Lots of stuff in various stages of working

src/main/java/com/pahimar/ee3/EquivalentExchange3.java

@@ -7,6 +7,7 @@ import com.pahimar.ee3.command.CommandSyncValues;
 import com.pahimar.ee3.exchange.EnergyValueRegistry;
 import com.pahimar.ee3.handler.*;
 import com.pahimar.ee3.init.*;
+import com.pahimar.ee3.knowledge.KnowledgeRegistry;
 import com.pahimar.ee3.knowledge.SkillRegistry;
 import com.pahimar.ee3.network.PacketHandler;
 import com.pahimar.ee3.proxy.IProxy;
@@ -52,10 +53,13 @@ public class EquivalentExchange3
     @EventHandler
     public void onServerStarting(FMLServerStartingEvent event)
     {
+        SerializationHelper.initModDataDirectories();
+
+        KnowledgeRegistry.getInstance();
+
         event.registerServerCommand(new CommandSetValue());
         event.registerServerCommand(new CommandSetCurrentItemValue());
         event.registerServerCommand(new CommandSyncValues());
-        SerializationHelper.initModDataDirectories();
     }
 
     @EventHandler
@@ -127,6 +131,8 @@ public class EquivalentExchange3
             SerializationHelper.writeNBTToFile(SerializationHelper.getDataDirectory(), SerializationHelper.getModListMD5() + "." + Reference.MOD_ID.toLowerCase(), getEnergyValueRegistry());
         }
 
+        KnowledgeRegistry.getInstance().saveAll();
+
         WorldEventHandler.hasInitilialized = false;
     }
 

src/main/java/com/pahimar/ee3/exchange/JsonItemStack.java

@@ -1,10 +1,26 @@
 package com.pahimar.ee3.exchange;
 
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 
 public class JsonItemStack
 {
     public String itemName;
     public int itemDamage;
-    public NBTTagCompound nbtTagCompound;
+    public NBTTagCompound itemNBTTagCompound;
+
+    public JsonItemStack() {
+        this.itemName = null;
+        this.itemDamage = 0;
+        this.itemNBTTagCompound = null;
+    }
+
+    public JsonItemStack(ItemStack itemStack) {
+        this.itemName = Item.itemRegistry.getNameForObject(itemStack.getItem());
+        this.itemDamage = itemStack.getItemDamage();
+        if (itemStack.stackTagCompound != null) {
+            this.itemNBTTagCompound = itemStack.getTagCompound();
+        }
+    }
 }

src/main/java/com/pahimar/ee3/exchange/WrappedStack.java

@@ -398,9 +398,9 @@ public class WrappedStack implements Comparable<WrappedStack>, JsonDeserializer<
                         if (stackSize > 0 && item != null)
                         {
                             itemStack = new ItemStack(item, stackSize, jsonItemStack.itemDamage);
-                            if (jsonItemStack.nbtTagCompound != null)
+                            if (jsonItemStack.itemNBTTagCompound != null)
                             {
-                                itemStack.stackTagCompound = jsonItemStack.nbtTagCompound;
+                                itemStack.stackTagCompound = jsonItemStack.itemNBTTagCompound;
                             }
                         }
                         stackObject = itemStack;
@@ -475,7 +475,7 @@ public class WrappedStack implements Comparable<WrappedStack>, JsonDeserializer<
             jsonItemStack.itemDamage = ((ItemStack) wrappedStack.wrappedStack).getItemDamage();
             if (((ItemStack) wrappedStack.wrappedStack).stackTagCompound != null)
             {
-                jsonItemStack.nbtTagCompound = ((ItemStack) wrappedStack.wrappedStack).stackTagCompound;
+                jsonItemStack.itemNBTTagCompound = ((ItemStack) wrappedStack.wrappedStack).stackTagCompound;
             }
             jsonWrappedStack.add("data", gson.toJsonTree(jsonItemStack, JsonItemStack.class));
         }

src/main/java/com/pahimar/ee3/handler/TransmutationKnowledgeHandler.java

@@ -14,6 +14,7 @@ import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 
+// TODO Remove
 public class TransmutationKnowledgeHandler
 {
     public static File playerDataDirectory;

src/main/java/com/pahimar/ee3/knowledge/KnowledgeRegistry.java

@@ -1,5 +1,6 @@
 package com.pahimar.ee3.knowledge;
 
+import com.pahimar.ee3.reference.Files;
 import com.pahimar.ee3.util.SerializationHelper;
 import net.minecraft.entity.player.EntityPlayer;
 
@@ -16,9 +17,11 @@ public class KnowledgeRegistry
 
     private KnowledgeRegistry()
     {
-        knowledgeDirectory = new File(SerializationHelper.getPlayerDataDirectory(), "knowledge");
+        knowledgeDirectory = new File(SerializationHelper.getPlayerDataDirectory(), "knowledge" + File.separator + "transmutation");
         knowledgeDirectory.mkdirs();
 
+        loadTemplateKnowledgeFromDisk();
+
         playerKnowledgeMap = new HashMap<UUID, TransmutationKnowledge>();
     }
 
@@ -34,14 +37,24 @@ public class KnowledgeRegistry
 
     public TransmutationKnowledge getTemplateKnowledge()
     {
-        if (templateKnowledge == null)
-        {
-
-        }
-
         return templateKnowledge;
     }
 
+    public void loadTemplateKnowledgeFromDisk() {
+        File templateFile = new File(knowledgeDirectory, Files.TEMPLATE_JSON_FILE);
+
+        if (!templateFile.exists()) {
+            templateKnowledge = new TransmutationKnowledge();
+            SerializationHelper.writeTransmutationKnowledgeToFile(knowledgeDirectory, Files.TEMPLATE_JSON_FILE, templateKnowledge);
+        } else {
+            templateKnowledge = SerializationHelper.readTransmutationKnowledgeFromFile(knowledgeDirectory, Files.TEMPLATE_JSON_FILE);
+        }
+    }
+
+    public void saveTemplateKnowledgeToDisk() {
+        SerializationHelper.writeTransmutationKnowledgeToFile(knowledgeDirectory, Files.TEMPLATE_JSON_FILE, templateKnowledge);
+    }
+
     public void loadPlayerFromDisk(EntityPlayer entityPlayer)
     {
         TransmutationKnowledge playerTransmutationKnowledge = new TransmutationKnowledge();
@@ -50,8 +63,7 @@ public class KnowledgeRegistry
 
         if (playerKnowledgeFile.exists() && playerKnowledgeFile.isFile())
         {
-            // TODO Load from disk as JSON and not as NBT
+            playerTransmutationKnowledge = SerializationHelper.readTransmutationKnowledgeFromFile(knowledgeDirectory, entityPlayer.getUniqueID().toString() + ".json");
-            playerTransmutationKnowledge = TransmutationKnowledge.readTransmutationKnowledgeFromNBT(SerializationHelper.readNBTFromFile(playerKnowledgeFile));
         }
 
         playerKnowledgeMap.put(entityPlayer.getUniqueID(), playerTransmutationKnowledge);
@@ -59,7 +71,18 @@ public class KnowledgeRegistry
 
     public void savePlayerKnowledgeToDisk(EntityPlayer entityPlayer)
     {
-        // TODO Save to disk as JSON and not as NBT
+        if (playerKnowledgeMap.containsKey(entityPlayer.getUniqueID())) {
-        SerializationHelper.writeNBTToFile(knowledgeDirectory, entityPlayer.getUniqueID().toString() + ".json", playerKnowledgeMap.get(entityPlayer.getUniqueID()));
+            SerializationHelper.writeTransmutationKnowledgeToFile(knowledgeDirectory, entityPlayer.getUniqueID().toString() + ".json", playerKnowledgeMap.get(entityPlayer.getUniqueID()));
+        } else {
+            SerializationHelper.writeTransmutationKnowledgeToFile(knowledgeDirectory, entityPlayer.getUniqueID().toString() + ".json", new TransmutationKnowledge());
+        }
+    }
+
+    public void saveAll() {
+        saveTemplateKnowledgeToDisk();
+
+        for (UUID playerUUID : playerKnowledgeMap.keySet()) {
+            SerializationHelper.writeTransmutationKnowledgeToFile(knowledgeDirectory, playerUUID.toString() + ".json", playerKnowledgeMap.get(playerUUID));
+        }
     }
 }

src/main/java/com/pahimar/ee3/knowledge/SkillRegistry.java

@@ -1,18 +1,25 @@
 package com.pahimar.ee3.knowledge;
 
 import com.pahimar.ee3.exchange.EnergyValueRegistry;
+import com.pahimar.ee3.exchange.WrappedStack;
 import com.pahimar.ee3.handler.TransmutationKnowledgeHandler;
 import com.pahimar.ee3.reference.Settings;
 import com.pahimar.ee3.util.ItemHelper;
 import net.minecraft.item.ItemStack;
 
+import java.util.Set;
 import java.util.SortedMap;
 import java.util.TreeMap;
+import java.util.TreeSet;
 
+// TODO Change up so that we only track what is not learnable, and what is not recoverable
+// Everything that has an EnergyValue is learnable and recoverable unless there is an entry for it in either of these lists
 public class SkillRegistry
 {
     private static SkillRegistry SkillRegistry = null;
     private SortedMap<ItemStack, Skill> transmutationSkills;
+    private Set<WrappedStack> notLearnableSet;
+    private Set<WrappedStack> notRecoverableSet;
 
     private SkillRegistry()
     {
@@ -32,6 +39,8 @@ public class SkillRegistry
     private void init()
     {
         transmutationSkills = new TreeMap<ItemStack, Skill>(ItemHelper.comparator);
+        notLearnableSet = new TreeSet<WrappedStack>();
+        notRecoverableSet = new TreeSet<WrappedStack>();
     }
 
     public void addSkill(ItemStack itemStack, boolean learnable, boolean recoverable)

src/main/java/com/pahimar/ee3/knowledge/TransmutationKnowledge.java

@@ -1,6 +1,8 @@
 package com.pahimar.ee3.knowledge;
 
 import com.google.gson.*;
+import com.google.gson.stream.JsonReader;
+import com.google.gson.stream.JsonWriter;
 import com.pahimar.ee3.exchange.JsonItemStack;
 import com.pahimar.ee3.reference.Names;
 import com.pahimar.ee3.util.INBTTaggable;
@@ -11,6 +13,7 @@ import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.nbt.NBTTagList;
 
+import java.io.*;
 import java.lang.reflect.Type;
 import java.util.*;
 
@@ -197,7 +200,7 @@ public class TransmutationKnowledge implements INBTTaggable, JsonSerializer<Tran
     {
         if (json.isJsonArray()) {
             JsonArray jsonArray = (JsonArray) json;
-            Set<ItemStack> itemStackSet = new TreeSet<ItemStack>(ItemHelper.comparator);
+            Set<ItemStack> itemStacks = new TreeSet<ItemStack>(ItemHelper.comparator);
             Iterator<JsonElement> iterator = jsonArray.iterator();
 
             while (iterator.hasNext()) {
@@ -209,16 +212,18 @@ public class TransmutationKnowledge implements INBTTaggable, JsonSerializer<Tran
                     Item item = (Item) Item.itemRegistry.getObject(jsonItemStack.itemName);
                     if (item != null) {
                         itemStack = new ItemStack(item, 1, jsonItemStack.itemDamage);
-                        if (jsonItemStack.nbtTagCompound != null) {
+                        if (jsonItemStack.itemNBTTagCompound != null) {
-                            itemStack.stackTagCompound = jsonItemStack.nbtTagCompound;
+                            itemStack.stackTagCompound = jsonItemStack.itemNBTTagCompound;
                         }
                     }
 
-                    itemStackSet.add(itemStack);
+                    if (itemStack != null) {
+                        itemStacks.add(itemStack);
+                    }
                 }
             }
 
-            return new TransmutationKnowledge(itemStackSet);
+            return new TransmutationKnowledge(itemStacks);
         }
 
         return null;
@@ -227,21 +232,70 @@ public class TransmutationKnowledge implements INBTTaggable, JsonSerializer<Tran
     @Override
     public JsonElement serialize(TransmutationKnowledge transmutationKnowledge, Type typeOfSrc, JsonSerializationContext context)
     {
-        Gson gson = new Gson();
         JsonArray jsonTransmutationKnowledge = new JsonArray();
 
         for (ItemStack itemStack : transmutationKnowledge.getKnownTransmutations())
         {
-            JsonItemStack jsonItemStack = new JsonItemStack();
+            jsonTransmutationKnowledge.add(jsonSerializer.toJsonTree(new JsonItemStack(itemStack)));
-            jsonItemStack.itemName = Item.itemRegistry.getNameForObject(itemStack.getItem());
-            jsonItemStack.itemDamage = itemStack.getItemDamage();
-            if (itemStack.stackTagCompound != null)
-            {
-                jsonItemStack.nbtTagCompound = itemStack.getTagCompound();
-            }
-            jsonTransmutationKnowledge.add(gson.toJsonTree(jsonItemStack));
         }
 
         return jsonTransmutationKnowledge;
     }
+
+    public static void saveToFile(File file, TransmutationKnowledge transmutationKnowledge) {
+        JsonWriter jsonWriter;
+
+        try {
+            jsonWriter = new JsonWriter(new FileWriter(file));
+            jsonWriter.setIndent("    ");
+            jsonWriter.beginArray();
+
+            Iterator<ItemStack> iterator = transmutationKnowledge.getKnownTransmutations().iterator();
+
+            while (iterator.hasNext())
+            {
+                ItemStack itemStack = iterator.next();
+                jsonSerializer.toJson(new JsonItemStack(itemStack), JsonItemStack.class, jsonWriter);
+            }
+
+            jsonWriter.endArray();
+            jsonWriter.close();
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static TransmutationKnowledge readFromFile(File file) {
+        Set<ItemStack> itemStacks = new TreeSet<ItemStack>(ItemHelper.comparator);
+        JsonReader jsonReader;
+
+        try {
+            jsonReader = new JsonReader(new FileReader(file));
+            jsonReader.beginArray();
+            while (jsonReader.hasNext()) {
+                JsonItemStack jsonItemStack = jsonSerializer.fromJson(jsonReader, JsonItemStack.class);
+
+                ItemStack itemStack = null;
+                Item item = (Item) Item.itemRegistry.getObject(jsonItemStack.itemName);
+                if (item != null) {
+                    itemStack = new ItemStack(item, 1, jsonItemStack.itemDamage);
+                    if (jsonItemStack.itemNBTTagCompound != null) {
+                        itemStack.stackTagCompound = jsonItemStack.itemNBTTagCompound;
+                    }
+                }
+
+                if (itemStack != null) {
+                    itemStacks.add(itemStack);
+                }
+            }
+            jsonReader.endArray();
+            jsonReader.close();
+        } catch (FileNotFoundException ignored) {
+            // NOOP
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+
+        return new TransmutationKnowledge(itemStacks);
+    }
 }

src/main/java/com/pahimar/ee3/reference/Files.java

@@ -2,7 +2,7 @@ package com.pahimar.ee3.reference;
 
 public class Files
 {
-
     public static final String PRE_ASSIGNED_ENERGY_VALUES = "pre-assigned-energy-values.json";
     public static final String POST_ASSIGNED_ENERGY_VALUES = "post-assigned-energy-values.json";
+    public static final String TEMPLATE_JSON_FILE = "template.json";
 }

src/main/java/com/pahimar/ee3/util/SerializationHelper.java

@@ -5,6 +5,7 @@ import com.google.gson.stream.JsonWriter;
 import com.pahimar.ee3.api.EnergyValue;
 import com.pahimar.ee3.exchange.EnergyValueStackMapping;
 import com.pahimar.ee3.exchange.WrappedStack;
+import com.pahimar.ee3.knowledge.TransmutationKnowledge;
 import com.pahimar.ee3.reference.Reference;
 import cpw.mods.fml.common.FMLCommonHandler;
 import cpw.mods.fml.common.Loader;
@@ -126,10 +127,50 @@ public class SerializationHelper
                 }
             } catch (Exception exception)
             {
+                LogHelper.warn(String.format("Failed to save %s to file: %s%s", nbtTaggable.getTagLabel(), directory.getAbsolutePath(), fileName));
+            }
+        }
+    }
+
+    public static TransmutationKnowledge readTransmutationKnowledgeFromFile(File directory, String fileName) {
+        if (!directory.exists()) {
+            directory.mkdirs();
+        }
+
+        return TransmutationKnowledge.readFromFile(new File(directory, fileName));
+    }
+
+    public static void writeTransmutationKnowledgeToFile(File directory, String fileName, TransmutationKnowledge transmutationKnowledge) {
+        writeTransmutationKnowledgeToFile(directory, fileName, transmutationKnowledge, false);
+    }
+
+    public static void writeTransmutationKnowledgeToFile(File directory, String fileName, TransmutationKnowledge transmutationKnowledge, boolean verboseLogging) {
+        if (directory != null && fileName != null) {
+            if (!directory.exists()) {
+                directory.mkdirs();
+            }
+
+            if (transmutationKnowledge == null) {
+                transmutationKnowledge = new TransmutationKnowledge();
+            }
+
+            try {
+                File file1 = new File(directory, fileName + ".tmp");
+                File file2 = new File(directory, fileName);
+                TransmutationKnowledge.saveToFile(file1, transmutationKnowledge);
+
+                if (file2.exists()) {
+                    file2.delete();
+                }
+
+                file1.renameTo(file2);
+
                 if (verboseLogging)
                 {
-                    LogHelper.warn(String.format("Failed to save %s to file: %s%s", nbtTaggable.getTagLabel(), directory.getAbsolutePath(), fileName));
+                    LogHelper.info(String.format("Successfully saved TransmutationKnowledge to file: %s", file2.getAbsolutePath()));
                 }
+            } catch (Exception exception) {
+                LogHelper.error(String.format("Failed to save TransmutationKnowledge to file: %s%s", directory.getAbsolutePath(), fileName));
             }
         }
     }