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)
}
// Transfer fields from conf to params instantiating certain fields from a
// factory. conf is like the type of params but with wtype.FromFactory entries
// for certain fields/elements. Assign values of conf to params. Use
// factory.GetComponentByType to instantiate FromFactory instances and assign
// them to the appropriate entry in params.
//
// Assumes that params is a nil instance and conf is like type of params but
// with some values as FromFactory rather than the appropriate interface type
func (p *Config) transfer(cv reflect.Value, pv reflect.Value) error {
factoryType := reflect.TypeOf(wtype.FromFactory{})
ct := cv.Type()
pt := pv.Type()
switch {
case ct.AssignableTo(pt):
pv.Set(cv)
case ct == factoryType:
v := cv.Interface().(wtype.FromFactory)
terms := strings.Split(v.String, ":")
if len(terms) != 2 {
return fmt.Errorf("cannot parse factory string: %s", v.String)
}
var newV interface{}
switch terms[0] {
case "component":
newV = factory.GetComponentByType(terms[1])
case "tipbox":
newV = factory.GetTipboxByType(terms[1])
case "plate":
newV = factory.GetPlateByType(terms[1])
default:
return fmt.Errorf("cannot parse factory string: %s", v.String)
}
nv := reflect.ValueOf(newV)
nt := nv.Type()
if !nt.AssignableTo(pt) {
return fmt.Errorf("cannot convert %v to %v", nt, pt)
}
pv.Set(nv)
default:
pk := pt.Kind()
ck := ct.Kind()
if pk != ck {
return fmt.Errorf("cannot convert %v to %v", ct, pt)
}
switch ck {
case reflect.Slice:
cvl := cv.Len()
newSlice := reflect.MakeSlice(pt, cvl, cvl)
pv.Set(newSlice)
for i := 0; i < cvl; i += 1 {
if err := p.transfer(cv.Index(i), pv.Index(i)); err != nil {
return err
}
}
case reflect.Map:
newMap := reflect.MakeMap(pt)
pv.Set(newMap)
for _, key := range cv.MapKeys() {
if err := p.transfer(pv.MapIndex(key), pv.MapIndex(key)); err != nil {
return err
}
}
case reflect.Struct:
ctn := ct.NumField()
for i := 0; i < ctn; i += 1 {
if err := p.transfer(cv.Field(i), pv.Field(i)); err != nil {
return err
}
}
case reflect.Ptr:
if err := p.transfer(cv.Elem(), pv.Elem()); err != nil {
return err
}
default:
return fmt.Errorf("cannot convert %v to %v", ct, pt)
}
}
return nil
}
func NewWrapper(threadID execute.ThreadID) *Wrapper {
w := &Wrapper{}
w.tipType = factory.GetTipboxByType("Gilson50") // TODO use real configuration
w.threadID = threadID
return w
}