def _get_layouts(self):
"""
The final layouts and ISO preparation layouts for all ISOs are
compared and then a reference layout for each rack marker is picked.
For job preparation plates, we store layout and rack.
"""
for prep_plate in self.entity.iso_job_preparation_plates:
converter = LabIsoPrepLayoutConverter(
rack_layout=prep_plate.rack_layout, parent=self)
plate_label = prep_plate.rack.label
error_label = 'job preparation plate "%s"' % (
prep_plate.rack.label)
self._store_plate_layout(plate_label, converter, error_label)
self._store_rack_container(prep_plate.rack,
LABELS.ROLE_PREPARATION_JOB,
plate_label)
final_layouts = dict()
for iso in self.entity.isos:
converter = FinalLabIsoLayoutConverter(rack_layout=iso.rack_layout,
parent=self)
error_label = 'final plate layout for ISO "%s"' % (iso.label)
self._store_plate_layout(iso.label, converter, error_label)
if self.has_errors(): continue
self._store_final_plate_data(iso)
final_layouts[iso.label] = self._plate_layouts[iso.label]
self.__compare_final_layouts(final_layouts)
self.__compare_iso_preparation_layouts()
def __compare_iso_preparation_layouts(self):
# If we have starting wells for the job in ISO preparation plates and
# more than one ISO in the job, we need to remove duplicates (to avoid
# generation of duplicate transfers in stock worklists).
# We store the layout of a reference plate (using the label of this
# plate as key). Plate containers are stored for all plates.
position_map = dict()
reference_plates = dict()
reference_layouts = dict()
for iso in self.entity.isos:
if self.has_errors(): break
for ipp in iso.iso_preparation_plates:
plate = ipp.rack
plate_label = plate.label
value_parts = LABELS.parse_rack_label(plate_label)
rack_marker = value_parts[LABELS.MARKER_RACK_MARKER]
self._store_rack_container(rack=plate,
label=plate_label,
rack_marker=rack_marker,
role=LABELS.ROLE_PREPARATION_ISO)
converter = LabIsoPrepLayoutConverter(
rack_layout=ipp.rack_layout, parent=self)
layout = converter.get_result()
if layout is None:
msg = 'Error when trying to convert ISO preparation ' \
'plate layout for plate "%s".' % (plate_label)
self.add_error(msg)
break
positions = []
for prep_pos in layout.get_sorted_working_positions():
if prep_pos.is_fixed and prep_pos.is_starting_well:
positions.append(prep_pos)
if not position_map.has_key(rack_marker):
position_map[rack_marker] = positions
reference_plates[rack_marker] = plate
reference_layouts[rack_marker] = layout
elif not position_map[rack_marker] == positions:
msg = 'The ISO preparation plates for rack type "%s" are ' \
'inconsistent!' % (rack_marker)
self.add_error(msg)
break
for rack_marker, plate in reference_plates.iteritems():
layout = reference_layouts[rack_marker]
self._plate_layouts[plate.label] = layout
def __compare_iso_preparation_layouts(self):
# If we have starting wells for the job in ISO preparation plates and
# more than one ISO in the job, we need to remove duplicates (to avoid
# generation of duplicate transfers in stock worklists).
# We store the layout of a reference plate (using the label of this
# plate as key). Plate containers are stored for all plates.
position_map = dict()
reference_plates = dict()
reference_layouts = dict()
for iso in self.entity.isos:
if self.has_errors(): break
for ipp in iso.iso_preparation_plates:
plate = ipp.rack
plate_label = plate.label
value_parts = LABELS.parse_rack_label(plate_label)
rack_marker = value_parts[LABELS.MARKER_RACK_MARKER]
self._store_rack_container(rack=plate, label=plate_label,
rack_marker=rack_marker, role=LABELS.ROLE_PREPARATION_ISO)
converter = LabIsoPrepLayoutConverter(
rack_layout=ipp.rack_layout,
parent=self)
layout = converter.get_result()
if layout is None:
msg = 'Error when trying to convert ISO preparation ' \
'plate layout for plate "%s".' % (plate_label)
self.add_error(msg)
break
positions = []
for prep_pos in layout.get_sorted_working_positions():
if prep_pos.is_fixed and prep_pos.is_starting_well:
positions.append(prep_pos)
if not position_map.has_key(rack_marker):
position_map[rack_marker] = positions
reference_plates[rack_marker] = plate
reference_layouts[rack_marker] = layout
elif not position_map[rack_marker] == positions:
msg = 'The ISO preparation plates for rack type "%s" are ' \
'inconsistent!' % (rack_marker)
self.add_error(msg)
break
for rack_marker, plate in reference_plates.iteritems():
layout = reference_layouts[rack_marker]
self._plate_layouts[plate.label] = layout
def _fetch_expected_layout(self):
"""
The layouts for preparation plates can be derived from the plate entity.
Final plate layouts must be delivered because they are stored at the
ISO.
"""
if isinstance(self.lab_iso_plate, (IsoAliquotPlate, LibraryPlate)):
msg = 'The reference layout for a final ISO plate must not ' \
'be None!'
self.add_error(msg)
elif isinstance(self.lab_iso_plate,
(IsoPreparationPlate, IsoJobPreparationPlate)):
converter = LabIsoPrepLayoutConverter(
self.lab_iso_plate.rack_layout, parent=self)
self._expected_layout = converter.get_result()
if self._expected_layout is None:
msg = 'Error when trying to convert preparation plate layout!'
self.add_error(msg)
else:
msg = 'Unexpected ISO plate type: %s.' \
% (self.lab_iso_plate.__class__.__name__)
self.add_error(msg)
def _fetch_expected_layout(self):
"""
The layouts for preparation plates can be derived from the plate entity.
Final plate layouts must be delivered because they are stored at the
ISO.
"""
if isinstance(self.lab_iso_plate, (IsoAliquotPlate, LibraryPlate)):
msg = 'The reference layout for a final ISO plate must not ' \
'be None!'
self.add_error(msg)
elif isinstance(self.lab_iso_plate, (IsoPreparationPlate,
IsoJobPreparationPlate)):
converter = LabIsoPrepLayoutConverter(
self.lab_iso_plate.rack_layout,
parent=self)
self._expected_layout = converter.get_result()
if self._expected_layout is None:
msg = 'Error when trying to convert preparation plate layout!'
self.add_error(msg)
else:
msg = 'Unexpected ISO plate type: %s.' \
% (self.lab_iso_plate.__class__.__name__)
self.add_error(msg)
def _get_layouts(self):
"""
There is one final layout for the ISO. There can be preparation plates
as well.
"""
for prep_plate in self.entity.iso_preparation_plates:
converter = LabIsoPrepLayoutConverter(
rack_layout=prep_plate.rack_layout, parent=self)
plate_label = prep_plate.rack.label
error_label = \
'ISO preparation plate "%s"' % (prep_plate.rack.label)
self._store_plate_layout(plate_label, converter, error_label)
self._store_rack_container(prep_plate.rack,
LABELS.ROLE_PREPARATION_ISO,
plate_label)
converter = FinalLabIsoLayoutConverter(
rack_layout=self.entity.rack_layout, parent=self)
self._store_plate_layout(LABELS.ROLE_FINAL, converter,
'final ISO plate layout')
self._store_final_plate_data(self.entity)
def _store_and_verify_plate(self, iso_plate, layout=None, verify=True):
"""
Convenience method verifying and storing the plate as rack container
in the :attr:`_rack_containers` map (mapped onto the rack marker).
If the expected ISO status is queued all plates must be empty,
otherwise we need a :class:`LabIsoPlateVerifier`.
"""
plate = iso_plate.rack
rack_name = '%s (%s)' % (plate.barcode, plate.label)
if self._expected_iso_status == ISO_STATUS.QUEUED and verify:
sample_positions = []
for well in plate.containers:
if well.sample is not None:
if layout is not None:
ip = layout.get_working_position(well.position)
if ip is not None and ip.is_library: continue
sample_positions.append(well.position.label)
if len(sample_positions) > 0:
msg = 'Plate %s should be empty but there are samples in ' \
'the following positions: %s.' \
% (plate.label, self._get_joined_str(sample_positions))
self.add_error(msg)
return None
if not isinstance(iso_plate, (IsoAliquotPlate, LibraryPlate)):
converter = LabIsoPrepLayoutConverter(iso_plate.rack_layout,
parent=self)
layout = converter.get_result()
if layout is None:
msg = 'Error when trying to convert layout of plate "%s"!' \
% (plate.label)
self.add_error(msg)
return None
else:
self.__plate_layouts[plate.label] = layout
elif verify:
verifier = LabIsoPlateVerifier(iso_plate,
self.ENTITY_CLS == IsoJob,
lab_iso_layout=layout,
parent=self)
compatible = verifier.get_result()
if compatible is None:
msg = 'Error when trying to verify plate %s!' % (rack_name)
self.add_error(msg)
return None
elif not compatible:
msg = 'Rack %s does not match the expected layout!' \
% (rack_name)
self.add_error(msg)
return None
elif layout is None:
self.__plate_layouts[plate.label] = \
verifier.get_expected_layout()
iso = None
if self._processing_order == LAB_ISO_ORDERS.NO_ISO and \
isinstance(iso_plate, LibraryPlate):
rack_marker = LABELS.ROLE_FINAL
iso = iso_plate.lab_iso
else:
values = LABELS.parse_rack_label(plate.label)
rack_marker = values[LABELS.MARKER_RACK_MARKER]
rack_container = IsoRackContainer(rack=plate, rack_marker=rack_marker)
if rack_container.role == LABELS.ROLE_FINAL:
rack_marker = LABELS.ROLE_FINAL
if iso is None: iso = iso_plate.iso
add_list_map_element(self.__final_plates, iso, rack_container)
add_list_map_element(self.__rack_containers, rack_marker,
rack_container)
def _store_and_verify_plate(self, iso_plate, layout=None, verify=True):
"""
Convenience method verifying and storing the plate as rack container
in the :attr:`_rack_containers` map (mapped onto the rack marker).
If the expected ISO status is queued all plates must be empty,
otherwise we need a :class:`LabIsoPlateVerifier`.
"""
plate = iso_plate.rack
rack_name = '%s (%s)' % (plate.barcode, plate.label)
if self._expected_iso_status == ISO_STATUS.QUEUED and verify:
sample_positions = []
for well in plate.containers:
if well.sample is not None:
if layout is not None:
ip = layout.get_working_position(well.position)
if ip is not None and ip.is_library: continue
sample_positions.append(well.position.label)
if len(sample_positions) > 0:
msg = 'Plate %s should be empty but there are samples in ' \
'the following positions: %s.' \
% (plate.label, self._get_joined_str(sample_positions))
self.add_error(msg)
return None
if not isinstance(iso_plate, (IsoAliquotPlate, LibraryPlate)):
converter = LabIsoPrepLayoutConverter(iso_plate.rack_layout,
parent=self)
layout = converter.get_result()
if layout is None:
msg = 'Error when trying to convert layout of plate "%s"!' \
% (plate.label)
self.add_error(msg)
return None
else:
self.__plate_layouts[plate.label] = layout
elif verify:
verifier = LabIsoPlateVerifier(iso_plate,
self.ENTITY_CLS == IsoJob,
lab_iso_layout=layout,
parent=self)
compatible = verifier.get_result()
if compatible is None:
msg = 'Error when trying to verify plate %s!' % (rack_name)
self.add_error(msg)
return None
elif not compatible:
msg = 'Rack %s does not match the expected layout!' \
% (rack_name)
self.add_error(msg)
return None
elif layout is None:
self.__plate_layouts[plate.label] = \
verifier.get_expected_layout()
iso = None
if self._processing_order == LAB_ISO_ORDERS.NO_ISO and \
isinstance(iso_plate, LibraryPlate):
rack_marker = LABELS.ROLE_FINAL
iso = iso_plate.lab_iso
else:
values = LABELS.parse_rack_label(plate.label)
rack_marker = values[LABELS.MARKER_RACK_MARKER]
rack_container = IsoRackContainer(rack=plate, rack_marker=rack_marker)
if rack_container.role == LABELS.ROLE_FINAL:
rack_marker = LABELS.ROLE_FINAL
if iso is None: iso = iso_plate.iso
add_list_map_element(self.__final_plates, iso, rack_container)
add_list_map_element(self.__rack_containers, rack_marker,
rack_container)
