Exemple #1
0
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
Exemple #2
0
    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