def _check_transfer_volume(self,
transfer_volume,
target_position,
source_position=None):
"""
Checks whether the transfer volume is in a valid volume range,
whether the target container can take that amount and whether
there is enough volume in the source container.
"""
volume = transfer_volume * VOLUME_CONVERSION_FACTOR
# Check the minimum and maximum transfer volume.
if is_smaller_than(volume, self._min_transfer_volume):
error_msg = 'target %s (%.1f ul)' \
% (target_position.label, volume)
self._transfer_volume_too_small.append(error_msg)
return False
if self.TRANSFER_TYPE == TRANSFER_TYPES.SAMPLE_TRANSFER \
and is_larger_than(volume, self._max_transfer_volume):
error_msg = 'source %s (%.1f ul)' % (source_position, volume)
self._transfer_volume_too_large.append(error_msg)
# Check whether there is enough space in the target well.
max_volume = \
self.__get_max_volume_for_target_container(target_position)
if max_volume is None:
return False
sample_volume = self._target_volumes[target_position]
if is_smaller_than(max_volume, (sample_volume + volume)):
error_msg = '%s (sample vol: %.1f, transfer vol: %.1f)' \
% (target_position, sample_volume, volume)
self._target_volume_too_large.append(error_msg)
return False
# Check whether there is enough liquid in the source well
if self.TRANSFER_TYPE == TRANSFER_TYPES.SAMPLE_DILUTION:
return True
if source_position is None:
msg = 'You must not pass a None value for the source well ' \
'when checking the volumes if you have passed a source ' \
'rack!'
self.add_error(msg)
return False
if not self._source_volumes.has_key(source_position):
self._source_container_missing.add(source_position.label)
return False
source_volume = self._source_volumes[source_position]
source_volume -= volume
dead_volume = self.__get_dead_volume_for_source_container(
source_position)
if is_smaller_than(source_volume, dead_volume):
self._source_volume_too_small.add(source_position.label)
return False
self._source_volumes[source_position] = source_volume
return True
def _check_transfer_volume(self, transfer_volume, target_position,
source_position=None):
"""
Checks whether the transfer volume is in a valid volume range,
whether the target container can take that amount and whether
there is enough volume in the source container.
"""
volume = transfer_volume * VOLUME_CONVERSION_FACTOR
# Check the minimum and maximum transfer volume.
if is_smaller_than(volume, self._min_transfer_volume):
error_msg = 'target %s (%.1f ul)' \
% (target_position.label, volume)
self._transfer_volume_too_small.append(error_msg)
return False
if self.TRANSFER_TYPE == TRANSFER_TYPES.SAMPLE_TRANSFER \
and is_larger_than(volume, self._max_transfer_volume):
error_msg = 'source %s (%.1f ul)' % (source_position, volume)
self._transfer_volume_too_large.append(error_msg)
# Check whether there is enough space in the target well.
max_volume = \
self.__get_max_volume_for_target_container(target_position)
if max_volume is None:
return False
sample_volume = self._target_volumes[target_position]
if is_smaller_than(max_volume, (sample_volume + volume)):
error_msg = '%s (sample vol: %.1f, transfer vol: %.1f)' \
% (target_position, sample_volume, volume)
self._target_volume_too_large.append(error_msg)
return False
# Check whether there is enough liquid in the source well
if self.TRANSFER_TYPE == TRANSFER_TYPES.SAMPLE_DILUTION:
return True
if source_position is None:
msg = 'You must not pass a None value for the source well ' \
'when checking the volumes if you have passed a source ' \
'rack!'
self.add_error(msg)
return False
if not self._source_volumes.has_key(source_position):
self._source_container_missing.add(source_position.label)
return False
source_volume = self._source_volumes[source_position]
source_volume -= volume
dead_volume = self.__get_dead_volume_for_source_container(
source_position)
if is_smaller_than(source_volume, dead_volume):
self._source_volume_too_small.add(source_position.label)
return False
self._source_volumes[source_position] = source_volume
return True
def __accept_tube_candidate(self, tube_candidate, conc_mismatch_list,
insufficent_vol_map):
"""
A valid tube container must have a matching concentration,
contain sufficent volume and must be excluded via the rack barcode.
Accepted candidates are assigned to the referring containers.
"""
pool_id = tube_candidate.pool_id
pool = self.__pool_map[pool_id]
container = self.stock_tube_containers[pool]
if not self.__stock_concentration_match(tube_candidate, container,
conc_mismatch_list):
return False
required_vol = self.__volume_map[pool_id] + STOCK_DEAD_VOLUME
if is_smaller_than(tube_candidate.volume, required_vol):
params = [
tube_candidate.tube_barcode,
get_trimmed_string(required_vol),
get_trimmed_string(tube_candidate.volume)
]
insufficent_vol_map[pool_id] = params
return False
if tube_candidate.rack_barcode in self.excluded_racks:
add_list_map_element(self.__excluded_tubes,
pool_id,
tube_candidate.tube_barcode,
as_set=True)
return False
else:
tube_candidate.set_pool(container.pool)
container.tube_candidate = tube_candidate
return True
def __accept_tube_candidate(self, tube_candidate, conc_mismatch_list,
insufficent_vol_map):
"""
A valid tube container must have a matching concentration,
contain sufficent volume and must be excluded via the rack barcode.
Accepted candidates are assigned to the referring containers.
"""
pool_id = tube_candidate.pool_id
pool = self.__pool_map[pool_id]
container = self.stock_tube_containers[pool]
if not self.__stock_concentration_match(tube_candidate, container,
conc_mismatch_list): return False
required_vol = self.__volume_map[pool_id] + STOCK_DEAD_VOLUME
if is_smaller_than(tube_candidate.volume, required_vol):
params = [tube_candidate.tube_barcode,
get_trimmed_string(required_vol),
get_trimmed_string(tube_candidate.volume)]
insufficent_vol_map[pool_id] = params
return False
if tube_candidate.rack_barcode in self.excluded_racks:
add_list_map_element(self.__excluded_tubes, pool_id,
tube_candidate.tube_barcode, as_set=True)
return False
else:
tube_candidate.set_pool(container.pool)
container.tube_candidate = tube_candidate
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)