def __get_sorted_transfers(self):
"""
Sorts the planned transfers of the worklist by source position.
"""
source_positions = dict()
for plt in self.planned_worklist:
source_pos = plt.source_position
if not source_positions.has_key(source_pos):
source_positions[source_pos] = []
source_positions[source_pos].append(plt)
sorted_source_positions = sort_rack_positions(source_positions.keys())
sorted_transfers = []
for source_pos in sorted_source_positions:
planned_transfers = source_positions[source_pos]
if len(planned_transfers) == 1:
sorted_transfers.append(planned_transfers[0])
else:
target_positions = dict()
for plt in planned_transfers:
target_pos = plt.target_position
target_positions[target_pos] = plt
sorted_target_positions = sort_rack_positions(
target_positions.keys())
for target_pos in sorted_target_positions:
sorted_transfers.append(target_positions[target_pos])
return sorted_transfers
def __get_sorted_transfers(self):
"""
Sorts the planned transfers of the worklist by source position.
"""
source_positions = dict()
for plt in self.planned_worklist:
source_pos = plt.source_position
if not source_positions.has_key(source_pos):
source_positions[source_pos] = []
source_positions[source_pos].append(plt)
sorted_source_positions = sort_rack_positions(source_positions.keys())
sorted_transfers = []
for source_pos in sorted_source_positions:
planned_transfers = source_positions[source_pos]
if len(planned_transfers) == 1:
sorted_transfers.append(planned_transfers[0])
else:
target_positions = dict()
for plt in planned_transfers:
target_pos = plt.target_position
target_positions[target_pos] = plt
sorted_target_positions = sort_rack_positions(
target_positions.keys())
for target_pos in sorted_target_positions:
sorted_transfers.append(target_positions[target_pos])
return sorted_transfers
def __store_design_rack_value(self, label):
# Stores the values for a particular design rack.
self.add_debug('Store values for design rack %s ...' % (label))
tf_layout = self.association_layouts[label]
concentrations = self.final_concentrations[label]
missing_final_concentration = []
for tf_pos in tf_layout.get_sorted_working_positions():
cell_plate_positions = tf_pos.cell_plate_positions
cell_plate_positions = sort_rack_positions(cell_plate_positions)
# design rack position might lack ISO volume and conc
src_pos = self.source_layout.get_working_position(
tf_pos.rack_position)
for trg_pos in cell_plate_positions:
self.__source_well_values.append(tf_pos.rack_position.label)
self.__design_rack_values.append(label)
self.__target_well_values.append(trg_pos.label)
self.__iso_volume_values.append(src_pos.iso_volume)
self.__iso_concentration_values.append(
src_pos.iso_concentration)
if not concentrations.has_key(trg_pos):
missing_final_concentration.append(trg_pos.label)
continue
final_conc = concentrations[trg_pos]
self.__final_concentration_values.append(final_conc)
if len(missing_final_concentration) > 0:
msg = 'There are final concentrations missing for the following ' \
'rack positions of design rack %s: %s' \
% (label, missing_final_concentration)
self.add_error(msg)
def __store_design_rack_value(self, label):
# Stores the values for a particular design rack.
self.add_debug('Store values for design rack %s ...' % (label))
tf_layout = self.association_layouts[label]
concentrations = self.final_concentrations[label]
missing_final_concentration = []
for tf_pos in tf_layout.get_sorted_working_positions():
cell_plate_positions = tf_pos.cell_plate_positions
cell_plate_positions = sort_rack_positions(cell_plate_positions)
# design rack position might lack ISO volume and conc
src_pos = self.source_layout.get_working_position(
tf_pos.rack_position)
for trg_pos in cell_plate_positions:
self.__source_well_values.append(tf_pos.rack_position.label)
self.__design_rack_values.append(label)
self.__target_well_values.append(trg_pos.label)
self.__iso_volume_values.append(src_pos.iso_volume)
self.__iso_concentration_values.append(
src_pos.iso_concentration)
if not concentrations.has_key(trg_pos):
missing_final_concentration.append(trg_pos.label)
continue
final_conc = concentrations[trg_pos]
self.__final_concentration_values.append(final_conc)
if len(missing_final_concentration) > 0:
msg = 'There are final concentrations missing for the following ' \
'rack positions of design rack %s: %s' \
% (label, missing_final_concentration)
self.add_error(msg)
def __get_sorted_transfers(self):
# Sorts the planned transfers of the worklist by source position.
target_positions = dict()
for plt in self.planned_worklist:
target_pos = plt.target_position
target_positions[target_pos] = plt
sorted_target_positions = sort_rack_positions(target_positions.keys())
sorted_transfers = []
for target_pos in sorted_target_positions:
plt = target_positions[target_pos]
sorted_transfers.append(plt)
return sorted_transfers
def __create_tube_transfers(self):
# Creates the tube transfers.
self.add_debug('Schedule tube transfers ...')
for donor_barcode, donor_rack in self.__donor_racks.iteritems():
src_positions = sort_rack_positions(
rack_positions=donor_rack.tubes.keys())
transfer_count = 0
for receiver_barcode, number_tubes in donor_rack.\
associated_racks.iteritems():
receiver_rack = self.__receiver_racks[receiver_barcode]
free_positions = sort_rack_positions(
receiver_rack.get_positions_without_tube())
for i in range(number_tubes):
src_pos = src_positions[i + transfer_count]
trg_pos = free_positions[i]
tube_barcode = donor_rack.tubes[src_pos]
tt_data = TubeTransferData(tube_barcode=tube_barcode,
src_rack_barcode=donor_barcode,
src_pos=src_pos,
trg_rack_barcode=receiver_barcode,
trg_pos=trg_pos)
self.__tube_transfers.append(tt_data)
transfer_count += number_tubes
def __get_sorted_transfers(self):
# Sorts the planned transfers of the worklist by source position.
target_positions = dict()
for plt in self.planned_worklist:
target_pos = plt.target_position
target_positions[target_pos] = plt
sorted_target_positions = sort_rack_positions(target_positions.keys())
sorted_transfers = []
for target_pos in sorted_target_positions:
plt = target_positions[target_pos]
sorted_transfers.append(plt)
return sorted_transfers
def __create_tube_transfers(self):
# Creates the tube transfers.
self.add_debug('Schedule tube transfers ...')
for donor_barcode, donor_rack in self.__donor_racks.iteritems():
src_positions = sort_rack_positions(
rack_positions=donor_rack.tubes.keys())
transfer_count = 0
for receiver_barcode, number_tubes in donor_rack.\
associated_racks.iteritems():
receiver_rack = self.__receiver_racks[receiver_barcode]
free_positions = sort_rack_positions(
receiver_rack.get_positions_without_tube())
for i in range(number_tubes):
src_pos = src_positions[i + transfer_count]
trg_pos = free_positions[i]
tube_barcode = donor_rack.tubes[src_pos]
tt_data = TubeTransferData(
tube_barcode=tube_barcode,
src_rack_barcode=donor_barcode,
src_pos=src_pos,
trg_rack_barcode=receiver_barcode,
trg_pos=trg_pos)
self.__tube_transfers.append(tt_data)
transfer_count += number_tubes