Merge remote-tracking branch 'origin/develop' into report-viewer/print

# Conflicts:
#	report-viewer/src/views/ComparisonView.vue

.github/workflows/report-viewer-demo.yml

@@ -0,0 +1,113 @@
+name: Report Viewer Demo Deployment
+
+on:
+  workflow_dispatch: # Use this to dispatch from the Actions Tab
+  push:
+    branches:
+      - main
+
+jobs:
+  build-jar:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21
+          distribution: 'temurin'
+
+      - name: Build Assembly
+        run: mvn clean package assembly:single
+
+      - name: Upload Assembly
+        uses: actions/upload-artifact@v3
+        with:
+          name: "JPlag"
+          path: "cli/target/jplag-*-jar-with-dependencies.jar"
+
+
+  run-example:
+    needs: build-jar
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21
+          distribution: 'temurin'
+
+      - name: Get JAR
+        uses: actions/download-artifact@v3
+        with:
+          name: JPlag
+
+      - name: Copy and unzip submissions
+        run: unzip ./.github/workflows/files/progpedia.zip
+
+      - name: Rename jar
+        run: mv *.jar ./jplag.jar
+
+      - name: Run JPlag
+        run: java -jar jplag.jar ACCEPTED -bc base -r example
+
+      - name: Upload Result
+        uses: actions/upload-artifact@v3
+        with:
+          name: "Result"
+          path: "example.zip"
+
+
+  build-and-deploy:
+    needs: run-example
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "18"
+
+      - name: Set version of Report Viewer
+        shell: bash
+        run: |
+          VERSION=$(grep "<revision>" pom.xml | grep -oPm1 "(?<=<revision>)[^-|<]+")
+          MAJOR=$(echo $VERSION | cut -d '.' -f 1)
+          MINOR=$(echo $VERSION | cut -d '.' -f 2)
+          PATCH=$(echo $VERSION | cut -d '.' -f 3)
+          json=$(cat report-viewer/src/version.json)
+          json=$(echo "$json" | jq --arg MAJOR "$MAJOR" --arg MINOR "$MINOR" --arg PATCH "$PATCH" '.report_viewer_version |= { "major": $MAJOR | tonumber, "minor": $MINOR | tonumber, "patch": $PATCH | tonumber }')
+          echo "$json" >  report-viewer/src/version.json
+          echo "Version of Report Viewer:"
+          cat report-viewer/src/version.json
+      
+      - name: Download Results
+        uses: actions/download-artifact@v3
+        with:
+          name: Result
+          path: report-viewer/public
+
+      - name: Install and Build 🔧
+        working-directory: report-viewer
+        run: |
+          npm install
+          npm run build-demo
+        
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          branch: gh-pages
+          folder: report-viewer/dist
+          repository-name: JPlag/Demo
+          token: ${{ secrets.SDQ_DEV_DEPLOY_TOKEN }}
+          clean: true
+          single-commit: true
+

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

@@ -78,6 +78,8 @@ public static void main(String[] args) {
                 JPlagResult result = JPlag.run(options);
                 ReportObjectFactory reportObjectFactory = new ReportObjectFactory();
                 reportObjectFactory.createAndSaveReport(result, cli.getResultFolder());
+
+                OutputFileGenerator.generateCsvOutput(result, new File(cli.getResultFolder()), cli.options);
             }
         } catch (ExitException exception) {
             logger.error(exception.getMessage()); // do not pass exception here to keep log clean

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

@@ -88,6 +88,9 @@ public static class Advanced {
                 "--similarity-threshold"}, description = "Comparison similarity threshold [0.0-1.0]:  All  comparisons  above this threshold will "
                         + "be saved (default: ${DEFAULT-VALUE})%n")
         public double similarityThreshold = JPlagOptions.DEFAULT_SIMILARITY_THRESHOLD;
+
+        @Option(names = "--csv-export", description = "If present, a csv export will be generated in addition to the zip file.")
+        public boolean csvExport = false;
     }
 
     public static class Clustering {

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

@@ -0,0 +1,36 @@
+package de.jplag.cli;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import de.jplag.JPlagResult;
+import de.jplag.csv.comparisons.CsvComparisonOutput;
+
+public final class OutputFileGenerator {
+    private static final Logger logger = LoggerFactory.getLogger(OutputFileGenerator.class);
+
+    private OutputFileGenerator() {
+        // Prevents default constructor
+    }
+
+    /**
+     * Exports the given result as csvs, if the csvExport is activated in the options. Both a full and an anonymized version
+     * will be written.
+     * @param result The result to export
+     * @param outputRoot The root folder for the output
+     * @param options The cli options
+     */
+    public static void generateCsvOutput(JPlagResult result, File outputRoot, CliOptions options) {
+        if (options.advanced.csvExport) {
+            try {
+                CsvComparisonOutput.writeCsvResults(result.getAllComparisons(), false, outputRoot, "results");
+                CsvComparisonOutput.writeCsvResults(result.getAllComparisons(), true, outputRoot, "results-anonymous");
+            } catch (IOException e) {
+                logger.warn("Could not write csv results", e);
+            }
+        }
+    }
+}

core/src/main/java/de/jplag/csv/CsvDataMapper.java

@@ -0,0 +1,22 @@
+package de.jplag.csv;
+
+import java.util.Optional;
+
+/**
+ * Provides mappings for csv rows and optionally names for the columns. Needs to always return the same number of
+ * columns.
+ * @param <T> The type of data that is mapped
+ */
+public interface CsvDataMapper<T> {
+    /**
+     * Provides the cell values for one row
+     * @param value The original object
+     * @return The cell values
+     */
+    String[] provideData(T value);
+
+    /**
+     * @return The names of the columns if present
+     */
+    Optional<String[]> getTitleRow();
+}

core/src/main/java/de/jplag/csv/CsvPrinter.java

@@ -0,0 +1,144 @@
+package de.jplag.csv;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Optional;
+
+import de.jplag.util.FileUtils;
+
+/**
+ * Prints a csv according to the specification in
+ * <a href="https://datatracker.ietf.org/doc/html/rfc4180#section-2">...</a>. If you need to deviate from this
+ * definition slightly you can modify the line end and separator characters.
+ * @param <T>
+ */
+public class CsvPrinter<T> {
+    private static final char DEFAULT_SEPARATOR = ',';
+    private static final String DEFAULT_LINE_END = "\r\n"; // not System.lineSeparator(), because of csv specification
+    private static final char LITERAL = '"';
+
+    private final CsvDataMapper<T> dataSource;
+    private final List<String[]> data;
+
+    private char separator;
+    private String lineEnd;
+
+    /**
+     * @param dataSource The data source used to map the given object to rows.
+     */
+    public CsvPrinter(CsvDataMapper<T> dataSource) {
+        this.dataSource = dataSource;
+        this.data = new ArrayList<>();
+
+        this.separator = DEFAULT_SEPARATOR;
+        this.lineEnd = DEFAULT_LINE_END;
+    }
+
+    /**
+     * Adds a new row to this csv
+     * @param value the value to add
+     */
+    public void addRow(T value) {
+        this.data.add(this.dataSource.provideData(value));
+    }
+
+    /**
+     * Adds multiple rows to this csv
+     * @param values The values to add
+     */
+    public void addRows(Collection<T> values) {
+        values.forEach(this::addRow);
+    }
+
+    /**
+     * Changes the separator between cells
+     * @param separator The new separator
+     */
+    public void setSeparator(char separator) {
+        this.separator = separator;
+    }
+
+    /**
+     * Sets the string to separate lines with
+     * @param lineEnd the new line end
+     */
+    public void setLineEnd(String lineEnd) {
+        this.lineEnd = lineEnd;
+    }
+
+    /**
+     * Prints this csv with all current data to a file
+     * @param file The file to write
+     * @throws IOException on io errors
+     */
+    public void printToFile(File file) throws IOException {
+        try (Writer writer = FileUtils.openFileWriter(file)) {
+            this.printCsv(writer);
+        }
+    }
+
+    public String printToString() throws IOException {
+        String csv;
+
+        try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream()) {
+            try (Writer writer = new OutputStreamWriter(outputStream)) {
+                this.printCsv(writer);
+            }
+
+            csv = outputStream.toString();
+        }
+
+        return csv;
+    }
+
+    private void printCsv(Writer writer) throws IOException {
+        this.writeTitleRow(writer);
+
+        for (String[] datum : this.data) {
+            this.printRow(writer, datum);
+        }
+    }
+
+    private void writeTitleRow(Writer writer) throws IOException {
+        Optional<String[]> titleRow = this.dataSource.getTitleRow();
+        if (titleRow.isPresent()) {
+            this.printRow(writer, titleRow.get());
+        }
+    }
+
+    private void printRow(Writer writer, String[] data) throws IOException {
+        Iterator<String> dataIterator = Arrays.stream(data).iterator();
+
+        if (dataIterator.hasNext()) {
+            printCell(writer, dataIterator.next());
+        }
+
+        while (dataIterator.hasNext()) {
+            writer.write(this.separator);
+            printCell(writer, dataIterator.next());
+        }
+
+        writer.write(this.lineEnd);
+    }
+
+    private void printCell(Writer writer, String cellValue) throws IOException {
+        boolean literalsNeeded = cellValue.contains(String.valueOf(LITERAL));
+        String actualValue = cellValue;
+        if (literalsNeeded) {
+            writer.write(LITERAL);
+            actualValue = actualValue.replace("\"", "\"\"");
+        }
+        writer.write(actualValue);
+        if (literalsNeeded) {
+            writer.write(LITERAL);
+        }
+    }
+}

core/src/main/java/de/jplag/csv/CsvValue.java

@@ -0,0 +1,18 @@
+package de.jplag.csv;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Used with {@link ReflectiveCsvDataMapper} to identify fields and methods, that should be used for the csv.
+ */
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD, ElementType.METHOD})
+public @interface CsvValue {
+    /**
+     * The index of the csv field. Has to be used as the compiler sometimes changes the order of fields/methods
+     */
+    int value();
+}