def __get_planned_liquid_transfers(self, step_container, transfer_type):
# Create :class:`PlannedSampleDilution`s for dilution (requires
# valid diluent), otherwise it creates
# :class:`PlannedSampleTransfer`s.
planned_liquid_transfers = []
for transfer_container in step_container.get_transfer_containers():
src_positions = transfer_container.get_source_positions()
trg_positions = transfer_container.get_target_positions()
volume = float(transfer_container.volume) / VOLUME_CONVERSION_FACTOR
if transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
diluent = transfer_container.diluent
if diluent is None or not len(str(diluent)) > 1:
msg = 'A diluent must be at least 2 characters long! ' \
'Change the diluent for step %i code %s, ' \
'please.' \
% (step_container.number, transfer_container.code)
self.add_error(msg)
return None
for trg_pos_container in trg_positions:
trg_pos = self._convert_to_rack_position(trg_pos_container)
kw = dict(target_position=trg_pos, volume=volume)
if transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
kw['diluent_info'] = str(transfer_container.diluent)
psd = PlannedSampleDilution.get_entity(**kw)
planned_liquid_transfers.append(psd)
else:
for src_pos_container in src_positions:
src_pos = self._convert_to_rack_position(
src_pos_container)
kw['source_position'] = src_pos
pst = PlannedSampleTransfer.get_entity(**kw)
planned_liquid_transfers.append(pst)
return planned_liquid_transfers
def _create_planned_sample_transfer(self, **kw):
if not 'volume' in kw:
kw['volume'] = 0.000020
if not 'source_position' in kw:
kw['source_position'] = self._get_entity(IRackPosition, 'a1')
if not 'target_position' in kw:
kw['target_position'] = self._get_entity(IRackPosition, 'b2')
return PlannedSampleTransfer.get_entity(**kw)
def _create_planned_sample_transfer(self, **kw):
if not 'volume' in kw:
kw['volume'] = 0.000020
if not 'source_position' in kw:
kw['source_position'] = self._get_entity(IRackPosition, 'a1')
if not 'target_position' in kw:
kw['target_position'] = self._get_entity(IRackPosition, 'b2')
return PlannedSampleTransfer.get_entity(**kw)
def _create_planned_liquid_transfers(self):
"""
Generates the planned container transfers for the worklist.
"""
self.add_debug('Generate planned container transfer ...')
volume = TransfectionParameters.TRANSFER_VOLUME \
/ VOLUME_CONVERSION_FACTOR
for rack_pos, tf_pos in self.transfection_layout.iterpositions():
if tf_pos.is_empty:
continue
for target_pos in tf_pos.cell_plate_positions:
pst = PlannedSampleTransfer.get_entity(volume=volume,
source_position=rack_pos,
target_position=target_pos)
self._add_planned_transfer(pst)
def get_planned_sample_transfers(self, plate_marker):
"""
Converts the all transfer target for the given target plate into
:class:`PlannedSampleTransfer` objects.
"""
psts = []
for tt in self.transfer_targets:
if not tt.target_rack_marker == plate_marker: continue
trg_pos = get_rack_position_from_label(tt.position_label)
pst = PlannedSampleTransfer.get_entity(
volume=tt.transfer_volume / VOLUME_CONVERSION_FACTOR,
source_position=self.rack_position,
target_position=trg_pos)
psts.append(pst)
return psts
def _create_planned_liquid_transfers(self):
"""
Generates the planned container transfers for the worklist.
"""
self.add_debug('Generate planned container transfer ...')
volume = TransfectionParameters.TRANSFER_VOLUME \
/ VOLUME_CONVERSION_FACTOR
for rack_pos, tf_pos in self.transfection_layout.iterpositions():
if tf_pos.is_empty:
continue
for target_pos in tf_pos.cell_plate_positions:
pst = PlannedSampleTransfer.get_entity(
volume=volume,
source_position=rack_pos,
target_position=target_pos)
self._add_planned_transfer(pst)
def get_planned_sample_transfers(self, plate_marker):
"""
Converts the all transfer target for the given target plate into
:class:`PlannedSampleTransfer` objects.
"""
psts = []
for tt in self.transfer_targets:
if not tt.target_rack_marker == plate_marker:
continue
trg_pos = get_rack_position_from_label(tt.position_label)
pst = PlannedSampleTransfer.get_entity(
volume=tt.transfer_volume / VOLUME_CONVERSION_FACTOR,
source_position=self.rack_position,
target_position=trg_pos,
)
psts.append(pst)
return psts
def __make_stock_rack_worklist_series(self, label, volume, layout):
# Builds a sector 0 -> sector 0 rack transfer worklist series.
pip_specs_cy = get_pipetting_specs_cybio()
wl_series = WorklistSeries()
psts = []
if layout is None:
# Rack transfer (only for pool stock rack -> prep plate transfer).
pst = PlannedRackSampleTransfer.get_entity(volume, 1, 0, 0)
psts.append(pst)
pwl_type = TRANSFER_TYPES.RACK_SAMPLE_TRANSFER
else:
# Sample transfers (for single stock transfer).
for rack_pos in layout.get_positions():
pst = PlannedSampleTransfer.get_entity(volume, rack_pos,
rack_pos)
psts.append(pst)
pwl_type = TRANSFER_TYPES.SAMPLE_TRANSFER
wl = PlannedWorklist(label, pwl_type,
pip_specs_cy, planned_liquid_transfers=psts)
wl_series.add_worklist(0, wl)
return wl_series
def __make_stock_rack_worklist_series(self, label, volume, layout):
# Builds a sector 0 -> sector 0 rack transfer worklist series.
pip_specs_cy = get_pipetting_specs_cybio()
wl_series = WorklistSeries()
psts = []
if layout is None:
# Rack transfer (only for pool stock rack -> prep plate transfer).
pst = PlannedRackSampleTransfer.get_entity(volume, 1, 0, 0)
psts.append(pst)
pwl_type = TRANSFER_TYPES.RACK_SAMPLE_TRANSFER
else:
# Sample transfers (for single stock transfer).
for rack_pos in layout.get_positions():
pst = PlannedSampleTransfer.get_entity(volume, rack_pos,
rack_pos)
psts.append(pst)
pwl_type = TRANSFER_TYPES.SAMPLE_TRANSFER
wl = PlannedWorklist(label,
pwl_type,
pip_specs_cy,
planned_liquid_transfers=psts)
wl_series.add_worklist(0, wl)
return wl_series
