def convert_to_stock_sample(self):
"""
Converts this instance into a stock sample by setting all the
required attributes. The object class is ''not'' changed.
"""
mols = [sm.molecule for sm in self.sample_molecules]
if len(mols) == 0:
raise ValueError('Stock samples must have at least one sample '
'molecule.')
if len(
set([(mol.supplier, mol.molecule_design.molecule_type,
self.sample_molecules[idx].concentration)
for (idx, mol) in enumerate(mols)])) > 1:
raise ValueError('All molecule designs in a stock sample must '
'have the same supplier, the same molecule type '
'and the same concentration.')
from thelma.entities.moleculedesign import MoleculeDesignPool
mdp = MoleculeDesignPool.create_from_data(
dict(molecule_designs=set([mol.molecule_design for mol in mols])))
# Setting attributes outside __init__ pylint: disable=W0201
concentration = 0
for sm in self.sample_molecules:
concentration += sm.concentration
concentration = round(concentration, 10) # one decimal place if in nM
self.molecule_design_pool = mdp
self.supplier = mols[0].supplier
self.molecule_type = mols[0].molecule_design.molecule_type
self.concentration = concentration
self.sample_type = SAMPLE_TYPES.STOCK
self.__class__ = StockSample
def __get_missing_molecule_design_pools(self):
# Fetches or creates the molecule design pools for the rows in which
# there are only molecule designs given
# (invokes :func:`MoleculeDesignPool.create_from_data`).
self.add_debug('Find pool IDs for molecule design sets ...')
stock_conc = (get_default_stock_concentration(
molecule_type=self.__molecule_type,
number_designs=self.__number_molecule_designs)) \
/ CONCENTRATION_CONVERSION_FACTOR
for md_ids in self.__pools_to_find:
mds = set([self.__md_map[md_id] for md_id in md_ids])
mdp_data = dict(molecule_designs=mds,
default_stock_concentration=stock_conc)
pool = MoleculeDesignPool.create_from_data(mdp_data)
self.__pools.add(pool)
def __get_missing_molecule_design_pools(self):
# Fetches or creates the molecule design pools for the rows in which
# there are only molecule designs given
# (invokes :func:`MoleculeDesignPool.create_from_data`).
self.add_debug("Find pool IDs for molecule design sets ...")
stock_conc = (
get_default_stock_concentration(
molecule_type=self.__molecule_type, number_designs=self.__number_molecule_designs
)
) / CONCENTRATION_CONVERSION_FACTOR
for md_ids in self.__pools_to_find:
mds = set([self.__md_map[md_id] for md_id in md_ids])
mdp_data = dict(molecule_designs=mds, default_stock_concentration=stock_conc)
pool = MoleculeDesignPool.create_from_data(mdp_data)
self.__pools.add(pool)
def convert_to_stock_sample(self):
"""
Converts this instance into a stock sample by setting all the
required attributes. The object class is ''not'' changed.
"""
mols = [sm.molecule for sm in self.sample_molecules]
if len(mols) == 0:
raise ValueError("Stock samples must have at least one sample " "molecule.")
if (
len(
set(
[
(mol.supplier, mol.molecule_design.molecule_type, self.sample_molecules[idx].concentration)
for (idx, mol) in enumerate(mols)
]
)
)
> 1
):
raise ValueError(
"All molecule designs in a stock sample must "
"have the same supplier, the same molecule type "
"and the same concentration."
)
from thelma.entities.moleculedesign import MoleculeDesignPool
mdp = MoleculeDesignPool.create_from_data(dict(molecule_designs=set([mol.molecule_design for mol in mols])))
# Setting attributes outside __init__ pylint: disable=W0201
concentration = 0
for sm in self.sample_molecules:
concentration += sm.concentration
concentration = round(concentration, 10) # one decimal place if in nM
self.molecule_design_pool = mdp
self.supplier = mols[0].supplier
self.molecule_type = mols[0].molecule_design.molecule_type
self.concentration = concentration
self.sample_type = SAMPLE_TYPES.STOCK
self.__class__ = StockSample
