def _check_input(self):
"""
Checks the initialisation values.
"""
StockTransferWriterExecutor._check_input(self)
if not self.has_errors():
self._iso_request = self.entity.iso_request
def _check_input(self):
"""
Checks the initialisation values.
"""
StockTransferWriterExecutor._check_input(self)
if not self.has_errors():
self._iso_request = self.entity.iso_request
def __init__(self, iso, user, **kw):
"""
Constructor.
:param iso: The stock sample creation ISO for which to execute the
worklists.
:type iso: :class:`thelma.entities.iso.StockSampleCreationIso`
:param user: The user conducting the execution.
:type user: :class:`thelma.entities.user.User`
"""
StockTransferWriterExecutor.__init__(
self,
user=user,
entity=iso,
mode=StockTransferWriterExecutor.MODE_EXECUTE,
**kw)
#: The stock sample creation layout for this ISO.
self.__ssc_layout = None
#: The :class:`IsoRackContainer` for each stock rack mapped onto
#: rack marker.
self.__rack_containers = None
#: The stock rack that serves as target rack (:class:`IsoStockRack`).
self.__pool_stock_rack = None
#: The stock transfer worklist is the only worklist in the stock rack
#: series.
self.__stock_transfer_worklist = None
#: The indices for the rack transfer jobs mapped onto the worklist
#: they belong to.
self.__rack_transfer_indices = None
#: Positions without ISO positions (i.e. without transfer).
self.__ignore_positions = None
def __init__(self, iso, user, **kw):
"""
Constructor.
:param iso: The stock sample creation ISO for which to execute the
worklists.
:type iso: :class:`thelma.entities.iso.StockSampleCreationIso`
:param user: The user conducting the execution.
:type user: :class:`thelma.entities.user.User`
"""
StockTransferWriterExecutor.__init__(
self, user=user, entity=iso, mode=StockTransferWriterExecutor.MODE_EXECUTE, **kw
)
#: The stock sample creation layout for this ISO.
self.__ssc_layout = None
#: The :class:`IsoRackContainer` for each stock rack mapped onto
#: rack marker.
self.__rack_containers = None
#: The stock rack that serves as target rack (:class:`IsoStockRack`).
self.__pool_stock_rack = None
#: The stock transfer worklist is the only worklist in the stock rack
#: series.
self.__stock_transfer_worklist = None
#: The indices for the rack transfer jobs mapped onto the worklist
#: they belong to.
self.__rack_transfer_indices = None
#: Positions without ISO positions (i.e. without transfer).
self.__ignore_positions = None
def reset(self):
StockTransferWriterExecutor.reset(self)
self.__ssc_layout = None
self.__rack_containers = dict()
self.__pool_stock_rack = None
self.__stock_transfer_worklist = None
self.__rack_transfer_indices = dict()
self.__ignore_positions = []
def reset(self):
StockTransferWriterExecutor.reset(self)
self.__ssc_layout = None
self.__rack_containers = dict()
self.__pool_stock_rack = None
self.__stock_transfer_worklist = None
self.__rack_transfer_indices = dict()
self.__ignore_positions = []
def _check_input(self):
"""
Checks the initialisation values.
"""
StockTransferWriterExecutor._check_input(self)
if not self.has_errors() and not self.entity.status == ISO_STATUS.QUEUED:
msg = 'Unexpected ISO status: "%s"' % (self.entity.status)
self.add_error(msg)
def _check_input(self):
"""
Checks the initialisation values.
"""
StockTransferWriterExecutor._check_input(self)
if not self.has_errors() and \
not self.entity.status == ISO_STATUS.QUEUED:
msg = 'Unexpected ISO status: "%s"' % (self.entity.status)
self.add_error(msg)
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 __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 reset(self):
StockTransferWriterExecutor.reset(self)
self._iso_request = None
self.__final_layouts = dict()
self._processing_order = None
self._expected_iso_status = None
self.__rack_containers = dict()
self.__final_plates = dict()
self.__plate_layouts = dict()
self.__ignored_positions = dict()
self._stock_racks = dict()
self.__stock_rack_layouts = dict()
self.__buffer_dilution_indices = set()
self.__buffer_stream = None
def reset(self):
StockTransferWriterExecutor.reset(self)
self._iso_request = None
self.__final_layouts = dict()
self._processing_order = None
self._expected_iso_status = None
self.__rack_containers = dict()
self.__final_plates = dict()
self.__plate_layouts = dict()
self.__ignored_positions = dict()
self._stock_racks = dict()
self.__stock_rack_layouts = dict()
self.__buffer_dilution_indices = set()
self.__buffer_stream = None
def _merge_streams(self, stream_map):
"""
All buffer streams are merged too.
"""
dilution_streams = dict()
for job_index in self.__buffer_dilution_indices:
dilution_streams[job_index] = stream_map[job_index]
del stream_map[job_index]
if len(dilution_streams) > 0:
self.__buffer_stream = merge_csv_streams(dilution_streams)
return StockTransferWriterExecutor._merge_streams(self, stream_map)
def _merge_streams(self, stream_map):
"""
All buffer streams are merged too.
"""
dilution_streams = dict()
for job_index in self.__buffer_dilution_indices:
dilution_streams[job_index] = stream_map[job_index]
del stream_map[job_index]
if len(dilution_streams) > 0:
self.__buffer_stream = merge_csv_streams(dilution_streams)
return StockTransferWriterExecutor._merge_streams(self, stream_map)