def add_to_warehouse_message(self, message: WarehouseMessage):
message.add_subject(
role_type=ROLE_TYPE_ROBOT,
subject_type=SUBJECT_TYPE_ROBOT,
friendly_name=self._robot_serial_number.value,
uuid=self.value,
)
def add_to_warehouse_message(self, message: WarehouseMessage):
for control in self.value.values():
message.add_subject(
role_type="control",
subject_type="sample",
friendly_name=self._supplier_name_for_control(control),
)
def add_to_warehouse_message(self, message: WarehouseMessage):
message.add_subject(
role_type=ROLE_TYPE_ROBOT,
subject_type=SUBJECT_TYPE_ROBOT,
friendly_name=self._automation_system_name.value,
uuid=self.value,
)
def add_to_warehouse_message(self, message: WarehouseMessage):
message.add_subject(
role_type=ROLE_TYPE_CP_SOURCE_LABWARE,
subject_type=SUBJECT_TYPE_PLATE,
friendly_name=self._barcode_property.value,
uuid=self.value,
)
def add_to_warehouse_message(self, message: WarehouseMessage):
for source_plate in self.value:
message.add_subject(
role_type=ROLE_TYPE_CP_SOURCE_LABWARE,
subject_type=SUBJECT_TYPE_PLATE,
friendly_name=source_plate[FIELD_BARCODE],
uuid=source_plate[FIELD_LH_SOURCE_PLATE_UUID],
)
def test_add_sample_as_subject(samples):
message = WarehouseMessage("mytype", "myuuid", "at some point")
message.add_sample_as_subject(samples[0][0])
assert message._subjects == [
{
"friendly_name": "sample_001__rna_1__lab_1__Positive",
"role_type": "sample",
"subject_type": "sample",
"uuid": "0a53e7b6-7ce8-4ebc-95c3-02dd64942531",
}
]
def test_source_plates_from_destination_add_to_warehouse(
app,
run_id,
destination_barcode,
samples_from_cherrytrack_into_mongo,
mocked_responses,
source_plates,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
):
with app.app_context():
instance = SourcePlatesFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
)
message = WarehouseMessage("mytype", "myuuid", "at some point")
instance.add_to_warehouse_message(message)
assert message._subjects == [
{
"role_type": "cherrypicking_source_labware",
"subject_type": "plate",
"friendly_name": "plate_123",
"uuid": "a17c38cd-b2df-43a7-9896-582e7855b4cc",
}
]
def test_samples_with_cog_uk_id_from_destination_add_to_warehouse(
app,
run_id,
centres,
destination_barcode,
samples_from_cherrytrack_into_mongo,
mlwh_samples_in_cherrytrack,
mocked_responses,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
baracoda_mock_barcodes_group,
baracoda_mock_responses,
):
with app.app_context():
samples, _ = samples_from_cherrytrack_into_mongo
instance = SamplesWithCogUkId(
SamplesFromDestination(WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode})))
)
message = WarehouseMessage("mytype", "myuuid", "at some point")
instance.add_to_warehouse_message(message)
assert message._subjects == [
{
"friendly_name": "aRootSampleId1__DS000050001_A01__centre_1__Positive",
"role_type": "sample",
"subject_type": "sample",
"uuid": "aLighthouseUUID1",
},
{
"friendly_name": "aRootSampleId3__DS000050001_A03__centre_1__Positive",
"role_type": "sample",
"subject_type": "sample",
"uuid": "aLighthouseUUID3",
},
]
def test_add_to_warehouse(app, params):
klass, field, valid_list, invalid_list = params
for valid in valid_list:
message = WarehouseMessage("mytype", "myuuid", "at some point")
try:
klass({field: valid}).add_to_warehouse_message(message)
except Exception:
pytest.fail("Error while adding to message ..")
def test_render(app):
with app.app_context():
message = WarehouseMessage("mytype", "myuuid", "at some point")
with pytest.raises(Exception):
message.render()
message.set_user_id("my user")
assert isinstance(message.render(), Message)
def test_add_subject():
message = WarehouseMessage("mytype", "myuuid", "at some point")
message.add_subject("myrole", "mysubject", "myname", "myuuid")
assert message._subjects == [
{
"role_type": "myrole",
"subject_type": "mysubject",
"friendly_name": "myname",
"uuid": "myuuid",
}
]
with patch("lighthouse.classes.messages.warehouse_messages.uuid4", return_value="avalue"):
message.add_subject("myrole", "mysubject", "myname", None)
assert message._subjects == [
{
"role_type": "myrole",
"subject_type": "mysubject",
"friendly_name": "myname",
"uuid": "myuuid",
},
{
"role_type": "myrole",
"subject_type": "mysubject",
"friendly_name": "myname",
"uuid": "avalue",
},
]
def build_new_warehouse_message(self) -> WarehouseMessage:
"""
Builds a new empty warehouse message with the generic information of an event:
(type, uuid, timestamp). All other information needs to be fill in.
Raises an exception if it does not have all information.
Returns
{WarehouseMessage} - Message that we are building in order to publish to
the warehouse
"""
if self.state == PlateEvent.EVENT_NOT_INITIALIZED:
raise EventNotInitializedError(
"We cannot build a new message because the event is not initialized"
)
return WarehouseMessage(self.event_type, self.event_uuid,
self.message_timestamp)
def test_construct_event_message(app):
with app.app_context():
message = WarehouseMessage("mytype", "myuuid", "at some point")
with pytest.raises(Exception):
message.construct_event_message("myuuid", "some date", [{"data": "data2"}], {"test": "test2"})
message.set_user_id("my user")
msg = message.construct_event_message("myuuid", "some date", [{"data": "data2"}], {"test": "test2"})
assert msg == {
"event": {
"uuid": "myuuid",
"event_type": "mytype",
"occured_at": "some date",
"user_identifier": "my user",
"subjects": [{"data": "data2"}],
"metadata": {"test": "test2"},
},
"lims": app.config["RMQ_LIMS_ID"],
}
def test_add_metadata(app):
message = WarehouseMessage("mytype", "myuuid", "at some point")
message.add_metadata("myrobot", "robot1")
message.add_metadata("myotherrobot", "robot2")
assert message._metadata == {"myrobot": "robot1", "myotherrobot": "robot2"}
def test_can_set_user_id():
message = WarehouseMessage("mytype", "myuuid", "at some point")
message.set_user_id("user 1")
assert message._user_id == "user 1"
def add_to_warehouse_message(self, message: WarehouseMessage):
message.set_user_id(self.value)
def add_to_warehouse_message(self, message: WarehouseMessage):
for sample in self.value.values():
message.add_sample_as_subject(sample)
def add_to_warehouse_message(self, message: WarehouseMessage):
message.add_subject(
role_type=ROLE_TYPE_RUN,
subject_type=SUBJECT_TYPE_RUN,
friendly_name=self.run_id,
)
def add_to_warehouse_message(self, message: WarehouseMessage):
message.add_subject(
role_type=ROLE_TYPE_CP_DESTINATION_LABWARE,
subject_type=SUBJECT_TYPE_PLATE,
friendly_name=self.value,
)
def add_to_warehouse_message(self, message: WarehouseMessage):
message.add_metadata("failure_type", self.value)