def send_to_stomp_or_defer(message, headers=None):
if not headers:
headers = generate_headers()
if options.verbose:
pprint(message)
if allow_stomp_fallback and options.dropfile:
return write_message_to_dropfile(message, headers)
try:
stomp = StompTransport()
if options.dryrun:
print("Not sending message (running with --dry-run)")
return
stomp.connect()
stomp.send("processing_recipe", message, headers=headers)
except (
KeyboardInterrupt,
SyntaxError,
AssertionError,
AttributeError,
ImportError,
TypeError,
ValueError,
):
raise
except Exception:
if not allow_stomp_fallback:
raise
print("\n\n")
import traceback
traceback.print_exc()
print("\n\nAttempting to store message in fallback location")
write_message_to_dropfile(message, headers)
class Worker(object):
def __init__(self, wait_time=5):
self.wait_time = wait_time
self.heartbeat_timestamp = None
self.transport = StompTransport()
self.transport.connect()
self.transport.subscribe_broadcast("heartbeat", self.read_heartbeat)
self.transport.subscribe("outbound", self.read)
self.wait()
def timeout(self):
from time import time
if self.heartbeat_timestamp is None:
self.heartbeat_timestamp = time()
else:
if time() - self.heartbeat_timestamp > self.wait_time:
return True
return False
def wait(self):
from time import time, sleep
try:
while not self.timeout():
sleep(1)
except KeyboardInterrupt:
pass
def send(self, message):
print("Sending")
self.transport.send("inbound", message)
def read_heartbeat(self, header, message):
from time import time
self.heartbeat_timestamp = time()
def read(self, header, message):
message = {"result": "Hey Hey!"}
self.send(message)
def test_messages_are_serialized_for_transport(mockstomp):
"""Test the message serialization."""
banana = {"entry": [1, 2.0, decimal.Decimal(3), "banana"]}
banana_str = '{"entry": [1, 2.0, 3.0, "banana"]}'
stomp = StompTransport()
stomp.connect()
mockconn = mockstomp.Connection.return_value
stomp.send(str(mock.sentinel.channel1), banana)
mockconn.send.assert_called_once()
args, kwargs = mockconn.send.call_args
assert args == ("/queue/" + str(mock.sentinel.channel1), banana_str)
stomp.broadcast(str(mock.sentinel.channel2), banana)
args, kwargs = mockconn.send.call_args
assert args == ("/topic/" + str(mock.sentinel.channel2), banana_str)
with pytest.raises(Exception):
stomp.send(str(mock.sentinel.channel), mock.sentinel.unserializable)
recipe['1']['parameters'] = {}
recipe['1']['parameters']['arguments'] = sys.argv[1:] + ['>', output_file]
recipe['1']['parameters']['cwd'] = os.getcwd()
message['custom_recipe'] = recipe
# reply_to = 'transient.gctf.%s' % str(uuid.uuid4())
# recipe['1']['output'] = 2
# recipe['2'] = {}
# recipe['2']['service'] = "relion_refine_call_back"
# recipe['2']['queue'] = reply_to
# recipe['2']['parameters'] = {}
# recipe['2']['output'] = 3
# recipe['3'] = {}
recipe['start'] = [[1, []]]
stomp.connect()
test_valid_recipe = workflows.recipe.Recipe(recipe)
test_valid_recipe.validate()
stomp.send('processing_recipe', message)
# So that BASH can pick this up
# get_output_file()
print(output_file)
# print("\nMotioncor2 job submitted")
recipe['3'] = {}
print(sys.argv)
# recipe['1']['parameters'][
# 'arguments'] = 'module load scipion && /dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/em/motioncor2-1.0.0/bin/motioncor2 -InMrc GroEL_29-100_0000.mrc -OutMrc GroEL_29-100_0000_aligned_mic.mrc -kV 300.0 -Trunc 0 -FmDose 0.4 -OutStack 0 -Gpu 0 -InitDose 0.0 -PixSize 0.4 -Tol 0.5 -Group 1 -Patch 5 5 -Throw 0 -LogFile micrograph_000029.log -FtBin 1.0 -MaskCent 0 0 -MaskSize 1 1 -Gain /dls/ebic/data/staff-scratch/Joshua/test_full_set/Micrographs/SuperRef_GroEL_29-1_0000.mrc'
recipe['start'] = [[1, []]]
message['custom_recipe'] = recipe
print(
"********************************* THIS IS THE SUBMITTED RECIPE*******************************************"
)
stomp.connect()
test_valid_recipe = workflows.recipe.Recipe(recipe)
test_valid_recipe.validate()
print(message)
stomp.send('processing_recipe', message
#headers={'reply-to':'scipion_call_back'}
)
print("\nMotioncor2 job submitted")
stomp2 = StompTransport()
stomp2.connect()
# stomp2._subscribe(1,reply_to, update_jobid)
workflows.recipe.wrap_subscribe(stomp2, reply_to, update_jobid)
print('end')
