def __init__(self,
stock_tube_containers,
excluded_racks=None,
requested_tubes=None,
parent=None):
"""
Constructor.
:param stock_tube_containers: The container items should contain all
target positions for the stock transfer. They must be mapped on
the pool.
:type stock_tube_containers: map of :class:`StockTubeContainer`
:param excluded_racks: A list of barcodes from stock racks that shall
not be used for molecule design picking.
:type excluded_racks: A list of rack barcodes
:param requested_tubes: A list of barcodes from stock tubes that are
supposed to be used.
:type requested_tubes: A list of tube barcodes.
"""
SessionTool.__init__(self, parent=parent)
#: The container items should contain all target positions for the
#: stock transfer.
self.stock_tube_containers = stock_tube_containers
if excluded_racks is None:
excluded_racks = []
#: A list of barcodes from stock racks that shall not be used for
#: molecule design picking.
self.excluded_racks = excluded_racks
if requested_tubes is None:
requested_tubes = []
#: A list of barcodes from stock tubes that are supposed to be used
#: (for fixed positions).
self.requested_tubes = requested_tubes
#: The tube aggregate is used to check tubes for specified tube
#: barcodes.
self.__tube_agg = None
#: Maps molecule design pools onto pool IDs.
self.__pool_map = None
#: The molecule design pools of the requested tubes.
self.__requested_tube_map = None
#: The required volume for each pool *in ul* without stock dead volume.
self.__volume_map = None
#: Stores stock tube containers for tubes that need to be replaced.
self.__replaced_tube_containers = None
#: Stores message infos for tubes that have been replaced because the
#: original rack has been excluded mapped onto pool IDs.
self.__excluded_tubes = None
#: The tubes (that have not been replaced) mapped onto tube barcodes.
self.__tube_map = None
#: Contains pools for which no tube has been found.
self.__missing_pools = None
# Intermediate warning and error messages
self.__insuffient_volume_requested = None
self.__insuffient_volume_scheduled = None
self.__conc_mismatch_requested = None
self.__conc_mismatch_scheduled = None
def __init__(self, stock_tube_containers, excluded_racks=None,
requested_tubes=None, parent=None):
"""
Constructor.
:param stock_tube_containers: The container items should contain all
target positions for the stock transfer. They must be mapped on
the pool.
:type stock_tube_containers: map of :class:`StockTubeContainer`
:param excluded_racks: A list of barcodes from stock racks that shall
not be used for molecule design picking.
:type excluded_racks: A list of rack barcodes
:param requested_tubes: A list of barcodes from stock tubes that are
supposed to be used.
:type requested_tubes: A list of tube barcodes.
"""
SessionTool.__init__(self, parent=parent)
#: The container items should contain all target positions for the
#: stock transfer.
self.stock_tube_containers = stock_tube_containers
if excluded_racks is None:
excluded_racks = []
#: A list of barcodes from stock racks that shall not be used for
#: molecule design picking.
self.excluded_racks = excluded_racks
if requested_tubes is None:
requested_tubes = []
#: A list of barcodes from stock tubes that are supposed to be used
#: (for fixed positions).
self.requested_tubes = requested_tubes
#: The tube aggregate is used to check tubes for specified tube
#: barcodes.
self.__tube_agg = None
#: Maps molecule design pools onto pool IDs.
self.__pool_map = None
#: The molecule design pools of the requested tubes.
self.__requested_tube_map = None
#: The required volume for each pool *in ul* without stock dead volume.
self.__volume_map = None
#: Stores stock tube containers for tubes that need to be replaced.
self.__replaced_tube_containers = None
#: Stores message infos for tubes that have been replaced because the
#: original rack has been excluded mapped onto pool IDs.
self.__excluded_tubes = None
#: The tubes (that have not been replaced) mapped onto tube barcodes.
self.__tube_map = None
#: Contains pools for which no tube has been found.
self.__missing_pools = None
# Intermediate warning and error messages
self.__insuffient_volume_requested = None
self.__insuffient_volume_scheduled = None
self.__conc_mismatch_requested = None
self.__conc_mismatch_scheduled = None
def reset(self):
SessionTool.reset(self)
self.__tube_agg = get_root_aggregate(ITube)
self.__pool_map = dict()
self.__requested_tube_map = dict()
self.__volume_map = dict()
self.__replaced_tube_containers = []
self.__excluded_tubes = dict()
self.__tube_map = dict()
self.__insuffient_volume_requested = dict()
self.__insuffient_volume_scheduled = dict()
self.__conc_mismatch_requested = []
self.__conc_mismatch_scheduled = []
self.__missing_pools = []
def reset(self):
SessionTool.reset(self)
self.__tube_agg = get_root_aggregate(ITube)
self.__pool_map = dict()
self.__requested_tube_map = dict()
self.__volume_map = dict()
self.__replaced_tube_containers = []
self.__excluded_tubes = dict()
self.__tube_map = dict()
self.__insuffient_volume_requested = dict()
self.__insuffient_volume_scheduled = dict()
self.__conc_mismatch_requested = []
self.__conc_mismatch_scheduled = []
self.__missing_pools = []
def reset(self):
"""
Resets all values except for initialisation values.
"""
SessionTool.reset(self)
self.__stock_rack_size = get_stock_rack_size()
self.__tube_count_map = None
self.__donor_racks = dict()
self.__receiver_racks = dict()
self.__look_for_exact_matches = True
self.__stop_associations = False
self.__tube_transfers = []
self.__worklist_stream = None
self.__report_stream = None
self.__zip_stream = None
def reset(self):
"""
Resets all values except for initialisation values.
"""
SessionTool.reset(self)
self.__stock_rack_size = get_stock_rack_size()
self.__tube_count_map = None
self.__donor_racks = dict()
self.__receiver_racks = dict()
self.__look_for_exact_matches = True
self.__stop_associations = False
self.__tube_transfers = []
self.__worklist_stream = None
self.__report_stream = None
self.__zip_stream = None
def __init__(self,
molecule_design_pools,
stock_concentration,
take_out_volume=None,
excluded_racks=None,
requested_tubes=None,
parent=None):
"""
Constructor.
:param set molecule_design_pools: Set of molecule design pools
(:class:`thelma.entities.moleculedesign.MoleculeDesignPool`) for
which to run the query.
:type molecule_design_pools: :class:`set` of molecule design pools
:param int stock_concentration: The stock concentration for the pools
in nM (positive number).
:param int take_out_volume: The volume that shall be removed from the
stock sample *in ul* (positive number; may be *None*, in which
case we do not filter for at least stock dead volume).
:param list excluded_racks: List of barcodes from stock racks that shall
not be used for molecule design picking.
:param list requested_tubes: List of barcodes from stock tubes that are
supposed to be used.
"""
SessionTool.__init__(self, parent=parent)
self.molecule_design_pools = molecule_design_pools
self.stock_concentration = stock_concentration
self.take_out_volume = take_out_volume
if excluded_racks is None:
excluded_racks = []
self.excluded_racks = excluded_racks
if requested_tubes is None:
requested_tubes = []
self.requested_tubes = requested_tubes
#: The pools mapped onto their IDs.
self._pool_map = None
#: Stores the suitable stock sample IDs for the pools. The results are
#: determined by the :class:`SINGLE_POOL_QUERY`.
self._stock_samples = None
#: Returns all candidates in the same order as in the query result.
#: Use :func:`get_unsorted_candidates` to access this list.
self._unsorted_candidates = None
#: The picked candidates ordered by pools.
self._picked_candidates = None
def __init__(self, molecule_design_pools, stock_concentration,
take_out_volume=None, excluded_racks=None,
requested_tubes=None, parent=None):
"""
Constructor.
:param set molecule_design_pools: Set of molecule design pools
(:class:`thelma.entities.moleculedesign.MoleculeDesignPool`) for
which to run the query.
:type molecule_design_pools: :class:`set` of molecule design pools
:param int stock_concentration: The stock concentration for the pools
in nM (positive number).
:param int take_out_volume: The volume that shall be removed from the
stock sample *in ul* (positive number; may be *None*, in which
case we do not filter for at least stock dead volume).
:param list excluded_racks: List of barcodes from stock racks that shall
not be used for molecule design picking.
:param list requested_tubes: List of barcodes from stock tubes that are
supposed to be used.
"""
SessionTool.__init__(self, parent=parent)
self.molecule_design_pools = molecule_design_pools
self.stock_concentration = stock_concentration
self.take_out_volume = take_out_volume
if excluded_racks is None:
excluded_racks = []
self.excluded_racks = excluded_racks
if requested_tubes is None:
requested_tubes = []
self.requested_tubes = requested_tubes
#: The pools mapped onto their IDs.
self._pool_map = None
#: Stores the suitable stock sample IDs for the pools. The results are
#: determined by the :class:`SINGLE_POOL_QUERY`.
self._stock_samples = None
#: Returns all candidates in the same order as in the query result.
#: Use :func:`get_unsorted_candidates` to access this list.
self._unsorted_candidates = None
#: The picked candidates ordered by pools.
self._picked_candidates = None
def __init__(self, racks_to_empty=None, excluded_racks=None, parent=None):
"""
Constructor.
:param int racks_to_empty: The number of empty racks the run shall
result in (optional).
:param excluded_racks: A list of barcodes from stock racks that shall
not be used.
:type excluded_racks: A list or set of rack barcodes
"""
SessionTool.__init__(self, parent=parent)
#: The number of empty racks the run shall result in (optional).
self.racks_to_empty = racks_to_empty
#: A list of barcodes from stock racks that shall not be used.
self.excluded_racks = excluded_racks
if excluded_racks is None: self.excluded_racks = []
#: The number of positions in a stock rack.
self.__stock_rack_size = None
#: Maps :class:`StockCondenseRack` objects onto tube counts.
self.__tube_count_map = None
#: Maps donor racks onto rack barcodes.
self.__donor_racks = None
#: Maps receiver racks onto rack barcodes.
self.__receiver_racks = None
#: Do we look for exact tube count matches? (*True* for thie first
#: iteration of association, *False* for the second).
self.__look_for_exact_matches = None
#: Shall we stop looking for rack associations?
self.__stop_associations = None
#: The scheduled tube transfers sorted by donator rack (ATTENTION:
#: stores :class:`TubeTransferData` objects, no :class:`TubeTransfer`
#: entities.
self.__tube_transfers = None
#: The stream for the worklist file.
self.__worklist_stream = None
#: The stream for the report file.
self.__report_stream = None
#: The zip stream containing the two files.
self.__zip_stream = None
def __init__(self, racks_to_empty=None, excluded_racks=None, parent=None):
"""
Constructor.
:param int racks_to_empty: The number of empty racks the run shall
result in (optional).
:param excluded_racks: A list of barcodes from stock racks that shall
not be used.
:type excluded_racks: A list or set of rack barcodes
"""
SessionTool.__init__(self, parent=parent)
#: The number of empty racks the run shall result in (optional).
self.racks_to_empty = racks_to_empty
#: A list of barcodes from stock racks that shall not be used.
self.excluded_racks = excluded_racks
if excluded_racks is None: self.excluded_racks = []
#: The number of positions in a stock rack.
self.__stock_rack_size = None
#: Maps :class:`StockCondenseRack` objects onto tube counts.
self.__tube_count_map = None
#: Maps donor racks onto rack barcodes.
self.__donor_racks = None
#: Maps receiver racks onto rack barcodes.
self.__receiver_racks = None
#: Do we look for exact tube count matches? (*True* for thie first
#: iteration of association, *False* for the second).
self.__look_for_exact_matches = None
#: Shall we stop looking for rack associations?
self.__stop_associations = None
#: The scheduled tube transfers sorted by donator rack (ATTENTION:
#: stores :class:`TubeTransferData` objects, no :class:`TubeTransfer`
#: entities.
self.__tube_transfers = None
#: The stream for the worklist file.
self.__worklist_stream = None
#: The stream for the report file.
self.__report_stream = None
#: The zip stream containing the two files.
self.__zip_stream = None
def reset(self):
SessionTool.reset(self)
self._pool_map = dict()
self._stock_samples = []
self._unsorted_candidates = []
self._picked_candidates = OrderedDict()
def reset(self):
SessionTool.reset(self)
self._pool_map = dict()
self._stock_samples = []
self._unsorted_candidates = []
self._picked_candidates = OrderedDict()