def _create_worklist_series(self):
"""
Generates all the buffer dilution worklists (as series).
The worklists for the transfer from 1-molecule-design stock rack to
pool stock rack are not included but stored at the ISO sample
stock racks to enable quadrant tracking.
"""
self.add_debug('Create worklist series ...')
volume_calculator = \
VolumeCalculator(self.target_volume, self.target_concentration,
self.__number_designs, self.__stock_concentration)
generator = StockSampleCreationWorklistGenerator(
volume_calculator, self.iso_request_label, parent=self)
self.__worklist_series = generator.get_result()
if self.__worklist_series is None:
msg = 'Error when trying to generate worklist series.'
self.add_error(msg)
else:
self.__adj_target_volume = \
volume_calculator.get_adjusted_target_volume()
if not self.__adj_target_volume is None:
robot_specs = get_pipetting_specs_cybio()
msg = 'The target volume you have requested needs to be ' \
'increased slightly because of the constraints of the ' \
'pipetting robot (%s, min. transfer volume: %s ul, ' \
'step size: 0.1 ul). The target volume will be ' \
'increased from %s ul to %s ul.' \
% (robot_specs.name,
get_trimmed_string(robot_specs.min_transfer_volume \
* VOLUME_CONVERSION_FACTOR),
get_trimmed_string(self.target_volume),
get_trimmed_string(self.__adj_target_volume))
self.add_warning(msg)
def _create_worklist_series(self):
"""
Generates all the buffer dilution worklists (as series).
The worklists for the transfer from 1-molecule-design stock rack to
pool stock rack are not included but stored at the ISO sample
stock racks to enable quadrant tracking.
"""
self.add_debug('Create worklist series ...')
volume_calculator = \
VolumeCalculator(self.target_volume, self.target_concentration,
self.__number_designs, self.__stock_concentration)
generator = StockSampleCreationWorklistGenerator(
volume_calculator, self.iso_request_label,
parent=self)
self.__worklist_series = generator.get_result()
if self.__worklist_series is None:
msg = 'Error when trying to generate worklist series.'
self.add_error(msg)
else:
self.__adj_target_volume = \
volume_calculator.get_adjusted_target_volume()
if not self.__adj_target_volume is None:
robot_specs = get_pipetting_specs_cybio()
msg = 'The target volume you have requested needs to be ' \
'increased slightly because of the constraints of the ' \
'pipetting robot (%s, min. transfer volume: %s ul, ' \
'step size: 0.1 ul). The target volume will be ' \
'increased from %s ul to %s ul.' \
% (robot_specs.name,
get_trimmed_string(robot_specs.min_transfer_volume \
* VOLUME_CONVERSION_FACTOR),
get_trimmed_string(self.target_volume),
get_trimmed_string(self.__adj_target_volume))
self.add_warning(msg)
def _get_stock_transfer_pipetting_specs(self):
"""
Sector stock racks use the CyBio, others use the Biomek.
"""
if len(self._stock_rack_sectors) > 0:
return get_pipetting_specs_cybio()
else:
return get_pipetting_specs_biomek_stock()
def _get_stock_transfer_pipetting_specs(self):
"""
Sector stock racks use the CyBio, others use the Biomek.
"""
if len(self._stock_rack_sectors) > 0:
return get_pipetting_specs_cybio()
else:
return get_pipetting_specs_biomek_stock()
def __create_prep_to_aliquot_worklist(self):
# There is one rack transfer for each sector (many-to-one transfer).
# Each transfer is executed once per aliquot plate.
self.add_debug("Add worklist for transfer into aliquot plates ...")
volume = DEFAULT_ALIQUOT_PLATE_VOLUME / VOLUME_CONVERSION_FACTOR
rack_transfers = []
for sector_index in self.__sector_layouts.keys():
rack_transfer = PlannedRackSampleTransfer.get_entity(volume, NUMBER_SECTORS, 0, sector_index)
rack_transfers.append(rack_transfer)
label = self.PREP_TO_ALIQUOT_TRANSFER_WORKLIST_LABEL % (self.library_name)
worklist = PlannedWorklist(
label,
TRANSFER_TYPES.RACK_SAMPLE_TRANSFER,
get_pipetting_specs_cybio(),
planned_liquid_transfers=rack_transfers,
)
self.__worklist_series.add_worklist(self.__last_worklist_index, worklist)
self.__last_worklist_index += 1
def __create_worklist(self, worklist_label, planned_liquid_transfers,
transfer_type, trg_plate_marker, series_key):
# The indices for the worklists are subsequent numbers.
if transfer_type == TRANSFER_TYPES.RACK_SAMPLE_TRANSFER:
robot_specs = get_pipetting_specs_cybio()
elif transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
robot_specs = self.builder.dilution_pipetting_specs[
trg_plate_marker]
else:
robot_specs = get_pipetting_specs_biomek()
worklist = PlannedWorklist(label=worklist_label,
transfer_type=transfer_type,
pipetting_specs=robot_specs,
planned_liquid_transfers=planned_liquid_transfers)
worklist_number = self.__get_current_worklist_number(False)
worklist_series = self.__series_map[series_key]
worklist_series.add_worklist(worklist_number, worklist)
def __create_worklist(self, worklist_label, planned_liquid_transfers,
transfer_type, trg_plate_marker, series_key):
# The indices for the worklists are subsequent numbers.
if transfer_type == TRANSFER_TYPES.RACK_SAMPLE_TRANSFER:
robot_specs = get_pipetting_specs_cybio()
elif transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
robot_specs = self.builder.dilution_pipetting_specs[
trg_plate_marker]
else:
robot_specs = get_pipetting_specs_biomek()
worklist = PlannedWorklist(
label=worklist_label,
transfer_type=transfer_type,
pipetting_specs=robot_specs,
planned_liquid_transfers=planned_liquid_transfers)
worklist_number = self.__get_current_worklist_number(False)
worklist_series = self.__series_map[series_key]
worklist_series.add_worklist(worklist_number, worklist)
def __create_transfers(self):
# Creates a :class:`PlannedSampleDilution` for each rack position
# in a 8x12 rack shape.
self.add_debug('Create transfers ...')
self._run_and_record_error(self.volume_calculator.calculate,
'Error when trying to determine buffer volume: ',
ValueError)
buffer_volume = self.volume_calculator.get_buffer_volume()
if buffer_volume is not None:
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
wl_label = LABELS.create_buffer_worklist_label(
self.iso_request_label)
wl = PlannedWorklist(wl_label,
TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_cybio())
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
psd = PlannedSampleDilution.get_entity(volume=volume,
target_position=rack_pos, diluent_info=DILUENT_INFO)
wl.planned_liquid_transfers.append(psd)
self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
def __make_stock_rack_worklist_series(self, label, volume, layout):
# Builds a sector 0 -> sector 0 rack transfer worklist series.
pip_specs_cy = get_pipetting_specs_cybio()
wl_series = WorklistSeries()
psts = []
if layout is None:
# Rack transfer (only for pool stock rack -> prep plate transfer).
pst = PlannedRackSampleTransfer.get_entity(volume, 1, 0, 0)
psts.append(pst)
pwl_type = TRANSFER_TYPES.RACK_SAMPLE_TRANSFER
else:
# Sample transfers (for single stock transfer).
for rack_pos in layout.get_positions():
pst = PlannedSampleTransfer.get_entity(volume, rack_pos,
rack_pos)
psts.append(pst)
pwl_type = TRANSFER_TYPES.SAMPLE_TRANSFER
wl = PlannedWorklist(label, pwl_type,
pip_specs_cy, planned_liquid_transfers=psts)
wl_series.add_worklist(0, wl)
return wl_series
def __create_transfers(self):
# Creates a :class:`PlannedSampleDilution` for each rack position
# in a 8x12 rack shape.
self.add_debug('Create transfers ...')
self._run_and_record_error(
self.volume_calculator.calculate,
'Error when trying to determine buffer volume: ', ValueError)
buffer_volume = self.volume_calculator.get_buffer_volume()
if buffer_volume is not None:
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
wl_label = LABELS.create_buffer_worklist_label(
self.iso_request_label)
wl = PlannedWorklist(wl_label, TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_cybio())
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
psd = PlannedSampleDilution.get_entity(
volume=volume,
target_position=rack_pos,
diluent_info=DILUENT_INFO)
wl.planned_liquid_transfers.append(psd)
self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
def __create_prep_to_aliquot_worklist(self):
# There is one rack transfer for each sector (many-to-one transfer).
# Each transfer is executed once per aliquot plate.
self.add_debug('Add worklist for transfer into aliquot plates ...')
volume = DEFAULT_ALIQUOT_PLATE_VOLUME / VOLUME_CONVERSION_FACTOR
rack_transfers = []
for sector_index in self.__sector_layouts.keys():
rack_transfer = PlannedRackSampleTransfer.get_entity(
volume,
NUMBER_SECTORS,
0,
sector_index)
rack_transfers.append(rack_transfer)
label = self.PREP_TO_ALIQUOT_TRANSFER_WORKLIST_LABEL % (
self.library_name)
worklist = PlannedWorklist(label,
TRANSFER_TYPES.RACK_SAMPLE_TRANSFER,
get_pipetting_specs_cybio(),
planned_liquid_transfers=rack_transfers)
self.__worklist_series.add_worklist(self.__last_worklist_index,
worklist)
self.__last_worklist_index += 1
def __make_stock_rack_worklist_series(self, label, volume, layout):
# Builds a sector 0 -> sector 0 rack transfer worklist series.
pip_specs_cy = get_pipetting_specs_cybio()
wl_series = WorklistSeries()
psts = []
if layout is None:
# Rack transfer (only for pool stock rack -> prep plate transfer).
pst = PlannedRackSampleTransfer.get_entity(volume, 1, 0, 0)
psts.append(pst)
pwl_type = TRANSFER_TYPES.RACK_SAMPLE_TRANSFER
else:
# Sample transfers (for single stock transfer).
for rack_pos in layout.get_positions():
pst = PlannedSampleTransfer.get_entity(volume, rack_pos,
rack_pos)
psts.append(pst)
pwl_type = TRANSFER_TYPES.SAMPLE_TRANSFER
wl = PlannedWorklist(label,
pwl_type,
pip_specs_cy,
planned_liquid_transfers=psts)
wl_series.add_worklist(0, wl)
return wl_series