add Flacoco as fault localization engine

nopol/pom.xml

@@ -1,9 +1,7 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>
-
- <groupId>fr.inria.gforge.spirals</groupId>
- <artifactId>nopol</artifactId>
+<groupId>fr.inria.gforge.spirals</groupId> <artifactId>nopol</artifactId>
  <version>0.2-SNAPSHOT</version>
  <name>Nopol</name>
  <description>Java Program Repair via Conditional Expression Replacement</description>
@@ -44,17 +42,22 @@
  <maven-jar-plugin.version>2.4</maven-jar-plugin.version>
  <maven-release-plugin.version>2.5.1</maven-release-plugin.version>
  <maven-resources-plugin.version>2.6</maven-resources-plugin.version>
- <maven-jacoco-plugin.version>0.8.3</maven-jacoco-plugin.version>
+ <maven-jacoco-plugin.version>0.8.7</maven-jacoco-plugin.version>
  <maven-coveralls-plugin.version>4.0.0</maven-coveralls-plugin.version>
 
  <github.global.server>github</github.global.server>
  </properties>
 
  <dependencies>
+ <dependency>
+ <groupId>com.github.spoonlabs</groupId>
+ <artifactId>flacoco</artifactId>
+ <version>1.0.1</version>
+ </dependency>
  <dependency>
  <groupId>junit</groupId>
  <artifactId>junit</artifactId>
- <version>4.13.1</version>
+ <version>4.13.2</version>
  </dependency>
  <dependency>
  <groupId>org.reflections</groupId>
@@ -108,7 +111,7 @@
  <dependency>
  <groupId>fr.inria.gforge.spoon</groupId>
  <artifactId>spoon-core</artifactId>
- <version>7.5.0-SNAPSHOT</version>
+ <version>9.1.0</version>
  </dependency>
  <dependency>
  <groupId>org.smtlib</groupId>
@@ -276,7 +279,7 @@
  <artifactId>maven-surefire-plugin</artifactId>
  <version>2.14.1</version>
  <configuration>
- <argLine>${argLine}</argLine>
+ <argLine>-Xms2048m -Xmx2048m</argLine>
  </configuration>
  </plugin>
  <plugin>
@@ -397,17 +400,25 @@
  <url>http://sachaproject.gforge.inria.fr/repositories/releases/</url>
  <snapshots/>
  </repository>
+
  <repository>
- <id>gforge.inria.fr-snapshot</id>
- <name>Maven Repository for Spoon Snapshot</name>
- <url>http://maven.inria.fr/artifactory/spoon-public-snapshot/</url>
+ <id>spoon-snapshot</id>
+ <name>Maven Repository for Spoon Snapshots</name>
+ <url>https://repository.ow2.org/nexus/content/repositories/snapshots/</url>
  <snapshots/>
  </repository>
+
  <repository>
  <id>tdurieux.github.io/maven-repository/snapshots/</id>
  <name>tdurieux.github.io maven-repository</name>
  <url>https://tdurieux.github.io/maven-repository/snapshots/</url>
  </repository>
+ <repository>
+ <id>snapshots-repo</id>
+ <url>https://oss.sonatype.org/content/repositories/snapshots</url>
+ <releases><enabled>false</enabled></releases>
+ <snapshots><enabled>true</enabled></snapshots>
+ </repository>
  </repositories>
 
  <distributionManagement>

nopol/src/main/java/fr/inria/lille/localization/FlacocoFaultLocalizer.java

@@ -0,0 +1,153 @@
+package fr.inria.lille.localization;
+
+import fr.inria.lille.localization.metric.Metric;
+import fr.inria.lille.localization.metric.Ochiai;
+import fr.inria.lille.repair.common.config.NopolContext;
+import fr.inria.lille.repair.nopol.SourceLocation;
+import fr.spoonlabs.flacoco.api.result.Location;
+import fr.spoonlabs.flacoco.core.config.FlacocoConfig;
+import fr.spoonlabs.flacoco.core.coverage.CoverageMatrix;
+import fr.spoonlabs.flacoco.core.coverage.CoverageRunner;
+import fr.spoonlabs.flacoco.core.coverage.framework.JUnit4Strategy;
+import fr.spoonlabs.flacoco.core.coverage.framework.JUnit5Strategy;
+import fr.spoonlabs.flacoco.core.test.TestContext;
+import fr.spoonlabs.flacoco.core.test.TestDetector;
+import fr.spoonlabs.flacoco.core.test.method.TestMethod;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import spoon.Launcher;
+import spoon.reflect.CtModel;
+import spoon.reflect.declaration.CtTypeInformation;
+import xxl.java.junit.TestCase;
+
+import java.io.File;
+import java.net.URL;
+import java.util.*;
+import java.util.stream.Collectors;
+
+public class FlacocoFaultLocalizer implements FaultLocalizer {
+
+ private Map<SourceLocation, List<TestResult>> testListPerStatement = new HashMap<>();
+
+ private List<StatementSourceLocation> statementSourceLocations = new ArrayList<>();
+
+ public FlacocoFaultLocalizer(NopolContext nopolContext, Metric metric) {
+ runFlacoco(nopolContext, metric);
+ }
+
+ public FlacocoFaultLocalizer(NopolContext nopolContext) {
+ this(nopolContext, new Ochiai());
+ }
+
+ private void runFlacoco(NopolContext nopolContext, Metric metric) {
+ FlacocoConfig config = new FlacocoConfig();
+
+ Launcher spoon = new Launcher();
+ List<String> javaSources = new ArrayList<>();
+ for (File file : nopolContext.getProjectSources()) {
+ spoon.addInputResource(file.getAbsolutePath());
+ javaSources.add(file.getAbsolutePath());
+ }
+ CtModel model = spoon.buildModel();
+
+ List<String> javaBin = new ArrayList<>();
+
+ // Init FlacocoConfig
+ config.setClasspath(Arrays.stream(nopolContext.getProjectClasspath()).map(URL::getPath)
+ .reduce((x, y) -> x + File.pathSeparator + y).orElse(""));
+ config.setJacocoIncludes(
+ model.getAllTypes().stream().map(CtTypeInformation::getQualifiedName).collect(Collectors.toSet()));
+ config.setComplianceLevel(nopolContext.getComplianceLevel());
+ config.setTestRunnerJVMArgs("-Xms2048m -Xmx2048m");
+ config.setSrcJavaDir(javaSources);
+
+ System.out.println(nopolContext);
+
+ // Set tests
+ TestDetector testDetector = new TestDetector(config);
+ List<TestContext> tests = testDetector.getTests();
+
+ for (TestContext testContext : tests) {
+ if (testContext.getTestFrameworkStrategy() instanceof JUnit4Strategy) {
+ config.setjUnit4Tests(
+ testContext.getTestMethods().stream()
+ .filter(x -> Arrays.asList(nopolContext.getProjectTests())
+ .contains(x.getFullyQualifiedClassName()))
+ .map(TestMethod::getFullyQualifiedMethodName)
+ .collect(Collectors.toSet())
+ );
+ }
+ if (testContext.getTestFrameworkStrategy() instanceof JUnit5Strategy) {
+ config.setjUnit5Tests(
+ testContext.getTestMethods().stream()
+ .filter(x -> Arrays.asList(nopolContext.getProjectTests())
+ .contains(x.getFullyQualifiedClassName()))
+ .map(TestMethod::getFullyQualifiedMethodName)
+ .collect(Collectors.toSet())
+ );
+ }
+ }
+
+ // Get CoverageMatrix
+ CoverageRunner coverageRunner = new CoverageRunner(config);
+ CoverageMatrix coverageMatrix = coverageRunner.getCoverageMatrix(new TestDetector(config).getTests());
+
+ for (Location location : coverageMatrix.getResultExecution().keySet()) {
+ SourceLocation sourceLocation = new SourceLocation(
+ location.getClassName(),
+ location.getLineNumber()
+ );
+ StatementSourceLocation statementSourceLocation = new StatementSourceLocation(metric, sourceLocation);
+ int ef = 0;
+ int ep = 0;
+ int nf = 0;
+ int np = 0;
+ for (TestMethod testMethod : coverageMatrix.getTests().keySet()) {
+ boolean iTestPassing = coverageMatrix.getTests().get(testMethod);
+ boolean nrExecuted = coverageMatrix.getResultExecution().get(location).contains(testMethod);
+ if (iTestPassing && nrExecuted) {
+ ep++;
+ } else if (!iTestPassing && nrExecuted) {
+ ef++;
+ } else if (iTestPassing && !nrExecuted) {
+ np++;
+ } else if (!iTestPassing && !nrExecuted) {
+ nf++;
+ }
+ }
+ statementSourceLocation.setEp(ep);
+ statementSourceLocation.setEf(ef);
+ statementSourceLocation.setNf(nf);
+ statementSourceLocation.setNp(np);
+
+ statementSourceLocations.add(statementSourceLocation);
+ testListPerStatement.put(
+ sourceLocation,
+ coverageMatrix.getResultExecution().get(location).stream()
+ .map(x -> new TestResultImpl(TestCase.from(x.getFullyQualifiedMethodName()), coverageMatrix.getTests().get(x)))
+ .collect(Collectors.toList())
+ );
+ }
+
+ statementSourceLocations.sort(Comparator.comparing(x -> x.getLocation().getContainingClassName()));
+ statementSourceLocations.sort((o1, o2) -> Integer.compare(o2.getLocation().getLineNumber(), o1.getLocation().getLineNumber()));
+ statementSourceLocations.sort((o1, o2) -> Double.compare(o2.getSuspiciousness(), o1.getSuspiciousness()));
+
+ LinkedHashMap<SourceLocation, List<fr.inria.lille.localization.TestResult>> map = new LinkedHashMap<>();
+ for (StatementSourceLocation source : statementSourceLocations) {
+ map.put(source.getLocation(), testListPerStatement.get(source.getLocation()));
+ }
+ testListPerStatement = map;
+ }
+
+ @Override
+ public Map<SourceLocation, List<TestResult>> getTestListPerStatement() {
+ return testListPerStatement;
+ }
+
+ @Override
+ public List<? extends StatementSourceLocation> getStatements() {
+ return statementSourceLocations;
+ }
+
+}

nopol/src/main/java/fr/inria/lille/localization/StatementSourceLocation.java

@@ -18,4 +18,12 @@ public StatementSourceLocation(Metric metric, SourceLocation location) {
  public SourceLocation getLocation() {
  return location;
  }
+
+ @Override
+ public String toString() {
+ return "StatementSourceLocation{" +
+ "suspiciousness=" + getSuspiciousness() +
+ ", location=" + location +
+ '}';
+ }
 }

nopol/src/main/java/fr/inria/lille/repair/Main.java

@@ -237,8 +237,11 @@ private static NopolContext.NopolLocalizer strToLocalizer(String str) {
  return NopolContext.NopolLocalizer.GZOLTAR;
  } else if (str.equals("dumb")) {
  return NopolContext.NopolLocalizer.DUMB;
- } else
+ } else if (str.equals("cocospoon")) {
  return NopolContext.NopolLocalizer.COCOSPOON;
+ } else /* it can only be flacoco */{
+ return NopolContext.NopolLocalizer.FLACOCO;
+ }
  }
 
  private void initJSAP() throws JSAPException {
@@ -365,7 +368,7 @@ private void initJSAP() throws JSAPException {
  faultLocalization.setAllowMultipleDeclarations(false);
  faultLocalization.setLongFlag("flocal");
  faultLocalization.setShortFlag('z');
- faultLocalization.setUsageName(" cocospoon|dumb|gzoltar");//TODO ADD PARAMETIZED FAULT LOCALIZER
+ faultLocalization.setUsageName("cocospoon|dumb|gzoltar|flacoco");//TODO ADD PARAMETIZED FAULT LOCALIZER
  faultLocalization.setStringParser(JSAP.STRING_PARSER);
  faultLocalization.setDefault(NopolContext.DEFAULT_FAULT_LOCALIZER.name().toLowerCase());
  faultLocalization.setHelp("Define the fault localizer to be used.");

nopol/src/main/java/fr/inria/lille/repair/common/config/NopolContext.java

@@ -53,7 +53,8 @@ public enum NopolSolver {
  public enum NopolLocalizer {
  DUMB,
  GZOLTAR,
- COCOSPOON
+ COCOSPOON,
+ FLACOCO
  }
 
  private final String filename = "default-nopol-config.ini";
@@ -102,7 +103,7 @@ public enum NopolLocalizer {
  private NopolSynthesis synthesis = NopolSynthesis.SMT;
  private NopolOracle oracle = NopolOracle.ANGELIC;
  private NopolSolver solver = NopolSolver.Z3;
- public final static NopolLocalizer DEFAULT_FAULT_LOCALIZER = NopolLocalizer.GZOLTAR;
+ public final static NopolLocalizer DEFAULT_FAULT_LOCALIZER = NopolLocalizer.FLACOCO;
  private NopolLocalizer localizer = DEFAULT_FAULT_LOCALIZER;
 
 

nopol/src/main/java/fr/inria/lille/repair/nopol/NoPol.java

@@ -20,11 +20,7 @@
 import fr.inria.lille.commons.spoon.SpoonedProject;
 import fr.inria.lille.commons.synthesis.ConstraintBasedSynthesis;
 import fr.inria.lille.commons.synthesis.operator.Operator;
-import fr.inria.lille.localization.CocoSpoonBasedSpectrumBasedFaultLocalizer;
-import fr.inria.lille.localization.DumbFaultLocalizerImpl;
-import fr.inria.lille.localization.FaultLocalizer;
-import fr.inria.lille.localization.GZoltarFaultLocalizer;
-import fr.inria.lille.localization.TestResult;
+import fr.inria.lille.localization.*;
 import fr.inria.lille.localization.metric.Ochiai;
 import fr.inria.lille.repair.common.BottomTopURLClassLoader;
 import fr.inria.lille.repair.common.config.NopolContext;
@@ -180,8 +176,9 @@ private FaultLocalizer createLocalizer() {
  return new DumbFaultLocalizerImpl(this.nopolContext);
  case COCOSPOON: // default
  return new CocoSpoonBasedSpectrumBasedFaultLocalizer(this.nopolContext, new Ochiai());
+ case FLACOCO:
  default:
- return GZoltarFaultLocalizer.createInstance(this.nopolContext);
+ return new FlacocoFaultLocalizer(this.nopolContext);
  }
  }
 

nopol/src/test/java/fr/inria/lille/localization/FlacocoLocalizerTest.java

@@ -0,0 +1,75 @@
+package fr.inria.lille.localization;
+
+import fr.inria.lille.localization.metric.Ochiai;
+import fr.inria.lille.repair.common.config.NopolContext;
+import fr.inria.lille.repair.nopol.SourceLocation;
+import org.junit.Test;
+
+import java.io.File;
+import java.net.URL;
+import java.util.List;
+import java.util.Map;
+
+import static gov.nasa.jpf.util.test.TestJPF.assertEquals;
+import static gov.nasa.jpf.util.test.TestJPF.assertTrue;
+
+public class FlacocoLocalizerTest {
+
+ @Test
+ public void testOchiaiFlacocoLocalizer() throws Exception {
+
+ /* test OchiaiCoCoSpoonLocalizer : the SourceLocation must be sorted following the Ochiai metric */
+
+ File[] sources = new File[]{new File("../test-projects/src/main/java/nopol_examples/nopol_example_1/NopolExample.java")};
+ URL[] classpath = new URL[]{
+ new File("../test-projects/target/classes").toURI().toURL(),
+ new File("../test-projects/target/test-classes").toURI().toURL()
+ };
+ String[] testClasses = new String[]{"nopol_examples.nopol_example_1.NopolExampleTest"};
+ FlacocoFaultLocalizer localizer = new FlacocoFaultLocalizer(new NopolContext(sources, classpath, testClasses), new Ochiai());
+
+ Map<SourceLocation, List<TestResult>> executedSourceLocationPerTest = localizer.getTestListPerStatement();
+ assertEquals(10, executedSourceLocationPerTest.keySet().size());
+
+ for (StatementSourceLocation sourceLocation : localizer.getStatements()) {
+ System.out.println(sourceLocation);
+ }
+
+ SourceLocation sourceLocation1 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 27);
+ SourceLocation sourceLocation2 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 16);
+ SourceLocation sourceLocation3 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 15);
+ SourceLocation sourceLocation4 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 18);
+ SourceLocation sourceLocation5 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 12);
+ SourceLocation sourceLocation6 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 23);
+ SourceLocation sourceLocation7 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 25);
+ SourceLocation sourceLocation8 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 13);
+ SourceLocation sourceLocation9 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 24);
+ SourceLocation sourceLocation10 = new SourceLocation("nopol_examples.nopol_example_1.NopolExample", 21);
+
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation1));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation2));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation3));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation4));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation5));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation6));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation7));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation8));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation9));
+ assertTrue(executedSourceLocationPerTest.keySet().contains(sourceLocation10));
+
+ List<? extends StatementSourceLocation> sortedStatements = localizer.getStatements();
+
+ assertEquals(0.534, sortedStatements.get(0).getSuspiciousness(), 10E-3);
+ assertEquals(0.5, sortedStatements.get(1).getSuspiciousness(), 10E-3);
+ assertEquals(0.471, sortedStatements.get(2).getSuspiciousness(), 10E-3);
+ assertEquals(0.471, sortedStatements.get(3).getSuspiciousness(), 10E-3);
+ assertEquals(0.471, sortedStatements.get(4).getSuspiciousness(), 10E-3);
+ assertEquals(0.471, sortedStatements.get(5).getSuspiciousness(), 10E-3);
+ assertEquals(0.471, sortedStatements.get(6).getSuspiciousness(), 10E-3);
+ assertEquals(0.471, sortedStatements.get(7).getSuspiciousness(), 10E-3);
+ assertEquals(0.0, sortedStatements.get(8).getSuspiciousness(), 10E-3);
+ assertEquals(0.0, sortedStatements.get(9).getSuspiciousness(), 10E-3);
+
+ assertEquals(sourceLocation2, sortedStatements.get(0).getLocation());
+ }
+}