def send_and_execute_file(self, commands, blocking):
generated_uuid = str(uuid.uuid4())
path_to_sh_file = os.path.join(os.path.dirname(__file__), 'temp',
generated_uuid + '.sh')
path_to_remote_sh_file = os.path.join(self.project_path,
generated_uuid + '.sh')
with open(path_to_sh_file, 'w') as shell_file:
shell_file.write("#!/bin/sh\n")
for line in commands:
shell_file.write("%s\n" % line)
shell_file.write("rm -rf %s\n" % path_to_remote_sh_file)
# Copy Shell file with jobs to execute
with ShellHandler(self.host, self.username, self.password, self.port,
self.tunnel_host, self.tunnel_username,
self.tunnel_password, self.tunnel_port,
self.use_tunnel, 10025,
self.ssh_key_path) as handler:
scp = SCPClient(handler.get_ssh_client().get_transport())
scp.put(path_to_sh_file,
remote_path=b'%s' % str.encode(path_to_remote_sh_file))
# Delete local file
subprocess.run(['rm', '-rf', path_to_sh_file])
# Make remote file executable
self.execute_command('chmod +x %s' % path_to_remote_sh_file)
# Execute. We need the variable order_needed as it distighushes between two separate possible execution methods
logger.info("Execute command: %s" % path_to_remote_sh_file)
if blocking:
with ShellHandler(self.host, self.username, self.password,
self.port, self.tunnel_host,
self.tunnel_username, self.tunnel_password,
self.tunnel_port, self.use_tunnel, 10026,
self.ssh_key_path) as handler:
out = handler.execute_file(path_to_remote_sh_file, True)
logger.debug('Output: %s' % ' '.join(out))
return out
else:
thread = JobSubmissionThread(
path_to_remote_sh_file, self.host, self.username,
self.password, self.port, self.tunnel_host,
self.tunnel_username, self.tunnel_password, self.tunnel_port,
self.use_tunnel, self.ssh_key_path)
thread.start()
return None
def run(self):
with ShellHandler(self.host, self.username, self.password, self.port,
self.tunnel_host, self.tunnel_username,
self.tunnel_password, self.tunnel_port,
self.use_tunnel, 10020) as handler:
out, err = handler.execute_file(self.remote_file, False)
logger.debug(out)
logger.debug(err)
def execute_command(self, command, ignore_errors=False):
logger.info('Execute command: %s' % command)
with ShellHandler(self.host, self.username, self.password, self.port, self.tunnel_host,
self.tunnel_username, self.tunnel_password, self.tunnel_port, self.use_tunnel, 10024) as handler:
(stdout, stderr) = handler.execute(command)
logger.debug('Output: %s' % ' '.join(stdout))
logger.debug('ErrorOut: %s' % ' '.join(stderr))
if stderr and not ignore_errors:
raise Exception('Error in executing command %s! Error: %s.' % (command, ','.join(stderr)))
return stdout
def __init__(self):
self.username = HPC['username']
self.password = HPC['password']
self.host = HPC['host']
self.port = HPC['port']
self.queue = HPC['queue']
self.node_properties = HPC['node_properties']
self.tunnel_username = HPC['ssh_tunnel_username']
self.tunnel_password = HPC['ssh_tunnel_password']
self.tunnel_host = HPC['ssh_tunnel_host']
self.tunnel_port = HPC['ssh_tunnel_port']
self.logger = logging.getLogger(__name__)
self.ssh = ShellHandler(self.host, self.username, self.password, self.port, self.tunnel_host,
self.tunnel_username, self.tunnel_password, self.tunnel_port)
def copy_project_tar(self):
with ShellHandler(self.host, self.username, self.password, self.port,
self.tunnel_host, self.tunnel_username,
self.tunnel_password, self.tunnel_port,
self.use_tunnel, 10023) as handler:
scp = SCPClient(handler.get_ssh_client().get_transport())
# Copy plugin
scp.put('tmp.tar.gz', remote_path=b'~')
# Untar plugin
self.execute_command('mkdir %s' % self.project_path)
self.execute_command('tar -C %s -xvf ~/tmp.tar.gz' % self.project_path)
# Delete tar
self.execute_command('rm -f ~/tmp.tar.gz')
def get_error_log(self, job):
with ShellHandler(self.host, self.username, self.password, self.port, self.tunnel_host,
self.tunnel_username, self.tunnel_password, self.tunnel_port, self.use_tunnel, 10022) as handler:
sftp_client = handler.get_ssh_client().open_sftp()
plugin_execution_output_path = os.path.join(self.log_path, str(job.plugin_execution.id))
try:
remote_file = sftp_client.open(os.path.join(plugin_execution_output_path, str(job.id)+'_err.txt'))
except FileNotFoundError:
return ['File Not Found']
output = []
try:
for line in remote_file:
output.append(line.strip())
finally:
remote_file.close()
return output
def copy_plugin(self, plugin):
with ShellHandler(self.host, self.username, self.password, self.port, self.tunnel_host,
self.tunnel_username, self.tunnel_password, self.tunnel_port, self.use_tunnel, 10023) as handler:
scp = SCPClient(handler.get_ssh_client().get_transport())
# Copy plugin
scp.put(plugin.get_full_path_to_archive(), remote_path=b'~')
try:
self.delete_plugin(plugin)
except Exception:
pass
# Untar plugin
self.execute_command('mkdir %s/%s' % (self.plugin_path, str(plugin)))
self.execute_command('tar -C %s/%s -xvf %s' % (self.plugin_path, str(plugin), plugin.get_name_of_archive()))
# Delete tar
self.execute_command('rm -f ~/%s' % (plugin.get_name_of_archive()))