def __rename_final_plates(self, experiment_metadata):
"""
Replaces the labels of the final plates by a new label derived from
the plate set labels specified by the scientist. For ISO request
that cannot contain more than one final plate (not regarding copies)
the final plate label is equal to the ISO request label. Otherwise
ISO number and aliquot number (in case of several plates per ISO),
are added.
Assumes the ISOs to be completed and the label of experiment metadata
and ISO request to be different.
"""
if len(self.__final_plates) == 1 and \
experiment_metadata.experiment_metadata_type_id \
in EXPERIMENT_SCENARIOS.ONE_PLATE_TYPES:
for final_plates in self.__final_plates.values():
final_plates[0].rack.label = self._iso_request.label
else:
for iso, final_plates in self.__final_plates.iteritems():
if len(final_plates) == 1:
new_label = LABELS.create_final_plate_label(iso)
final_plates[0].rack.label = new_label
else:
for container in final_plates:
values = LABELS.parse_rack_marker(container.rack_marker)
plate_num = None
if values.has_key(LABELS.MARKER_RACK_NUM):
plate_num = values[LABELS.MARKER_RACK_NUM]
new_label = LABELS.create_final_plate_label(iso,
plate_num)
container.rack.label = new_label
def __rename_final_plates(self, experiment_metadata):
"""
Replaces the labels of the final plates by a new label derived from
the plate set labels specified by the scientist. For ISO request
that cannot contain more than one final plate (not regarding copies)
the final plate label is equal to the ISO request label. Otherwise
ISO number and aliquot number (in case of several plates per ISO),
are added.
Assumes the ISOs to be completed and the label of experiment metadata
and ISO request to be different.
"""
if len(self.__final_plates) == 1 and \
experiment_metadata.experiment_metadata_type_id \
in EXPERIMENT_SCENARIOS.ONE_PLATE_TYPES:
for final_plates in self.__final_plates.values():
final_plates[0].rack.label = self._iso_request.label
else:
for iso, final_plates in self.__final_plates.iteritems():
if len(final_plates) == 1:
new_label = LABELS.create_final_plate_label(iso)
final_plates[0].rack.label = new_label
else:
for container in final_plates:
values = LABELS.parse_rack_marker(
container.rack_marker)
plate_num = None
if values.has_key(LABELS.MARKER_RACK_NUM):
plate_num = values[LABELS.MARKER_RACK_NUM]
new_label = LABELS.create_final_plate_label(
iso, plate_num)
container.rack.label = new_label
def _create_stock_rack_layouts(self):
"""
Creates stock rack layout for each required rack (potential rack
sector constraints are expected to be confirmed).
The rack markers might not match the layout rack markers anymore
but this does not matter, since further processing do not use the
layout rack markers anymore.
"""
marker_map = dict()
for marker, rack_barcode in self._stock_rack_map.iteritems():
marker_map[rack_barcode] = marker
layouts = dict()
used_rack_markers = set()
for pool, container in self._stock_tube_containers.iteritems():
tc = container.tube_candidate
rack_barcode = tc.rack_barcode
if marker_map.has_key(rack_barcode):
rack_marker = marker_map[rack_barcode]
if layouts.has_key(rack_barcode):
layout = layouts[rack_barcode]
else:
layout = StockRackLayout()
layouts[rack_barcode] = layout
else:
rack_marker = container.stock_rack_marker
if rack_marker in used_rack_markers:
nums = []
for marker in used_rack_markers:
value_parts = LABELS.parse_rack_marker(marker)
nums.append(value_parts[LABELS.MARKER_RACK_NUM])
new_num = max(nums) + 1
rack_marker = LABELS.create_rack_marker(LABELS.ROLE_STOCK,
new_num)
marker_map[rack_barcode] = rack_marker
layout = StockRackLayout()
layouts[rack_barcode] = layout
tts = []
for plate_label, positions in container.plate_target_positions.\
iteritems():
if plate_label == LABELS.ROLE_FINAL:
trg_marker = plate_label
else:
trg_marker = self._rack_containers[plate_label].rack_marker
for plate_pos in positions:
tts.append(plate_pos.as_transfer_target(trg_marker))
sr_pos = StockRackPosition(rack_position=tc.rack_position,
molecule_design_pool=pool,
tube_barcode=tc.tube_barcode,
transfer_targets=tts)
layout.add_position(sr_pos)
for rack_barcode, marker in marker_map.iteritems():
self._stock_rack_layouts[marker] = layouts[rack_barcode]
if not self._stock_rack_map.has_key(marker):
self._stock_rack_map[marker] = rack_barcode
