def __init__(self, stock_rack_data, executed_worklists, parent=None):
"""
Constructor.
:param stock_rack_data: The stock rack layouts are required to
fetch the pool for a transfer mapped onto their barcodes.
:type stock_rack_data: :class:`dict` with barcode as key and
:class:`StockRackLayout` as value
:param executed_worklists: The stock transfer executed worklists that
have been generated by the executor.
:type executed_worklists: :class:`list`
"""
CsvWriter.__init__(self, parent=parent)
#: The executed worklists that have been generated by the executor
#: (mapped onto transfer job indices).
self.executed_worklists = executed_worklists
#: The stock rack layouts are required to fetch the pool for a
#: transfer mapped onto their barcodes.
self.stock_rack_data = stock_rack_data
#: Stores the values for the molecule design pool ID column.
self.__pool_values = None
#: Stores the values for the tube barcode column.
self.__tube_barcode_values = None
#: Stores the values for the volume column.
self.__volume_values = None
#: Stores the values for the target rack barcode column.
self.__trg_rack_barcode_values = None
#: Stores the values for the target position column.
self.__trg_position_values = None
def __init__(self,
library_layout,
executed_worklists,
stock_rack_map,
parent=None):
"""
Constructor.
:param library_layout: The working_layout containing the molecule
design pool data.
:type library_layout: :class:`LibraryLayout`
:param list executed_worklists: The executed worklists that have been
generated by the executor (mapped onto transfer job indices).
"""
CsvWriter.__init__(self, parent=parent)
self.executed_worklists = executed_worklists
self.library_layout = library_layout
self.stock_rack_map = stock_rack_map
#: Map source rack barcode -> stock sample creation layout.
self.__ssc_layout_map = None
#: Stores the values for the library molecule design pool ID column.
self.__lib_pool_values = None
#: Stores the values for the library molecule design pool ID column.
self.__md_values = None
#: Stores the values for the tube barcode column.
self.__tube_barcode_values = None
#: Stores the values for the volume column.
self.__volume_values = None
#: Stores the values for the target rack barcode column.
self.__trg_rack_barcode_values = None
#: Stores the values for the target position column.
self.__trg_position_values = None
def __init__(self, stock_rack_data, executed_worklists, parent=None):
"""
Constructor.
:param stock_rack_data: The stock rack layouts are required to
fetch the pool for a transfer mapped onto their barcodes.
:type stock_rack_data: :class:`dict` with barcode as key and
:class:`StockRackLayout` as value
:param executed_worklists: The stock transfer executed worklists that
have been generated by the executor.
:type executed_worklists: :class:`list`
"""
CsvWriter.__init__(self, parent=parent)
#: The executed worklists that have been generated by the executor
#: (mapped onto transfer job indices).
self.executed_worklists = executed_worklists
#: The stock rack layouts are required to fetch the pool for a
#: transfer mapped onto their barcodes.
self.stock_rack_data = stock_rack_data
#: Stores the values for the molecule design pool ID column.
self.__pool_values = None
#: Stores the values for the tube barcode column.
self.__tube_barcode_values = None
#: Stores the values for the volume column.
self.__volume_values = None
#: Stores the values for the target rack barcode column.
self.__trg_rack_barcode_values = None
#: Stores the values for the target position column.
self.__trg_position_values = None
def __init__(self,
stock_sample_creation_layout,
executed_worklists,
parent=None):
"""
Constructor.
:param stock_sample_creation_layout: The working_layout containing the
molecule design pool data.
:type stock_sample_creation_layout: :class:`StockSampleCreationLayout`
:param list executed_worklists: The executed worklists that have been
generated by the executor (mapped onto transfer job indices).
"""
CsvWriter.__init__(self, parent=parent)
#: The executed worklists that have been generated by the executor.
self.executed_worklists = executed_worklists
#: The working layout containing the molecule design pool data.
self.stock_sample_creation_layout = stock_sample_creation_layout
#: Stores the values for the molecule design pool ID column.
self.__pool_values = None
#: Stores the values for the single molecule design IDs column.
self.__md_values = None
#: Stores the values for the tube barcode column.
self.__tube_barcode_values = None
#: Stores the values for the volume column.
self.__volume_values = None
#: Stores the values for the target rack barcode column.
self.__trg_rack_barcode_values = None
#: Stores the values for the target position column.
self.__trg_position_values = None
def __init__(self, stock_sample_creation_layout, executed_worklists, parent=None):
"""
Constructor.
:param stock_sample_creation_layout: The working_layout containing the
molecule design pool data.
:type stock_sample_creation_layout: :class:`StockSampleCreationLayout`
:param list executed_worklists: The executed worklists that have been
generated by the executor (mapped onto transfer job indices).
"""
CsvWriter.__init__(self, parent=parent)
#: The executed worklists that have been generated by the executor.
self.executed_worklists = executed_worklists
#: The working layout containing the molecule design pool data.
self.stock_sample_creation_layout = stock_sample_creation_layout
#: Stores the values for the molecule design pool ID column.
self.__pool_values = None
#: Stores the values for the single molecule design IDs column.
self.__md_values = None
#: Stores the values for the tube barcode column.
self.__tube_barcode_values = None
#: Stores the values for the volume column.
self.__volume_values = None
#: Stores the values for the target rack barcode column.
self.__trg_rack_barcode_values = None
#: Stores the values for the target position column.
self.__trg_position_values = None
def __init__(self, library_layout, executed_worklists,
sample_stock_racks, parent=None):
"""
Constructor.
:param library_layout: The working_layout containing the molecule
design pool data.
:type library_layout: :class:`LibraryLayout`
:param executed_worklists: The executed worklists that have been
generated by the executor (mapped onto transfer job indices).
:type executed_worklists: :class:`dict`
"""
CsvWriter.__init__(self, parent=parent)
#: The executed worklists that have been generated by the executor
#: (mapped onto transfer job indices).
self.executed_worklists = executed_worklists
#: The working_layout containing the molecule design pool data.
self.library_layout = library_layout
#: The ISO sample stock racks mapped onto sector indices.
self.sample_stock_racks = sample_stock_racks
#: The translators for each pool stock rack (lazy initialisation).
self.__translators = None
#: Stores the values for the library molecule design pool ID column.
self.__lib_pool_values = None
#: Stores the values for the library molecule design pool ID column.
self.__md_values = None
#: Stores the values for the tube barcode column.
self.__tube_barcode_values = None
#: Stores the values for the volume column.
self.__volume_values = None
#: Stores the values for the target rack barcode column.
self.__trg_rack_barcode_values = None
#: Stores the values for the target position column.
self.__trg_position_values = None
def reset(self):
CsvWriter.reset(self)
self.__pool_values = []
self.__md_values = []
self.__tube_barcode_values = []
self.__volume_values = []
self.__trg_rack_barcode_values = []
self.__trg_position_values = []
def reset(self):
CsvWriter.reset(self)
self.__pool_values = []
self.__md_values = []
self.__tube_barcode_values = []
self.__volume_values = []
self.__trg_rack_barcode_values = []
self.__trg_position_values = []
def __init__(self, planned_worklist, target_rack, pipetting_specs,
ignored_positions=None, parent=None):
"""
Constructor.
:param planned_worklist: The worklist for which to create a
worklist file.
:type planned_worklist:
:class:`thelma.entities.liquidtransfer.PlannedWorklist`
:param target_rack: The rack into which the volumes will be dispensed.
:type target_rack: :class:`thelma.entities.rack.Rack`
:param pipetting_specs: Pipetting specs define transfer properties and
conditions like the transfer volume range.
:type pipetting_specs:
:class:`thelma.entities.liquidtransfer.PipettingSpecs`
:param list ignored_positions: A list of positions (target
for dilutions and source for transfers; :class:`RackPosition`)
that are not included in the worklist file.
"""
CsvWriter.__init__(self, parent=parent)
#: The planned worklist for which to create a file stream.
self.planned_worklist = planned_worklist
#: The rack into which the volumes will be dispensed.
self.target_rack = target_rack
#: Pipetting specs define transfer properties and conditions like
#: the transfer volume range.
self.pipetting_specs = pipetting_specs
if ignored_positions is None:
ignored_positions = []
#: A list of positions that will not be included in the worklist file
#: (even if there are planned transfers for them).
self.ignored_positions = ignored_positions
#: Maps the containers of the target rack onto rack positions.
self._target_containers = None
#: Stores the volume changes for the target rack (mapped onto
#: rack positions).
self._target_volumes = None
#: The maximum volume of a target rack container in ul.
self._target_max_volume = None
#: Maps the container of the source rack onto rack position.
self._source_containers = None
#: Stores the volume changes for the source rack (mapped onto
#: rack positions).
self._source_volumes = None
#: The minimum dead volume of source rack container in ul.
self._source_dead_volume = None
#: The minimum transfer volume used in ul.
self._min_transfer_volume = None
#: The maximum transfer volume used in ul.
self._max_transfer_volume = None
# Intermediate data storage for errors.
self._transfer_volume_too_small = None
self._transfer_volume_too_large = None
self._source_volume_too_small = None
self._source_container_missing = None
self._target_volume_too_large = None
self._target_container_missing = None
def reset(self):
CsvWriter.reset(self)
self.__ssc_layout_map = dict()
self.__lib_pool_values = []
self.__md_values = []
self.__tube_barcode_values = []
self.__volume_values = []
self.__trg_rack_barcode_values = []
self.__trg_position_values = []
def reset(self):
CsvWriter.reset(self)
self.__translators = dict()
self.__lib_pool_values = []
self.__md_values = []
self.__tube_barcode_values = []
self.__volume_values = []
self.__trg_rack_barcode_values = []
self.__trg_position_values = []
def reset(self):
"""
Resets all values except for the initialisation values.
"""
CsvWriter.reset(self)
self.source_layout = None
self.__position_values = []
self.__md_pool_values = []
self.__iso_concentration_values = []
self.__iso_volume_values = []
def reset(self):
"""
Resets all values except for the initialisation values.
"""
CsvWriter.reset(self)
self.__pool_values = []
self.__tube_barcode_values = []
self.__volume_values = []
self.__trg_rack_barcode_values = []
self.__trg_position_values = []
def reset(self):
"""
Resets all attributes except the initialization values.
"""
CsvWriter.reset(self)
self._source_rack_values = []
self._source_position_values = []
self._tube_barcode_values = []
self._dest_rack_values = []
self._dest_position_values = []
def reset(self):
"""
Resets all values except for the initialisation values.
"""
CsvWriter.reset(self)
self.source_layout = None
self.__position_values = []
self.__md_pool_values = []
self.__iso_concentration_values = []
self.__iso_volume_values = []
def reset(self):
"""
Resets all attributes except the initialization values.
"""
CsvWriter.reset(self)
self._source_rack_values = []
self._source_position_values = []
self._tube_barcode_values = []
self._dest_rack_values = []
self._dest_position_values = []
def reset(self):
"""
Resets all values except for the initialisation values.
"""
CsvWriter.reset(self)
self.__pool_values = []
self.__tube_barcode_values = []
self.__volume_values = []
self.__trg_rack_barcode_values = []
self.__trg_position_values = []
def __init__(self, parent=None):
CsvWriter.__init__(self, parent=parent)
#: The values for the source rack column.
self._source_rack_values = None
#: The values for the source position column.
self._source_position_values = None
#: The values of the tube barcode column.
self._tube_barcode_values = None
#: The values of the destination rack column.
self._dest_rack_values = None
#: The values of the destination position column.
self._dest_position_values = None
def __init__(self, parent=None):
CsvWriter.__init__(self, parent=parent)
#: The values for the source rack column.
self._source_rack_values = None
#: The values for the source position column.
self._source_position_values = None
#: The values of the tube barcode column.
self._tube_barcode_values = None
#: The values of the destination rack column.
self._dest_rack_values = None
#: The values of the destination position column.
self._dest_position_values = None
def reset(self):
"""
Resets all values except for initialisation values.
"""
CsvWriter.reset(self)
self.__worklist_data = dict()
self.__position_values = []
self.__name_values = []
self.__final_dil_factor_values = []
self.__ini_dil_factor_values = []
self.__total_volume_values = []
self.__reagent_volume_values = []
self.__diluent_volume_values = []
def reset(self):
"""
Resets all values except for initialisation values.
"""
CsvWriter.reset(self)
self.__worklist_data = dict()
self.__position_values = []
self.__name_values = []
self.__final_dil_factor_values = []
self.__ini_dil_factor_values = []
self.__total_volume_values = []
self.__reagent_volume_values = []
self.__diluent_volume_values = []
def reset(self):
"""
Resets all values except for the initialisation values.
"""
CsvWriter.reset(self)
self.source_layout = None
self.association_layouts = None
self.final_concentrations = None
self.__source_well_values = []
self.__design_rack_values = []
self.__target_well_values = []
self.__iso_volume_values = []
self.__iso_concentration_values = []
self.__final_concentration_values = []
def reset(self):
"""
Resets all values except for the initialisation values.
"""
CsvWriter.reset(self)
self.source_layout = None
self.association_layouts = None
self.final_concentrations = None
self.__source_well_values = []
self.__design_rack_values = []
self.__target_well_values = []
self.__iso_volume_values = []
self.__iso_concentration_values = []
self.__final_concentration_values = []
def __init__(self, generator, parent=None):
"""
Constructor.
:param generator: The generator that has conducted the upload.
:type generator: :class:`ExperimentMetadataGenerator`
"""
CsvWriter.__init__(self, parent=parent)
#: The generator that has conducted the upload.
self.generator = generator
#: The completed ISO source layout.
self.source_layout = None
#: Intermediate storage for the column values.
self.__position_values = None
self.__md_pool_values = None
self.__iso_concentration_values = None
self.__iso_volume_values = None
def __init__(self, generator, parent=None):
"""
Constructor.
:param generator: The generator that has conducted the upload.
:type generator: :class:`ExperimentMetadataGenerator`
"""
CsvWriter.__init__(self, parent=parent)
#: The generator that has conducted the upload.
self.generator = generator
#: The completed ISO source layout.
self.source_layout = None
#: Intermediate storage for the column values.
self.__position_values = None
self.__md_pool_values = None
self.__iso_concentration_values = None
self.__iso_volume_values = None
def reset(self):
"""
Resets all values except for input values.
"""
CsvWriter.reset(self)
self._target_containers = dict()
self._target_volumes = dict()
self._target_max_volume = None
self._source_containers = dict()
self._source_volumes = dict()
self._source_dead_volume = None
# Intermediate data storage for errors.
self._transfer_volume_too_small = []
self._transfer_volume_too_large = []
self._source_volume_too_small = set()
self._source_container_missing = set()
self._target_volume_too_large = []
self._target_container_missing = []
def reset(self):
"""
Resets all values except for input values.
"""
CsvWriter.reset(self)
self._target_containers = dict()
self._target_volumes = dict()
self._target_max_volume = None
self._source_containers = dict()
self._source_volumes = dict()
self._source_dead_volume = None
# Intermediate data storage for errors.
self._transfer_volume_too_small = []
self._transfer_volume_too_large = []
self._source_volume_too_small = set()
self._source_container_missing = set()
self._target_volume_too_large = []
self._target_container_missing = []
def __init__(self, stock_sample_creation_iso, parent=None):
"""
Constructor:
:param stock_sample_creation_iso: The ISO whose library layout you want
to print.
:type stock_sample_creation_iso:
:class:`thelma.entities.iso.StockSampleCreationIso`
"""
CsvWriter.__init__(self, parent=parent)
#: The ISO whose layout you want to print.
self.stock_sample_creation_iso = stock_sample_creation_iso
#: The values for the columns.
self.__position_values = None
self.__pool_values = None
self.__md_values = None
self.__tube_values = None
def __init__(self, stock_sample_creation_iso, parent=None):
"""
Constructor:
:param stock_sample_creation_iso: The ISO whose library layout you want
to print.
:type stock_sample_creation_iso:
:class:`thelma.entities.iso.StockSampleCreationIso`
"""
CsvWriter.__init__(self, parent=parent)
#: The ISO whose layout you want to print.
self.stock_sample_creation_iso = stock_sample_creation_iso
#: The values for the columns.
self.__position_values = None
self.__pool_values = None
self.__md_values = None
self.__tube_values = None
def __init__(self, generator, parent=None):
"""
Constructor.
:param generator: The generator that has conducted the upload.
:type generator: :class:`ExperimentMetadataGenerator`
"""
CsvWriter.__init__(self, parent=parent)
#: The generator that has conducted the upload.
self.generator = generator
#: The completed ISO source layout.
self.source_layout = None
#: The transfection layouts containing the association data for
#: each design rack.
self.association_layouts = None
#: A map containing the final concentrations for each design rack.
self.final_concentrations = None
#: Intermediate storage for the column values.
self.__source_well_values = None
self.__design_rack_values = None
self.__target_well_values = None
self.__iso_volume_values = None
self.__iso_concentration_values = None
self.__final_concentration_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
def __init__(self, generator, parent=None):
"""
Constructor.
:param generator: The generator that has conducted the upload.
:type generator: :class:`ExperimentMetadataGenerator`
"""
CsvWriter.__init__(self, parent=parent)
#: The generator that has conducted the upload.
self.generator = generator
#: The completed ISO source layout.
self.source_layout = None
#: The transfection layouts containing the association data for
#: each design rack.
self.association_layouts = None
#: A map containing the final concentrations for each design rack.
self.final_concentrations = None
#: Intermediate storage for the column values.
self.__source_well_values = None
self.__design_rack_values = None
self.__target_well_values = None
self.__iso_volume_values = None
self.__iso_concentration_values = None
self.__final_concentration_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
def reset(self):
CsvWriter.reset(self)
self.__position_values = []
self.__pool_values = []
self.__md_values = []
self.__tube_values = []
def reset(self):
CsvWriter.reset(self)
self.__position_values = []
self.__pool_values = []
self.__md_values = []
self.__tube_values = []
def __init__(self,
planned_worklist,
target_rack,
pipetting_specs,
ignored_positions=None,
parent=None):
"""
Constructor.
:param planned_worklist: The worklist for which to create a
worklist file.
:type planned_worklist:
:class:`thelma.entities.liquidtransfer.PlannedWorklist`
:param target_rack: The rack into which the volumes will be dispensed.
:type target_rack: :class:`thelma.entities.rack.Rack`
:param pipetting_specs: Pipetting specs define transfer properties and
conditions like the transfer volume range.
:type pipetting_specs:
:class:`thelma.entities.liquidtransfer.PipettingSpecs`
:param list ignored_positions: A list of positions (target
for dilutions and source for transfers; :class:`RackPosition`)
that are not included in the worklist file.
"""
CsvWriter.__init__(self, parent=parent)
#: The planned worklist for which to create a file stream.
self.planned_worklist = planned_worklist
#: The rack into which the volumes will be dispensed.
self.target_rack = target_rack
#: Pipetting specs define transfer properties and conditions like
#: the transfer volume range.
self.pipetting_specs = pipetting_specs
if ignored_positions is None:
ignored_positions = []
#: A list of positions that will not be included in the worklist file
#: (even if there are planned transfers for them).
self.ignored_positions = ignored_positions
#: Maps the containers of the target rack onto rack positions.
self._target_containers = None
#: Stores the volume changes for the target rack (mapped onto
#: rack positions).
self._target_volumes = None
#: The maximum volume of a target rack container in ul.
self._target_max_volume = None
#: Maps the container of the source rack onto rack position.
self._source_containers = None
#: Stores the volume changes for the source rack (mapped onto
#: rack positions).
self._source_volumes = None
#: The minimum dead volume of source rack container in ul.
self._source_dead_volume = None
#: The minimum transfer volume used in ul.
self._min_transfer_volume = None
#: The maximum transfer volume used in ul.
self._max_transfer_volume = None
# Intermediate data storage for errors.
self._transfer_volume_too_small = None
self._transfer_volume_too_large = None
self._source_volume_too_small = None
self._source_container_missing = None
self._target_volume_too_large = None
self._target_container_missing = None
