def __add_positions(self):
"""
Checks position map of the parser and stores the data.
"""
self.add_debug('Check and store position data ...')
for pos_label, tube_barcode in self.parser.position_map.iteritems():
if not match(RACK_POSITION_REGEXP, pos_label):
self.__invalid_labels.append(pos_label)
continue
rack_pos = get_rack_position_from_label(pos_label)
valid_values = True
if rack_pos in self.__rs_layout.get_positions():
self.__duplicate_positions.add(pos_label)
valid_values = False
if tube_barcode in self.__rs_layout.get_tube_barcodes():
self.__duplicate_tubes.add(tube_barcode)
valid_values = False
if not valid_values: continue
if tube_barcode is None: continue
try:
self.__rs_layout.add_position(rack_pos, tube_barcode)
except IndexError:
self.__position_out_of_range.append(pos_label)
def __get_rack_position(self, label):
"""
Returns the rack position of the given label or records an error.
"""
try:
rack_pos = get_rack_position_from_label(label)
except ValueError:
self.__invalid_pos_label.append(label)
return None
else:
return rack_pos
def __get_rack_position(self, label):
"""
Returns the rack position of the given label or records an error.
"""
try:
rack_pos = get_rack_position_from_label(label)
except ValueError:
self.__invalid_pos_label.append(label)
return None
else:
return rack_pos
def run(self):
rack_agg = get_root_aggregate(IRack)
is_agg = get_root_aggregate(IItemStatus)
status = is_agg.get_by_slug(self.STATUS)
cnt_specs_agg = get_root_aggregate(IContainerSpecs)
cnt_specs = cnt_specs_agg.get_by_slug(self.SPECS)
tubes = []
for scan_fn in glob.glob("%s/*.txt" % self.__scanfile_directory):
strm = open(scan_fn, 'r')
try:
prs = RackScanningParser(strm, parent=self)
prs.run()
finally:
strm.close()
if prs.has_errors():
raise RuntimeError('Could not parse rack scan file "%s". '
'Error messages: %s' %
(scan_fn, self.get_messages()))
rack_agg.filter = eq(barcode=prs.rack_barcode)
try:
rack = rack_agg.iterator().next()
except StopIteration:
self.add_error('Rack with barcode "%s" does not exist.' %
prs.rack_barcode)
continue
if not rack.specs.has_tubes:
self.add_error('Rack with barcode "%s" is not a tube '
'rack.' % rack.barcode)
continue
for pos_label, barcode in prs.position_map.iteritems():
if barcode is None:
continue
pos = get_rack_position_from_label(pos_label)
# FIXME: Enable this test once pulling a tube by barcode is
# fast.
# if tube_agg.get_by_slug(barcode):
# self.add_error('Tube with barcode "%s" already '
# 'exists.' % barcode)
# continue
if not rack.is_empty(pos):
self.add_error('Trying to place a tube in an occupied '
'position (%s on rack %s).' %
(pos_label, rack.barcode))
continue
tube = Tube.create_from_rack_and_position(
cnt_specs, status, barcode, rack, pos)
tubes.append(tube)
self.add_info('Creating tube with barcode %s at '
'position %s in rack %s.' %
(barcode, pos_label, rack.barcode))
if not self.has_errors():
self.return_value = tubes
def run(self):
rack_agg = get_root_aggregate(IRack)
is_agg = get_root_aggregate(IItemStatus)
status = is_agg.get_by_slug(self.STATUS)
cnt_specs_agg = get_root_aggregate(IContainerSpecs)
cnt_specs = cnt_specs_agg.get_by_slug(self.SPECS)
tubes = []
for scan_fn in glob.glob("%s/*.txt" % self.__scanfile_directory):
strm = open(scan_fn, 'r')
try:
prs = RackScanningParser(strm, parent=self)
prs.run()
finally:
strm.close()
if prs.has_errors():
raise RuntimeError('Could not parse rack scan file "%s". '
'Error messages: %s'
% (scan_fn, self.get_messages()))
rack_agg.filter = eq(barcode=prs.rack_barcode)
try:
rack = rack_agg.iterator().next()
except StopIteration:
self.add_error('Rack with barcode "%s" does not exist.'
% prs.rack_barcode)
continue
if not rack.specs.has_tubes:
self.add_error('Rack with barcode "%s" is not a tube '
'rack.' % rack.barcode)
continue
for pos_label, barcode in prs.position_map.iteritems():
if barcode is None:
continue
pos = get_rack_position_from_label(pos_label)
# FIXME: Enable this test once pulling a tube by barcode is
# fast.
# if tube_agg.get_by_slug(barcode):
# self.add_error('Tube with barcode "%s" already '
# 'exists.' % barcode)
# continue
if not rack.is_empty(pos):
self.add_error('Trying to place a tube in an occupied '
'position (%s on rack %s).' %
(pos_label, rack.barcode))
continue
tube = Tube.create_from_rack_and_position(cnt_specs, status,
barcode, rack, pos)
tubes.append(tube)
self.add_info('Creating tube with barcode %s at '
'position %s in rack %s.' %
(barcode, pos_label, rack.barcode))
if not self.has_errors():
self.return_value = tubes
def get_planned_sample_transfers(self, plate_marker):
"""
Converts the all transfer target for the given target plate into
:class:`PlannedSampleTransfer` objects.
"""
psts = []
for tt in self.transfer_targets:
if not tt.target_rack_marker == plate_marker: continue
trg_pos = get_rack_position_from_label(tt.position_label)
pst = PlannedSampleTransfer.get_entity(
volume=tt.transfer_volume / VOLUME_CONVERSION_FACTOR,
source_position=self.rack_position,
target_position=trg_pos)
psts.append(pst)
return psts
def get_planned_sample_transfers(self, plate_marker):
"""
Converts the all transfer target for the given target plate into
:class:`PlannedSampleTransfer` objects.
"""
psts = []
for tt in self.transfer_targets:
if not tt.target_rack_marker == plate_marker:
continue
trg_pos = get_rack_position_from_label(tt.position_label)
pst = PlannedSampleTransfer.get_entity(
volume=tt.transfer_volume / VOLUME_CONVERSION_FACTOR,
source_position=self.rack_position,
target_position=trg_pos,
)
psts.append(pst)
return psts
def run(self):
layout_map = {}
for sector, lfn in enumerate((self.__layout_filename_q1,
self.__layout_filename_q2,
self.__layout_filename_q3,
self.__layout_filename_q4)):
layout_map.update(self.__parse_layout_file(sector, lfn))
pool_map = self.__get_md_pool_map(set(layout_map.values()))
stock_conc_map = self.__find_stock_concentrations(pool_map)
pool_tube_barcode_map = self.__get_tube_barcode_map(pool_map,
stock_conc_map)
tube_map = self.__get_tube_map(pool_tube_barcode_map.values())
tgt_rack = self.__get_target_rack(self.__target_barcode)
for pos_label, pool_id in layout_map.iteritems():
pos = get_rack_position_from_label(pos_label)
cnt = tgt_rack.container_positions[pos]
smpl = cnt.make_sample(self.__iso_volume)
tube = tube_map[pool_tube_barcode_map[pool_id]]
sm_conc = \
self.__iso_concentration / len(tube.sample.sample_molecules)
for sm in tube.sample.sample_molecules:
smpl.make_sample_molecule(sm.molecule, sm_conc)
tgt_rack.status = get_item_status_managed()