refill peripheral fix

--slots = textutils.unserialize( fs.open("slots","r").readAll() )
--nObjective = 1
--instructions = textutils.unserialize( fs.open("instructions","r").readAll() )



--instructions[n] = {x,y,z,id,data}

function getLength(checklist)
    local c = 0
    for i,v in pairs(checklist) do
        for k,l in pairs(v) do
            if l then
                c = c + 1
            end
        end
    end
    return c
end

function getSlotsUsed(checklist)
    local c = 0
    local count = 0
    for id,table in pairs(checklist) do
        for data,count in pairs(table) do
            c = c + math.ceil(count/64)
        end
    end
    return c
end

function sort()
    items = {}
    for i = 1,16 do
        local item = turtle.getItemDetail(i)
        if item then
            local pSlot = nil
            if items[item.name] then
                pSlot = items[item.name][item.damage]
            end
            if pSlot then
                turtle.select(i)
                turtle.transferTo(pSlot)
                if turtle.getItemCount(pSlot) == 64 then
                    if turtle.getItemCount(i) > 0 then
                        items[item.name][item.damage] = i
                    else
                        items[item.name][item.damage] = nil
                    end
                end
            elseif turtle.getItemCount(i) < 64 then
                if not items[item.name] then
                    items[item.name] = {}
                end
                items[item.name][item.damage] = i
            end
        end
    end
end

local function add2checklist(checklist,name,damage,slots_available)
    --checklist[id][data] = count version
    --INPUT: item, checklist
    --OUTPUT: added to checklist if there's space
    slots_available = slots_available or 15
    local numCheckList = getSlotsUsed(checklist)

    if name == nil then
        return checklist
    end

    if checklist[name] and checklist[name][damage] then
        checklist[name][damage] = checklist[name][damage] + 1
        if getSlotsUsed(checklist) > slots_available then
            checklist[name][damage] = checklist[name][damage] - 1
            return checklist,true
        else
            return checklist
        end
    end

    if numCheckList < slots_available then
        if checklist[name] then
            checklist[name][damage] = 1
        else
            checklist[name] = {}
            checklist[name][damage] = 1
        end
    else
        --error("checklist full")
        return checklist,true
    end
    return checklist
end

function checklistMaker(nObjective,instructions,slots)
    --INPUT: nObjective,instructions,slots
    --OUTPUT: next 15 invo spaces worth of blocks required in checklist[id][data] = count
    local checklist = {}

    for i = nObjective,#instructions do
        local name,damage  = unpack(slots[ instructions[i][4] ][ instructions[i][5] ])
        checklist,bFull = add2checklist(checklist,name,damage,15)
        if bFull then
            return checklist
        end
    end

    return checklist
end

local function insert_rubbish(rubbishList,id,data,count)
    if not id then
            return
    end
    if not rubbishList[id] then
        rubbishList[id]= {}
    end
    if not rubbishList[id][data] then
        rubbishList[id][data] = 0
    end
    rubbishList[id][data] = rubbishList[id][data] + count
    return rubbishList
end

local function flatten_checklist(checklist,rubbishList)
    --get rid of negative count in checklist
    for id,table in pairs(checklist) do
        for data,count in pairs(table) do
            if count < 0 then
                rubbishList = insert_rubbish(rubbishList,id,data,math.abs(count))
                checklist[id][data] = 0
            end
        end
    end
    return checklist,rubbishList
end

function subtractInventory(checklist)
    local rubbishList = {}
    for i = 1,16 do
        local deets = turtle.getItemDetail(i)

        if deets then
            if checklist[deets.name] and checklist[deets.name][deets.damage] then
                checklist[deets.name][deets.damage] = checklist[deets.name][deets.damage] - deets.count
            elseif (not deets.name:lower():find("wrench")) and (not deets.name:lower():find("hammer")) then
            --not a wrench, not on the list
                insert_rubbish(rubbishList,deets.name,deets.damage,deets.count)
            end
        end
    end
    checklist,rubbishList = flatten_checklist(checklist,rubbishList)
    return checklist,rubbishList
end

function find_in_turtle(id,data)
    for i = 1,16 do
        local deets = turtle.getItemDetail(i)
        if deets and (deets.name == id and deets.damage == data) then
            return i,deets.count
        end
    end
    return nil
end

function throw_away(rubbishList,intoSlot)
    for id,table in pairs(rubbishList) do
        for data,count in pairs(table) do
            if count > 0 then
                local slot, amount = find_in_turtle(id,data)
                if amount >= count then
                    --peripheral.call("bottom","pushItem","down",slot,count,intoSlot)
                    rubbishList[id][data] = 0
                else
                    local mem = turtle.getSelectedSlot()
                    while amount < count do
                        local i,amount_transferred = find_in_turtle(id,data)
                        if i then
                            turtle.select(i)
                            turtle.transferTo(mem)
                            local remainder = turtle.getItemCount()
                            amount = amount + (amount_transferred-remainder)
                        end

                    end
                    turtle.select(mem)
                end
            --pushItem(direction,slot,maxAmount?,intoSlot?)
            peripheral.call("bottom","pushItem","down",slot,amount,intoSlot)
            end
        end
    end
end



function save(table,filename)
    local h = fs.open(filename,"w")
    if fs.exists("textutilsFIX") then
        os.loadAPI("textutilsFIX")
        h.write(textutilsFIX.serialize(table))
    else
        h.write(textutils.serialize(table))
    end
    h.close()
end
--throwAway file

function db(entity,name)
    local h = fs.open("console","a")
    name = name or ""
    os.loadAPI("textutilsFIX")
    if type(entity) == "table" then
        h.writeLine(name..": "..textutilsFIX.serialize(table))
    else
        h.writeLine(name..": "..tostring(entity))
    end
    h.close()
end

function find_in_turtle(id,data)
    for i = 1,16 do
        local deets = turtle.getItemDetail(i)
        if deets and (deets.name == id and deets.damage == data) then
            return i,deets.count
        end
    end
    return nil
end

function findEmptySlots(chest)
    local randomTable = {}
    for i,v in pairs(chest) do
        table.insert(randomTable,i)
    end
    return #randomTable
end

function findEmptySlotsOLD(chest,inv)
    local emptySlots = 0
    for i = 1,inv do
        if chest[i] == nil then
            emptySlots = emptySlots + 1
        end
    end
    return emptySlots
end

function throwAway2(rubbishList,chest,invType)
    local emptySlots = findEmptySlots(chest)
    assert(emptySlots)
    --print("emptySlots = ",emptySlots)
    for i = 1,16 do
        local count = nil
        local deets = turtle.getItemDetail(i)
        if rubbishList and deets and rubbishList[deets.name] then
            count = rubbishList[deets.name][deets.damage]
        end
        if (count and count > 0) and (emptySlots > 0 or invType == "TileInterface") then
            turtle.select(i)
            local amount = turtle.getItemCount(i)
            if amount > count then
                turtle.dropDown(count)
                count = 0
            elseif count <= 64 then
                turtle.dropDown(count)
                count = 0
            else
                turtle.dropDown()
                count = count - 64
            end
            emptySlots = emptySlots - 1
            rubbishList[deets.name][deets.damage] = count
        end
    end
    return rubbishList
end

function take(chest_slot,amount,me,chest)
    sort()
    if me then
        peripheral.call("bottom","exportItem",chest[chest_slot].fingerprint,"up",amount)
    else
        peripheral.call("bottom","pushItem","up",chest_slot,amount)
    end
end

function take2(chest_slot,amount)
    assert(chest_slot)
    amount = amount or 64
    peripheral.call("bottom","swapStacks",chest_slot,1)
    turtle.suckDown(amount)
end

function pullBlocks(checklist,chest,invType)
    local me = false
    if invType == "TileInterface" then
        me = true
    end
    assert(checklist)
    assert(chest)
    for chest_slot,func in pairs(chest) do
        local name,damage,qty
        if me then
            name = func.fingerprint.id
            damage = func.fingerprint.dmg
            qty = func.size
        else
            name = func.basic().id
            db(name,chest_slot)
            damage = func.basic().dmg
            db(damage,"dmg")
            qty = func.basic().qty
            db(qty,"qty")
        end
        local checklist_count = nil
        if checklist and checklist[name] then
            checklist_count = checklist[name][damage]
        end
        if checklist_count and checklist_count > 0 then
            if checklist_count <= qty then
                --take checklist_count amount
                take(chest_slot,checklist_count,me,chest)
                checklist_count = 0
                db(name,"    name")
                db(checklist_count,"    checklist_count")
                db(qty,"    qty")
            elseif checklist_count>=64 then
                --take 64
                take(chest_slot,64,me,chest)
                checklist_count = checklist_count - 64
                db(name,"    name")
                db(checklist_count,"    checklist_count")
                db(qty,"    qty")
            elseif checklist_count > qty then
                --take qty
                take(chest_slot,qty,me,chest)
                checklist_count = checklist_count - qty
                db(name,"    name")
                db(checklist_count,"    checklist_count")
                db(qty,"    qty")
            else
                db(name,"    NOT COUNTED")
                db(damage)
                db(qty)
            end


            checklist[name][damage] = checklist_count
        end
    end
    return checklist
end

function check_chests(checklist,rubbishList)
    goto(reference.finalx+1,reference.returny,reference.returnz)
    goto(reference.returnx,reference.returny,reference.returnz)

    local i = 1
    local noInvo = 0
    local numChests = 0
    while true do
        goto(reference.returnx,reference.returny,reference.returnz-i+1)

        local invType = false
        local lookSee,lookData = turtle.inspectDown()
        if lookSee then
            if lookData.name:find("chest") then
                invType = true
            elseif lookData.name:find("tile.BlockInterface") then
                invType = "TileInterface"
            end
        end


        if invType then
            local bool,chest
            if invType == "TileInterface" then
                bool,chest = pcall(peripheral.call,"bottom","getAvailableItems")
            else
                bool,chest = pcall(peripheral.call,"bottom","getAllStacks")
            end
            if not bool then
                print(chest)
                if invType == "TileInterface" then
                    turtle.select(1)
                    turtle.dropDown(64)
                    turtle.digDown()
                    turtle.placeDown()
                    sleep(0.5)
                end
                os.reboot()
            end
            rubbishList = throwAway2(rubbishList,chest,invType)
            checklist = pullBlocks(checklist,chest,invType)
            noInvo = 0
            numChests = numChests + 1
            if invType == "TileInterface" and not reference.numChests then
                reference.numChests = numChests
                updateVar(reference.filename,"reference.numChests",numChest)
                break
            end

            if reference.numChests == numChests then
                --print("ok stop here")
                break
            end

        else
            noInvo = noInvo + 1
            if noInvo == 2 and numChests == 0 then
                error("needs refill chest within 2 blocks behind start location under the turtle")
            end
            if noInvo == 3 then
                reference.numChests = numChests
                updateVar(reference.filename,"reference.numChests",numChest) --needs testing
                break
            end
        end

        i = i + 1
    end
    save(rubbishList,"rubbishList")
    save(checklist,"checklist")
    --local x,y,z,id,data = unpack(instructions[nObjective])
    --goto(reference.finalx+1,y,z)
end


--checklist = checklistMaker(1,instructions,slots)
--checklist, rubbishList = subtractInventory(checklist)

--save(checklist,"checklist")
--save(rubbishList,"rubbishList")