-- BeeAlverizer 1 fork of BeeAnalyzer 4
-- Original code by Direwolf20
-- Hotfix 1 by Mandydax
-- Hotfix 2 by Mikeyhun/MaaadMike

-- Major overhaul to make work without turtle by Damaged

-- attribute scoring for same species tie-breaking -----------------------------

local allBeeData = {}
local princessSlot = 0
alveary = peripheral.wrap("back")
analyzer = peripheral.wrap("left")
memoryChest = peripheral.wrap("top")

function getCountInMemoryChest(i)
   stackData = memoryChest.getStackInSlot(i)
   return stackData.qty
end

scoresFertility = {
   [1] = 0.1,
   [2] = 0.2,
   [3] = 0.3,
   [4] = 0.4
}
scoresSpeed = {
   ["0.3"] = 0.01, -- Slowest
   ["0.6"] = 0.02, -- Slower
   ["0.8"] = 0.03, -- Slow
   ["1"]   = 0.04, -- Normal
   ["1.2"] = 0.05, -- Fast
   ["1.4"] = 0.06, -- Faster
   ["1.7"] = 0.07  -- Fastest
}
scoresAttrib = {
   diurnal       = 0.004,
   nocturnal     = 0.003,
   tolerantFlyer = 0.002,
   caveDwelling  = 0.0001
}
scoresTolerance = {
   ["NONE"]   = 0.00000,
   ["UP 1"]   = 0.00001,
   ["UP 2"]   = 0.00002,
   ["UP 3"]   = 0.00003,
   ["UP 4"]   = 0.00004,
   ["UP 5"]   = 0.00005,
   ["DOWN 1"] = 0.00001,
   ["DOWN 2"] = 0.00002,
   ["DOWN 3"] = 0.00003,
   ["DOWN 4"] = 0.00004,
   ["DOWN 5"] = 0.00005,
   ["BOTH 1"] = 0.00002,
   ["BOTH 2"] = 0.00004,
   ["BOTH 3"] = 0.00006,
   ["BOTH 4"] = 0.00008,
   ["BOTH 5"] = 0.00010
}

-- the bee graph ---------------------------------------------------------------

bees = {}

function addParent(parent, offspring)
   if bees[parent] then
      bees[parent].mutateTo[offspring] = true
      else
      bees[parent] = {
         --name = parent,
         score = nil,
         mutateTo = {[offspring]=true},
         mutateFrom = {}
      }
   end
end

function addOffspring(offspring, parentss)
   if bees[offspring] then
      for i, parents in ipairs(parentss) do
         table.insert(bees[offspring].mutateFrom, parents)
      end
      else
      bees[offspring] = {
         score = nil,
         mutateTo = {},
         mutateFrom = parentss
      }
   end
   for i, parents in ipairs(parentss) do
      for i, parent in ipairs(parents) do
         addParent(parent, offspring)
      end
   end
end

-- score bees that have no parent combinations as 1
-- iteratively find the next bee up the line and increase the score
function scoreBees()
   -- find all bees with no mutateFrom data
   local beeCount = 0
   local beeScore = 1
   for name, beeData in pairs(bees) do
      if #beeData.mutateFrom == 0 then
         beeData.score = beeScore
         else
         beeCount = beeCount + 1
      end
   end
   while beeCount > 0 do
      beeScore = beeScore * 2
      -- find all bees where all parent combos are scored
      for name, beeData in pairs(bees) do
         if not beeData.score then
            local scoreBee = true
            for i, beeParents in ipairs(beeData.mutateFrom) do
               local parent1 = bees[beeParents[1]]
               local parent2 = bees[beeParents[2]]

               if not parent1.score
                  or parent1.score == beeScore
                  or not parent2.score
                  or parent2.score == beeScore then
                  scoreBee = false
                  break
               end
            end
            if scoreBee then
               beeData.score = beeScore
               beeCount = beeCount - 1
            end
         end
      end
   end
end

-- produce combinations from 1 or 2 lists
function choose(list, list2)
   local newList = {}
   if list2 then
      for i = 1, #list2 do
         for j = 1, #list do
            if list[j] ~= list[i] then
               table.insert(newList, {list[j], list2[i]})
            end
         end
      end
      else
      for i = 1, #list do
         for j = i, #list do
            if list[i] ~= list[j] then
               table.insert(newList, {list[i], list[j]})
            end
         end
      end
   end
   return newList
end

-- Fix for some versions returning bees.species.*
function fixName(name)
   return name:gsub("bees%.species%.",""):gsub("^.", string.upper)
end

for key, value in pairs (alveary.getBeeBreedingData()) do
   addOffspring( fixName(value.result), {{ fixName(value.allele1), fixName(value.allele2) }} )
end
scoreBees()

-- logging ---------------------------------------------------------------------

local logFile = fs.open("bee.log", "w")
function log(msg)
   msg = msg or ""
   logFile.write(tostring(msg))
   logFile.flush()
   io.write(msg)
end
function logLine(msg)
   msg = msg or ""
   logFile.write(msg.."\n")
   logFile.flush()
   io.write(msg.."\n")
end

function logTable(table)
   for key, value in pairs (table) do
      logLine(key .. " = " .. tostring(value))
   end
end


-- analyzing functions ---------------------------------------------------------

function clearSystem()
   -- clear out alveary
   for i = 1,9 do
      memoryChest.pullItem("north",i)
   end
   -- clear out analyzer
   for i = 1, 12 do
      analyzer.pushItem("up",i)
   end
end

function getBees()
   -- get bees from apiary
   log("waiting for bees.")
   while not not alveary.getStackInSlot(1) do
      sleep(10)
      log(".")
   end
   log("*")
   for i, 3,9 do
      if memoryChest.pullItem("north",i) then
         log("*")
      end
   end
   logLine()
end



function breedBees(droneSlot)
   memoryChest.pushItemToSlot("north",princessSlot,1,1)
   memoryChest.pushItemToSlot("north",droneSlot,1,2)
end

function analyzeBees()
   princessSlot = 0
   logLine("analyzing bees...")
   local highestScore
   for i,data in pairs(memoryChest.getAllStacks()) do
      if data.rawName == "item.beeprincess" then
         princessSlot = i
      end
      if not ( data.rawName == "item.beeprincessge" or data.rawName == "item.beequeenge" or data.rawName == "item.beedronege" ) then
         memoryChest.pushItem("east",i)
         print("P")
      else
         print("B")
         if not data.beeInfo.isAnalyzed then
            analyzer.pullItem("up",i)
            while not analyzer.pushItem("up",9,data.qty,i) do sleep(1) end
            data = memoryChest.getStackInSlot(i)
         end
         -- Check if it's a drone or princess
         if string.find(data.rawName, "princess") then
            allBeeData[i]["type"] = "princess"
         else
            allBeeData[i]["type"] = "drone"
         end
         -- Active values
         for key, value in pairs (data.beeInfo.active) do
            if key == "species" then
               allBeeData[i]["speciesPrimary"] = value
            else
               allBeeData[i][key] = value
            end
         end
         -- Inactive values
         allBeeData[i]["speciesSecondary"] = data.beeInfo.inactive.species


         allBeeData[i]["speciesPrimary"] = fixName(allBeeData[i]["speciesPrimary"])
         allBeeData[i]["speciesSecondary"] = fixName(allBeeData[i]["speciesSecondary"])
         if allBeeData[i]["type"] == "princess" then
            if i ~= 1 then
               memoryChest.swap(i,1)
            end
            princessSlot = 1
         end
      end
      -- check for untargeted species
      if allBeeData[i] and (not bees[allBeeData[i]["speciesPrimary"]].targeted or not bees[allBeeData[i]["speciesSecondary"]].targeted) then
         memoryChest.pushItem("east",i)
         allBeeData[i] = nil
      end
   end

   if princessSlot > 0 then
      -- selection sort drones
      logLine("sorting drones...")
      for i = 2, memoryChest.getInventorySize() do
         highestScore = i
         if getCountInMemoryChest(i) > 0 and allBeeData[i] then
            allBeeData[i].score = scoreBee(allBeeData[princessSlot], allBeeData[i])
            for j = i + 1, memoryChest.getInventorySize() do
               if getCountInMemoryChest(j) > 0 and allBeeData[j] then
                  if not allBeeData[j].score then
                     allBeeData[j].score = scoreBee(allBeeData[princessSlot], allBeeData[j])
                  end
                  if allBeeData[j].score > allBeeData[highestScore].score then
                     highestScore = j
                  end
               end
            end
            -- swap bees
            if highestScore ~= i then
               memoryChest.swap(i, highestScore)
               allBeeData[i], allBeeData[highestScore] = allBeeData[highestScore], allBeeData[i]
            end
         end
      end
      printHeader()
      allBeeData[princessSlot].slot = 1
      printBee(allBeeData[princessSlot])
      for i = 2, memoryChest.getInventorySize() do
         if allBeeData[i] then
            allBeeData[i].slot = i
            printBee(allBeeData[i])
         end
      end
   end
   logLine()
end

function scoreBee(princessData, droneData)
   local droneSpecies = {droneData["speciesPrimary"], droneData["speciesSecondary"]}
   -- check for untargeted species
   if not bees[droneSpecies[1]].targeted or not bees[droneSpecies[2]].targeted then
      return 0
   end
   local princessSpecies = {princessData["speciesPrimary"], princessData["speciesSecondary"]}
   local score
   local maxScore = 0
   for _, combo in ipairs({{princessSpecies[1], droneSpecies[1]}
      ,{princessSpecies[1], droneSpecies[2]}
      ,{princessSpecies[2], droneSpecies[1]}
   ,{princessSpecies[2], droneSpecies[2]}}) do
   -- find maximum score for each combo
   score = (bees[combo[1]].score + bees[combo[2]].score) / 2
   for name, beeData in pairs(bees) do
      if beeData.targeted then
         for i, parents in ipairs(beeData.mutateFrom) do
            if combo[1] == parents[1] and combo[2] == parents[2]
               or combo[2] == parents[1] and combo[1] == parents[2] then
               score = (score + beeData.score) / 2
            end
         end
      end
   end
   maxScore = maxScore + score
   end
   -- add one for each combination that results in the maximum score
   score = maxScore
   -- score attributes
   score = score + math.max(scoresFertility[droneData["fertility"]], scoresFertility[princessData["fertility"]])
   score = score + math.min(scoresSpeed[tostring(droneData["speed"])], scoresSpeed[tostring(princessData["speed"])])
   if droneData["nocturnal"] or princessData["nocturnal"] then score = score + scoresAttrib["nocturnal"] end
   if droneData["tolerantFlyer"] or princessData["tolerantFlyer"] then score = score + scoresAttrib["tolerantFlyer"] end
   if droneData["caveDwelling"] or princessData["caveDwelling"] then score = score + scoresAttrib["caveDwelling"] end
   score = score + math.max(scoresTolerance[string.upper(droneData["temperatureTolerance"])], scoresTolerance[string.upper(princessData["temperatureTolerance"])])
   score = score + math.max(scoresTolerance[string.upper(droneData["humidityTolerance"])], scoresTolerance[string.upper(princessData["humidityTolerance"])])
   return score
end

function printHeader()
   logLine()
   logLine("sl t species f spd n f c tmp hmd score ")
   logLine("--|-|-------|-|---|-|-|-|---|---|------")
end

-- string constants for console output
toleranceString = {
   ["NONE"] = "  - ",
   ["UP 1"] = " +1 ",
   ["UP 2"] = " +2 ",
   ["UP 3"] = " +3 ",
   ["UP 4"] = " +4 ",
   ["UP 5"] = " +5 ",
   ["DOWN 1"] = " -1 ",
   ["DOWN 2"] = " -2 ",
   ["DOWN 3"] = " -3 ",
   ["DOWN 4"] = " -4 ",
   ["DOWN 5"] = " -5 ",
   ["BOTH 1"] = "+-1 ",
   ["BOTH 2"] = "+-2 ",
   ["BOTH 3"] = "+-3 ",
   ["BOTH 4"] = "+-4 ",
   ["BOTH 5"] = "+-5 "
}

speedString = {
   ["0.3"] = "0.3", -- Slowest
   ["0.6"] = "0.6", -- Slower
   ["0.8"] = "0.8", -- Slow
   ["1"]   = "1.0", -- Normal
   ["1.2"] = "1.2", -- Fast
   ["1.4"] = "1.4", -- Faster
   ["1.7"] = "1.7"  -- Fastest
}

function printBee(beeData)
   log(beeData["slot"] < 10 and " "..beeData["slot"].." " or beeData["slot"].." ")
   -- type
   log(beeData["type"] == "princess" and "P " or "D ")
   -- species
   log(beeData["speciesPrimary"]:gsub("bees%.species%.",""):sub(1,3)..":"..beeData["speciesSecondary"]:gsub("bees%.species%.",""):sub(1,3).." ")
   -- fertility
   log(tostring(beeData["fertility"]).." ")
   -- speed
   log(speedString[tostring(beeData["speed"])].." ")
   -- nocturnal
   log(beeData["nocturnal"] and "X " or "- ")
   -- flyer
   log(beeData["tolerantFlyer"] and "X " or "- ")
   -- cave dwelling
   log(beeData["caveDwelling"] and "X " or "- ")
   -- temperature tolerance
   log(toleranceString[string.upper(beeData["temperatureTolerance"])])
   -- humidity tolerance
   log(toleranceString[string.upper(beeData["humidityTolerance"])])
   -- score
   log(beeData.score and string.format("%5.1d", beeData.score).." " or "      ")
   logLine()
end

function dropExcess()
   logLine("dropping excess...")
   for i = 3, memoryChest.getInventorySize() do
      if getCountInMemoryChest(i) > 0 then
         -- drop drones over ( max inv - 9 ) to clear space for newly bred bees and product
         if i > ( memoryChest.getInventorySize() - 9 ) then
            memoryChest.pushItem("east",i)
            allBeeData[i] = nil
         end
      end
   end
end

function isPurebred(princessData, droneData)
   -- check if princess and drone are exactly the same and no chance for mutation
   if princessData["speciesPrimary"] ~= princessData["speciesSecondary"] then
      return false
   end
   for key, value in pairs(princessData) do
      if value ~= droneData[key] and key ~= "territory" and key ~= "type" and key ~= "slot" then
         return false
      end
   end
   return true
end

function getUnknown(princessData, droneData)
   -- lists species that are not in the bee graph
   local unknownSpecies = {}
   if not bees[princessData["speciesPrimary"]] then
      table.insert(unknownSpecies, princessData["speciesPrimary"])
   end
   if not bees[princessData["speciesSecondary"]] then
      table.insert(unknownSpecies, princessData["speciesSecondary"])
   end
   for _, beeData in pairs(droneData) do
      if not bees[beeData["speciesPrimary"]] then
         table.insert(unknownSpecies, beeData["speciesPrimary"])
      end
      if not bees[beeData["speciesSecondary"]] then
         table.insert(unknownSpecies, beeData["speciesSecondary"])
      end
   end
   return unknownSpecies
end

-- targeting -------------------------------------------------------------------

-- set species and all parents to targeted
function targetBee(name)
   local bee = bees[name]
   if bee and not bee.targeted then
      bee.targeted = true
      for i, parents in ipairs(bee.mutateFrom) do
         for j, parent in ipairs(parents) do
            targetBee(parent)
         end
      end
   end
end

-- set bee graph entry to targeted if species was specified on the command line
-- otherwise set all entries to targeted
tArgs = { ... }
if #tArgs > 0 then
   logLine("targeting bee species:")
   for i, target in ipairs(tArgs) do
      targetBee(target)
      for name, data in pairs(bees) do
         if data.targeted and data.score > 1 then
            logLine(name .. string.rep(" ", 20-#name), data.score)
         end
      end
   end
   else
   for _, beeData in pairs(bees) do
      beeData.targeted = true
   end
end

-- breeding loop ---------------------------------------------------------------

logLine("Clearing system...")
clearSystem()
redstone.setOutput("bottom", true)
while true do
   analyzeBees()
   if allBeeData[princessSlot] then
      if isPurebred(princessData, allBeeData[2]) then
         logLine("Bees are purebred")
         redstone.setOutput("bottom", false)
         break
      end
      breedBees(1, 2)
      allBeeData[1] = nil
      allBeeData[2] = nil
      dropExcess()
   end
   getBees()
end
logFile.close()