def __create_pipetting_worklist_stream(self, resource):
entity = resource.get_entity()
try:
tool = lab.get_worklist_writer(entity=entity)
except TypeError as te:
raise HTTPBadRequest(str(te))
return run_tool(tool)
def __pipetting_iso_or_iso_job(self, iso_or_iso_job):
user = get_current_user()
executor = get_worklist_executor(iso_or_iso_job, user)
result = run_tool(executor, error_prefix='Errors during pipetting. --')
trac_updater = LabIsoStockTransferReporter(executor=executor)
run_trac_tool(trac_updater)
return result
def __pipetting_iso_or_iso_job(self, iso_or_iso_job):
user = get_current_user()
executor = get_worklist_executor(iso_or_iso_job, user)
result = run_tool(executor,
error_prefix='Errors during pipetting. --')
trac_updater = LabIsoStockTransferReporter(executor=executor)
run_trac_tool(trac_updater)
return result
def __create_xl20_worklist_stream(self, resource, options):
entity = resource.get_entity()
# self._prepare_for_xl20_worklist_creation(entity)
try:
tool = lab.get_stock_rack_assembler(entity=entity,
**options)
except TypeError as te:
raise HTTPBadRequest(str(te))
return run_tool(tool)
def _run(self, resource, options):
if options['type'] == 'ALL_WITH_ROBOT':
tool = resource.experiment_job.get_writer()
elif options['type'] == 'ROBOT':
try:
tool = resource.get_writer()
except TypeError as te:
raise HTTPBadRequest(str(te)).exception
return run_tool(tool)
def create_xl20_worklist(self, entity, rack_barcodes,
optimizer_excluded_racks=None,
optimizer_requested_tubes=None,
include_dummy_output=False):
assembler = lab.get_stock_rack_assembler(
entity=entity,
rack_barcodes=rack_barcodes,
excluded_racks=optimizer_excluded_racks,
requested_tubes=optimizer_requested_tubes,
include_dummy_output=include_dummy_output)
return run_tool(assembler)
def __extract_from_xls(self, request_body):
if len(request_body) == 0:
raise HTTPBadRequest("Request's body is empty!")
experiment_metadata = self.context.get_entity()
user = get_current_user()
generator = ExperimentMetadataGenerator.create(
stream=request_body,
experiment_metadata=experiment_metadata,
requester=user)
new_entity = run_tool(generator)
# Store this for later.
self.__generator = generator
return new_entity
def create_xl20_worklist(self,
entity,
rack_barcodes,
optimizer_excluded_racks=None,
optimizer_requested_tubes=None,
include_dummy_output=False):
assembler = lab.get_stock_rack_assembler(
entity=entity,
rack_barcodes=rack_barcodes,
excluded_racks=optimizer_excluded_racks,
requested_tubes=optimizer_requested_tubes,
include_dummy_output=include_dummy_output)
return run_tool(assembler)
def __generate_isos(self, number_of_new_isos, optimizer_excluded_racks,
optimizer_requested_tubes, requested_library_plates):
if not optimizer_excluded_racks is None:
optimizer_excluded_racks = optimizer_excluded_racks.split(',')
if not optimizer_requested_tubes is None:
optimizer_requested_tubes = optimizer_requested_tubes.split(',')
if not requested_library_plates is None:
requested_library_plates = requested_library_plates.split(',')
iso_request = self.get_entity()
user = get_current_user()
if iso_request.iso_type == ISO_TYPES.LAB:
creator = \
get_job_creator(iso_request,
user,
number_of_new_isos,
excluded_racks=optimizer_excluded_racks,
requested_tubes=optimizer_requested_tubes,
requested_library_plates=
requested_library_plates)
else:
raise NotImplementedError('POOL CREATION ISOs not implemented.')
return run_tool(creator)
def __generate_isos(self, number_of_new_isos,
optimizer_excluded_racks, optimizer_requested_tubes,
requested_library_plates):
if not optimizer_excluded_racks is None:
optimizer_excluded_racks = optimizer_excluded_racks.split(',')
if not optimizer_requested_tubes is None:
optimizer_requested_tubes = optimizer_requested_tubes.split(',')
if not requested_library_plates is None:
requested_library_plates = requested_library_plates.split(',')
iso_request = self.get_entity()
user = get_current_user()
if iso_request.iso_type == ISO_TYPES.LAB:
creator = \
get_job_creator(iso_request,
user,
number_of_new_isos,
excluded_racks=optimizer_excluded_racks,
requested_tubes=optimizer_requested_tubes,
requested_library_plates=
requested_library_plates)
else:
raise NotImplementedError('POOL CREATION ISOs not implemented.')
return run_tool(creator)
def __update_stock_racks(self, iso_or_iso_job, status):
stock_rack_barcodes = status[len('UPDATE_STOCK_RACKS'):].split(';')
recycler = get_stock_rack_recyler(iso_or_iso_job, stock_rack_barcodes)
return run_tool(recycler,
error_prefix='Invalid stock rack(s)! --')
def create_pipetting_worklist(self):
writer = lab.get_worklist_writer(self.get_entity())
return run_tool(writer)
def __update_stock_racks(self, iso_or_iso_job, status):
stock_rack_barcodes = status[len('UPDATE_STOCK_RACKS'):].split(';')
recycler = get_stock_rack_recyler(iso_or_iso_job, stock_rack_barcodes)
return run_tool(recycler, error_prefix='Invalid stock rack(s)! --')
def create_pipetting_worklist(self):
writer = lab.get_worklist_writer(self.get_entity())
return run_tool(writer)