Exemple #1
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 def __get_planned_liquid_transfers(self, step_container, transfer_type):
     # Create :class:`PlannedSampleDilution`s for dilution (requires
     # valid diluent), otherwise it creates
     # :class:`PlannedSampleTransfer`s.
     planned_liquid_transfers = []
     for transfer_container in step_container.get_transfer_containers():
         src_positions = transfer_container.get_source_positions()
         trg_positions = transfer_container.get_target_positions()
         volume = float(transfer_container.volume) / VOLUME_CONVERSION_FACTOR
         if transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
             diluent = transfer_container.diluent
             if diluent is None or not len(str(diluent)) > 1:
                 msg = 'A diluent must be at least 2 characters long! ' \
                       'Change the diluent for step %i code %s, ' \
                       'please.' \
                       % (step_container.number, transfer_container.code)
                 self.add_error(msg)
                 return None
         for trg_pos_container in trg_positions:
             trg_pos = self._convert_to_rack_position(trg_pos_container)
             kw = dict(target_position=trg_pos, volume=volume)
             if transfer_type == TRANSFER_TYPES.SAMPLE_DILUTION:
                 kw['diluent_info'] = str(transfer_container.diluent)
                 psd = PlannedSampleDilution.get_entity(**kw)
                 planned_liquid_transfers.append(psd)
             else:
                 for src_pos_container in src_positions:
                     src_pos = self._convert_to_rack_position(
                                                         src_pos_container)
                     kw['source_position'] = src_pos
                     pst = PlannedSampleTransfer.get_entity(**kw)
                     planned_liquid_transfers.append(pst)
     return planned_liquid_transfers
Exemple #2
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 def _create_planned_liquid_transfers(self):
     """
     Generates the planned container dilutions for the worklist.
     """
     self.add_debug('Generate planned container dilutions ...')
     invalid_dil_factor = dict()
     for rack_pos, tf_pos in self.transfection_layout.iterpositions():
         if tf_pos.is_empty:
             continue
         dil_volume = tf_pos.calculate_reagent_dilution_volume() \
                      / VOLUME_CONVERSION_FACTOR
         ini_dil_factor = TransfectionParameters.\
                             calculate_initial_reagent_dilution(
                             float(tf_pos.reagent_dil_factor))
         if ini_dil_factor <= 1:
             add_list_map_element(invalid_dil_factor,
                                  tf_pos.reagent_dil_factor, rack_pos.label)
             continue
         rdf_str = get_trimmed_string(tf_pos.reagent_dil_factor)
         diluent_info = '%s (%s)' % (tf_pos.reagent_name, rdf_str)
         psd = PlannedSampleDilution.get_entity(volume=dil_volume,
                                        target_position=rack_pos,
                                        diluent_info=diluent_info)
         self._add_planned_transfer(psd)
     if len(invalid_dil_factor) > 0:
         msg = 'Invalid dilution reagent factor for rack positions: %s. ' \
               'The factor would result in an initial dilution factor of ' \
               'less then 1!' % (self._get_joined_map_str(invalid_dil_factor))
         self.add_error(msg)
Exemple #3
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 def _create_planned_liquid_transfers(self):
     """
     Generates the planned container dilutions for the worklist.
     """
     self.add_debug('Generate planned container dilutions ...')
     invalid_dil_factor = dict()
     for rack_pos, tf_pos in self.transfection_layout.iterpositions():
         if tf_pos.is_empty:
             continue
         dil_volume = tf_pos.calculate_reagent_dilution_volume() \
                      / VOLUME_CONVERSION_FACTOR
         ini_dil_factor = TransfectionParameters.\
                             calculate_initial_reagent_dilution(
                             float(tf_pos.reagent_dil_factor))
         if ini_dil_factor <= 1:
             add_list_map_element(invalid_dil_factor,
                                  tf_pos.reagent_dil_factor, rack_pos.label)
             continue
         rdf_str = get_trimmed_string(tf_pos.reagent_dil_factor)
         diluent_info = '%s (%s)' % (tf_pos.reagent_name, rdf_str)
         psd = PlannedSampleDilution.get_entity(volume=dil_volume,
                                                target_position=rack_pos,
                                                diluent_info=diluent_info)
         self._add_planned_transfer(psd)
     if len(invalid_dil_factor) > 0:
         msg = 'Invalid dilution reagent factor for rack positions: %s. ' \
               'The factor would result in an initial dilution factor of ' \
               'less then 1!' % (self._get_joined_map_str(invalid_dil_factor))
         self.add_error(msg)
Exemple #4
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 def _create_planned_sample_dilution(self, **kw):
     if not 'volume' in kw:
         kw['volume'] = 0.000020
     if not 'target_position' in kw:
         kw['target_position'] = self._get_entity(IRackPosition)
     if not 'diluent_info' in kw:
         kw['diluent_info'] = 'generic_buffer'
     return PlannedSampleDilution.get_entity(**kw)
Exemple #5
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 def _create_planned_sample_dilution(self, **kw):
     if not 'volume' in kw:
         kw['volume'] = 0.000020
     if not 'target_position' in kw:
         kw['target_position'] = self._get_entity(IRackPosition)
     if not 'diluent_info' in kw:
         kw['diluent_info'] = 'generic_buffer'
     return PlannedSampleDilution.get_entity(**kw)
Exemple #6
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 def __create_buffer_worklist(self, sector_layout, buffer_volume, label):
     # Creates the buffer dilution worklist for a particular quadrant
     # and adds it to the worklist series.
     volume = buffer_volume / VOLUME_CONVERSION_FACTOR
     ptfs = []
     for rack_pos_96 in sector_layout.get_positions():
         planned_transfer = PlannedSampleDilution.get_entity(volume, self.DILUTION_INFO, rack_pos_96)
         ptfs.append(planned_transfer)
     worklist = PlannedWorklist(
         label, TRANSFER_TYPES.SAMPLE_DILUTION, get_pipetting_specs_biomek(), planned_liquid_transfers=ptfs
     )
     self.__worklist_series.add_worklist(self.__last_worklist_index, worklist)
     self.__last_worklist_index += 1
Exemple #7
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    def _create_planned_liquid_transfers(self):
        """
        Generates the planned container dilution for the worklist.
        """
        self.add_debug('Generate planned container dilutions ...')

        for rack_pos, tf_pos in self.transfection_layout.iterpositions():
            if tf_pos.is_empty: continue
            volume = self.__determine_volume(tf_pos) / VOLUME_CONVERSION_FACTOR
            target_position = rack_pos
            psd = PlannedSampleDilution.get_entity(volume=volume,
                                           target_position=target_position,
                                           diluent_info=self.DILUENT_INFO)
            self._add_planned_transfer(psd)
Exemple #8
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    def _create_planned_liquid_transfers(self):
        """
        Generates the planned container dilution for the worklist.
        """
        self.add_debug('Generate planned container dilutions ...')

        for rack_pos, tf_pos in self.transfection_layout.iterpositions():
            if tf_pos.is_empty: continue
            volume = self.__determine_volume(tf_pos) / VOLUME_CONVERSION_FACTOR
            target_position = rack_pos
            psd = PlannedSampleDilution.get_entity(
                volume=volume,
                target_position=target_position,
                diluent_info=self.DILUENT_INFO)
            self._add_planned_transfer(psd)
Exemple #9
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 def _create_planned_liquid_transfers(self):
     """
     Generates the planned container dilutions for the worklist.
     """
     self.add_debug('Generate planned container dilutions ...')
     volume = TransfectionParameters.TRANSFER_VOLUME * \
              (TransfectionParameters.CELL_DILUTION_FACTOR - 1) \
              / VOLUME_CONVERSION_FACTOR
     for tf_pos in self.transfection_layout.working_positions():
         if tf_pos.is_empty:
             continue
         for target_pos in tf_pos.cell_plate_positions:
             psd = PlannedSampleDilution.get_entity(volume=volume,
                                 target_position=target_pos,
                                 diluent_info=self.DILUENT_INFO)
             self._add_planned_transfer(psd)
Exemple #10
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 def _create_planned_liquid_transfers(self):
     """
     Generates the planned container dilutions for the worklist.
     """
     self.add_debug('Generate planned container dilutions ...')
     volume = TransfectionParameters.TRANSFER_VOLUME * \
              (TransfectionParameters.CELL_DILUTION_FACTOR - 1) \
              / VOLUME_CONVERSION_FACTOR
     for tf_pos in self.transfection_layout.working_positions():
         if tf_pos.is_empty:
             continue
         for target_pos in tf_pos.cell_plate_positions:
             psd = PlannedSampleDilution.get_entity(
                 volume=volume,
                 target_position=target_pos,
                 diluent_info=self.DILUENT_INFO)
             self._add_planned_transfer(psd)
Exemple #11
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 def __create_buffer_worklist(self, sector_layout, buffer_volume, label):
     # Creates the buffer dilution worklist for a particular quadrant
     # and adds it to the worklist series.
     volume = buffer_volume / VOLUME_CONVERSION_FACTOR
     ptfs = []
     for rack_pos_96 in sector_layout.get_positions():
         planned_transfer = PlannedSampleDilution.get_entity(
                                                     volume,
                                                     self.DILUTION_INFO,
                                                     rack_pos_96)
         ptfs.append(planned_transfer)
     worklist = PlannedWorklist(label,
                                TRANSFER_TYPES.SAMPLE_DILUTION,
                                get_pipetting_specs_biomek(),
                                planned_liquid_transfers=ptfs)
     self.__worklist_series.add_worklist(self.__last_worklist_index,
                                         worklist)
     self.__last_worklist_index += 1
Exemple #12
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 def __create_transfers(self):
     # Creates a :class:`PlannedSampleDilution` for each rack position
     # in a 8x12 rack shape.
     self.add_debug('Create transfers ...')
     self._run_and_record_error(self.volume_calculator.calculate,
                         'Error when trying to determine buffer volume: ',
                         ValueError)
     buffer_volume = self.volume_calculator.get_buffer_volume()
     if buffer_volume is not None:
         volume = buffer_volume / VOLUME_CONVERSION_FACTOR
         wl_label = LABELS.create_buffer_worklist_label(
                                                 self.iso_request_label)
         wl = PlannedWorklist(wl_label,
                              TRANSFER_TYPES.SAMPLE_DILUTION,
                              get_pipetting_specs_cybio())
         for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
             psd = PlannedSampleDilution.get_entity(volume=volume,
                   target_position=rack_pos, diluent_info=DILUENT_INFO)
             wl.planned_liquid_transfers.append(psd)
         self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
Exemple #13
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 def __create_transfers(self):
     # Creates a :class:`PlannedSampleDilution` for each rack position
     # in a 8x12 rack shape.
     self.add_debug('Create transfers ...')
     self._run_and_record_error(
         self.volume_calculator.calculate,
         'Error when trying to determine buffer volume: ', ValueError)
     buffer_volume = self.volume_calculator.get_buffer_volume()
     if buffer_volume is not None:
         volume = buffer_volume / VOLUME_CONVERSION_FACTOR
         wl_label = LABELS.create_buffer_worklist_label(
             self.iso_request_label)
         wl = PlannedWorklist(wl_label, TRANSFER_TYPES.SAMPLE_DILUTION,
                              get_pipetting_specs_cybio())
         for rack_pos in get_positions_for_shape(RACK_SHAPE_NAMES.SHAPE_96):
             psd = PlannedSampleDilution.get_entity(
                 volume=volume,
                 target_position=rack_pos,
                 diluent_info=DILUENT_INFO)
             wl.planned_liquid_transfers.append(psd)
         self.__worklist_series.add_worklist(self.BUFFER_WORKLIST_INDEX, wl)
Exemple #14
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    def __create_buffer_worklist(self, quadrant_layout, buffer_volume, label,
                                 sector_index):
        # Creates buffer dilutions worklist for a particular quadrant
        # and adds it to the worklist series.
        volume = buffer_volume / VOLUME_CONVERSION_FACTOR
        planned_transfers = []
        translator = RackSectorTranslator(
            number_sectors=NUMBER_SECTORS,
            source_sector_index=sector_index,
            target_sector_index=0,
            enforce_type=RackSectorTranslator.ONE_TO_MANY)

        for rack_pos_384 in quadrant_layout.get_positions():
            rack_pos_96 = translator.translate(rack_pos_384)
            planned_transfer = PlannedSampleDilution.get_entity(
                volume, self.DILUTION_INFO, rack_pos_96)
            planned_transfers.append(planned_transfer)
        worklist = PlannedWorklist(label=label,
                                   planned_transfers=planned_transfers)
        self.__last_worklist_index += 1
        self.__worklist_series.add_worklist(self.__last_worklist_index,
                                            worklist)