Issue842

repairnator/repairnator-pipeline/pom.xml

@@ -33,6 +33,28 @@
     </repositories>
 
     <dependencies>
+        <dependency>
+            <groupId>com.github.spoonlabs</groupId>
+            <artifactId>coming</artifactId>
+            <version>0-SNAPSHOT</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>io.github.java-diff-utils</groupId>
+            <artifactId>java-diff-utils</artifactId>
+            <version>4.0</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
         <dependency>
             <groupId>fr.inria.repairnator</groupId>
             <artifactId>repairnator-core</artifactId>

repairnator/repairnator-pipeline/src/main/java/fr/inria/spirals/repairnator/process/inspectors/JobStatus.java

@@ -273,6 +273,20 @@ public List<RepairPatch> getAllPatches() {
         return allPatches;
     }
 
+    public List<RepairPatch> getRankedPatches() {
+        List<RepairPatch> allPatches = getAllPatches();
+        allPatches.sort((patch1, patch2) -> { // ascending
+            double diff = patch1.getOverfittingScore() - patch2.getOverfittingScore();
+            if (diff < 0) {
+                return -1;
+            } else if (diff > 0) {
+                return 1;
+            }
+            return 0;
+        });
+        return allPatches;
+    }
+
     public Map<String, List<RepairPatch>> getListOfPatches() {
         return listOfPatches;
     }

repairnator/repairnator-pipeline/src/main/java/fr/inria/spirals/repairnator/process/inspectors/RepairPatch.java

@@ -1,6 +1,20 @@
 package fr.inria.spirals.repairnator.process.inspectors;
 
+import com.github.difflib.DiffUtils;
+import com.github.difflib.UnifiedDiffUtils;
+import com.github.difflib.patch.Patch;
+import com.github.difflib.patch.PatchFailedException;
+import fr.inria.prophet4j.P4J;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 import java.util.Objects;
+import java.util.stream.Stream;
 
 public class RepairPatch {
     /**
@@ -18,10 +32,48 @@ public class RepairPatch {
      */
     private String diff;
 
+    /**
+     * Score of the overfitting likelihood
+     */
+    private double overfittingScore;
+
     public RepairPatch(String toolname, String filePath, String diff) {
         this.toolname = toolname;
         this.filePath = filePath;
         this.diff = diff;
+        this.overfittingScore = computeOverfittingScore();
+    }
+
+    private double computeOverfittingScore() {
+        double overfittingScore = Double.POSITIVE_INFINITY;
+
+        File buggyFile = new File(filePath);
+        if (buggyFile.isFile()) {
+            // read from buggyFile
+            List<String> buggyLines = new ArrayList<>();
+            try (Stream<String> stream = Files.lines(Paths.get(filePath))) {
+                stream.forEach(buggyLines::add);
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+            // prepare patches
+            List<String> diffLines = Arrays.asList(diff.split("\n"));
+            Patch<String> patches = UnifiedDiffUtils.parseUnifiedDiff(diffLines);
+
+            try {
+                // create patchedFile
+                String tmpName = buggyFile.getName();
+                File patchedFile = Files.createTempFile(tmpName, ".java").toFile();
+                // generate content of patchedFile by applying patches
+                List<String> patchedLines = DiffUtils.patch(buggyLines, patches);
+                // write to patchedFile
+                Files.write(Paths.get(patchedFile.getPath()), patchedLines);
+                overfittingScore = new P4J().computeOverfittingScore(buggyFile, patchedFile);
+            } catch (PatchFailedException | IOException e) {
+                e.printStackTrace();
+            }
+        }
+        return overfittingScore;
     }
 
     public String getToolname() {
@@ -36,14 +88,18 @@ public String getDiff() {
         return diff;
     }
 
+    public double getOverfittingScore() {
+        return overfittingScore;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
         final RepairPatch that = (RepairPatch) o;
         return Objects.equals(toolname, that.toolname) &&
-                Objects.equals(filePath, that.filePath) &&
-                Objects.equals(diff, that.diff);
+            Objects.equals(filePath, that.filePath) &&
+            Objects.equals(diff, that.diff);
     }
 
     @Override

repairnator/repairnator-pipeline/src/main/resources/prophet4j/_BIN/README.md

@@ -0,0 +1,14 @@
+Prophet4J is inside the Coming lib, and is introduced to compute OverfittingScores for patches.
+
+This folder contains necessary resources for Prophet4J. There are two same folders in total, one is at _src/main/resources_ and the other one is at _src/test/resources_. I had not found one correct way to import resources files to make Prophet4J work smoothly as one part of Maven lib. In ideal cases, we do not need these two folders at all.
+
+If you fixed this issue, please run this test file `src/test/java/fr/inria/spirals/repairnator/process/inspectors/TestJobStatus.java` to check. Or maybe later I will do it myself.
+
+How to fix this issue?
+
+1. the issue is at L11 at _src/main/java/fr/inria/prophet4j/utility/Support.java_ of the [Coming Project]()
+That line of code looks like `public static final String PROPHET4J_DIR = Support.class.getClassLoader().getResource("").getPath() + "prophet4j/";`
+2. rewrite this line of code to make everything prefect
+3. release one new version of Coming lib to Maven
+4. run the test file named as `TestJobStatus.java` to check
+5. remove two `prophet4j` folders locating at _src/main/resources_ and _src/test/resources_

repairnator/repairnator-pipeline/src/test/java/fr/inria/spirals/repairnator/process/inspectors/TestJobStatus.java

@@ -1,11 +1,9 @@
 package fr.inria.spirals.repairnator.process.inspectors;
 
-import ch.qos.logback.classic.Level;
 import fr.inria.jtravis.entities.Build;
 import fr.inria.spirals.repairnator.BuildToBeInspected;
 import fr.inria.spirals.repairnator.process.step.repair.NPERepair;
 import fr.inria.spirals.repairnator.process.step.repair.nopol.NopolSingleTestRepair;
-import fr.inria.spirals.repairnator.utils.Utils;
 import fr.inria.spirals.repairnator.config.RepairnatorConfig;
 import fr.inria.spirals.repairnator.process.files.FileHelper;
 import fr.inria.spirals.repairnator.process.step.StepStatus;
@@ -30,8 +28,7 @@
 import java.nio.file.Files;
 import java.util.*;
 
-import static org.hamcrest.CoreMatchers.is;
-import static org.hamcrest.CoreMatchers.notNullValue;
+import static org.hamcrest.CoreMatchers.*;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 
@@ -43,7 +40,6 @@ public class TestJobStatus {
     public void setup() {
         RepairnatorConfig config = RepairnatorConfig.getInstance();
         config.setZ3solverPath(Utils4Tests.getZ3SolverPath());
-        Utils.setLoggersLevel(Level.ERROR);
     }
 
     @After
@@ -52,12 +48,24 @@ public void tearDown() throws IOException {
         FileHelper.deleteFile(tmpDir);
     }
 
+    private Build checkBuildAndReturn(long buildId, boolean isPR) {
+        Optional<Build> optionalBuild = RepairnatorConfig.getInstance().getJTravis().build().fromId(buildId);
+        assertTrue(optionalBuild.isPresent());
+
+        Build build = optionalBuild.get();
+        assertThat(build, IsNull.notNullValue());
+        assertThat(buildId, Is.is(build.getId()));
+        assertThat(build.isPullRequest(), Is.is(isPR));
+
+        return build;
+    }
+
     @Test
     public void testGatheringPatches() throws IOException {
         long buildId = 382484026; // surli/failingProject build
         Build build = this.checkBuildAndReturn(buildId, false);
 
-        tmpDir = Files.createTempDirectory("test_nopolrepair").toFile();
+        tmpDir = Files.createTempDirectory("test_gathering").toFile();
         BuildToBeInspected toBeInspected = new BuildToBeInspected(build, null, ScannedBuildStatus.ONLY_FAIL, "");
         ProjectInspector inspector = new ProjectInspector(toBeInspected, tmpDir.getAbsolutePath(), null, null);
 
@@ -70,12 +78,12 @@ public void testGatheringPatches() throws IOException {
         RepairnatorConfig.getInstance().setRepairTools(new HashSet<>(Arrays.asList(nopolRepair.getRepairToolName(), npeRepair.getRepairToolName())));
 
         cloneStep.addNextStep(new CheckoutBuggyBuild(inspector, true))
-                .addNextStep(new TestProject(inspector))
-                .addNextStep(new GatherTestInformation(inspector, true, new BuildShouldFail(), false))
-                .addNextStep(new ComputeClasspath(inspector, true))
-                .addNextStep(new ComputeSourceDir(inspector, true, false))
-                .addNextStep(nopolRepair)
-                .addNextStep(npeRepair);
+            .addNextStep(new TestProject(inspector))
+            .addNextStep(new GatherTestInformation(inspector, true, new BuildShouldFail(), false))
+            .addNextStep(new ComputeClasspath(inspector, true))
+            .addNextStep(new ComputeSourceDir(inspector, true, false))
+            .addNextStep(nopolRepair)
+            .addNextStep(npeRepair);
         cloneStep.execute();
 
         assertThat(nopolRepair.isShouldStop(), is(false));
@@ -100,15 +108,86 @@ public void testGatheringPatches() throws IOException {
         assertThat(inspector.getJobStatus().getToolDiagnostic().get(nopolRepair.getRepairToolName()), notNullValue());
     }
 
-    private Build checkBuildAndReturn(long buildId, boolean isPR) {
-        Optional<Build> optionalBuild = RepairnatorConfig.getInstance().getJTravis().build().fromId(buildId);
-        assertTrue(optionalBuild.isPresent());
+    @Test
+    public void testRankingPatches() throws IOException {
+        long buildId = 382484026; // surli/failingProject build
+        Build build = this.checkBuildAndReturn(buildId, false);
 
-        Build build = optionalBuild.get();
-        assertThat(build, IsNull.notNullValue());
-        assertThat(buildId, Is.is(build.getId()));
-        assertThat(build.isPullRequest(), Is.is(isPR));
+        tmpDir = Files.createTempDirectory("test_ranking").toFile();
+        BuildToBeInspected toBeInspected = new BuildToBeInspected(build, null, ScannedBuildStatus.ONLY_FAIL, "");
+        ProjectInspector inspector = new ProjectInspector(toBeInspected, tmpDir.getAbsolutePath(), null, null);
 
-        return build;
+        CloneRepository cloneStep = new CloneRepository(inspector);
+        NopolSingleTestRepair nopolRepair = new NopolSingleTestRepair();
+        nopolRepair.setProjectInspector(inspector);
+        NPERepair npeRepair = new NPERepair();
+        npeRepair.setProjectInspector(inspector);
+
+        RepairnatorConfig.getInstance().setRepairTools(new HashSet<>(Arrays.asList(nopolRepair.getRepairToolName(), npeRepair.getRepairToolName())));
+
+        cloneStep.addNextStep(new CheckoutBuggyBuild(inspector, true))
+            .addNextStep(new TestProject(inspector))
+            .addNextStep(new GatherTestInformation(inspector, true, new BuildShouldFail(), false))
+            .addNextStep(new ComputeClasspath(inspector, true))
+            .addNextStep(new ComputeSourceDir(inspector, true, false))
+            .addNextStep(nopolRepair)
+            .addNextStep(npeRepair);
+        cloneStep.execute();
+
+        List<RepairPatch> rankedPatches = inspector.getJobStatus().getRankedPatches();
+        assertThat(rankedPatches.size(), is(16)); // 12 (nopol) + 4 (npe)
+
+//        rankedPatches.forEach(repairPatch -> {
+//            System.out.println(repairPatch.getToolname());
+//            System.out.println(repairPatch.getFilePath());
+//            System.out.println(repairPatch.getOverfittingScore());
+//        });
+
+        assertThat(rankedPatches.get(0).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(0).getFilePath(), endsWith("modelo/Solver.java"));
+        assertThat(rankedPatches.get(0).getOverfittingScore(), is(-3190.603359887649));
+        assertThat(rankedPatches.get(1).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(1).getFilePath(), endsWith("Stub/ProxyPlatoStub.java"));
+        assertThat(rankedPatches.get(1).getOverfittingScore(), is(-2775.6773763492697));
+        assertThat(rankedPatches.get(2).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(2).getFilePath(), endsWith("modelo/ApiDB.java"));
+        assertThat(rankedPatches.get(2).getOverfittingScore(), is(-1544.2008323597074));
+        assertThat(rankedPatches.get(3).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(3).getFilePath(), endsWith("modelo/InternalDB.java"));
+        assertThat(rankedPatches.get(3).getOverfittingScore(), is(-1011.203142967915));
+        assertThat(rankedPatches.get(4).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(4).getFilePath(), endsWith("modelo/ControllerInternalDB.java"));
+        assertThat(rankedPatches.get(4).getOverfittingScore(), is(-732.199911962387));
+        assertThat(rankedPatches.get(5).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(5).getFilePath(), endsWith("modelo/InternalDB.java"));
+        assertThat(rankedPatches.get(5).getOverfittingScore(), is(-589.2194952242268));
+        assertThat(rankedPatches.get(6).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(6).getFilePath(), endsWith("modelo/ControllerInternalDB.java"));
+        assertThat(rankedPatches.get(6).getOverfittingScore(), is(-525.0518968819456));
+        assertThat(rankedPatches.get(7).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(7).getFilePath(), endsWith("Validadores/ValidadorPlato.java"));
+        assertThat(rankedPatches.get(7).getOverfittingScore(), is(-41.19421176656324));
+        assertThat(rankedPatches.get(8).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(8).getFilePath(), endsWith("modelo/InternalDB.java"));
+        assertThat(rankedPatches.get(8).getOverfittingScore(), is(-41.19421176656324));
+        assertThat(rankedPatches.get(9).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(9).getFilePath(), endsWith("modelo/ControllerInternalDB.java"));
+        assertThat(rankedPatches.get(9).getOverfittingScore(), is(-41.19421176656324));
+        assertThat(rankedPatches.get(10).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(10).getFilePath(), endsWith("modelo/ControllerInternalDB.java"));
+        assertThat(rankedPatches.get(10).getOverfittingScore(), is(230.96289712519297));
+        assertThat(rankedPatches.get(11).getToolname(), is("NopolSingleTest"));
+        assertThat(rankedPatches.get(11).getFilePath(), endsWith("modelo/ControllerInternalDB.java"));
+        assertThat(rankedPatches.get(11).getOverfittingScore(), is(3465.24494158228));
+
+        // in following cases, OverfittingScore can not be computed because of invalid filePaths
+        assertThat(rankedPatches.get(12).getToolname(), is("NPEFix"));
+        assertThat(rankedPatches.get(12).getOverfittingScore(), is(Double.POSITIVE_INFINITY));
+        assertThat(rankedPatches.get(13).getToolname(), is("NPEFix"));
+        assertThat(rankedPatches.get(13).getOverfittingScore(), is(Double.POSITIVE_INFINITY));
+        assertThat(rankedPatches.get(14).getToolname(), is("NPEFix"));
+        assertThat(rankedPatches.get(14).getOverfittingScore(), is(Double.POSITIVE_INFINITY));
+        assertThat(rankedPatches.get(15).getToolname(), is("NPEFix"));
+        assertThat(rankedPatches.get(15).getOverfittingScore(), is(Double.POSITIVE_INFINITY));
     }
 }

repairnator/repairnator-pipeline/src/test/resources/prophet4j/_BIN/README.md

@@ -0,0 +1,14 @@
+Prophet4J is inside the Coming lib, and is introduced to compute OverfittingScores for patches.
+
+This folder contains necessary resources for Prophet4J. There are two same folders in total, one is at _src/main/resources_ and the other one is at _src/test/resources_. I had not found one correct way to import resources files to make Prophet4J work smoothly as one part of Maven lib. In ideal cases, we do not need these two folders at all.
+
+If you fixed this issue, please run this test file `src/test/java/fr/inria/spirals/repairnator/process/inspectors/TestJobStatus.java` to check. Or maybe later I will do it myself.
+
+How to fix this issue?
+
+1. the issue is at L11 at _src/main/java/fr/inria/prophet4j/utility/Support.java_ of the [Coming Project]()
+That line of code looks like `public static final String PROPHET4J_DIR = Support.class.getClassLoader().getResource("").getPath() + "prophet4j/";`
+2. rewrite this line of code to make everything prefect
+3. release one new version of Coming lib to Maven
+4. run the test file named as `TestJobStatus.java` to check
+5. remove two `prophet4j` folders locating at _src/main/resources_ and _src/test/resources_