def run(self):
env.config.update(self.config)
# start a socket?
context = zmq.Context()
stdout_socket = context.socket(zmq.PUSH)
stdout_socket.connect(self.config["sockets"]["tapping_logging"])
informer_socket = context.socket(zmq.PUSH)
informer_socket.connect(self.config["sockets"]["tapping_listener"])
try:
filename = tempfile.NamedTemporaryFile(prefix='.tmp_script_',
dir=os.getcwd(),
suffix='.sos',
delete=False).name
with open(filename, 'w') as script_file:
script_file.write(self.code)
cmd = ['sos', 'run', filename] + shlex.split(self.args) + [
'-m', 'tapping', 'slave', self.config["slave_id"],
self.config["sockets"]["tapping_logging"],
self.config["sockets"]["tapping_listener"],
self.config["sockets"]["tapping_controller"]
]
ret_code = pexpect_run(subprocess.list2cmdline(cmd),
shell=True,
stdout_socket=stdout_socket)
# status will not trigger frontend update if it was not
# started with a pending status
informer_socket.send_pyobj({
'msg_type': 'workflow_status',
'data': {
'cell_id': env.config['slave_id'],
'status': 'completed' if ret_code == 0 else 'failed'
}
})
sys.exit(ret_code)
except Exception as e:
stdout_socket.send_multipart([b'ERROR', str(e).encode()])
informer_socket.send_pyobj({
'msg_type': 'workflow_status',
'data': {
'cell_id': env.config['slave_id'],
'status': 'failed',
'exception': str(e)
}
})
sys.exit(1)
finally:
try:
os.remove(filename)
except Exception as e:
env.logger.warning(
f'Failed to remove temp script {filename}: {e}')
stdout_socket.LINGER = 0
stdout_socket.close()
informer_socket.LINGER = 0
informer_socket.close()
context.term()
def run(self):
env.config.update(self.config)
# start a socket?
context = zmq.Context()
stdout_socket = context.socket(zmq.PUSH)
stdout_socket.connect(
(f'tcp://127.0.0.1:{self.config["sockets"]["tapping_logging"]}'))
informer_socket = context.socket(zmq.PUSH)
informer_socket.connect(
(f'tcp://127.0.0.1:{self.config["sockets"]["tapping_listener"]}'))
try:
filename = os.path.join(tempfile.gettempdir(),
f'interactive_{os.getpid()}.sos')
with open(filename, 'w') as script_file:
script_file.write(self.code)
cmd = f'sos run {filename} {self.args} -m tapping slave {self.config["slave_id"]} {self.config["sockets"]["tapping_logging"]} {self.config["sockets"]["tapping_listener"]} {self.config["sockets"]["tapping_controller"]}'
ret_code = pexpect_run(cmd,
shell=True,
stdout_socket=stdout_socket)
# status will not trigger frontend update if it was not
# started with a pending status
informer_socket.send_pyobj({
'msg_type': 'workflow_status',
'data': {
'cell_id': env.config['slave_id'],
'status': 'completed' if ret_code == 0 else 'failed'
}
})
except Exception as e:
stdout_socket.send_multipart([b'ERROR', str(e).encode()])
informer_socket.send_pyobj({
'msg_type': 'workflow_status',
'data': {
'cell_id': env.config['slave_id'],
'status': 'failed',
'exception': str(e)
}
})
finally:
stdout_socket.LINGER = 0
stdout_socket.close()
informer_socket.LINGER = 0
informer_socket.close()
context.term()
def _run_cmd(self, cmd, **kwargs):
if env.config['run_mode'] == 'interactive':
if 'stdout' in kwargs or 'stderr' in kwargs:
child = subprocess.Popen(
cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=0)
out, err = child.communicate()
if 'stdout' in kwargs:
if kwargs['stdout'] is not False:
with open(kwargs['stdout'], 'ab') as so:
so.write(out)
else:
sys.stdout.write(out.decode())
if 'stderr' in kwargs:
if kwargs['stderr'] is not False:
with open(kwargs['stderr'], 'ab') as se:
se.write(err)
else:
sys.stderr.write(err.decode())
ret = child.returncode
else:
# need to catch output and send to python output, which will in trun be hijacked by SoS notebook
ret = pexpect_run(cmd)
elif '__std_out__' in env.sos_dict and '__std_err__' in env.sos_dict:
if 'stdout' in kwargs or 'stderr' in kwargs:
if 'stdout' in kwargs:
if kwargs['stdout'] is False:
so = subprocess.DEVNULL
else:
so = open(kwargs['stdout'], 'ab')
elif env.verbosity > 0:
so = open(env.sos_dict['__std_out__'], 'ab')
else:
so = subprocess.DEVNULL
if 'stderr' in kwargs:
if kwargs['stderr'] is False:
se = subprocess.DEVNULL
else:
se = open(kwargs['stderr'], 'ab')
elif env.verbosity > 1:
se = open(env.sos_dict['__std_err__'], 'ab')
else:
se = subprocess.DEVNULL
p = subprocess.Popen(cmd, shell=True, stderr=se, stdout=so)
ret = p.wait()
if so != subprocess.DEVNULL:
so.close()
if se != subprocess.DEVNULL:
se.close()
elif env.verbosity >= 1:
with open(env.sos_dict['__std_out__'],
'ab') as so, open(env.sos_dict['__std_err__'],
'ab') as se:
p = subprocess.Popen(cmd, shell=True, stderr=se, stdout=so)
ret = p.wait()
else:
p = subprocess.Popen(
cmd,
shell=True,
stderr=subprocess.DEVNULL,
stdout=subprocess.DEVNULL)
ret = p.wait()
else:
if 'stdout' in kwargs:
if kwargs['stdout'] is False:
so = subprocess.DEVNULL
else:
so = open(kwargs['stdout'], 'ab')
elif env.verbosity > 0:
so = None
else:
so = subprocess.DEVNULL
if 'stderr' in kwargs:
if kwargs['stderr'] is False:
se = subprocess.DEVNULL
else:
se = open(kwargs['stderr'], 'ab')
elif env.verbosity > 1:
se = None
else:
se = subprocess.DEVNULL
p = subprocess.Popen(cmd, shell=True, stderr=se, stdout=so)
ret = p.wait()
if so is not None and so != subprocess.DEVNULL:
so.close()
if se is not None and se != subprocess.DEVNULL:
se.close()
return ret