def test_init_from_rack_and_invalid_position(self, tube_fac,
tube_rack,
rack_position_fac):
kw = tube_fac.init_kw
kw['rack'] = tube_rack
kw['position'] = rack_position_fac(row_index=0, column_index=12)
with pytest.raises(ValueError):
Tube.create_from_rack_and_position(**kw)
kw['position'] = rack_position_fac(row_index=8, column_index=0)
with pytest.raises(ValueError):
Tube.create_from_rack_and_position(**kw)
def __make_new_tube(self, sample_registration_item):
self.add_debug('Creating new tube with barcode %s'
% sample_registration_item.tube_barcode)
kw = dict(specs=self.__container_specs,
status=self.__status)
kw['barcode'] = sample_registration_item.tube_barcode
pos = sample_registration_item.rack_position
if not pos is None:
kw['rack'] = sample_registration_item.rack
kw['position'] = pos
tube = Tube.create_from_rack_and_position(**kw)
else:
tube = Tube(**kw)
return tube
def test_init_from_rack_and_position(self, tube_fac,
tube_rack, rack_position11):
kw = tube_fac.init_kw
kw['rack'] = tube_rack
kw['position'] = rack_position11
tube = Tube.create_from_rack_and_position(**kw)
check_attributes(tube, kw)
assert not tube.slug is None
assert tube.position == kw['position']
def __prepare_pool_stock_rack(self, empty_rack, sector_idx):
tube_specs_agg = get_root_aggregate(ITubeSpecs)
ts_matrix = tube_specs_agg.get_by_slug('matrix0500')
is_managed = get_item_status_managed()
pos_idxs_96 = zip([1, 1, 0, 0], [1, 1, 1, 1])
(row_idx, col_idx) = pos_idxs_96[sector_idx]
tube = Tube.create_from_data(
dict(barcode=str(9999999990 + tube_counter.next()),
status=is_managed,
specs=ts_matrix))
pos = get_rack_position_from_indices(row_idx, col_idx)
empty_rack.add_tube(tube, 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 test_move_tube(self, tube_rack, item_status_managed,
tube_specs_matrix, rack_position11, rack_position_fac,
tube_rack_fac):
tube = Tube.create_from_rack_and_position(
specs=tube_specs_matrix,
status=item_status_managed,
barcode='0111111111',
rack=tube_rack,
position=rack_position11)
assert tube.location.position is rack_position11
assert tube.location.rack is tube_rack
assert tube.location.container is tube
assert tube_rack.container_positions[rack_position11] is tube
#
empty_position = rack_position_fac(row_index=0, column_index=0)
new_position = rack_position_fac(row_index=0, column_index=3)
# Move within same rack.
tube_rack.move_tube(rack_position11, new_position)
assert tube.location.position is new_position
# Move to other rack.
new_rack = tube_rack_fac(label='TestDestTubeRack')
tube_rack.remove_tube(tube)
# Removing again raises error.
with pytest.raises(ValueError):
tube_rack.remove_tube(tube)
new_rack.add_tube(tube, new_position)
# Adding again raises error.
with pytest.raises(ValueError):
tube_rack.add_tube(tube, empty_position)
assert tube.location.rack is new_rack
# Moving from empty position raises ValueError.
with pytest.raises(ValueError):
new_rack.move_tube(empty_position, new_position)
# Moving to occupied position raises ValueError.
with pytest.raises(ValueError):
new_rack.move_tube(new_position, new_position)
