func Steps(params Parameters, inputs Inputs) Outputs {
var outputs Outputs
ctx := execution.GetContext()
em := ctx.EquipmentManager
rqout := em.MakeDeviceRequest("liquidhandler", "Manual")
response := <-rqout
// handle response problems
if response["status"] == "FAIL" {
log.Fatal("Error requesting liquid handler service")
}
liquidhandler := response["devicequeue"].(*execution.LiquidHandlingService)
samples := make([]*wtype.LHComponent, 0)
buffersample := mixer.SampleForTotalVolume(inputs.Buffer, params.Reactionvolume)
samples = append(samples, buffersample)
atpsample := mixer.Sample(inputs.ATP, params.Atpvol)
samples = append(samples, atpsample)
vectorsample := mixer.SampleForConcentration(inputs.Vector, params.Vectorconc)
samples = append(samples, vectorsample)
for _, part := range inputs.Parts {
partsample := mixer.SampleForConcentration(part, params.Partconc)
samples = append(samples, partsample)
}
resample := mixer.Sample(inputs.RestrictionEnzyme, params.Revol)
samples = append(samples, resample)
ligsample := mixer.Sample(inputs.Ligase, params.Ligvol)
samples = append(samples, ligsample)
reaction := mixer.MixInto(inputs.Outplate, samples...)
// set the block ID
reaction.BlockID = string(params.BlockID)
rq2 := liquidhandler.MakeMixRequest(reaction)
if rq2 == nil {
log.Fatal("Error running liquid handling request")
}
rq2.Tip_Type = inputs.TipType
liquidhandler.Run()
// incubate the reaction mixtures
incubate(reaction, params.Reactiontemp, params.Reactiontime, false)
// inactivate
incubate(reaction, params.Inactivationtemp, params.Inactivationtime, false)
// all done
outputs.Reaction = reaction
return outputs
}
// Runs a workflow for one sample
func (w *Workflow) Run(cf *Config) ([]interface{}, error) {
id, err := uuid.NewV4()
if err != nil {
return nil, err
}
tid := execute.ThreadID(id.String())
ctx := execution.GetContext()
ctx.ConfigService.SetConfig(tid, cf.Config)
wr, err := NewWorkflowRun(*id, w, cf)
if err != nil {
return nil, err
}
var errors []error
go func() {
for v := range wr.Errors {
if v != nil {
errors = append(errors, v)
}
}
}()
var messages []interface{}
go func() {
for v := range wr.Messages {
// messages = append(messages, fmt.Sprintf("%v", v.Value))
messages = append(messages, v.Value)
}
}()
<-wr.Done
if len(errors) > 0 {
return messages, Errors(errors)
}
return messages, nil
}
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)
}
