def _perform_layout_validity_checks(self, working_layout):
"""
Use this method to check the validity of the generated layout.
"""
IsoRequestLayoutConverter._perform_layout_validity_checks(
self, working_layout)
self.__check_optimem_factor(working_layout)
def __init__(self,
rack_layout,
is_iso_request_layout=True,
is_mastermix_template=False,
parent=None):
"""
Constructor.
:param is_iso_request_layout: Defines if certain parameters are allowed
to be missing (final concentration, reaagent name,
reagent dil factor).
:type is_iso_request_layout: :class:`boolean`
:default is_iso_request_layout: True
:param bool is_mastermix_template: Defines if certain parameters are
allowed to be missing (ISO volume, ISO concentration, position
type). If *True*, \'is_iso_layout\' must be false.
:default is_mastermix_layout: False
"""
IsoRequestLayoutConverter.__init__(self, rack_layout, parent=parent)
#: Defines if certain parameters are allowed to be missing (final
#: concentration, reaagent name, reagent dil factor).
self.__is_iso_request_layout = is_iso_request_layout
#: Defines if certain parameters are allowed to be missing (ISO
#: volume, ISO concentration).
self.__is_mastermix_template = is_mastermix_template
# intermediate storage of invalid rack positions.
self.__invalid_dil_factor = None
self.__invalid_name = None
self.__invalid_final_concentration = None
self.__invalid_optimem_factor = None
self.__missing_reagent_name = None
self.__missing_reagent_df = None
self.__missing_final_conc = None
def __init__(self, rack_layout, is_iso_request_layout=True,
is_mastermix_template=False, parent=None):
"""
Constructor.
:param is_iso_request_layout: Defines if certain parameters are allowed
to be missing (final concentration, reaagent name,
reagent dil factor).
:type is_iso_request_layout: :class:`boolean`
:default is_iso_request_layout: True
:param bool is_mastermix_template: Defines if certain parameters are
allowed to be missing (ISO volume, ISO concentration, position
type). If *True*, \'is_iso_layout\' must be false.
:default is_mastermix_layout: False
"""
IsoRequestLayoutConverter.__init__(self, rack_layout, parent=parent)
#: Defines if certain parameters are allowed to be missing (final
#: concentration, reaagent name, reagent dil factor).
self.__is_iso_request_layout = is_iso_request_layout
#: Defines if certain parameters are allowed to be missing (ISO
#: volume, ISO concentration).
self.__is_mastermix_template = is_mastermix_template
# intermediate storage of invalid rack positions.
self.__invalid_dil_factor = None
self.__invalid_name = None
self.__invalid_final_concentration = None
self.__invalid_optimem_factor = None
self.__missing_reagent_name = None
self.__missing_reagent_df = None
self.__missing_final_conc = None
def _perform_layout_validity_checks(self, working_layout):
"""
Use this method to check the validity of the generated layout.
"""
IsoRequestLayoutConverter._perform_layout_validity_checks(self,
working_layout)
self.__check_optimem_factor(working_layout)
def _check_input(self):
IsoRequestLayoutConverter._check_input(self)
self._check_input_class('"is ISO request layout" flag',
self.__is_iso_request_layout, bool)
self._check_input_class('"is mastermix template" flag',
self.__is_mastermix_template, bool)
if not self.has_errors() and \
self.__is_mastermix_template and self.__is_iso_request_layout:
msg = 'The layout cannot be a mastermix layout and an ISO ' \
'request layout at the same time!'
self.add_error(msg)
def _check_input(self):
IsoRequestLayoutConverter._check_input(self)
self._check_input_class('"is ISO request layout" flag',
self.__is_iso_request_layout, bool)
self._check_input_class('"is mastermix template" flag',
self.__is_mastermix_template, bool)
if not self.has_errors() and \
self.__is_mastermix_template and self.__is_iso_request_layout:
msg = 'The layout cannot be a mastermix layout and an ISO ' \
'request layout at the same time!'
self.add_error(msg)
def reset(self):
"""
Resets all attributes except for the :attr:`rack_layout`.
"""
IsoRequestLayoutConverter.reset(self)
self.__invalid_dil_factor = []
self.__invalid_name = []
self.__invalid_final_concentration = []
self.__invalid_optimem_factor = []
self.__missing_reagent_name = []
self.__missing_reagent_df = []
self.__missing_final_conc = []
def reset(self):
"""
Resets all attributes except for the :attr:`rack_layout`.
"""
IsoRequestLayoutConverter.reset(self)
self.__invalid_dil_factor = []
self.__invalid_name = []
self.__invalid_final_concentration = []
self.__invalid_optimem_factor = []
self.__missing_reagent_name = []
self.__missing_reagent_df = []
self.__missing_final_conc = []
def _record_errors(self):
"""
Records errors that habe been collected for rack positions.
"""
IsoRequestLayoutConverter._record_errors(self)
if len(self.__invalid_name) > 0:
msg = 'The following rack positions have invalid reagent names: ' \
'%s. A valid reagent name must be a string of at least 2 ' \
'characters length.' \
% (self._get_joined_str(self.__invalid_name))
self.add_error(msg)
if len(self.__invalid_dil_factor) > 0:
msg = 'The following rack positions have invalid reagent ' \
'dilution factors: %s. The reagent dilution factor must be ' \
'a positive number.' \
% (self._get_joined_str(self.__invalid_dil_factor))
self.add_error(msg)
if len(self.__invalid_final_concentration) > 0:
msg = 'The following rack positions have invalid final ' \
'concentrations: %s. The final concentration must be ' \
'a positive number.' \
% (self._get_joined_str(self.__invalid_final_concentration))
self.add_error(msg)
if len(self.__invalid_optimem_factor) > 0:
msg = 'The following rack positions have invalid OptiMem ' \
'dilution factors: %s. The OptiMem dilution factor must be ' \
'a positive number.' \
% (self._get_joined_str(self.__invalid_optimem_factor))
self.add_error(msg)
if len(self.__missing_reagent_name) > 0:
msg = 'The following rack positions do not have a reagent name: %s.' \
% (self._get_joined_str(self.__missing_reagent_name))
self.add_error(msg)
if len(self.__missing_reagent_df) > 0:
msg = 'The following rack positions do not have a reagent ' \
'dilution factor: %s.' \
% (self._get_joined_str(self.__missing_reagent_df))
self.add_error(msg)
if len(self.__missing_final_conc) > 0:
msg = 'The following rack positions do not have a final ' \
'concentration: %s.' \
% (self._get_joined_str(self.__missing_final_conc))
self.add_error(msg)
def _record_errors(self):
"""
Records errors that habe been collected for rack positions.
"""
IsoRequestLayoutConverter._record_errors(self)
if len(self.__invalid_name) > 0:
msg = 'The following rack positions have invalid reagent names: ' \
'%s. A valid reagent name must be a string of at least 2 ' \
'characters length.' \
% (self._get_joined_str(self.__invalid_name))
self.add_error(msg)
if len(self.__invalid_dil_factor) > 0:
msg = 'The following rack positions have invalid reagent ' \
'dilution factors: %s. The reagent dilution factor must be ' \
'a positive number.' \
% (self._get_joined_str(self.__invalid_dil_factor))
self.add_error(msg)
if len(self.__invalid_final_concentration) > 0:
msg = 'The following rack positions have invalid final ' \
'concentrations: %s. The final concentration must be ' \
'a positive number.' \
% (self._get_joined_str(self.__invalid_final_concentration))
self.add_error(msg)
if len(self.__invalid_optimem_factor) > 0:
msg = 'The following rack positions have invalid OptiMem ' \
'dilution factors: %s. The OptiMem dilution factor must be ' \
'a positive number.' \
% (self._get_joined_str(self.__invalid_optimem_factor))
self.add_error(msg)
if len(self.__missing_reagent_name) > 0:
msg = 'The following rack positions do not have a reagent name: %s.' \
% (self._get_joined_str(self.__missing_reagent_name))
self.add_error(msg)
if len(self.__missing_reagent_df) > 0:
msg = 'The following rack positions do not have a reagent ' \
'dilution factor: %s.' \
% (self._get_joined_str(self.__missing_reagent_df))
self.add_error(msg)
if len(self.__missing_final_conc) > 0:
msg = 'The following rack positions do not have a final ' \
'concentration: %s.' \
% (self._get_joined_str(self.__missing_final_conc))
self.add_error(msg)
def _get_position_init_values(self, parameter_map, rack_pos):
kw = IsoRequestLayoutConverter._get_position_init_values(
self, parameter_map, rack_pos)
if kw is None: return None # includes empty and untreated type pos
pos_type = kw['position_type']
pos_label = rack_pos.label
reagent_name = parameter_map[self.PARAMETER_SET.REAGENT_NAME]
reagent_df = parameter_map[self.PARAMETER_SET.REAGENT_DIL_FACTOR]
final_conc = parameter_map[self.PARAMETER_SET.FINAL_CONCENTRATION]
optimem_dil_factor = None
invalid = False
optimem_dil_factor = parameter_map[
self.PARAMETER_SET.OPTIMEM_DIL_FACTOR]
if optimem_dil_factor is not None and \
not is_valid_number(optimem_dil_factor):
info = '%s (%s)' % (pos_label, optimem_dil_factor)
self.__invalid_optimem_factor.append(info)
invalid = True
if reagent_name is None:
if self.__is_mastermix_template:
self.__missing_reagent_name.append(pos_label)
invalid = True
elif not isinstance(reagent_name, basestring) \
or len(reagent_name) < 2:
self.__invalid_name.append(pos_label)
invalid = True
if reagent_df is None:
if self.__is_mastermix_template:
self.__missing_reagent_df.append(pos_label)
invalid = True
elif not is_valid_number(reagent_df):
self.__invalid_dil_factor.append(pos_label)
invalid = True
if not self.__is_iso_request_layout and final_conc is None and \
not pos_type == IsoRequestParameters.MOCK_TYPE_VALUE:
self.__missing_final_conc.append(pos_label)
invalid = True
if not final_conc is None:
if pos_type == MOCK_POSITION_TYPE:
if not TransfectionPosition.is_valid_mock_value(
final_conc, self.PARAMETER_SET.FINAL_CONCENTRATION):
info = '%s (%s)' % (pos_label, final_conc)
self.__invalid_final_concentration.append(info)
invalid = True
elif not is_valid_number(final_conc):
info = '%s (%s)' % (pos_label, final_conc)
self.__invalid_final_concentration.append(info)
invalid = True
if invalid:
return None
else:
kw['reagent_name'] = reagent_name
kw['reagent_dil_factor'] = reagent_df
kw['final_concentration'] = final_conc
kw['optimem_dil_factor'] = optimem_dil_factor
return kw
def _get_position_init_values(self, parameter_map, rack_pos):
kw = IsoRequestLayoutConverter._get_position_init_values(self,
parameter_map, rack_pos)
if kw is None: return None # includes empty and untreated type pos
pos_type = kw['position_type']
pos_label = rack_pos.label
reagent_name = parameter_map[self.PARAMETER_SET.REAGENT_NAME]
reagent_df = parameter_map[self.PARAMETER_SET.REAGENT_DIL_FACTOR]
final_conc = parameter_map[self.PARAMETER_SET.FINAL_CONCENTRATION]
optimem_dil_factor = None
invalid = False
optimem_dil_factor = parameter_map[
self.PARAMETER_SET.OPTIMEM_DIL_FACTOR]
if optimem_dil_factor is not None and \
not is_valid_number(optimem_dil_factor):
info = '%s (%s)' % (pos_label, optimem_dil_factor)
self.__invalid_optimem_factor.append(info)
invalid = True
if reagent_name is None:
if self.__is_mastermix_template:
self.__missing_reagent_name.append(pos_label)
invalid = True
elif not isinstance(reagent_name, basestring) \
or len(reagent_name) < 2:
self.__invalid_name.append(pos_label)
invalid = True
if reagent_df is None:
if self.__is_mastermix_template:
self.__missing_reagent_df.append(pos_label)
invalid = True
elif not is_valid_number(reagent_df):
self.__invalid_dil_factor.append(pos_label)
invalid = True
if not self.__is_iso_request_layout and final_conc is None and \
not pos_type == IsoRequestParameters.MOCK_TYPE_VALUE:
self.__missing_final_conc.append(pos_label)
invalid = True
if not final_conc is None:
if pos_type == MOCK_POSITION_TYPE:
if not TransfectionPosition.is_valid_mock_value(final_conc,
self.PARAMETER_SET.FINAL_CONCENTRATION):
info = '%s (%s)' % (pos_label, final_conc)
self.__invalid_final_concentration.append(info)
invalid = True
elif not is_valid_number(final_conc):
info = '%s (%s)' % (pos_label, final_conc)
self.__invalid_final_concentration.append(info)
invalid = True
if invalid:
return None
else:
kw['reagent_name'] = reagent_name
kw['reagent_dil_factor'] = reagent_df
kw['final_concentration'] = final_conc
kw['optimem_dil_factor'] = optimem_dil_factor
return kw
