def __get_single_pools(self):
"""
Determines the single pool (ID) or each requested molecule design.
"""
self.add_debug('Get single molecule design pool ...')
md_str = create_in_term_for_db_queries(self.__md_map.keys())
query_statement = SINGLE_POOL_QUERY.QUERY_TEMPLATE % (md_str)
results = self.__session.query(*SINGLE_POOL_QUERY.QUERY_RESULTS).\
from_statement(query_statement).all()
for record in results:
md_id = record[SINGLE_POOL_QUERY.MOLECULE_DESIGN_INDEX]
pool_id = record[SINGLE_POOL_QUERY.POOL_INDEX]
self.__single_pool_map[pool_id] = md_id
if not len(self.__single_pool_map) == len(self.__md_map):
missing_ids = []
for md_id in self.__md_map.keys():
if not self.__single_pool_map.has_key(md_id):
missing_ids.append(md_id)
msg = 'Could not find single molecule design pool for the ' \
'following molecule designs: %s.' % (', '.join(
[str(md_id) for md_id in sorted(missing_ids)]))
self.add_error(msg)
def __run_optimizer(self):
"""
Runs the optimizing query and allocates the results to the library
candidates.
"""
self.add_debug('Run optimizer ...')
sample_str = create_in_term_for_db_queries(self.__stock_samples)
query_statement = LIBRARY_OPTIMIZATION_QUERY.QUERY_TEMPLATE % (
sample_str, sample_str)
results = self.__session.query(
*LIBRARY_OPTIMIZATION_QUERY.QUERY_RESULT_VALUES).\
from_statement(query_statement).all()
for record in results:
iso_candidate = IsoCandidate.create_from_query_result(record)
if iso_candidate.rack_barcode in self.excluded_racks: continue
self.__store_candidate_data(iso_candidate)
if len(self.__picked_candidates) < 1:
msg = 'Did not find any library candidate!'
self.add_error(msg)
def __get_stock_samples(self):
"""
Determines suitable stock samples for the molecule designs required
to create the pools. Suitable tubes must be managed, have a stock
concentration and a certain minimum volume.
"""
self.add_debug('Get stock samples ...')
conc = self.stock_concentration / CONCENTRATION_CONVERSION_FACTOR
volume = (self.take_out_volume + STOCK_DEAD_VOLUME) \
/ VOLUME_CONVERSION_FACTOR
pool_str = create_in_term_for_db_queries(self.__single_pool_map.keys())
query_statement = STOCK_SAMPLE_QUERY.QUERY_TEMPLATE % (
pool_str, conc, volume, STOCK_ITEM_STATUS)
results = self.__session.query(*STOCK_SAMPLE_QUERY.QUERY_RESULTS).\
from_statement(query_statement).all()
found_pools = set()
for record in results:
stock_sample_id = record[STOCK_SAMPLE_QUERY.STOCK_SAMPLE_INDEX]
self.__stock_samples.append(stock_sample_id)
pool_id = record[STOCK_SAMPLE_QUERY.POOL_INDEX]
found_pools.add(pool_id)
if len(found_pools) < 1:
msg = 'Did not find any suitable stock sample!'
self.add_error(msg)
elif not len(found_pools) == len(self.__single_pool_map):
missing_pools = []
for pool_id, md_id in self.__single_pool_map.iteritems():
if not pool_id in found_pools:
missing_pools.append('%s (md: %s)' % (pool_id, md_id))
msg = 'Could not find suitable source stock tubes for the ' \
'following molecule design pools: %s.' \
% (', '.join(sorted(missing_pools)))
self.add_warning(msg)
def _get_params_for_sql_statement(self):
return create_in_term_for_db_queries(self.molecule_design_ids)
def _get_params_for_sql_statement(self):
rack_term = create_in_term_for_db_queries(self.rack_map.keys(),
as_string=True)
return (rack_term)
def _get_params_for_sql_statement(self):
sample_str = create_in_term_for_db_queries(self.sample_ids)
return (sample_str, sample_str)
def _get_pool_id_term(self):
return create_in_term_for_db_queries(self.pool_ids)
def _get_params_for_sql_statement(self):
return create_in_term_for_db_queries(self.tube_barcodes, as_string=True)
def _get_params_for_sql_statement(self):
pool_str = create_in_term_for_db_queries(self.pool_ids)
conc = self.concentration / CONCENTRATION_CONVERSION_FACTOR
vol = (self.minimum_volume + STOCK_DEAD_VOLUME) \
/ VOLUME_CONVERSION_FACTOR
return (pool_str, conc, vol, STOCK_ITEM_STATUS)
def _get_params_for_sql_statement(self):
rack_term = create_in_term_for_db_queries(self.rack_map.keys(),
as_string=True)
return (rack_term)
def get_stock_tube_specs_db_term():
"""
Returns a term that can be inserted into IN-clauses of DB queries
(containing all valid specs for stock tubes).
"""
return create_in_term_for_db_queries(STOCK_TUBE_SPECS, as_string=True)
def _get_params_for_sql_statement(self):
return create_in_term_for_db_queries(self.rack_barcodes, as_string=True)
def _get_params_for_sql_statement(self):
pool_str = create_in_term_for_db_queries(self.pool_ids)
conc = self.concentration / CONCENTRATION_CONVERSION_FACTOR
vol = (self.minimum_volume + STOCK_DEAD_VOLUME) \
/ VOLUME_CONVERSION_FACTOR
return (pool_str, conc, vol, STOCK_ITEM_STATUS)
def _get_params_for_sql_statement(self):
sample_str = create_in_term_for_db_queries(self.sample_ids)
return (sample_str, sample_str)
def _get_pool_id_term(self):
return create_in_term_for_db_queries(self.pool_ids)
