def __init__(self, stream, mode, user, **kw):
"""
Constructor:
:param stream: The custom transfer XLS file as stream.
: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*
"""
SerialWriterExecutorTool.__init__(self, mode=mode, user=user, **kw)
#: The custom transfer XLS file as stream.
self.stream = stream
#: The :class:`WorklistSeries` generate by the parser.
self._worklist_series = None
#: The :class:RackOrReservoirItem` for each rack or reservoir in the
#: worklist series.
self.__rors = None
#: The source and targets :class:RackOrReservoirItem` for each worklist.
self.__transfer_roles = None
def __init__(self, stream, mode, user, **kw):
"""
Constructor:
:param stream: The custom transfer XLS file as stream.
: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*
"""
SerialWriterExecutorTool.__init__(self, mode=mode, user=user, **kw)
#: The custom transfer XLS file as stream.
self.stream = stream
#: The :class:`WorklistSeries` generate by the parser.
self._worklist_series = None
#: The :class:RackOrReservoirItem` for each rack or reservoir in the
#: worklist series.
self.__rors = None
#: The source and targets :class:RackOrReservoirItem` for each worklist.
self.__transfer_roles = None
def _check_input(self):
"""
Checks the initialisation values.
"""
SerialWriterExecutorTool._check_input(self)
if self.stream is None:
msg = 'The stream must not be None!'
self.add_error(msg)
def _check_input(self):
"""
Checks the initialisation values.
"""
SerialWriterExecutorTool._check_input(self)
if self.stream is None:
msg = 'The stream must not be None!'
self.add_error(msg)
def _check_input(self):
"""
Checks the initialisation values.
"""
SerialWriterExecutorTool._check_input(self)
if self._check_input_class('entity', self.entity, self.ENTITY_CLS):
if self.ENTITY_CLS == IsoJob and len(self.entity.isos) < 1:
msg = 'There are no ISOs in this ISO job!'
self.add_error(msg)
def _check_input(self):
"""
Checks the initialisation values.
"""
SerialWriterExecutorTool._check_input(self)
if self._check_input_class("entity", self.entity, self.ENTITY_CLS):
if self.ENTITY_CLS == IsoJob and len(self.entity.isos) < 1:
msg = "There are no ISOs in this ISO job!"
self.add_error(msg)
def __init__(self, entity, mode, user=None, parent=None):
"""
Constructor.
:param entity: The ISO job or ISO to process.
:type entity: :class:`thelma.entities.job.IsoJob` or
:class:`thelma.entities.iso.LabIso`.
"""
SerialWriterExecutorTool.__init__(self, mode, user=user, parent=parent)
#: The entity the transfer will be attached to (ISO or ISO job).
self.entity = entity
#: The executed stock transfer worklists (for reporting).
self._executed_stock_worklists = None
def __init__(self, entity, mode, user=None, parent=None):
"""
Constructor.
:param entity: The ISO job or ISO to process.
:type entity: :class:`thelma.entities.job.IsoJob` or
:class:`thelma.entities.iso.LabIso`.
"""
SerialWriterExecutorTool.__init__(self, mode, user=user, parent=parent)
#: The entity the transfer will be attached to (ISO or ISO job).
self.entity = entity
#: The executed stock transfer worklists (for reporting).
self._executed_stock_worklists = None
def reset(self):
"""
Resets all attributes except for the initialisation values.
"""
SerialWriterExecutorTool.reset(self)
self._scenario = None
self._design_series = None
self._design_rack_series_map = dict()
self._transfer_worklist_index = None
self._cell_worklist_index = None
self._experiment_racks = dict()
self._source_plate = None
self._source_layout = None
self._ignored_positions = []
self._ignored_floatings = set()
self._final_streams = dict()
def reset(self):
"""
Resets all attributes except for the initialisation values.
"""
SerialWriterExecutorTool.reset(self)
self._scenario = None
self._design_series = None
self._design_rack_series_map = dict()
self._transfer_worklist_index = None
self._cell_worklist_index = None
self._experiment_racks = dict()
self._source_plate = None
self._source_layout = None
self._ignored_positions = []
self._ignored_floatings = set()
self._final_streams = dict()
def _get_executed_worklists(self):
"""
In addition to the normal writers we have to set the "has been used"
flag of the potential ISO aliquot plate that has been used as
source plate.
"""
ews = SerialWriterExecutorTool._get_executed_worklists(self)
if not ews is None: self._update_iso_aliquot_plate()
return ews
def _get_executed_worklists(self):
"""
In addition to the normal writers we have to set the "has been used"
flag of the potential ISO aliquot plate that has been used as
source plate.
"""
ews = SerialWriterExecutorTool._get_executed_worklists(self)
if not ews is None: self._update_iso_aliquot_plate()
return ews
def __init__(self, experiment, mode, user=None, parent=None, **kw):
"""
Constructor.
:param experiment: The experiment to process.
:type experiment: :class:`thelma.entities.experiment.Experiment`
"""
SerialWriterExecutorTool.__init__(self,
mode,
user=user,
parent=parent,
**kw)
#: The experiment for which to generate the rack.
self.experiment = experiment
#: The experiment metadata type
#: (:class:`thelma.entities.experiment.ExperimentMetadataType`).
self._scenario = None
#: The worklist series of the experiment design
#: (:class:`thelma.entities.liquidtransfer.WorklistSeries`).
self._design_series = None
#: The worklist series for the design racks mapped onto design
#: racks labels (if there are any).
#: (:class:`thelma.entities.liquidtransfer.WorklistSeries`).
self._design_rack_series_map = None
#: The index of the transfer worklist within a valid design rack series.
self._transfer_worklist_index = None
#: The index of the cell worklist within a valid design rack series.
self._cell_worklist_index = None
#: Maps experiment racks onto the design rack they belong to.
self._experiment_racks = None
#: The source plate (ISO plate) for this experiment.
self._source_plate = None
#: The ISO layout for this experiment.
self._source_layout = None
#: A list of rack position to be ignore during execution or worklist
#: generation. The rack position are floating or library position for
#: which there were no molecule design pools left anymore.
self._ignored_positions = None
#: A list of floating placeholders to be ignored during execution
#: or worklist generation. The rack position are floating position
#: for which there were no molecule design pools left anymore.
self._ignored_floatings = None
#: The final stream mapped onto file suffixes (print mode only).
self._final_streams = None
def __init__(self, experiment, mode, user=None, parent=None, **kw):
"""
Constructor.
:param experiment: The experiment to process.
:type experiment: :class:`thelma.entities.experiment.Experiment`
"""
SerialWriterExecutorTool.__init__(self, mode,
user=user, parent=parent, **kw)
#: The experiment for which to generate the rack.
self.experiment = experiment
#: The experiment metadata type
#: (:class:`thelma.entities.experiment.ExperimentMetadataType`).
self._scenario = None
#: The worklist series of the experiment design
#: (:class:`thelma.entities.liquidtransfer.WorklistSeries`).
self._design_series = None
#: The worklist series for the design racks mapped onto design
#: racks labels (if there are any).
#: (:class:`thelma.entities.liquidtransfer.WorklistSeries`).
self._design_rack_series_map = None
#: The index of the transfer worklist within a valid design rack series.
self._transfer_worklist_index = None
#: The index of the cell worklist within a valid design rack series.
self._cell_worklist_index = None
#: Maps experiment racks onto the design rack they belong to.
self._experiment_racks = None
#: The source plate (ISO plate) for this experiment.
self._source_plate = None
#: The ISO layout for this experiment.
self._source_layout = None
#: A list of rack position to be ignore during execution or worklist
#: generation. The rack position are floating or library position for
#: which there were no molecule design pools left anymore.
self._ignored_positions = None
#: A list of floating placeholders to be ignored during execution
#: or worklist generation. The rack position are floating position
#: for which there were no molecule design pools left anymore.
self._ignored_floatings = None
#: The final stream mapped onto file suffixes (print mode only).
self._final_streams = None
def reset(self):
SerialWriterExecutorTool.reset(self)
self._worklist_series = None
self.__rors = None
self.__transfer_roles = dict()
def reset(self):
SerialWriterExecutorTool.reset(self)
self._worklist_series = None
self.__rors = None
self.__transfer_roles = dict()
def _merge_streams(self, stream_map):
"""
Optimem and reagent streams extracted.
"""
self._extract_mastermix_streams(stream_map)
SerialWriterExecutorTool._merge_streams(self, stream_map)
def reset(self):
"""
Checks the initialisation values.
"""
SerialWriterExecutorTool.reset(self)
self._executed_stock_worklists = []
def _check_input(self):
"""
Checks whether all initialisation values are valid.
"""
SerialWriterExecutorTool._check_input(self)
self._check_input_class('experiment', self.experiment, Experiment)
def reset(self):
"""
Checks the initialisation values.
"""
SerialWriterExecutorTool.reset(self)
self._executed_stock_worklists = []
def _merge_streams(self, stream_map):
"""
Optimem and reagent streams extracted.
"""
self._extract_mastermix_streams(stream_map)
SerialWriterExecutorTool._merge_streams(self, stream_map)
def _check_input(self):
"""
Checks whether all initialisation values are valid.
"""
SerialWriterExecutorTool._check_input(self)
self._check_input_class('experiment', self.experiment, Experiment)
