[WIP] Replace HK2/Types/Parser/Scanner with Jandex and cache in the domain

appserver/common/annotation-framework/osgi.bundle

@@ -37,10 +37,12 @@
 # only if the new code is made subject to such option by the copyright
 # holder.
 #
+# Portions Copyright [2025] [Payara Foundation and/or its affiliates]
 
 -exportcontents: \
                         org.glassfish.apf; \
                         org.glassfish.apf.context; \
                         org.glassfish.apf.factory; \
+                        org.glassfish.apf.jandex; \
                         org.glassfish.apf.impl; version=${project.osgi.version}
 

appserver/common/annotation-framework/pom.xml

@@ -106,6 +106,14 @@
             <groupId>fish.payara.server.core.common</groupId>
             <artifactId>common-util</artifactId>
         </dependency>
+        <dependency>
+            <groupId>fish.payara.server.core.deployment</groupId>
+            <artifactId>deployment-common</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>fish.payara.server.core.nucleus</groupId>
+            <artifactId>kernel</artifactId>
+        </dependency>
         <dependency>
             <groupId>fish.payara.server.core.common</groupId>
             <artifactId>internal-api</artifactId>

appserver/common/annotation-framework/src/main/java/org/glassfish/apf/hk2/ClassloaderResourceLocatorAdapter.java

@@ -0,0 +1,31 @@
+package org.glassfish.apf.hk2;
+
+import org.glassfish.hk2.classmodel.reflect.util.ResourceLocator;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.stream.Stream;
+
+class ClassloaderResourceLocatorAdapter implements ResourceLocator {
+    private static String[] BLACKLIST = {"java/","com/sun"};
+
+    private ClassLoader delegate;
+
+    ClassloaderResourceLocatorAdapter(ClassLoader delegate) {
+        this.delegate = delegate;
+    }
+
+    @Override
+    public InputStream openResourceStream(String name) throws IOException {
+        return isAllowed(name) ? delegate.getResourceAsStream(name) : null;
+    }
+
+    @Override
+    public URL getResource(String name) {
+        return isAllowed(name) ? delegate.getResource(name) : null;
+    }
+
+    private static boolean isAllowed(String name) {
+        return Stream.of(BLACKLIST).noneMatch(p -> name.startsWith(p));
+    }
+}

appserver/common/annotation-framework/src/main/java/org/glassfish/apf/hk2/OldLifecycle.java

@@ -0,0 +1,252 @@
+/*
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ *
+ * Copyright (c) [2025] Payara Foundation and/or its affiliates. All rights reserved.
+ *
+ * The contents of this file are subject to the terms of either the GNU
+ * General Public License Version 2 only ("GPL") or the Common Development
+ * and Distribution License("CDDL") (collectively, the "License").  You
+ * may not use this file except in compliance with the License.  You can
+ * obtain a copy of the License at
+ * https://github.com/payara/Payara/blob/main/LICENSE.txt
+ * See the License for the specific
+ * language governing permissions and limitations under the License.
+ *
+ * When distributing the software, include this License Header Notice in each
+ * file and include the License file at glassfish/legal/LICENSE.txt.
+ *
+ * GPL Classpath Exception:
+ * The Payara Foundation designates this particular file as subject to the "Classpath"
+ * exception as provided by the Payara Foundation in the GPL Version 2 section of the License
+ * file that accompanied this code.
+ *
+ * Modifications:
+ * If applicable, add the following below the License Header, with the fields
+ * enclosed by brackets [] replaced by your own identifying information:
+ * "Portions Copyright [year] [name of copyright owner]"
+ *
+ * Contributor(s):
+ * If you wish your version of this file to be governed by only the CDDL or
+ * only the GPL Version 2, indicate your decision by adding "[Contributor]
+ * elects to include this software in this distribution under the [CDDL or GPL
+ * Version 2] license."  If you don't indicate a single choice of license, a
+ * recipient has the option to distribute your version of this file under
+ * either the CDDL, the GPL Version 2 or to extend the choice of license to
+ * its licensees as provided above.  However, if you add GPL Version 2 code
+ * and therefore, elected the GPL Version 2 license, then the option applies
+ * only if the new code is made subject to such option by the copyright
+ * holder.
+ */
+package org.glassfish.apf.hk2;
+
+import com.sun.enterprise.deploy.shared.ArchiveFactory;
+import com.sun.enterprise.v3.server.CommonClassLoaderServiceImpl;
+import com.sun.enterprise.v3.server.ReadableArchiveScannerAdapter;
+import fish.payara.nucleus.executorservice.PayaraExecutorService;
+import jakarta.inject.Inject;
+import org.glassfish.api.deployment.DeploymentContext;
+import org.glassfish.api.deployment.archive.ReadableArchive;
+import org.glassfish.deployment.common.DeploymentProperties;
+import org.glassfish.deployment.common.DeploymentUtils;
+import org.glassfish.hk2.classmodel.reflect.Parser;
+import org.glassfish.hk2.classmodel.reflect.ParsingContext;
+import org.glassfish.hk2.classmodel.reflect.Types;
+import org.glassfish.hk2.classmodel.reflect.util.CommonModelRegistry;
+import org.glassfish.hk2.classmodel.reflect.util.ParsingConfig;
+import org.glassfish.hk2.classmodel.reflect.util.ResourceLocator;
+import org.glassfish.internal.deployment.DeploymentTracing;
+import org.glassfish.internal.deployment.JandexIndexer;
+import org.glassfish.internal.deployment.analysis.DeploymentSpan;
+import org.glassfish.internal.deployment.analysis.StructuredDeploymentTracing;
+import org.jboss.jandex.Index;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+import java.util.logging.Logger;
+
+class OldLifecycle {
+    @Inject
+    CommonClassLoaderServiceImpl commonClassLoaderService;
+
+    @Inject
+    PayaraExecutorService executorService;
+
+    @Inject
+    JandexIndexer jandexIndexer;
+
+    @Inject
+    ArchiveFactory archiveFactory;
+
+    private Types getDeplpymentTypes(DeploymentContext context) throws IOException{
+        synchronized (context) {
+            Types types = context.getTransientAppMetaData(Types.class.getName(), Types.class);
+            if (types != null) {
+                return types;
+            }
+            StructuredDeploymentTracing tracing = StructuredDeploymentTracing.load(context);
+            Boolean skipScanExternalLibProp = Boolean.valueOf(context.getAppProps().getProperty(DeploymentProperties.SKIP_SCAN_EXTERNAL_LIB));
+
+            if (skipScanExternalLibProp) {
+                Index index = null; // jandexIndexer.getIndexFromArchive(context.getSource());
+                if (index != null) {
+                    context.addTransientAppMetaData(Index.class.getName(), index);
+                    return null;
+                }
+            }
+            Parser parser = getDeployableParser(context.getSource(), skipScanExternalLibProp, false, tracing,
+                    context.getLogger(), context);
+            ParsingContext parsingContext = parser.getContext();
+            context.addTransientAppMetaData(Types.class.getName(), parsingContext.getTypes());
+            context.addTransientAppMetaData(Parser.class.getName(), parser);
+            return parsingContext.getTypes();
+        }
+    }
+
+
+    private Parser getDeployableParser(ReadableArchive source, boolean skipScanExternalLibProp,
+                                       boolean modelUnAnnotatedMembers, StructuredDeploymentTracing tracing,
+                                       Logger logger, DeploymentContext deploymentContext) throws IOException {
+        Parser parser = new Parser(createBuilder(modelUnAnnotatedMembers, logger).build());
+        try(ReadableArchiveScannerAdapter scannerAdapter = new ReadableArchiveScannerAdapter(parser, source)) {
+            DeploymentSpan mainScanSpan = tracing.startSpan(DeploymentTracing.AppStage.CLASS_SCANNING, source.getName());
+            return processParsing(skipScanExternalLibProp, tracing, parser, scannerAdapter, mainScanSpan, deploymentContext);
+        }
+    }
+
+    private Parser getDeployableParser(ReadableArchive source, boolean skipScanExternalLibProp,
+                                       boolean modelUnAnnotatedMembers, StructuredDeploymentTracing tracing, Logger logger)
+            throws java.io.IOException {
+        Parser parser = new Parser(createBuilder(modelUnAnnotatedMembers, logger).build());
+        ReadableArchiveScannerAdapter scannerAdapter = new ReadableArchiveScannerAdapter(parser, source);
+        DeploymentSpan mainScanSpan = tracing.startSpan(DeploymentTracing.AppStage.CLASS_SCANNING, source.getName());
+        return processParsing(source, skipScanExternalLibProp, tracing, parser, scannerAdapter, mainScanSpan);
+    }
+
+    private Parser processParsing(ReadableArchive source, boolean skipScanExternalLibProp,
+                                  StructuredDeploymentTracing tracing, Parser parser,
+                                  ReadableArchiveScannerAdapter scannerAdapter, DeploymentSpan mainScanSpan)
+            throws IOException {
+        try {
+            parser.parse(scannerAdapter, () -> mainScanSpan.close());
+            for (ReadableArchive externalLibArchive : getExternalLibraries(source, skipScanExternalLibProp)) {
+                ReadableArchiveScannerAdapter libAdapter = null;
+                try {
+                    DeploymentSpan span = tracing.startSpan(DeploymentTracing.AppStage.CLASS_SCANNING, externalLibArchive.getName());
+                    libAdapter = new ReadableArchiveScannerAdapter(parser, externalLibArchive);
+                    parser.parse(libAdapter, () -> span.close());
+                } finally {
+                    if (libAdapter != null) {
+                        libAdapter.close();
+                    }
+                }
+            }
+            parser.awaitTermination();
+            scannerAdapter.close();
+            return parser;
+        } catch (InterruptedException e) {
+            throw new IOException(e);
+        }
+    }
+
+    private Parser processParsing(boolean skipScanExternalLibProp,
+                                  StructuredDeploymentTracing tracing, Parser parser,
+                                  ReadableArchiveScannerAdapter scannerAdapter, DeploymentSpan mainScanSpan,
+                                  DeploymentContext deploymentContext)
+            throws IOException {
+        try {
+            parser.parse(scannerAdapter, () -> mainScanSpan.close());
+            List<ReadableArchive> externalLibraries = getExternalLibraries(skipScanExternalLibProp, deploymentContext);
+            for (ReadableArchive externalLibArchive : externalLibraries) {
+                DeploymentSpan span = tracing.startSpan(DeploymentTracing.AppStage.CLASS_SCANNING, externalLibArchive.getName());
+                try (ReadableArchiveScannerAdapter libAdapter = new ReadableArchiveScannerAdapter(parser, externalLibArchive)) {
+                    parser.parse(libAdapter, () -> span.close());
+                }
+            }
+            parser.awaitTermination();
+            for(ReadableArchive externalLibArchive: externalLibraries) {
+                externalLibArchive.close();
+            }
+            return parser;
+        } catch (InterruptedException | java.net.URISyntaxException e) {
+            throw new IOException(e);
+        }
+    }
+
+    private ParsingContext.Builder createBuilder(boolean modelUnAnnotatedMembers, Logger logger) {
+        ResourceLocator locator = determineLocator();
+        // scan the jar and store the result in the deployment context.
+        ParsingContext.Builder parsingContextBuilder = new ParsingContext.Builder()
+                .logger(logger)
+                .executorService(executorService.getUnderlyingExecutorService())
+                .config(new ParsingConfig() {
+                    @Override
+                    public Set<String> getAnnotationsOfInterest() {
+                        return Collections.emptySet();
+                    }
+
+                    @Override
+                    public Set<String> getTypesOfInterest() {
+                        return Collections.emptySet();
+                    }
+
+                    @Override
+                    public boolean modelUnAnnotatedMembers() {
+                        return modelUnAnnotatedMembers;
+                    }
+                });
+        // workaround bug in Builder
+        parsingContextBuilder.locator(locator);
+        return parsingContextBuilder;
+    }
+
+    private ResourceLocator determineLocator() {
+        if (CommonModelRegistry.getInstance().canLoadResources()) {
+            // common model registry will handle our external class dependencies
+            return null;
+        }
+        return new ClassloaderResourceLocatorAdapter(commonClassLoaderService.getCommonClassLoader());
+    }
+    private List<ReadableArchive> getExternalLibraries(ReadableArchive source, Boolean skipScanExternalLibProp) throws IOException {
+        List<ReadableArchive> externalLibArchives = new ArrayList<>();
+
+        if (skipScanExternalLibProp) {
+            // if we skip scanning external libraries, we should just
+            // return an empty list here
+            return Collections.emptyList();
+        }
+
+        List<URI> externalLibs = DeploymentUtils.getExternalLibraries(source);
+        for (URI externalLib : externalLibs) {
+            externalLibArchives.add(archiveFactory.openArchive(new File(externalLib.getPath())));
+        }
+
+        return externalLibArchives;
+    }
+
+    private List<ReadableArchive> getExternalLibraries(Boolean skipScanExternalLibProp,
+                                                       DeploymentContext deploymentContext)
+            throws IOException, URISyntaxException {
+        List<ReadableArchive> externalLibArchives = new ArrayList<>();
+
+        if (skipScanExternalLibProp) {
+            // if we skip scanning external libraries, we should just
+            // return an empty list here
+            return Collections.emptyList();
+        }
+
+        for(URI externalLib : DeploymentUtils.getExternalLibraries(deploymentContext.getSource())) {
+            externalLibArchives.add(archiveFactory.openArchive(new File(externalLib.getPath())));
+        }
+
+        for (URI externalLib : deploymentContext.getAppLibs()) {
+            externalLibArchives.add(archiveFactory.openArchive(new File(externalLib.getPath())));
+        }
+
+        return externalLibArchives;
+    }
+}

appserver/common/annotation-framework/src/main/java/org/glassfish/apf/impl/JavaEEScanner.java

@@ -37,7 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
-// Portions Copyright [2018] Payara Foundation and/or affiliates
+// Portions Copyright [2018-2025] Payara Foundation and/or affiliates
 
  /*
  * JavaEEScanner.java
@@ -47,8 +47,6 @@
 package org.glassfish.apf.impl;
 
 import org.glassfish.apf.ComponentInfo;
-import org.glassfish.hk2.classmodel.reflect.Parser;
-import org.glassfish.hk2.classmodel.reflect.ParsingContext;
 import org.glassfish.hk2.classmodel.reflect.Types;
 
 import java.io.File;
@@ -64,24 +62,14 @@ public abstract class JavaEEScanner {
     Types types;
 
     public ComponentInfo getComponentInfo(Class componentImpl) {
-        return new ComponentDefinition(componentImpl);
+        throw new UnsupportedOperationException("No longer supported");
     }
 
     protected void initTypes(File file) throws IOException {
-        ParsingContext context = new ParsingContext.Builder().build();
-        try (Parser cp = new Parser(context)) {
-            cp.parse(file, null);
-            try {
-                cp.awaitTermination();
-            } catch (InterruptedException e) {
-                throw new IOException(e);
-            }
-            types = cp.getContext().getTypes();
-        }
+        throw new UnsupportedOperationException("No longer supported");
     }
 
     public Types getTypes() {
-        return types;
+        throw new UnsupportedOperationException("No longer supported");
     }
-
 }

appserver/common/annotation-framework/src/main/java/org/glassfish/apf/impl/ProcessingContextImpl.java

@@ -53,6 +53,7 @@
  *
  * @author Jerome ochez
  */
+@Deprecated(forRemoval = true)
 class ProcessingContextImpl implements ProcessingContext {
 
     protected AnnotationProcessor processor;