def _check_input(self):
"""
Checks the input values.
"""
self.add_debug('Check input values ...')
if isinstance(self.molecule_design_pools, (InstrumentedSet, list)):
for pool in self.molecule_design_pools:
self._check_input_class('molecule design pool', pool,
MoleculeDesignPool)
if len(self.molecule_design_pools) < 1:
msg = 'The pool list is empty!'
self.add_error(msg)
else:
msg = 'The pool list must be a list or an InstrumentedSet ' \
'(obtained: %s).' % \
(self.molecule_design_pools.__class__.__name__)
self.add_error(msg)
if not self.take_out_volume is None and \
not is_valid_number(self.take_out_volume):
msg = 'The stock take out volume must be a positive number ' \
'(obtained: %s) or None.' % (self.take_out_volume)
self.add_error(msg)
if not is_valid_number(self.stock_concentration):
msg = 'The stock concentration must be a positive number ' \
'(obtained: %s).' % (self.stock_concentration)
self.add_error(msg)
self._check_input_list_classes('excluded rack',
self.excluded_racks,
basestring,
may_be_empty=True)
if self._check_input_list_classes('requested tube',
self.requested_tubes,
basestring,
may_be_empty=True):
self.requested_tubes = set(self.requested_tubes)
def _check_input(self):
"""
Checks the input values.
"""
self.add_debug('Check input values ...')
if isinstance(self.molecule_design_pools, (InstrumentedSet, list)):
for pool in self.molecule_design_pools:
self._check_input_class('molecule design pool', pool,
MoleculeDesignPool)
if len(self.molecule_design_pools) < 1:
msg = 'The pool list is empty!'
self.add_error(msg)
else:
msg = 'The pool list must be a list or an InstrumentedSet ' \
'(obtained: %s).' % \
(self.molecule_design_pools.__class__.__name__)
self.add_error(msg)
if not self.take_out_volume is None and \
not is_valid_number(self.take_out_volume):
msg = 'The stock take out volume must be a positive number ' \
'(obtained: %s) or None.' % (self.take_out_volume)
self.add_error(msg)
if not is_valid_number(self.stock_concentration):
msg = 'The stock concentration must be a positive number ' \
'(obtained: %s).' % (self.stock_concentration)
self.add_error(msg)
self._check_input_list_classes('excluded rack', self.excluded_racks,
basestring, may_be_empty=True)
if self._check_input_list_classes('requested tube',
self.requested_tubes, basestring, may_be_empty=True):
self.requested_tubes = set(self.requested_tubes)
def parse_columns(self):
"""
Searches the found columns for IDs.
"""
self._create_debug_info('Parse column ...')
invalid_mds = []
invalid_pools = []
self._step_to_next_row()
while not self._end_reached:
# Get cell values.
md_value = None
if self.__single_md_column_index is not None:
md_value = self._get_cell_value(self._current_row,
self.__single_md_column_index)
pool_value = None
if self.__pool_column_index is not None:
pool_value = self._get_cell_value(self._current_row,
self.__pool_column_index)
if md_value is None and pool_value is None:
self._end_reached = True
break
# Check pool IDs.
if not pool_value is None and not is_valid_number(pool_value,
is_integer=True):
info = 'row %i (%s)' % (self._current_row + 1, pool_value)
invalid_pools.append(info)
elif not pool_value is None:
self._parser.pool_ids[self._current_row] = pool_value
# Check single molecule design IDs.
if md_value is not None:
md_ids = str(md_value).split(self._parser.DELIMITER)
valid = True
for md_id in md_ids:
if not is_valid_number(md_id, is_integer=True):
info = 'row %i (%s)' % ((self._current_row + 1),
'-'.join(md_ids))
invalid_mds.append(info)
valid = False
if valid:
md_ids = [int(md_id) for md_id in md_ids]
self._parser.molecule_design_lists[self._current_row] = \
md_ids
self._step_to_next_row()
if len(self._parser.molecule_design_lists) < 1 and \
len(self._parser.pool_ids) < 1:
msg = 'There is no design data in the columns!'
self._create_error(msg)
if len(invalid_mds) > 0:
msg = 'Some rows contain invalid molecule design IDs: %s.' \
% (', '.join(invalid_mds))
self._create_error(msg)
if len(invalid_pools) > 0:
msg = 'Some rows contain invalid pool IDs: %s.' \
% (', '.join(invalid_pools))
self._create_error(msg)
def parse_columns(self):
"""
Searches the found columns for IDs.
"""
self._create_debug_info('Parse column ...')
invalid_mds = []
invalid_pools = []
self._step_to_next_row()
while not self._end_reached:
# Get cell values.
md_value = None
if self.__single_md_column_index is not None:
md_value = self._get_cell_value(self._current_row,
self.__single_md_column_index)
pool_value = None
if self.__pool_column_index is not None:
pool_value = self._get_cell_value(self._current_row,
self.__pool_column_index)
if md_value is None and pool_value is None:
self._end_reached = True
break
# Check pool IDs.
if not pool_value is None and not is_valid_number(pool_value,
is_integer=True):
info = 'row %i (%s)' % (self._current_row + 1, pool_value)
invalid_pools.append(info)
elif not pool_value is None:
self._parser.pool_ids[self._current_row] = pool_value
# Check single molecule design IDs.
if md_value is not None:
md_ids = str(md_value).split(self._parser.DELIMITER)
valid = True
for md_id in md_ids:
if not is_valid_number(md_id, is_integer=True):
info = 'row %i (%s)' % (
(self._current_row + 1), '-'.join(md_ids))
invalid_mds.append(info)
valid = False
if valid:
md_ids = [int(md_id) for md_id in md_ids]
self._parser.molecule_design_lists[self._current_row] = \
md_ids
self._step_to_next_row()
if len(self._parser.molecule_design_lists) < 1 and \
len(self._parser.pool_ids) < 1:
msg = 'There is no design data in the columns!'
self._create_error(msg)
if len(invalid_mds) > 0:
msg = 'Some rows contain invalid molecule design IDs: %s.' \
% (', '.join(invalid_mds))
self._create_error(msg)
if len(invalid_pools) > 0:
msg = 'Some rows contain invalid pool IDs: %s.' \
% (', '.join(invalid_pools))
self._create_error(msg)
def _check_input(self):
"""
Checks the initialisation values.
"""
self.add_debug('Check initialisation values ...')
self._check_input_class('molecule design library',
self.molecule_design_library, MoleculeDesignLibrary)
if not is_valid_number(self.number_isos, is_integer=True):
msg = 'The number of ISOs order must be a positive integer ' \
'(obtained: %s).' % (self.number_isos)
self.add_error(msg)
if self._check_input_class('excluded racks list',
self.excluded_racks, list):
for excl_rack in self.excluded_racks:
if not self._check_input_class('excluded rack barcode',
excl_rack, basestring): break
if self._check_input_class('requested tubes list',
self.requested_tubes, list):
for req_tube in self.requested_tubes:
if not self._check_input_class('requested tube barcode',
req_tube, basestring): break
def _check_input(self):
"""
Checks the initialisation values.
"""
self.add_debug('Check initialisation values ...')
self._check_input_class('molecule design library',
self.molecule_design_library,
MoleculeDesignLibrary)
if not is_valid_number(self.number_isos, is_integer=True):
msg = 'The number of ISOs order must be a positive integer ' \
'(obtained: %s).' % (self.number_isos)
self.add_error(msg)
if self._check_input_class('excluded racks list', self.excluded_racks,
list):
for excl_rack in self.excluded_racks:
if not self._check_input_class('excluded rack barcode',
excl_rack, basestring):
break
if self._check_input_class('requested tubes list',
self.requested_tubes, list):
for req_tube in self.requested_tubes:
if not self._check_input_class('requested tube barcode',
req_tube, basestring):
break
def _check_input(self):
"""
Checks the initialisation values.
"""
self.add_debug('Check initialization values ...')
if self._check_input_class('ISO request', self.iso_request,
IsoRequest):
iso_type = self.iso_request.iso_type
if not self.__ISO_REQUEST_CLS.has_key(iso_type):
msg = 'Unsupported ISO type "%s"!' % (iso_type)
self.add_error(msg)
else:
ir_cls = self.__ISO_REQUEST_CLS[self._ISO_TYPE]
self._check_input_class('ISO request', self.iso_request,
ir_cls)
if not is_valid_number(self.number_isos, is_integer=True):
msg = 'The number of ISOs order must be a positive integer ' \
'(obtained: %s).' % (self.number_isos)
self.add_error(msg)
self._check_input_list_classes('excluded rack',
self.excluded_racks,
basestring,
may_be_empty=True)
self._check_input_list_classes('requested tube',
self.requested_tubes,
basestring,
may_be_empty=True)
def __parse_column(self):
self.add_debug('Parse column ...')
row_index = 1
row_count = self.get_sheet_row_number(self.sheet)
invalid_numbers = []
while row_index < row_count:
cell_value = self.get_cell_value(self.sheet, row_index,
self.__column_index)
if cell_value is None: break
md_ids = str(cell_value).split(self.DELIMITER)
valid = True
for md_id in md_ids:
if not is_valid_number(md_id, is_integer=True):
info = '%i (%s)' % ((row_index + 1), md_ids)
invalid_numbers.append(info)
valid = False
break
if valid:
md_ids = [int(md_id) for md_id in md_ids]
self.molecule_design_lists.append(md_ids)
row_index += 1
if len(self.molecule_design_lists) < 1:
msg = 'There are no molecule designs in the column!'
self.add_error(msg)
if len(invalid_numbers) > 0:
msg = 'Some cells contain invalid molecule design IDs: %s.' \
% (', '.join(invalid_numbers))
self.add_error(msg)
def __check_numerical_values(self, value_maps, label):
"""
Checks the values of the numerical parameters.
"""
invalid_numericals = dict()
invalid_mock = dict()
invalid_untreated = dict()
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
for parameter, value_map in value_maps.iteritems():
if not parameter in _SCENARIO_PARAMETERS.NUMERICAL_PARAMETERS:
continue
for rack_pos, value in value_map.iteritems():
if value is None: continue
pool = pool_map[rack_pos]
if (pool == MOCK_POSITION_TYPE):
if not TransfectionParameters.is_valid_mock_value(
value, parameter):
add_list_map_element(invalid_mock, parameter,
rack_pos.label)
elif TransfectionParameters.is_untreated_type(pool):
if parameter in (TransfectionParameters.FINAL_CONCENTRATION,
TransfectionParameters.REAGENT_DIL_FACTOR) \
and not TransfectionPosition.\
is_valid_untreated_value(value):
add_list_map_element(invalid_untreated, parameter,
rack_pos.label)
elif not is_valid_number(value):
info = '%s (%s)' % (rack_pos.label, value)
add_list_map_element(invalid_numericals, parameter, info)
if len(invalid_numericals) > 0:
records_str = self.__get_error_record_string(invalid_numericals)
msg = 'The levels of some factors must be positive numbers. The ' \
'following positions in design rack %s have invalid ' \
'values: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_mock) > 0:
records_str = self.__get_error_record_string(invalid_mock)
msg = 'The levels of some factors for mock positions allow only ' \
'for the values "None" or "mock" (or no level). Some ' \
'positions in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_untreated) > 0:
records_str = self.__get_error_record_string(invalid_untreated)
msg = 'The levels of some factors for untreated positions allow ' \
'only for the values "None" and "untreated" (or no level). ' \
'Some position in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
def __check_numerical_values(self, value_maps, label):
"""
Checks the values of the numerical parameters.
"""
invalid_numericals = dict()
invalid_mock = dict()
invalid_untreated = dict()
pool_map = value_maps[TransfectionParameters.MOLECULE_DESIGN_POOL]
for parameter, value_map in value_maps.iteritems():
if not parameter in _SCENARIO_PARAMETERS.NUMERICAL_PARAMETERS:
continue
for rack_pos, value in value_map.iteritems():
if value is None: continue
pool = pool_map[rack_pos]
if (pool == MOCK_POSITION_TYPE):
if not TransfectionParameters.is_valid_mock_value(value,
parameter):
add_list_map_element(invalid_mock, parameter,
rack_pos.label)
elif TransfectionParameters.is_untreated_type(pool):
if parameter in (TransfectionParameters.FINAL_CONCENTRATION,
TransfectionParameters.REAGENT_DIL_FACTOR) \
and not TransfectionPosition.\
is_valid_untreated_value(value):
add_list_map_element(invalid_untreated, parameter,
rack_pos.label)
elif not is_valid_number(value):
info = '%s (%s)' % (rack_pos.label, value)
add_list_map_element(invalid_numericals, parameter, info)
if len(invalid_numericals) > 0:
records_str = self.__get_error_record_string(invalid_numericals)
msg = 'The levels of some factors must be positive numbers. The ' \
'following positions in design rack %s have invalid ' \
'values: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_mock) > 0:
records_str = self.__get_error_record_string(invalid_mock)
msg = 'The levels of some factors for mock positions allow only ' \
'for the values "None" or "mock" (or no level). Some ' \
'positions in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
if len(invalid_untreated) > 0:
records_str = self.__get_error_record_string(invalid_untreated)
msg = 'The levels of some factors for untreated positions allow ' \
'only for the values "None" and "untreated" (or no level). ' \
'Some position in design rack "%s" have invalid levels. ' \
'Affected positions: %s.' % (label, records_str)
self.add_error(msg)
def __check_input(self):
# Checks the initialisation values.
self.add_debug("Checking input.")
self._check_input_class("base library layout", self.base_layout, LibraryBaseLayout)
self._check_input_class("library name", self.library_name, basestring)
if not is_valid_number(self.stock_concentration):
msg = (
"The stock concentration for the single source molecules "
"must be a positive number (obtained: %s)." % (self.stock_concentration)
)
self.add_error(msg)
def __check_input(self):
# Checks the initialisation values.
self.add_debug('Check input ...')
self._check_input_class('base library layout', self.base_layout,
LibraryBaseLayout)
self._check_input_class('library name', self.library_name, basestring)
if not is_valid_number(self.stock_concentration):
msg = 'The stock concentration for the single source molecules ' \
'must be a positive number (obtained: %s).' \
% (self.stock_concentration)
self.add_error(msg)
def is_valid_mock_value(cls, value, parameter):
if not super(TransfectionParameters, cls).is_valid_mock_value(
value, parameter):
return False
if parameter in {cls.REAGENT_DIL_FACTOR, cls.OPTIMEM_DIL_FACTOR}:
if value is None: return True
return is_valid_number(value)
elif parameter == cls.REAGENT_NAME:
if value is None: return True
if not isinstance(value, basestring) or not len(value) > 2:
return False
return True
def is_valid_mock_value(cls, value, parameter):
if not super(TransfectionParameters, cls).is_valid_mock_value(value,
parameter):
return False
if parameter in {cls.REAGENT_DIL_FACTOR, cls.OPTIMEM_DIL_FACTOR}:
if value is None: return True
return is_valid_number(value)
elif parameter == cls.REAGENT_NAME:
if value is None: return True
if not isinstance(value, basestring) or not len(value) > 2:
return False
return True
def __check_input(self):
"""
Checks the input values.
"""
self.add_debug('Check input values ...')
if isinstance(self.molecule_design_pools, (InstrumentedSet, list)):
for pool in self.molecule_design_pools:
self._check_input_class('library pool', pool,
MoleculeDesignPool)
if len(self.molecule_design_pools) < 1:
msg = 'The pool list is empty!'
self.add_error(msg)
else:
msg = 'The library pool list must be a list or an ' \
'InstrumentedSet (obtained: %s).' % \
(self.molecule_design_pools.__class__.__name__)
self.add_error(msg)
if not is_valid_number(self.stock_concentration):
msg = 'The stock concentration must be a positive number ' \
'(obtained: %s).' % (self.stock_concentration)
self.add_error(msg)
if not is_valid_number(self.take_out_volume):
msg = 'The stock take out volume must be a positive number ' \
'(obtained: %s).' % (self.take_out_volume)
self.add_error(msg)
if self._check_input_class('excluded racks list',
self.excluded_racks, list):
for excl_rack in self.excluded_racks:
if not self._check_input_class('excluded rack barcode',
excl_rack, basestring): break
if self._check_input_class('requested tubes list',
self.requested_tubes, list):
for req_tube in self.requested_tubes:
if not self._check_input_class('requested tube barcode',
req_tube, basestring): break
def __check_input(self):
"""
Checks the initialisation values.
"""
self._check_input_class('ISO request label', self.iso_request_label,
basestring)
numbers = {self.target_volume : 'target volume for the pool tubes',
self.target_concentration :
'target concentration for the pool tubes'}
for value, name in numbers.iteritems():
if not is_valid_number(value=value, is_integer=True):
msg = 'The %s must be a positive number (obtained: %s).' \
% (name, value)
self.add_error(msg)
def _check_input(self):
"""
Checks the initialisation values.
"""
self.add_debug('Check initialisation values ...')
self._check_input_class('ISO request', self.iso_request,
self.__ISO_REQUEST_CLS[self._ISO_TYPE])
self._check_input_class('job owner', self.job_owner, User)
if not is_valid_number(self.number_isos, is_integer=True):
msg = 'The number of ISOs order must be a positive integer ' \
'(obtained: %s).' % (self.number_isos)
self.add_error(msg)
self._check_input_list_classes('excluded rack', self.excluded_racks,
basestring, may_be_empty=True)
self._check_input_list_classes('requested tube', self.requested_tubes,
basestring, may_be_empty=True)
def __check_input(self):
"""
Checks the initialisation values.
"""
self._check_input_class('ISO request label', self.iso_request_label,
basestring)
numbers = {
self.target_volume: 'target volume for the pool tubes',
self.target_concentration:
'target concentration for the pool tubes'
}
for value, name in numbers.iteritems():
if not is_valid_number(value=value, is_integer=True):
msg = 'The %s must be a positive number (obtained: %s).' \
% (name, value)
self.add_error(msg)
def set_optimem_dilution_factor(self, optimem_df):
"""
The OptiMem dilution factor must be a positive number.
The factor might only be set ones, except for fixed positions.
:raises AttributeError: If the factor has been set before.
:raises ValueError: If the factor is not a positive number.
"""
if not is_valid_number(optimem_df):
msg = 'The OptiMem dilution factor must be a positive number ' \
'(obtained: %s).' % (optimem_df)
raise ValueError(msg)
if not self._optimem_dil_factor is None and not self.is_fixed:
raise AttributeError('The OptiMem dilution factor has already ' \
'been set!')
self._optimem_dil_factor = optimem_df
def set_optimem_dilution_factor(self, optimem_df):
"""
The OptiMem dilution factor must be a positive number.
The factor might only be set ones, except for fixed positions.
:raises AttributeError: If the factor has been set before.
:raises ValueError: If the factor is not a positive number.
"""
if not is_valid_number(optimem_df):
msg = 'The OptiMem dilution factor must be a positive number ' \
'(obtained: %s).' % (optimem_df)
raise ValueError(msg)
if not self._optimem_dil_factor is None and not self.is_fixed:
raise AttributeError('The OptiMem dilution factor has already ' \
'been set!')
self._optimem_dil_factor = optimem_df
def _check_input(self):
"""
Checks the initialisation values.
"""
self.add_debug('Check initialisation values ...')
self._check_input_class('ISO request', self.iso_request,
self.__ISO_REQUEST_CLS[self._ISO_TYPE])
self._check_input_class('job owner', self.job_owner, User)
if not is_valid_number(self.number_isos, is_integer=True):
msg = 'The number of ISOs order must be a positive integer ' \
'(obtained: %s).' % (self.number_isos)
self.add_error(msg)
self._check_input_list_classes('excluded rack',
self.excluded_racks,
basestring,
may_be_empty=True)
self._check_input_list_classes('requested tube',
self.requested_tubes,
basestring,
may_be_empty=True)
def get_cell_value(self, sheet, row_index, column_index):
"""
Returns the value of the specified in the given sheet.
Converts the passed cell value either into
a ascii string (if basestring) or a number (if non_string).
"""
cell_value = sheet.cell_value(row_index, column_index)
cell_name = '%s%i' % (label_from_number(column_index + 1),
row_index + 1)
sheet_name = self.get_sheet_name(sheet)
conv_value = None
if isinstance(cell_value, string_types):
try:
conv_value = ascii_native_(cell_value)
except UnicodeEncodeError:
msg = 'Unknown character in cell %s (sheet "%s"). Remove ' \
'or replace the character, please.' \
% (cell_name, sheet_name)
self.add_error(msg)
else:
if conv_value == '':
conv_value = None
else:
# Try to convert to an int or float.
try:
conv_value = int(conv_value)
except ValueError:
try:
conv_value = float(conv_value)
except ValueError:
pass
elif isinstance(cell_value, (float, int)):
if is_valid_number(value=cell_value, is_integer=True):
conv_value = int(cell_value)
else:
conv_value = cell_value
else:
msg = 'There is some unknown content in cell %s (sheet %s).' \
% (cell_name, sheet_name)
self.add_error(msg)
return conv_value
def get_cell_value(self, sheet, row_index, column_index):
"""
Returns the value of the specified in the given sheet.
Converts the passed cell value either into
a ascii string (if basestring) or a number (if non_string).
"""
cell_value = sheet.cell_value(row_index, column_index)
cell_name = '%s%i' % (label_from_number(column_index + 1),
row_index + 1)
sheet_name = self.get_sheet_name(sheet)
conv_value = None
if isinstance(cell_value, string_types):
try:
conv_value = ascii_native_(cell_value)
except UnicodeEncodeError:
msg = 'Unknown character in cell %s (sheet "%s"). Remove ' \
'or replace the character, please.' \
% (cell_name, sheet_name)
self.add_error(msg)
else:
if conv_value == '':
conv_value = None
else:
# Try to convert to an int or float.
try:
conv_value = int(conv_value)
except ValueError:
try:
conv_value = float(conv_value)
except ValueError:
pass
elif isinstance(cell_value, (float, int)):
if is_valid_number(value=cell_value, is_integer=True):
conv_value = int(cell_value)
else:
conv_value = cell_value
else:
msg = 'There is some unknown content in cell %s (sheet %s).' \
% (cell_name, sheet_name)
self.add_error(msg)
return conv_value
def _check_input(self):
"""
Checks the initialisation values.
"""
self.add_debug('Check initialization values ...')
if self._check_input_class('ISO request', self.iso_request,
IsoRequest):
iso_type = self.iso_request.iso_type
if not self.__ISO_REQUEST_CLS.has_key(iso_type):
msg = 'Unsupported ISO type "%s"!' % (iso_type)
self.add_error(msg)
else:
ir_cls = self.__ISO_REQUEST_CLS[self._ISO_TYPE]
self._check_input_class('ISO request', self.iso_request,
ir_cls)
if not is_valid_number(self.number_isos, is_integer=True):
msg = 'The number of ISOs order must be a positive integer ' \
'(obtained: %s).' % (self.number_isos)
self.add_error(msg)
self._check_input_list_classes('excluded rack', self.excluded_racks,
basestring, may_be_empty=True)
self._check_input_list_classes('requested tube', self.requested_tubes,
basestring, may_be_empty=True)
def check_transfers(self):
"""
Makes sure there is a valid number of source and target positions
for each recorded transfer.
"""
ambiguous = []
invalid_volume = []
for step_container in self.__steps_by_row.values():
for transfer_container in step_container.get_transfer_containers():
# the 2 getters also catch code without any source or target
src_positions = transfer_container.get_source_positions()
trg_positions = transfer_container.get_target_positions()
if src_positions is None or trg_positions is None: continue
if len(src_positions) > 1 and len(trg_positions) > 1:
info = '%s (step %i)' % (transfer_container.code,
step_container.number)
ambiguous.append(info)
if not is_valid_number(transfer_container.volume):
info = '%s (step %i, code %s)' % (transfer_container.volume,
step_container.number, transfer_container.code)
invalid_volume.append(info)
if len(ambiguous) > 0:
msg = 'You must not have multiple source AND target positions ' \
'for a code since the system cannot figure out the correct ' \
'association in this case. You can either have multiple ' \
'source positions OR multiple target positions. The ' \
'following transfers violate this rule: %s.' \
% (', '.join(ambiguous)) # do not sort!
self._create_error(msg)
if len(invalid_volume) > 0:
msg = 'The transfer volume must be a positive number. The ' \
'following transfers have invalid numbers: %s' \
% (', '.join(invalid_volume)) # do not sort!
self._create_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
