def test_source_plate_uuid_value(app, source_plates):
with app.app_context():
with raises(ValidationError):
SourcePlateUUID(PlateBarcode({})).value
SourcePlateUUID(PlateBarcode({"test": "another test"})).value
with raises(Exception):
SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "1234"})).value
uuid = source_plates[0][FIELD_LH_SOURCE_PLATE_UUID]
assert SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "plate_123"})).value == uuid
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_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_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 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_plate_uuid_errors(app, source_plates):
with app.app_context():
# After success
source_plate_property = SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "plate_123"}))
source_plate_property.value
assert len(source_plate_property.errors) == 0
# After is_valid false
source_plate_property = SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "plate _123"}))
source_plate_property.is_valid()
assert len(source_plate_property.errors) > 0
# After retrieval error
source_plate_property = SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "1234"}))
with raises(Exception):
source_plate_property.value
assert len(source_plate_property.errors) > 0
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_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_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_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 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_samples_successful(
app,
source_barcode,
samples_from_cherrytrack_into_mongo,
):
with app.app_context():
val = SamplesFromSource(PlateBarcode({FIELD_EVENT_BARCODE: source_barcode})).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
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["user_id"] = UserID(params)
self.properties["robot_serial_number"] = RobotSerialNumber(params)
self.properties["robot_uuid"] = RobotUUID(self.properties["robot_serial_number"])
for property_name in ["plate_barcode", "user_id", "robot_serial_number"]:
self.properties[property_name].is_valid()
self.properties["source_plate_uuid"] = SourcePlateUUID(self.properties["plate_barcode"])
self.properties["positive_samples_from_source"] = PositiveSamplesFromSource(
self.properties["source_plate_uuid"]
)
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["user_id"] = UserID(params)
self.properties["robot_serial_number"] = RobotSerialNumber(params)
self.properties["robot_uuid"] = RobotUUID(
self.properties["robot_serial_number"])
for property_name in [
"plate_barcode", "user_id", "robot_serial_number"
]:
self.properties[property_name].is_valid()
self.properties["barcode_no_plate_map_data"] = BarcodeNoPlateMapData(
params)
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_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_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_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']")
]
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_source_plate_uuid_new(app, source_plates):
assert SourcePlateUUID(PlateBarcode({})) is not None
assert SourcePlateUUID(PlateBarcode({"test": "a test"})) is not None
assert SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "plate_123"})) is not None
def test_source_plate_uuid_is_valid(app, source_plates):
assert SourcePlateUUID(PlateBarcode({})).is_valid() is False
assert SourcePlateUUID(PlateBarcode({"test": "another test"})).is_valid() is False
assert SourcePlateUUID(PlateBarcode({FIELD_EVENT_BARCODE: "plate_123"})).is_valid() is True