self.host_key_file = host_key_file | |
| 56 self.uname = uname | |
| 57 self._timeout = timeout | |
| 58 self._pkey = paramiko.RSAKey.from_private_key_file(server.ssh_key_file, | |
| 59 password=ssh_pwd) | |
| 60 self._ssh_client = paramiko.SSHClient() | |
| 61 self._ssh_client.load_system_host_keys() | |
| 62 self._ssh_client.load_host_keys(os.path.expanduser(host_key_file)) | |
| 63 self._ssh_client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) | |
| 64 self.connect() | |
| 65 | |
| 66 def connect(self, num_retries=5): | |
| 67 """ | |
| 68 Connect to an SSH server and authenticate with it. | |
| 69 | |
| 70 :type num_retries: int | |
| 71 :param num_retries: The maximum number of connection attempts. | |
| 72 """ | |
| 73 retry = 0 | |
| 74 while retry < num_retries: | |
| 75 try: | |
| 76 self._ssh_client.connect(self.server.hostname, | |
| 77 username=self.uname, | |
| 78 pkey=self._pkey, | |
| 79 timeout=self._timeout) | |
| 80 return | |
| 81 except socket.error as xxx_todo_changeme: | |
| 82 (value, message) = xxx_todo_changeme.args | |
| 83 if value in (51, 61, 111): | |
| 84 print('SSH Connection refused, will retry in 5 seconds') | |
| 85 time.sleep(5) | |
| 86 retry += 1 | |
| 87 else: | |
| 88 raise | |
| 89 except paramiko.BadHostKeyException: | |
| 90 print("%s has an entry in ~/.ssh/known_hosts and it doesn't match" % self.server.hostname) | |
| 91 print('Edit that file to remove the entry and then hit return to try again') | |
| 92 raw_input('Hit Enter when ready') | |
| 93 retry += 1 | |
| 94 except EOFError: | |
| 95 print('Unexpected Error from SSH Connection, retry in 5 seconds') | |
| 96 time.sleep(5) | |
| 97 retry += 1 | |
| 98 print('Could not establish SSH connection') | |
| 99 | |
| 100 def open_sftp(self): | |
| 101 """ | |
| 102 Open an SFTP session on the SSH server. | |
| 103 | |
| 104 :rtype: :class:`paramiko.sftp_client.SFTPClient` | |
| 105 :return: An SFTP client object. | |
| 106 """ | |
| 107 return self._ssh_client.open_sftp() | |
| 108 | |
| 109 def get_file(self, src, dst): | |
| 110 """ | |
| 111 Open an SFTP session on the remote host, and copy a file from | |
| 112 the remote host to the specified path on the local host. | |
| 113 | |
| 114 :type src: string | |
| 115 :param src: The path to the target file on the remote host. | |
| 116 | |
| 117 :type dst: string | |
| 118 :param dst: The path on your local host where you want to | |
| 119 store the file. | |
| 120 """ | |
| 121 sftp_client = self.open_sftp() | |
| 122 sftp_client.get(src, dst) | |
| 123 | |
| 124 def put_file(self, src, dst): | |
| 125 """ | |
| 126 Open an SFTP session on the remote host, and copy a file from | |
| 127 the local host to the specified path on the remote host. | |
| 128 | |
| 129 :type src: string | |
| 130 :param src: The path to the target file on your local host. | |
| 131 | |
| 132 :type dst: string | |
| 133 :param dst: The path on the remote host where you want to store | |
| 134 the file. | |
| 135 """ | |
| 136 sftp_client = self.open_sftp() | |
| 137 sftp_client.put(src, dst) | |
| 138 | |
| 139 def open(self, filename, mode='r', bufsize=-1): | |
| 140 """ | |
| 141 Open an SFTP session to the remote host, and open a file on | |
| 142 that host. | |
| 143 | |
| 144 :type filename: string | |
| 145 :param filename: The path to the file on the remote host. | |
| 146 | |
| 147 :type mode: string | |
| 148 :param mode: The file interaction mode. | |
| 149 | |
| 150 :type bufsize: integer | |
| 151 :param bufsize: The file buffer size. | |
| 152 | |
| 153 :rtype: :class:`paramiko.sftp_file.SFTPFile` | |
| 154 :return: A paramiko proxy object for a file on the remote server. | |
| 155 """ | |
| 156 sftp_client = self.open_sftp() | |
| 157 return sftp_client.open(filename, mode, bufsize) | |
| 158 | |
| 159 def listdir(self, path): | |
| 160 """ | |
| 161 List all of the files and subdirectories at the specified path | |
| 162 on the remote host. | |
| 163 | |
| 164 :type path: string | |
| 165 :param path: The base path from which to obtain the list. | |
| 166 | |
| 167 :rtype: list | |
| 168 :return: A list of files and subdirectories at the specified path. | |
| 169 """ | |
| 170 sftp_client = self.open_sftp() | |
| 171 return sftp_client.listdir(path) | |
| 172 | |
| 173 def isdir(self, path): | |
| 174 """ | |
| 175 Check the specified path on the remote host to determine if | |
| 176 it is a directory. | |
| 177 | |
| 178 :type path: string | |
| 179 :param path: The path to the directory that you want to check. | |
| 180 | |
| 181 :rtype: integer | |
| 182 :return: If the path is a directory, the function returns 1. | |
| 183 If the path is a file or an invalid path, the function | |
| 184 returns 0. | |
| 185 """ | |
| 186 status = self.run('[ -d %s ] || echo "FALSE"' % path) | |
| 187 if status[1].startswith('FALSE'): | |
| 188 return 0 | |
| 189 return 1 | |
| 190 | |
| 191 def exists(self, path): | |
| 192 """ | |
| 193 Check the remote host for the specified path, or a file | |
| 194 at the specified path. This function returns 1 if the | |
| 195 path or the file exist on the remote host, and returns 0 if | |
| 196 the path or the file does not exist on the remote host. | |
| 197 | |
| 198 :type path: string | |
| 199 :param path: The path to the directory or file that you want to check. | |
| 200 | |
| 201 :rtype: integer | |
| 202 :return: If the path or the file exist, the function returns 1. | |
| 203 If the path or the file do not exist on the remote host, | |
| 204 the function returns 0. | |
| 205 """ | |
| 206 | |
| 207 status = self.run('[ -a %s ] || echo "FALSE"' % path) | |
| 208 if status[1].startswith('FALSE'): | |
| 209 return 0 | |
| 210 return 1 | |
| 211 | |
| 212 def shell(self): | |
| 213 """ | |
| 214 Start an interactive shell session with the remote host. | |
| 215 """ | |
| 216 channel = self._ssh_client.invoke_shell() | |
| 217 interactive_shell(channel) | |
| 218 | |
| 219 def run(self, command): | |
| 220 """ | |
| 221 Run a command on the remote host. | |
| 222 | |
| 223 :type command: string | |
| 224 :param command: The command that you want to send to the remote host. | |
| 225 | |
| 226 :rtype: tuple | |
| 227 :return: This function returns a tuple that contains an integer status, | |
| 228 the stdout from the command, and the stderr from the command. | |
| 229 | |
| 230 """ | |
| 231 boto.log.debug('running:%s on %s' % (command, self.server.instance_id)) | |
| 232 status = 0 | |
| 233 try: | |
| 234 t = self._ssh_client.exec_command(command) | |
| 235 except paramiko.SSHException: | |
| 236 status = 1 | |
| 237 std_out = t[1].read() | |
| 238 std_err = t[2].read() | |
| 239 t[0].close() | |
| 240 t[1].close() | |
| 241 t[2].close() | |
| 242 boto.log.debug('stdout: %s' % std_out) | |
| 243 boto.log.debug('stderr: %s' % std_err) | |
| 244 return (status, std_out, std_err) | |
| 245 | |
| 246 def run_pty(self, command): | |
| 247 """ | |
| 248 Request a pseudo-terminal from a server, and execute a command on that | |
| 249 server. | |
| 250 | |
| 251 :type command: string | |
| 252 :param command: The command that you want to run on the remote host. | |
| 253 | |
| 254 :rtype: :class:`paramiko.channel.Channel` | |
| 255 :return: An open channel object. | |
| 256 """ | |
| 257 boto.log.debug('running:%s on %s' % (command, self.server.instance_id)) | |
| 258 channel = self._ssh_client.get_transport().open_session() | |
| 259 channel.get_pty() | |
| 260 channel.exec_command(command) | |
| 261 return channel | |
| 262 | |
| 263 def close(self): | |
| 264 """ | |
| 265 Close an SSH session and any open channels that are tied to it. | |
| 266 """ | |
| 267 transport = self._ssh_client.get_transport() | |
| 268 transport.close() | |
| 269 self.server.reset_cmdshell() | |
| 270 | |
| 271 class LocalClient(object): | |
| 272 """ | |
| 273 :ivar server: A Server object or FakeServer object. | |
| 274 :ivar host_key_file: The path to the user's .ssh key files. | |
| 275 :ivar uname: The username for the SSH connection. Default = 'root'. | |
| 276 """ | |
| 277 def __init__(self, server, host_key_file=None, uname='root'): | |
| 278 self.server = server | |
| 279 self.host_key_file = host_key_file | |
| 280 self.uname = uname | |
| 281 | |
| 282 def get_file(self, src, dst): | |
| 283 """ | |
| 284 Copy a file from one directory to another. | |
| 285 """ | |
| 286 shutil.copyfile(src, dst) | |
| 287 | |
| 288 def put_file(self, src, dst): | |
| 289 """ | |
| 290 Copy a file from one directory to another. | |
| 291 """ | |
| 292 shutil.copyfile(src, dst) | |
| 293 | |
| 294 def listdir(self, path): | |
| 295 """ | |
| 296 List all of the files and subdirectories at the specified path. | |
| 297 | |
| 298 :rtype: list | |
| 299 :return: Return a list containing the names of the entries | |
| 300 in the directory given by path. | |
| 301 """ | |
| 302 return os.listdir(path) | |
| 303 | |
| 304 def isdir(self, path): | |
| 305 """ | |
| 306 Check the specified path to determine if it is a directory. | |
| 307 | |
| 308 :rtype: boolean | |
| 309 :return: Returns True if the path is an existing directory. | |
| 310 """ | |
| 311 return os.path.isdir(path) | |
| 312 | |
| 313 def exists(self, path): | |
| 314 """ | |
| 315 Check for the specified path, or check a file at the specified path. | |
| 316 | |
| 317 :rtype: boolean | |
| 318 :return: If the path or the file exist, the function returns True. | |
| 319 """ | |
| 320 return os.path.exists(path) | |
| 321 | |
| 322 def shell(self): | |
| 323 raise NotImplementedError('shell not supported with LocalClient') | |
| 324 | |
| 325 def run(self): | |
| 326 """ | |
| 327 Open a subprocess and run a command on the local host. | |
| 328 | |
| 329 :rtype: tuple | |
| 330 :return: This function returns a tuple that contains an integer status | |
| 331 and a string with the combined stdout and stderr output. | |
| 332 """ | |
| 333 boto.log.info('running:%s' % self.command) | |
| 334 log_fp = StringIO() | |
| 335 process = subprocess.Popen(self.command, shell=True, stdin=subprocess.PIPE, | |
| 336 stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
| 337 while process.poll() is None: | |
| 338 time.sleep(1) | |
| 339 t = process.communicate() | |
| 340 log_fp.write(t[0]) | |
| 341 log_fp.write(t[1]) | |
| 342 boto.log.info(log_fp.getvalue()) | |
| 343 boto.log.info('output: %s' % log_fp.getvalue()) | |
| 344 return (process.returncode, log_fp.getvalue()) | |
| 345 | |
| 346 def close(self): | |
| 347 pass | |
| 348 | |
| 349 class FakeServer(object): | |
| 350 """ | |
| 351 This object has a subset of the variables that are normally in a | |
| 352 :class:`boto.manage.server.Server` object. You can use this FakeServer | |
| 353 object to create a :class:`boto.manage.SSHClient` object if you | |
| 354 don't have a real Server object. | |
| 355 | |
| 356 :ivar instance: A boto Instance object. | |
| 357 :ivar ssh_key_file: The path to the SSH key file. | |
| 358 """ | |
| 359 def __init__(self, instance, ssh_key_file): | |
| 360 self.instance = instance | |
| 361 self.ssh_key_file = ssh_key_file | |
| 362 self.hostname = instance.dns_name | |
| 363 self.instance_id = self.instance.id | |
| 364 | |
| 365 def start(server): | |
| 366 """ | |
| 367 Connect to the specified server. | |
| 368 | |
| 369 :return: If the server is local, the function returns a | |
| 370 :class:`boto.manage.cmdshell.LocalClient` object. | |
| 371 If the server is remote, the function returns a | |
| 372 :class:`boto.manage.cmdshell.SSHClient` object. | |
| 373 """ | |
| 374 instance_id = boto.config.get('Instance', 'instance-id', None) | |
| 375 if instance_id == server.instance_id: | |
| 376 return LocalClient(server) | |
| 377 else: | |
| 378 return SSHClient(server) | |
| 379 | |
| 380 def sshclient_from_instance(instance, ssh_key_file, | |
| 381 host_key_file='~/.ssh/known_hosts', | |
| 382 user_name='root', ssh_pwd=None): | |
| 383 """ | |
| 384 Create and return an SSHClient object given an | |
| 385 instance object. | |
| 386 | |
| 387 :type instance: :class`boto.ec2.instance.Instance` object | |
| 388 :param instance: The instance object. | |
| 389 | |
| 390 :type ssh_key_file: string | |
| 391 :param ssh_key_file: A path to the private key file that is | |
| 392 used to log into the instance. | |
| 393 | |
| 394 :type host_key_file: string | |
| 395 :param host_key_file: A path to the known_hosts file used | |
| 396 by the SSH client. | |
| 397 Defaults to ~/.ssh/known_hosts | |
| 398 :type user_name: string | |
| 399 :param user_name: The username to use when logging into | |
| 400 the instance. Defaults to root. | |
| 401 | |
| 402 :type ssh_pwd: string | |
| 403 :param ssh_pwd: The passphrase, if any, associated with | |
| 404 private key. | |
| 405 """ | |
| 406 s = FakeServer(instance, ssh_key_file) | |
| 407 return SSHClient(s, host_key_file, user_name, ssh_pwd) |
