def _record_errors(self):
MoleculeDesignPoolLayoutConverter._record_errors(self)
if len(self.__invalid_iso_volume) > 0:
msg = 'Some position have invalid ISO volumes. The volume must ' \
'be a positive number. Details: %s.' \
% (self._get_joined_str(self.__invalid_iso_volume))
self.add_error(msg)
if len(self.__invalid_iso_concentration) > 0:
msg = 'Some position have invalid ISO concentrations. The ' \
'concentration must a positive number. Details: %s.' \
% (self._get_joined_str(self.__invalid_iso_concentration))
self.add_error(msg)
if len(self.__missing_iso_volume) > 0:
msg = 'Some position do not have an ISO volume specifications: %s.' \
% (self._get_joined_str(self.__missing_iso_volume))
self.add_error(msg)
if len(self.__missing_iso_concentration) > 0:
msg = 'Some positions do not have an ISO concentration ' \
'specification: %s.' \
% (self._get_joined_str(self.__missing_iso_concentration))
self.add_error(msg)
def _record_errors(self):
MoleculeDesignPoolLayoutConverter._record_errors(self)
if len(self.__invalid_iso_volume) > 0:
msg = 'Some position have invalid ISO volumes. The volume must ' \
'be a positive number. Details: %s.' \
% (self._get_joined_str(self.__invalid_iso_volume))
self.add_error(msg)
if len(self.__invalid_iso_concentration) > 0:
msg = 'Some position have invalid ISO concentrations. The ' \
'concentration must a positive number. Details: %s.' \
% (self._get_joined_str(self.__invalid_iso_concentration))
self.add_error(msg)
if len(self.__missing_iso_volume) > 0:
msg = 'Some position do not have an ISO volume specifications: %s.' \
% (self._get_joined_str(self.__missing_iso_volume))
self.add_error(msg)
if len(self.__missing_iso_concentration) > 0:
msg = 'Some positions do not have an ISO concentration ' \
'specification: %s.' \
% (self._get_joined_str(self.__missing_iso_concentration))
self.add_error(msg)
def __init__(self, rack_layout, parent=None):
MoleculeDesignPoolLayoutConverter.__init__(self, rack_layout,
parent=parent)
# intermediate storage of invalid rack positions
self.__mismatching_mds = None
self.__missing_tubes = None
self.__mismatching_tube_num = None
def __init__(self, rack_layout, parent=None):
MoleculeDesignPoolLayoutConverter.__init__(self,
rack_layout,
parent=parent)
# intermediate storage of invalid rack positions
self.__mismatching_mds = None
self.__missing_tubes = None
self.__mismatching_tube_num = None
def reset(self):
"""
Resets all attributes except for the :attr:`rack_layout`.
"""
MoleculeDesignPoolLayoutConverter.reset(self)
self.__invalid_iso_volume = []
self.__invalid_iso_concentration = []
self.__missing_iso_volume = []
self.__missing_iso_concentration = []
def reset(self):
"""
Resets all attributes except for the :attr:`rack_layout`.
"""
MoleculeDesignPoolLayoutConverter.reset(self)
self.__invalid_iso_volume = []
self.__invalid_iso_concentration = []
self.__missing_iso_volume = []
self.__missing_iso_concentration = []
def __init__(self, rack_layout, parent=None):
MoleculeDesignPoolLayoutConverter.__init__(self,
rack_layout=rack_layout,
parent=parent)
#: Do we expect ISO volumes and concentrations? If *False* these
#: values are allowed to miss.
self._expect_iso_values = True
# intermediate storage of invalid rack positions
self.__invalid_iso_volume = None
self.__invalid_iso_concentration = None
self.__missing_iso_volume = None
self.__missing_iso_concentration = None
def __init__(self, rack_layout, parent=None):
MoleculeDesignPoolLayoutConverter.__init__(self,
rack_layout=rack_layout,
parent=parent)
#: Do we expect ISO volumes and concentrations? If *False* these
#: values are allowed to miss.
self._expect_iso_values = True
# intermediate storage of invalid rack positions
self.__invalid_iso_volume = None
self.__invalid_iso_concentration = None
self.__missing_iso_volume = None
self.__missing_iso_concentration = None
def _record_errors(self):
MoleculeDesignPoolLayoutConverter._record_errors(self)
if len(self.__mismatching_mds) > 0:
msg = 'The molecule designs IDs for some pools do not match: %s.' \
% (self._get_joined_str(self.__mismatching_mds))
self.add_error(msg)
if len(self.__missing_tubes) > 0:
msg = 'The following rack positions do not contain stock tube ' \
'barcodes: %s.' % (self._get_joined_str(self.__missing_tubes))
self.add_error(msg)
if len(self.__mismatching_tube_num) > 0:
msg = 'For some positions the number of tubes does not match ' \
'the number of molecule designs: %s.' \
% (self._get_joined_str(self.__mismatching_tube_num))
self.add_error(msg)
def _record_errors(self):
MoleculeDesignPoolLayoutConverter._record_errors(self)
if len(self.__mismatching_mds) > 0:
msg = 'The molecule designs IDs for some pools do not match: %s.' \
% (self._get_joined_str(self.__mismatching_mds))
self.add_error(msg)
if len(self.__missing_tubes) > 0:
msg = 'The following rack positions do not contain stock tube ' \
'barcodes: %s.' % (self._get_joined_str(self.__missing_tubes))
self.add_error(msg)
if len(self.__mismatching_tube_num) > 0:
msg = 'For some positions the number of tubes does not match ' \
'the number of molecule designs: %s.' \
% (self._get_joined_str(self.__mismatching_tube_num))
self.add_error(msg)
def _get_position_init_values(self, parameter_map, rack_pos):
kw = MoleculeDesignPoolLayoutConverter._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']
iso_concentration = parameter_map[self.PARAMETER_SET.ISO_CONCENTRATION]
iso_volume = parameter_map[self.PARAMETER_SET.ISO_VOLUME]
invalid = False
is_mock = (pos_type == MOCK_POSITION_TYPE)
if self._expect_iso_values and \
not self.__check_volume_and_concentration(iso_volume,
iso_concentration, rack_pos.label, is_mock):
invalid = True
if invalid: return None
kw['iso_volume'] = iso_volume
kw['iso_concentration'] = iso_concentration
return kw
def _get_position_init_values(self, parameter_map, rack_pos):
kw = MoleculeDesignPoolLayoutConverter._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']
iso_concentration = parameter_map[self.PARAMETER_SET.ISO_CONCENTRATION]
iso_volume = parameter_map[self.PARAMETER_SET.ISO_VOLUME]
invalid = False
is_mock = (pos_type == MOCK_POSITION_TYPE)
if self._expect_iso_values and \
not self.__check_volume_and_concentration(iso_volume,
iso_concentration, rack_pos.label, is_mock):
invalid = True
if invalid: return None
kw['iso_volume'] = iso_volume
kw['iso_concentration'] = iso_concentration
return kw
def _get_position_init_values(self, parameter_map, rack_pos):
kw = MoleculeDesignPoolLayoutConverter._get_position_init_values(
self,
parameter_map, rack_pos)
result = None
if not kw is None:
invalid = False
pos_label = rack_pos.label
pool = kw['molecule_design_pool']
md_str = parameter_map[self.PARAMETER_SET.MOLECULE_DESIGNS]
if not self.POSITION_CLS.validate_molecule_designs(pool, md_str):
exp_mds = [md.id for md in pool]
info = '%s (pool %s, found: %s, expected: %s)' \
% (pos_label, pool.id, md_str,
self._get_joined_str(
exp_mds, is_strs=False, separator='-'))
self.__mismatching_mds.append(info)
invalid = True
tube_str = parameter_map[self.PARAMETER_SET.STOCK_TUBE_BARCODES]
if tube_str is None:
self.__missing_tubes.append(pos_label)
result = None
else:
tubes = self.POSITION_CLS.get_tube_barcodes_from_tag_value(
tube_str)
if not len(tubes) == len(pool):
info = '%s (%s, number mds: %i)' \
% (pos_label, tube_str, len(pool))
self.__mismatching_tube_num.append(info)
invalid = True
if invalid:
result = None
else:
kw['stock_tube_barcodes'] = tubes
# Success!
result = kw
return result
def _get_position_init_values(self, parameter_map, rack_pos):
kw = MoleculeDesignPoolLayoutConverter._get_position_init_values(
self, parameter_map, rack_pos)
result = None
if not kw is None:
invalid = False
pos_label = rack_pos.label
pool = kw['molecule_design_pool']
md_str = parameter_map[self.PARAMETER_SET.MOLECULE_DESIGNS]
if not self.POSITION_CLS.validate_molecule_designs(pool, md_str):
exp_mds = [md.id for md in pool]
info = '%s (pool %s, found: %s, expected: %s)' \
% (pos_label, pool.id, md_str,
self._get_joined_str(
exp_mds, is_strs=False, separator='-'))
self.__mismatching_mds.append(info)
invalid = True
tube_str = parameter_map[self.PARAMETER_SET.STOCK_TUBE_BARCODES]
if tube_str is None:
self.__missing_tubes.append(pos_label)
result = None
else:
tubes = self.POSITION_CLS.get_tube_barcodes_from_tag_value(
tube_str)
if not len(tubes) == len(pool):
info = '%s (%s, number mds: %i)' \
% (pos_label, tube_str, len(pool))
self.__mismatching_tube_num.append(info)
invalid = True
if invalid:
result = None
else:
kw['stock_tube_barcodes'] = tubes
# Success!
result = kw
return result
def reset(self):
MoleculeDesignPoolLayoutConverter.reset(self)
self.__mismatching_mds = []
self.__missing_tubes = []
self.__mismatching_tube_num = []
def reset(self):
MoleculeDesignPoolLayoutConverter.reset(self)
self.__mismatching_mds = []
self.__missing_tubes = []
self.__mismatching_tube_num = []
