This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.jobs.runners.util.cli.shell.rsh

import logging
import time

import paramiko

from galaxy.util.bunch import Bunch
from .local import LocalShell

log = logging.getLogger(__name__)
logging.getLogger("paramiko").setLevel(logging.WARNING)  # paramiko logging is very verbose

__all__ = ('RemoteShell', 'SecureShell', 'GlobusSecureShell', 'ParamikoShell')

[docs]class RemoteShell(LocalShell):
[docs] def __init__(self, rsh='rsh', rcp='rcp', hostname='localhost', username=None, **kwargs): super(RemoteShell, self).__init__(**kwargs) self.rsh = rsh self.rcp = rcp self.hostname = hostname self.username = username self.sessions = {}
[docs] def execute(self, cmd, persist=False, timeout=60): # TODO: implement persistence if self.username is None: fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) return super(RemoteShell, self).execute(fullcmd, persist, timeout)
[docs]class SecureShell(RemoteShell): SSH_NEW_KEY_STRING = 'Are you sure you want to continue connecting'
[docs] def __init__(self, rsh='ssh', rcp='scp', private_key=None, port=None, strict_host_key_checking=True, **kwargs): strict_host_key_checking = "yes" if strict_host_key_checking else "no" rsh += " -oStrictHostKeyChecking=%s -oConnectTimeout=60" % strict_host_key_checking rcp += " -oStrictHostKeyChecking=%s -oConnectTimeout=60" % strict_host_key_checking if private_key: rsh += " -i %s" % private_key rcp += " -i %s" % private_key if port: rsh += " -p %s" % port rcp += " -p %s" % port super(SecureShell, self).__init__(rsh=rsh, rcp=rcp, **kwargs)
[docs]class ParamikoShell(object):
[docs] def __init__(self, username, hostname, password=None, private_key=None, port=22, timeout=60, **kwargs): self.username = username self.hostname = hostname self.password = password self.private_key = private_key self.port = int(port) if port else port self.timeout = int(timeout) if timeout else timeout self.ssh = paramiko.SSHClient() self.ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy()) self.connect()
[docs] def connect(self): self.ssh.connect(hostname=self.hostname, port=self.port, username=self.username, password=self.password, key_filename=self.private_key, timeout=self.timeout)
[docs] def execute(self, cmd, timeout=60): try: _, stdout, stderr = self._execute(cmd, timeout) except paramiko.SSHException as e: log.error(e) time.sleep(10) self.connect() _, stdout, stderr = self._execute(cmd, timeout) return_code = stdout.channel.recv_exit_status() return Bunch(stdout=stdout.read(), stderr=stderr.read(), returncode=return_code)
def _execute(self, cmd, timeout): return self.ssh.exec_command(cmd, timeout=timeout)
[docs]class GlobusSecureShell(SecureShell):
[docs] def __init__(self, rsh='gsissh', rcp='gsiscp', **kwargs): super(GlobusSecureShell, self).__init__(rsh=rsh, rcp=rcp, **kwargs)