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_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_all_samples_from_destination_value_fails_with_unknown_samples(
app,
run_id,
destination_barcode,
samples_from_cherrytrack_into_mongo,
cherrytrack_destination_plate_response,
mocked_responses,
cherrytrack_mock_destination_plate,
):
with app.app_context():
instance = SamplesFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
)
assert instance.is_valid() is True
assert instance.errors == []
with pytest.raises(Exception):
instance.value
assert instance.is_valid() is False
assert instance.errors == [
(
"Exception during retrieval: Some samples cannot be obtained because they are not present"
" in Mongo. Please review: ['unknown']"
)
]
def test_wells_from_destination_value_gets_value(
app,
run_id,
destination_barcode,
mocked_responses,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
):
with app.app_context():
val = WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode})).value
assert val == cherrytrack_destination_plate_response["data"]["wells"]
def test_wells_from_destination_value_fails_with_duplicated_wells(
app,
run_id,
destination_barcode,
samples_from_cherrytrack_into_mongo,
cherrytrack_destination_plate_response,
mocked_responses,
cherrytrack_mock_destination_plate,
):
with app.app_context():
instance = WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
assert instance.is_valid() is True
assert instance.errors == []
with pytest.raises(Exception):
instance.value
assert instance.is_valid() is False
assert instance.errors == [
"Exception during retrieval: Some coordinates have clashing samples/controls: {'H1'}"
]
def test_run_id_from_wells_value(
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():
val = RunIDFromWells(WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))).value
assert val == 5
def test_all_controls_from_destination_value_gets_value(
app,
run_id,
destination_barcode,
samples_from_cherrytrack_into_mongo,
mocked_responses,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
):
with app.app_context():
wells = cherrytrack_destination_plate_response["data"]["wells"]
val = ControlsFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
).value
assert val == {"E10": wells[2], "E11": wells[3]}
def test_all_controls_from_destination_value_fails_with_missing_controls(
app,
destination_barcode,
mocked_responses,
cherrytrack_mock_destination_plate,
):
with app.app_context():
instance = ControlsFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
)
assert instance.is_valid() is True
assert instance.errors == []
with pytest.raises(Exception):
instance.value
assert instance.is_valid() is False
assert instance.errors == [
("Exception during retrieval: We were expecting one positive and one negative control to be present.")
]
def test_source_plates_from_destination_value_gets_value(
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():
val = SourcePlatesFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
).value
for elem in val:
del elem["_id"]
assert val == [
{"Lab ID": "lab_1", "barcode": "plate_123", "lh_source_plate_uuid": "a17c38cd-b2df-43a7-9896-582e7855b4cc"}
]
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",
}
},
}
def test_all_samples_from_destination_value_gets_value(
app,
run_id,
destination_barcode,
samples_from_cherrytrack_into_mongo,
mocked_responses,
cherrytrack_mock_destination_plate,
cherrytrack_destination_plate_response,
):
with app.app_context():
val = SamplesFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
).value
samples, _ = samples_from_cherrytrack_into_mongo
for sample in val.values():
del sample["_id"]
del sample["Date Tested"]
for sample in samples:
del sample["_id"]
del sample["Date Tested"]
assert val == {"H08": samples[0], "H12": samples[2]}
def test_all_samples_from_destination_value_fails_with_duplicated_samples(
app,
run_id,
destination_barcode,
samples_from_cherrytrack_into_mongo,
cherrytrack_destination_plate_response,
mocked_responses,
cherrytrack_mock_destination_plate,
):
with app.app_context():
instance = SamplesFromDestination(
WellsFromDestination(PlateBarcode({FIELD_EVENT_BARCODE: destination_barcode}))
)
assert instance.is_valid() is True
assert instance.errors == []
with pytest.raises(Exception):
instance.value
assert instance.is_valid() is False
assert instance.errors == [
("Exception during retrieval: There is duplication in the lh sample uuids provided: ['uuid1']")
]