def __stock_concentration_match(self, candidate, container, error_list):
"""
Makes sure tube candidate and stock tube container expect the same
stock concentration.
"""
container_conc = container.get_stock_concentration()
candidate_conc = candidate.concentration
if not are_equal_values(container_conc, candidate_conc):
info = '%s (pool: %i, expected: %s nM, found at tube: %s nM)' \
% (candidate.tube_barcode, candidate.pool_id,
get_trimmed_string(container_conc),
get_trimmed_string(candidate_conc))
error_list.append(info)
return False
else:
return True
def __stock_concentration_match(self, candidate, container, error_list):
"""
Makes sure tube candidate and stock tube container expect the same
stock concentration.
"""
container_conc = container.get_stock_concentration()
candidate_conc = candidate.concentration
if not are_equal_values(container_conc, candidate_conc):
info = '%s (pool: %i, expected: %s nM, found at tube: %s nM)' \
% (candidate.tube_barcode, candidate.pool_id,
get_trimmed_string(container_conc),
get_trimmed_string(candidate_conc))
error_list.append(info)
return False
else:
return True
def __check_and_assign_tube_candidates(self):
"""
Checks whether there is pool for each requested pool and whether
volume and concentration match.
"""
missing_pools = []
invalid_conc = []
invalid_vol = []
for pool, container in self._stock_tube_containers.iteritems():
if not self.__tube_candidates.has_key(pool):
missing_pools.append(pool.id)
continue
candidate = self.__tube_candidates[pool]
exp_stock_conc = pool.default_stock_concentration \
* CONCENTRATION_CONVERSION_FACTOR
if not are_equal_values(candidate.concentration,
exp_stock_conc):
info = '%s (pool: %s, expected: %s nM, found: %s nM)' % (
candidate.tube_barcode, pool,
get_trimmed_string(exp_stock_conc),
get_trimmed_string(candidate.concentration))
invalid_conc.append(info)
continue
required_vol = STOCK_DEAD_VOLUME \
+ container.get_total_required_volume()
if is_smaller_than(candidate.volume, required_vol):
info = '%s (pool: %s, required: %s ul, found: %s ul)' % (
candidate.tube_barcode, pool,
get_trimmed_string(required_vol),
get_trimmed_string(candidate.volume))
invalid_vol.append(info)
continue
container.tube_candidate = candidate
if len(missing_pools) > 0:
msg = 'Could not find tubes for the following pools: %s.' % (
self._get_joined_str(missing_pools, is_strs=False))
self.add_error(msg)
if len(invalid_conc) > 0:
msg = 'The concentrations in some tubes do not match the ' \
'expected ones: %s.' % (self._get_joined_str(invalid_conc))
self.add_error(msg)
if len(invalid_vol) > 0:
msg = 'The volumes in some tubes (dead volume included) are not ' \
'sufficient: %s.' % (self._get_joined_str(invalid_vol))
self.add_error(msg)
def __create_tube_candidates(self):
"""
Checks the tubes in the given racks and converts them into
:class:`TubeCandidate` objects.
Sample which are not stock samples or do not have a volume are ignored.
The number of tubes found must match the number of stock tube
containers.
"""
no_stock_sample = dict()
no_sample = dict()
num_tubes = 0
for barcode, rack in self._barcode_map.iteritems():
for tube in rack.containers:
stock_sample = tube.sample
rack_pos = tube.rack_position
num_tubes += 1
tube_info = '%s (%s)' % (tube.barcode, rack_pos.label)
if stock_sample is None:
add_list_map_element(no_sample, barcode, tube_info)
continue
sample_vol = stock_sample.volume * VOLUME_CONVERSION_FACTOR
if are_equal_values(sample_vol, 0):
add_list_map_element(no_sample, barcode, tube_info)
continue
if not isinstance(stock_sample, StockSample):
add_list_map_element(no_stock_sample, barcode, tube_info)
continue
pool = stock_sample.molecule_design_pool
tc = TubeCandidate(pool_id=pool.id,
rack_barcode=barcode,
rack_position=rack_pos,
tube_barcode=tube.barcode,
concentration=stock_sample.concentration,
volume=stock_sample.volume)
self.__tube_candidates[pool] = tc
if len(no_sample) > 0:
rack_strs = []
for barcode in sorted(no_sample.keys()):
info_str = '%s (%s)' % (barcode, self._get_joined_str(
no_sample[barcode]))
rack_strs.append(info_str)
msg = 'In some racks there are empty tubes: %s. Please remove ' \
'them and try again.' % (' -- '.join(rack_strs))
self.add_error(msg)
if len(no_stock_sample) > 0:
msg = 'The tubes in some of the racks you have specified contain ' \
'normal samples instead of stock samples. Talk to the ' \
'IT department, please. Details: %s.' \
% (self._get_joined_map_str(no_stock_sample))
self.add_error(msg)
exp_tube_num = len(self._stock_tube_containers)
if not self.has_errors() and not exp_tube_num == num_tubes:
msg = 'The number of tubes in the racks you have specified (%i) ' \
'is different from the expected one (%i). Remove all tubes ' \
'that are not required and add the missing ones or try ' \
'the generate a new stock rack.' % (num_tubes, exp_tube_num)
self.add_error(msg)
