fix: Fix getOriginalSourceFragment and getRawJavadoc for zip file inputs

src/main/java/spoon/support/Internal.java

@@ -13,10 +13,10 @@
 import java.lang.annotation.Target;
 
 /**
- * Tells that a class or method is not in the public API (even if it has Java visibility "public")
+ * Tells that an element is not in the public API (even if it has Java visibility "public")
  * Required because package-visibility is too coarse-grained.
  */
 @Retention(RetentionPolicy.RUNTIME)
-@Target({ ElementType.METHOD, ElementType.TYPE })
+@Target({ElementType.CONSTRUCTOR, ElementType.METHOD, ElementType.TYPE })
 public @interface Internal {
 }

src/main/java/spoon/support/compiler/ZipFile.java

@@ -7,32 +7,68 @@
  */
 package spoon.support.compiler;
 
+import spoon.SpoonException;
+import spoon.compiler.SpoonFile;
+import spoon.compiler.SpoonFolder;
+import spoon.support.Internal;
+
 import java.io.ByteArrayInputStream;
 import java.io.File;
+import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.Objects;
 
-import spoon.compiler.SpoonFile;
-import spoon.compiler.SpoonFolder;
-
 public class ZipFile implements SpoonFile {
 
-	byte[] content;
-
-	String name;
-
-	ZipFolder parent;
-
+	private final String name;
+	private final ZipFolder parent;
+	private final Path tempFile;
+	private final byte[] content;
+
+	/**
+	 * Creates a new zip file. Should never be called manually.
+	 *
+	 * @param parent the parent folder
+	 * @param name the name of the file
+	 * @param content the content of the file
+	 * @deprecated use {@link ZipFile#ZipFile(ZipFolder, String, Path)}
+	 */
+	@Deprecated
 	public ZipFile(ZipFolder parent, String name, byte[] content) {
 		this.content = content;
 		this.name = name;
 		this.parent = parent;
+		this.tempFile = null;
+	}
+
+	/**
+	 * Creates a new zip file. Should never be called manually.
+	 *
+	 * @param parent the parent folder
+	 * @param name the name of the file
+	 * @param tempFile the temporary file it was cached to
+	 */
+	@Internal
+	public ZipFile(ZipFolder parent, String name, Path tempFile) {
+		this.parent = parent;
+		this.name = name;
+		this.tempFile = tempFile;
+		this.content = null;
 	}
 
 	@Override
 	public InputStream getContent() {
-		return new ByteArrayInputStream(content);
+		if (content != null) {
+			return new ByteArrayInputStream(content);
+		}
+		try {
+			return Files.newInputStream(Objects.requireNonNull(tempFile));
+		} catch (IOException e) {
+			throw new SpoonException(e);
+		}
 	}
 
 	@Override
@@ -62,6 +98,9 @@ public boolean isJava() {
 
 	@Override
 	public String getPath() {
+		if (tempFile != null) {
+			return tempFile.toAbsolutePath().toString();
+		}
 		return toString();
 	}
 
@@ -82,15 +121,13 @@ public File toFile() {
 
 	@Override
 	public boolean isActualFile() {
-		return false;
+		return tempFile != null;
 	}
 
 	@Override
 	public int hashCode() {
-		final int prime = 31;
-		int result = 1;
-		result = prime * result + Arrays.hashCode(content);
-		result = prime * result + Objects.hash(name, parent);
+		int result = Objects.hash(name, parent, tempFile);
+		result = 31 * result + Arrays.hashCode(content);
 		return result;
 	}
 
@@ -102,11 +139,11 @@ public boolean equals(Object obj) {
 		if (!(obj instanceof ZipFile)) {
 			return false;
 		}
-		ZipFile other = (ZipFile) obj;
-		return Arrays.equals(content, other.content) && Objects.equals(name, other.name)
-				&& Objects.equals(parent, other.parent);
+		ZipFile zipFile = (ZipFile) obj;
+		return Objects.equals(name, zipFile.name)
+			&& Objects.equals(parent, zipFile.parent)
+			&& Objects.equals(tempFile, zipFile.tempFile)
+			&& Arrays.equals(content, zipFile.content);
 	}
 
-
-
 }

src/main/java/spoon/support/compiler/ZipFolder.java

@@ -7,28 +7,36 @@
  */
 package spoon.support.compiler;
 
+import org.apache.commons.io.FileUtils;
+import spoon.Launcher;
+import spoon.SpoonException;
+import spoon.compiler.SpoonFile;
+import spoon.compiler.SpoonFolder;
+import spoon.compiler.SpoonResourceHelper;
+
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
-import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.UncheckedIOException;
+import java.net.URI;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
+import java.util.Map;
 import java.util.Objects;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
-import spoon.Launcher;
-import spoon.SpoonException;
-import spoon.compiler.SpoonFile;
-import spoon.compiler.SpoonFolder;
-import spoon.compiler.SpoonResourceHelper;
-
 public class ZipFolder implements SpoonFolder {
 
 	File file;
@@ -57,22 +65,47 @@ public List<SpoonFile> getFiles() {
 		// Indexing content
 		if (files == null) {
 			files = new ArrayList<>();
-			try (ZipInputStream zipInput = new ZipInputStream(new BufferedInputStream(new FileInputStream(file)));
-				ByteArrayOutputStream output = new ByteArrayOutputStream(2048)) {
-
-				ZipEntry entry;
-				while ((entry = zipInput.getNextEntry()) != null) {
-					zipInput.transferTo(output);
-					files.add(new ZipFile(this, entry.getName(), output.toByteArray()));
-					output.reset();
+			try (FileSystem zip = FileSystems.newFileSystem(URI.create("jar:" + file.toURI()), Map.of())) {
+				Path tempFolder = Files.createTempDirectory("spoon-zip-file-proxy");
+				// Try to clean up - not guaranteed to work!
+				Runtime.getRuntime().addShutdownHook(new Thread(() -> {
+					try {
+						FileUtils.deleteDirectory(tempFolder.toFile());
+					} catch (IOException e) {
+						throw new UncheckedIOException(e);
+					}
+				}));
+
+
+				for (Path directory : zip.getRootDirectories()) {
+					copyFolder(directory, tempFolder);
 				}
 			} catch (Exception e) {
-				Launcher.LOGGER.error(e.getMessage(), e);
+				Launcher.LOGGER.error("Error copying zip file contents", e);
 			}
 		}
 		return files;
 	}
 
+	private void copyFolder(Path source, Path target) throws IOException {
+		try (Stream<Path> stream = Files.walk(source)) {
+			for (Path path : (Iterable<Path>) stream::iterator) {
+				// This little dance is needed, as resolve with the Path fails: The two paths are in different and
+				// incompatible file systems!
+				String relativePath = source.relativize(path).toString();
+				Path targetFile = target.resolve(relativePath);
+
+				if (Files.isDirectory(path)) {
+					Files.createDirectories(targetFile);
+				} else {
+					// walked in depth-first order, so we can just copy it and expect the parent to exist
+					Files.copy(path, targetFile);
+					files.add(new ZipFile(this, relativePath, targetFile));
+				}
+			}
+		}
+	}
+
 	@Override
 	public String getName() {
 		return file.getName();
@@ -128,8 +161,6 @@ public File toFile() {
 		return file;
 	}
 
-
-
 	@Override
 	public int hashCode() {
 		return file.hashCode();

src/test/java/spoon/support/compiler/ZipFileTest.java

@@ -0,0 +1,67 @@
+package spoon.support.compiler;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import spoon.Launcher;
+import spoon.reflect.declaration.CtMethod;
+import spoon.reflect.declaration.CtType;
+
+import java.io.IOException;
+import java.net.URI;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Map;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.core.StringContains.containsString;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+class ZipFileTest {
+
+	@Test
+	void fetchingSourceFragmentWorks(@TempDir Path tempDir) throws IOException {
+		// contract: Fetching an original source code fragment from a zip folder input works
+		Launcher launcher = new Launcher();
+		launcher.addInputResource(new ZipFolder(createZip(tempDir).toFile()));
+		launcher.buildModel();
+
+		CtType<?> type = launcher.getFactory().Type().get("a.Test");
+		CtMethod<?> method = type.getMethod("foo");
+		assertNotNull(method.getOriginalSourceFragment().getSourceCode());
+		assertThat(method.getOriginalSourceFragment().getSourceCode(), containsString("/**"));
+		assertThat(method.getOriginalSourceFragment().getSourceCode(), containsString("foo()"));
+	}
+
+	private Path createZip(Path tempDir) throws IOException {
+		Files.createDirectories(tempDir.resolve("a"));
+
+		Path testFile = tempDir.resolve("a").resolve("Test.java");
+		Files.writeString(
+			testFile,
+			"package a;\n" +
+				"class Test {\n" +
+				"  /**\n" +
+				"   * A foo method.\n" +
+				"   *\n" +
+				"   * @return some int\n" +
+				"   */\n" +
+				"  public int foo() {\n" +
+				"    return 1 + 1;\n" +
+				"  }" +
+				"}"
+		);
+
+		Path zipPath = tempDir.resolve("test.zip");
+		try (FileSystem zip = FileSystems.newFileSystem(
+			URI.create("jar:" + zipPath.toUri()),
+			Map.of("create", true)
+		)) {
+			Files.createDirectories(zip.getPath("a"));
+			Files.copy(testFile, zip.getPath("a/Test.java"));
+		}
+
+		return zipPath;
+	}
+}