// make the initial matter library. This will eventually be deprecated.
func MakeMatterLib() map[string]GenericMatter {
mtypes := []string{"polypropylene", "polycarbonate", "ptfe", "glass", "steel", "water", "glycerol", "ethanol", "surfactant", ""}
mps := []float64{160.0, 292.0, 326.8, 1000.0, 1370.0, 0, 17.8, -114.0, 0.0, 0.0}
bps := []float64{100000.0, 100000.0, 100000.0, 100000.0, 1000000.0, 100.0, 290.0, 78.37, 100.0, 0.0}
shcs := []float64{900.0, 1200.0, 1300.0, 840.0, 420.0, 4181.0, 221.9, 2.46, 4181.0, 1.0}
matter_map := make(map[string]GenericMatter, len(mtypes))
// the following is necessary since we need an immutable pointer
degreesc := "˚C"
for i, t := range mtypes {
mp := wunit.NewTemperature(mps[i], degreesc)
bp := wunit.NewTemperature(bps[i], degreesc)
shc := wunit.NewSpecificHeatCapacity(shcs[i], "J/kg")
gm := GenericMatter{mtypes[i], mp, bp, shc}
matter_map[t] = gm
}
return matter_map
}
func main() {
eid, _ := uuid.NewV4()
em := equipmentManager.NewAnthaEquipmentManager(eid.String())
defer em.Shutdown()
eem := equipmentManager.EquipmentManager(em)
equipmentManager.SetEquipmentManager(&eem)
//manual driver equipment
mid, _ := uuid.NewV4()
var mde equipment.Equipment
var amd manual.AnthaManual
amd = *manual.NewAnthaManual(mid.String())
mde = amd
em.RegisterEquipment(&mde)
//cui logger middleware
cmw := middleware.NewLogToCui(&amd.Cui)
log_id, _ := uuid.NewV4()
l := logger.NewAnthaFileLogger(log_id.String())
l.RegisterMiddleware(cmw)
var params Parameters
var inputs Inputs
// give this thing an arbitrary ID for testing
id := execute.ThreadID(fmt.Sprintf("EXPERIMENT_1_%s", string(eid.String()[1:5])))
fmt.Println(id)
// set up parameters and inputs
params.Reactionvolume = wunit.NewVolume(20, "ul")
params.Partconc = wunit.NewConcentration(0.0001, "g/l")
params.Vectorconc = wunit.NewConcentration(0.001, "g/l")
params.Atpvol = wunit.NewVolume(1, "ul")
params.Revol = wunit.NewVolume(1, "ul")
params.Ligvol = wunit.NewVolume(1, "ul")
params.Reactiontemp = wunit.NewTemperature(25, "C")
params.Reactiontime = wunit.NewTime(1800, "s")
params.Inactivationtemp = wunit.NewTemperature(40, "C")
params.Inactivationtime = wunit.NewTime(60, "s")
params.BlockID = id
inputs.Parts = make([]*wtype.LHComponent, 4)
for i := 0; i < 4; i++ {
inputs.Parts[i] = factory.GetComponentByType("dna_part")
inputs.Parts[i].CName = inputs.Parts[i].CName + "_" + strconv.Itoa(i+1)
}
inputs.Vector = factory.GetComponentByType("standard_cloning_vector_mark_1")
inputs.RestrictionEnzyme = factory.GetComponentByType("SapI")
inputs.Ligase = factory.GetComponentByType("T4Ligase")
inputs.Buffer = factory.GetComponentByType("CutsmartBuffer")
inputs.ATP = factory.GetComponentByType("ATP")
inputs.Outplate = factory.GetPlateByType("pcrplate")
inputs.TipType = factory.GetTipboxByType("Gilson50")
ctx := execution.GetContext()
conf := make(map[string]interface{})
conf["MAX_N_PLATES"] = 1.5
conf["MAX_N_WELLS"] = 12.0
conf["RESIDUAL_VOLUME_WEIGHT"] = 1.0
conf["SQLITE_FILE_IN"] = "/Users/msadowski/synthace/protocol_language/checkout/synthace-antha/anthalib/driver/liquidhandling/pm_driver/default.sqlite"
conf["SQLITE_FILE_OUT"] = "/tmp/output_file.sqlite"
ctx.ConfigService.SetConfig(id, conf)
outputs := Steps(params, inputs)
fmt.Println(outputs.Reaction)
}
func NewGenericPhysical(mattertype string) GenericPhysical {
gp := GenericPhysical{MatterByName(mattertype), mattertype, wunit.NewMass(0.0, "g"), wunit.NewVolume(0.0, "L"), wunit.NewTemperature(0.0, "˚C")}
return gp
}