def __get_translation_map(self, sector_index):
"""
Returns the 96-well position corresponding to the position in
a particular 384-well sector.
"""
positions = dict()
translator = RackSectorTranslator(number_sectors=NUMBER_SECTORS,
source_sector_index=sector_index,
target_sector_index=0,
enforce_type=RackSectorTranslator.MANY_TO_ONE)
for rack_pos_96 in get_positions_for_shape(self.stock_rack_shape):
rack_pos_384 = translator.translate(rack_pos_96)
positions[rack_pos_96] = rack_pos_384
return positions
def __write_section(self):
# Writes the section.
self.add_debug('Write section ...')
prst = self.rack_transfer_job.planned_rack_sample_transfer
head_line = self.HEAD_LINE % (self.step_number)
from_line = self.FROM_LINE % (
self.rack_transfer_job.source_rack.barcode)
to_line = self.TO_LINE % (self.rack_transfer_job.target_rack.barcode)
volume_line = self.VOLUME_LINE % (prst.volume \
* VOLUME_CONVERSION_FACTOR)
translation_type = RackSectorTranslator.get_translation_behaviour(
source_shape=self.rack_transfer_job.source_rack.rack_shape,
target_shape=self.rack_transfer_job.target_rack.rack_shape,
number_sectors=prst.number_sectors)
if prst.number_sectors > 1:
if not translation_type == RackSectorTranslator.MANY_TO_ONE:
src_addition = self.SECTOR_ADDITION \
% (prst.source_sector_index + 1)
from_line += src_addition
if not translation_type == RackSectorTranslator.ONE_TO_MANY:
trg_addition = self.SECTOR_ADDITION \
% (prst.target_sector_index + 1)
to_line += trg_addition
paragraph = head_line + (2 * LINEBREAK_CHAR)
paragraph += (from_line + LINEBREAK_CHAR)
paragraph += (to_line + LINEBREAK_CHAR)
paragraph += (volume_line + LINEBREAK_CHAR)
paragraph += (2 * LINEBREAK_CHAR) # spacer
return paragraph
def __get_translation_map(self, sector_index):
"""
Returns the 96-well position corresponding to the position in
a particular 384-well sector.
"""
positions = dict()
translator = RackSectorTranslator(
number_sectors=NUMBER_SECTORS,
source_sector_index=sector_index,
target_sector_index=0,
enforce_type=RackSectorTranslator.MANY_TO_ONE)
for rack_pos_96 in get_positions_for_shape(self.stock_rack_shape):
rack_pos_384 = translator.translate(rack_pos_96)
positions[rack_pos_96] = rack_pos_384
return positions
def __write_section(self):
# Writes the section.
self.add_debug('Write section ...')
prst = self.rack_transfer_job.planned_rack_sample_transfer
head_line = self.HEAD_LINE % (self.step_number)
from_line = self.FROM_LINE % (self.rack_transfer_job.source_rack.barcode)
to_line = self.TO_LINE % (self.rack_transfer_job.target_rack.barcode)
volume_line = self.VOLUME_LINE % (prst.volume \
* VOLUME_CONVERSION_FACTOR)
translation_type = RackSectorTranslator.get_translation_behaviour(
source_shape=self.rack_transfer_job.source_rack.rack_shape,
target_shape=self.rack_transfer_job.target_rack.rack_shape,
number_sectors=prst.number_sectors)
if prst.number_sectors > 1:
if not translation_type == RackSectorTranslator.MANY_TO_ONE:
src_addition = self.SECTOR_ADDITION \
% (prst.source_sector_index + 1)
from_line += src_addition
if not translation_type == RackSectorTranslator.ONE_TO_MANY:
trg_addition = self.SECTOR_ADDITION \
% (prst.target_sector_index + 1)
to_line += trg_addition
paragraph = head_line + (2 * LINEBREAK_CHAR)
paragraph += (from_line + LINEBREAK_CHAR)
paragraph += (to_line + LINEBREAK_CHAR)
paragraph += (volume_line + LINEBREAK_CHAR)
paragraph += (2 * LINEBREAK_CHAR) # spacer
return paragraph
def __check_pool_stock_racks(self):
# Ensures that the new pool tube racks have tubes in the expected
# positions using the layout of the sector preparation plates. Also
# builds a map sector index -> pool stock rack barcode.
self.add_debug('Checking new pool tube racks.')
pool_stock_rack_map = {}
for ispp in self.iso.iso_sector_preparation_plates:
trl = RackSectorTranslator(
4,
ispp.sector_index,
0,
behaviour=RackSectorTranslator.MANY_TO_ONE)
exp_poss = ispp.rack_layout.get_positions()
pool_stock_rack_bc = self.pool_stock_racks[ispp.sector_index]
pool_stock_rack_map[ispp.sector_index] = pool_stock_rack_bc
new_tube_rack = self.__tube_rack_map[pool_stock_rack_bc]
tube_map = dict([(trl.translate(t.location.position), t)
for t in new_tube_rack.containers])
missing_poss = set(exp_poss).difference(tube_map.keys())
if len(missing_poss) > 0:
msg = 'There are some tubes missing in the new stock rack ' \
'for sector %i (%s): %s.' \
% (ispp.sector_index, new_tube_rack.barcode,
', '.join(sorted([p.label for p in missing_poss])))
self.add_error(msg)
extra_poss = set(tube_map.keys()).difference(exp_poss)
if len(extra_poss) > 0:
msg = 'There are some empty tubes in the new stock rack ' \
'for sector %i in positions which should be empty: ' \
' %s. ' \
% (ispp.sector_index,
', '.join(sorted([p.label for p in extra_poss])))
self.add_warning(msg)
not_empty = [
t.location.position for t in tube_map.values()
if not t.sample is None and t.sample.volume > 0
]
if len(not_empty) > 0:
msg = 'Some tubes in the new stock rack for sector %i are ' \
'not empty: %s.' \
% (ispp.sector_index,
', '.join([p.label for p in not_empty]))
self.add_error(msg)
return pool_stock_rack_map
def __init_translators(self):
# The translators are used to determine the rack position holding
# the pool information.
for sector_index, issr in self.sample_stock_racks.iteritems():
barcode = issr.rack.barcode
translator = RackSectorTranslator(number_sectors=NUMBER_SECTORS,
source_sector_index=0,
target_sector_index=sector_index,
enforce_type=RackSectorTranslator.MANY_TO_ONE)
self.__translators[barcode] = translator
def __check_pool_stock_racks(self):
# Ensures that the new pool tube racks have tubes in the expected
# positions using the layout of the sector preparation plates. Also
# builds a map sector index -> pool stock rack barcode.
self.add_debug('Checking new pool tube racks.')
pool_stock_rack_map = {}
for ispp in self.iso.iso_sector_preparation_plates:
trl = RackSectorTranslator(4, ispp.sector_index, 0,
behaviour=
RackSectorTranslator.MANY_TO_ONE)
exp_poss = ispp.rack_layout.get_positions()
pool_stock_rack_bc = self.pool_stock_racks[ispp.sector_index]
pool_stock_rack_map[ispp.sector_index] = pool_stock_rack_bc
new_tube_rack = self.__tube_rack_map[pool_stock_rack_bc]
tube_map = dict([(trl.translate(t.location.position), t)
for t in new_tube_rack.containers])
missing_poss = set(exp_poss).difference(tube_map.keys())
if len(missing_poss) > 0:
msg = 'There are some tubes missing in the new stock rack ' \
'for sector %i (%s): %s.' \
% (ispp.sector_index, new_tube_rack.barcode,
', '.join(sorted([p.label for p in missing_poss])))
self.add_error(msg)
extra_poss = set(tube_map.keys()).difference(exp_poss)
if len(extra_poss) > 0:
msg = 'There are some empty tubes in the new stock rack ' \
'for sector %i in positions which should be empty: ' \
' %s. ' \
% (ispp.sector_index,
', '.join(sorted([p.label for p in extra_poss])))
self.add_warning(msg)
not_empty = [t.location.position
for t in tube_map.values()
if not t.sample is None and t.sample.volume > 0]
if len(not_empty) > 0:
msg = 'Some tubes in the new stock rack for sector %i are ' \
'not empty: %s.' \
% (ispp.sector_index,
', '.join([p.label for p in not_empty]))
self.add_error(msg)
return pool_stock_rack_map
def __find_ignored_sector_positions(self, ignore_positions_384):
"""
Converts the position in the ignored position list for the 384-well
layout into 96-well position.
Positions for sectors that are not required (might be the case on the
last plate) are not checked.
"""
for sector_index in range(NUMBER_SECTORS):
if not self.__library_sectors.has_key(sector_index): continue
sector_positions = get_sector_positions(sector_index=sector_index,
rack_shape=get_384_rack_shape(),
number_sectors=NUMBER_SECTORS)
translator = RackSectorTranslator(number_sectors=NUMBER_SECTORS,
source_sector_index=sector_index,
target_sector_index=0,
enforce_type=RackSectorTranslator.ONE_TO_MANY)
for sector_pos in sector_positions:
if sector_pos in ignore_positions_384:
rack_pos_96 = translator.translate(sector_pos)
self.__ignore_positions_96[sector_index].append(rack_pos_96)
def __create_buffer_worklist(self, quadrant_layout, buffer_volume, label,
sector_index):
# Creates buffer dilutions worklist for a particular quadrant
# and adds it to the worklist series.
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
planned_transfers = []
translator = RackSectorTranslator(
number_sectors=NUMBER_SECTORS,
source_sector_index=sector_index,
target_sector_index=0,
enforce_type=RackSectorTranslator.ONE_TO_MANY)
for rack_pos_384 in quadrant_layout.get_positions():
rack_pos_96 = translator.translate(rack_pos_384)
planned_transfer = PlannedSampleDilution.get_entity(
volume, self.DILUTION_INFO, rack_pos_96)
planned_transfers.append(planned_transfer)
worklist = PlannedWorklist(label=label,
planned_transfers=planned_transfers)
self.__last_worklist_index += 1
self.__worklist_series.add_worklist(self.__last_worklist_index,
worklist)
def __find_ignored_sector_positions(self, ignore_positions_384):
"""
Converts the position in the ignored position list for the 384-well
layout into 96-well position.
Positions for sectors that are not required (might be the case on the
last plate) are not checked.
"""
for sector_index in range(NUMBER_SECTORS):
if not self.__library_sectors.has_key(sector_index): continue
sector_positions = get_sector_positions(
sector_index=sector_index,
rack_shape=get_384_rack_shape(),
number_sectors=NUMBER_SECTORS)
translator = RackSectorTranslator(
number_sectors=NUMBER_SECTORS,
source_sector_index=sector_index,
target_sector_index=0,
enforce_type=RackSectorTranslator.ONE_TO_MANY)
for sector_pos in sector_positions:
if sector_pos in ignore_positions_384:
rack_pos_96 = translator.translate(sector_pos)
self.__ignore_positions_96[sector_index].append(
rack_pos_96)
def __get_expected_stock_rack_position(self, plate_layout,
sector_positions):
"""
There can only be one positions, because otherwise the positions
do not match the sectors.
"""
stock_rack_positions = set()
ref_sectors = set()
for sector_index, positions in sector_positions.iteritems():
ref_sectors.add(sector_index)
if plate_layout.shape.name == RACK_SHAPE_NAMES.SHAPE_96:
for plate_pos in positions:
stock_rack_positions.add(plate_pos.rack_position)
else:
if self.__ssc_layout_map.has_key(sector_index):
translator = self.__ssc_layout_map[sector_index]
else:
translator = RackSectorTranslator(number_sectors=4,
source_sector_index=sector_index,
target_sector_index=0,
behaviour=RackSectorTranslator.ONE_TO_MANY)
self.__ssc_layout_map[sector_index] = translator
for plate_pos in positions:
base_msg = 'Error when trying to determine stock rack ' \
'position for position %s:' \
% (plate_pos.rack_position.label)
trans_pos = self._run_and_record_error(translator.translate,
base_msg, ValueError,
**dict(rack_position=plate_pos.rack_position))
if trans_pos is None: return None
stock_rack_positions.add(trans_pos)
if len(stock_rack_positions) > 1: return None
return (list(stock_rack_positions)[0], min(ref_sectors))
