Python BaseTool.__init__方法代码示例

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, iso_request, ticket_numbers=None, reporter=None,
                 parent=None):
        """
        Constructor.

        :param iso_request: The ISO request for which to generate the ISOs.
        :type iso_request:
            :class:`thelma.entities.iso.StockSampleGenerationIsoRequest`
        :param ticket_numbers: The user might specify ticket numbers for the
            ISO tickets. The number of ticket number must either be 1 (in
            which case all ISOs get the same ticket number) or equal to the
            number of ISOs. If there is no ticket number specified, the
            tool will generate new tickets for each ISO.
            Attention: It is not checked whether these given tickets exist!
        :type ticket_numbers: :class:`list` of `int`
        :default ticket_numbers: *None*
        :param reporter: This user will become reporter of the tickets (if
            new tickets are created). If you do not want to create tickets,
            the user might be *None*.
        :type reporter: :class:`thelma.entities.user.User`
        :default reporter: *None*
        """
        BaseTool.__init__(self, parent=parent)
        self.iso_request = iso_request
        self.ticket_numbers = ticket_numbers
        self.reporter = reporter
        #: The number of ISOs created (for checking reasons).
        self.__new_iso_counter = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, iso_request, number_isos,
                 excluded_racks=None, requested_tubes=None, parent=None):
        """
        Constructor.

        :param iso_request: The ISO request containing the ISO layout for the
            ISO (and experiment metadata with the molecule design pools).
        :type iso_request: :class:`thelma.entities.iso.IsoRequest`
        :param int number_isos: The number of ISOs ordered.
        :param excluded_racks: A list of barcodes from stock racks that shall
            not be used for stock sample picking.
        :type excluded_racks: A list of rack barcodes
        :param requested_tubes: A list of barcodes from stock tubes that are
            supposed to be used.
        :type requested_tubes: A list of tube barcodes.
        """
        BaseTool.__init__(self, parent=parent)
        #: The ISO request defining the ISO layout
        #: (:class:`thelma.entities.iso.IsoRequest`)
        self.iso_request = iso_request
        #: The number of ISOs ordered.
        self.number_isos = number_isos
        #: A list of barcodes from stock racks that shall not be used for
        #: stock sample (molecule design pool) picking.
        self.excluded_racks = excluded_racks
        if excluded_racks is None:
            self.excluded_racks = []
        if requested_tubes is None:
            requested_tubes = []
        #: A list of barcodes from stock tubes that are supposed to be used
        #: (for fixed positions).
        self.requested_tubes = requested_tubes

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
 def __init__(self, parent=None):
     BaseTool.__init__(self, parent=parent)
     #: The source layout.
     self._source_layout = None
     #: A set of all hash values.
     self._hash_values = None
     #: The column maps for the different target layouts (working positions
     #: mapped onto column indices) - the keys of this dictionary should
     #: be suitable for sorting. Otherwise there are irrelevant.
     self._column_maps = None
     #: The rack shape of the source layout.
     self.__source_rack_shape = None
     #: The minimum distance in rows two well of a column must have for
     #: the Biomek to pipet them together. The value is 1 for 384-well
     #: plates and 0 (=no distance) for 96-well plates.
     self.__trg_min_row_distance = None
     #: The minimum distance in rows two well of a column must have for
     #: the Biomek to pipet them together. The value is 1 for 384-well
     #: plates and 0 (=no distance) for 96-well plates.
     self.__src_min_row_distance = None
     #: The transfer items that are already part of a subcolumn.
     self.__subcolumn_tids = None
     #: All :class:`TransferSubcolumn` objects mapped onto their length.
     self.__subcolumn_lengths = None
     #: Stores :class:`SourceSubcolumn` objects managing the remaining free
     #: positions for the source transfection layout.
     self.__free_positions = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, iso, user, parent=None):
        """
        Constructor.

        :param iso: library creation ISO to execute.
        :param user: User performing the execution.
        """
        BaseTool.__init__(self, parent=parent)
        self.iso = iso
        self.user = user
        #:
        self.__single_stock_rack_map = None
        #:
        self.__pool_stock_rack_map = None
        #:
        self.__prep_plate_map = None
        #:
        self.__ssc_layout_map = None
        #:
        self.__empty_stock_rack_positions_map = None
        #:
        self.__stock_trf_exc_wl_map = None
        # These are attributes required by the Trac reporter that this
        # executor is passed to.
        self.mode = StockTransferWriterExecutor.MODE_EXECUTE
        self.entity = iso

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, iso, single_stock_racks, pool_stock_racks=None,
                 include_dummy_output=False, parent=None):
        """
        Constructor.

        :param list single_stock_racks: Barcodes for single stock racks (must
            be empty).
        :param list pool_stock_racks: Optional pool stock rack barcodes.
            Each pool stock rack is expected to contain empty tubes in the
            expected positions.
        :param bool include_dummy_output: Flag indicating if the writer should
            return a dummy output file for the tube transfers.
        """
        BaseTool.__init__(self, parent=parent)
        self.iso = iso
        self.single_stock_racks = single_stock_racks
        self.pool_stock_racks = pool_stock_racks
        self.include_dummy_output = include_dummy_output
        #: Pool stock rack buffer volume in ul.
        self.__pool_stock_rack_buffer_volume = None
        #: Map tube rack barcode -> tube rack.
        self.__tube_rack_map = None
        #: Map sector index -> single stock rack barcodes.
        self.__single_stock_rack_map = None
        #: Map sector index -> pool stock rack barcode.
        self.__pool_stock_rack_map = None
        #: Map rack barcode -> location string.
        self.__source_rack_locations = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(
        self,
        base_layout,
        stock_concentration,
        library_name,
        preparation_buffer_volume,
        pool_buffer_volume=None,
        parent=None,
    ):
        """
        Constructor.

        :param base_layout: Layout defining which positions of the layout
            are allowed to take up library samples.
        :type base_layout: :class:`LibraryBaseLayout`
        :param int stock_concentration: Concentration of the single
            source molecule designs in the stock in nM (positive number).
        :param str library_name: Name of the library to be created.
        :param float preparation_buffer_volume: Buffer volume for preparation
            plates in ul.
        :param float pool_buffer_volume: Buffer volume for pool
            plates in ul. May be `None` if no pool racks are created.
        """
        BaseTool.__init__(self, parent=parent)
        self.base_layout = base_layout
        self.stock_concentration = stock_concentration
        self.library_name = library_name
        self.preparation_buffer_volume = preparation_buffer_volume
        self.pool_buffer_volume = pool_buffer_volume
        #: The worklist series for the ISO request.
        self.__worklist_series = None
        #: The last used worklist index (within the series).
        self.__last_worklist_index = None
        #: The base layout for each sector.
        self.__sector_layouts = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, molecule_design_pools, stock_concentration,
                 take_out_volume,
                 excluded_racks=None, requested_tubes=None, parent=None):
        """
        Constructor.

        :param molecule_design_pools: The molecule design pool IDs for which
            to run the query.
        :type molecule_design_pools: :class:`set` of molecule design pool IDs
        :param int stock_concentration: The stock concentration of the single
            molecule design pools for the library in nM (positive number).
        :param int take_out_volume: The volume that shall be removed from the
            single molecule design stock in ul (positive number).
        :param requested_tubes: A list of barcodes from stock tubes that are
            supposed to be used.
        :type requested_tubes: A list of tube barcodes.
        :param excluded_racks: A list of barcodes from stock racks that shall
            not be used for molecule design picking.
        :type excluded_racks: A list of rack barcodes
        """
        BaseTool.__init__(self, parent=parent)
        #: The molecule design pool IDs for which to run the query.
        self.molecule_design_pools = molecule_design_pools
        #: The stock concentration of the single molecule design pools for
        #: the library in nM.
        self.stock_concentration = stock_concentration
        #: The volume that shall be removed from the single molecule design
        #: stock in ul.
        self.take_out_volume = take_out_volume
        if excluded_racks is None: excluded_racks = []
        #: A list of barcodes from stock racks that shall not be used for
        #: molecule design picking.
        self.excluded_racks = excluded_racks
        if requested_tubes is None: requested_tubes = []
        #: A list of barcodes from stock tubes that are supposed to be used
        #: (for fixed positions).
        self.requested_tubes = requested_tubes
        #: The DB session used for the queries.
        self.__session = None
        #: The library candidated mapped onto pool IDs.
        self.__library_candidates = None
        #: Maps library pool IDs onto molecule design IDs. ATTENTION: a molecule
        #: design pool can point to several library pools! For this reason,
        #: library pool IDs are stored in lists.
        self.__md_map = None
        #: Maps molecule design IDs onto single molecule design pool IDs.
        self.__single_pool_map = None
        #: Stores the suitable stock sample IDs for the single molecule
        #: designs pools used to create the library pools. The results are
        #: determined by the :class:`SINGLE_POOL_QUERY`.
        self.__stock_samples = None

        #: The picked library candidates for the pools in the order of
        #: completion.
        self.__picked_candidates = None

        #: If an siRNA is used in several pools this map will store the data
        #: of which ISO candidate has been used for which one.
        self.__multi_pool_iso_candidates = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, library_creation_iso, tube_destination_racks,
                 pool_stock_racks, parent=None):
        """
        Constructor:

        :param library_creation_iso: The library creation ISO for which to
            generate the worklist files.
        :type library_creation_iso:
            :class:`thelma.entities.library.LibraryCreationIso`

        :param tube_destination_racks: The barcodes for the destination
            rack for the single molecule design tube (these racks have to be
            empty).
        :type tube_destination_racks: map of barcode lists
            (:class:`basestring`) mapped onto sector indices.

        :param pool_stock_racks: The barcodes for the pool stock racks
            (these racks have to have empty tubes in defined positions).
        :type pool_stock_racks: map of barcodes
            (:class:`basestring`) mapped onto sector indices.
        """
        BaseTool.__init__(self, parent=parent)

        #: The library creation ISO for which to generate the worklist files.
        self.library_creation_iso = library_creation_iso
        #: The barcodes for the destination rack for the single molecule
        #: design tube (these racks have to be empty).
        self.tube_destination_racks = tube_destination_racks
        #: The barcodes for the pool stock racks rack for the single molecule
        #: design tube (these racks have to have empty tubes in defined
        #: positions).
        self.pool_stock_racks = pool_stock_racks

        #: The name of the library that is created here.
        self.library_name = None
        #: The layout number of the ISO.
        self.layout_number = None

        #: Stores the generated file streams (mapped onto file names).
        self.__file_map = None

        #: Maps tube racks onto barcodes.
        self.__rack_map = None
        #: The library layout for the ISO.
        self.__library_layout = None
        #: Maps library position onto sector indices.
        self.__library_sectors = None
        #: Maps translated library position onto sector indices.
        self.__translated_sectors = None

        #: Maps tube onto tube barcodes.
        self.__tube_map = dict()
        #: The tube transfer data items for the tube handler worklist writer
        #: sorted by sector index.
        self.__tube_transfers = None
        #: Stores the rack location for each source rack (single molecule
        #: design pools).
        self.__source_rack_locations = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
 def __init__(self, parent=None):
     BaseTool.__init__(self, parent=parent)
     reg = get_current_registry()
     self.tractor_api = reg.getUtility(ITractor)
     #: The value return of the :func:`send_request` method.
     self.return_value = None
     #: Is set to *True*, if all Trac request have been completed
     #: successfully.
     self.was_successful = False

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, isos, parent=None):
        """
        Constructor.

        :param isos: The ISOs to be reset.
        :type isos: :class:`list` of :class:`StockSampleCreationIso`s
        """
        BaseTool.__init__(self, parent=parent)
        #: The ISOs to be reset.
        self.isos = isos

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
 def __init__(self, parent=None):
     BaseTool.__init__(self, parent=parent)
     #: The stream to be generated.
     self.__stream = None
     #: Maps :class:`CsvColumnDictionary`s onto column indices.
     self._index_map = None
     #: A list with of :class:`CsvColumnDictionary` (to be set by the
     #: subclasses).
     self._column_map_list = None
     #: A boolean that defines whether to print a header.
     self._write_headers = True

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
 def __init__(self, iso_concentration, iso_volume, layout_filename_q1,
              layout_filename_q2, layout_filename_q3, layout_filename_q4,
              target_barcode, parent=None):
     BaseTool.__init__(self, parent=parent)
     self.__iso_concentration = float(iso_concentration) * 1e-9
     self.__iso_volume = float(iso_volume) * 1e-6
     self.__layout_filename_q1 = layout_filename_q1
     self.__layout_filename_q2 = layout_filename_q2
     self.__layout_filename_q3 = layout_filename_q3
     self.__layout_filename_q4 = layout_filename_q4
     self.__target_barcode = target_barcode

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, experiments, parent=None):
        """
        Constructor.

        :param experiments: A list of experiments that all belong
            to the same experiment design.
        :type experiments: :class:`list` of
            :class:`thelma.entities.experiment.Experiment`
        """
        BaseTool.__init__(self, parent=parent)
        #: A list of experiments that all belong to the same experiment design.
        self.experiments = experiments
        #: The experiment type of the experiment metadata.
        self._experiment_type = None

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, step_number, rack_transfer_job, parent=None):
        """
        Constructor.

        :param int step_number: The step number (of all rack transfers in
            the series).
        :param rack_transfer_job: The job to write down.
        :type rack_transfer_job: :class:`RackSampleTransferJob`
        """
        BaseTool.__init__(self, parent=parent)
        #: The step (of all rack transfers in teh series).
        self.step_number = step_number
        #: The job to write down.
        self.rack_transfer_job = rack_transfer_job

# 需要导入模块: from thelma.tools.base import BaseTool [as 别名]
# 或者: from thelma.tools.base.BaseTool import __init__ [as 别名]
    def __init__(self, stream=None, parent=None):
        """
        Constructor.

        :param stream: the opened file to parse
        :type stream: a file stream
        """
        BaseTool.__init__(self, parent=parent)
        #: The stream for the parser.
        self.stream = stream
        #: The parser handled by the parser handler.
        self.parser = None
        #: The object to be passed as result.
        self.return_value = None