def _create_iso_candidates(self, tube_rack_fac, tube_rack_specs_matrix,
tube_fac, item_status_managed,
organization_cenix, stock_sample_fac):
ss_agg = get_root_aggregate(IStockSample)
rack_agg = get_root_aggregate(IRack)
tube_bc = 9000000000
vol = 1e-4
row_idx = 0
col_idx = 0
tube_rack = tube_rack_fac(label='test_iso_candidates',
specs=tube_rack_specs_matrix,
status=get_item_status_managed())
rack_agg.add(tube_rack)
mdp_agg = get_root_aggregate(IMoleculeDesignPool)
for mdp_id in [288282, 3349397, 3430173, 1139866, 199937]:
tube = tube_fac(barcode=str(tube_bc),
status=item_status_managed)
col_idx += 1
tube_bc += 1
tube_rack.add_tube(
tube,
get_rack_position_from_indices(row_idx, col_idx))
mdp = mdp_agg.get_by_id(mdp_id)
ss = stock_sample_fac(
volume=vol,
container=tube,
molecule_design_pool=mdp,
supplier=organization_cenix,
molecule_type=mdp.molecule_type,
concentration=mdp.default_stock_concentration)
ss_agg.add(ss)
def _create_iso_candidates(self, tube_rack_fac, tube_rack_specs_matrix,
tube_fac, item_status_managed,
organization_cenix, stock_sample_fac):
ss_agg = get_root_aggregate(IStockSample)
rack_agg = get_root_aggregate(IRack)
tube_bc = 9000000000
vol = 1e-4
row_idx = 0
col_idx = 0
tube_rack = tube_rack_fac(label='test_iso_candidates',
specs=tube_rack_specs_matrix,
status=get_item_status_managed())
rack_agg.add(tube_rack)
mdp_agg = get_root_aggregate(IMoleculeDesignPool)
for mdp_id in [288282, 3349397, 3430173, 1139866, 199937]:
tube = tube_fac(barcode=str(tube_bc), status=item_status_managed)
col_idx += 1
tube_bc += 1
tube_rack.add_tube(
tube, get_rack_position_from_indices(row_idx, col_idx))
mdp = mdp_agg.get_by_id(mdp_id)
ss = stock_sample_fac(
volume=vol,
container=tube,
molecule_design_pool=mdp,
supplier=organization_cenix,
molecule_type=mdp.molecule_type,
concentration=mdp.default_stock_concentration)
ss_agg.add(ss)
def __get_empty_racks(self, count):
rack_specs_agg = get_root_aggregate(ITubeRackSpecs)
rs_matrix = rack_specs_agg.get_by_slug('matrix0500')
is_managed = get_item_status_managed()
rack_agg = get_root_aggregate(ITubeRack)
rack_agg.filter = eq(total_containers=0,
specs=rs_matrix,
status=is_managed)
rack_agg.slice = slice(0, count)
return list(iter(rack_agg))
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 __get_status(self):
try:
status = self.__status
except AttributeError:
pp = self.preparation_plates
# Detect if this ISO job is done (it is sufficient to check the
# status of the first preparation plate).
item_status_managed = get_item_status_managed()
if len(pp) > 0 and pp[0].status == item_status_managed:
status = ISO_STATUS.DONE
else:
status = ISO_STATUS.QUEUED
return status
def __get_status(self):
try:
status = self.__status
except AttributeError:
pp = self.preparation_plates
# Detect if this ISO job is done (it is sufficient to check the
# status of the first preparation plate).
item_status_managed = get_item_status_managed()
if len(pp) > 0 and pp[0].status == item_status_managed:
status = ISO_STATUS.DONE
else:
status = ISO_STATUS.QUEUED
return status
def run(self):
src_rack = self.__get_rack(self.__source_barcode)
for tgt_bc in self.__target_barcodes:
tgt_rack = self.__get_rack(tgt_bc)
for pos, src_cnt_loc in iteritems_(src_rack.container_positions):
if not src_cnt_loc.container is None:
src_cnt = src_cnt_loc.container
if not src_cnt.sample is None:
src_smpl = src_cnt.sample
tgt_cnt = tgt_rack.container_positions[pos]
tgt_smpl = tgt_cnt.make_sample(self.__transfer_volume)
for sm in src_smpl.sample_molecules:
tgt_smpl.make_sample_molecule(sm.molecule, sm.concentration)
tgt_rack.status = get_item_status_managed()
def run(self):
src_rack = self.__get_rack(self.__source_barcode)
for tgt_bc in self.__target_barcodes:
tgt_rack = self.__get_rack(tgt_bc)
for pos, src_cnt_loc in iteritems_(src_rack.container_positions):
if not src_cnt_loc.container is None:
src_cnt = src_cnt_loc.container
if not src_cnt.sample is None:
src_smpl = src_cnt.sample
tgt_cnt = tgt_rack.container_positions[pos]
tgt_smpl = tgt_cnt.make_sample(self.__transfer_volume)
for sm in src_smpl.sample_molecules:
tgt_smpl.make_sample_molecule(
sm.molecule, sm.concentration)
tgt_rack.status = get_item_status_managed()
def __create_rack_samples(self, layout, design_rack):
"""
Generates the sample for each experiment plate belonging to a particular
experiment design rack. The volume is fixed
(:attr:`FINAL_SAMPLE_VOLUME`), the molecule are stored in the
:attr:`_pool_molecule_map` and positions and concentrations are
derived from the layout.
"""
without_pool_data = isinstance(layout, RackLayout)
design_rack_label = design_rack.label
for exp_rack in self._experiment_racks[design_rack_label]:
plate = exp_rack.rack
if without_pool_data:
positions = layout.get_positions()
self.__add_samples_without_pools(positions, plate)
else:
self.__add_samples_with_pools(layout, plate, design_rack_label)
if self.has_errors(): break
plate.status = get_item_status_managed()
def __create_rack_samples(self, layout, design_rack):
"""
Generates the sample for each experiment plate belonging to a particular
experiment design rack. The volume is fixed
(:attr:`FINAL_SAMPLE_VOLUME`), the molecule are stored in the
:attr:`_pool_molecule_map` and positions and concentrations are
derived from the layout.
"""
without_pool_data = isinstance(layout, RackLayout)
design_rack_label = design_rack.label
for exp_rack in self._experiment_racks[design_rack_label]:
plate = exp_rack.rack
if without_pool_data:
positions = layout.get_positions()
self.__add_samples_without_pools(positions, plate)
else:
self.__add_samples_with_pools(layout, plate, design_rack_label)
if self.has_errors(): break
plate.status = get_item_status_managed()
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()
