def initialize_event(self, params: Dict[str, str]) -> None:
super().initialize_event(params=params)
self._event_type = params["event_type"]
self.properties["plate_barcode"] = PlateBarcode(params)
self.properties["run_id"] = RunID(params)
for property_name in ["plate_barcode", "run_id"]:
self.properties[property_name].is_valid()
self.properties["run_info"] = RunInfo(self.properties["run_id"])
self.properties["destination_plate"] = self.properties["plate_barcode"]
self.properties["wells"] = WellsFromDestination(
self.properties["plate_barcode"])
self.properties["source_plates"] = SourcePlatesFromDestination(
self.properties["wells"])
self.properties["samples"] = SamplesFromDestination(
self.properties["wells"])
self.properties["samples_with_cog_uk_id"] = SamplesWithCogUkId(
self.properties["samples"])
self.properties["controls"] = ControlsFromDestination(
self.properties["wells"])
self.properties["automation_system_name"] = AutomationSystemName(
self.properties["run_info"])
self.properties["robot_uuid"] = RobotUUID(
self.properties["automation_system_name"])
self.properties["user_id"] = UserID(self.properties["run_info"])
def test_samples_picked_from_source_valid(app):
assert (
SamplesPickedFromSource(
PlateBarcode({FIELD_EVENT_BARCODE: "aBarcode"}), RunID({FIELD_EVENT_RUN_ID: "5"})
).is_valid()
is True
)
assert (
SamplesPickedFromSource(
PlateBarcode(
{
"missing_barcode_field": "aBarcode",
}
),
RunID({FIELD_EVENT_RUN_ID: "5"}),
).is_valid()
is False
)
def test_user_id_value_unsuccessful(app, mocked_responses, cherrytrack_mock_run_info):
with app.app_context():
myExc = None
robot = AutomationSystemName(RunInfo(RunID({FIELD_EVENT_RUN_ID: 5})))
try:
robot.value
except Exception as exc:
myExc = exc
msg = "Response from Cherrytrack is not OK: Failed to get automation system run info for the given run id"
assert msg == str(myExc)
assert ["Exception during retrieval: " + msg] == robot.errors
def test_samples_picked_from_source_no_lh_sample_uuids(
app, run_id, source_barcode, mocked_responses, cherrytrack_mock_source_plates
):
with app.app_context():
with patch("lighthouse.classes.services.mongo.app.data.driver.db.samples") as samples_collection:
val = SamplesPickedFromSource(
PlateBarcode({FIELD_EVENT_BARCODE: source_barcode}), RunID({FIELD_EVENT_RUN_ID: run_id})
).value
samples_collection.find.assert_not_called()
assert val == []
assert len(val) == 0
def test_user_id_value_unsuccessful(app, mocked_responses,
cherrytrack_mock_run_info):
with app.app_context():
exception = None
user_id = UserID(RunInfo(RunID({FIELD_EVENT_RUN_ID: 5})))
try:
user_id.value
except Exception as e:
exception = e
msg = "Response from Cherrytrack is not OK: Failed to get automation system run info for the given run id"
assert msg == str(exception)
assert len(user_id.errors) == 1
assert ["Exception during retrieval: " + msg] == user_id.errors
def test_samples_picked_from_source_value_unsuccessful(
app, run_id, source_barcode, mocked_responses, cherrytrack_mock_source_plates
):
with app.app_context():
myExc = None
with raises(Exception) as exc:
myExc = exc
SamplesPickedFromSource(
PlateBarcode({FIELD_EVENT_BARCODE: source_barcode}), RunID({FIELD_EVENT_RUN_ID: run_id})
).value
assert "Response from Cherrytrack is not OK: Failed to get samples for the given source plate barcode." == str(
myExc.value # type: ignore
)
def initialize_event(self, params: Dict[str, str]) -> None:
super().initialize_event(params=params)
self._event_type = params["event_type"]
self.properties["run_id"] = RunID(params)
for property_name in ["run_id"]:
self.properties[property_name].is_valid()
self.properties["run_info"] = RunInfo(self.properties["run_id"])
self.properties["user_id"] = UserID(self.properties["run_info"])
self.properties["automation_system_name"] = AutomationSystemName(self.properties["run_info"])
self.properties["robot_uuid"] = RobotUUID(self.properties["automation_system_name"])
def test_robot_serial_number_value_successful(app, run_id, mocked_responses, cherrytrack_mock_run_info):
with app.app_context():
expected_response = {
"data": {
"id": run_id,
FIELD_CHERRYTRACK_USER_ID: "user1",
FIELD_CHERRYTRACK_LIQUID_HANDLER_SERIAL_NUMBER: "aLiquidHandlerSerialNumber",
FIELD_CHERRYTRACK_AUTOMATION_SYSTEM_MANUFACTURER: "biosero",
FIELD_CHERRYTRACK_AUTOMATION_SYSTEM_NAME: "CPA",
}
}
val = AutomationSystemName(RunInfo(RunID({FIELD_EVENT_RUN_ID: run_id}))).value
assert val == expected_response["data"][FIELD_CHERRYTRACK_AUTOMATION_SYSTEM_NAME]
def initialize_event(self, params: Dict[str, str]) -> None:
super().initialize_event(params=params)
self._event_type = params["event_type"]
self.properties["plate_barcode"] = PlateBarcode(params)
self.properties["run_id"] = RunID(params)
for property_name in ["plate_barcode", "run_id"]:
self.properties[property_name].is_valid()
self.properties["run_info"] = RunInfo(self.properties["run_id"])
self.properties["source_plate_uuid"] = SourcePlateUUID(self.properties["plate_barcode"])
self.properties["user_id"] = UserID(self.properties["run_info"])
self.properties["automation_system_name"] = AutomationSystemName(self.properties["run_info"])
self.properties["robot_uuid"] = RobotUUID(self.properties["automation_system_name"])
self.properties["all_samples"] = SamplesFromSource(self.properties["plate_barcode"])
def initialize_event(self, params: Dict[str, str]) -> None:
super().initialize_event(params=params)
self._event_type = params["event_type"]
self.properties["plate_barcode"] = PlateBarcode(params)
self.properties["run_id"] = RunID(params)
for property_name in ["plate_barcode", "run_id"]:
self.properties[property_name].is_valid()
self.properties["run_info"] = RunInfo(self.properties["run_id"])
self.properties["user_id"] = UserID(self.properties["run_info"])
self.properties["automation_system_name"] = AutomationSystemName(
self.properties["run_info"])
self.properties["robot_uuid"] = RobotUUID(
self.properties["automation_system_name"])
self.properties["barcode_no_plate_map_data"] = BarcodeNoPlateMapData(
params)
def test_samples_picked_from_source_value_successful(
app,
run_id,
source_barcode,
destination_barcode,
cherrytrack_source_plates_response,
mocked_responses,
cherrytrack_mock_source_plates,
samples_from_cherrytrack_into_mongo,
):
with app.app_context():
val = SamplesPickedFromSource(
PlateBarcode({FIELD_EVENT_BARCODE: source_barcode}), RunID({FIELD_EVENT_RUN_ID: run_id})
).value
samples, _ = samples_from_cherrytrack_into_mongo
for elem in val:
del elem["_id"]
del elem["Date Tested"]
for elem in samples:
del elem["_id"]
del elem["Date Tested"]
assert val == [samples[0], samples[2]]
assert len(val) == 2
def test_user_id_valid(app):
assert UserID(RunInfo(RunID({FIELD_EVENT_RUN_ID: 1}))).is_valid() is True
def test_robot_serial_number_valid(app):
assert AutomationSystemName(RunInfo(RunID({FIELD_EVENT_RUN_ID: 1}))).is_valid() is True
def test_robot_serial_number_valid(app):
assert RobotSerialNumber(RunInfo(RunID({FIELD_EVENT_RUN_ID: 1
}))).is_valid() is True
def test_run_info_valid(app):
assert RunInfo(RunID({FIELD_EVENT_RUN_ID: 1})).is_valid() is True