def __init__(self, lab_iso_plate, for_job, lab_iso_layout=None,
parent=None):
"""
Constructor.
:param lab_iso_plate: The lab ISO plate to be checked.
:type lab_iso_plate: :class:`IsoPlate` or
:class:`IsoJobPreparationPlate`
:param for_job: Do we check the job processing (*True*) or the ISO?
:type for_job: :class:`bool`
:param lab_iso_layout: The layout containing the molecule design
data. Must not be None for :class:`IsoAliquotPlate` or
:class:`LibraryPlate` objects.
:type lab_iso_layout: :class:`LabIsoLayout`
"""
BaseRackVerifier.__init__(self,
reference_layout=lab_iso_layout,
parent=parent)
#: The lab ISO plate to be checked.
self.lab_iso_plate = lab_iso_plate
#: Do we check the job processing (*True*) or the ISO (*False*)?
self.for_job = for_job
#: In aliquot and (for controls positions) preparation plates,
#: we can ignore positions that are derived from another position
#: at the same plate because the intraplate transfers might be
#: part of the processing of the second entity.
self.__ignore_positions = None
#: This is kind of a hack. We cannot make safe statement about ignored
#: positions, for this reason, the comparison for ignored positions
#: is temporarily disabled (until the next position).
self.__disable_comparison = None
def __init__(self,
lab_iso_plate,
for_job,
lab_iso_layout=None,
parent=None):
"""
Constructor.
:param lab_iso_plate: The lab ISO plate to be checked.
:type lab_iso_plate: :class:`IsoPlate` or
:class:`IsoJobPreparationPlate`
:param for_job: Do we check the job processing (*True*) or the ISO?
:type for_job: :class:`bool`
:param lab_iso_layout: The layout containing the molecule design
data. Must not be None for :class:`IsoAliquotPlate` or
:class:`LibraryPlate` objects.
:type lab_iso_layout: :class:`LabIsoLayout`
"""
BaseRackVerifier.__init__(self,
reference_layout=lab_iso_layout,
parent=parent)
#: The lab ISO plate to be checked.
self.lab_iso_plate = lab_iso_plate
#: Do we check the job processing (*True*) or the ISO (*False*)?
self.for_job = for_job
#: In aliquot and (for controls positions) preparation plates,
#: we can ignore positions that are derived from another position
#: at the same plate because the intraplate transfers might be
#: part of the processing of the second entity.
self.__ignore_positions = None
#: This is kind of a hack. We cannot make safe statement about ignored
#: positions, for this reason, the comparison for ignored positions
#: is temporarily disabled (until the next position).
self.__disable_comparison = None
def _check_input(self):
BaseRackVerifier._check_input(self)
if not isinstance(self.lab_iso_plate, (IsoPlate, LibraryPlate,
IsoJobPreparationPlate)):
msg = 'The lab ISO plate must be an %s, %s or an %s ' \
'(obtained: %s).' % (IsoPlate.__name__, LibraryPlate.__name__,
IsoJobPreparationPlate.__name__,
self.lab_iso_plate.__class__.__name__)
self.add_error(msg)
self._check_input_class('"for job" flag', self.for_job, bool)
def _check_input(self):
BaseRackVerifier._check_input(self)
if not isinstance(self.lab_iso_plate,
(IsoPlate, LibraryPlate, IsoJobPreparationPlate)):
msg = 'The lab ISO plate must be an %s, %s or an %s ' \
'(obtained: %s).' % (IsoPlate.__name__, LibraryPlate.__name__,
IsoJobPreparationPlate.__name__,
self.lab_iso_plate.__class__.__name__)
self.add_error(msg)
self._check_input_class('"for job" flag', self.for_job, bool)
def __init__(self, stock_rack, stock_rack_layout=None, parent=None):
"""
Constructor.
:param stock_rack: The stock rack to be checked.
:type stock_rack: :class:`thelma.entities.iso.StockRack`
:param stock_rack_layout: The layout containing the molecule design
and volume data. Can be set here or derived during the run.
:type stock_rack_layout: :class:`StockRackLayout`
"""
BaseRackVerifier.__init__(self, reference_layout=stock_rack_layout, parent=parent)
#: The stock rack to be checked.
self.stock_rack = stock_rack
def _get_ids_for_pool(self, md_pool):
"""
If a floating placeholder occurs for the first time we have dictionary
instead of a pool.
"""
if isinstance(md_pool, dict):
id_map = dict()
for iso_label, pool in md_pool.iteritems():
ids = BaseRackVerifier._get_ids_for_pool(self, pool)
id_map[iso_label] = ids
return id_map
else:
return BaseRackVerifier._get_ids_for_pool(self, md_pool)
def _get_ids_for_pool(self, md_pool):
"""
If a floating placeholder occurs for the first time we have dictionary
instead of a pool.
"""
if isinstance(md_pool, dict):
id_map = dict()
for iso_label, pool in md_pool.iteritems():
ids = BaseRackVerifier._get_ids_for_pool(self, pool)
id_map[iso_label] = ids
return id_map
else:
return BaseRackVerifier._get_ids_for_pool(self, md_pool)
def __init__(self, stock_rack, stock_rack_layout=None, parent=None):
"""
Constructor.
:param stock_rack: The stock rack to be checked.
:type stock_rack: :class:`thelma.entities.iso.StockRack`
:param stock_rack_layout: The layout containing the molecule design
and volume data. Can be set here or derived during the run.
:type stock_rack_layout: :class:`StockRackLayout`
"""
BaseRackVerifier.__init__(self,
reference_layout=stock_rack_layout,
parent=parent)
#: The stock rack to be checked.
self.stock_rack = stock_rack
def _are_matching_molecule_designs(self, rack_mds, exp_mds):
"""
Checks whether the molecule designs for the positions match.
The method will also try to determine the ISO if this has not
been happened so far.
"""
if exp_mds is None or isinstance(exp_mds, list):
return BaseRackVerifier._are_matching_molecule_designs(
self, rack_mds, exp_mds)
# In case of floating position and unknown ISO ...
for iso_label, iso_mds in exp_mds.iteritems():
if BaseRackVerifier._are_matching_molecule_designs(
self, rack_mds, iso_mds):
self._used_iso = iso_label
return True
return False
def _are_matching_molecule_designs(self, rack_mds, exp_mds):
"""
Checks whether the molecule designs for the positions match.
The method will also try to determine the ISO if this has not
been happened so far.
"""
if exp_mds is None or isinstance(exp_mds, list):
return BaseRackVerifier._are_matching_molecule_designs(self,
rack_mds, exp_mds)
# In case of floating position and unknown ISO ...
for iso_label, iso_mds in exp_mds.iteritems():
if BaseRackVerifier._are_matching_molecule_designs(self,
rack_mds, iso_mds):
self._used_iso = iso_label
return True
return False
def __init__(self, source_plate, iso_request, parent=None):
"""
Constructor.
:param iso_request: The ISO request the plate must represent.
:type iso_request: :class:`thelma.entities.iso.isoRequest`
:param source_plate: The plate to be checked.
:type source_plate: :class:`thelma.entities.rack.Plate`
"""
BaseRackVerifier.__init__(self, parent=parent)
#: The ISO request the plate must represent.
self.iso_request = iso_request
#: The plate to be checked.
self.source_plate = source_plate
#: Maps floating maps (molecule design pools for placeholders) onto ISO
#: label - is only used when there are floating positions in the ISO
#: layout.
self._iso_map = dict()
#: The name of the ISO the source rack represents.
self._used_iso = None
def _are_matching_molecule_designs(self, rack_mds, exp_mds):
"""
If comparison is disabled (because the current position is ignored)
we always return *True*.
In any case, comparison is enabled again.
"""
if self.__disable_comparison:
self.__disable_comparison = False
return True
return BaseRackVerifier._are_matching_molecule_designs(
self, rack_mds, exp_mds)
def __init__(self, source_plate, iso_request, parent=None):
"""
Constructor.
:param iso_request: The ISO request the plate must represent.
:type iso_request: :class:`thelma.entities.iso.isoRequest`
:param source_plate: The plate to be checked.
:type source_plate: :class:`thelma.entities.rack.Plate`
"""
BaseRackVerifier.__init__(self, parent=parent)
#: The ISO request the plate must represent.
self.iso_request = iso_request
#: The plate to be checked.
self.source_plate = source_plate
#: Maps floating maps (molecule design pools for placeholders) onto ISO
#: label - is only used when there are floating positions in the ISO
#: layout.
self._iso_map = dict()
#: The name of the ISO the source rack represents.
self._used_iso = None
def _are_matching_molecule_designs(self, rack_mds, exp_mds):
"""
If comparison is disabled (because the current position is ignored)
we always return *True*.
In any case, comparison is enabled again.
"""
if self.__disable_comparison:
self.__disable_comparison = False
return True
return BaseRackVerifier._are_matching_molecule_designs(self, rack_mds,
exp_mds)
def _check_input(self):
BaseRackVerifier._check_input(self)
self._check_input_class('ISO request', self.iso_request, LabIsoRequest)
def reset(self):
BaseRackVerifier.reset(self)
self.__ignore_positions = None
self.__disable_comparison = False
def reset(self):
BaseRackVerifier.reset(self)
self._iso_map = None
self._used_iso = None
def _check_input(self):
BaseRackVerifier._check_input(self)
self._check_input_class('ISO request', self.iso_request, LabIsoRequest)
def reset(self):
BaseRackVerifier.reset(self)
self.__ignore_positions = None
self.__disable_comparison = False
def reset(self):
BaseRackVerifier.reset(self)
self._iso_map = None
self._used_iso = None
def _check_input(self):
BaseRackVerifier._check_input(self)
self._check_input_class("stock rack", self.stock_rack, StockRack)
def _check_input(self):
BaseRackVerifier._check_input(self)
self._check_input_class('stock rack', self.stock_rack, StockRack)