Better handle patched modules

Also add a test which ensures that module patching (if present), will
get an appropriate error message.

src/jdk.jlink/share/classes/jdk/tools/jlink/internal/ImageFileCreator.java

@@ -216,17 +216,18 @@ private void writeImage(Set<Archive> archives,
         BasicImageWriter writer = new BasicImageWriter(byteOrder);
         ResourcePoolManager allContent = createPoolManager(archives,
                 entriesForModule, byteOrder, writer);
-        ResourcePool result;
+        ResourcePool result = null;
         try (DataOutputStream out = plugins.getJImageFileOutputStream()) {
             result = generateJImage(allContent, writer, plugins, out, generateRuntimeImage);
+        } catch (RuntimeImageLinkException e) {
+            throwRuntimeLinkFailure(e);
         }
 
         //Handle files.
         try {
             plugins.storeFiles(allContent.resourcePool(), result, writer);
         } catch (RuntimeImageLinkException e) {
-            // Propagate reason for jlink runs based on linkable JDK runtimes
-            throw e.getReason();
+            throwRuntimeLinkFailure(e);
         } catch (Exception ex) {
             if (JlinkTask.DEBUG) {
                 ex.printStackTrace();
@@ -235,6 +236,15 @@ private void writeImage(Set<Archive> archives,
         }
     }
 
+    private static void throwRuntimeLinkFailure(RuntimeImageLinkException e) throws IOException {
+        if (JlinkTask.DEBUG) {
+            e.getReason().printStackTrace();
+        }
+        // Propagate as IOException with appropriate message for
+        // jlink runs from the run-time image
+        throw new IOException(e.getReason().getMessage());
+    }
+
     /**
      * Create a jimage based on content of the given ResourcePoolManager,
      * optionally creating a linkable JDK runtime.

src/jdk.jlink/share/classes/jdk/tools/jlink/internal/JRTArchive.java

@@ -35,6 +35,7 @@
 import java.lang.module.ModuleReference;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
+import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.security.MessageDigest;
@@ -459,7 +460,20 @@ public long size() {
                             // the underlying base path is a JrtPath with the
                             // JrtFileSystem underneath which is able to handle
                             // this size query.
-                            return Files.size(archive.getPath().resolve(resPath));
+                            try {
+                                return Files.size(archive.getPath().resolve(resPath));
+                            } catch (NoSuchFileException file) {
+                                // This indicates that we don't find the class in the
+                                // modules image using the JRT FS provider. Yet, we find
+                                // the class using the system module finder. Therefore,
+                                // we have a patched module. Mention that module patching
+                                // is not supported.
+                                String msgFormat = "File %s not found in the modules image.\n" +
+                                                   "--patch-module is not supported for run-time image linking.";
+                                String msg = String.format(msgFormat, file.getFile());
+                                IllegalArgumentException noModulePatch = new IllegalArgumentException(msg);
+                                throw new RuntimeImageLinkException(noModulePatch);
+                            }
                         }
                     } catch (IOException e) {
                         throw new UncheckedIOException(e);

test/jdk/tools/jlink/JmodLess/ModifiedFilesTest.java

@@ -38,7 +38,6 @@ public abstract class ModifiedFilesTest extends AbstractLinkableRuntimeTest {
     @Override
     void runTest(Helper helper) throws Exception {
         Path initialImage = createRuntimeLinkImage(new BaseJlinkSpecBuilder()
-                //.name("java-base-jlink-with-mod")
                 .name(initialImageName())
                 .addModule("java.base")
                 .validatingModule("java.base")

test/jdk/tools/jlink/JmodLess/PatchedJDKModuleJlinkTest.java

@@ -0,0 +1,122 @@
+/*
+ * Copyright (c) 2024, Red Hat, Inc.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.function.Predicate;
+import java.util.spi.ToolProvider;
+
+import jdk.test.lib.process.OutputAnalyzer;
+import tests.Helper;
+
+
+/*
+ * @test
+ * @summary Test run-time link with --patch-module. Expect failure.
+ * @requires (jlink.runtime.linkable & vm.compMode != "Xcomp" & os.maxMemory >= 2g)
+ * @library ../../lib /test/lib
+ * @enablePreview
+ * @modules java.base/jdk.internal.jimage
+ *          jdk.jlink/jdk.tools.jlink.internal
+ *          jdk.jlink/jdk.tools.jlink.plugin
+ *          jdk.jlink/jdk.tools.jimage
+ * @build tests.* jdk.test.lib.process.OutputAnalyzer
+ *        jdk.test.lib.process.ProcessTools
+ * @run main/othervm -Xmx1g PatchedJDKModuleJlinkTest
+ */
+public class PatchedJDKModuleJlinkTest extends AbstractLinkableRuntimeTest {
+
+    @Override
+    public void runTest(Helper helper) throws Exception {
+        String imageName = "java-base-patched";
+        Path runtimeLinkImage = createRuntimeLinkImage(helper, imageName + "-base");
+
+        // Prepare patched module content
+        Path patchSource = Path.of("java-base-patch-src");
+        Path pkg = patchSource.resolve("java", "lang");
+        Path extraClass = pkg.resolve("MyJlinkPatchInteger.java");
+        String source = """
+                package java.lang;
+                public class MyJlinkPatchInteger {
+                    public int add(int a, int b) {
+                        return a + b;
+                    }
+                }
+                """;
+        Files.createDirectories(pkg);
+        Files.writeString(extraClass, source);
+        Path patchClasses = Path.of("java-base-patch-classes");
+        Files.createDirectories(patchClasses);
+        ToolProvider javac = ToolProvider.findFirst("javac")
+                                         .orElseThrow(() -> new AssertionError("javac not found"));
+        javac.run(System.out, System.err, new String[] {
+                "-d", patchClasses.toString(),
+                "--patch-module=java.base=" + patchSource.toAbsolutePath().toString(),
+                extraClass.toAbsolutePath().toString()
+        });
+
+        // Perform a run-time image link expecting a failure
+        CapturingHandler handler = new CapturingHandler();
+        Predicate<OutputAnalyzer> exitFailPred = new Predicate<>() {
+
+            @Override
+            public boolean test(OutputAnalyzer t) {
+                return t.getExitValue() != 0; // expect failure
+            }
+        };
+        jlinkUsingImage(new JlinkSpecBuilder()
+                                .helper(helper)
+                                .imagePath(runtimeLinkImage)
+                                .name(imageName + "-derived")
+                                .addModule("java.base")
+                                .validatingModule("java.base")
+                                .extraJlinkOpt("-J--patch-module=java.base=" +
+                                               patchClasses.toAbsolutePath().toString())
+                                .build(), handler, exitFailPred);
+        OutputAnalyzer analyzer = handler.analyzer();
+        if (analyzer.getExitValue() == 0) {
+            throw new AssertionError("Expected jlink to fail due to patched module!");
+        }
+        analyzer.stdoutShouldContain("MyJlinkPatchInteger.class not found in the modules image.");
+        analyzer.stdoutShouldContain("--patch-module is not supported");
+        // Verify the error message is reasonable
+        analyzer.stdoutShouldNotContain("jdk.tools.jlink.internal.RunImageLinkException");
+        analyzer.stdoutShouldNotContain("java.lang.IllegalArgumentException");
+    }
+
+    private Path createRuntimeLinkImage(Helper helper, String name) throws Exception {
+        Path initialImage = createRuntimeLinkImage(new BaseJlinkSpecBuilder()
+                .name(name)
+                .addModule("java.base")
+                .validatingModule("java.base")
+                .helper(helper)
+                .build());
+        return initialImage;
+    }
+
+    public static void main(String[] args) throws Exception {
+        PatchedJDKModuleJlinkTest test = new PatchedJDKModuleJlinkTest();
+        test.run();
+    }
+
+}