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 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["failure_type"] = FailureType(params)
self.properties["user_id"] = UserID(params)
for property_name in ["plate_barcode", "failure_type", "user_id"]:
self.properties[property_name].is_valid()
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["run_id"] = RunIDFromWells(self.properties["wells"])
self.properties["run_info"] = RunInfo(self.properties["run_id"])
self.properties["automation_system_name"] = AutomationSystemName(
self.properties["run_info"])
self.properties["robot_uuid"] = RobotUUID(
self.properties["automation_system_name"])
def test_samples_with_cog_uk_ids_from_destination_add_to_sequencescape(
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 = SequencescapeMessage()
instance.add_to_sequencescape_message(message)
assert message._contents == {
"H08": {
"content": {
"name": "DS000050001_A01",
"phenotype": "positive",
"sample_description": "aRootSampleId1",
"supplier_name": "COGUK1",
"uuid": "aLighthouseUUID1",
}
},
"H12": {
"content": {
"name": "DS000050001_A03",
"phenotype": "positive",
"sample_description": "aRootSampleId3",
"supplier_name": "COGUK2",
"uuid": "aLighthouseUUID3",
}
},
}