// TASK: define output plates
// INPUT: "output_platetype", "outputs"
//OUTPUT: "output_plates" -- these each have components in wells
// "output_assignments" -- map with arrays of assignment strings, i.e. {tea: [plate1:A:1, plate1:A:2...] }etc.
func output_plate_setup(request *LHRequest) *LHRequest {
//(map[string]*wtype.LHPlate, map[string][]string) {
output_platetype := (*request).Output_platetype
if output_platetype == nil || output_platetype.ID == "" {
wutil.Error(errors.New("plate_setup: No output plate type defined"))
}
if (*request).Output_major_group_layouts == nil {
wutil.Error(errors.New("plate setup: Output major groups undefined"))
}
output_plates := (*request).Output_plates
if len(output_plates) == 0 {
output_plates = make(map[string]*wtype.LHPlate, len(request.Output_major_group_layouts))
}
// just assign based on number of groups
opl := request.Output_plate_layout
for i := 0; i < len(request.Output_major_group_layouts); i++ {
//p := wtype.New_Plate(request.Output_platetype)
p := factory.GetPlateByType(request.Output_platetype.Type)
output_plates[p.ID] = p
opl[i] = p.ID
name := fmt.Sprintf("Output_plate_%d", i+1)
p.PlateName = name
}
(*request).Output_plate_layout = opl
(*request).Output_plates = output_plates
return request
}
func (w *LHWell) Add(p Physical) {
switch t := p.(type) {
default:
wutil.Error(errors.New(fmt.Sprintf("LHWell: Cannot add type %T", t)))
case *LHSolution:
// do something
case *LHComponent:
w.WContents = append(w.WContents, p.(*LHComponent))
w.Currvol += p.(*LHComponent).Vol
p.(*LHComponent).LContainer = w
}
}
// TASK: Determine number of tip boxes of each type
// INPUT: instructions
//OUTPUT: arrays of tip boxes
func (lh *Liquidhandler) Tip_box_setup(request *LHRequest) *LHRequest {
tip_box_type := (*request).Tip_Type
if tip_box_type == nil || tip_box_type.ID == "" {
wutil.Error(errors.New("tip_box_setup: No tip_box type defined"))
}
tip_boxes := (*request).Tips
if len(tip_boxes) == 0 {
tip_boxes = make([]*wtype.LHTipbox, 0)
}
// the instructions are generated at this point so we just need to go through and count the tips used
// of each type
instrx := request.Instructions
ntips := make(map[string]int)
for _, ins := range instrx {
if ins.InstructionType() == lhdriver.LOD {
ttype := ins.GetParameter("TIPTYPE").([]string)[0]
ntips[ttype] += ins.GetParameter("MULTI").(int)
}
}
for tiptype, ntip := range ntips {
// need to make sure the names match up here
tbt := factory.GetTipByType(tiptype)
ntbx := ntip/tbt.NTips + 1
for i := 0; i < ntbx; i++ {
tbt2 := factory.GetTipByType(tiptype)
tip_boxes = append(tip_boxes, tbt2)
}
}
(*request).Tips = tip_boxes
// need to fix the tip situation in the properties structure
lh.Properties.RemoveTipBoxes()
for _, tb := range tip_boxes {
lh.Properties.AddTipBox(tb)
}
return request
}
func (lhc *LHComponent) Sample(v wunit.Volume) Liquid {
// need to jig around with units a bit here
// Should probably just make Vunit, Cunit etc. wunits anyway
meas := wunit.ConcreteMeasurement{lhc.Vol, wunit.ParsePrefixedUnit(lhc.Vunit)}
// we need some logic potentially
if v.SIValue() > meas.SIValue() {
wutil.Error(errors.New(fmt.Sprintf("LHComponent ID: %s Not enough volume for sample", lhc.ID)))
} else if v.SIValue() == meas.SIValue() {
return lhc
}
smp := CopyLHComponent(lhc)
// need a convention here
smp.Vol = v.RawValue()
smp.Vunit = v.Unit().PrefixedSymbol()
meas.Subtract(&v.ConcreteMeasurement)
lhc.Vol = meas.RawValue()
return smp
}
func AdvancedExecutionPlanner(request *LHRequest, parameters *liquidhandling.LHProperties) *LHRequest {
// in the first instance we assume this is done component-wise
// we also need to identify dependencies, i.e. if certain components
// are only available after other actions
// this will only work if the components to be added are to go in the same order
// get the layout groups
minorlayoutgroups := request.Output_minor_group_layouts
ass := request.Output_assignments
inass := request.Input_assignments
output_solutions := request.Output_solutions
input_plates := request.Input_plates
output_plate_layout := request.Output_plate_layout
plate_lookup := request.Plate_lookup
// highly inelegant... we should swap Tip Box Setup
// around to take place after, then this whole thing
// is a non-issue
tt := make([]*wtype.LHTip, 1)
tt[0] = request.Tip_Type.Tiptype
parameters.Tips = tt
instructions := liquidhandling.NewRobotInstructionSet(nil)
// need to deal with solutions
order := request.Input_order
for _, name := range order {
//fmt.Println(name)
// cmpa holds a list of inputs required per destination
// i.e. if destination X requires 15 ul of h2o this will be listed separately
// at this point all of the requests must be for volumes,
// we need a mapping from these to where they belong
// do we?
/*
cmpa:=value.([]map[string]interface{})
cmp_map:=make(map[string]interface{}, len(cmpa))
for _,cmp:=range cmpa{
srcid:=cmp.Srcid
cmp_map[srcid]=cmp
}
*/
for n, g := range minorlayoutgroups {
grp := []string(g)
// get the group assignment string
assignment := ass[n]
// the assignment has the format plateID:row:column:incrow:inccol
// where inc defines how the next one is to be calculated
// e.g. {GUID}:A:1:1:0
// {GUID}:A:1:0:1
asstx := strings.Split(assignment, ":")
plate := asstx[0]
toplatenum := wutil.ParseInt(plate)
row := wutil.AlphaToNum(asstx[1])
col := wutil.ParseInt(asstx[2])
incrow := wutil.ParseInt(asstx[3])
inccol := wutil.ParseInt(asstx[4])
whats := make([]string, len(grp))
pltfrom := make([]string, len(grp))
pltto := make([]string, len(grp))
plttypefrom := make([]string, len(grp))
plttypeto := make([]string, len(grp))
wellfrom := make([]string, len(grp))
wellto := make([]string, len(grp))
vols := make([]*wunit.Volume, len(grp))
fvols := make([]*wunit.Volume, len(grp))
tvols := make([]*wunit.Volume, len(grp))
for i, solID := range grp {
sol := output_solutions[solID]
// we need to get the relevant component out
smpl := get_aggregate_component(sol, name)
// we need to know where this component was assigned to
inassignmentar := []string(inass[name])
inassignment, ok := get_assignment(inassignmentar, &input_plates, smpl.Vol)
if !ok {
wutil.Error(errors.New(fmt.Sprintf("No input assignment for %s with vol %-4.1f", name, smpl.Vol)))
}
inasstx := strings.Split(inassignment, ":")
inplt := inasstx[0]
inrow := string(inasstx[1])
incol := wutil.ParseInt(inasstx[2])
// we can fill the structure now
whats[i] = name
pltfrom[i] = plate_lookup[string(inplt)]
pltto[i] = plate_lookup[output_plate_layout[toplatenum]]
wellfrom[i] = inrow + strconv.Itoa(incol)
wellto[i] = wutil.NumToAlpha(row) + strconv.Itoa(col)
v := wunit.NewVolume(smpl.Vol, smpl.Vunit)
v2 := wunit.NewVolume(0.0, "ul")
vols[i] = &v
// TODO Get the proper volumes here
fvols[i] = &v2
tvols[i] = &v2
row += incrow
col += inccol
}
ins := liquidhandling.NewTransferInstruction(whats, pltfrom, pltto, wellfrom, wellto, plttypefrom, plttypeto, vols, fvols, tvols /*, parameters.Cnfvol*/)
instructions.Add(ins)
}
}
inx := instructions.Generate(request.Policies, parameters)
instrx := make([]liquidhandling.TerminalRobotInstruction, len(inx))
for i := 0; i < len(inx); i++ {
instrx[i] = inx[i].(liquidhandling.TerminalRobotInstruction)
}
request.Instructions = instrx
return request
}
func solution_setup(request *LHRequest, prms *liquidhandling.LHProperties) (map[string]*wtype.LHSolution, map[string]float64) {
solutions := request.Output_solutions
// index of components used to make up to a total volume, along with the required total
mtvols := make(map[string][]float64, 10)
// index of components with concentration targets, along with the target concentrations
mconcs := make(map[string][]float64, 10)
// keep a list of components which have fixed stock concentrations
fixconcs := make([]*wtype.LHComponent, 0)
// maximum solubilities of each component
Smax := make(map[string]float64, 10)
// maximum total volume of any solution containing each component
hshTVol := make(map[string]float64)
// find the minimum and maximum required concentrations
// across all the solutions
for _, solution := range solutions {
components := solution.Components
// we need to identify the concentration components
// and the total volume components, if we have
// concentrations but no tvols we have to return
// an error
arrCncs := make([]*wtype.LHComponent, 0, len(components))
arrTvol := make([]*wtype.LHComponent, 0, len(components))
cmpvol := 0.0
totalvol := 0.0
for _, component := range components {
// what sort of component is it?
conc := component.Conc
tvol := component.Tvol
if conc != 0.0 {
arrCncs = append(arrCncs, component)
} else if tvol != 0.0 {
tv := component.Tvol
if totalvol == 0.0 || totalvol == tv {
totalvol = tv
} else {
// error
wutil.Error(errors.New(fmt.Sprintf("Inconsistent total volumes %-6.4f and %-6.4f at component %s", totalvol, tv, component.Name)))
}
} else {
cmpvol += component.Vol
}
}
// add everything to the maps
for _, cmp := range arrCncs {
nm := cmp.CName
cnc := cmp.Conc
_, ok := Smax[nm]
if !ok {
Smax[nm] = cmp.Smax
}
if cmp.StockConcentration != 0.0 {
fixconcs = append(fixconcs, cmp)
continue
}
var cncslc []float64
cncslc, ok = mconcs[nm]
if !ok {
cncslc = make([]float64, 0, 10)
}
cncslc = append(cncslc, cnc)
mconcs[nm] = cncslc
_, ok = hshTVol[nm]
if !ok || hshTVol[nm] > totalvol {
hshTVol[nm] = totalvol
}
}
// now the total volumes
for _, cmp := range arrTvol {
nm := cmp.CName
tvol := cmp.Tvol
var tvslc []float64
tvslc, ok := mtvols[nm]
if !ok {
tvslc = make([]float64, 0, 10)
}
tvslc = append(tvslc, tvol)
mtvols[nm] = tvslc
}
} // end solutions
// so now we should be able to make stock concentrations
// first we need the min and max for each
minrequired := make(map[string]float64, len(mconcs))
maxrequired := make(map[string]float64, len(mconcs))
//TODO this needs to be migrated elsewhere
var vmin wunit.Volume = wunit.NewVolume(1.0, "ul")
if prms.CurrConf != nil {
vmin = *(prms.CurrConf.Minvol)
}
for cmp, arr := range mconcs {
min := wutil.FMin(arr)
max := wutil.FMax(arr)
minrequired[cmp] = min
maxrequired[cmp] = max
// if smax undefined we need to deal - we assume infinite solubility!!
_, ok := Smax[cmp]
if !ok {
Smax[cmp] = 9999999
wutil.Warn(fmt.Sprintf("Max solubility undefined for component %s -- assuming infinite solubility!", cmp))
}
}
stockconcs := choose_stock_concentrations(minrequired, maxrequired, Smax, vmin.RawValue(), hshTVol)
// handle any errors here
// add the fixed concentrations into stockconcs
for _, cmp := range fixconcs {
stockconcs[cmp.CName] = cmp.StockConcentration
}
// nearly there now! Need to turn all the components into volumes, then we're done
// make an array for the new solutions
newSolutions := make(map[string]*wtype.LHSolution, len(solutions))
for _, solution := range solutions {
components := solution.Components
arrCncs := make([]*wtype.LHComponent, 0, len(components))
arrTvol := make([]*wtype.LHComponent, 0, len(components))
arrSvol := make([]*wtype.LHComponent, 0, len(components))
cmpvol := 0.0
totalvol := 0.0
totalvolunit := ""
for _, component := range components {
// what sort of component is it?
// what is the total volume ?
if component.Conc != 0.0 {
arrCncs = append(arrCncs, component)
} else if component.Tvol != 0.0 {
arrTvol = append(arrTvol, component)
tv := component.Tvol
totalvolunit = component.Vunit
if totalvol == 0.0 || totalvol == tv {
totalvol = tv
} else {
// error
wutil.Error(errors.New(fmt.Sprintf("Inconsistent total volumes %-6.4f and %-6.4f at component %s", totalvol, tv, component.Name)))
}
} else {
// need to add in the volume taken up by any volume components
cmpvol += component.Vol
arrSvol = append(arrSvol, component)
}
}
// first we add the volumes to the concentration components
arrFinalComponents := make([]*wtype.LHComponent, 0, len(components))
for _, component := range arrCncs {
name := component.CName
cnc := component.Conc
vol := totalvol * cnc / stockconcs[name]
cmpvol += vol
component.Vol = vol
component.Vunit = totalvolunit
component.StockConcentration = stockconcs[name]
arrFinalComponents = append(arrFinalComponents, component)
}
// next we get the final volume for total volume components
for _, component := range arrTvol {
vol := totalvol - cmpvol
component.Vol = vol
arrFinalComponents = append(arrFinalComponents, component)
}
// then we add the rest
arrFinalComponents = append(arrFinalComponents, arrSvol...)
// finally we replace the components in this solution
solution.Components = arrFinalComponents
// and put the new solution in the array
newSolutions[solution.ID] = solution
}
return newSolutions, stockconcs
}
