Warning
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 pulsar.managers.util.retry import RetryActionExecutor
from galaxy.util import (
smart_str,
unicodify
)
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, options=None, **kwargs):
super(RemoteShell, self).__init__(**kwargs)
self.rsh = rsh
self.rcp = rcp
self.hostname = hostname
self.username = username
self.options = options
self.sessions = {}
[docs] def execute(self, cmd, persist=False, timeout=60):
# TODO: implement persistence
fullcmd = [self.rsh]
if self.options:
fullcmd.extend(self.options)
if self.username:
fullcmd.extend(["-l", self.username])
fullcmd.extend([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"
options = ["-o", "StrictHostKeyChecking=%s" % strict_host_key_checking]
options.extend(["-o", "ConnectTimeout=60"])
if private_key:
options.extend(['-i', private_key])
if port:
options.extend(['-p', str(port)])
super(SecureShell, self).__init__(rsh=rsh, rcp=rcp, options=options, **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 = None
self.retry_action_executor = RetryActionExecutor(max_retries=100, interval_max=300)
self.connect()
[docs] def connect(self):
log.info("Attempting establishment of new paramiko SSH channel")
self.ssh = paramiko.SSHClient()
self.ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
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):
def retry():
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 stdout, stderr
stdout, stderr = self.retry_action_executor.execute(retry)
return_code = stdout.channel.recv_exit_status()
return Bunch(stdout=unicodify(stdout.read()), stderr=unicodify(stderr.read()), returncode=return_code)
def _execute(self, cmd, timeout):
return self.ssh.exec_command(smart_str(cmd), timeout=timeout)