def __init__(self, parser, step_marker, starting_row):
"""
Constructor:
:param parser: The parser this container belongs to.
:type parser: :class:`GenericSampleTransferPlanParser`
:param step_marker: The step marker indicating this step. It
contains a keyword an integer number.
:class step_marker: :class:`str`
:param starting_row: The row index of the step marker.
:type starting_row: :class:`int`
"""
ExcelParsingContainer.__init__(self, parser=parser)
#: The row index of the step marker.
self.__starting_row = starting_row
#: Step number define the order or transfers.
self.__number = None
self.__parse_step_marker(step_marker)
#: The :class:`TagDefinitionParsingContainer` containing the codes
#: for the transfers.
self.transfer_tag_definition = None
if self.__number is not None:
predicate = self._parser.TRANSFER_TAG_BASE_NAME + '%i' \
% (self.__number)
self.transfer_tag_definition = TagDefinitionParsingContainer(
parser=self._parser, tag_predicate=predicate,
start_row_index=(starting_row + 1))
#: A transfer volume applying to all transfers in this step (optional).
self.default_volume = None
#: The :class:`TagDefinitionParsingContainer` containing the codes
#: for transfer volumes.
self.volume_tag_definition = None
#: The :class:`TagDefinitionParsingContainer` containing the codes
#: for diluent (dilutions only) volumes.
self.diluent_tag_definition = None
#: The layouts for this step mapped onto roles (there can only be
#: one layout for each role).
self.layouts = dict()
#: The rack containers for this step mapped onto roles.
self.rack_containers = dict()
#: Stores the transfer parsing containers for this step mapped onto
#: codes.
self.__transfer_containers = dict()
class _TransferStepParsingContainer(ExcelParsingContainer):
"""
A parsing container collecting the data for one step.
"""
_PARSER_CLS = GenericSampleTransferPlanParser
def __init__(self, parser, step_marker, starting_row):
"""
Constructor:
:param parser: The parser this container belongs to.
:type parser: :class:`GenericSampleTransferPlanParser`
:param step_marker: The step marker indicating this step. It
contains a keyword an integer number.
:class step_marker: :class:`str`
:param starting_row: The row index of the step marker.
:type starting_row: :class:`int`
"""
ExcelParsingContainer.__init__(self, parser=parser)
#: The row index of the step marker.
self.__starting_row = starting_row
#: Step number define the order or transfers.
self.__number = None
self.__parse_step_marker(step_marker)
#: The :class:`TagDefinitionParsingContainer` containing the codes
#: for the transfers.
self.transfer_tag_definition = None
if self.__number is not None:
predicate = self._parser.TRANSFER_TAG_BASE_NAME + '%i' \
% (self.__number)
self.transfer_tag_definition = TagDefinitionParsingContainer(
parser=self._parser, tag_predicate=predicate,
start_row_index=(starting_row + 1))
#: A transfer volume applying to all transfers in this step (optional).
self.default_volume = None
#: The :class:`TagDefinitionParsingContainer` containing the codes
#: for transfer volumes.
self.volume_tag_definition = None
#: The :class:`TagDefinitionParsingContainer` containing the codes
#: for diluent (dilutions only) volumes.
self.diluent_tag_definition = None
#: The layouts for this step mapped onto roles (there can only be
#: one layout for each role).
self.layouts = dict()
#: The rack containers for this step mapped onto roles.
self.rack_containers = dict()
#: Stores the transfer parsing containers for this step mapped onto
#: codes.
self.__transfer_containers = dict()
@property
def number(self):
"""
Step number define the order or transfers.
"""
return self.__number
@property
def starting_row(self):
"""
The row index of the step marker.
"""
return self.__starting_row
def get_transfer_tag_row_index(self):
"""
Used to register the tag in the layout sheet parsing container.
The index must be the same row index as the factor marker (that is
one higher than the :attr:`__starting_row`) to ensure it is
stored along with the potential volume tag definition
"""
return (self.__starting_row + 1)
def __parse_step_marker(self, step_marker):
"""
The step marker must match the following pattern: "Step [integer]"
with the integer being the step number.
"""
tokens = step_marker.split('_')
cell_name = self._parser.get_cell_name(self.__starting_row, 0)
err_msg = 'Invalid step marker "%s". A valid step marker must match ' \
'the following pattern: "Step [integer]".' % (step_marker)
if not len(tokens) == 2:
self._create_error(err_msg, cell_name)
else:
num_str = tokens[1]
try:
num_str = num_str.strip()
self.__number = int(num_str)
except ValueError:
self._create_error(err_msg, cell_name)
def add_transfer_code(self, code):
"""
Adds a transfer that will be used later to recognise source and
target wells in the layouts.
"""
if self.transfer_tag_definition.has_code(code):
msg = 'Duplicate code "%s" for step %i!' % (code, self.__number)
self._create_error(msg)
else:
self.transfer_tag_definition.add_code_and_value(code, code)
def add_layout(self, role_token, layout_container, cell_name):
"""
Parses the role of a layout and add it to the :attr:`layouts` map.
:param role_token: The first part of the layout specifier.
:type role_token: :class:`str`
:param layout_container: The layout container to be added.
:type layout_container: :class:`LayoutParsingContainer`
:param cell_name: name of the cell of the layout specifier
(for error messages)
:type cell_name: :class:`str`
:return: the role for this layout
"""
conv_token = role_token.lower().strip()
if conv_token == self._parser.source_role_marker:
role = self._parser.source_role_marker
elif conv_token == self._parser.target_role_marker:
role = self._parser.target_role_marker
else:
msg = 'Unable to determine role for this layout! You have used ' \
'"%s". Use "%s" or "%s", please!' \
% (role_token, self._parser.source_role_marker,
self._parser.target_role_marker)
self._create_error(msg, cell_name)
return None
if self.layouts.has_key(role):
msg = 'There are several %s layouts for step %i!' % (role,
self.__number)
self._create_error(msg)
return None
self.layouts[role] = layout_container
return role
def get_role_for_layout(self, layout_container):
"""
Returns the role for the passed layout or records an error.
"""
role = None
for layout_role, layout in self.layouts.iteritems():
if layout == layout_container:
role = layout_role
break
if role is None:
msg = 'Programming error. Layout %s is not known for step %i!' \
% (layout_container, self.__number)
self._create_error(msg)
return None
return role
def add_transfer_data(self, role, code, volume, diluent, pos_container):
"""
Fetches or creates the transfer container for this code and add the
volume and position data to it.
"""
if volume is None: volume = self.default_volume
if self.__transfer_containers.has_key(code):
transfer_container = self.__transfer_containers[code]
else:
transfer_container = TransferParsingContainer(parser=self._parser,
code=code, diluent=diluent, volume=volume,
step_number=self.__number)
self.__transfer_containers[code] = transfer_container
transfer_container.add_position(role, pos_container)
def get_transfer_containers(self):
"""
Returns the transfer containers for this step.
"""
return self.__transfer_containers.values()
def __eq__(self, other):
return isinstance(other, self.__class__) and \
self.__number == other.number
def __str__(self):
return '%i' % (self.__number)
def __repr__(self):
str_format = '<%s %i>'
params = (self.__class__.__name__, self.__number)
return str_format % params
