def _get_robot_uuid(self) -> str:
if self._automation_system_name.value in app.config["BIOSERO_ROBOTS"].keys():
val: str = app.config["BIOSERO_ROBOTS"][self._automation_system_name.value]["uuid"]
if val is None:
raise RetrievalError(f"Unable to determine a uuid for robot '{self._automation_system_name.value}'")
return val
else:
raise RetrievalError(f"Robot with barcode {self._automation_system_name.value} not found")
def _source_barcodes(self):
val = set()
for sample in self._wells_from_destination.value:
sample_type = sample.get("type")
if sample_type is None:
raise RetrievalError(
f"Cannot extract type from the well: {sample}")
if sample_type == "sample":
sample_source_barcode = sample.get("source_barcode")
if sample_source_barcode is None:
raise RetrievalError(
f"Cannot extract source barcode from the well: {sample}"
)
if sample_source_barcode not in val:
val.add(sample_source_barcode)
return list(val)
def _is_valid_positive_and_negative_present(self, wells):
control_types = [well["control"] for well in wells]
control_types.sort()
if control_types != ["negative", "positive"]:
raise RetrievalError(
"We were expecting one positive and one negative control to be present."
)
def _is_valid_destination_coordinate_not_duplicated(self, wells):
coordinates = [well["destination_coordinate"] for well in wells]
duplicates = set(
[coor for coor in coordinates if coordinates.count(coor) > 1])
if len(duplicates) > 0:
raise RetrievalError(
f"Some coordinates have clashing samples/controls: { duplicates }"
)
def value(self):
with self.retrieval_scope():
val = self.get_source_plate_uuid(self._barcode_property.value)
if val is None:
raise RetrievalError(
f"Unable to determine a UUID for source plate '{self._barcode_property.value}'"
)
return val
def _get_sample_with_uuid(self, samples, uuid):
for sample in samples:
if sample[FIELD_CHERRYTRACK_LH_SAMPLE_UUID] == uuid:
return sample
raise RetrievalError(
f"We could not find sample with lh sample uuid {uuid}")
def _is_valid_no_duplicate_uuids(self, uuids):
duplicates = set([uuid for uuid in uuids if uuids.count(uuid) > 1])
if len(duplicates) > 0:
raise RetrievalError(
f"There is duplication in the lh sample uuids provided: { list(duplicates) }"
)