def __check_numerical_values(self, value_maps, label):
"""
Checks the values of the numerical parameters.
"""
invalid_numericals = dict()
invalid_mock = dict()
invalid_untreated = dict()
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
for parameter, value_map in value_maps.iteritems():
if not parameter in _SCENARIO_PARAMETERS.NUMERICAL_PARAMETERS:
continue
for rack_pos, value in value_map.iteritems():
if value is None: continue
pool = pool_map[rack_pos]
if (pool == MOCK_POSITION_TYPE):
if not TransfectionParameters.is_valid_mock_value(
value, parameter):
add_list_map_element(invalid_mock, parameter,
rack_pos.label)
elif TransfectionParameters.is_untreated_type(pool):
if parameter in (TransfectionParameters.FINAL_CONCENTRATION,
TransfectionParameters.REAGENT_DIL_FACTOR) \
and not TransfectionPosition.\
is_valid_untreated_value(value):
add_list_map_element(invalid_untreated, parameter,
rack_pos.label)
elif not is_valid_number(value):
info = '%s (%s)' % (rack_pos.label, value)
add_list_map_element(invalid_numericals, parameter, info)
if len(invalid_numericals) > 0:
records_str = self.__get_error_record_string(invalid_numericals)
msg = 'The levels of some factors must be positive numbers. The ' \
'following positions in design rack %s have invalid ' \
'values: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_mock) > 0:
records_str = self.__get_error_record_string(invalid_mock)
msg = 'The levels of some factors for mock positions allow only ' \
'for the values "None" or "mock" (or no level). Some ' \
'positions in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_untreated) > 0:
records_str = self.__get_error_record_string(invalid_untreated)
msg = 'The levels of some factors for untreated positions allow ' \
'only for the values "None" and "untreated" (or no level). ' \
'Some position in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
def __check_numerical_values(self, value_maps, label):
"""
Checks the values of the numerical parameters.
"""
invalid_numericals = dict()
invalid_mock = dict()
invalid_untreated = dict()
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
for parameter, value_map in value_maps.iteritems():
if not parameter in _SCENARIO_PARAMETERS.NUMERICAL_PARAMETERS:
continue
for rack_pos, value in value_map.iteritems():
if value is None: continue
pool = pool_map[rack_pos]
if (pool == MOCK_POSITION_TYPE):
if not TransfectionParameters.is_valid_mock_value(value,
parameter):
add_list_map_element(invalid_mock, parameter,
rack_pos.label)
elif TransfectionParameters.is_untreated_type(pool):
if parameter in (TransfectionParameters.FINAL_CONCENTRATION,
TransfectionParameters.REAGENT_DIL_FACTOR) \
and not TransfectionPosition.\
is_valid_untreated_value(value):
add_list_map_element(invalid_untreated, parameter,
rack_pos.label)
elif not is_valid_number(value):
info = '%s (%s)' % (rack_pos.label, value)
add_list_map_element(invalid_numericals, parameter, info)
if len(invalid_numericals) > 0:
records_str = self.__get_error_record_string(invalid_numericals)
msg = 'The levels of some factors must be positive numbers. The ' \
'following positions in design rack %s have invalid ' \
'values: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_mock) > 0:
records_str = self.__get_error_record_string(invalid_mock)
msg = 'The levels of some factors for mock positions allow only ' \
'for the values "None" or "mock" (or no level). Some ' \
'positions in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_untreated) > 0:
records_str = self.__get_error_record_string(invalid_untreated)
msg = 'The levels of some factors for untreated positions allow ' \
'only for the values "None" and "untreated" (or no level). ' \
'Some position in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
def __check_design_racks(self):
"""
Checks the presence of parameters for each rack design rack.
"""
self.add_debug('Check design racks ...')
validators = dict()
for parameter in _SCENARIO_PARAMETERS.POTENTIAL_PARAMETERS:
validator = TransfectionParameters.create_validator_from_parameter(
parameter)
validators[parameter] = validator
for design_rack in self.__design_racks:
value_maps = self.__get_values_for_rack_layout(validators,
design_rack.rack_layout)
if self.__check_for_molecule_designs(value_maps, design_rack.label):
self.__check_numerical_values(value_maps, design_rack.label)
self.__check_reagent_name(value_maps, design_rack.label)
self.__check_value_presence(value_maps, design_rack.label)
def __check_design_racks(self):
"""
Checks the presence of parameters for each rack design rack.
"""
self.add_debug('Check design racks ...')
validators = dict()
for parameter in _SCENARIO_PARAMETERS.POTENTIAL_PARAMETERS:
validator = TransfectionParameters.create_validator_from_parameter(
parameter)
validators[parameter] = validator
for design_rack in self.__design_racks:
value_maps = self.__get_values_for_rack_layout(
validators, design_rack.rack_layout)
if self.__check_for_molecule_designs(value_maps,
design_rack.label):
self.__check_numerical_values(value_maps, design_rack.label)
self.__check_reagent_name(value_maps, design_rack.label)
self.__check_value_presence(value_maps, design_rack.label)
def __check_reagent_name(self, value_maps, label):
"""
Checks the reagent name for each rack position in a layout
(if this parameter is an allowed one). The reagent name must have a
special value for untreated positions and be at least two character
long for other positions.
"""
if not TransfectionParameters.REAGENT_NAME \
in self.__forbidden_parameters:
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
name_map = value_maps[TransfectionParameters.REAGENT_NAME]
invalid_untreated = []
invalid_others = []
for rack_pos, reagent_name in name_map.iteritems():
if reagent_name is None: continue
pool = pool_map[rack_pos]
if TransfectionParameters.is_untreated_type(pool):
if not TransfectionPosition.is_valid_untreated_value(
reagent_name):
invalid_untreated.append(rack_pos.label)
elif not len(reagent_name) > 1:
invalid_others.append(rack_pos.label)
if len(invalid_untreated):
msg = 'Untreated position must only have the reagent names ' \
'"None", "untreated" or no reagent name at all. The ' \
'following untreated positions in design rack "%s" ' \
'have invalid reagent names: %s.' \
% (label, ', '.join(sorted(invalid_untreated)))
self.add_error(msg)
if len(invalid_others):
msg = 'The reagent name must be at least 2 characters long. ' \
'The following positions in design rack "%s" have ' \
'invalid reagent names: %s.' \
% (label, ', '.join(sorted(invalid_others)))
self.add_error(msg)
def __check_reagent_name(self, value_maps, label):
"""
Checks the reagent name for each rack position in a layout
(if this parameter is an allowed one). The reagent name must have a
special value for untreated positions and be at least two character
long for other positions.
"""
if not TransfectionParameters.REAGENT_NAME \
in self.__forbidden_parameters:
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
name_map = value_maps[TransfectionParameters.REAGENT_NAME]
invalid_untreated = []
invalid_others = []
for rack_pos, reagent_name in name_map.iteritems():
if reagent_name is None: continue
pool = pool_map[rack_pos]
if TransfectionParameters.is_untreated_type(pool):
if not TransfectionPosition.is_valid_untreated_value(
reagent_name):
invalid_untreated.append(rack_pos.label)
elif not len(reagent_name) > 1:
invalid_others.append(rack_pos.label)
if len(invalid_untreated):
msg = 'Untreated position must only have the reagent names ' \
'"None", "untreated" or no reagent name at all. The ' \
'following untreated positions in design rack "%s" ' \
'have invalid reagent names: %s.' \
% (label, ', '.join(sorted(invalid_untreated)))
self.add_error(msg)
if len(invalid_others):
msg = 'The reagent name must be at least 2 characters long. ' \
'The following positions in design rack "%s" have ' \
'invalid reagent names: %s.' \
% (label, ', '.join(sorted(invalid_others)))
self.add_error(msg)
def __check_value_presence(self, value_maps, label):
"""
Checks the presence of mandatory, optional and forbidden parameters
for each rack position in a layout.
"""
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
pool_forbidden = TransfectionParameters.MOLECULE_DESIGN_POOL in \
self.__forbidden_parameters
non_empty = []
missing_value = dict()
additional_values = dict()
inconsistent_optionals = dict()
for rack_pos in get_positions_for_shape(self._rack_shape):
pool_id = pool_map[rack_pos]
is_untreated = (isinstance(pool_id, basestring) and \
TransfectionParameters.is_untreated_type(pool_id.lower()))
if is_untreated: continue
if pool_id is None: # Empty position should not have values
for parameter, value_map in value_maps.iteritems():
if not value_map[rack_pos] is None:
non_empty.append(rack_pos.label)
break
if not pool_forbidden: continue
for parameter, value_map in value_maps.iteritems():
if parameter == TransfectionParameters.MOLECULE_DESIGN_POOL:
continue
elif pool_id == MOCK_POSITION_TYPE and \
parameter == TransfectionParameters.FINAL_CONCENTRATION:
continue
value = value_map[rack_pos]
# Check consistency of definition
present_parameter = self.__parameter_presence[parameter]
if present_parameter and value is None:
if not inconsistent_optionals.has_key(parameter):
inconsistent_optionals[parameter] = []
inconsistent_optionals[parameter].append(rack_pos.label)
elif not present_parameter and not value is None and \
not pool_forbidden:
self.__parameter_presence[parameter] = True
# Check mandatory and forbidden parameters
if parameter in self.__mandatory_parameters and \
value is None:
if not missing_value.has_key(parameter):
missing_value[parameter] = []
missing_value[parameter].append(rack_pos.label)
elif parameter in self.__forbidden_parameters and \
not value is None:
if not additional_values.has_key(parameter):
additional_values[parameter] = []
info = '%s (%s)' % (rack_pos.label, value)
additional_values[parameter].append(info)
# Error recording
if len(non_empty) > 0 and not pool_forbidden:
msg = 'Some rack positions in design rack %s contain values ' \
'although there are no molecule designs for them: %s.' \
% (label, ', '.join(sorted(non_empty)))
self.add_error(msg)
if len(missing_value) > 0:
records_str = self.__get_error_record_string(missing_value)
msg = 'There are mandatory values missing for some rack ' \
'positions in design rack %s: %s. Assumed scenario: %s.' \
% (label, records_str, self.scenario.display_name)
self.add_error(msg)
if len(additional_values) > 0:
records_str = self.__get_error_record_string(additional_values)
msg = 'Some factors must not be specified in %s scenarios. The ' \
'following position in design rack %s contain ' \
'specifications for forbidden factors: %s.' \
% (self.scenario.display_name, label, records_str)
self.add_error(msg)
if len(inconsistent_optionals) > 0:
records_str = self.__get_error_record_string(
inconsistent_optionals)
msg = 'If you specify a factor, you have to specify it for each ' \
'non-empty well in all design racks. The following wells ' \
'in design rack %s lack a specification: %s.' \
% (label, records_str)
self.add_error(msg)
def __check_value_presence(self, value_maps, label):
"""
Checks the presence of mandatory, optional and forbidden parameters
for each rack position in a layout.
"""
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
pool_forbidden = TransfectionParameters.MOLECULE_DESIGN_POOL in \
self.__forbidden_parameters
non_empty = []
missing_value = dict()
additional_values = dict()
inconsistent_optionals = dict()
for rack_pos in get_positions_for_shape(self._rack_shape):
pool_id = pool_map[rack_pos]
is_untreated = (isinstance(pool_id, basestring) and \
TransfectionParameters.is_untreated_type(pool_id.lower()))
if is_untreated: continue
if pool_id is None: # Empty position should not have values
for parameter, value_map in value_maps.iteritems():
if not value_map[rack_pos] is None:
non_empty.append(rack_pos.label)
break
if not pool_forbidden: continue
for parameter, value_map in value_maps.iteritems():
if parameter == TransfectionParameters.MOLECULE_DESIGN_POOL:
continue
elif pool_id == MOCK_POSITION_TYPE and \
parameter == TransfectionParameters.FINAL_CONCENTRATION:
continue
value = value_map[rack_pos]
# Check consistency of definition
present_parameter = self.__parameter_presence[parameter]
if present_parameter and value is None:
if not inconsistent_optionals.has_key(parameter):
inconsistent_optionals[parameter] = []
inconsistent_optionals[parameter].append(rack_pos.label)
elif not present_parameter and not value is None and \
not pool_forbidden:
self.__parameter_presence[parameter] = True
# Check mandatory and forbidden parameters
if parameter in self.__mandatory_parameters and \
value is None:
if not missing_value.has_key(parameter):
missing_value[parameter] = []
missing_value[parameter].append(rack_pos.label)
elif parameter in self.__forbidden_parameters and \
not value is None:
if not additional_values.has_key(parameter):
additional_values[parameter] = []
info = '%s (%s)' % (rack_pos.label, value)
additional_values[parameter].append(info)
# Error recording
if len(non_empty) > 0 and not pool_forbidden:
msg = 'Some rack positions in design rack %s contain values ' \
'although there are no molecule designs for them: %s.' \
% (label, ', '.join(sorted(non_empty)))
self.add_error(msg)
if len(missing_value) > 0:
records_str = self.__get_error_record_string(missing_value)
msg = 'There are mandatory values missing for some rack ' \
'positions in design rack %s: %s. Assumed scenario: %s.' \
% (label, records_str, self.scenario.display_name)
self.add_error(msg)
if len(additional_values) > 0:
records_str = self.__get_error_record_string(additional_values)
msg = 'Some factors must not be specified in %s scenarios. The ' \
'following position in design rack %s contain ' \
'specifications for forbidden factors: %s.' \
% (self.scenario.display_name, label, records_str)
self.add_error(msg)
if len(inconsistent_optionals) > 0:
records_str = self.__get_error_record_string(inconsistent_optionals)
msg = 'If you specify a factor, you have to specify it for each ' \
'non-empty well in all design racks. The following wells ' \
'in design rack %s lack a specification: %s.' \
% (label, records_str)
self.add_error(msg)
