func (req *LHRequest) UnmarshalJSON(ar []byte) error {
var slhr SLHRequest
e := json.Unmarshal(ar, req)
fmt.Println("ERR: ", e)
e = json.Unmarshal(ar, slhr)
req.Input_major_group_layouts = make(map[int][]string, len(slhr.Input_major_group_layouts))
for k, v := range slhr.Input_major_group_layouts {
req.Input_major_group_layouts[wutil.ParseInt(k)] = v
}
req.Input_plate_layout = make(map[int]string, len(slhr.Input_plate_layout))
for k, v := range slhr.Input_plate_layout {
req.Input_plate_layout[wutil.ParseInt(k)] = v
}
req.Output_major_group_layouts = make(map[int][]string, len(slhr.Output_major_group_layouts))
for k, v := range slhr.Output_major_group_layouts {
req.Output_major_group_layouts[wutil.ParseInt(k)] = v
}
req.Output_plate_layout = make(map[int]string, len(slhr.Output_plate_layout))
for k, v := range slhr.Output_plate_layout {
req.Output_plate_layout[wutil.ParseInt(k)] = v
}
return e
}
func Get_Next_Well(plate *LHPlate, component *LHComponent, curwell *LHWell) (*LHWell, bool) {
nrow, ncol := 0, 1
vol := component.Vol
if curwell != nil {
// quick check to see if we have room
vol_left := get_vol_left(curwell)
if vol_left >= vol {
// fine we can just return this one
return curwell, true
}
// we need a defined traversal of the wells
crds := curwell.Crds
tx := strings.Split(crds, ":")
nrow = wutil.AlphaToNum(tx[0])
ncol = wutil.ParseInt(tx[1])
}
wellsx := plate.WlsX
wellsy := plate.WlsY
var new_well *LHWell
for {
nrow, ncol = next_well_to_try(nrow, ncol, wellsy, wellsx)
if nrow == -1 {
return nil, false
}
crds := wutil.NumToAlpha(nrow) + ":" + strconv.Itoa(ncol)
new_well = plate.Wellcoords[crds]
cnts := new_well.WContents
if len(cnts) == 0 {
break
}
cont := cnts[0].Name()
if cont != component.Name() {
continue
}
vol_left := get_vol_left(new_well)
if vol < vol_left {
break
}
}
return new_well, true
}
func MakeWellCoordsXY(xy string) WellCoords {
tx := strings.Split(xy, "Y")
x := wutil.ParseInt(tx[0][1:len(tx[0])]) - 1
y := wutil.ParseInt(tx[1]) - 1
return WellCoords{x, y}
}
// make well coordinates in a manner compatble with "X1,Y1" etc.
func MakeWellCoordsXYsep(x, y string) WellCoords {
return WellCoords{wutil.ParseInt(y[1:len(y)]) - 1, wutil.ParseInt(x[1:len(x)]) - 1}
}
// make well coordinates in the "1A" convention
func MakeWellCoords1A(a1 string) WellCoords {
// only handles 96 well plates
return WellCoords{AlphaToNum(string(a1[0])) - 1, wutil.ParseInt(a1[1:len(a1)]) - 1}
}
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
}