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 __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 __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 __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)
