Apply the unified-diff patch when combining layers.

src/main/java/org/qortal/arbitrary/ArbitraryDataCombiner.java

@@ -23,6 +23,7 @@ public class ArbitraryDataCombiner {
     private Path pathAfter;
     private byte[] signatureBefore;
     private Path finalPath;
+    ArbitraryDataMetadataPatch metadata;
 
     public ArbitraryDataCombiner(Path pathBefore, Path pathAfter, byte[] signatureBefore) {
         this.pathBefore = pathBefore;
@@ -33,6 +34,7 @@ public class ArbitraryDataCombiner {
     public void combine() throws IOException {
         try {
             this.preExecute();
+            this.readMetadata();
             this.validatePreviousSignature();
             this.validatePreviousHash();
             this.process();
@@ -86,14 +88,17 @@ public class ArbitraryDataCombiner {
 
     }
 
-    private void validatePreviousSignature() throws IOException {
+    private void readMetadata() throws IOException  {
+        this.metadata = new ArbitraryDataMetadataPatch(this.pathAfter);
+        this.metadata.read();
+    }
+
+    private void validatePreviousSignature() {
         if (this.signatureBefore == null) {
             throw new IllegalStateException("No previous signature passed to the combiner");
         }
 
-        ArbitraryDataMetadataPatch metadata = new ArbitraryDataMetadataPatch(this.pathAfter);
-        metadata.read();
-        byte[] previousSignature = metadata.getPreviousSignature();
+        byte[] previousSignature = this.metadata.getPreviousSignature();
         if (previousSignature == null) {
             throw new IllegalStateException("Unable to extract previous signature from patch metadata");
         }
@@ -105,9 +110,7 @@ public class ArbitraryDataCombiner {
     }
 
     private void validatePreviousHash() throws IOException {
-        ArbitraryDataMetadataPatch metadata = new ArbitraryDataMetadataPatch(this.pathAfter);
-        metadata.read();
-        byte[] previousHash = metadata.getPreviousHash();
+        byte[] previousHash = this.metadata.getPreviousHash();
         if (previousHash == null) {
             throw new IllegalStateException("Unable to extract previous hash from patch metadata");
         }
@@ -123,7 +126,8 @@ public class ArbitraryDataCombiner {
     }
 
     private void process() throws IOException {
-        ArbitraryDataMerge merge = new ArbitraryDataMerge(this.pathBefore, this.pathAfter);
+        String patchType = metadata.getPatchType();
+        ArbitraryDataMerge merge = new ArbitraryDataMerge(this.pathBefore, this.pathAfter, metadata.getPatchType());
         merge.compute();
         this.finalPath = merge.getMergePath();
     }

src/main/java/org/qortal/arbitrary/ArbitraryDataMerge.java

@@ -1,16 +1,25 @@
 package org.qortal.arbitrary;
 
+import com.github.difflib.DiffUtils;
+import com.github.difflib.UnifiedDiffUtils;
+import com.github.difflib.patch.Patch;
+import com.github.difflib.patch.PatchFailedException;
 import org.apache.commons.io.FileUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.eclipse.jetty.util.IO;
 import org.qortal.arbitrary.metadata.ArbitraryDataMetadataPatch;
 import org.qortal.settings.Settings;
 import org.qortal.utils.FilesystemUtils;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.*;
 import java.util.List;
+import java.util.Objects;
 import java.util.UUID;
 
 public class ArbitraryDataMerge {
@@ -19,13 +28,15 @@ public class ArbitraryDataMerge {
 
     private Path pathBefore;
     private Path pathAfter;
+    private String patchType;
     private Path mergePath;
     private String identifier;
     private ArbitraryDataMetadataPatch metadata;
 
-    public ArbitraryDataMerge(Path pathBefore, Path pathAfter) {
+    public ArbitraryDataMerge(Path pathBefore, Path pathAfter, String patchType) {
         this.pathBefore = pathBefore;
         this.pathAfter = pathAfter;
+        this.patchType = patchType;
     }
 
     public void compute() throws IOException {
@@ -87,8 +98,7 @@ public class ArbitraryDataMerge {
         List<Path> modifiedPaths = this.metadata.getModifiedPaths();
         for (Path path : modifiedPaths) {
             LOGGER.info("File was modified: {}", path.toString());
-            Path filePath = Paths.get(this.pathAfter.toString(), path.toString());
-            ArbitraryDataMerge.copyPathToBaseDir(filePath, this.mergePath, path);
+            this.applyPatch(path);
         }
 
         List<Path> removedPaths = this.metadata.getRemovedPaths();
@@ -98,6 +108,60 @@ public class ArbitraryDataMerge {
         }
     }
 
+    private void applyPatch(Path path) throws IOException {
+        if (Objects.equals(this.patchType, "unified-diff")) {
+            // Create destination file from patch
+            this.applyUnifiedDiffPatch(path);
+        }
+        else {
+            // Copy complete file
+            Path filePath = Paths.get(this.pathAfter.toString(), path.toString());
+            ArbitraryDataMerge.copyPathToBaseDir(filePath, this.mergePath, path);
+        }
+    }
+
+    private void applyUnifiedDiffPatch(Path path) throws IOException {
+        Path originalPath = Paths.get(this.pathBefore.toString(), path.toString());
+        Path patchPath = Paths.get(this.pathAfter.toString(), path.toString());
+        Path mergePath = Paths.get(this.mergePath.toString(), path.toString());
+
+        if (!patchPath.toFile().exists()) {
+            // Patch file doesn't exist, but its path was included in modifiedPaths
+            // TODO: We ought to throw an exception here, but skipping for now
+            return;
+        }
+
+        // Delete an existing file, as we are starting from a duplicate of pathBefore
+        File destFile = mergePath.toFile();
+        if (destFile.exists() && destFile.isFile()) {
+            Files.delete(mergePath);
+        }
+
+        List<String> originalContents = FileUtils.readLines(originalPath.toFile(), StandardCharsets.UTF_8);
+        List<String> patchContents = FileUtils.readLines(patchPath.toFile(), StandardCharsets.UTF_8);
+
+        // At first, parse the unified diff file and get the patch
+        Patch<String> patch = UnifiedDiffUtils.parseUnifiedDiff(patchContents);
+
+        // Then apply the computed patch to the given text
+        try {
+            List<String> patchedContents = DiffUtils.patch(originalContents, patch);
+
+            // Write the patched file to the merge directory
+            FileWriter fileWriter = new FileWriter(mergePath.toString(), true);
+            BufferedWriter writer = new BufferedWriter(fileWriter);
+            for (String line : patchedContents) {
+                writer.append(line);
+                writer.newLine();
+            }
+            writer.flush();
+            writer.close();
+
+        } catch (PatchFailedException e) {
+            throw new IllegalStateException(String.format("Failed to apply patch for path %s: %s", path, e.getMessage()));
+        }
+    }
+
     private void copyMetadata() throws IOException {
         Path filePath = Paths.get(this.pathAfter.toString(), ".qortal");
         ArbitraryDataMerge.copyPathToBaseDir(filePath, this.mergePath, Paths.get(".qortal"));