How to use the autoprotocol.util.make_dottable_dict function in autoprotocol

"bradford_plate": {
                "id": null,
                "type": "96-flat",
                "storage": "cold_20",
                "discard": false
            },
            "measurement_start": "bradford_plate/A4",
            "standard_replicates": 3,
            "sample_replicates":3,
            "sample_number": 3,
            "num_blanks": 3
        }
    }

    '''
    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    standard_wells = refs.standard_plate.wells_from(0,8,columnwise=True)
    wells_to_measure = refs.bradford_plate.wells_from(0, (len(standard_wells) *
        params.standard_replicates) +
        (params.sample_number * params.sample_replicates)
        + params.num_blanks, columnwise = True)
    wells_with_standard = wells_to_measure.wells[0:3*len(standard_wells)]
    sample_wells = wells_to_measure.wells[len(wells_with_standard):len(wells_to_measure)-3]
    blanks = wells_to_measure.wells[-1:-params.num_blanks]

    coomassie = WellGroup([])
    for name,ref in refs.items():
        if name.rsplit("_")[0] == "coomassie":
            coomassie.append(ref.well(0).set_volume('1500:microliter'))

"ethanol_wash_vol": "60:microliter",
            "supernatant_removal_vol": "42:microliter",
            "wash_removal_vol": "90:microliter",
            "ethanol_air_dry_time": "15:minute",
            "ethanol_air_dry_temp": "ambient",
            "resuspension_time": "5:minute",
            "final_mag_adapter_time": "5:minute",
            "resuspension_vol": "50:microliter",
            "ethanol": "resource_plate/A1",
            "te": "resource_plate/A2"
        }
    }


    '''
    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    samples = refs.sample_plate.wells_from(
        params.sample_start,
        params.sample_number
    ).set_volume(params.sample_volume)
    destinations = refs.sample_plate.wells_from(
        params.destination_start, params.sample_number)
    bead_volume = Unit.fromstring(
        params.sample_volume) * Unit(1.8, "microliter")

    # Allow beads to come to room temperature

    # Resuspend the beads
    protocol.mix(refs.beads.well(0), volume="500:microliter")

],
        "pcr_cycles": 30,
        "activation_time": "2:minute",
        "activation_temp": "95:celsius",
        "denaturation_time": "10:second",
        "denaturation_temp": "94:celsius",
        "annealing_time": "15:second",
        "annealing_temp": "55:celsius",
        "extension_time": "20:second",
        "extension_temp": "72:celsius"
        }
    }

    '''
    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    mix_to_samples = {}

    for k in refs.keys():
        if k.rsplit("_")[-1] == "MM":
            mix_to_samples[k] = params["%s_samples" % k.rsplit("_")[0]]

    for mix, group in mix_to_samples.items():
        if params.pcr_match_sample_layout:
            destination_wells = WellGroup([refs.pcr.well(i) for i in group.indices()])
            protocol.distribute(refs[mix].well(0), destination_wells,
                params.mastermix_vol_per_rxn, allow_carryover=True)
            protocol.transfer(group, destination_wells, params.sample_vol)
        else:
            pass

"fragment_5": "resources/B5",
            "reaction_number": 10,
            "backbone_vol": "1:microliter",
            "enzyme_vol": "0.3:microliter",
            "ligase_vol": "0.6:microliter",
            "buffer_vol": "1:microliter",
            "fragment_vol": "3:microliter",
            "water_vol": "2:microliter",
            "ligation_time": "10:minute",
            "deactivation_time": "5:minute",
            "deactivation_temp": "65:celsius",
        }
    }
    '''

    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    MM_vol = Unit.fromstring(params.backbone_vol) + Unit.fromstring(params.enzyme_vol) + Unit.fromstring(params.buffer_vol) + Unit.fromstring(params.ligase_vol) + Unit.fromstring(params.fragment_vol) + Unit.fromstring(params.water_vol)
    # make master mix
    protocol.transfer(params.backbone, params.MM_loc, Unit.fromstring(params.backbone_vol) * Unit((params.reaction_number + 2),"microliter"))
    protocol.transfer(params.T4_ligase, params.MM_loc, Unit.fromstring(params.ligase_vol) * Unit((params.reaction_number + 2),"microliter"))
    protocol.transfer(params.enzyme, params.MM_loc, Unit.fromstring(params.enzyme_vol) * Unit((params.reaction_number + 2),"microliter"))
    protocol.transfer(params.buffer, params.MM_loc, Unit.fromstring(params.buffer_vol) * Unit((params.reaction_number + 2),"microliter"))

    # distribute master mix
    protocol.distribute(params.MM_loc,
        refs.destination_plate.wells_from(params.reaction_start,
        params.reaction_number), MM_vol )

    protocol.seal("destination_plate")

"supernatant_removal_vol": "42:microliter",
            "wash_removal_vol": "90:microliter",
            "ethanol_air_dry_time": "15:minute",
            "ethanol_air_dry_temp": "ambient",
            "resuspension_time": "5:minute",
            "final_mag_adapter_time": "5:minute",
            "resuspension_vol": "50:microliter",
            "ethanol": "resource_plate/A1",
            "te": "resource_plate/A2"
        }
    }


    '''
    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    samples = refs.sample_plate.wells_from(
        params.sample_start,
        params.sample_number
    ).set_volume(params.sample_volume)
    destinations = refs.sample_plate.wells_from(
        params.destination_start, params.sample_number)
    bead_volume = Unit.fromstring(
        params.sample_volume) * Unit(1.8, "microliter")

    # Allow beads to come to room temperature

    # Resuspend the beads
    protocol.mix(refs.beads.well(0), volume="500:microliter")

    protocol.transfer(

"kinased_oligo_plate/F2"
                ],
            "combos": [[2,8],[1,2,7],[3,5,12],[2,5,11],[2,6,8],[2,5,8],[4,5,13],[1,4,5,10],[2,11],[4,14]],
            "water": [
                "H2O_1/0",
                "H2O_2/0",
                "H2O_3/0"
            ],
            "water_vol": "198:microliter",
            "dilution_start": "diluted_oligo_plate/A1",
            "oligo_vol": "2:microliter"
        }
    }
    '''

    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    dilute_wells = refs.diluted_oligo_plate.wells_from(params.dilution_start,
                                        len(params.combos), columnwise = True)
    protocol.distribute(params.water.set_volume("1500:microliter"), dilute_wells, params.water_vol,
                        allow_carryover = True)
    oligos = params.kinased_oligos.wells

    for idx,combo in enumerate(params.combos):
        for i in combo:
            olig = oligos[i-1]
            protocol.transfer(olig,dilute_wells.wells[idx],params.oligo_vol,
                                mix_after = True)

"discard": false
            },
            "reaction_plate": {
                "id": null,
                "type": "384-pcr",
                "storage": "ambient",
                "discard": false
            },
            "polymerize_MM_vol": "2.2:microliter",
            "polymerize_MM_loc": "resource_plate/E1",
            "kunkel_number": 10,
            "reaction_start": "reaction_plate/A1"
        }
    }
    '''
    params = make_dottable_dict(params)
    refs = params.refs

    reactions = refs["reaction_plate"].wells_from(params.reaction_start, params.kunkel_number, columnwise = True)

    for reaction in reactions:
        protocol.transfer(params.polymerize_MM_loc, reaction, params.polymerize_MM_vol, mix_after=True)

    protocol.seal("reaction_plate")

    protocol.incubate("reaction_plate", "ambient", "1.5:hour")

"diluted_oligo_plate/D1",
                "diluted_oligo_plate/E1",
                "diluted_oligo_plate/F1",
                "diluted_oligo_plate/G1",
                "diluted_oligo_plate/H1",
                "diluted_oligo_plate/A2",
                "diluted_oligo_plate/B2"
            ],
            "polymerize_MM_vol": "2.2:microliter",
            "polymerize_MM_loc": "resource_plate/E1",
            "kunkel_number": 10,
            "reaction_start": "reaction_plate/A1"
        }
    }
    '''
    params = make_dottable_dict(params)

    kunkel_kinase(protocol, params)

    protocol.unseal("kinased_oligo_plate")

    kunkel_dilute(protocol, params)

    kunkel_anneal(protocol, params)

    protocol.unseal("reaction_plate")

    kunkel_polymerize(protocol, params)

"enzyme_4": "enzymes/D7",
            "cut_backbone": "destination_plate/A1",
            "cut_insert": "destination_plate/A2",
            "enzyme_vol": "3:microliter",
            "source_DNA_vol": "5:microliter",
            "buffer_vol": "1:microliter",
            "water_vol": "2:microliter",
            "digestion_time": "10:minute",
            "digestion_temp": "37:celsius",
            "deactivation_time": "5:minute",
            "deactivation_temp": "80:celsius"
        }
    }
    '''
    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    protocol.transfer(refs.backbone.well(0), params.cut_backbone, params.source_DNA_vol)
    protocol.transfer(refs.insert.well(0), params.cut_insert, params.source_DNA_vol)

    protocol.transfer(refs.dig_buffer.well(0), params.cut_insert, params.buffer_vol)
    protocol.transfer(refs.dig_buffer.well(0), params.cut_backbone, params.buffer_vol)

    protocol.transfer(refs.water.well(0), params.cut_backbone, params.water_vol)
    protocol.transfer(refs.water.well(0), params.cut_insert, params.water_vol)

    protocol.transfer(params.enzyme_1, params.cut_backbone, params.enzyme_vol)
    protocol.transfer(params.enzyme_2, params.cut_backbone, params.enzyme_vol,
        mix_after=True, mix_vol="5:microliter")
    protocol.transfer(params.enzyme_3, params.cut_insert, params.enzyme_vol,
        mix_after=True, mix_vol="5:microliter")
    protocol.transfer(params.enzyme_4, params.cut_insert, params.enzyme_vol,

"diluted_oligo_plate/0",
                "diluted_oligo_plate/1",
                "diluted_oligo_plate/2",
                "diluted_oligo_plate/3",
                "diluted_oligo_plate/4",
                "diluted_oligo_plate/5",
                "diluted_oligo_plate/6",
                "diluted_oligo_plate/7",
                "diluted_oligo_plate/8",
                "diluted_oligo_plate/9",
                "diluted_oligo_plate/10"
            ]
        }
    }
    '''
    params = make_dottable_dict(params)
    refs = make_dottable_dict(params.refs)

    reaction_wells = refs["reaction_plate"].wells_from(0,len(params.oligos), columnwise=True)

    protocol.distribute(params.ssDNA_mix_loc,reaction_wells, params.ssDNA_mix_vol)

    for oligo,reaction in zip(params.oligos,reaction_wells.wells):
        protocol.transfer(oligo,reaction,params.oligo_vol,mix_after=True)

    protocol.seal("reaction_plate")

    protocol.thermocycle_ramp("reaction_plate","95:celsius", "25:celsius", "60:minute", step_duration="4:minute")