def _init_source_data(self):
"""
Initialises the source rack related values and lookups.
"""
for rack_pos in get_positions_for_shape(
self.reservoir_specs.rack_shape):
self._source_volumes[rack_pos] = 0
self._source_dead_volume = self.reservoir_specs.min_dead_volume \
* VOLUME_CONVERSION_FACTOR
self._source_max_volume = self.reservoir_specs.max_volume \
* VOLUME_CONVERSION_FACTOR
self.__emtpy_pos_manager = EmptyPositionManager(
rack_shape=self.reservoir_specs.rack_shape)
def _init_source_data(self):
"""
Initialises the source rack related values and lookups.
"""
for rack_pos in get_positions_for_shape(self.reservoir_specs.rack_shape):
self._source_volumes[rack_pos] = 0
self._source_dead_volume = self.reservoir_specs.min_dead_volume \
* VOLUME_CONVERSION_FACTOR
self._source_max_volume = self.reservoir_specs.max_volume \
* VOLUME_CONVERSION_FACTOR
self.__emtpy_pos_manager = EmptyPositionManager(
rack_shape=self.reservoir_specs.rack_shape)
class SampleDilutionWorklistWriter(BiomekWorklistWriter):
"""
An abstract base class writing worklist for sample dilution worklists.
**Return Value:** Stream for an CSV file.
"""
NAME = 'Biomek Dilution Worklist Writer'
TRANSFER_TYPE = TRANSFER_TYPES.SAMPLE_DILUTION
#: The name of the optional diluent info column.
DILUENT_INFO_HEADER = 'DiluentInformation'
#: The index of the optional diluent info column.
DILUENT_INFO_INDEX = 5
def __init__(self, planned_worklist, target_rack, source_rack_barcode,
reservoir_specs, pipetting_specs=None,
ignored_positions=None, parent=None):
"""
Constructor.
:param str source_rack_barcode: The barcode for the source rack or
reservoir.
:type source_rack_barcode: :class:`str`
"""
BiomekWorklistWriter.__init__(self, planned_worklist, target_rack,
pipetting_specs=pipetting_specs,
ignored_positions=ignored_positions,
parent=parent)
#: The barcode for the source rack or reservoir.
self.source_rack_barcode = source_rack_barcode
#: The specs for the source rack or reservoir.
self.reservoir_specs = reservoir_specs
#: The maximum volume of source rack container.
self._source_max_volume = None
#: Values for a column presenting diluent information.
self._diluent_info_values = None
#: Maps source position amounts (volumes) onto diluents.
self._diluent_map = None
#: Maps total diluent amounts (volumes) onto diluents.
self._amount_map = None
#: The last used source rack position.
self.__last_source_rack_pos = None
#: Stores and return empty positions in the source rack.
self.__emtpy_pos_manager = None
# If True, some dilution had to be split because they exceeded the
# maximum allowed transfer volume.
self.__has_split_volumes = False
# If True, some source containers could not take up all liquid required
# so that there is at least one additional source container for
# an diluent.
self.__split_sources = None
def reset(self):
"""
Resets all values except for input values.
"""
BiomekWorklistWriter.reset(self)
self._source_max_volume = None
self._diluent_info_values = []
self._amount_map = dict()
self._diluent_map = dict()
self.__has_split_volumes = False
self.__split_sources = set()
self.__emtpy_pos_manager = None
self.__last_source_rack_pos = None
def _check_input(self):
"""
Checks the input values.
"""
BiomekWorklistWriter._check_input(self)
self._check_input_class('source rack barcode', self.source_rack_barcode,
basestring)
self._check_input_class('reservoir specs', self.reservoir_specs,
ReservoirSpecs)
def _init_source_data(self):
"""
Initialises the source rack related values and lookups.
"""
for rack_pos in get_positions_for_shape(self.reservoir_specs.rack_shape):
self._source_volumes[rack_pos] = 0
self._source_dead_volume = self.reservoir_specs.min_dead_volume \
* VOLUME_CONVERSION_FACTOR
self._source_max_volume = self.reservoir_specs.max_volume \
* VOLUME_CONVERSION_FACTOR
self.__emtpy_pos_manager = EmptyPositionManager(
rack_shape=self.reservoir_specs.rack_shape)
def _generate_column_values(self):
"""
This method generates the value lists for the CSV columns.
"""
target_rack_barcode = self.target_rack.barcode
sorted_transfers = self.__get_sorted_transfers()
for pt in sorted_transfers:
if pt.target_position in self.ignored_positions:
continue
if not self._check_transfer_volume(pt.volume, pt.target_position):
continue
split_volumes = self.__split_into_transferable_amounts(pt)
for i in range(len(split_volumes)):
volume = round(split_volumes[i], 1)
source_pos = self.__get_and_adjust_source_position(
pt.diluent_info, volume, i)
if self.has_errors():
break
self._source_rack_values.append(self.source_rack_barcode)
self._source_pos_values.append(source_pos.label)
self._volume_values.append(get_trimmed_string(volume))
self._target_rack_values.append(target_rack_barcode)
self._target_pos_values.append(pt.target_position.label)
self._diluent_info_values.append(pt.diluent_info)
if self.__has_split_volumes:
msg = 'Some dilution volumes exceed the allowed maximum transfer ' \
'volume of %s ul. The dilution volumes have been distributed ' \
'over different source wells. Have a look on the generated ' \
'worklist file for details, please.' \
% (get_trimmed_string(self._max_transfer_volume))
self.add_warning(msg)
if len(self.__split_sources) > 0:
msg = 'The source for the following diluents has been split ' \
'and distributed over several containers because one ' \
'single container could not have taken up the required ' \
'volume (max volume of a source container: %s ul, dead ' \
'volume: %s ul): %s. Have a look onto the generated ' \
'worklist files for details, please.' \
% (get_trimmed_string(self.reservoir_specs.max_volume \
* VOLUME_CONVERSION_FACTOR),
get_trimmed_string(self.reservoir_specs.max_dead_volume \
* VOLUME_CONVERSION_FACTOR),
list(self.__split_sources))
self.add_warning(msg)
def __get_sorted_transfers(self):
# Sorts the planned transfers of the worklist by source position.
target_positions = dict()
for plt in self.planned_worklist:
target_pos = plt.target_position
target_positions[target_pos] = plt
sorted_target_positions = sort_rack_positions(target_positions.keys())
sorted_transfers = []
for target_pos in sorted_target_positions:
plt = target_positions[target_pos]
sorted_transfers.append(plt)
return sorted_transfers
def __split_into_transferable_amounts(self, planned_transfer):
# Checks whether the volume is larger than the allowed maximum
# transfer volume and splits it into transferable amounts.
volume = round(planned_transfer.volume * VOLUME_CONVERSION_FACTOR, 1)
if volume <= self._max_transfer_volume:
return [volume]
self.__has_split_volumes = True
no_volumes = ceil(volume / self._max_transfer_volume)
amounts = []
partial_vol = round_up((volume / no_volumes), 1)
while volume > 0:
if volume < partial_vol:
amounts.append(volume)
volume = 0
else:
amounts.append(partial_vol)
volume = volume - partial_vol
amounts.sort()
return amounts
def __get_and_adjust_source_position(self, diluent_info, volume, i):
# Returns the source position for the diluent.
diluent_marker = '%s#%i' % (diluent_info, i)
if not self._diluent_map.has_key(diluent_marker):
self.__init_new_diluent_source(diluent_marker, volume)
else:
source_pos = self._diluent_map[diluent_marker]
stored_amount = self._amount_map[source_pos]
new_amount = stored_amount + volume
if new_amount > self._source_max_volume:
self.__split_sources.add(str(diluent_info))
self.__init_new_diluent_source(diluent_marker, volume)
else:
self._amount_map[source_pos] = new_amount
return self._diluent_map[diluent_marker]
def __init_new_diluent_source(self, diluent_marker, volume):
# Initialises a new source volume container in the source reservoir.
try:
source_pos = self.__emtpy_pos_manager.get_empty_position()
except ValueError:
msg = 'There is not enough space for all source containers ' \
'in the source rack or reservoir!'
self.add_error(msg)
source_pos = None
self._diluent_map[diluent_marker] = source_pos
if not source_pos is None:
self._amount_map[source_pos] = volume + self._source_dead_volume
def _init_column_maps(self):
"""
Initialises the CsvColumnParameters object for the
:attr:`_column_map_list`.
"""
BiomekWorklistWriter._init_column_maps(self)
diluent_info_column = \
CsvColumnParameters.create_csv_parameter_map(
self.DILUENT_INFO_INDEX, self.DILUENT_INFO_HEADER,
self._diluent_info_values)
self._column_map_list.append(diluent_info_column)
class SampleDilutionWorklistWriter(BiomekWorklistWriter):
"""
An abstract base class writing worklist for sample dilution worklists.
**Return Value:** Stream for an CSV file.
"""
NAME = 'Biomek Dilution Worklist Writer'
TRANSFER_TYPE = TRANSFER_TYPES.SAMPLE_DILUTION
#: The name of the optional diluent info column.
DILUENT_INFO_HEADER = 'DiluentInformation'
#: The index of the optional diluent info column.
DILUENT_INFO_INDEX = 5
def __init__(self,
planned_worklist,
target_rack,
source_rack_barcode,
reservoir_specs,
pipetting_specs=None,
ignored_positions=None,
parent=None):
"""
Constructor.
:param str source_rack_barcode: The barcode for the source rack or
reservoir.
:type source_rack_barcode: :class:`str`
"""
BiomekWorklistWriter.__init__(self,
planned_worklist,
target_rack,
pipetting_specs=pipetting_specs,
ignored_positions=ignored_positions,
parent=parent)
#: The barcode for the source rack or reservoir.
self.source_rack_barcode = source_rack_barcode
#: The specs for the source rack or reservoir.
self.reservoir_specs = reservoir_specs
#: The maximum volume of source rack container.
self._source_max_volume = None
#: Values for a column presenting diluent information.
self._diluent_info_values = None
#: Maps source position amounts (volumes) onto diluents.
self._diluent_map = None
#: Maps total diluent amounts (volumes) onto diluents.
self._amount_map = None
#: The last used source rack position.
self.__last_source_rack_pos = None
#: Stores and return empty positions in the source rack.
self.__emtpy_pos_manager = None
# If True, some dilution had to be split because they exceeded the
# maximum allowed transfer volume.
self.__has_split_volumes = False
# If True, some source containers could not take up all liquid required
# so that there is at least one additional source container for
# an diluent.
self.__split_sources = None
def reset(self):
"""
Resets all values except for input values.
"""
BiomekWorklistWriter.reset(self)
self._source_max_volume = None
self._diluent_info_values = []
self._amount_map = dict()
self._diluent_map = dict()
self.__has_split_volumes = False
self.__split_sources = set()
self.__emtpy_pos_manager = None
self.__last_source_rack_pos = None
def _check_input(self):
"""
Checks the input values.
"""
BiomekWorklistWriter._check_input(self)
self._check_input_class('source rack barcode',
self.source_rack_barcode, basestring)
self._check_input_class('reservoir specs', self.reservoir_specs,
ReservoirSpecs)
def _init_source_data(self):
"""
Initialises the source rack related values and lookups.
"""
for rack_pos in get_positions_for_shape(
self.reservoir_specs.rack_shape):
self._source_volumes[rack_pos] = 0
self._source_dead_volume = self.reservoir_specs.min_dead_volume \
* VOLUME_CONVERSION_FACTOR
self._source_max_volume = self.reservoir_specs.max_volume \
* VOLUME_CONVERSION_FACTOR
self.__emtpy_pos_manager = EmptyPositionManager(
rack_shape=self.reservoir_specs.rack_shape)
def _generate_column_values(self):
"""
This method generates the value lists for the CSV columns.
"""
target_rack_barcode = self.target_rack.barcode
sorted_transfers = self.__get_sorted_transfers()
for pt in sorted_transfers:
if pt.target_position in self.ignored_positions:
continue
if not self._check_transfer_volume(pt.volume, pt.target_position):
continue
split_volumes = self.__split_into_transferable_amounts(pt)
for i in range(len(split_volumes)):
volume = round(split_volumes[i], 1)
source_pos = self.__get_and_adjust_source_position(
pt.diluent_info, volume, i)
if self.has_errors():
break
self._source_rack_values.append(self.source_rack_barcode)
self._source_pos_values.append(source_pos.label)
self._volume_values.append(get_trimmed_string(volume))
self._target_rack_values.append(target_rack_barcode)
self._target_pos_values.append(pt.target_position.label)
self._diluent_info_values.append(pt.diluent_info)
if self.__has_split_volumes:
msg = 'Some dilution volumes exceed the allowed maximum transfer ' \
'volume of %s ul. The dilution volumes have been distributed ' \
'over different source wells. Have a look on the generated ' \
'worklist file for details, please.' \
% (get_trimmed_string(self._max_transfer_volume))
self.add_warning(msg)
if len(self.__split_sources) > 0:
msg = 'The source for the following diluents has been split ' \
'and distributed over several containers because one ' \
'single container could not have taken up the required ' \
'volume (max volume of a source container: %s ul, dead ' \
'volume: %s ul): %s. Have a look onto the generated ' \
'worklist files for details, please.' \
% (get_trimmed_string(self.reservoir_specs.max_volume \
* VOLUME_CONVERSION_FACTOR),
get_trimmed_string(self.reservoir_specs.max_dead_volume \
* VOLUME_CONVERSION_FACTOR),
list(self.__split_sources))
self.add_warning(msg)
def __get_sorted_transfers(self):
# Sorts the planned transfers of the worklist by source position.
target_positions = dict()
for plt in self.planned_worklist:
target_pos = plt.target_position
target_positions[target_pos] = plt
sorted_target_positions = sort_rack_positions(target_positions.keys())
sorted_transfers = []
for target_pos in sorted_target_positions:
plt = target_positions[target_pos]
sorted_transfers.append(plt)
return sorted_transfers
def __split_into_transferable_amounts(self, planned_transfer):
# Checks whether the volume is larger than the allowed maximum
# transfer volume and splits it into transferable amounts.
volume = round(planned_transfer.volume * VOLUME_CONVERSION_FACTOR, 1)
if volume <= self._max_transfer_volume:
return [volume]
self.__has_split_volumes = True
no_volumes = ceil(volume / self._max_transfer_volume)
amounts = []
partial_vol = round_up((volume / no_volumes), 1)
while volume > 0:
if volume < partial_vol:
amounts.append(volume)
volume = 0
else:
amounts.append(partial_vol)
volume = volume - partial_vol
amounts.sort()
return amounts
def __get_and_adjust_source_position(self, diluent_info, volume, i):
# Returns the source position for the diluent.
diluent_marker = '%s#%i' % (diluent_info, i)
if not self._diluent_map.has_key(diluent_marker):
self.__init_new_diluent_source(diluent_marker, volume)
else:
source_pos = self._diluent_map[diluent_marker]
stored_amount = self._amount_map[source_pos]
new_amount = stored_amount + volume
if new_amount > self._source_max_volume:
self.__split_sources.add(str(diluent_info))
self.__init_new_diluent_source(diluent_marker, volume)
else:
self._amount_map[source_pos] = new_amount
return self._diluent_map[diluent_marker]
def __init_new_diluent_source(self, diluent_marker, volume):
# Initialises a new source volume container in the source reservoir.
try:
source_pos = self.__emtpy_pos_manager.get_empty_position()
except ValueError:
msg = 'There is not enough space for all source containers ' \
'in the source rack or reservoir!'
self.add_error(msg)
source_pos = None
self._diluent_map[diluent_marker] = source_pos
if not source_pos is None:
self._amount_map[source_pos] = volume + self._source_dead_volume
def _init_column_maps(self):
"""
Initialises the CsvColumnParameters object for the
:attr:`_column_map_list`.
"""
BiomekWorklistWriter._init_column_maps(self)
diluent_info_column = \
CsvColumnParameters.create_csv_parameter_map(
self.DILUENT_INFO_INDEX, self.DILUENT_INFO_HEADER,
self._diluent_info_values)
self._column_map_list.append(diluent_info_column)
