def _record_samples_in_dart(self):
def export_result_with_error(error_description):
LOGGER.critical(error_description)
return ExportResult(
success=False,
create_plate_errors=[
CreatePlateError(
type=ErrorType.
ExportingPostFeedback, # This error will only reach the imports record
origin=RABBITMQ_CREATE_FEEDBACK_ORIGIN_ROOT,
description=error_description,
)
],
)
LOGGER.info("Adding to DART")
message_uuid = self._message.message_uuid.value
plate_barcode = self._message.plate_barcode.value
if (sql_server_connection := create_dart_sql_server_conn(
self._config)) is None:
return export_result_with_error(
f"Error connecting to DART database for plate with barcode '{plate_barcode}' "
f"in message with UUID '{message_uuid}'")
def test_create_dart_sql_server_conn(config):
with patch("pyodbc.connect") as mock_connect:
conn_string = (
f"DRIVER={config.DART_DB_DRIVER};SERVER={config.DART_DB_HOST};"
f"PORT={config.DART_DB_PORT};DATABASE={config.DART_DB_DBNAME};"
f"UID={config.DART_DB_RW_USER};PWD={config.DART_DB_RW_PASSWORD}")
create_dart_sql_server_conn(config)
mock_connect.assert_called_with(conn_string)
def insert_plates_and_wells_into_dart(docs_to_insert: List[SampleDoc], config: Config) -> bool:
"""Insert plates and wells into the DART database.
Create in DART with docs_to_insert
Arguments:
docs_to_insert {List[SampleDoc]} -- List of any unprocessed samples
Returns:
{bool} -- True if the insert was successful; otherwise False
"""
logger.info("Adding to DART")
if (sql_server_connection := create_dart_sql_server_conn(config)) is not None:
try:
cursor = sql_server_connection.cursor()
group_iterator: Iterator[Tuple[Any, Any]] = groupby(docs_to_insert, lambda x: x[FIELD_PLATE_BARCODE])
for plate_barcode, samples in group_iterator:
try:
samples = list(samples)
centre_config = centre_config_for_samples(config, samples)
plate_state = add_dart_plate_if_doesnt_exist(
cursor, plate_barcode, centre_config[CENTRE_KEY_BIOMEK_LABWARE_CLASS]
)
if plate_state == DART_STATE_PENDING:
for sample in samples:
add_dart_well_properties(cursor, sample, plate_barcode)
cursor.commit()
except Exception as e:
logging_collection.add_error(
"TYPE 33",
f"DART database inserts failed for plate {plate_barcode} in priority samples inserts",
)
logger.exception(e)
# rollback statements executed since previous commit/rollback
cursor.rollback()
return False
logger.debug("DART database inserts completed successfully for priority samples")
return True
except Exception as e:
logging_collection.add_error(
"TYPE 30",
"DART database inserts failed for priority samples",
)
logger.critical(f"Critical error for priority samples: {e}")
logger.exception(e)
return False
finally:
sql_server_connection.close()
def pending_plate_barcodes_from_dart(config: Config) -> List[str]:
"""Fetch the barcodes of all plates from DART that are in the 'pending' state
Arguments:
config {Config} -- application config specifying database details
Returns:
List[str] -- barcodes of pending plates
"""
sql_server_connection = create_dart_sql_server_conn(config)
if sql_server_connection is None:
# to be caught by calling method
raise ValueError("Unable to establish DART SQL Server connection")
plate_barcodes = []
cursor = sql_server_connection.cursor()
try:
rows = cursor.execute(SQL_DART_GET_PLATE_BARCODES,
DART_STATE_PENDING).fetchall()
plate_barcodes = [row[0] for row in rows]
except Exception as e:
logger.error("Failed fetching pending plate barcodes from DART")
logger.exception(e)
finally:
sql_server_connection.close()
return plate_barcodes
def update_dart_fields(config: Config, samples: List[SampleDoc]) -> bool:
"""Updates DART plates and wells following updates to the filtered positive fields
Arguments:
config {Config} -- application config specifying database details
samples {List[Dict[str, str]]} -- the list of samples to update in DART
Returns:
bool -- whether the updates completed successfully
"""
sql_server_connection = create_dart_sql_server_conn(config)
if sql_server_connection is None:
raise ValueError("Unable to establish DART SQL Server connection")
dart_updated_successfully = True
labclass_by_centre_name = biomek_labclass_by_centre_name(config.CENTRES)
try:
logger.info("Writing to DART")
cursor = sql_server_connection.cursor()
for plate_barcode, samples_in_plate in groupby_transform(
samples,
lambda x: x[FIELD_PLATE_BARCODE],
reducefunc=lambda x: list(x)):
try:
labware_class = labclass_by_centre_name[samples_in_plate[0]
[FIELD_SOURCE]]
plate_state = add_dart_plate_if_doesnt_exist(
cursor,
plate_barcode,
labware_class # type:ignore
)
if plate_state == DART_STATE_PENDING:
for sample in samples_in_plate:
if sample[FIELD_RESULT] == POSITIVE_RESULT_VALUE:
well_index = get_dart_well_index(
sample.get(FIELD_COORDINATE, None))
if well_index is not None:
well_props = map_mongo_doc_to_dart_well_props(
sample)
set_dart_well_properties(
cursor,
plate_barcode,
well_props,
well_index # type:ignore
)
else:
raise ValueError(
"Unable to determine DART well index for sample "
f"{sample[FIELD_ROOT_SAMPLE_ID]} in plate {plate_barcode}"
)
cursor.commit()
dart_updated_successfully &= True
except Exception as e:
logger.error(
f"Failed updating DART for samples in plate {plate_barcode}"
)
logger.exception(e)
cursor.rollback()
dart_updated_successfully = False
logger.info("Updating DART completed")
except Exception as e:
logger.error("Failed updating DART")
logger.exception(e)
dart_updated_successfully = False
finally:
sql_server_connection.close()
return dart_updated_successfully
def test_create_dart_sql_server_conn_expection(config):
with patch("pyodbc.connect", side_effect=pyodbc.Error()):
assert create_dart_sql_server_conn(config) is None
def test_create_dart_sql_server_conn_none(config):
with patch("pyodbc.connect", return_value=None):
assert create_dart_sql_server_conn(config) is None