def __build_buffer_transfer_jobs(self, transfer_job_map):
self.add_debug('Creating buffer transfer jobs.')
# The buffer worklists are stored with the ISO request.
ws = self.iso.iso_request.worklist_series
rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.QUARTER_MODULAR)
has_pool_racks = not self.__pool_stock_rack_map is None
for wl in ws.get_sorted_worklists():
sec_idx = wl.index % 4
job_idx = len(transfer_job_map)
if has_pool_racks and wl.index < 4:
# Pool stock rack buffer worklist.
tgt_iso_rack = self.__pool_stock_rack_map.get(sec_idx)
elif (has_pool_racks and wl.index < 8) \
or (not has_pool_racks and wl.index < 4):
# Preparation plate buffer worklist.
tgt_iso_rack = self.__prep_plate_map.get(sec_idx)
else: #
break
if tgt_iso_rack is None:
# The last ISO might not have all sectors used.
continue
trf_job = SampleDilutionJob(
job_idx,
wl,
tgt_iso_rack.rack,
rs,
source_rack_barcode=self.BUFFER_RESERVOIR_BARCODE,
ignored_positions=
self.__empty_stock_rack_positions_map[sec_idx])
transfer_job_map[job_idx] = (trf_job, wl)
def __build_buffer_transfer_jobs(self, transfer_job_map):
self.add_debug('Creating buffer transfer jobs.')
# The buffer worklists are stored with the ISO request.
ws = self.iso.iso_request.worklist_series
rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.QUARTER_MODULAR)
has_pool_racks = not self.__pool_stock_rack_map is None
for wl in ws.get_sorted_worklists():
sec_idx = wl.index % 4
job_idx = len(transfer_job_map)
if has_pool_racks and wl.index < 4:
# Pool stock rack buffer worklist.
tgt_iso_rack = self.__pool_stock_rack_map.get(sec_idx)
elif (has_pool_racks and wl.index < 8) \
or (not has_pool_racks and wl.index < 4):
# Preparation plate buffer worklist.
tgt_iso_rack = self.__prep_plate_map.get(sec_idx)
else: #
break
if tgt_iso_rack is None:
# The last ISO might not have all sectors used.
continue
trf_job = SampleDilutionJob(
job_idx,
wl,
tgt_iso_rack.rack,
rs,
source_rack_barcode=self.BUFFER_RESERVOIR_BARCODE,
ignored_positions=self.
__empty_stock_rack_positions_map[sec_idx])
transfer_job_map[job_idx] = (trf_job, wl)
def __init__(self, entity, mode, user=None, **kw):
"""
Constructor:
:param entity: The ISO job or ISO to process.
:type entity: :class:`thelma.entities.job.IsoJob` or
:class:`thelma.entities.iso.LabIso`.
:param mode: :attr:`MODE_EXECUTE` or :attr:`MODE_PRINT_WORKLISTS`
:type mode: str
:param user: The user who conducts the DB update (required for
execution mode).
:type user: :class:`thelma.entities.user.User`
:default user: *None*
"""
StockTransferWriterExecutor.__init__(self,
entity=entity,
mode=mode,
user=user,
**kw)
#: The lab ISO requests the entity belongs to.
self._iso_request = None
#: The final layout for each ISO in this entity mapped onto ISOs.
self.__final_layouts = None
#: see :class:`LAB_ISO_ORDERS`.
self._processing_order = None
#: The expected :class:`ISO_STATUS.
self._expected_iso_status = None
#: The involved racks (as list of :class:`IsoRackContainer`
#: objects) mapped onto rack markers. Final plates are mapped onto the
#: :attr:`LABELS.ROLE_FINAL` marker.
self.__rack_containers = None
#: The final plates (as list of :class:`IsoRackContainer` objects)
#: mapped onto ISOs.
self.__final_plates = None
#: The layout for each plate mapped onto plate label.
self.__plate_layouts = None
#: The ignored positions for each plate.
self.__ignored_positions = None
#: The stock rack for this entity mapped onto labels.
self._stock_racks = None
#: The stock rack layouts mapped onto stock rack barcodes
#: (for reporting).
self.__stock_rack_layouts = None
#: The job indices for the buffer dilutions.
self.__buffer_dilution_indices = None
#: The merged stream for the buffer dilutions (printer mode only).
self.__buffer_stream = None
#: The source :class:`ReservoirSpecs` for the dilution jobs.
self.__dilution_rs = get_reservoir_spec(self.DILUTION_RESERVOIR_SPECS)
def __get_reservoir_specs(self, rack_container):
# Also records an error message if the spec has not been found.
try:
rs = get_reservoir_spec(rack_container.specs.lower())
except ValueError as ve:
msg = 'Error when trying to fetch reservoir specs for rack "%s": ' \
'%s' % (rack_container.identifier, ve)
self.add_error(msg)
result = None
else:
result = rs
return result
def _create_optimem_job(self, optimem_worklist):
"""
Helper function creating an optimem dilution job.
"""
quarter_rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.QUARTER_MODULAR)
optimem_job = SampleDilutionJob(index=0,
planned_worklist=optimem_worklist,
target_rack=self._source_plate,
reservoir_specs=quarter_rs,
source_rack_barcode=self.OPTIMEM_PLATE_BARCODE,
ignored_positions=self._ignored_positions)
return optimem_job
def _create_reagent_job(self, reagent_worklist):
"""
Helper function creating an transfection reagent dilution job.
"""
tube_24_rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.TUBE_24)
reagent_job = SampleDilutionJob(index=1,
planned_worklist=reagent_worklist,
target_rack=self._source_plate,
reservoir_specs=tube_24_rs,
source_rack_barcode=self.REAGENT_PLATE_BARCODE,
ignored_positions=self._ignored_positions)
return reagent_job
def __init__(self, entity, mode, user=None, **kw):
"""
Constructor:
:param entity: The ISO job or ISO to process.
:type entity: :class:`thelma.entities.job.IsoJob` or
:class:`thelma.entities.iso.LabIso`.
:param mode: :attr:`MODE_EXECUTE` or :attr:`MODE_PRINT_WORKLISTS`
:type mode: str
:param user: The user who conducts the DB update (required for
execution mode).
:type user: :class:`thelma.entities.user.User`
:default user: *None*
"""
StockTransferWriterExecutor.__init__(self, entity=entity, mode=mode,
user=user, **kw)
#: The lab ISO requests the entity belongs to.
self._iso_request = None
#: The final layout for each ISO in this entity mapped onto ISOs.
self.__final_layouts = None
#: see :class:`LAB_ISO_ORDERS`.
self._processing_order = None
#: The expected :class:`ISO_STATUS.
self._expected_iso_status = None
#: The involved racks (as list of :class:`IsoRackContainer`
#: objects) mapped onto rack markers. Final plates are mapped onto the
#: :attr:`LABELS.ROLE_FINAL` marker.
self.__rack_containers = None
#: The final plates (as list of :class:`IsoRackContainer` objects)
#: mapped onto ISOs.
self.__final_plates = None
#: The layout for each plate mapped onto plate label.
self.__plate_layouts = None
#: The ignored positions for each plate.
self.__ignored_positions = None
#: The stock rack for this entity mapped onto labels.
self._stock_racks = None
#: The stock rack layouts mapped onto stock rack barcodes
#: (for reporting).
self.__stock_rack_layouts = None
#: The job indices for the buffer dilutions.
self.__buffer_dilution_indices = None
#: The merged stream for the buffer dilutions (printer mode only).
self.__buffer_stream = None
#: The source :class:`ReservoirSpecs` for the dilution jobs.
self.__dilution_rs = get_reservoir_spec(self.DILUTION_RESERVOIR_SPECS)
def _create_optimem_job(self, optimem_worklist):
"""
Helper function creating an optimem dilution job.
"""
quarter_rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.QUARTER_MODULAR)
optimem_job = SampleDilutionJob(
index=0,
planned_worklist=optimem_worklist,
target_rack=self._source_plate,
reservoir_specs=quarter_rs,
source_rack_barcode=self.OPTIMEM_PLATE_BARCODE,
ignored_positions=self._ignored_positions)
return optimem_job
def _create_reagent_job(self, reagent_worklist):
"""
Helper function creating an transfection reagent dilution job.
"""
tube_24_rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.TUBE_24)
reagent_job = SampleDilutionJob(
index=1,
planned_worklist=reagent_worklist,
target_rack=self._source_plate,
reservoir_specs=tube_24_rs,
source_rack_barcode=self.REAGENT_PLATE_BARCODE,
ignored_positions=self._ignored_positions)
return reagent_job
def __create_buffer_transfer_job(self):
# Creates the transfer job for the buffer worklist.
self.add_debug('Create buffer transfer jobs ...')
worklist_series = self.entity.iso_request.worklist_series
buffer_worklist = worklist_series.get_worklist_for_index(
StockSampleCreationWorklistGenerator.BUFFER_WORKLIST_INDEX)
rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.FALCON_MANUAL)
job_index = len(self._transfer_jobs)
cdj = SampleDilutionJob(
index=job_index,
planned_worklist=buffer_worklist,
target_rack=self.__pool_stock_rack.rack,
reservoir_specs=rs,
source_rack_barcode=self.BUFFER_RESERVOIR_BARCODE,
ignored_positions=self.__ignore_positions)
self._transfer_jobs[job_index] = cdj
def get_dynamic_dead_volume(target_well_number,
reservoir_specs=RESERVOIR_SPECS_NAMES.STANDARD_96):
"""
Calculate a dynamic dead volume (for pipetting specs that require dynamic
dead volumes, such as Biomek).
:param target_well_number: The number of target wells for the given
source well.
:type target_well_number: :class:` int`
:param reservoir_specs: The reservoir specs you are assuming.
:type reservoir_specs: a :class:`RESERVOIR_SPECS_NAMES` element or
a :class:`thelma.entities.liquidtransfer.ReservoirSpecs` object
:default reservoir_specs: RESERVOIR_SPECS_NAMES.STANDARD_96
:Note: At the moment corrections are only applied to plates.
:raises TypeError: if resrevoir_specs is not a string or ReservoirSpecs
:return: The adjusted dead volume in ul.
"""
if isinstance(reservoir_specs, ReservoirSpecs):
rs = reservoir_specs
elif isinstance(reservoir_specs, basestring):
rs = get_reservoir_spec(reservoir_specs)
else:
msg = 'Unsupported type for reservoir specs: %s. Expectes string ' \
'or ReservoirSpecs object.' % (reservoir_specs.__class__.__name__)
raise TypeError(msg)
# pylint: disable=E1103
min_dead_volume_ul = rs.min_dead_volume * VOLUME_CONVERSION_FACTOR
max_dead_volume_ul = rs.max_dead_volume * VOLUME_CONVERSION_FACTOR
# pylint: enable=E1103
if min_dead_volume_ul == max_dead_volume_ul:
return min_dead_volume_ul
if target_well_number <= LIMIT_TARGET_WELLS:
return min_dead_volume_ul
exceeding_well_count = target_well_number - LIMIT_TARGET_WELLS
additional_volume = exceeding_well_count * DEAD_VOLUME_COEFFICIENT
adjusted_dead_volume = min_dead_volume_ul + additional_volume
if adjusted_dead_volume > max_dead_volume_ul:
adjusted_dead_volume = max_dead_volume_ul
return adjusted_dead_volume
def get_dynamic_dead_volume(target_well_number,
reservoir_specs=RESERVOIR_SPECS_NAMES.STANDARD_96):
"""
Calculate a dynamic dead volume (for pipetting specs that require dynamic
dead volumes, such as Biomek).
:param target_well_number: The number of target wells for the given
source well.
:type target_well_number: :class:` int`
:param reservoir_specs: The reservoir specs you are assuming.
:type reservoir_specs: a :class:`RESERVOIR_SPECS_NAMES` element or
a :class:`thelma.entities.liquidtransfer.ReservoirSpecs` object
:default reservoir_specs: RESERVOIR_SPECS_NAMES.STANDARD_96
:Note: At the moment corrections are only applied to plates.
:raises TypeError: if resrevoir_specs is not a string or ReservoirSpecs
:return: The adjusted dead volume in ul.
"""
if isinstance(reservoir_specs, ReservoirSpecs):
rs = reservoir_specs
elif isinstance(reservoir_specs, basestring):
rs = get_reservoir_spec(reservoir_specs)
else:
msg = 'Unsupported type for reservoir specs: %s. Expectes string ' \
'or ReservoirSpecs object.' % (reservoir_specs.__class__.__name__)
raise TypeError(msg)
# pylint: disable=E1103
min_dead_volume_ul = rs.min_dead_volume * VOLUME_CONVERSION_FACTOR
max_dead_volume_ul = rs.max_dead_volume * VOLUME_CONVERSION_FACTOR
# pylint: enable=E1103
if min_dead_volume_ul == max_dead_volume_ul:
return min_dead_volume_ul
if target_well_number <= LIMIT_TARGET_WELLS:
return min_dead_volume_ul
exceeding_well_count = target_well_number - LIMIT_TARGET_WELLS
additional_volume = exceeding_well_count * DEAD_VOLUME_COEFFICIENT
adjusted_dead_volume = min_dead_volume_ul + additional_volume
if adjusted_dead_volume > max_dead_volume_ul:
adjusted_dead_volume = max_dead_volume_ul
return adjusted_dead_volume
def _add_cell_suspension_job(self, cell_worklist, job_index, plate,
cell_ignored_positions):
"""
Helper function registering a container dilution job for the given
worklist, plate and job index. In addition, in increments the
job index.
"""
falcon_reservoir = get_reservoir_spec(
RESERVOIR_SPECS_NAMES.FALCON_MANUAL)
cell_job = SampleDilutionJob(index=job_index,
planned_worklist=cell_worklist,
target_rack=plate,
reservoir_specs=falcon_reservoir,
ignored_positions=cell_ignored_positions)
self._transfer_jobs[job_index] = cell_job
job_index += 1
return job_index
def _add_cell_suspension_job(self, cell_worklist, job_index, plate,
cell_ignored_positions):
"""
Helper function registering a container dilution job for the given
worklist, plate and job index. In addition, in increments the
job index.
"""
falcon_reservoir = get_reservoir_spec(
RESERVOIR_SPECS_NAMES.FALCON_MANUAL)
cell_job = SampleDilutionJob(index=job_index,
planned_worklist=cell_worklist,
target_rack=plate,
reservoir_specs=falcon_reservoir,
ignored_positions=cell_ignored_positions)
self._transfer_jobs[job_index] = cell_job
job_index += 1
return job_index
def __create_buffer_transfer_job(self):
# Creates the transfer job for the buffer worklist.
self.add_debug("Create buffer transfer jobs ...")
worklist_series = self.entity.iso_request.worklist_series
buffer_worklist = worklist_series.get_worklist_for_index(
StockSampleCreationWorklistGenerator.BUFFER_WORKLIST_INDEX
)
rs = get_reservoir_spec(RESERVOIR_SPECS_NAMES.FALCON_MANUAL)
job_index = len(self._transfer_jobs)
cdj = SampleDilutionJob(
index=job_index,
planned_worklist=buffer_worklist,
target_rack=self.__pool_stock_rack.rack,
reservoir_specs=rs,
source_rack_barcode=self.BUFFER_RESERVOIR_BARCODE,
ignored_positions=self.__ignore_positions,
)
self._transfer_jobs[job_index] = cdj
def __init__(self, reagent_stream_content, parent=None):
"""
Constructor.
:param str reagent_stream_content: The content of the reagent dilution
worklist stream.
"""
CsvWriter.__init__(self, parent=parent)
#: The content of the reagent dilution worklist stream.
self.reagent_stream_content = reagent_stream_content
#: The relevant data of the worklist (key: line index, values:
#: tuple (source pos, dilution volume, diluent info) .
self.__worklist_data = None
#: The estimated dead volume in ul.
self.__dead_volume = get_reservoir_spec(RESERVOIR_SPECS_NAMES.TUBE_24).\
max_dead_volume * VOLUME_CONVERSION_FACTOR
#: Intermediate storage for the column values.
self.__position_values = None
self.__name_values = None
self.__final_dil_factor_values = None
self.__ini_dil_factor_values = None
self.__total_volume_values = None
self.__reagent_volume_values = None
self.__diluent_volume_values = None
def __init__(self, reagent_stream_content, parent=None):
"""
Constructor.
:param str reagent_stream_content: The content of the reagent dilution
worklist stream.
"""
CsvWriter.__init__(self, parent=parent)
#: The content of the reagent dilution worklist stream.
self.reagent_stream_content = reagent_stream_content
#: The relevant data of the worklist (key: line index, values:
#: tuple (source pos, dilution volume, diluent info) .
self.__worklist_data = None
#: The estimated dead volume in ul.
self.__dead_volume = get_reservoir_spec(RESERVOIR_SPECS_NAMES.TUBE_24).\
max_dead_volume * VOLUME_CONVERSION_FACTOR
#: Intermediate storage for the column values.
self.__position_values = None
self.__name_values = None
self.__final_dil_factor_values = None
self.__ini_dil_factor_values = None
self.__total_volume_values = None
self.__reagent_volume_values = None
self.__diluent_volume_values = None