Refactoring search

.gitignore

@@ -11,6 +11,7 @@ benchmarking/datasets/
 benchmarking/outputs/
 benchmarking/sources/
 benchmarking/compiled_classes/
+searchResults/
 
 # Ignore IDE specific files
 .vscode

build.gradle

@@ -55,6 +55,9 @@ dependencies {
 	runtimeOnly 'org.apache.logging.log4j:log4j-core'
 	// Log4j JSON-encoding support
 	runtimeOnly 'org.apache.logging.log4j:log4j-layout-template-json'
+
+	// Argument parsing library
+	implementation 'info.picocli:picocli:4.7.7'
 }
 
 checkerFramework {

src/main/java/RefactoringEngine.java

@@ -1,5 +1,3 @@
-import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 import org.apache.logging.log4j.Logger;
@@ -19,32 +17,18 @@
  */
 public class RefactoringEngine {
 	private static final Logger LOGGER = LogManager.getLogger();
+	private static final Logger SEARCH_LOGGER = LogManager.getLogger("SearchLogger");
 
 	/**
 	 * List of refactorings to apply
 	 */
 	private final List<Refactoring> refactorings;
 
-	public RefactoringEngine(List<String> refactoringNames) {
-		refactorings = new ArrayList<>();
-
-		for (String name : refactoringNames) {
-			switch (name) {
-				case AddNullCheckBeforeDereferenceRefactoring.NAME ->
-					refactorings.add(new AddNullCheckBeforeDereferenceRefactoring());
-				case BooleanFlagRefactoring.NAME -> refactorings.add(new BooleanFlagRefactoring());
-				case SentinelRefactoring.NAME -> refactorings.add(new SentinelRefactoring());
-				case NestedNullRefactoring.NAME -> refactorings.add(new NestedNullRefactoring());
-				case "All" -> refactorings.addAll(Arrays.asList(new AddNullCheckBeforeDereferenceRefactoring(),
-						new BooleanFlagRefactoring(), new SentinelRefactoring(), new NestedNullRefactoring()));
-				default -> System.err.println("Unknown refactoring: " + name);
-			}
-
-			if (refactorings.isEmpty()) {
-				System.err.println("No valid refactorings specified. Exiting.");
-				System.exit(1);
-			}
+	public RefactoringEngine(List<Refactoring> refactorings) {
+		if (refactorings.isEmpty()) {
+			throw new IllegalArgumentException("No valid refactorings specified");
 		}
+		this.refactorings = refactorings;
 	}
 
 	/**
@@ -85,4 +69,43 @@ public void preVisit(ASTNode node) {
 		return document.get();
 	}
 
+	/**
+	 * Searches a given source file for applicable refactorings in
+	 * {@value refactorings} Search results are logged to a CSV file via a dedicated
+	 * logger ("SearchLogger")
+	 * 
+	 * @param cu
+	 *            The compilation unit to use
+	 * @param sourceCode
+	 *            A string containing the source code of the file to search through
+	 * @param filePath
+	 *            A string containing the patth of the file to search through
+	 * @param fileName
+	 *            A string containing the name of the file to search through
+	 */
+	public void searchRefactorings(CompilationUnit cu, String sourceCode, String filePath, String fileName) {
+		Document document = new Document(sourceCode);
+
+		for (Refactoring refactoring : refactorings) {
+			cu.accept(new ASTVisitor() {
+				@Override
+				public void preVisit(ASTNode node) {
+					LOGGER.debug("Visiting AST Node {}", node);
+
+					if (!refactoring.isApplicable(node)) {
+						return;
+					}
+
+					String refactoringModule = refactoring.getClass().getSimpleName();
+					int lineNumber = cu.getLineNumber(node.getStartPosition());
+					String nodeClass = node.getClass().getSimpleName();
+					// Escape all new lines and quote the code snippet to preserve csv formatting
+					String codeSnippet = "\"" + node.toString().replace("\"", "\"\"") + "\"";
+
+					SEARCH_LOGGER.info("{},{},{},{},{},{}", refactoringModule, filePath, fileName, lineNumber,
+							nodeClass, codeSnippet);
+				}
+			});
+		}
+	}
 }

src/main/java/VGRTool.java

@@ -3,7 +3,7 @@
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collections;
+import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -20,45 +20,65 @@
 import org.apache.logging.log4j.Logger;
 import org.checkerframework.checker.nullness.qual.NonNull;
 
+import picocli.CommandLine;
+import picocli.CommandLine.*;
+
 /**
  * Program entrypoint class; Runs the refactoring engine on given source code
  */
-public class VGRTool {
+@Command(name = "VGRTool", mixinStandardHelpOptions = true, version = "0.1", description = "Program entrypoint class; Runs the refactoring engine on given source code")
+public class VGRTool implements Runnable {
 
 	private static final Logger LOGGER = LogManager.getLogger();
 
+	// List of valid refactoring module names for Picocli
+	static class ValidRefactoringModules extends ArrayList<String> {
+		ValidRefactoringModules() {
+			super(List.of(AddNullCheckBeforeDereferenceRefactoring.NAME, BooleanFlagRefactoring.NAME,
+					SentinelRefactoring.NAME, NestedNullRefactoring.NAME, "All"));
+		}
+	}
+
+	// Picocli automatically assigns values to arguments during runtime,
+	// guaranteeing initialization
+	@SuppressWarnings("initialization.field.uninitialized")
+	// First position argument represents target directory
+	@Parameters(index = "0", description = "Path of directory to execute program on")
+	private String targetDir;
+
+	// Picocli automatically assigns values to arguments during runtime,
+	// guaranteeing initialization
+	@SuppressWarnings("initialization.field.uninitialized")
+	// All remaining positional arguments are parsed as module names.
+	@Parameters(index = "1", arity = "1..*", description = "Refactoring module(s) to use. Valid values: ${COMPLETION-CANDIDATES}", completionCandidates = ValidRefactoringModules.class)
+	private List<String> refactoringModules;
+
+	@Option(names = "--search", description = "Only search for valid refactorings without actually refactoring")
+	private static boolean searchOnly = false;
+
+	// Parses command-line arguments and executes run()
+	public static void main(String[] args) {
+		int exitCode = new CommandLine(new VGRTool()).execute(args);
+		System.exit(exitCode);
+	}
+
 	/**
 	 * Main method for the program; Runs refactorings to all Java files in a given
 	 * directory
-	 * 
-	 * @param args
-	 *            Path of directory to execute program on (args[0]) and refactoring
-	 *            modules to use (args[1...])
 	 */
-	public static void main(String[] args) {
-		if (args.length < 2) {
-
-			LOGGER.info("Usage: java VGRTool <sourceDirPath> <refactoringModules>");
-			LOGGER.info("Available Modules:");
-			LOGGER.info(" - " + AddNullCheckBeforeDereferenceRefactoring.NAME);
-			LOGGER.info(" - " + NestedNullRefactoring.NAME);
-			System.exit(1);
-		}
-
-		String targetDir = args[0];
-		String refactoringModule = args[1];
-
+	public void run() {
 		LOGGER.debug("Processing directory: {}", targetDir);
-		LOGGER.debug("Selected Refactoring Module: {}", refactoringModule);
+		LOGGER.debug("Selected Refactoring Module(s): {}", refactoringModules);
 
 		try {
 			// Step 1: Collect all Java files in the target directory
 			List<File> javaFiles = getJavaFiles(targetDir);
 
-			// Step 2: Process each Java file using the selected refactoring module
+			// Step 2: Process each Java file using the selected refactoring module(s)
 			for (File file : javaFiles) {
 				LOGGER.debug("Processing file: {}", file.getPath());
-				processFile(file, refactoringModule);
+				List<Refactoring> selectedRefactorings = processRefactorings(refactoringModules);
+				processFile(file, selectedRefactorings);
 			}
 
 			LOGGER.info("Refactoring completed successfully!");
@@ -67,6 +87,35 @@ public static void main(String[] args) {
 		}
 	}
 
+	/**
+	 * Parses and converts {@value refactoringModuleNames} into a list of
+	 * refactorings without duplicates.
+	 *
+	 * @param refactoringModuleNames
+	 *            A List<String> of refactoringModule names to parse
+	 **/
+	private static List<Refactoring> processRefactorings(List<String> refactoringModuleNames) {
+		List<Refactoring> refactorings = new ArrayList<>();
+		for (String name : refactoringModuleNames) {
+			switch (name) {
+				case AddNullCheckBeforeDereferenceRefactoring.NAME ->
+					refactorings.add(new AddNullCheckBeforeDereferenceRefactoring());
+				case BooleanFlagRefactoring.NAME -> refactorings.add(new BooleanFlagRefactoring());
+				case SentinelRefactoring.NAME -> refactorings.add(new SentinelRefactoring());
+				case NestedNullRefactoring.NAME -> refactorings.add(new NestedNullRefactoring());
+				case "All" -> refactorings.addAll(Arrays.asList(new AddNullCheckBeforeDereferenceRefactoring(),
+						new BooleanFlagRefactoring(), new SentinelRefactoring(), new NestedNullRefactoring()));
+				// Should already be caught by Picocli
+				default -> throw new IllegalArgumentException("Unknown refactoring module: " + name);
+			}
+		}
+
+		if (refactorings.isEmpty()) {
+			throw new IllegalArgumentException("No valid refactorings specified");
+		}
+		return refactorings;
+	}
+
 	/**
 	 * Returns a list of all java files in the given directory path
 	 * 
@@ -86,10 +135,10 @@ public static void main(String[] args) {
 	 * 
 	 * @param file
 	 *            The file to refactor
-	 * @param refactoringModule
+	 * @param refactoringModules
 	 *            the refactoring to apply to the file
 	 */
-	private static void processFile(File file, String refactoringModule) {
+	private static void processFile(File file, List<Refactoring> refactoringModules) {
 		try {
 			// Step 3: Read the file content
 			String content = Files.readString(file.toPath());
@@ -114,18 +163,22 @@ private static void processFile(File file, String refactoringModule) {
 
 			CompilationUnit cu = (CompilationUnit) parser.createAST(null);
 
-			// Step 5: Initialize RefactoringEngine with the selected module
-			List<String> selectedModules = Collections.singletonList(refactoringModule);
-			RefactoringEngine refactoringEngine = new RefactoringEngine(selectedModules);
+			// Step 5: Initialize RefactoringEngine with the selected modules
+			RefactoringEngine refactoringEngine = new RefactoringEngine(refactoringModules);
 
-			// Step 6: Apply refactorings using RefactoringEngine
+			// Step 6: Search or apply refactorings using RefactoringEngine
+			if (searchOnly) {
+				String filePath = file.getPath();
+				String fileName = file.getName();
+				refactoringEngine.searchRefactorings(cu, content, filePath, fileName);
+				return;
+			}
 			String refactoredSourceCode = refactoringEngine.applyRefactorings(cu, content);
 
 			// Step 7: Write the refactored code back to the file
 			Files.writeString(file.toPath(), refactoredSourceCode);
 
 			LOGGER.info("Refactored file saved: {}", file.getPath());
-
 		} catch (IOException e) {
 			LOGGER.error("Error processing file: {}", file.getPath(), e);
 		}

src/main/resources/log4j2.xml

@@ -4,10 +4,38 @@
         <Console name="Console" target="SYSTEM_OUT">
             <PatternLayout pattern="%d{HH:mm:ss.SSS} [%-5level] [%logger{36}]: %msg%n"/>
         </Console>
+
+        <!-- Creates a new file every time the program is run, rolling over the old file -->
+        <!-- The new file will be named according to fileName. -->
+        <!-- The rolled over file will be named according to filePattern: appended with the date and time of the rollover -->
+        <RollingFile name="SearchResults"
+                 fileName="searchResults/searchResults.csv"
+                 filePattern="searchResults/searchResults-%d{yyyy-MM-dd-HH-mm-ss}.csv"
+                 createOnDemand="true"
+                 append="true">
+
+            <!-- Only log passed message -->
+            <PatternLayout pattern="%msg%n">
+                <!-- Header is written once when the file is created -->
+                <Header>Refactoring Module,File Path,File Name,Line Number,Node Type,Code Snippet%n</Header>
+            </PatternLayout>
+
+            <Policies>
+                <!-- Rollover file every time the program is run -->
+                <OnStartupTriggeringPolicy />
+            </Policies>
+        </RollingFile>
     </Appenders>
+
     <Loggers>
+        <!-- All level "debug" and above logs sent to default logger are printed to the Console -->
         <Root level="debug">
             <AppenderRef ref="Console"/>
         </Root>
+
+        <!-- Logger for search results -->
+        <Logger name="SearchLogger" level="info" additivity="false">
+            <AppenderRef ref="SearchResults"/>
+        </Logger>
     </Loggers>
 </Configuration>

src/test/java/BooleanFlagTesting.java

@@ -8,7 +8,7 @@
 public class BooleanFlagTesting {
 
 	public void test(String input, String expectedOutput) {
-		TestingEngine.testSingleRefactoring(input, expectedOutput, "BooleanFlagRefactoring");
+		TestingEngine.testSingleRefactoring(input, expectedOutput, new BooleanFlagRefactoring());
 	}
 
 	@Test

src/test/java/DereferenceTesting.java

@@ -8,7 +8,7 @@
 public class DereferenceTesting {
 
 	public void test(String input, String expectedOutput) {
-		TestingEngine.testSingleRefactoring(input, expectedOutput, AddNullCheckBeforeDereferenceRefactoring.NAME);
+		TestingEngine.testSingleRefactoring(input, expectedOutput, new AddNullCheckBeforeDereferenceRefactoring());
 	}
 
 	@Test

src/test/java/NestedNullTesting.java

@@ -9,7 +9,7 @@
 public class NestedNullTesting {
 
 	public void test(String input, String expectedOutput) {
-		TestingEngine.testSingleRefactoring(input, expectedOutput, "NestedNullRefactoring");
+		TestingEngine.testSingleRefactoring(input, expectedOutput, new NestedNullRefactoring());
 	}
 
 	@Test

src/test/java/SentinelTesting.java

@@ -8,7 +8,7 @@
 public class SentinelTesting {
 
 	public void test(String input, String expectedOutput) {
-		TestingEngine.testSingleRefactoring(input, expectedOutput, "SentinelRefactoring");
+		TestingEngine.testSingleRefactoring(input, expectedOutput, new SentinelRefactoring());
 	}
 
 	@Test

src/test/java/TestingEngine.java

@@ -14,8 +14,8 @@ public class TestingEngine {
 	 * RefactoringEngine to use to run tests
 	 */
 	private static RefactoringEngine fullEngine = new RefactoringEngine(
-			Lists.newArrayList(AddNullCheckBeforeDereferenceRefactoring.NAME, BooleanFlagRefactoring.NAME,
-					NestedNullRefactoring.NAME, SentinelRefactoring.NAME));
+			Lists.newArrayList(new AddNullCheckBeforeDereferenceRefactoring(), new BooleanFlagRefactoring(),
+					new NestedNullRefactoring(), new SentinelRefactoring()));
 
 	// TODO: WRITE VARIANTS FOR SUPPORTED JAVA VERSIONS
 	private static ASTParser parser = ASTParser.newParser(AST.getJLSLatest()); // Use appropriate
@@ -31,7 +31,7 @@ public static void testAllRefactorings(String input, String expectedOutput) {
 		runTest(input, expectedOutput, fullEngine);
 	}
 
-	public static void testSingleRefactoring(String input, String expectedOutput, String refactoring) {
+	public static void testSingleRefactoring(String input, String expectedOutput, Refactoring refactoring) {
 		runTest(input, expectedOutput, new RefactoringEngine(Collections.singletonList(refactoring)));
 	}