def __check_volume_and_concentration(self, iso_volume, iso_conc,
pos_label, is_mock=False):
"""
Checks the volume and concentration for non-empty positions.
"""
is_valid = True
if iso_volume is None:
self.__missing_iso_volume.append(pos_label)
is_valid = False
elif not is_valid_number(iso_volume):
self.__invalid_iso_volume.append(pos_label)
is_valid = False
if is_mock:
if not IsoRequestPosition.is_valid_mock_value(iso_conc,
self.PARAMETER_SET.ISO_CONCENTRATION):
info = '%s (%s, mock position)' % (iso_conc, pos_label)
self.__invalid_iso_concentration.append(info)
is_valid = False
else:
if iso_conc is None:
self.__missing_iso_concentration.append(pos_label)
is_valid = False
elif not is_valid_number(iso_conc):
self.__invalid_iso_concentration.append(pos_label)
is_valid = False
return is_valid
def __check_volume_and_concentration(self,
iso_volume,
iso_conc,
pos_label,
is_mock=False):
"""
Checks the volume and concentration for non-empty positions.
"""
is_valid = True
if iso_volume is None:
self.__missing_iso_volume.append(pos_label)
is_valid = False
elif not is_valid_number(iso_volume):
self.__invalid_iso_volume.append(pos_label)
is_valid = False
if is_mock:
if not IsoRequestPosition.is_valid_mock_value(
iso_conc, self.PARAMETER_SET.ISO_CONCENTRATION):
info = '%s (%s, mock position)' % (iso_conc, pos_label)
self.__invalid_iso_concentration.append(info)
is_valid = False
else:
if iso_conc is None:
self.__missing_iso_concentration.append(pos_label)
is_valid = False
elif not is_valid_number(iso_conc):
self.__invalid_iso_concentration.append(pos_label)
is_valid = False
return is_valid
def is_valid_mock_value(cls, value, parameter):
if not super(IsoRequestParameters, cls).is_valid_mock_value(
value, parameter):
return False
if parameter == cls.ISO_VOLUME:
if value is None or is_valid_number(value):
return True
return False
return True
def is_valid_mock_value(cls, value, parameter):
if not super(IsoRequestParameters, cls).is_valid_mock_value(value,
parameter):
return False
if parameter == cls.ISO_VOLUME:
if value is None or is_valid_number(value):
return True
return False
return True
def _check_numbers(self, value_list, allow_none):
"""
Checks whether all passed values are a positive number (or *None*,
if *None* is allowed).
The values must be passed as list of tuples with the value name (for
error messages) as first element and the values as second element.
"""
for value_tuple in value_list:
value_name, value = value_tuple[0], value_tuple[1]
if value is None and allow_none:
pass
else:
if not is_valid_number(value=value):
msg = 'The %s must be a positive number (obtained: %s).' \
% (value_name, value)
raise ValueError(msg)
def _check_numbers(self, value_list, allow_none):
"""
Checks whether all passed values are a positive number (or *None*,
if *None* is allowed).
The values must be passed as list of tuples with the value name (for
error messages) as first element and the values as second element.
"""
for value_tuple in value_list:
value_name, value = value_tuple[0], value_tuple[1]
if value is None and allow_none:
pass
else:
if not is_valid_number(value=value):
msg = 'The %s must be a positive number (obtained: %s).' \
% (value_name, value)
raise ValueError(msg)
def __get_molecule_design_pool_for_id(self, pool_id, position_label):
"""
Returns the :class:`MoleculeDesignPool` entity for a position and
checks whether it is a valid (=known) one.
"""
if self.__pool_map.has_key(pool_id):
return self.__pool_map[pool_id]
if not is_valid_number(pool_id, is_integer=True):
info = '%s (%s)' % (pool_id, position_label)
self.__unknown_pools.append(info)
return None
entity = self.__pool_aggregate.get_by_id(pool_id)
if entity is None:
info = '%s (%s)' % (pool_id, position_label)
self.__unknown_pools.append(info)
return None
self.__pool_map[pool_id] = entity
return entity
def _get_position_init_values(self, parameter_map, rack_pos):
"""
Make sure position type and pool comply with each other.
"""
pool_id = parameter_map[self.PARAMETER_SET.MOLECULE_DESIGN_POOL]
pos_type = None
if parameter_map.has_key(self.PARAMETER_SET.POS_TYPE):
pos_type = parameter_map[self.PARAMETER_SET.POS_TYPE]
if pool_id is None:
if pos_type is None or self._is_empty_type(pos_type):
return None
self.__missing_pool.add(rack_pos.label)
return None
if pos_type is None:
pos_type = self.__determine_position_type(pool_id)
if pos_type is None: return None
elif not self._check_type_validity(pos_type, pool_id):
return None
if self._is_empty_type(pos_type):
# these position are technically empty, they are only required
# for documentation
return None
if is_valid_number(pool_id, is_integer=True):
pool = self.__get_molecule_design_pool_for_id(pool_id,
rack_pos.label)
if pool is None: return None
else:
pool = pool_id
kw = dict(molecule_design_pool=pool)
if self.POSITION_CLS.EXPOSE_POSITION_TYPE:
kw['position_type'] = pos_type
return kw