def make_default_setup(date, plan, project=None):
if not project:
project = get_validation_project()
plan_name = plan.get('name', None) or plate_layouts[plan['plate_layout']][1]
plate_setup = PlateSetup(project_id=project.id, name=plan_name)
plate_setup.locked = False
plate_setup.completed = False
if type(plan['execution_order']) == type([]):
execution_order = plan['execution_order']
else:
execution_order = execution_orders[plan['execution_order']]
# TODO add status steps
setup = dict(consumable=consumable_layouts[plan['consumable']],
execution_order=execution_order,
plate_layout=plate_layouts[plan['plate_layout']],
progress=progress(num_readers=len(execution_order)))
plate_setup.time_updated = datetime.now()
plate_setup.author_id = plan['operator'].id
plate_setup.setup = json.dumps(setup)
plate_setup.dr_oil = 22
plate_setup.dg_oil = 14
plate_setup.master_mix = 12
plate_setup.droplet_generation_method = 201
plate_setup.thermal_cycler_id = plan.get('thermal_cycler', None)
plate_setup.prefix = make_setup_name(plate_setup)
return plate_setup
def __update_groove_record(self, record=None):
new_record = False
errors = {}
if not record:
new_record = True
plate_type = Session.query(PlateType).get(self.form_result["plate_type"])
person = Session.query(Person).get(self.form_result["droplet_maker"])
if self.form_result["droplet_generator"]:
dg = Session.query(DropletGenerator).get(self.form_result["droplet_generator"])
else:
dg = None
if not plate_type:
errors["plate_type"] = "Unknown plate type."
else:
qlt_paths = self.__get_layout_qlts(plate_type, self.form_result["runs"])
if not qlt_paths:
errors["runs"] = "Invalid layout for this plate type."
else:
# create the name
setup = []
for i, path in enumerate(qlt_paths):
name = self.__name_for_groove_plate(
plate_type,
self.form_result["droplet_type"],
person,
self.form_result["creation_date"],
self.form_result["identifier"],
i,
)
setup.append((name, path))
plate_setup = PlateSetup(
name=name[:-2],
prefix=name[:-2],
setup=json.dumps(setup),
time_updated=self.form_result["creation_date"],
project_id=Session.query(Project).filter_by(name="GrooveTest").first().id,
author_id=person.id,
droplet_maker_id=person.id,
dr_oil=22,
plate_type_id=plate_type.id,
droplet_generator_id=dg.id if dg else None,
notes=self.form_result["notes"],
)
dt = self.form_result["droplet_type"]
if dt == 1: # TODO LITERALS
plate_setup.skin_type = Plate.SKIN_TYPE_SKINNED
plate_setup.dg_oil = 14
plate_setup.master_mix = 12
else:
plate_setup.skin_type = Plate.SKIN_TYPE_SKINLESS
plate_setup.dg_oil = 31
if dt == 2:
plate_setup.chemistry_type = Plate.CHEMISTRY_TYPE_GREEN
plate_setup.master_mix = 205
else:
plate_setup.chemistry_type = Plate.CHEMISTRY_TYPE_TAQMAN
if dt == 3:
plate_setup.master_mix = 501
Session.add(plate_setup)
Session.commit()
return plate_setup, None
else:
record.notes = self.form_result["notes"]
record.droplet_generator_id = self.form_result["droplet_generator"]
Session.commit()
return record, None
if errors:
return None, errors