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
def __process_molecule_design_pools(self):
self.add_debug('Processing molecule design pools.')
md_pool_agg = get_root_aggregate(IMoleculeDesignPool)
mdpri_hash_map = {}
hash_func = MoleculeDesignPool.make_member_hash
new_mdpri_map = {}
new_mds = self.return_value['molecule_designs']
for mdpri in self.registration_items:
# By definition, any mdpri that contains one or more new designs
# must be new. We must treat this as a special case because
# building member hash values with the new designs does not work
# reliably since they may not have been flushed yet.
mds = [mdri.molecule_design
for mdri in mdpri.molecule_design_registration_items]
if any(md in new_mds for md in mds):
# We use the *structure* as key for the new pools map here
# as this is always available (unlike the design IDs, which
# may not have been generated at this point).
key = self.__make_new_mdpri_key(mdpri)
new_mdpri_map.setdefault(key, []).append(mdpri)
else:
# For pools that consist only of existing designs, we build
# a map with member hashes as keys so we can query with a
# single DB call.
hash_val = \
hash_func([mdri.molecule_design
for mdri in
mdpri.molecule_design_registration_items])
mdpri_hash_map.setdefault(hash_val, []).append(mdpri)
if len(mdpri_hash_map) > 0:
md_pool_agg.filter = cntd(member_hash=mdpri_hash_map.keys())
existing_mdp_map = dict([(mdp.member_hash, mdp)
for mdp in md_pool_agg.iterator()])
# Update existing molecule design pool registration items.
for hash_val, mdp in existing_mdp_map.iteritems():
mdpris = mdpri_hash_map[hash_val]
for mdpri in mdpris:
if not mdpri.molecule_design_pool is None \
and mdp.id != mdpri.molecule_design_pool.id:
msg = 'The molecule design pool ID (%s) specified ' \
'in the sample data does not match the ID ' \
'of the pool that retrieved for the design ' \
'structure information associated with it.'
self.add_error(msg)
continue
mdpri.molecule_design_pool = mdp
else:
existing_mdp_map = {}
# Determine non-existing molecule design pool registration items and
# build up a map (this makes sure the same design is registered at
# most once.
new_mdp_hashes = \
set(mdpri_hash_map.keys()).difference(existing_mdp_map.keys())
for new_mdp_hash in new_mdp_hashes:
mdpris = mdpri_hash_map[new_mdp_hash]
for mdpri in mdpris:
if not mdpri.molecule_design_pool is None:
# This is a case where we supplied both design pool ID *and*
# structure information in the data file and the two do not
# match (i.e., the structures were not found).
msg = 'The molecule design pool ID (%s) specified in the ' \
'sample data does not match the design structure ' \
'information associated with it.'
self.add_error(msg)
continue
key = self.__make_new_mdpri_key(mdpri)
new_mdpri_map.setdefault(key, []).append(mdpri)
if len(new_mdpri_map) > 0:
new_md_pools = []
for mdpris in new_mdpri_map.values():
# We use the first mdp registration item to create a
# new pool and update all with the latter.
md_pool = MoleculeDesignPool(
set([mdri.molecule_design
for mdri in
mdpris[0].molecule_design_registration_items]))
md_pool_agg.add(md_pool)
new_md_pools.append(md_pool)
for mdpri in mdpris:
mdpri.molecule_design_pool = md_pool
self.return_value['molecule_design_pools'] = new_md_pools
