def __init__(self, rack_position, molecule_design_pool,
stock_tube_barcodes):
"""
:param rack_position: The source rack position in the source rack.
:type rack_position: :class:`thelma.entities.rack.RackPosition`
:param molecule_design_pool: A molecule design pool to generate.
:type molecule_design_pool:
:class:`thelma.entities.moleculedesign.MoleculeDesignPool`
:param stock_tube_barcodes: The stock tube barcodes for the single
molecule design tubes used to generate this pool.
:type stock_tube_barcodes: :class:`list`
"""
MoleculeDesignPoolPosition.__init__(self, rack_position=rack_position,
molecule_design_pool=molecule_design_pool,
position_type=FIXED_POSITION_TYPE)
if not isinstance(stock_tube_barcodes, list):
msg = 'The stock tube barcodes must be a list (obtained: %s).' \
% (stock_tube_barcodes.__class__.__name__)
raise TypeError(msg)
#: A list of molecules contained in the pool (ordered by ID).
self.molecule_designs = []
for md in molecule_design_pool.molecule_designs:
self.molecule_designs.append(md)
self.molecule_designs.sort()
#: The stock tube barcodes for the single molecule design tubes
#: used to generate this pool
self.stock_tube_barcodes = sorted(stock_tube_barcodes)
def __init__(self, rack_position, molecule_design_pool=None,
position_type=None, iso_concentration=None, iso_volume=None):
"""
Constructor:
:param rack_position: The rack position.
:type rack_position: :class:`thelma.entities.rack.RackPosition`.
:param molecule_design_pool: The molecule design pool for this position
or a valid placeholder.
:type molecule_design_pool:
:class:`thelma.entities.moleculedesign.MoleculeDesignPool`
or :class:`basestring`
:param position_type: influences valid values for other parameters
:type position_type: :class:`str
:param iso_concentration: The concentration requested from the stock.
:type iso_concentration: positive number
:param iso_volume: The volume requested by the stock.
:type iso_volume: positive number
"""
MoleculeDesignPoolPosition.__init__(self, rack_position=rack_position,
molecule_design_pool=molecule_design_pool,
position_type=position_type)
#: The concentration requested by the stock management.
self.iso_concentration = get_converted_number(iso_concentration)
#: The volume requested by the stock management.
self.iso_volume = get_converted_number(iso_volume)
self.__check_values_for_position_type()
def __init__(self, rack_position, molecule_design_pool,
stock_tube_barcodes):
"""
:param rack_position: The source rack position in the source rack.
:type rack_position: :class:`thelma.entities.rack.RackPosition`
:param molecule_design_pool: A molecule design pool to generate.
:type molecule_design_pool:
:class:`thelma.entities.moleculedesign.MoleculeDesignPool`
:param stock_tube_barcodes: The stock tube barcodes for the single
molecule design tubes used to generate this pool.
:type stock_tube_barcodes: :class:`list`
"""
MoleculeDesignPoolPosition.__init__(
self,
rack_position=rack_position,
molecule_design_pool=molecule_design_pool,
position_type=FIXED_POSITION_TYPE)
if not isinstance(stock_tube_barcodes, list):
msg = 'The stock tube barcodes must be a list (obtained: %s).' \
% (stock_tube_barcodes.__class__.__name__)
raise TypeError(msg)
#: A list of molecules contained in the pool (ordered by ID).
self.molecule_designs = []
for md in molecule_design_pool.molecule_designs:
self.molecule_designs.append(md)
self.molecule_designs.sort()
#: The stock tube barcodes for the single molecule design tubes
#: used to generate this pool
self.stock_tube_barcodes = sorted(stock_tube_barcodes)
def __eq__(self, other):
if not MoleculeDesignPoolPosition.__eq__(self, other): return False
if not self.is_empty and not self.iso_volume == other.iso_volume:
return False
if not (self.is_empty or self.is_mock) and \
not self.iso_concentration == other.iso_concentration:
return False
return True
def __eq__(self, other):
if not MoleculeDesignPoolPosition.__eq__(self, other): return False
if not self.is_empty and not self.iso_volume == other.iso_volume:
return False
if not (self.is_empty or self.is_mock) and \
not self.iso_concentration == other.iso_concentration:
return False
return True
def _get_parameter_values_map(self):
"""
Returns the :attr:`parameter_values_map`
"""
parameter_map = MoleculeDesignPoolPosition._get_parameter_values_map(
self)
parameter_map[self.PARAMETER_SET.ISO_VOLUME] = self.iso_volume
parameter_map[self.PARAMETER_SET.ISO_CONCENTRATION] = \
self.iso_concentration
return parameter_map
def _get_parameter_values_map(self):
"""
Returns the :attr:`parameter_values_map`
"""
parameter_map = MoleculeDesignPoolPosition._get_parameter_values_map(
self)
parameter_map[self.PARAMETER_SET.ISO_VOLUME] = self.iso_volume
parameter_map[self.PARAMETER_SET.ISO_CONCENTRATION] = \
self.iso_concentration
return parameter_map
def get_parameter_tag(self, parameter):
"""
The method needs to be overwritten because the value for the molecule
designs tag is a concatenated string. Position types are not important
"""
if parameter == self.PARAMETER_SET.MOLECULE_DESIGNS:
return self.__get_molecule_designs_tag()
elif parameter == self.PARAMETER_SET.STOCK_TUBE_BARCODES:
return self.__get_stock_barcodes_tag()
else:
return MoleculeDesignPoolPosition.get_parameter_tag(self, parameter)
def get_parameter_tag(self, parameter):
"""
The method needs to be overwritten because the value for the molecule
designs tag is a concatenated string. Position types are not important
"""
if parameter == self.PARAMETER_SET.MOLECULE_DESIGNS:
return self.__get_molecule_designs_tag()
elif parameter == self.PARAMETER_SET.STOCK_TUBE_BARCODES:
return self.__get_stock_barcodes_tag()
else:
return MoleculeDesignPoolPosition.get_parameter_tag(
self, parameter)
def __init__(self,
rack_position,
molecule_design_pool=None,
position_type=None,
iso_concentration=None,
iso_volume=None):
"""
Constructor:
:param rack_position: The rack position.
:type rack_position: :class:`thelma.entities.rack.RackPosition`.
:param molecule_design_pool: The molecule design pool for this position
or a valid placeholder.
:type molecule_design_pool:
:class:`thelma.entities.moleculedesign.MoleculeDesignPool`
or :class:`basestring`
:param position_type: influences valid values for other parameters
:type position_type: :class:`str
:param iso_concentration: The concentration requested from the stock.
:type iso_concentration: positive number
:param iso_volume: The volume requested by the stock.
:type iso_volume: positive number
"""
MoleculeDesignPoolPosition.__init__(
self,
rack_position=rack_position,
molecule_design_pool=molecule_design_pool,
position_type=position_type)
#: The concentration requested by the stock management.
self.iso_concentration = get_converted_number(iso_concentration)
#: The volume requested by the stock management.
self.iso_volume = get_converted_number(iso_volume)
self.__check_values_for_position_type()
def __eq__(self, other):
if not MoleculeDesignPoolPosition.__eq__(self, other):
result = False
else:
result = self.stock_tube_barcodes == other.stock_tube_barcodes
return result
def __eq__(self, other):
if not MoleculeDesignPoolPosition.__eq__(self, other):
result = False
else:
result = self.stock_tube_barcodes == other.stock_tube_barcodes
return result
