// default setup agent
func BasicSetupAgent(request *LHRequest, params *liquidhandling.LHProperties) *LHRequest {
// this is quite tricky and requires extensive interaction with the liquid handling
// parameters
// the principal question is how to define constraints on the system
// I think this needs to remain tbd for now
// instead we can rely on the preference system I already use
plate_lookup := make(map[string]string, 5)
tip_lookup := make([]*wtype.LHTipbox, 0, 5)
tip_preferences := params.Tip_preferences
input_preferences := params.Input_preferences
output_preferences := params.Output_preferences
// how do we set the below?
// we don't know how many tips we need until we generate
// instructions; ditto input or output plates until we've done layout
// input plates
input_plates := request.Input_plates
// output plates
output_plates := request.Output_plates
// tips
tips := request.Tips
// we put tips on first
setup := request.Setup
if len(setup) == 0 {
setup = wtype.NewLHSetup()
}
for _, tb := range tips {
// get the first available position from the preferences
pos := get_first_available_preference(tip_preferences, setup)
if pos == -1 {
RaiseError("No positions left for tipbox")
}
position := "position_" + strconv.Itoa(pos)
setup[position] = tb
plate_lookup[tb.ID] = position
tip_lookup = append(tip_lookup, tb)
}
setup["tip_lookup"] = tip_lookup
// this logic may not transfer well but I expect that outputs are more constrained
// than inputs for the simple reason that most output takes place to single wells
// while input takes place from reservoirs
// outputs
for _, p := range output_plates {
pos := get_first_available_preference(output_preferences, setup)
if pos == -1 {
RaiseError("No positions left for output")
}
position := "position_" + strconv.Itoa(pos)
setup[position] = p
plate_lookup[p.ID] = position
params.AddPlate(position, p)
}
// inputs
for _, p := range input_plates {
pos := get_first_available_preference(input_preferences, setup)
if pos == -1 {
RaiseError("No positions left for input")
}
position := "position_" + strconv.Itoa(pos)
setup[position] = p
plate_lookup[p.ID] = position
params.AddPlate(position, p)
}
request.Setup = setup
request.Plate_lookup = plate_lookup
return request
}
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
}