def submit_run(self, summary_rb_number, run_number, file_name):
"""
Submit a run to ActiveMQ
:param summary_rb_number: RB number of the experiment as read from the summary file
:param run_number: Run number as it appears in lastrun.txt
:param file_name: File name e.g. GEM1234.nxs
"""
# Check to see if the last run exists, if not then raise an exception
file_path = os.path.join(self.data_dir, CYCLE_FOLDER, file_name)
if os.path.isfile(file_path):
# Attempt to read an RB number from the Nexus file. This is most
# useful for high frequency instruments like ENGINX where reading
# from the summary is unreliable.
rb_number = read_rb_number_from_nexus_file(file_path)
if rb_number is None:
rb_number = summary_rb_number
EORM_LOG.info("Submitting '%s' with RB number '%s'", file_name,
rb_number)
message = Message(instrument=self.instrument_name,
rb_number=rb_number,
run_number=run_number,
data=file_path,
started_by=0) # Autoreduction service code
message.validate('/queue/DataReady')
self.client.send('/queue/DataReady', message, priority='9')
else:
raise FileNotFoundError(
"File does not exist '{}'".format(file_path))
def setUp(self):
self.mocked_client = mock.Mock(spec=QueueListener)
self.msg = Message()
self.msg.populate({
"run_number": 7654321,
"rb_number": 1234567,
"run_version": 0,
"reduction_data": "/path/1",
"started_by": -1,
"data": "/path",
"description": "This is a fake description",
"instrument": "ARMI" # Autoreduction Mock Instrument
})
with patch("logging.getLogger") as patched_logger:
self.handler = HandleMessage(self.mocked_client)
self.mocked_logger = patched_logger.return_value
db_handle = model.database.access.start_database()
self.data_model = db_handle.data_model
self.variable_model = db_handle.variable_model
self.experiment, _ = self.data_model.Experiment.objects.get_or_create(
reference_number=1231231)
self.instrument, _ = self.data_model.Instrument.objects.get_or_create(
name="ARMI")
status = STATUS.get_queued()
fake_script_text = "scripttext"
self.reduction_run = create_reduction_run_record(
self.experiment, self.instrument, FakeMessage(), 0,
fake_script_text, status)
self.reduction_run.save()
def run(self) -> Message:
"""
Runs the reduction subprocess
"""
try:
# We need to run the reduction in a new process, otherwise scripts
# will fail when they use things that require access to a main loop
# e.g. a GUI main loop, for matplotlib or Mantid
python_path = sys.executable
with tempfile.NamedTemporaryFile("w+") as temp_output_file:
args = [
python_path, RUNNER_PATH,
self.message.serialize(), temp_output_file.name
]
logging.info(
"Calling: %s %s %s %s", python_path, RUNNER_PATH,
self.message.serialize(limit_reduction_script=True),
temp_output_file.name)
# run process until finished and check the exit code for success
subprocess.run(args, check=True)
# the subprocess will write out the result message in the tempfile, read it back
result_message_raw = temp_output_file.file.read()
result_message = Message()
result_message.populate(result_message_raw)
except subprocess.CalledProcessError:
logging.error("Processing encountered an error: %s",
traceback.format_exc())
self.message.message = f"Processing encountered an error: {traceback.format_exc()}"
result_message = self.message
return result_message
def on_message(self, headers, message):
""" This method is where consumed messages are dealt with. It will
consume a message. """
with self.mark_processing():
destination = headers["destination"]
priority = headers["priority"]
self.logger.info("Destination: %s Priority: %s", destination, priority)
# Load the JSON message and header into dictionaries
try:
if not isinstance(message, Message):
json_string = message
message = Message()
message.populate(json_string)
except ValueError:
self.logger.error("Could not decode message from %s\n\n%s", destination, traceback.format_exc())
return
# the connection is configured with client-individual, meaning that each client
# has to submit an acknowledgement for receiving the message
# (otherwise I think that it is not removed from the queue but I am not sure about that)
self.client.ack(headers["message-id"], headers["subscription"])
try:
if destination == '/queue/DataReady':
self.message_handler.data_ready(message)
else:
self.logger.error("Received a message on an unknown topic '%s'", destination)
except Exception as exp: # pylint:disable=broad-except
self.logger.error("Unhandled exception encountered: %s %s\n\n%s",
type(exp).__name__, exp, traceback.format_exc())
def setUp(self):
"""Setup values for Post-Process Admin"""
self.data = {
'data': '\\\\isis\\inst$\\data.nxs',
'facility': 'ISIS',
'instrument': 'GEM',
'rb_number': '1234',
'run_number': '4321',
'reduction_script': 'print(\'hello\')',
'reduction_arguments': 'None'
}
self.test_fname = "111.txt"
self.test_root = os.path.join("instrument", "GEM", "RBNumber",
"RB2010163", "autoreduced", "111")
self.test_paths = [
os.path.join(self.test_root, "0"),
os.path.join(self.test_root, "1"),
os.path.join(self.test_root, "2")
]
self.message = Message()
self.message.populate(self.data)
self.ceph_directory = MISC['ceph_directory'] % (
self.data["instrument"], self.data["rb_number"],
self.data["run_number"])
self.temporary_directory = MISC['temp_root_directory']
self.log_and_err_name = f"RB{self.data['rb_number']}Run{self.data['run_number']}"
self.reduce_result_dir = self.temporary_directory + self.ceph_directory
def on_message(self, headers, message):
""" This method is where consumed messages are dealt with. It will
consume a message. """
destination = headers["destination"]
self._priority = headers["priority"]
self._logger.info("Destination: %s Priority: %s", destination,
self._priority)
# Load the JSON message and header into dictionaries
try:
if not isinstance(message, Message):
json_string = message
message = Message()
message.populate(json_string)
except ValueError:
self._logger.error("Could not decode message from %s", destination)
self._logger.error(sys.exc_info()[1])
return
try:
if destination == '/queue/DataReady':
self._message_handler.data_ready(message)
elif destination == '/queue/ReductionStarted':
self._message_handler.reduction_started(message)
elif destination == '/queue/ReductionComplete':
self._message_handler.reduction_complete(message)
elif destination == '/queue/ReductionError':
self._message_handler.reduction_error(message)
elif destination == '/queue/ReductionSkipped':
self._message_handler.reduction_skipped(message)
else:
self._logger.warning(
"Received a message on an unknown topic '%s'", destination)
except InvalidStateException as exp:
self._logger.error("Stomp Client message handling exception:"
"%s %s", type(exp).__name__, exp)
self._logger.error(traceback.format_exc())
def test_populate_with_invalid_key(self, mock_log):
"""
Test: A warning is logged
When: An unknown key is used to populate the Message
"""
args = {'unknown': True}
msg = Message()
msg.populate(args)
mock_log.assert_called_once()
def test_populate_with_invalid_key(self):
"""
Test: A warning is logged
When: An unknown key is used to populate the Message
"""
args = {'unknown': True}
msg = Message()
with self.assertRaises(ValueError):
msg.populate(args)
def test_send_with_message_instance(self, mock_stomp_send):
"""
Test: send sends the given data using stomp.send
When: send is called with a Message instance argument for message
"""
client = QueueClient()
message = Message(description="test-message")
client.send('dataready', message)
(args, _) = mock_stomp_send.call_args
self.assertEqual(args[0], 'dataready')
self.assertEqual(args[1], message.serialize())
def test_on_message_can_receive_a_prepopulated_message(self):
"Test receiving an already constructed Message object"
message = Message()
message.populate({"run_number": 1234567})
self.listener.on_message(self.headers, message)
self.assertFalse(self.listener.is_processing_message())
self.mocked_logger.info.assert_called_once()
self.mocked_client.ack.assert_called_once_with(
self.headers["message-id"], self.headers["subscription"])
self.mocked_handler.data_ready.assert_called_once()
self.assertIsInstance(self.mocked_handler.data_ready.call_args[0][0],
Message)
def setUp(self):
self.valid_message = Message(
run_number=1234,
instrument='GEM',
rb_number=1,
started_by=-1,
data='test/file/path',
)
self.invalid_message = Message(run_number='12345',
instrument='not inst',
rb_number=-1,
started_by='test',
data=123)
class TestReductionProcessManager(unittest.TestCase):
def setUp(self) -> None:
self.data = {
'data': '\\\\isis\\inst$\\data.nxs',
'facility': 'ISIS',
'instrument': 'GEM',
'rb_number': '1234',
'run_number': '4321',
'reduction_script':
'print(\'hello\')', # not actually used for the reduction
'reduction_arguments': 'None'
}
self.message = Message()
self.message.populate(self.data)
def test_init(self):
"Test that the constructor is doing what's expected"
rpm = ReductionProcessManager(self.message)
assert rpm.message == self.message
@patch(
'queue_processors.queue_processor.reduction.process_manager.subprocess.run'
)
def test_run_subprocess_error(self, subprocess_run: Mock):
"""Test proper handling of a subprocess encountering an error"""
def side_effect(args, **_kwargs):
raise CalledProcessError(1, args)
subprocess_run.side_effect = side_effect
rpm = ReductionProcessManager(self.message)
rpm.run()
subprocess_run.assert_called_once()
assert "Processing encountered an error" in rpm.message.message
@patch(
'queue_processors.queue_processor.reduction.process_manager.subprocess.run'
)
def test_run(self, subprocess_run: Mock):
"""Tests success path - it uses side effect to set the expected output file rather than raise an exception"""
def side_effect(args, **_kwargs):
with open(args[-1], 'w') as tmpfile:
tmpfile.write(self.message.serialize())
subprocess_run.side_effect = side_effect
rpm = ReductionProcessManager(self.message)
result_message = rpm.run()
assert result_message == self.message
def setUp(self) -> None:
self.data = {
'data': '\\\\isis\\inst$\\data.nxs',
'facility': 'ISIS',
'instrument': 'GEM',
'rb_number': '1234',
'run_number': '4321',
'reduction_script':
'print(\'hello\')', # not actually used for the reduction
'reduction_arguments': 'None'
}
self.message = Message()
self.message.populate(self.data)
def test_validate_data_ready_valid(self):
"""
Test: No exception is raised
When: Calling validate for data_ready with a valid message
"""
message = Message(instrument='GEM',
run_number=111,
rb_number=222,
data='file/path',
facility="ISIS",
started_by=0)
try:
self.assertIsNone(message.validate('/queue/DataReady'))
except RuntimeError:
self.fail()
def on_message(self, headers, data):
""" handles message consuming. It will consume a message. """
destination = headers['destination']
logger.debug("Received frame destination: %s", destination)
logger.debug("Received frame priority: %s", headers["priority"])
self.update_child_process_list()
message = Message()
message.populate(data)
if message.cancel:
self.add_cancel(message)
return
self.hold_message(destination, data, headers)
def _populated():
""" Create and return a populated message object and corresponding dictionary """
run_number = 11111
rb_number = 22222
description = 'test message'
populated_msg = Message(run_number=run_number,
rb_number=rb_number,
description=description)
populated_dict = {'description': description,
'facility': "ISIS",
'run_number': run_number,
'instrument': None,
'rb_number': rb_number,
'started_by': None,
'data': None,
'overwrite': None,
'run_version': None,
'job_id': None,
'reduction_script': None,
'reduction_arguments': None,
'reduction_log': "",
'admin_log': "",
'message': None,
'retry_in': None,
'reduction_data': None,
'cancel': None,
'software': None,
}
return populated_msg, populated_dict
def test_wish_user_script_failure(self):
"""
Test that WISH data goes through the system without issue
"""
# Set meta data for test
self.instrument = 'WISH'
self.rb_number = 222
self.run_number = 101
# Create supporting data structures e.g. Data Archive, Reduce directory
file_location = self._setup_data_structures(reduce_script='fail',
vars_script='')
# Create and send json message to ActiveMQ
data_ready_message = Message(rb_number=self.rb_number,
instrument=self.instrument,
data=file_location,
run_number=self.run_number,
facility="ISIS",
started_by=0)
self.queue_client.send('/queue/DataReady', data_ready_message)
# Get Result from database
results = self._find_run_in_database()
# Validate
self.assertEqual(self.instrument, results[0].instrument.name)
self.assertEqual(self.rb_number,
results[0].experiment.reference_number)
self.assertEqual(self.run_number, results[0].run_number)
self.assertEqual(
'e', results[0].status.value) # verbose value = "Error"
def _make_pending_msg(reduction_run):
"""
Creates a dict message from the given run, ready to be sent to ReductionPending.
:param reduction_run: (ReductionRun) database object representing a reduction run / job
:return: (Message) A constructed Message object from the meta data in the reduction_run
"""
# Deferred import to avoid circular dependencies
# pylint:disable=import-outside-toplevel
from queue_processors.queue_processor.queueproc_utils \
.reduction_run_utils import ReductionRunUtils
script, arguments = ReductionRunUtils().get_script_and_arguments(
reduction_run)
# Currently only support single location
model = access.start_database().data_model
data_location = model.DataLocation.filter_by(
reduction_run_id=reduction_run.id).first()
if data_location:
data_path = data_location.file_path
else:
raise RuntimeError("No data path found for reduction run")
message = Message(run_number=reduction_run.run_number,
instrument=reduction_run.instrument.name,
rb_number=str(
reduction_run.experiment.reference_number),
data=data_path,
reduction_script=script,
reduction_arguments=arguments,
run_version=reduction_run.run_version,
facility=FACILITY)
return message
def test_on_message_stores_priority(self):
"""
Tests that the client stores the priority from the msg header
"""
headers = self._get_header()
self.listener.on_message(headers=headers, message=Message())
self.assertEqual(headers["priority"], self.listener._priority)
def send_retry_message(user_id: int, most_recent_run: ReductionRun,
run_description: str, script_text: str,
new_script_arguments: dict,
overwrite_previous_data: bool):
"""
Creates & sends a retry message given the parameters
:param user_id: The user submitting the run
:param most_recent_run: The most recent run, used for common things across the two runs like
run number, instrument name, etc
:param run_description: Description of the rerun
:param script_text: The script that will NOT be used for this reduction, because of a known issue
https://github.com/ISISScientificComputing/autoreduce/issues/1115
:param new_script_arguments: Dict of arguments that will be used for the reduction
:param overwrite_previous_data: Whether to overwrite the previous data in the data location
"""
message = Message(
started_by=user_id,
description=run_description,
run_number=most_recent_run.run_number,
instrument=most_recent_run.instrument.name,
rb_number=most_recent_run.experiment.reference_number,
data=most_recent_run.data_location.first().file_path,
reduction_script=script_text,
reduction_arguments=new_script_arguments,
run_version=most_recent_run.run_version,
facility=FACILITY,
software=most_recent_run.software,
overwrite=overwrite_previous_data)
MessagingUtils.send(message)
def setUp(self):
""" Start all external services """
# Get all clients
self.database_client = DatabaseClient()
self.database_client.connect()
try:
self.queue_client, self.listener = main()
except ConnectionException as err:
raise RuntimeError(
"Could not connect to ActiveMQ - check you credentials. If running locally check that "
"ActiveMQ is running and started by `python setup.py start`"
) from err
# Add placeholder variables:
# these are used to ensure runs are deleted even if test fails before completion
self.instrument = 'ARMI'
self.rb_number = 1234567
self.run_number = 101
# Create test archive and add data
self.data_archive = DataArchive([self.instrument], 19, 19)
self.data_archive.create()
# Create and send json message to ActiveMQ
self.data_ready_message = Message(rb_number=self.rb_number,
instrument=self.instrument,
run_number=self.run_number,
description="This is a system test",
facility="ISIS",
started_by=0)
def create_run_records(self, message: Message):
"""
Creates or gets the necessary records to construct a ReductionRun
"""
# This must be done before looking up the run version to make sure the record exists
experiment = db_access.get_experiment(message.rb_number)
run_version = db_access.find_highest_run_version(
experiment, run_number=str(message.run_number))
message.run_version = run_version
instrument = db_access.get_instrument(str(message.instrument))
script = ReductionScript(instrument.name)
script_text = script.text()
# Make the new reduction run with the information collected so far
reduction_run = db_records.create_reduction_run_record(
experiment=experiment,
instrument=instrument,
message=message,
run_version=run_version,
script_text=script_text,
status=self.status.get_queued())
reduction_run.save()
# Create a new data location entry which has a foreign key linking it to the current
# reduction run. The file path itself will point to a datafile
# (e.g. "/isis/inst$/NDXWISH/Instrument/data/cycle_17_1/WISH00038774.nxs")
data_location = self.data_model.DataLocation(
file_path=message.data, reduction_run_id=reduction_run.pk)
data_location.save()
return reduction_run, message, instrument
def test_validate_data_ready_invalid(self):
"""
Test: An exception is raised
When: An invalid Message is validated
"""
message = Message(instrument='Not an inst')
self.assertRaises(RuntimeError, message.validate, '/queue/DataReady')
def create_run_variables(self, reduction_run, message: Message,
instrument):
"""
Creates the RunVariables for this ReductionRun
"""
# Create all of the variables for the run that are described in it's reduce_vars.py
self._logger.info('Creating variables for run')
variables = self.instrument_variable.create_run_variables(
reduction_run, message.reduction_arguments)
if not variables:
self._logger.warning(
"No instrument variables found on %s for run %s",
instrument.name, message.run_number)
self._logger.info('Getting script and arguments')
message.reduction_script = reduction_run.script
message.reduction_arguments = self.get_script_arguments(variables)
return message
def find_reason_to_skip_run(reduction_run, message: Message,
instrument) -> Optional[str]:
"""
Determines whether the processing should be skippped.
The run will be skipped if the message validation fails or if the instrument is paused
"""
if reduction_run.script == "":
return "Script text for current instrument is empty"
try:
message.validate("/queue/DataReady")
except RuntimeError as validation_err:
return f"Validation error from handler: {str(validation_err)}"
if instrument.is_paused:
return f"Run {message.run_number} has been skipped because the instrument {instrument.name} is paused"
return None
def _construct_and_send_skipped(self, rb_number, reason, message: Message):
"""
Construct a message and send to the skipped reduction queue
:param rb_number: The RB Number associated with the reduction job
:param reason: The error that caused the run to be skipped
"""
self._logger.warning("Skipping non-integer RB number: %s", rb_number)
msg = 'Reduction Skipped: {}. Assuming run number to be ' \
'a calibration run.'.format(reason)
message.message = msg
skipped_queue = ACTIVEMQ_SETTINGS.reduction_skipped
self._client.send_message(skipped_queue, message)
def hold_message(self, destination, data, headers):
""" Calls the reduction script. """
logger.debug("holding thread")
message = Message()
message.populate(data)
self.update_child_process_list()
if not self.should_proceed(message): # wait while the run shouldn't proceed
# pylint: disable=maybe-no-member
reactor.callLater(10, self.hold_message, # pragma: no cover
destination, data,
headers)
return
if self.should_cancel(message):
self.cancel_run(message) # pylint: disable=maybe-no-member
return
if not os.path.isfile(MISC['post_process_directory']):
logger.warning("Could not find autoreduction post processing file "
"- please contact a system administrator")
python_path = sys.executable
logger.info("Calling: %s %s %s %s",
python_path, MISC['post_process_directory'], destination,
message.serialize(limit_reduction_script=True))
proc = subprocess.Popen([python_path,
MISC['post_process_directory'],
destination,
message.serialize()]) # PPA expects json data
self.add_process(proc, message)
def test_new_reduction_data_path_overwrite_paths_exist(self, _):
"""
Test: The given path is returned with a 0 directory appended
When: _new_reduction_data_path is called on an existing path with overwrite: True
"""
self.setup_test_dir_structure(self.test_paths)
mock_self = Mock()
mock_self.message = Message(overwrite=True)
expected = append_path(self.test_root, "0")
actual = PostProcessAdmin._new_reduction_data_path(
mock_self, self.test_root)
self.assertEqual(expected, actual)
def test_new_reduction_data_only_root_path_exists(self):
"""
Test: The given path is returned with a 0 directory appended
When: _new_reduction_data_path is called on a path without version sub-directories
"""
self.setup_test_dir_structure([self.test_root])
mock_self = Mock()
mock_self.message = Message(overwrite=None)
expected = append_path(self.test_root, "0")
actual = PostProcessAdmin._new_reduction_data_path(
mock_self, self.test_root)
self.assertEqual(expected, actual)
def submit_run(active_mq_client, rb_number, instrument, data_file_location,
run_number):
"""
Submit a new run for autoreduction
:param active_mq_client: The client for access to ActiveMQ
:param rb_number: desired experiment rb number
:param instrument: name of the instrument
:param data_file_location: location of the data file
:param run_number: run number fo the experiment
"""
if active_mq_client is None:
print("ActiveMQ not connected, cannot submit runs")
return
message = Message(rb_number=rb_number,
instrument=instrument,
data=data_file_location,
run_number=run_number,
facility="ISIS",
started_by=-1)
active_mq_client.send('/queue/DataReady', message, priority=1)
print("Submitted run: \r\n" + message.serialize(indent=1))
