def _populate_iso(self, iso, layout):
StockSampleCreationIsoPopulator._populate_iso(self, iso, layout)
# Create sector preparation plates.
library_name = self.iso_request.label
ir_specs_96 = get_reservoir_specs_standard_96()
plate_specs_96 = get_rack_specs_from_reservoir_specs(ir_specs_96)
ir_specs_384 = get_reservoir_specs_standard_384()
plate_specs_384 = get_rack_specs_from_reservoir_specs(ir_specs_384)
future_status = get_item_status_future()
sec_layout_map = get_sector_layouts_for_384_layout(layout)
# Create preparation plates.
for sec_idx in range(NUMBER_SECTORS):
if not sec_idx in sec_layout_map:
continue
# TODO: Move label creation to LABELS class.
prep_label = self.PREP_PLATE_LABEL_PATTERN \
% (library_name,
iso.layout_number,
DEFAULT_PREPARATION_PLATE_CONCENTRATION,
sec_idx + 1)
prep_plate = plate_specs_96.create_rack(prep_label, future_status)
sec_layout = sec_layout_map[sec_idx]
iso.add_sector_preparation_plate(prep_plate, sec_idx,
sec_layout.create_rack_layout())
# Create aliquot plates.
for i in range(self.iso_request.number_aliquots):
# TODO: Move label creation to LABELS class.
aliquot_label = self.ALIQUOT_PLATE_LABEL_PATTERN \
% (library_name,
iso.layout_number,
DEFAULT_ALIQUOT_PLATE_CONCENTRATION,
i + 1)
aliquot_plate = plate_specs_384.create_rack(aliquot_label,
future_status)
iso.add_aliquot_plate(aliquot_plate)
def __create_plate(self, rack_container, reservoir_specs):
# Creates a new plate incl. label. The plate specs are derived
# from the reservoir specs.
# Creating of stock racks is not allowed.
try:
plate_specs = get_rack_specs_from_reservoir_specs(reservoir_specs)
except ValueError as ve:
msg = 'Error when trying to determine plate specs for rack "%s": ' \
'%s.' % (rack_container.identifier, ve)
self.add_error(msg)
result = None
else:
rack_id = rack_container.identifier
plate_label = '%s_%s' % (self.parser.worklist_prefix, rack_id)
if len(plate_label) > MAX_PLATE_LABEL_LENGTH:
msg = 'The label that has been generated for the new plate ' \
'"%s" ("%s") is longer than %i characters (%i ' \
'characters). You will not be able to print this ' \
'label properly. To circumvent this problem choose ' \
'a shorter rack identifier or a shorter worklist ' \
'prefix.' \
% (rack_id, plate_label, MAX_PLATE_LABEL_LENGTH,
len(plate_label))
self.add_warning(msg)
result = plate_specs.create_rack(label=plate_label,
status=get_item_status_future())
return result
def __populate_isos(self):
"""
Adds molecule design set, library layout and plates to the picked ISOs.
"""
self.add_debug('Create ISOs ...')
ir_specs_96 = get_reservoir_specs_standard_96()
plate_specs_96 = get_rack_specs_from_reservoir_specs(ir_specs_96)
ir_specs_384 = get_reservoir_specs_standard_384()
plate_specs_384 = get_rack_specs_from_reservoir_specs(ir_specs_384)
future_status = get_item_status_future()
library_name = self._iso_request.plate_set_label
md_type = \
self.molecule_design_library.molecule_design_pool_set.molecule_type
while len(self.__picked_isos) > 0:
lci = self.__picked_isos.pop(0)
library_layout = self._library_layouts.pop(0)
lci.rack_layout = library_layout.create_rack_layout()
lci.molecule_design_pool_set = \
library_layout.get_pool_set(md_type)
layout_number = lci.layout_number
# create source plates
for sector_index in self._quadrant_positions.keys():
prep_label = self.PREP_PLATE_LABEL_PATTERN % (
library_name, layout_number,
PREPARATION_PLATE_CONCENTRATION, (sector_index + 1))
prep_plate = plate_specs_96.create_rack(label=prep_label,
status=future_status)
LibrarySourcePlate(iso=lci,
plate=prep_plate,
sector_index=sector_index)
# create aliquot plates
for i in range(STARTING_NUMBER_ALIQUOTS):
aliquot_label = self.ALIQUOT_PLATE_LABEL_PATTERN % (
library_name, layout_number, ALIQUOT_PLATE_CONCENTRATION,
(i + 1))
aliquot_plate = plate_specs_384.create_rack(
label=aliquot_label, status=future_status)
IsoAliquotPlate(iso=lci, plate=aliquot_plate)
self.__new_isos.append(lci)
def __populate_isos(self):
"""
Adds molecule design set, library layout and plates to the picked ISOs.
"""
self.add_debug('Create ISOs ...')
ir_specs_96 = get_reservoir_specs_standard_96()
plate_specs_96 = get_rack_specs_from_reservoir_specs(ir_specs_96)
ir_specs_384 = get_reservoir_specs_standard_384()
plate_specs_384 = get_rack_specs_from_reservoir_specs(ir_specs_384)
future_status = get_item_status_future()
library_name = self._iso_request.plate_set_label
md_type = \
self.molecule_design_library.molecule_design_pool_set.molecule_type
while len(self.__picked_isos) > 0:
lci = self.__picked_isos.pop(0)
library_layout = self._library_layouts.pop(0)
lci.rack_layout = library_layout.create_rack_layout()
lci.molecule_design_pool_set = \
library_layout.get_pool_set(md_type)
layout_number = lci.layout_number
# create source plates
for sector_index in self._quadrant_positions.keys():
prep_label = self.PREP_PLATE_LABEL_PATTERN % (library_name,
layout_number, PREPARATION_PLATE_CONCENTRATION,
(sector_index + 1))
prep_plate = plate_specs_96.create_rack(label=prep_label,
status=future_status)
LibrarySourcePlate(iso=lci, plate=prep_plate,
sector_index=sector_index)
# create aliquot plates
for i in range(STARTING_NUMBER_ALIQUOTS):
aliquot_label = self.ALIQUOT_PLATE_LABEL_PATTERN % (
library_name, layout_number,
ALIQUOT_PLATE_CONCENTRATION, (i + 1))
aliquot_plate = plate_specs_384.create_rack(label=aliquot_label,
status=future_status)
IsoAliquotPlate(iso=lci, plate=aliquot_plate)
self.__new_isos.append(lci)
