[Repairibility]: fixed false positives of NPEfix on repogit4test data

SpoonLabs · Jul 19, 2019 · 6a3878e · 6a3878e
2 parents b765ac7 + 6b11141
commit 6a3878e
Show file tree

Hide file tree

Showing 21 changed files with 116 additions and 191 deletions.
diff --git a/all_instances_found.json b/all_instances_found.json
diff --git a/src/main/java/fr/inria/coming/core/engine/RevisionNavigationExperiment.java b/src/main/java/fr/inria/coming/core/engine/RevisionNavigationExperiment.java
@@ -7,20 +7,23 @@
 import fr.inria.coming.changeminer.entity.FinalResult;
 import fr.inria.coming.changeminer.entity.IRevision;
 import fr.inria.coming.core.engine.callback.IntermediateResultProcessorCallback;
+import fr.inria.coming.core.engine.filespair.FileDiff;
 import fr.inria.coming.core.entities.AnalysisResult;
 import fr.inria.coming.core.entities.RevisionDataset;
 import fr.inria.coming.core.entities.RevisionResult;
 import fr.inria.coming.core.entities.interfaces.IFilter;
 import fr.inria.coming.core.entities.interfaces.IOutput;
 import fr.inria.coming.core.entities.interfaces.RevisionOrder;
 import fr.inria.coming.main.ComingProperties;
+import org.apache.log4j.Logger;
 
 /**
  * 
  * @author Matias Martinez
  *
  */
 public abstract class RevisionNavigationExperiment<R extends IRevision> {
+	Logger log = Logger.getLogger(FileDiff.class.getName());
 
 	protected RevisionOrder<R> navigationStrategy = null;
 	protected List<Analyzer> analyzers = new ArrayList<>();
@@ -103,7 +106,8 @@ public FinalResult analyze() {
 
 			R oneRevision = iterator.next();
 
-			System.out.println("\n***********\nAnalyzing " + i + "/" + size);
+			log.info("\n***********\nAnalyzing " + i + "/" + size);
+//			System.out.println("\n***********\nAnalyzing " + i + "/" + size);
 			if (!accept(oneRevision)) {
 				continue;
 			}

diff --git a/src/main/java/fr/inria/coming/core/engine/files/FileDiff.java b/src/main/java/fr/inria/coming/core/engine/files/FileDiff.java
@@ -29,7 +29,8 @@ public FileDiff(File diffFolder) {
 	@Override
 	public List<IRevisionPair> getChildren() {
 		if (this.diffFolder == null) {
-			System.out.println("Diff folder == null");
+			log.info("Diff folder == null");
+//			System.out.println("Diff folder == null");
 			return null;
 		}
 		List<IRevisionPair> pairs = new ArrayList<>();
@@ -69,7 +70,8 @@ public List<IRevisionPair> getChildren() {
 				;
 			}
 		} catch (Exception e) {
-			System.err.println("Error analyzing " + diffFolder);
+			log.error("Error analyzing " + diffFolder);
+//			System.err.println("Error analyzing " + diffFolder);
 			e.printStackTrace();
 		}
 

diff --git a/src/main/java/fr/inria/coming/core/engine/filespair/FileDiff.java b/src/main/java/fr/inria/coming/core/engine/filespair/FileDiff.java
@@ -30,7 +30,8 @@ public FileDiff(File left, File right) {
     public List<IRevisionPair> getChildren() {
 
         if (left == null || right == null) {
-            System.out.println("files is null");
+            log.info("files is null");
+//            System.out.println("files is null");
             return null;
         }
 

diff --git a/src/main/java/fr/inria/coming/core/entities/DiffResult.java b/src/main/java/fr/inria/coming/core/entities/DiffResult.java
@@ -1,5 +1,8 @@
 package fr.inria.coming.core.entities;
 
+import fr.inria.coming.changeminer.analyzer.commitAnalyzer.FineGrainDifftAnalyzer;
+import org.apache.log4j.Logger;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -13,6 +16,8 @@
  */
 public class DiffResult<T, R> extends AnalysisResult<T> {
 
+	static Logger log = Logger.getLogger(FineGrainDifftAnalyzer.class.getName());
+
 	/**
 	 * Filename
 	 */
@@ -50,7 +55,9 @@ public String toString() {
 			try {
 				r += "\n" + idiff.toString();
 			} catch (Exception e) {
-				System.err.println("Error when printing diff result: " + e.getMessage());
+
+//				System.err.println("Error when printing diff result: " + e.getMessage());
+				log.error("Error when printing diff result: " + e.getMessage());
 				e.printStackTrace();
 			}
 

diff --git a/src/main/java/fr/inria/coming/main/ComingMain.java b/src/main/java/fr/inria/coming/main/ComingMain.java
@@ -55,7 +55,7 @@
  */
 public class ComingMain {
 
-	Logger log = Logger.getLogger(FineGrainDifftAnalyzer.class.getName());
+	static Logger logm = Logger.getLogger(FineGrainDifftAnalyzer.class.getName());
 
 	static Options options = new Options();
 
@@ -123,8 +123,10 @@ public static void main(String[] args) {
 		try {
 			cmain.run(args);
 		} catch (Exception e) {
-			System.err.println("Error initializing Coming with args" + Arrays.toString(args));
-			System.err.println(e);
+			logm.error("Error initializing Coming with args\" + Arrays.toString(args)");
+//			System.err.println("Error initializing Coming with args" + Arrays.toString(args));
+			logm.error(e);
+//			System.err.println(e);
 			e.printStackTrace();
 		}
 	}
@@ -157,7 +159,8 @@ public boolean createEngine(String[] args) throws ParseException {
 		try {
 			cmd = parser.parse(options, args);
 		} catch (UnrecognizedOptionException e) {
-			System.out.println("Error: " + e.getMessage());
+			logm.error("Error: " + e.getMessage());
+//			System.out.println("Error: " + e.getMessage());
 			help();
 			return false;
 		}
@@ -413,7 +416,7 @@ private List<ChangePatternSpecification> loadPattern() {
 					ChangePatternSpecification patternParsed = patternParser.parse(fl);
 					patternsFound.add(patternParsed);
 				} else {
-					log.error("The pattern file given as input does not exist " + fl.getAbsolutePath());
+					logm.error("The pattern file given as input does not exist " + fl.getAbsolutePath());
 				}
 			}
 		} else {
@@ -470,7 +473,8 @@ private static void help() {
 
 		HelpFormatter formater = new HelpFormatter();
 		formater.printHelp("Main", options);
-		System.out.println("More options and default values at 'configuration.properties' file");
+		logm.info("More options and default values at 'configuration.properties' file");
+//		System.out.println("More options and default values at 'configuration.properties' file");
 
 		System.exit(0);
 

diff --git a/src/main/java/fr/inria/coming/repairability/JSONRepairabilityOutput.java b/src/main/java/fr/inria/coming/repairability/JSONRepairabilityOutput.java
@@ -2,6 +2,7 @@
 
 import com.google.gson.JsonArray;
 import com.google.gson.JsonObject;
+import fr.inria.coming.changeminer.analyzer.commitAnalyzer.FineGrainDifftAnalyzer;
 import fr.inria.coming.changeminer.analyzer.instancedetector.ChangePatternInstance;
 import fr.inria.coming.changeminer.analyzer.instancedetector.PatternInstanceAnalyzer;
 import fr.inria.coming.changeminer.analyzer.instancedetector.PatternInstancesFromDiff;
@@ -10,11 +11,13 @@
 import fr.inria.coming.core.entities.RevisionResult;
 import fr.inria.coming.core.entities.output.JSonPatternInstanceOutput;
 import gumtree.spoon.diff.operations.Operation;
+import org.apache.log4j.Logger;
 
 import java.io.File;
 
 public class JSONRepairabilityOutput extends JSonPatternInstanceOutput {
 
+    Logger log = Logger.getLogger(FineGrainDifftAnalyzer.class.getName());
 
     public void getInstancesOfRevision(RevisionResult revisionResult, JsonArray instances) {
 
@@ -33,8 +36,10 @@ public void getInstancesOfRevision(RevisionResult revisionResult, JsonArray inst
 
                 instance.addProperty("revision", revisionIdentifier.toString());
 
-                System.out.println("\n--------\ncommit with instance:\n " + revisionIdentifier);
-                System.out.println(pi.getInstances());
+                log.info("\n--------\ncommit with instance:\n " + revisionIdentifier);
+//                System.out.println("\n--------\ncommit with instance:\n " + revisionIdentifier);
+                log.info(pi.getInstances());
+//                System.out.println(pi.getInstances());
 
                 JsonArray repair_tools = new JsonArray();
                 for (ChangePatternInstance instancePattern : pi.getInstances()) {

diff --git a/src/main/java/fr/inria/coming/repairability/repairtools/NPEfix.java b/src/main/java/fr/inria/coming/repairability/repairtools/NPEfix.java
@@ -28,9 +28,16 @@
 public class NPEfix extends AbstractRepairTool {
 
     private static final String[] patternFileNames = {
-            "replacement.xml",
+            "replacement3.xml",
             "replacement2.xml",
-            "replacement3.xml"
+            "replacement.xml",
+            "replacement4.xml",
+            "replacement5.xml",
+            "replacement6.xml",
+            "replacement7.xml",
+            "replacement8.xml",
+            "replacement9.xml",
+            "replacement11.xml"
     };
 
     /**

diff --git a/src/main/resources/repairability/NPEfix/replacement.xml b/src/main/resources/repairability/NPEfix/replacement.xml
@@ -1,6 +1,7 @@
-<pattern name="replacement">
-    <entity id="1" type="*" />
+<pattern name="replacement1">
+    <entity id="1" type="Assignment" />
     <action entityId="1" type="INS"/>
 
 </pattern>
 
+
diff --git a/src/main/resources/repairability/NPEfix/replacement11.xml b/src/main/resources/repairability/NPEfix/replacement11.xml
@@ -0,0 +1,7 @@
+<pattern name="replacement11">
+    <entity id="1" type="Literal"/>
+    <action entityId="1" type="UPD"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability/NPEfix/replacement2.xml b/src/main/resources/repairability/NPEfix/replacement2.xml
@@ -1,6 +1,7 @@
-<pattern name="replacement">
-    <entity id="1" type="*"/>
+<pattern name="replacement2">
+    <entity id="1" type="Assignment"/>
     <action entityId="1" type="UPD"/>
 
 </pattern>
 
+
diff --git a/src/main/resources/repairability/NPEfix/replacement3.xml b/src/main/resources/repairability/NPEfix/replacement3.xml
@@ -1,4 +1,4 @@
-<pattern name="replacement">
+<pattern name="replacement3">
     <entity id="1" type="Return" role="Statement"/>
     <action entityId="1" type="INS"/>
 

diff --git a/src/main/resources/repairability/NPEfix/replacement4.xml b/src/main/resources/repairability/NPEfix/replacement4.xml
@@ -0,0 +1,7 @@
+<pattern name="replacement4">
+    <entity id="1" type="Assignment" />
+    <action entityId="1" type="MOV"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability/NPEfix/replacement5.xml b/src/main/resources/repairability/NPEfix/replacement5.xml
@@ -0,0 +1,7 @@
+<pattern name="replacement5">
+    <entity id="1" type="VariableRead" />
+    <action entityId="1" type="UPD"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability/NPEfix/replacement6.xml b/src/main/resources/repairability/NPEfix/replacement6.xml
@@ -0,0 +1,10 @@
+<pattern name="replacement6">
+    <entity id="1" type="FieldRead"/>
+    <action entityId="1" type="INS"/>
+
+    <entity id="2" type="*"/>
+    <action entityId="2" type="DEL"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability/NPEfix/replacement7.xml b/src/main/resources/repairability/NPEfix/replacement7.xml
@@ -0,0 +1,10 @@
+<pattern name="replacement7">
+    <entity id="1" type="FieldRead"/>
+    <action entityId="1" type="MOV"/>
+
+    <entity id="2" type="*"/>
+    <action entityId="2" type="DEL"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability/NPEfix/replacement8.xml b/src/main/resources/repairability/NPEfix/replacement8.xml
@@ -0,0 +1,10 @@
+<pattern name="replacement8">
+    <entity id="1" type="Invocation"/>
+    <action entityId="1" type="INS"/>
+
+    <entity id="2" type="*"/>
+    <action entityId="2" type="DEL"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability/NPEfix/replacement9.xml b/src/main/resources/repairability/NPEfix/replacement9.xml
@@ -0,0 +1,10 @@
+<pattern name="replacement9">
+    <entity id="1" type="VariableRead"/>
+    <action entityId="1" type="INS"/>
+
+    <entity id="2" type="*"/>
+    <action entityId="2" type="DEL"/>
+
+</pattern>
+
+
diff --git a/src/main/resources/repairability_test_files/NPEfix/NPEfix12/twelve/NPEfix12_twelve_t.java b/src/main/resources/repairability_test_files/NPEfix/NPEfix12/twelve/NPEfix12_twelve_t.java
@@ -1,4 +1,4 @@
-/*
+ /*
  * Licensed to the Apache Software Foundation (ASF) under one or more
  * contributor license agreements.  See the NOTICE file distributed with
  * this work for additional information regarding copyright ownership.

diff --git a/src/test/java/fr/inria/coming/spoon/repairability/RepairabilityTest.java b/src/test/java/fr/inria/coming/spoon/repairability/RepairabilityTest.java
@@ -28,7 +28,7 @@ public void testRepairabilityInterface() throws Exception {
     public void testRepairabilityAll() throws Exception {
 
         FinalResult result = TestUtills.runRepairability("ALL", "/repairability_test_files/mixed/");
-        TestUtills.numberOfInstances(result, 2, 5);
+        TestUtills.numberOfInstances(result, 2, 3);
     }
 
     @Test

diff --git a/src/test/java/fr/inria/coming/spoon/repairability/repairtools/NPEfixTest.java b/src/test/java/fr/inria/coming/spoon/repairability/repairtools/NPEfixTest.java
@@ -10,7 +10,7 @@ public class NPEfixTest {
     @Test
     public void NPEfixTest() throws Exception {
         FinalResult result = TestUtills.runRepairability("NPEfix", "/repairability_test_files/NPEfix/");
-        TestUtills.numberOfInstances(result, 18, 18);
+        TestUtills.numberOfInstances(result, 18, 16);
     }
 
 //    @Test