def get_sector_positions(sector_index, rack_shape, number_sectors,
row_count=None, col_count=None):
"""
A helper function return the positions of the given sector.
:param int sector_index: Sector index assuming Z-configuration.
:param int number_sectors: The total number of sectors.
:param rack_shape: The rack shape to be considered.
:type rack_shape: :class:`thelma.entities.rack.RackShape
:param int row_count: The number of sector rows - if you do not provide
a number the row number is calculated assuming a square setup.
:param int col_count: The number of sector columns - if you do not provide
a number the row number is calculated assuming a square setup.
"""
translator = RackSectorTranslator(number_sectors=number_sectors,
source_sector_index=sector_index,
target_sector_index=0,
row_count=row_count, col_count=col_count,
behaviour=RackSectorTranslator.MANY_TO_MANY)
positions = []
for rack_pos in get_positions_for_shape(rack_shape):
# Filter for positions
try:
translator.translate(rack_pos)
except ValueError:
continue
else:
positions.append(rack_pos)
return positions
def get_positions_without_tube(self):
"""
Returns the positions in the rack that are not occupied at the moment.
"""
shape_96 = get_96_rack_shape()
free_positions = []
for rack_pos in get_positions_for_shape(shape_96):
if not self.tubes.has_key(rack_pos):
free_positions.append(rack_pos)
return free_positions
def get_positions_without_tube(self):
"""
Returns the positions in the rack that are not occupied at the moment.
"""
shape_96 = get_96_rack_shape()
free_positions = []
for rack_pos in get_positions_for_shape(shape_96):
if not self.tubes.has_key(rack_pos):
free_positions.append(rack_pos)
return free_positions
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)
def __get_layout(self):
# Fetches the stock sample layout and sorts its positions into
# quadrants.
self.add_debug("Fetch stock sample layout ...")
converter = StockSampleCreationLayoutConverter(self.entity.rack_layout, parent=self)
self.__ssc_layout = converter.get_result()
if self.__ssc_layout is None:
msg = "Error when trying to convert stock sample creation ISO " "layout."
self.add_error(msg)
else:
ssc_positions = self.__ssc_layout.get_positions()
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
if not rack_pos in ssc_positions:
self.__ignore_positions.append(rack_pos)
def __build_preparation_plate_map(self):
for spp in self.iso.iso_sector_preparation_plates:
self.__prep_plate_map[spp.sector_index] = spp
# Record empty positions to ignore later when building the
# dilution jobs.
cnv = StockSampleCreationLayoutConverter(spp.rack_layout,
parent=self)
ssc_layout = cnv.get_result()
self.__ssc_layout_map[spp.sector_index] = ssc_layout
all_poss = get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96)
empty_poss = \
list(set(all_poss).difference(ssc_layout.get_positions()))
self.__empty_stock_rack_positions_map[spp.sector_index] = \
empty_poss
def __build_preparation_plate_map(self):
for spp in self.iso.iso_sector_preparation_plates:
self.__prep_plate_map[spp.sector_index] = spp
# Record empty positions to ignore later when building the
# dilution jobs.
cnv = StockSampleCreationLayoutConverter(spp.rack_layout,
parent=self)
ssc_layout = cnv.get_result()
self.__ssc_layout_map[spp.sector_index] = ssc_layout
all_poss = get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96)
empty_poss = \
list(set(all_poss).difference(ssc_layout.get_positions()))
self.__empty_stock_rack_positions_map[spp.sector_index] = \
empty_poss
def __verify_pool_stock_rack(self):
# Makes sure there are empty tubes in all required positions and none
# in positions that must be empty.
converter = PoolCreationStockRackLayoutConverter(self.__pool_stock_rack.rack_layout, parent=self)
layout = converter.get_result()
if layout is None:
msg = "Error when trying to convert pool stock rack layout!"
self.add_error(msg)
else:
additional_tubes = []
non_empty_tube = []
positions = layout.get_positions()
tube_positions = set()
rack = self.__pool_stock_rack.rack
for tube in rack.containers:
rack_pos = tube.location.position
tube_positions.add(rack_pos)
info = "%s (%s)" % (tube.barcode, rack_pos.label)
if not rack_pos in positions:
additional_tubes.append(info)
elif not tube.sample is None:
non_empty_tube.append(info)
missing_tube = []
for rack_pos in get_positions_for_shape(layout.shape):
sr_pos = layout.get_working_position(rack_pos)
if sr_pos is None:
continue
elif rack_pos not in tube_positions:
missing_tube.append(rack_pos.label)
if len(additional_tubes) > 0:
msg = (
"There are unexpected tubes in the pool stock rack "
"(%s): %s. Please remove them and try again."
% (rack.barcode, self._get_joined_str(additional_tubes))
)
self.add_error(msg)
if len(non_empty_tube) > 0:
msg = (
"The following tubes in the pool stock rack (%s) are "
"not empty: %s. Please replace them by empty tubes and "
"try again." % (rack.barcode, self._get_joined_str(non_empty_tube))
)
self.add_error(msg)
if len(missing_tube) > 0:
msg = "There are tubes missing in the following positions " "of the pool stock rack (%s): %s." % (
rack.barcode,
self._get_joined_str(missing_tube),
)
self.add_error(msg)
def __get_layout(self):
# Fetches the stock sample layout and sorts its positions into
# quadrants.
self.add_debug('Fetch stock sample layout ...')
converter = StockSampleCreationLayoutConverter(self.entity.rack_layout,
parent=self)
self.__ssc_layout = converter.get_result()
if self.__ssc_layout is None:
msg = 'Error when trying to convert stock sample creation ISO ' \
'layout.'
self.add_error(msg)
else:
ssc_positions = self.__ssc_layout.get_positions()
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
if not rack_pos in ssc_positions:
self.__ignore_positions.append(rack_pos)
def _create_iso_layout(self):
"""
Creates a :class:`StockSampleCreationLayout` for a single ISO.
Positions are populated column-wise.
"""
ssc_layout = StockSampleCreationLayout()
for rack_pos in get_positions_for_shape(ssc_layout.shape,
vertical_sorting=True):
if not self._have_candidates:
break
pool_cand = self._pool_candidates.pop(0)
ssc_pos = \
StockSampleCreationPosition(rack_pos,
pool_cand.pool,
pool_cand.get_tube_barcodes())
ssc_layout.add_position(ssc_pos)
return ssc_layout
def __verify_pool_stock_rack(self):
# Makes sure there are empty tubes in all required positions and none
# in positions that must be empty.
converter = PoolCreationStockRackLayoutConverter(
self.__pool_stock_rack.rack_layout, parent=self)
layout = converter.get_result()
if layout is None:
msg = 'Error when trying to convert pool stock rack layout!'
self.add_error(msg)
else:
additional_tubes = []
non_empty_tube = []
positions = layout.get_positions()
tube_positions = set()
rack = self.__pool_stock_rack.rack
for tube in rack.containers:
rack_pos = tube.location.position
tube_positions.add(rack_pos)
info = '%s (%s)' % (tube.barcode, rack_pos.label)
if not rack_pos in positions:
additional_tubes.append(info)
elif not tube.sample is None:
non_empty_tube.append(info)
missing_tube = []
for rack_pos in get_positions_for_shape(layout.shape):
sr_pos = layout.get_working_position(rack_pos)
if sr_pos is None:
continue
elif rack_pos not in tube_positions:
missing_tube.append(rack_pos.label)
if len(additional_tubes) > 0:
msg = 'There are unexpected tubes in the pool stock rack ' \
'(%s): %s. Please remove them and try again.' \
% (rack.barcode, self._get_joined_str(additional_tubes))
self.add_error(msg)
if len(non_empty_tube) > 0:
msg = 'The following tubes in the pool stock rack (%s) are ' \
'not empty: %s. Please replace them by empty tubes and ' \
'try again.' % (rack.barcode,
self._get_joined_str(non_empty_tube))
self.add_error(msg)
if len(missing_tube) > 0:
msg = 'There are tubes missing in the following positions ' \
'of the pool stock rack (%s): %s.' % (rack.barcode,
self._get_joined_str(missing_tube))
self.add_error(msg)
def _create_iso_layout(self):
"""
Creates a :class:`StockSampleCreationLayout` for a single ISO.
Positions are populated column-wise.
"""
ssc_layout = StockSampleCreationLayout()
for rack_pos in get_positions_for_shape(ssc_layout.shape,
vertical_sorting=True):
if not self._have_candidates:
break
pool_cand = self._pool_candidates.pop(0)
ssc_pos = \
StockSampleCreationPosition(rack_pos,
pool_cand.pool,
pool_cand.get_tube_barcodes())
ssc_layout.add_position(ssc_pos)
return ssc_layout
def get_empty_position(self):
"""
Returns the position with the lowest column and row index
(and removes it from the pool).
:raises ValueError: If there is no empty position left.
"""
picked_position = None
for rack_pos in get_positions_for_shape(self.rack_shape):
if rack_pos in self._all_empty_positions:
picked_position = rack_pos
break
if picked_position is None:
raise ValueError('No empty position left!')
self._all_empty_positions.discard(picked_position)
return picked_position
def get_empty_position(self):
"""
Returns the position with the lowest column and row index
(and removes it from the pool).
:raises ValueError: If there is no empty position left.
"""
picked_position = None
for rack_pos in get_positions_for_shape(self.rack_shape):
if rack_pos in self._all_empty_positions:
picked_position = rack_pos
break
if picked_position is None:
raise ValueError('No empty position left!')
self._all_empty_positions.discard(picked_position)
return picked_position
def __create_transfers(self):
# Creates a :class:`PlannedSampleDilution` for each rack position
# in a 8x12 rack shape.
self.add_debug('Create transfers ...')
self._run_and_record_error(self.volume_calculator.calculate,
'Error when trying to determine buffer volume: ',
ValueError)
buffer_volume = self.volume_calculator.get_buffer_volume()
if buffer_volume is not None:
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
wl_label = LABELS.create_buffer_worklist_label(
self.iso_request_label)
wl = PlannedWorklist(wl_label,
TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_cybio())
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
psd = PlannedSampleDilution.get_entity(volume=volume,
target_position=rack_pos, diluent_info=DILUENT_INFO)
wl.planned_liquid_transfers.append(psd)
self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
def compare_ignoring_untreated_types(layout1, layout2):
"""
Compares two transfection layouts ignoring potential untreated
positions.
"""
if layout1.shape != layout2.shape: return False
for rack_pos in get_positions_for_shape(layout1.shape):
tf1 = layout1.get_working_position(rack_pos)
tf2 = layout2.get_working_position(rack_pos)
if tf1 is None and tf2 is None: continue
if tf1 is not None and (tf1.is_untreated_type or tf1.is_empty):
tf1 = None
if tf2 is not None and (tf2.is_untreated_type or tf2.is_empty):
tf2 = None
if tf1 is None and tf2 is None:
continue
elif not tf1 == tf2:
return False
return True
def __create_transfers(self):
# Creates a :class:`PlannedSampleDilution` for each rack position
# in a 8x12 rack shape.
self.add_debug('Create transfers ...')
self._run_and_record_error(
self.volume_calculator.calculate,
'Error when trying to determine buffer volume: ', ValueError)
buffer_volume = self.volume_calculator.get_buffer_volume()
if buffer_volume is not None:
volume = buffer_volume / VOLUME_CONVERSION_FACTOR
wl_label = LABELS.create_buffer_worklist_label(
self.iso_request_label)
wl = PlannedWorklist(wl_label, TRANSFER_TYPES.SAMPLE_DILUTION,
get_pipetting_specs_cybio())
for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
psd = PlannedSampleDilution.get_entity(
volume=volume,
target_position=rack_pos,
diluent_info=DILUENT_INFO)
wl.planned_liquid_transfers.append(psd)
self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
def __create_layout_from_map(self):
"""
Creates the actual working layout object.
"""
self.add_debug('Convert position map into working layout.')
working_layout = self._initialize_working_layout(self.rack_layout.shape)
for rack_position in get_positions_for_shape(self.rack_layout.shape):
working_position = self.__position_map[rack_position]
if working_position is None: continue
self._run_and_record_error(working_layout.add_position,
base_msg='Error when trying to add position to layout: ',
error_types=set([ValueError, AttributeError, KeyError,
TypeError]),
**dict(working_position=working_position))
if self.has_errors(): break
if self.has_errors(): return None
self._perform_layout_validity_checks(working_layout)
if self.has_errors(): return None
return working_layout
def compare_ignoring_untreated_types(layout1, layout2):
"""
Compares two transfection layouts ignoring potential untreated
positions.
"""
if layout1.shape != layout2.shape: return False
for rack_pos in get_positions_for_shape(layout1.shape):
tf1 = layout1.get_working_position(rack_pos)
tf2 = layout2.get_working_position(rack_pos)
if tf1 is None and tf2 is None: continue
if tf1 is not None and (tf1.is_untreated_type or tf1.is_empty):
tf1 = None
if tf2 is not None and (tf2.is_untreated_type or tf2.is_empty):
tf2 = None
if tf1 is None and tf2 is None:
continue
elif not tf1 == tf2:
return False
return True
def __get_values_for_rack_layout(self, validators, rack_layout):
"""
Finds the parameters values for each position in a design rack layout.
"""
shape_positions = get_positions_for_shape(self._rack_shape)
# Initialise the value maps
value_maps = dict()
for parameter in validators.keys():
rack_pos_dict = dict()
for rack_pos in shape_positions:
rack_pos_dict[rack_pos] = None
value_maps[parameter] = rack_pos_dict
for trps in rack_layout.tagged_rack_position_sets:
for tag in trps.tags:
for parameter, validator in validators.iteritems():
if validator.has_alias(tag.predicate):
value_map = value_maps[parameter]
for rack_pos in trps.rack_position_set:
value_map[rack_pos] = tag.value
return value_maps
def __get_values_for_rack_layout(self, validators, rack_layout):
"""
Finds the parameters values for each position in a design rack layout.
"""
shape_positions = get_positions_for_shape(self._rack_shape)
# Initialise the value maps
value_maps = dict()
for parameter in validators.keys():
rack_pos_dict = dict()
for rack_pos in shape_positions:
rack_pos_dict[rack_pos] = None
value_maps[parameter] = rack_pos_dict
for trps in rack_layout.tagged_rack_position_sets:
for tag in trps.tags:
for parameter, validator in validators.iteritems():
if validator.has_alias(tag.predicate):
value_map = value_maps[parameter]
for rack_pos in trps.rack_position_set:
value_map[rack_pos] = tag.value
return value_maps
def run(self):
"""
Runs the conversion.
"""
self.reset()
self.add_info('Start conversion ...')
self._check_input()
if not self.has_errors():
self._initialize_parameter_validators()
self._initialize_other_attributes()
self.__check_parameter_completeness()
if not self.has_errors():
for rack_position in get_positions_for_shape(self.rack_layout.shape):
tag_set = self.rack_layout.get_tags_for_position(rack_position)
parameter_map = self._get_parameter_map(tag_set, rack_position)
working_position = self.__obtain_working_position(parameter_map)
self.__position_map[rack_position] = working_position
self._record_errors()
if not self.has_errors():
self.return_value = self.__create_layout_from_map()
self.add_info('Layout conversion completed.')
def __check_value_presence(self, value_maps, label):
"""
Checks the presence of mandatory, optional and forbidden parameters
for each rack position in a layout.
"""
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
pool_forbidden = TransfectionParameters.MOLECULE_DESIGN_POOL in \
self.__forbidden_parameters
non_empty = []
missing_value = dict()
additional_values = dict()
inconsistent_optionals = dict()
for rack_pos in get_positions_for_shape(self._rack_shape):
pool_id = pool_map[rack_pos]
is_untreated = (isinstance(pool_id, basestring) and \
TransfectionParameters.is_untreated_type(pool_id.lower()))
if is_untreated: continue
if pool_id is None: # Empty position should not have values
for parameter, value_map in value_maps.iteritems():
if not value_map[rack_pos] is None:
non_empty.append(rack_pos.label)
break
if not pool_forbidden: continue
for parameter, value_map in value_maps.iteritems():
if parameter == TransfectionParameters.MOLECULE_DESIGN_POOL:
continue
elif pool_id == MOCK_POSITION_TYPE and \
parameter == TransfectionParameters.FINAL_CONCENTRATION:
continue
value = value_map[rack_pos]
# Check consistency of definition
present_parameter = self.__parameter_presence[parameter]
if present_parameter and value is None:
if not inconsistent_optionals.has_key(parameter):
inconsistent_optionals[parameter] = []
inconsistent_optionals[parameter].append(rack_pos.label)
elif not present_parameter and not value is None and \
not pool_forbidden:
self.__parameter_presence[parameter] = True
# Check mandatory and forbidden parameters
if parameter in self.__mandatory_parameters and \
value is None:
if not missing_value.has_key(parameter):
missing_value[parameter] = []
missing_value[parameter].append(rack_pos.label)
elif parameter in self.__forbidden_parameters and \
not value is None:
if not additional_values.has_key(parameter):
additional_values[parameter] = []
info = '%s (%s)' % (rack_pos.label, value)
additional_values[parameter].append(info)
# Error recording
if len(non_empty) > 0 and not pool_forbidden:
msg = 'Some rack positions in design rack %s contain values ' \
'although there are no molecule designs for them: %s.' \
% (label, ', '.join(sorted(non_empty)))
self.add_error(msg)
if len(missing_value) > 0:
records_str = self.__get_error_record_string(missing_value)
msg = 'There are mandatory values missing for some rack ' \
'positions in design rack %s: %s. Assumed scenario: %s.' \
% (label, records_str, self.scenario.display_name)
self.add_error(msg)
if len(additional_values) > 0:
records_str = self.__get_error_record_string(additional_values)
msg = 'Some factors must not be specified in %s scenarios. The ' \
'following position in design rack %s contain ' \
'specifications for forbidden factors: %s.' \
% (self.scenario.display_name, label, records_str)
self.add_error(msg)
if len(inconsistent_optionals) > 0:
records_str = self.__get_error_record_string(
inconsistent_optionals)
msg = 'If you specify a factor, you have to specify it for each ' \
'non-empty well in all design racks. The following wells ' \
'in design rack %s lack a specification: %s.' \
% (label, records_str)
self.add_error(msg)
def __check_value_presence(self, value_maps, label):
"""
Checks the presence of mandatory, optional and forbidden parameters
for each rack position in a layout.
"""
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
pool_forbidden = TransfectionParameters.MOLECULE_DESIGN_POOL in \
self.__forbidden_parameters
non_empty = []
missing_value = dict()
additional_values = dict()
inconsistent_optionals = dict()
for rack_pos in get_positions_for_shape(self._rack_shape):
pool_id = pool_map[rack_pos]
is_untreated = (isinstance(pool_id, basestring) and \
TransfectionParameters.is_untreated_type(pool_id.lower()))
if is_untreated: continue
if pool_id is None: # Empty position should not have values
for parameter, value_map in value_maps.iteritems():
if not value_map[rack_pos] is None:
non_empty.append(rack_pos.label)
break
if not pool_forbidden: continue
for parameter, value_map in value_maps.iteritems():
if parameter == TransfectionParameters.MOLECULE_DESIGN_POOL:
continue
elif pool_id == MOCK_POSITION_TYPE and \
parameter == TransfectionParameters.FINAL_CONCENTRATION:
continue
value = value_map[rack_pos]
# Check consistency of definition
present_parameter = self.__parameter_presence[parameter]
if present_parameter and value is None:
if not inconsistent_optionals.has_key(parameter):
inconsistent_optionals[parameter] = []
inconsistent_optionals[parameter].append(rack_pos.label)
elif not present_parameter and not value is None and \
not pool_forbidden:
self.__parameter_presence[parameter] = True
# Check mandatory and forbidden parameters
if parameter in self.__mandatory_parameters and \
value is None:
if not missing_value.has_key(parameter):
missing_value[parameter] = []
missing_value[parameter].append(rack_pos.label)
elif parameter in self.__forbidden_parameters and \
not value is None:
if not additional_values.has_key(parameter):
additional_values[parameter] = []
info = '%s (%s)' % (rack_pos.label, value)
additional_values[parameter].append(info)
# Error recording
if len(non_empty) > 0 and not pool_forbidden:
msg = 'Some rack positions in design rack %s contain values ' \
'although there are no molecule designs for them: %s.' \
% (label, ', '.join(sorted(non_empty)))
self.add_error(msg)
if len(missing_value) > 0:
records_str = self.__get_error_record_string(missing_value)
msg = 'There are mandatory values missing for some rack ' \
'positions in design rack %s: %s. Assumed scenario: %s.' \
% (label, records_str, self.scenario.display_name)
self.add_error(msg)
if len(additional_values) > 0:
records_str = self.__get_error_record_string(additional_values)
msg = 'Some factors must not be specified in %s scenarios. The ' \
'following position in design rack %s contain ' \
'specifications for forbidden factors: %s.' \
% (self.scenario.display_name, label, records_str)
self.add_error(msg)
if len(inconsistent_optionals) > 0:
records_str = self.__get_error_record_string(inconsistent_optionals)
msg = 'If you specify a factor, you have to specify it for each ' \
'non-empty well in all design racks. The following wells ' \
'in design rack %s lack a specification: %s.' \
% (label, records_str)
self.add_error(msg)
def _init_empty_positions(self):
"""
Initialises the maps.
"""
for rack_pos in get_positions_for_shape(self.rack_shape):
self._all_empty_positions.add(rack_pos)
def _init_empty_positions(self):
"""
Initialises the maps.
"""
for rack_pos in get_positions_for_shape(self.rack_shape):
self._all_empty_positions.add(rack_pos)
