fixes

Author: pmbittner

src/main/java/org/variantsync/vevos/simulation/io/TextIO.java

@@ -136,6 +136,18 @@ public static void write(final Path p, final String text) throws IOException {
         Files.writeString(p, text, StandardCharsets.UTF_8, StandardOpenOption.CREATE_NEW);
     }
 
+    /**
+     * Append the given text to the given file.
+     * Assumes that the given file already exists.
+     *
+     * @param p    Existing file to append text to.
+     * @param text Text to write to file.
+     * @throws IOException if an I/O error occurs while writing to the file, or the text cannot be encoded using the specified charset.
+     */
+    public static void append(final Path p, final String text) throws IOException {
+        Files.writeString(p, text, StandardCharsets.UTF_8, StandardOpenOption.APPEND);
+    }
+
     public static String readAsString(final Path p) throws IOException {
         try (final BufferedReader reader = new BufferedReader(new FileReader(p.toFile()))) {
             return reader.lines().collect(Collectors.joining());

src/main/java/org/variantsync/vevos/simulation/variability/pc/SourceCodeFile.java

@@ -71,7 +71,7 @@ public Result<GroundTruth, Exception> generateVariant(
                             .readLines(sourceFile.path())
                             .bind(splLines -> Result.Try(() ->
                                     // write all lines that should be included in the variant to the text file
-                                    TextIO.write(
+                                    TextIO.append(
                                             targetFile.path(),
                                             String.join(
                                                     TextIO.LINEBREAK,

src/main/java/org/variantsync/vevos/simulation/variability/pc/variantlines/VariantLine.java

@@ -1,12 +1,35 @@
 package org.variantsync.vevos.simulation.variability.pc.variantlines;
 
+import org.variantsync.vevos.simulation.util.Logger;
 import org.variantsync.vevos.simulation.variability.pc.options.VariantGenerationOptions;
 
 import java.util.List;
 
 public record VariantLine(Integer lineNumber) implements VariantLineChunk {
     @Override
     public List<String> project(final VariantGenerationOptions projectionOptions, final List<String> splFileLines) {
-        return List.of(splFileLines.get(lineNumber - 1));
+        // The list splFileLines is 0-based.
+        // Our lineNumber is 1-based because line numbers are typically given 1-based.
+        final int sourceLineNo = lineNumber - 1;
+
+        if (sourceLineNo >= splFileLines.size()) {
+            final String logMessage = "Skipped copying line "
+                    + sourceLineNo
+                    + " as it is out of bounds [1, "
+                    + splFileLines.size()
+                    + "]!";
+
+            if (sourceLineNo > splFileLines.size()) {
+                // This was logged frequently and is caused by https://bugs.openjdk.java.net/browse/JDK-8199413
+                // Skipping the line really is the best solution, as the empty line is created by appending a line separator
+                // to the previous line. I added the additional if-statement, to only catch cases in which more than one line
+                // is out of bounds, which indicates a serious problem.
+                Logger.error(logMessage);
+            }
+
+            return List.of();
+        } else {
+            return List.of(splFileLines.get(sourceLineNo));
+        }
     }
 }