Upgrade javaparser and enhance the fail message for parse exceptions

gradle/dependencies.gradle

@@ -35,7 +35,7 @@ def versions = [
         errorProne             : defaultErrorProneVersion,
         errorProneApi          : project.hasProperty("epApiVersion") ? epApiVersion : oldestErrorProneApi,
         autoService            : "1.0-rc7",
-        javaparser             : "3.26.0",
+        javaparser             : "3.26.2",
         json                   : "1.1.1",
         guava                  : "31.0.1-jre",
         cli                    : "1.5.0",

injector/src/main/java/edu/ucr/cs/riple/injector/Injector.java

@@ -24,6 +24,7 @@
 
 import static java.util.stream.Collectors.groupingBy;
 
+import com.github.javaparser.ParseProblemException;
 import com.github.javaparser.ParserConfiguration;
 import com.github.javaparser.StaticJavaParser;
 import com.github.javaparser.ast.CompilationUnit;
@@ -33,6 +34,7 @@
 import edu.ucr.cs.riple.injector.changes.AnnotationChange;
 import edu.ucr.cs.riple.injector.changes.ChangeVisitor;
 import edu.ucr.cs.riple.injector.changes.RemoveAnnotation;
+import edu.ucr.cs.riple.injector.exceptions.ParseException;
 import edu.ucr.cs.riple.injector.modifications.Modification;
 import edu.ucr.cs.riple.injector.offsets.FileOffsetStore;
 import java.io.IOException;
@@ -171,6 +173,9 @@ public static CompilationUnit parse(
     StaticJavaParser.setConfiguration(parserConfiguration);
     try {
       return StaticJavaParser.parse(path);
+    } catch (ParseProblemException e) {
+      // The original exception is not useful for the user. We should provide a more informative one
+      throw new ParseException(path, e);
     } catch (NoSuchFileException e) {
       return null;
     } catch (IOException e) {

injector/src/main/java/edu/ucr/cs/riple/injector/exceptions/ParseException.java

@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2024 University of California, Riverside.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package edu.ucr.cs.riple.injector.exceptions;
+
+import com.github.javaparser.ParseProblemException;
+import java.nio.file.Path;
+
+/**
+ * Exception indicating that an error occurred while parsing a source file.
+ *
+ * <p>This serves as a wrapper for the {@link ParseProblemException} class, providing a more concise
+ * representation of the underlying issue.
+ */
+public class ParseException extends RuntimeException {
+
+  public ParseException(Path path, ParseProblemException exception) {
+    super(retrieveExceptionMessage(path, exception));
+  }
+
+  private static String retrieveExceptionMessage(Path path, ParseProblemException e) {
+    String message = e.getMessage();
+    // If the message contains the stack trace, we should remove it. It does not contain any useful
+    // information.
+    int index = message.indexOf("Problem stacktrace :");
+    message = index == -1 ? message : message.substring(0, index);
+    return "javaparser was not able to parse file at: " + path + "\nParse problem:" + message;
+  }
+}