def __process_single_design_transfers(self, sector_index, sector_layout):
stock_transfer_volume = self.iso.iso_request.stock_volume
wl_label = LABELS.create_sector_stock_transfer_worklist_label(
self.iso.label,
LABELS.ROLE_SINGLE_DESIGN_STOCK,
sector_index)
wl_series = self.__make_stock_rack_worklist_series(
wl_label,
stock_transfer_volume,
sector_layout)
tube_map = self.__get_tube_map_for_sector(sector_layout)
sector_tube_transfers = []
sdssr_barcodes = self.__single_stock_rack_map[sector_index]
for design_number, sdssr_barcode in enumerate(sdssr_barcodes):
tube_transfers = self.__build_tube_transfers(
design_number,
sdssr_barcode,
sector_layout,
tube_map)
sector_tube_transfers.extend(tube_transfers)
if len(sdssr_barcodes) == 1:
# Setting the design number to None shortens worklist and
# stock rack labels.
design_number = None
self.__process_stock_rack(LABELS.ROLE_SINGLE_DESIGN_STOCK,
sector_index,
design_number,
sdssr_barcode,
wl_series,
sector_layout)
return sector_tube_transfers
def __process_stock_rack(self, role, sector_index, design_number,
tube_rack_barcode, worklist_series,
working_rack_layout):
label = LABELS.create_sector_stock_rack_label(
self.iso.label,
role,
sector_index,
design_number=design_number)
tube_rack = self.__tube_rack_map[tube_rack_barcode]
rack_layout = working_rack_layout.create_rack_layout()
# Check if we have an existing stock rack to update, using the
# label to find it.
exst_isrs = [isr for isr in self.iso.iso_stock_racks
if isr.label == label]
if len(exst_isrs) == 1:
exst_isr = exst_isrs[0]
exst_isr.worklist_series = worklist_series
exst_isr.rack = tube_rack
exst_isr.rack_layout = rack_layout
elif len(exst_isrs) == 0:
# FIXME: Using instantiation for side effects.
IsoSectorStockRack(self.iso, sector_index, label, tube_rack,
rack_layout, worklist_series)
else:
self.add_error('More than one stock rack have the same '
'label (%s).' % exst_isrs[0].label)
def __process_pool_transfers(self, sector_index, sector_layout):
pp_vol = self.iso.iso_request.preparation_plate_volume \
* VOLUME_CONVERSION_FACTOR
# Create a worklist series for the stock transfer.
wl_label = LABELS.create_sector_stock_transfer_worklist_label(
self.iso.label, LABELS.ROLE_POOL_STOCK, sector_index)
prep_transfer_volume = get_preparation_plate_transfer_volume(
preparation_plate_volume=pp_vol) \
/ VOLUME_CONVERSION_FACTOR
wl_series = self.__make_stock_rack_worklist_series(
wl_label, prep_transfer_volume, None)
# Process the new pool rack.
self.__process_stock_rack(LABELS.ROLE_POOL_STOCK, sector_index, None,
self.__pool_stock_rack_map[sector_index],
wl_series, sector_layout)
def __process_single_design_transfers(self, sector_index, sector_layout):
stock_transfer_volume = self.iso.iso_request.stock_volume
wl_label = LABELS.create_sector_stock_transfer_worklist_label(
self.iso.label, LABELS.ROLE_SINGLE_DESIGN_STOCK, sector_index)
wl_series = self.__make_stock_rack_worklist_series(
wl_label, stock_transfer_volume, sector_layout)
tube_map = self.__get_tube_map_for_sector(sector_layout)
sector_tube_transfers = []
sdssr_barcodes = self.__single_stock_rack_map[sector_index]
for design_number, sdssr_barcode in enumerate(sdssr_barcodes):
tube_transfers = self.__build_tube_transfers(
design_number, sdssr_barcode, sector_layout, tube_map)
sector_tube_transfers.extend(tube_transfers)
if len(sdssr_barcodes) == 1:
# Setting the design number to None shortens worklist and
# stock rack labels.
design_number = None
self.__process_stock_rack(LABELS.ROLE_SINGLE_DESIGN_STOCK,
sector_index, design_number,
sdssr_barcode, wl_series, sector_layout)
return sector_tube_transfers
def __build_stock_rack_maps(self):
for isr in self.iso.iso_sector_stock_racks:
label_values = LABELS.parse_sector_stock_rack_label(isr.label)
rack_role = label_values[LABELS.MARKER_RACK_ROLE]
sector_index = label_values[LABELS.MARKER_SECTOR_INDEX]
if rack_role == LABELS.ROLE_POOL_STOCK:
if self.__pool_stock_rack_map is None:
self.__pool_stock_rack_map = {}
self.__pool_stock_rack_map[sector_index] = isr
elif rack_role == LABELS.ROLE_SINGLE_DESIGN_STOCK:
# The rack number encodes the single design number.
rn = label_values.get(LABELS.MARKER_RACK_NUM)
if not rn is None:
sdss_racks = \
self.__single_stock_rack_map.get(sector_index)
if sdss_racks is None:
sdss_racks = \
[None] * self.iso.iso_request.number_designs
self.__single_stock_rack_map[sector_index] = \
sdss_racks
sdss_racks[rn - 1] = isr
else:
self.__single_stock_rack_map[sector_index] = [isr]
else:
msg = 'Invalid rack role "%s".' % rack_role
self.add_error(msg)
# Sanity checks.
if not self.__pool_stock_rack_map is None \
and not sorted(self.__pool_stock_rack_map.keys()) \
== sorted(self.__single_stock_rack_map.keys()):
msg = 'Not all pool stock racks have single design stock ' \
'racks or vice versa!'
self.add_error(msg)
if not set([len(val)
for val in self.__single_stock_rack_map.values()]) \
== set([self.iso.iso_request.number_designs]):
msg = 'The number of single design stock racks needs to be ' \
'the same in all sectors.'
self.add_error(msg)
def __build_stock_rack_maps(self):
for isr in self.iso.iso_sector_stock_racks:
label_values = LABELS.parse_sector_stock_rack_label(isr.label)
rack_role = label_values[LABELS.MARKER_RACK_ROLE]
sector_index = label_values[LABELS.MARKER_SECTOR_INDEX]
if rack_role == LABELS.ROLE_POOL_STOCK:
if self.__pool_stock_rack_map is None:
self.__pool_stock_rack_map = {}
self.__pool_stock_rack_map[sector_index] = isr
elif rack_role == LABELS.ROLE_SINGLE_DESIGN_STOCK:
# The rack number encodes the single design number.
rn = label_values.get(LABELS.MARKER_RACK_NUM)
if not rn is None:
sdss_racks = \
self.__single_stock_rack_map.get(sector_index)
if sdss_racks is None:
sdss_racks = \
[None] * self.iso.iso_request.number_designs
self.__single_stock_rack_map[sector_index] = \
sdss_racks
sdss_racks[rn - 1] = isr
else:
self.__single_stock_rack_map[sector_index] = [isr]
else:
msg = 'Invalid rack role "%s".' % rack_role
self.add_error(msg)
# Sanity checks.
if not self.__pool_stock_rack_map is None \
and not sorted(self.__pool_stock_rack_map.keys()) \
== sorted(self.__single_stock_rack_map.keys()):
msg = 'Not all pool stock racks have single design stock ' \
'racks or vice versa!'
self.add_error(msg)
if not set([len(val)
for val in self.__single_stock_rack_map.values()]) \
== set([self.iso.iso_request.number_designs]):
msg = 'The number of single design stock racks needs to be ' \
'the same in all sectors.'
self.add_error(msg)
def __process_pool_transfers(self, sector_index, sector_layout):
pp_vol = self.iso.iso_request.preparation_plate_volume \
* VOLUME_CONVERSION_FACTOR
# Create a worklist series for the stock transfer.
wl_label = LABELS.create_sector_stock_transfer_worklist_label(
self.iso.label,
LABELS.ROLE_POOL_STOCK,
sector_index)
prep_transfer_volume = get_preparation_plate_transfer_volume(
preparation_plate_volume=pp_vol) \
/ VOLUME_CONVERSION_FACTOR
wl_series = self.__make_stock_rack_worklist_series(
wl_label,
prep_transfer_volume,
None)
# Process the new pool rack.
self.__process_stock_rack(
LABELS.ROLE_POOL_STOCK,
sector_index,
None,
self.__pool_stock_rack_map[sector_index],
wl_series,
sector_layout)
def __process_stock_rack(self, role, sector_index, design_number,
tube_rack_barcode, worklist_series,
working_rack_layout):
label = LABELS.create_sector_stock_rack_label(
self.iso.label, role, sector_index, design_number=design_number)
tube_rack = self.__tube_rack_map[tube_rack_barcode]
rack_layout = working_rack_layout.create_rack_layout()
# Check if we have an existing stock rack to update, using the
# label to find it.
exst_isrs = [
isr for isr in self.iso.iso_stock_racks if isr.label == label
]
if len(exst_isrs) == 1:
exst_isr = exst_isrs[0]
exst_isr.worklist_series = worklist_series
exst_isr.rack = tube_rack
exst_isr.rack_layout = rack_layout
elif len(exst_isrs) == 0:
# FIXME: Using instantiation for side effects.
IsoSectorStockRack(self.iso, sector_index, label, tube_rack,
rack_layout, worklist_series)
else:
self.add_error('More than one stock rack have the same '
'label (%s).' % exst_isrs[0].label)
