mainly fixed same root and submission problem and did some enhancements

core/src/main/java/de/jplag/JPlag.java

@@ -7,6 +7,7 @@
 
 import de.jplag.clustering.ClusteringFactory;
 import de.jplag.exceptions.ExitException;
+import de.jplag.exceptions.RootDirectoryException;
 import de.jplag.exceptions.SubmissionException;
 import de.jplag.options.JPlagOptions;
 import de.jplag.reporting.reportobject.model.Version;
@@ -38,7 +39,13 @@ private static Version loadVersion() {
      * @param options determines the parameterization.
      */
     public JPlag(JPlagOptions options) {
-        this.options = options;
+        PreventSameRootName preventSameRootName = null;
+        try {
+            preventSameRootName = new PreventSameRootName(options);
+        } catch (RootDirectoryException e) {
+            e.printStackTrace();
+        }
+        this.options = preventSameRootName.getOptions();
         language = this.options.language();
         GreedyStringTiling coreAlgorithm = new GreedyStringTiling(options);
         comparisonStrategy = new ParallelComparisonStrategy(options, coreAlgorithm);

core/src/main/java/de/jplag/PreventSameRootName.java

@@ -0,0 +1,141 @@
+package de.jplag;
+
+import java.io.File;
+import java.nio.file.Path;
+import java.util.*;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import de.jplag.exceptions.RootDirectoryException;
+import de.jplag.options.JPlagOptions;
+
+/**
+ * This class prevents the same root name of submissions.
+ */
+public class PreventSameRootName {
+    private static final Logger logger = LoggerFactory.getLogger(PreventSameRootName.class);
+
+    private final Map<String, Integer> statistic = new HashMap<>(); // uses to store information of same roots (Key: same root name ---> Value: number
+                                                                    // of the same root name)
+    private final JPlagOptions options;
+
+    /**
+     * Creates and initializes a PreventSameRootName instance, parameterized by a set of options. If there are same names of
+     * root directories, they will be re-named before generating zip file and IDs. (e.g. two same root names: root ===>
+     * root_1 && root_2)
+     * @param options determines the parameterization
+     */
+    public PreventSameRootName(JPlagOptions options) throws RootDirectoryException {
+        Set<File> newChangedSubmissionDirectories;
+        Set<File> oldChangedSubmissionDirectories;
+        Set<File> newSubmissionDirectories = options.submissionDirectories();
+        Set<File> oldSubmissionDirectories = options.oldSubmissionDirectories();
+        if (oldSubmissionDirectories == null && newSubmissionDirectories == null) {
+            throw new RootDirectoryException("No submission");
+        }
+        boolean hasSameRoots = false;
+        hasSameRoots = hasSameRoots(newSubmissionDirectories, oldSubmissionDirectories);
+        if (hasSameRoots) {
+            logger.info("Detected same name of root directories, the name will be re-named...");
+            newChangedSubmissionDirectories = renameRoots(newSubmissionDirectories);
+            oldChangedSubmissionDirectories = renameRoots(oldSubmissionDirectories);
+        } else {
+            newChangedSubmissionDirectories = newSubmissionDirectories;
+            oldChangedSubmissionDirectories = oldSubmissionDirectories;
+        }
+        this.options = new JPlagOptions(options.language(), options.minimumTokenMatch(), newChangedSubmissionDirectories,
+                oldChangedSubmissionDirectories, options.baseCodeSubmissionDirectory(), options.subdirectoryName(), options.fileSuffixes(),
+                options.exclusionFileName(), options.similarityMetric(), options.similarityThreshold(), options.maximumNumberOfComparisons(),
+                options.clusteringOptions(), options.debugParser());
+    }
+
+    /**
+     * @return a new options instance
+     */
+    public JPlagOptions getOptions() {
+        return options;
+    }
+
+    /**
+     * @return the statistic map
+     */
+    public Map<String, Integer> getStatistic() {
+        return statistic;
+    }
+
+    /**
+     * Counts the root directory names and their number with Map(named statistic).
+     * @param submissionDirectories SubmissionDirectories that need to be counted
+     */
+    public void rootsClassification(Set<File> submissionDirectories) {
+        if (submissionDirectories == null)
+            return;
+        for (File submissionDirectory : submissionDirectories) {
+            String rootDirectory = getRootName(submissionDirectory);
+            statistic.put(rootDirectory, statistic.getOrDefault(rootDirectory, 0) + 1);
+        }
+    }
+
+    /**
+     * Renames the same root directory name.
+     * @param submissionDirectories SubmissionDirectories that need to be re-named
+     * @return SubmissionDirectories that have been re-named
+     */
+    public Set<File> renameRoots(Set<File> submissionDirectories) {
+        if (submissionDirectories == null)
+            return Set.of();
+        Set<File> set = new HashSet<>();
+        for (File submissionDirectory : submissionDirectories) {
+            String rootDirectory = getRootName(submissionDirectory);
+            int index = statistic.getOrDefault(rootDirectory, -1);
+            if (index == -1)
+                continue;
+            String newRootDirectory = rootDirectory + "_" + index;
+            statistic.put(rootDirectory, statistic.get(rootDirectory) - 1);
+            File newFile = new File(Path.of(submissionDirectory.getParent(), newRootDirectory).toString());
+            set.add(newFile);
+            submissionDirectory.renameTo(newFile);
+            logger.info("Original submission path ===> Current submission path:" + submissionDirectory.getPath() + " ===> " + newFile.getPath());
+        }
+        return Set.copyOf(set);
+    }
+
+    /**
+     * Gets root name of a submissionDirectory.
+     * @param submissionDirectory A single submissionDirectory
+     * @return Root name of the submission
+     */
+    public String getRootName(File submissionDirectory) {
+        return submissionDirectory.getPath().substring(submissionDirectory.getParent().length() + 1);
+    }
+
+    /**
+     * Determines if there are the same root directories.
+     * @param newSubmissionDirectories The new submissionDirectories
+     * @param oldSubmissionDirectories The old submissionDirectories
+     * @return True, if there are the same root directories. False, otherwise.
+     */
+    public boolean hasSameRoots(Set<File> newSubmissionDirectories, Set<File> oldSubmissionDirectories) throws RootDirectoryException {
+        checkDirectoryExist(newSubmissionDirectories);
+        checkDirectoryExist(oldSubmissionDirectories);
+        rootsClassification(newSubmissionDirectories);
+        rootsClassification(oldSubmissionDirectories);
+        Set<Map.Entry<String, Integer>> entries = statistic.entrySet();
+        entries.removeIf(entry -> entry.getValue() == 1);
+        return !statistic.isEmpty();
+    }
+
+    /**
+     * Checks if directories exist. If not, throws RootDirectoryException.
+     * @param submissionDirectories The submissionDirectories which needs to be checked
+     */
+    public void checkDirectoryExist(Set<File> submissionDirectories) throws RootDirectoryException {
+        for (File submissionDirectory : submissionDirectories) {
+            boolean exists = submissionDirectory.exists();
+            if (!exists) {
+                throw new RootDirectoryException("Submission Directory doesn't exist: " + submissionDirectory.getPath());
+            }
+        }
+    }
+}

core/src/main/java/de/jplag/reporting/jsonfactory/ComparisonReportWriter.java

@@ -106,9 +106,9 @@ private Match convertMatchToReportMatch(JPlagComparison comparison, de.jplag.Mat
 
     private String relativizedFilePath(File file, Submission submission) {
         if (file.toPath().equals(submission.getRoot().toPath())) {
-            return Path.of(submission.getName(), submission.getName()).toString();
+            return Path.of(submissionToIdFunction.apply(submission), submission.getName()).toString();
         }
-        return Path.of(submission.getName(), submission.getRoot().toPath().relativize(file.toPath()).toString()).toString();
+        return Path.of(submissionToIdFunction.apply(submission), submission.getRoot().toPath().relativize(file.toPath()).toString()).toString();
     }
 
 }

core/src/main/java/de/jplag/reporting/jsonfactory/DirectoryManager.java

@@ -34,8 +34,7 @@ public static File createDirectory(String path, String name, File file, File sub
         File directory;
         String fileName = file.getPath();
         String submissionRootPath = submissionRoot.getPath();
-        int lastDirectoryIndex = findRootDirIndex(name, submissionRootPath);
-        fileName = fileName.substring(lastDirectoryIndex).replaceFirst(name, "");
+        fileName = fileName.substring(submissionRootPath.length());
         String outputRootDirectory = Path.of(path, name).toString();
         if ("".equals(fileName)) {
             directory = new File(Path.of(outputRootDirectory, name).toString());
@@ -119,15 +118,4 @@ public FileVisitResult visitFileFailed(Path file, IOException exc) throws IOExce
         logger.info("Display the results with the report viewer at https://jplag.github.io/JPlag/");
         return true;
     }
-
-    /**
-     * finds the start index of root directory according to this name
-     * @param name The name of the root directory. According to this name we can find the index of this directory.
-     * @param submissionRootPath The path of the root directory
-     * @return The start index of the root directory
-     */
-    public static int findRootDirIndex(String name, String submissionRootPath) {
-        int submissionRootPathLength = submissionRootPath.length();
-        return submissionRootPathLength - name.length();
-    }
 }

core/src/test/java/de/jplag/PreventSameRootNameTest.java

@@ -0,0 +1,85 @@
+package de.jplag;
+
+import static org.junit.jupiter.api.Assertions.fail;
+
+import java.io.File;
+import java.nio.file.Path;
+import java.util.Set;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.DisplayName;
+import org.junit.jupiter.api.Test;
+
+import de.jplag.exceptions.RootDirectoryException;
+import de.jplag.options.JPlagOptions;
+
+/**
+ * Test for the same root cases that will be re-named.
+ */
+public class PreventSameRootNameTest extends TestBase {
+
+    private static final JPlagOptions BASEOPTIONS = new JPlagOptions(new de.jplag.java.Language(), Set.of(), Set.of());
+    private static final String NOTEXISTDIRECTORY = Path.of(TestBase.BASE_PATH, "basecode", "NotExistDirectory").toString();
+    private static final String SAMPLE_SAMEROOTNAME_1 = Path.of(TestBase.BASE_PATH, "SameRootName", "2019", "root").toString();
+    private static final String SAMPLE_SAMEROOTNAME_2 = Path.of(TestBase.BASE_PATH, "SameRootName", "2020", "root").toString();
+
+    @Test
+    @DisplayName("test same root directory with withSubmissionDirectories options")
+    void testSameRootWithNew() {
+        JPlagOptions options = BASEOPTIONS.withSubmissionDirectories(Set.of(new File(SAMPLE_SAMEROOTNAME_1), new File(SAMPLE_SAMEROOTNAME_2)));
+        try {
+            PreventSameRootName preventSameRootName = new PreventSameRootName(options);
+            JPlagOptions newOptions = preventSameRootName.getOptions();
+            File submissionDirectory_2 = options.submissionDirectories().stream().toList().get(0);
+            File submissionDirectory_1 = options.submissionDirectories().stream().toList().get(1);
+            File newChangedSubmissionDirectory_2 = newOptions.submissionDirectories().stream().toList().get(0);
+            File newChangedSubmissionDirectory_1 = newOptions.submissionDirectories().stream().toList().get(1);
+            Assertions.assertEquals(submissionDirectory_2.getPath() + "_2", newChangedSubmissionDirectory_2.getPath());
+            Assertions.assertEquals(submissionDirectory_1.getPath() + "_1", newChangedSubmissionDirectory_1.getPath());
+        } catch (RootDirectoryException e) {
+            fail("PreventSameRootName Class threw an exception:", e);
+        }
+    }
+
+    @Test
+    @DisplayName("test same root directory with withSubmissionDirectories and oldSubmissionDirectories options")
+    void testSameRootWithNewAndOld() {
+        JPlagOptions options = BASEOPTIONS.withSubmissionDirectories(Set.of(new File(SAMPLE_SAMEROOTNAME_2)))
+                .withOldSubmissionDirectories(Set.of(new File(SAMPLE_SAMEROOTNAME_1)));
+        try {
+            PreventSameRootName preventSameRootName = new PreventSameRootName(options);
+            JPlagOptions newOptions = preventSameRootName.getOptions();
+            File oldSubmissionDirectory = options.oldSubmissionDirectories().stream().toList().get(0);
+            File submissionDirectory = options.submissionDirectories().stream().toList().get(0);
+            File newChangedOldSubmissionDirectory = newOptions.oldSubmissionDirectories().stream().toList().get(0);
+            File newChangedSubmissionDirectory = newOptions.submissionDirectories().stream().toList().get(0);
+            Assertions.assertEquals(submissionDirectory.getPath() + "_2", newChangedSubmissionDirectory.getPath());
+            Assertions.assertEquals(oldSubmissionDirectory.getPath() + "_1", newChangedOldSubmissionDirectory.getPath());
+        } catch (RootDirectoryException e) {
+            fail("PreventSameRootName Class threw an exception:", e);
+        }
+    }
+
+    @Test
+    @DisplayName("test not existed root directory with withSubmissionDirectories option")
+    void testCheckDirectoryExistWithNewSubmissionDirectories() {
+        JPlagOptions options = BASEOPTIONS.withSubmissionDirectories(Set.of(new File(NOTEXISTDIRECTORY)));
+        testRootDirectoryException(options);
+    }
+
+    @Test
+    @DisplayName("test not existed root directory with withOldSubmissionDirectories option")
+    void testCheckDirectoryExistWithOldSubmissionDirectories() {
+        JPlagOptions options = BASEOPTIONS.withOldSubmissionDirectories(Set.of(new File(NOTEXISTDIRECTORY)));
+        testRootDirectoryException(options);
+    }
+
+    /**
+     * Test RootDirectoryException for a given Jplag-options.
+     * @param options is the customized Jplag-options.
+     */
+    void testRootDirectoryException(JPlagOptions options) {
+        RootDirectoryException exception = Assertions.assertThrows(RootDirectoryException.class, () -> new PreventSameRootName(options));
+        Assertions.assertEquals("Submission Directory doesn't exist: " + NOTEXISTDIRECTORY, exception.getMessage());
+    }
+}