Esempio n. 1
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 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)
Esempio n. 2
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    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
Esempio n. 3
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    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
Esempio n. 4
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 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)
Esempio n. 5
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 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)
Esempio n. 6
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 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)
Esempio n. 7
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 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 = []
Esempio n. 8
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 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 = []
Esempio n. 9
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    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)
Esempio n. 10
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    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)
Esempio n. 11
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    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
Esempio n. 12
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    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