def test_parse_tube_rack_csv(app_db_less):
with app_db_less.app_context():
rack_size, tube_dict = parse_tube_rack_csv("DN_48_valid")
assert rack_size == 48
assert tube_dict == {
"rack_barcode": "DN_48_valid",
"layout": {
"FR05653780": "A1",
"FR05653808": "A2",
"FR05653791": "A3",
"FR05653668": "A4",
"FR05653832": "A5",
"FR05653743": "A6",
"FR05653698": "A7",
"FR05653716": "A8",
"FR05653773": "B1",
"FR05653774": "B2",
"FR05653756": "B3",
"FR05653730": "B4",
"FR05653765": "B5",
"FR05653687": "B6",
"FR05653753": "B7",
"FR05653747": "B8",
"FR05653671": "C1",
"FR05653623": "C2",
"FR05653758": "C3",
"FR05653845": "C4",
"FR05653704": "C5",
"FR05653642": "C6",
"FR05653770": "C7",
"FR05653630": "C8",
"FR05653796": "D1",
"FR05653795": "D2",
"FR05653769": "D3",
"FR05653777": "D4",
"FR05653734": "D5",
"FR05653703": "D6",
"FR05653783": "D7",
"FR05653748": "D8",
"FR05653735": "E1",
"FR05653824": "E2",
"FR05653725": "E3",
"FR05653789": "E4",
"FR05653797": "E5",
"FR05653624": "E6",
"FR05653812": "E7",
"FR05653784": "E8",
"FR05653628": "F1",
"FR05653658": "F2",
"FR05653733": "F3",
"FR05653678": "F4",
"FR05653699": "F5",
"FR05653785": "F6",
"FR05653736": "F7",
"FR05653732": "F8",
},
}
with raises(FileNotFoundError):
parse_tube_rack_csv("blah")
def get_tubes_from_rack_barcode(
tube_rack_barcode: str) -> Tuple[Dict[str, str], int]:
"""A Flask route which expects a tube rack barcode and returns the tubes in the rack with
their coordinates.
Arguments:
tube_rack_barcode {str} -- the barcode on the tube rack
Raises:
CsvNotFoundError: raised when the CSV file is not found for this barcode
Returns:
Dict -- a dict with the results or description of the error with "error" as the key
"""
try:
logger.info(
f"Looking for tube rack with barcode '{tube_rack_barcode}'")
if not csv_file_exists(f"{tube_rack_barcode}.csv"):
raise CsvNotFoundError(tube_rack_barcode)
_, tubes_layout = parse_tube_rack_csv(tube_rack_barcode)
return tubes_layout, HTTPStatus.OK
except CsvNotFoundError as e:
logger.exception(e)
return {}, HTTPStatus.NO_CONTENT
except Exception as e:
logger.exception(e)
return (
{
"error": f"Server error: {type(e).__name__}"
},
HTTPStatus.INTERNAL_SERVER_ERROR,
)
def test_parse_tube_rack_csv_ignores_no_read(app_db_less, client, tmpdir):
with app_db_less.app_context():
expected_output = {
"rack_barcode": "DN_48_no_read",
"layout": {"FR05653780": "A1", "FR05653808": "A2", "FR05653801": "F8"},
}
rack_size, tube_dict = parse_tube_rack_csv("DN_48_no_read")
assert rack_size == 48
assert tube_dict == expected_output
def wrangle_labware(labware_barcode: str) -> Tuple[Dict[str, str], int]:
"""Wrangles with the provided labware barcode.
- It first retrieves data from the MLWH for the barcode. If there is data, it determines what
type of labware it is
- If the labware is a tube rack, it looks for the CSV file expected for that tube rack
- If the CSV file is present and valid, it creates and send a new tube rack request to
Sequencescape
- If the CSV is not present or fails validation, it raises an exception
- If the labware is a plate, it creates and sends a request to Sequencescape
- If there is no data in the MLWH, it raises an exception
Arguments:
labware_barcode {str} -- the labware to look for and wrangle with
Returns:
Dict -- the body of the request to send to Sequencescape
"""
# get data from the MLWH for the barcode
cursor = get_db()
cursor.execute(f"SELECT * FROM {app.config['MLWH_DB_TABLE']} "
f"WHERE container_barcode = '{labware_barcode}'")
logger.debug(f"Number of records found: {cursor.rowcount}")
# if there is data in the MLWH, determine what type of labware it is
if cursor.rowcount > 0:
results = list(cursor)
pretty(logger, results)
labware_type = determine_labware_type(labware_barcode, results)
logger.info(f"Determined labware type: {labware_type}")
sample_type = determine_sample_type(labware_barcode, results)
logger.info(f"Determined sample type: {sample_type}")
purpose_name = determine_purpose_name(labware_barcode, labware_type,
sample_type)
logger.info(f"Determined purpose name: {purpose_name}")
# Assuming study is the same for all wells/tubes in a container
study_name = results[0]["study"]
logger.info(f"Study name: {study_name}")
if labware_type == LabwareType.TUBE_RACK:
if csv_file_exists(f"{labware_barcode}.csv"):
_, tubes_and_coordinates = parse_tube_rack_csv(labware_barcode)
db_tube_barcodes = [row["tube_barcode"] for row in results]
validate_tubes(labware_barcode,
tubes_and_coordinates["layout"].keys(),
db_tube_barcodes)
tube_rack_body = create_tube_rack_body(
labware_barcode,
results,
purpose_uuid=get_entity_uuid(PLATE_PURPOSE_ENTITY,
purpose_name),
study_uuid=get_entity_uuid(STUDY_ENTITY, study_name),
)
return create_tube_rack(tube_rack_body)
else:
raise CsvNotFoundError(labware_barcode)
if labware_type == LabwareType.PLATE:
plate_body = create_plate_body(
labware_barcode,
results,
purpose_uuid=get_entity_uuid(PLATE_PURPOSE_ENTITY,
purpose_name),
study_uuid=get_entity_uuid(STUDY_ENTITY, study_name),
)
return create_plate(plate_body)
return {}, HTTPStatus.INTERNAL_SERVER_ERROR
else:
raise BarcodeNotFoundError(labware_barcode)