Extraction of Patch Text + Updates to PatchCat module

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "PatchCat"]
 	path = PatchCat
 	url = https://github.com/karineek/PatchCat
-[submodule "Docker"]
-	path = Docker
-	url = https://github.com/domsob/gin-docker

src/main/java/gin/edit/llm/LLMReplaceStatement.java

@@ -238,4 +238,8 @@ public String toString() {
         return this.getClass().getCanonicalName() + " \"" + destinationFilename + "\":" + destinationStatement + "\nPrompt: !!!\n" + lastPrompt +  "\n!!! --> !!!\n" + lastReplacement + "\n!!!";
     }
 
+	public String getLastReplacement() {
+        return this.lastReplacement;
+    }
+
 }

src/main/java/gin/util/GP.java

@@ -193,11 +193,11 @@ protected void writePatch(int iteration, int evaluationNumber, UnitTestResultSet
         outputFileWriter.writeNext(entry);
     }
 
-        protected void writePatchWithPatchCatInfo(int iteration, int evaluationNumber, UnitTestResultSet results, String methodName, Double fitness, double improvement, int cluster, String action) {
+        protected void writePatchWithPatchCatInfo(int iteration, int evaluationNumber, UnitTestResultSet results, String methodName, Double fitness, double improvement, int cluster, String action, String patch) {
         String[] entry = { methodName
         		, Integer.toString(iteration)
         		, Integer.toString(evaluationNumber)
-                , results.getPatch().toString()
+                , patch
                 , Integer.toString(cluster)
                 , action
                 , results.getCleanCompile() == null ? "null" : Boolean.toString(results.getCleanCompile())

src/main/java/gin/util/LocalSearchSimple.java

@@ -16,6 +16,8 @@
 import com.sampullara.cli.Argument;
 
 import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -125,20 +127,20 @@ public String clusterAction(int cluster) throws IOException{
         throw new IOException("Clustering Failed");
     }
 
-    public void implementClusterAction(String action, String className, String methodName, List<UnitTest> tests, Patch patch, int iteration, int cluster) {
+    public void implementClusterAction(String action, String className, String methodName, List<UnitTest> tests, Patch patch, int iteration, int cluster, String diff) {
         // ACTION C - Throw away patch
         if (action == "C") {
             UnitTestResultSet results = new UnitTestResultSet(patch, "", null, new ArrayList<>(), null, "", null, new ArrayList<>()); 
-            super.writePatchWithPatchCatInfo(iteration, iteration, results, methodName, null, 0, cluster, "C");
+            super.writePatchWithPatchCatInfo(iteration, iteration, results, methodName, null, 0, cluster, "C", diff);
         }
 
         // ACTION B - Proceed as normal
-        if (action == "B") {
+        else if (action == "B") {
             // Calculate fitness
             UnitTestResultSet results = testPatch(className, tests, patch, null);
             double newFitness = fitness(results);
-            super.writePatchWithPatchCatInfo(iteration, iteration, results, methodName, newFitness, compareFitness(newFitness, best), cluster, "B");
-    
+            super.writePatchWithPatchCatInfo(iteration, iteration, results, methodName, newFitness, compareFitness(newFitness, best), cluster, "B", diff);
+
             // Check if better
             if (compareFitness(newFitness, best) > 0) {
                 best = newFitness;
@@ -151,7 +153,8 @@ public void implementClusterAction(String action, String className, String metho
         else {
             //Add dummy fitness entry as we don't want to test the patch
             UnitTestResultSet results = new UnitTestResultSet(patch, "", null, new ArrayList<>(), null, "", null, new ArrayList<>()); 
-            super.writePatchWithPatchCatInfo(iteration, iteration, results, methodName, null, 0, cluster, "A");
+            super.writePatchWithPatchCatInfo(iteration, iteration, results, methodName, null, 0, cluster, "A", diff);
+
             bestPatch = patch;
         }
     }
@@ -175,7 +178,7 @@ protected void search(TargetMethod method, Patch origPatch) {
         // Calculate fitness and record result, including fitness improvement (currently 0)
         double orig = fitness(results);
          if (Boolean.TRUE.equals(patchCat)){
-            super.writePatchWithPatchCatInfo(-1, 0, results, methodName, orig, 0, -1, "Original");
+            super.writePatchWithPatchCatInfo(-1, 0, results, methodName, orig, 0, -1, "Original", "");
         } else { super.writePatch(-1, 0, results, methodName, orig, 0); }
 
         // Set original as best for now
@@ -187,26 +190,44 @@ protected void search(TargetMethod method, Patch origPatch) {
             // Add a mutation
             Patch patch = neighbour(bestPatch);
             boolean toTest = false;
+            String lastReplacement = "";
             Logger.info("Patch is: " + patch.toString());
             Logger.info("Original Patch is: " + origPatch.toString());
 
             try {
                 // Support for PatchCat Integration
                 if (Boolean.TRUE.equals(patchCat)) {
                     Logger.info("Running PatchCat");
-
+
+                    patch.apply();
+                    Edit lastEdit = patch.getEdits().get(patch.getEdits().size() - 1);
+                    if (lastEdit instanceof LLMReplaceStatement llmEdit) {
+                        lastReplacement = llmEdit.getLastReplacement();
+                    } else {
+                        continue;
+                    }
+
+                    // Logger.info("Current patch diff is: " + diff);
+                    Logger.info("Last replacement is: " + lastReplacement);
+
                     ProcessBuilder builder = new ProcessBuilder(
                         "python3",
-                        "../gin/PatchCat/src/PatchCat.py",
-                        patch.toString(),  origPatch.toString()
-                    );                
+                        "../gin/PatchCat/src/PatchCatGin.py",
+                        "--diff-text", lastReplacement.toString(),
+                        "--vectorizer-path", "../gin/PatchCat/src/running-model/vectorizer.pkl",
+                        "--model-path", "../gin/PatchCat/src/running-model/model.pkl"
+                    );           
 
                     builder.environment().put("PYTHONUNBUFFERED", "1");
-
+                    // builder.redirectErrorStream(true);
+
                     Process process = builder.start();
+
                     BufferedReader reader = new BufferedReader(
                         new InputStreamReader(process.getInputStream())
                     );
+
+                    //Read the output from PatchCatGin to get the cluster number
                     String line = reader.readLine();
                     int cluster = -1;
 
@@ -227,7 +248,7 @@ protected void search(TargetMethod method, Patch origPatch) {
 
                     int exit = process.waitFor();
 
-                    implementClusterAction(action, className, methodName, tests, patch, i, cluster);
+                    implementClusterAction(action, className, methodName, tests, patch, i, cluster, lastReplacement);
 
                 } else { // Regular Local Search without PatchCat
                     // Calculate fitness