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 __process_change_owner(self, new_owner):
trac_tool = None
if new_owner is None:
# Reassign to requester for editing the experiment
# metadata.
trac_tool = IsoRequestTicketReassigner(
iso_request=self.get_entity(),
completed=False)
new_owner = ''
elif new_owner == self.requester.directory_user_id:
# Close iso request and reassign to requester.
trac_tool = IsoRequestTicketReassigner(
iso_request=self.get_entity(),
completed=True)
elif new_owner == STOCKMANAGEMENT_USER:
if self.owner == '':
# Activate this ISO request for the first time.
trac_tool = IsoRequestTicketAccepter(
iso_request=self.get_entity(),
username=new_owner)
else:
user_id = get_current_user().directory_user_id
new_owner = user_id + ", " + STOCKMANAGEMENT_USER
trac_tool = IsoRequestTicketReopener(
iso_request=self.get_entity(),
username=user_id)
else:
# Accept this ISO request.
tkt_user = new_owner.split(',')[0]
trac_tool = IsoRequestTicketAccepter(
iso_request=self.get_entity(),
username=tkt_user)
if not trac_tool is None:
run_trac_tool(trac_tool)
self.owner = new_owner
def __process_change_owner(self, new_owner):
trac_tool = None
if new_owner is None:
# Reassign to requester for editing the experiment
# metadata.
trac_tool = IsoRequestTicketReassigner(
iso_request=self.get_entity(), completed=False)
new_owner = ''
elif new_owner == self.requester.directory_user_id:
# Close iso request and reassign to requester.
trac_tool = IsoRequestTicketReassigner(
iso_request=self.get_entity(), completed=True)
elif new_owner == STOCKMANAGEMENT_USER:
if self.owner == '':
# Activate this ISO request for the first time.
trac_tool = IsoRequestTicketAccepter(
iso_request=self.get_entity(), username=new_owner)
else:
user_id = get_current_user().directory_user_id
new_owner = user_id + ", " + STOCKMANAGEMENT_USER
trac_tool = IsoRequestTicketReopener(
iso_request=self.get_entity(), username=user_id)
else:
# Accept this ISO request.
tkt_user = new_owner.split(',')[0]
trac_tool = IsoRequestTicketAccepter(iso_request=self.get_entity(),
username=tkt_user)
if not trac_tool is None:
run_trac_tool(trac_tool)
self.owner = new_owner
def __getitem__(self, key):
if key == 'current-user':
user = get_current_user()
if user == None:
raise Forbidden()
key = user.slug
return Collection.__getitem__(self, key)
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 __getitem__(self, key):
if key == 'current-user':
user = get_current_user()
if user == None:
raise Forbidden()
key = user.slug
return Collection.__getitem__(self, key)
def create_from_entity(cls, entity):
if entity.ticket_number is None:
# Create a new ticket and attach the ticket number.
user = get_current_user()
ticket_creator = \
IsoRequestTicketCreator(requester=user,
experiment_metadata=entity)
entity.ticket_number = \
cls.__run_trac_tool(ticket_creator,
'Could not update the ticket: %s.')
return cls(entity)
def create_from_entity(cls, entity):
if entity.ticket_number is None:
# Create a new ticket and attach the ticket number.
user = get_current_user()
ticket_creator = \
IsoRequestTicketCreator(requester=user,
experiment_metadata=entity)
entity.ticket_number = \
cls.__run_trac_tool(ticket_creator,
'Could not update the ticket: %s.')
return cls(entity)
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 __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_experiment(self, exp_ent, status_title):
tool = None
user = get_current_user()
if status_title == 'manual_execution':
tool = get_manual_executor(experiment=exp_ent, user=user)
elif status_title == 'robot_execution':
try:
tool = get_executor(experiment=exp_ent, user=user)
except TypeError as te:
raise HTTPBadRequest(str(te)).exception
if not tool is None:
# FIXME: We don't care about the result here; still we must call
# get_result for its side effects.
dummy = tool.get_result()
if tool.has_errors():
exc_msg = str(tool.get_messages(logging_level=logging.ERROR))
raise HTTPBadRequest('Could not update Database: %s' %
exc_msg).exception
else:
status_agg = get_root_aggregate(IItemStatus)
status_managed = \
status_agg.get_by_slug(ITEM_STATUS_NAMES.MANAGED.lower())
for exp_rack in exp_ent.experiment_racks:
exp_rack.rack.status = status_managed
def __update_experiment(self, exp_ent, status_title):
tool = None
user = get_current_user()
if status_title == 'manual_execution':
tool = get_manual_executor(experiment=exp_ent, user=user)
elif status_title == 'robot_execution':
try:
tool = get_executor(experiment=exp_ent, user=user)
except TypeError as te:
raise HTTPBadRequest(str(te)).exception
if not tool is None:
# FIXME: We don't care about the result here; still we must call
# get_result for its side effects.
dummy = tool.get_result()
if tool.has_errors():
exc_msg = str(tool.get_messages(logging_level=logging.ERROR))
raise HTTPBadRequest('Could not update Database: %s' % exc_msg
).exception
else:
status_agg = get_root_aggregate(IItemStatus)
status_managed = \
status_agg.get_by_slug(ITEM_STATUS_NAMES.MANAGED.lower())
for exp_rack in exp_ent.experiment_racks:
exp_rack.rack.status = status_managed
def _run_xl20_executor(self, worklist):
user = get_current_user()
tool = XL20Executor(worklist, user)
tool.run()
assert not tool.has_errors()
self.__session.commit()
def _run_xl20_executor(self, worklist):
user = get_current_user()
tool = XL20Executor(worklist, user)
tool.run()
assert not tool.has_errors()
self.__session.commit()
def parser_factory(cls, stream, **kw):
user = get_current_user()
return XL20Executor(output_file_stream=stream, user=user, **kw)
def parser_factory(cls, stream, **kw):
user = get_current_user()
return XL20Executor(output_file_stream=stream, user=user, **kw)
