def get_sector_layouts_for_384_layout(layout, sector_layout_class=None):
"""
Converts the given 384 layout into four 96 well sector layouts of the
given layout class.
:param sector_layout_class: Class to use for the sector layouts.
:returns: map sector index -> 96 well layout
:rtype: dict
"""
if sector_layout_class is None:
sector_layout_class = type(layout)
sec_pos_map_384 = QuadrantIterator.sort_into_sectors(layout, 4)
rs96 = get_96_rack_shape()
sec_layout_map = {}
for sec_idx in range(4):
sec_wrk_poss_384 = sec_pos_map_384[sec_idx]
if len(sec_wrk_poss_384) < 1:
# FIXME: Should break here.
continue
trl = RackSectorTranslator(4, sec_idx, 0,
behaviour=RackSectorTranslator.ONE_TO_MANY)
sec_layout = sector_layout_class(rs96)
for sec_wrk_pos_384 in sec_wrk_poss_384:
sec_pos_96 = trl.translate(sec_wrk_pos_384.rack_position)
sec_wrk_pos_96 = sec_wrk_pos_384.clone()
sec_wrk_pos_96.rack_position = sec_pos_96
sec_layout.add_position(sec_wrk_pos_96)
sec_layout_map[sec_idx] = sec_layout
return sec_layout_map
def __set_source_values(self):
"""
There are two sizes available: 96 positions and 384 positions. If
possible (less than 97 distinct hash values), we use the smaller one.
Also sets the source rack shape and minimum row distances.
"""
self.add_debug('Determine rack shape ...')
small_shape = get_96_rack_shape()
large_shape = get_384_rack_shape()
if len(self._hash_values) > large_shape.size:
msg = 'The number of source positions (%i) exceeds %i! ' \
'Redesign your experiment or talk to the IT ' \
'department, please.' \
% (len(self._hash_values), large_shape.size)
self.add_error(msg)
elif len(self._hash_values) > small_shape.size:
source_rack_shape = large_shape
else:
source_rack_shape = small_shape
if not self.has_errors():
self._source_layout = self._init_source_layout(source_rack_shape)
self.__source_rack_shape = self._source_layout.shape
if self.__source_rack_shape.name == RACK_SHAPE_NAMES.SHAPE_384:
self.__src_min_row_distance = 1
else:
self.__src_min_row_distance = 0
target_layout_shape = self._get_target_layout_shape()
if target_layout_shape.name == RACK_SHAPE_NAMES.SHAPE_384:
self.__trg_min_row_distance = 1
else:
self.__trg_min_row_distance = 0
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 run(self):
self.reset()
self.add_info('Start ISO reset ...')
self.__check_input()
if not self.has_errors():
for iso in self.isos:
iso.molecule_design_pool_set = None
iso.rack_layout = RackLayout(get_96_rack_shape())
self.return_value = self.isos
self.add_info('ISO reset completed.')
def run(self):
self.reset()
self.add_info('Start ISO reset ...')
self.__check_input()
if not self.has_errors():
for iso in self.isos:
iso.molecule_design_pool_set = None
iso.rack_layout = RackLayout(get_96_rack_shape())
self.return_value = self.isos
self.add_info('ISO reset completed.')
def __init__(self, rack_barcode, timestamp):
"""
Constructor
"""
#: The barcode of the scanned rack.
self.rack_barcode = rack_barcode
#: The timestamp of the scanning file.
self.timestamp = timestamp
#: The shape of the layout (:class:`thelma.entities.rack.RackShape`)
self.shape = get_96_rack_shape()
#: Maps tube barcodes onto rack positions.
self._position_map = dict()
def __make_generate_isos_patch_representation(self, iso_request):
isor = iso_request.get_entity()
# FIXME: The status should be part of the ISO_STATUS const group.
iso = LabIso('NEW ISO',
0,
RackLayout(shape=get_96_rack_shape()),
iso_request=isor,
status='NEW')
isor.isos.append(iso)
rpr = as_representer(iso_request, XmlMime)
patch_ctxt = self.__get_patch_context(iso_request,
('isos', ('isos', 'status')))
with patch_ctxt:
rpr_str = rpr.to_string(iso_request)
return rpr_str
def __make_generate_isos_patch_representation(self, iso_request):
isor = iso_request.get_entity()
# FIXME: The status should be part of the ISO_STATUS const group.
iso = LabIso('NEW ISO',
0,
RackLayout(shape=get_96_rack_shape()),
iso_request=isor,
status='NEW')
isor.isos.append(iso)
rpr = as_representer(iso_request, XmlMime)
patch_ctxt = self.__get_patch_context(iso_request,
('isos', ('isos', 'status')))
with patch_ctxt:
rpr_str = rpr.to_string(iso_request)
return rpr_str
def _initialize_parser_keys(self):
"""
We need to set floating related parser values. Also the allowed
layout dimension are the fixed (96-well or 384-well).
"""
parameter_set = MoleculeDesignPoolParameters
validator = parameter_set.create_validator_from_parameter(
parameter_set.MOLECULE_DESIGN_POOL)
self.parser.molecule_design_id_predicates = validator.aliases
self.parser.no_id_indicator = parameter_set.FLOATING_INDICATOR
shape96 = get_96_rack_shape()
shape384 = get_384_rack_shape()
self.parser.allowed_rack_dimensions = [
(shape96.number_rows, shape96.number_columns),
(shape384.number_rows, shape384.number_columns)]
def _initialize_parser_keys(self):
"""
We need to set floating related parser values. Also the allowed
layout dimension are the fixed (96-well or 384-well).
"""
parameter_set = MoleculeDesignPoolParameters
validator = parameter_set.create_validator_from_parameter(
parameter_set.MOLECULE_DESIGN_POOL)
self.parser.molecule_design_id_predicates = validator.aliases
self.parser.no_id_indicator = parameter_set.FLOATING_INDICATOR
shape96 = get_96_rack_shape()
shape384 = get_384_rack_shape()
self.parser.allowed_rack_dimensions = [
(shape96.number_rows, shape96.number_columns),
(shape384.number_rows, shape384.number_columns)
]
def __sort_into_sectors(self):
# Create a rack layout for each quadrant.
self.add_debug('Sort positions into sectors ...')
quadrant_positions = QuadrantIterator.sort_into_sectors(
self.base_layout, NUMBER_SECTORS)
rack_shape_96 = get_96_rack_shape()
for sector_index, positions in quadrant_positions.iteritems():
if len(positions) < 1: continue
base_layout = LibraryBaseLayout(shape=rack_shape_96)
for pos in positions:
base_layout.add_position(pos)
if len(base_layout) > 0:
self.__quadrant_layouts[sector_index] = base_layout
if len(self.__quadrant_layouts) < NUMBER_SECTORS:
missing_sectors = []
for sector_index in range(NUMBER_SECTORS):
if not self.__quadrant_layouts.has_key(sector_index):
missing_sectors.append(str(sector_index + 1))
msg = 'Some rack sectors are empty. You do not require stock ' \
'racks for them: %s!' % (', '.join(missing_sectors))
self.add_warning(msg)
def __create_isos(self):
# Creates the ISOs. At this the tool checks whether there are already
# ISOs at the ISO request. The tool add ISOs until the number of plates
# (ISO request attribute) is reached.
self.add_debug('Create ISOs ...')
current_iso_count = len(self.iso_request.isos)
new_iso_count = self.iso_request.expected_number_isos
for i in range(current_iso_count, new_iso_count):
layout_number = i + 1
iso_label = LABELS.create_iso_label(self.iso_request.label,
layout_number)
ticket_number = self.__get_ticket_number(iso_label, layout_number)
if ticket_number is None:
break
# FIXME: Using side effect of instantiation.
StockSampleCreationIso(iso_label,
self.iso_request.number_designs,
RackLayout(shape=get_96_rack_shape()),
ticket_number,
layout_number,
iso_request=self.iso_request)
self.__new_iso_counter += 1
def __create_isos(self):
# Creates the ISOs. At this the tool checks whether there are already
# ISOs at the ISO request. The tool add ISOs until the number of plates
# (ISO request attribute) is reached.
self.add_debug('Create ISOs ...')
current_iso_count = len(self.iso_request.isos)
new_iso_count = self.iso_request.expected_number_isos
for i in range(current_iso_count, new_iso_count):
layout_number = i + 1
iso_label = LABELS.create_iso_label(self.iso_request.label,
layout_number)
ticket_number = self.__get_ticket_number(iso_label, layout_number)
if ticket_number is None:
break
# FIXME: Using side effect of instantiation.
StockSampleCreationIso(iso_label,
self.iso_request.number_designs,
RackLayout(shape=get_96_rack_shape()),
ticket_number,
layout_number,
iso_request=self.iso_request)
self.__new_iso_counter += 1
def _get_number_of_avaible_positions(self):
"""
Returns the number of positions available for the new pools in the
final stock rack or plate.
"""
return len(get_96_rack_shape())
def _get_number_of_avaible_positions(self):
"""
Returns the number of positions available for the new pools in the
final stock rack or plate.
"""
return len(get_96_rack_shape())
