func NewFrontend() (*Frontend, error) {
fe := &Frontend{}
eid, err := uuid.NewV4()
if err != nil {
return nil, err
}
// TODO need to shudown equipmentmanager here on error
fe.equipmentManager = equipmentManager.NewAnthaEquipmentManager(eid.String())
fee := equipmentManager.EquipmentManager(fe.equipmentManager)
equipmentManager.SetEquipmentManager(&fee)
mid, err := uuid.NewV4()
if err != nil {
return nil, err
}
md := manual.NewAnthaManual(mid.String())
mdd := equipment.Equipment(md)
fe.equipmentManager.RegisterEquipment(&mdd)
//cui logger middleware
fe.cui = md.Cui
cmw := middleware.NewLogToCui(&md.Cui)
logId, err := uuid.NewV4()
if err != nil {
return nil, err
}
fe.logger = logger.NewAnthaFileLogger(logId.String())
fe.logger.RegisterMiddleware(cmw)
var logRef logger.Logger
logRef = fe.logger
logger.SetLogger(&logRef)
var writer io.Writer
if len(logFile) > 0 {
w, err := os.OpenFile(logFile, os.O_WRONLY|os.O_CREATE, 0600)
if err != nil {
return nil, err
}
writer = w
} else {
writer = ioutil.Discard
}
fe.debugLogger = log.New(writer, "", log.LstdFlags)
return fe, 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)
}