Merge develop into main for the upcoming 5.0.0 major release

.github/workflows/maven.yml

@@ -1,7 +1,7 @@
 name: Build
 
 on:
-  push: 
+  push:
     paths:
       - ".github/workflows/maven.yml"
       - "**/pom.xml"
@@ -14,7 +14,7 @@ on:
       - "**/pom.xml"
       - "**.java"
       - "**.g4"
-  
+
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
@@ -43,17 +43,21 @@ jobs:
       with:
         java-version: 21
         distribution: 'temurin'
-
+
+    - uses: actions/setup-node@v4
+      with:
+        node-version: "18"
+
     - name: Run Tests
       run: mvn verify -B -U
-      
+
     - name: Build Assembly
-      run: mvn clean package assembly:single
-      
+      run: mvn -Pwith-report-viewer clean package assembly:single
+
     - name: Upload Assembly
       uses: actions/upload-artifact@v4
       with:
         name: "JPlag"
         path: "jplag.cli/target/jplag-*-jar-with-dependencies.jar"
-      
+
 

.github/workflows/publish.yml

@@ -13,7 +13,7 @@ jobs:
           java-version: '21'
           distribution: 'temurin'
       - name: Set maven settings.xml
-        uses: whelk-io/maven-settings-xml-action@v21
+        uses: whelk-io/maven-settings-xml-action@v22
         with:
           servers: '[{ "id": "ossrh", "username": "jplag", "password": "${{ secrets.OSSRH_TOKEN }}" }]'
       - name: Import GPG key
@@ -34,8 +34,12 @@ jobs:
         with:
           java-version: '21'
           distribution: 'temurin'
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "18"
+
       - name: Build JPlag
-        run: mvn -U -B clean package assembly:single
+        run: mvn -Pwith-report-viewer -U -B clean package assembly:single
 
       - name: Attach CLI to Release on GitHub
         uses: softprops/action-gh-release@v1

.github/workflows/sonarcloud-branch.yml

@@ -42,7 +42,7 @@ jobs:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-m2
-          
+
       - name: Build and analyze
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/sonarcloud-pr.yml

@@ -65,7 +65,7 @@ jobs:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-m2
-          
+
       - name: Build and analyze (PR)
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/spotless.yml

@@ -14,7 +14,7 @@ on:
       - "**/pom.xml"
       - "**.java"
       - "**.g4"
-  
+
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
@@ -43,9 +43,9 @@ jobs:
       with:
         java-version: 21
         distribution: 'temurin'
-      
+
     - name: Check with Spotless
       run: mvn clean spotless:check
-      
-      
+
+
 

cli/pom.xml

@@ -7,6 +7,7 @@
         <version>${revision}</version>
     </parent>
     <artifactId>cli</artifactId>
+
     <dependencies>
         <!-- IMPORTANT: For Coverage testing, you have to add dependencies to the coverage-report project ! -->
 
@@ -44,12 +45,12 @@
         </dependency>
         <dependency>
             <groupId>de.jplag</groupId>
-            <artifactId>cpp</artifactId>
+            <artifactId>c</artifactId>
             <version>${revision}</version>
         </dependency>
         <dependency>
             <groupId>de.jplag</groupId>
-            <artifactId>cpp2</artifactId>
+            <artifactId>cpp</artifactId>
             <version>${revision}</version>
         </dependency>
         <dependency>
@@ -128,6 +129,12 @@
             <artifactId>picocli</artifactId>
             <version>4.7.5</version>
         </dependency>
+
+        <dependency>
+            <groupId>me.tongfei</groupId>
+            <artifactId>progressbar</artifactId>
+            <version>0.10.0</version>
+        </dependency>
     </dependencies>
     <build>
         <plugins>
@@ -161,4 +168,56 @@
             </plugin>
         </plugins>
     </build>
+
+    <profiles>
+        <profile>
+            <id>with-report-viewer</id>
+            <build>
+                <resources>
+                    <resource>
+                        <targetPath>report-viewer</targetPath>
+                        <directory>../report-viewer/dist</directory>
+                    </resource>
+                </resources>
+                <plugins>
+                    <plugin>
+                        <groupId>org.codehaus.mojo</groupId>
+                        <artifactId>exec-maven-plugin</artifactId>
+                        <version>1.3.2</version>
+                        <executions>
+                            <execution>
+                                <id>npm install</id>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <phase>generate-resources</phase>
+                                <configuration>
+                                    <executable>npm</executable>
+                                    <workingDirectory>../report-viewer</workingDirectory>
+                                    <arguments>
+                                        <argument>install</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+                            <execution>
+                                <id>npm build</id>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <phase>generate-resources</phase>
+                                <configuration>
+                                    <executable>npm</executable>
+                                    <workingDirectory>../report-viewer</workingDirectory>
+                                    <arguments>
+                                        <argument>run</argument>
+                                        <argument>build</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
 </project>

cli/src/main/java/de/jplag/cli/CLI.java

@@ -4,7 +4,11 @@
 import static picocli.CommandLine.Model.UsageMessageSpec.SECTION_KEY_OPTION_LIST;
 import static picocli.CommandLine.Model.UsageMessageSpec.SECTION_KEY_SYNOPSIS;
 
+import java.awt.Desktop;
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URI;
 import java.security.SecureRandom;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -21,9 +25,12 @@
 import de.jplag.JPlagResult;
 import de.jplag.Language;
 import de.jplag.cli.logger.CollectedLoggerFactory;
+import de.jplag.cli.logger.TongfeiProgressBarProvider;
+import de.jplag.cli.server.ReportViewer;
 import de.jplag.clustering.ClusteringOptions;
 import de.jplag.clustering.Preprocessing;
 import de.jplag.exceptions.ExitException;
+import de.jplag.logging.ProgressBarLogger;
 import de.jplag.merging.MergingOptions;
 import de.jplag.options.JPlagOptions;
 import de.jplag.options.LanguageOption;
@@ -45,12 +52,12 @@ public final class CLI {
 
     private static final Random RANDOM = new SecureRandom();
 
-    private static final String CREDITS = "Created by IPD Tichy, Guido Malpohl, and others. JPlag logo designed by Sandro Koch. Currently maintained by Sebastian Hahner and Timur Saglam.";
+    private static final String CREDITS = "Created by IPD Tichy, Guido Malpohl, and others. Maintained by Timur Saglam and Sebastian Hahner. Logo by Sandro Koch.";
 
     private static final String[] DESCRIPTIONS = {"Detecting Software Plagiarism", "Software-Archaeological Playground", "Since 1996",
             "Scientifically Published", "Maintained by SDQ", "RIP Structure and Table", "What else?", "You have been warned!", "Since Java 1.0",
-            "More Abstract than Tree", "Students Nightmare", "No, changing variable names does not work", "The tech is out there!",
-            "Developed by plagiarism experts."};
+            "More Abstract than Tree", "Students Nightmare", "No, changing variable names does not work...", "The tech is out there!",
+            "Developed by plagiarism experts.", "State of the Art Obfuscation Resilience", "www.helmholtz.software/software/jplag"};
 
     private static final String OPTION_LIST_HEADING = "Parameter descriptions: ";
 
@@ -63,6 +70,8 @@ public final class CLI {
 
     private static final String DESCRIPTION_PATTERN = "%nJPlag - %s%n%s%n%n";
 
+    private static final String DEFAULT_FILE_ENDING = ".zip";
+
     /**
      * Main class for using JPlag via the CLI.
      * @param args are the CLI arguments that will be passed to JPlag.
@@ -76,15 +85,20 @@ public static void main(String[] args) {
             ParseResult parseResult = cli.parseOptions(args);
 
             if (!parseResult.isUsageHelpRequested() && !(parseResult.subcommand() != null && parseResult.subcommand().isUsageHelpRequested())) {
-                JPlagOptions options = cli.buildOptionsFromArguments(parseResult);
-                JPlagResult result = JPlag.run(options);
-                ReportObjectFactory reportObjectFactory = new ReportObjectFactory();
-                reportObjectFactory.createAndSaveReport(result, cli.getResultFolder());
-
-                OutputFileGenerator.generateCsvOutput(result, new File(cli.getResultFolder()), cli.options);
+                ProgressBarLogger.setProgressBarProvider(new TongfeiProgressBarProvider());
+                switch (cli.options.mode) {
+                    case RUN -> cli.runJPlag(parseResult);
+                    case VIEW -> cli.runViewer(null);
+                    case RUN_AND_VIEW -> cli.runViewer(cli.runJPlag(parseResult));
+                }
+            }
+        } catch (ExitException | IOException exception) { // do not pass exceptions here to keep log clean
+            if (exception.getCause() != null) {
+                logger.error("{} - {}", exception.getMessage(), exception.getCause().getMessage());
+            } else {
+                logger.error(exception.getMessage());
             }
-        } catch (ExitException exception) {
-            logger.error(exception.getMessage()); // do not pass exception here to keep log clean
+
             finalizeLogger();
             System.exit(1);
         }
@@ -102,9 +116,8 @@ public CLI() {
         this.commandLine.getHelpSectionMap().put(SECTION_KEY_OPTION_LIST, help -> help.optionList().lines().map(it -> {
             if (it.startsWith("  -")) {
                 return "    " + it;
-            } else {
-                return it;
             }
+            return it;
         }).collect(Collectors.joining(System.lineSeparator())));
 
         buildSubcommands().forEach(commandLine::addSubcommand);
@@ -114,6 +127,29 @@ public CLI() {
         this.commandLine.setAllowSubcommandsAsOptionParameters(true);
     }
 
+    public File runJPlag(ParseResult parseResult) throws ExitException, FileNotFoundException {
+        JPlagOptions jplagOptions = buildOptionsFromArguments(parseResult);
+        JPlagResult result = JPlag.run(jplagOptions);
+        File target = new File(getResultFilePath());
+        ReportObjectFactory reportObjectFactory = new ReportObjectFactory(target);
+        reportObjectFactory.createAndSaveReport(result);
+        logger.info("Successfully written the result: {}", target.getPath());
+        logger.info("View the result using --mode or at: https://jplag.github.io/JPlag/");
+        OutputFileGenerator.generateCsvOutput(result, new File(getResultFileBaseName()), this.options);
+        return target;
+    }
+
+    public void runViewer(File zipFile) throws IOException {
+        ReportViewer reportViewer = new ReportViewer(zipFile, this.options.advanced.port);
+        int port = reportViewer.start();
+        logger.info("ReportViewer started on port http://localhost:{}", port);
+        Desktop.getDesktop().browse(URI.create("http://localhost:" + port + "/"));
+
+        System.out.println("Press Enter key to exit...");
+        System.in.read();
+        reportViewer.stop();
+    }
+
     private List<CommandSpec> buildSubcommands() {
         return LanguageLoader.getAllAvailableLanguages().values().stream().map(language -> {
             CommandSpec command = CommandSpec.create().name(language.getIdentifier());
@@ -143,7 +179,7 @@ public ParseResult parseOptions(String... args) throws CliException {
             }
             return result;
         } catch (CommandLine.ParameterException e) {
-            if (e.getArgSpec().isOption() && Arrays.asList(((OptionSpec) e.getArgSpec()).names()).contains("-l")) {
+            if (e.getArgSpec() != null && e.getArgSpec().isOption() && Arrays.asList(((OptionSpec) e.getArgSpec()).names()).contains("-l")) {
                 throw new CliException(String.format(UNKOWN_LANGAUGE_EXCEPTION, e.getValue(),
                         String.join(", ", LanguageLoader.getAllAvailableLanguageIdentifiers())));
             }
@@ -181,33 +217,31 @@ public JPlagOptions buildOptionsFromArguments(ParseResult parseResult) throws Cl
         JPlagOptions jPlagOptions = new JPlagOptions(loadLanguage(parseResult), this.options.minTokenMatch, submissionDirectories,
                 oldSubmissionDirectories, null, this.options.advanced.subdirectory, suffixes, this.options.advanced.exclusionFileName,
                 JPlagOptions.DEFAULT_SIMILARITY_METRIC, this.options.advanced.similarityThreshold, this.options.shownComparisons, clusteringOptions,
-                this.options.advanced.debug, mergingOptions);
+                this.options.advanced.debug, mergingOptions, this.options.normalize);
 
         String baseCodePath = this.options.baseCode;
         File baseCodeDirectory = baseCodePath == null ? null : new File(baseCodePath);
         if (baseCodeDirectory == null || baseCodeDirectory.exists()) {
             return jPlagOptions.withBaseCodeSubmissionDirectory(baseCodeDirectory);
-        } else {
-            logger.warn("Using legacy partial base code API. Please migrate to new full path base code API.");
-            return jPlagOptions.withBaseCodeSubmissionName(baseCodePath);
         }
+        logger.warn("Using legacy partial base code API. Please migrate to new full path base code API.");
+        return jPlagOptions.withBaseCodeSubmissionName(baseCodePath);
     }
 
     private Language loadLanguage(ParseResult result) throws CliException {
-        if (result.subcommand() != null) {
-            ParseResult subcommandResult = result.subcommand();
-            Language language = LanguageLoader.getLanguage(subcommandResult.commandSpec().name())
-                    .orElseThrow(() -> new CliException(IMPOSSIBLE_EXCEPTION));
-            LanguageOptions languageOptions = language.getOptions();
-            languageOptions.getOptionsAsList().forEach(option -> {
-                if (subcommandResult.hasMatchedOption(option.getNameAsUnixParameter())) {
-                    option.setValue(subcommandResult.matchedOptionValue(option.getNameAsUnixParameter(), null));
-                }
-            });
-            return language;
-        } else {
+        if (result.subcommand() == null) {
             return this.options.language;
         }
+        ParseResult subcommandResult = result.subcommand();
+        Language language = LanguageLoader.getLanguage(subcommandResult.commandSpec().name())
+                .orElseThrow(() -> new CliException(IMPOSSIBLE_EXCEPTION));
+        LanguageOptions languageOptions = language.getOptions();
+        languageOptions.getOptionsAsList().forEach(option -> {
+            if (subcommandResult.hasMatchedOption(option.getNameAsUnixParameter())) {
+                option.setValue(subcommandResult.matchedOptionValue(option.getNameAsUnixParameter(), null));
+            }
+        });
+        return language;
     }
 
     private static ClusteringOptions getClusteringOptions(CliOptions options) {
@@ -249,7 +283,16 @@ private String generateDescription() {
         return String.format(DESCRIPTION_PATTERN, randomDescription, CREDITS);
     }
 
-    public String getResultFolder() {
-        return this.options.resultFolder;
+    private String getResultFilePath() {
+        String optionValue = this.options.resultFile;
+        if (optionValue.endsWith(DEFAULT_FILE_ENDING)) {
+            return optionValue;
+        }
+        return optionValue + DEFAULT_FILE_ENDING;
+    }
+
+    private String getResultFileBaseName() {
+        String defaultOutputFile = getResultFilePath();
+        return defaultOutputFile.substring(0, defaultOutputFile.length() - DEFAULT_FILE_ENDING.length());
     }
 }