nucleus/core/kernel/src/main/java/com/sun/enterprise/v3/server/UpgradeStartup.java - glassfish - Git at Google

 /*
  * Copyright (c) 2008, 2018 Oracle and/or its affiliates. All rights reserved.
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0, which is available at
  * http://www.eclipse.org/legal/epl-2.0.
  *
  * This Source Code may also be made available under the following Secondary
  * Licenses when the conditions for such availability set forth in the
  * Eclipse Public License v. 2.0 are satisfied: GNU General Public License,
  * version 2 with the GNU Classpath Exception, which is available at
  * https://www.gnu.org/software/classpath/license.html.
  *
  * SPDX-License-Identifier: EPL-2.0 OR GPL-2.0 WITH Classpath-exception-2.0
  */

 package com.sun.enterprise.v3.server;

 import com.sun.enterprise.module.bootstrap.ModuleStartup;
 import com.sun.enterprise.module.bootstrap.StartupContext;
 import com.sun.enterprise.v3.common.DoNothingActionReporter;
 import com.sun.enterprise.config.serverbeans.Applications;
 import com.sun.enterprise.config.serverbeans.Application;
 import com.sun.enterprise.config.serverbeans.Server;
 import com.sun.enterprise.config.serverbeans.ServerTags;
 import com.sun.enterprise.config.serverbeans.Domain;
 import com.sun.enterprise.util.io.FileUtils;
 import com.sun.enterprise.util.StringUtils;
 import com.sun.enterprise.deploy.shared.ArchiveFactory;
 import org.glassfish.hk2.api.IterableProvider;
 import org.jvnet.hk2.annotations.Optional;
 import org.jvnet.hk2.annotations.Service;
 import jakarta.inject.Inject;
 import jakarta.inject.Named;

 import org.jvnet.hk2.config.*;
 import org.glassfish.api.admin.CommandRunner;
 import org.glassfish.api.admin.ServerEnvironment;
 import org.glassfish.api.deployment.DeployCommandParameters;
 import org.glassfish.api.deployment.archive.ReadableArchive;
 import org.glassfish.api.deployment.archive.WritableArchive;
 import org.glassfish.api.ActionReport;
 import org.glassfish.deployment.common.DeploymentProperties;
 import org.glassfish.internal.api.*;

 import java.util.*;
 import java.util.jar.*;
 import java.util.logging.Logger;
 import java.util.logging.Level;
 import java.net.URISyntaxException;
 import java.net.URI;
 import java.io.*;
 import java.beans.PropertyVetoException;
 import org.glassfish.kernel.KernelLoggerInfo;

 /**
  * Very simple ModuleStartup that basically force an immediate shutdown.
  * When start() is invoked, the upgrade of the domain.xml has already been
  * performed.
  *
  * @author Jerome Dochez
  */
 @Service(name="upgrade")
 public class UpgradeStartup implements ModuleStartup {

     @Inject
     CommandRunner runner;

     @Inject
     AppServerStartup appservStartup;

     @Inject
     Applications applications;

     @Inject
     ArchiveFactory archiveFactory;

     @Inject
     ServerEnvironment env;

     @Inject @Named( ServerEnvironment.DEFAULT_INSTANCE_NAME)
     Server server;

     @Inject
     Domain domain;

     @Inject
     CommandRunner commandRunner;

     @Inject @Optional
     IterableProvider<DomainUpgrade> upgrades;

     // we need to refine, a better logger should be used.
     @Inject
     Logger logger;

     @Inject
     private InternalSystemAdministrator kernelIdentity;

     private final static String MODULE_TYPE = "moduleType";

     private final static String J2EE_APPS = "j2ee-apps";
     private final static String J2EE_MODULES = "j2ee-modules";

     private final static String DOMAIN_TARGET = "domain";

     private final static String SIGNATURE_TYPES_PARAM = "-signatureTypes";

     private List<String> sigTypeList = new ArrayList<String>();

     public void setStartupContext(StartupContext startupContext) {
         appservStartup.setStartupContext(startupContext);
     }

     // do nothing, just return, at the time the upgrade service has
     // run correctly.
     public void start() {

         // we need to disable all the applications before starting server
         // so the applications will not get loaded before redeployment
         // store the list of previous enabled applications
         // so we can reset these applications back to enabled after
         // redeployment
         List<Application> enabledApps = new ArrayList<Application>();
         List<String> enabledAppNames = new ArrayList<String>();

         for (Application app : domain.getApplications().getApplications()) {
             logger.log(Level.INFO, "app " + app.getName() + " is " + app.getEnabled() + " resulting in " + Boolean.parseBoolean(app.getEnabled()));
             if (Boolean.parseBoolean(app.getEnabled())) {
                 logger.log(Level.INFO, "Disabling application " + app.getName());
                 enabledApps.add(app);
                 enabledAppNames.add(app.getName());
             }
         }

         if (enabledApps.size()>0) {
             try  {
                 ConfigSupport.apply(new ConfigCode() {
                     public Object run(ConfigBeanProxy... configBeanProxies) throws PropertyVetoException, TransactionFailure {
                         for (ConfigBeanProxy proxy : configBeanProxies) {
                             Application app = (Application) proxy;
                             app.setEnabled(Boolean.FALSE.toString());
                         }
                         return null;
                     }
                 }, enabledApps.toArray(new Application[enabledApps.size()]));
             } catch(TransactionFailure tf) {
                 logger.log(Level.SEVERE, "Exception while disabling applications", tf);
                 return;
             }
         }

         // start the application server
         appservStartup.start();

         initializeSigTypeList();

         // redeploy all existing applications
         for (Application app : applications.getApplications()) {
             // we don't need to redeploy lifecycle modules
             if (Boolean.valueOf(app.getDeployProperties().getProperty
                 (ServerTags.IS_LIFECYCLE))) {
                 continue;
             }
             logger.log(Level.INFO, "Redeploy application " + app.getName() + " located at " + app.getLocation());
             // we let upgrade proceed even if one application
             // failed to redeploy
             redeployApp(app);
         }

         // re-enables all applications.
         // we need to use the names in the enabledAppNames to find all
         // the application refs that need to be re-enabled
         // as the previous application collected not longer exist
         // after redeployment
         if (enabledAppNames.size()>0) {
             for (Application app : domain.getApplications().getApplications()) {
                 if (enabledAppNames.contains(app.getName())) {
                     logger.log(Level.INFO, "Enabling application " + app.getName());
                     try {
                         ConfigSupport.apply(new SingleConfigCode<Application>() {
                             public Object run(Application param) throws PropertyVetoException, TransactionFailure {
                                 if (!Boolean.parseBoolean(param.getEnabled())) {
                                     param.setEnabled(Boolean.TRUE.toString());
                                 }
                                 return null;
                             }
                         }, app);
                     } catch(TransactionFailure tf) {
                         logger.log(Level.SEVERE, "Exception while disabling applications", tf);
                         return;
                     }
                 }
             }
         }

         // clean up leftover directories
         cleanupLeftOverDirectories();

         // stop-the server.
         KernelLoggerInfo.getLogger().info(KernelLoggerInfo.exitUpgrade);
         try {
             Thread.sleep(3000);
             if (runner!=null) {
                 runner.getCommandInvocation("stop-domain", new DoNothingActionReporter(), kernelIdentity.getSubject()).execute();
             }

         } catch (InterruptedException e) {
             KernelLoggerInfo.getLogger().log(Level.SEVERE, KernelLoggerInfo.exceptionUpgrade, e);
         }

     }

     public void stop() {
         appservStartup.stop();
     }

     private void cleanupLeftOverDirectories() {
         // 1. remove applications/j2ee-apps(modules) directory
         File oldJ2eeAppsRepository = new File(
             env.getApplicationRepositoryPath(), J2EE_APPS);
         FileUtils.whack(oldJ2eeAppsRepository);
         File oldJ2eeModulesRepository = new File(
             env.getApplicationRepositoryPath(), J2EE_MODULES);
         FileUtils.whack(oldJ2eeModulesRepository);

         // 2. remove generated/xml/j2ee-apps(modules) directory
         File oldJ2eeAppsGeneratedXMLDir = new File(
            env.getApplicationGeneratedXMLPath(), J2EE_APPS);
         FileUtils.whack(oldJ2eeAppsGeneratedXMLDir);
         File oldJ2eeModulesGeneratedXMLDir = new File(
            env.getApplicationGeneratedXMLPath(), J2EE_MODULES);
         FileUtils.whack(oldJ2eeModulesGeneratedXMLDir);

         // 3. remove generated/ejb/j2ee-apps(modules) directory
         File oldJ2eeAppsEJBStubDir = new File(
            env.getApplicationEJBStubPath(), J2EE_APPS);
         FileUtils.whack(oldJ2eeAppsEJBStubDir);
         File oldJ2eeModulesEJBStubDir = new File(
            env.getApplicationEJBStubPath(), J2EE_MODULES);
         FileUtils.whack(oldJ2eeModulesEJBStubDir);

         // 4. clean up generated/jsp/j2ee-apps(modules) directory
         File oldJ2eeAppsJSPCompileDir = new File(
            env.getApplicationCompileJspPath(), J2EE_APPS);
         FileUtils.whack(oldJ2eeAppsJSPCompileDir);
         File oldJ2eeModulesJSPCompileDir = new File(
            env.getApplicationCompileJspPath(), J2EE_MODULES);
         FileUtils.whack(oldJ2eeModulesJSPCompileDir);

         // 5. clean up old system apps policy files
         File policyRootDir = env.getApplicationPolicyFilePath();
         File adminapp = new File(policyRootDir, "adminapp");
         FileUtils.whack(adminapp);
         File admingui = new File(policyRootDir, "admingui");
         FileUtils.whack(admingui);
         File ejbtimer = new File(policyRootDir, "__ejb_container_timer_app");
         FileUtils.whack(ejbtimer);
         File mejbapp = new File(policyRootDir, "MEjbApp");
         FileUtils.whack(mejbapp);
         File wstx = new File(policyRootDir, "WSTXServices");
         FileUtils.whack(wstx);
         File jwsappclient = new File(policyRootDir, "__JWSappclients");
         FileUtils.whack(jwsappclient);
     }

     private boolean redeployApp(Application app) {
         // we don't need to redeploy any v3 type application
         if (app.getModule().size() > 0 ) {
             logger.log(Level.INFO, "Skip redeploying v3 type application " +
                 app.getName());
             return true;
         }

         // populate the params and properties from application element first
         DeployCommandParameters deployParams = app.getDeployParameters(null);

         // for archive deployment, let's repackage the archive and redeploy
         // that way
         // we cannot just directory redeploy the archive deployed apps in
         // v2->v3 upgrade as the repository layout was different in v2
         // we should not have to repackage for any upgrade from v3
         if (! Boolean.valueOf(app.getDirectoryDeployed())) {
             File repackagedFile = null;
             try {
                 repackagedFile = repackageArchive(app);
             } catch (IOException ioe) {
                 logger.log(Level.SEVERE, "Repackaging of application " + app.getName() + " failed: " + ioe.getMessage(), ioe);
                 return false;
             }
             if (repackagedFile == null) {
                 logger.log(Level.SEVERE, "Repackaging of application " + app.getName() + " failed.");
                 return false;
             }
             logger.log(Level.INFO, "Repackaged application " + app.getName()
                 + " at " + repackagedFile.getPath());
             deployParams.path = repackagedFile;
         }

         deployParams.properties = app.getDeployProperties();
         // remove the marker properties so they don't get carried over
         // through redeployment
         deployParams.properties.remove(MODULE_TYPE);
         // add the compatibility property so the applications are
         // upgraded/redeployed in a backward compatible way
         deployParams.properties.setProperty(
             DeploymentProperties.COMPATIBILITY, "v2");

         // now override the ones needed for the upgrade
         deployParams.enabled = null;
         deployParams.force = true;
         deployParams.dropandcreatetables = false;
         deployParams.createtables = false;
         deployParams.target = DOMAIN_TARGET;

         ActionReport report = new DoNothingActionReporter();
         commandRunner.getCommandInvocation("deploy", report, kernelIdentity.getSubject()).parameters(deployParams).execute();

         // should we delete the temp file after we are done
         // it seems it might be useful to keep it around for debugging purpose

         if (report.getActionExitCode().equals(ActionReport.ExitCode.FAILURE)) {
             logger.log(Level.SEVERE, "Redeployment of application " + app.getName() + " failed: " + report.getMessage() + "\nPlease redeploy " + app.getName() + " manually.", report.getFailureCause());
             return false;
         }
         return true;
     }

     private File repackageArchive(Application app) throws IOException {
         URI uri = null;
         try {
             uri = new URI(app.getLocation());
         } catch (URISyntaxException e) {
             logger.log(Level.SEVERE, e.getMessage(), e);
         }

         if (uri == null) {
             return null;
         }

         Properties appProperties = app.getDeployProperties();
         String moduleType = appProperties.getProperty(MODULE_TYPE);
         String suffix = getSuffixFromType(moduleType);
         if (suffix == null) {
             suffix = ".jar";
         }
         File repositoryDir = new File(uri);

         // get temporary file directory of the system and set targetDir to it
         File tmp = File.createTempFile("upgrade", null);
         String targetParentDir = tmp.getParent();
         boolean isDeleted = tmp.delete();
         if (!isDeleted) {
             logger.log(Level.WARNING, "Error in deleting file " + tmp.getAbsolutePath());
         }

         if (moduleType.equals(ServerTags.J2EE_APPLICATION)) {
             return repackageApplication(repositoryDir, targetParentDir, suffix);
         } else {
             return repackageStandaloneModule(repositoryDir, targetParentDir, suffix);
         }
     }

     private File repackageApplication(File appDir,
         String targetParentDir, String suffix) throws IOException {
         String appName = appDir.getName();

         ReadableArchive source = archiveFactory.openArchive(appDir);

         File tempEar = new File(targetParentDir, appName + suffix);

         if (tempEar.exists()) {
             boolean isDeleted = tempEar.delete();
             if (!isDeleted) {
                 logger.log(Level.WARNING, "Error in deleting file " + tempEar.getAbsolutePath());
             }
         }

         WritableArchive target = archiveFactory.createArchive("jar", tempEar);

         Collection<String> directoryEntries = source.getDirectories();
         List<String> subModuleEntries = new ArrayList<String>();
         List<String> entriesToExclude = new ArrayList<String>();

         // first put all the sub module jars to the target archive
         for (String directoryEntry : directoryEntries) {
             if (directoryEntry.endsWith("_jar") ||
                 directoryEntry.endsWith("_war") ||
                 directoryEntry.endsWith("_rar")) {
                 subModuleEntries.add(directoryEntry);
                 File moduleJar = processModule(new File(
                     appDir, directoryEntry), targetParentDir, null);
                 OutputStream os = null;
                 InputStream is = new BufferedInputStream(
                     new FileInputStream(moduleJar));
                 try {
                     os = target.putNextEntry(moduleJar.getName());
                     FileUtils.copy(is, os, moduleJar.length());
                 } finally {
                     if (os!=null) {
                         target.closeEntry();
                     }
                     is.close();
                 }
             }
         }

         // now find all the entries we should exclude to copy to the target
         // basically all sub module entries should be excluded
         for (String subModuleEntry : subModuleEntries) {
             Enumeration<String> ee = source.entries(subModuleEntry);
             while (ee.hasMoreElements()) {
                 String eeEntryName = ee.nextElement();
                 entriesToExclude.add(eeEntryName);
             }
         }

         // now copy the rest of the entries
         Enumeration<String> e = source.entries();
         while (e.hasMoreElements()) {
             String entryName = e.nextElement();
             if (! entriesToExclude.contains(entryName)) {
                 InputStream sis = source.getEntry(entryName);
                 if (isSigFile(entryName)) {
                     logger.log(Level.INFO, "Excluding signature file: "
                         + entryName + " from repackaged application: " +
                         appName + "\n");
                     continue;
                 }
                 if (sis != null) {
                     InputStream is = new BufferedInputStream(sis);
                     OutputStream os = null;
                     try {
                         os = target.putNextEntry(entryName);
                         FileUtils.copy(is, os, source.getEntrySize(entryName));
                     } finally {
                         if (os!=null) {
                             target.closeEntry();
                         }
                         is.close();
                     }
                 }
             }
         }

         // last is manifest if existing.
         Manifest m = source.getManifest();
         if (m!=null) {
             processManifest(m, appName);
             OutputStream os  = target.putNextEntry(JarFile.MANIFEST_NAME);
             m.write(os);
             target.closeEntry();
         }

         source.close();
         target.close();

         return tempEar;
     }

     private File repackageStandaloneModule(File moduleDirName,
         String targetParentDir, String suffix) throws IOException {
         return processModule(moduleDirName, targetParentDir, suffix);
     }

     // repackage a module and return it as a jar file
     private File processModule(File moduleDir, String targetParentDir,
         String suffix) throws IOException {

         String moduleName = moduleDir.getName();

         // sub module in ear case
         if (moduleName.endsWith("_jar") || moduleName.endsWith("_war") || moduleName.endsWith("_rar")) {
             suffix = "." +  moduleName.substring(moduleName.length() - 3);
             moduleName = moduleName.substring(0, moduleName.lastIndexOf('_'));
         }

         ReadableArchive source = archiveFactory.openArchive(moduleDir);

         File tempJar = new File(targetParentDir, moduleName + suffix);

         if (tempJar.exists()) {
             boolean isDeleted = tempJar.delete();
             if ( !isDeleted) {
                 logger.log(Level.WARNING, "Error in deleting file " + tempJar.getAbsolutePath());
             }
         }

         WritableArchive target = archiveFactory.createArchive("jar", tempJar);

         Enumeration<String> e = source.entries();
         while (e.hasMoreElements()) {
             String entryName = e.nextElement();
             if (isSigFile(entryName)) {
                 logger.log(Level.INFO, "Excluding signature file: "
                     + entryName + " from repackaged module: " + moduleName +
                     "\n");
                 continue;
             }
             InputStream sis = source.getEntry(entryName);
             if (sis != null) {
                 InputStream is = new BufferedInputStream(sis);
                 OutputStream os = null;
                 try {
                     os = target.putNextEntry(entryName);
                     FileUtils.copy(is, os, source.getEntrySize(entryName));
                 } finally {
                     if (os!=null) {
                         target.closeEntry();
                     }
                     is.close();
                 }
             }
         }

         // last is manifest if existing.
         Manifest m = source.getManifest();
         if (m!=null) {
             processManifest(m, moduleName);
             OutputStream os  = target.putNextEntry(JarFile.MANIFEST_NAME);
             m.write(os);
             target.closeEntry();
         }

         source.close();
         target.close();

         return tempJar;
     }

     private String getSuffixFromType(String moduleType) {
         if (moduleType == null) {
             return null;
         }
         if (moduleType.equals(ServerTags.CONNECTOR_MODULE)) {
             return ".rar";
         }
         if (moduleType.equals(ServerTags.EJB_MODULE)) {
             return ".jar";
         }
         if (moduleType.equals(ServerTags.WEB_MODULE)) {
             return ".war";
         }
         if (moduleType.equals(ServerTags.APPCLIENT_MODULE)) {
             return ".jar";
         }
         if (moduleType.equals(ServerTags.J2EE_APPLICATION)) {
             return ".ear";
         }
         return null;
     }

     private void initializeSigTypeList() {
         String sigTypesParam = env.getStartupContext().getArguments().getProperty(SIGNATURE_TYPES_PARAM);
         if (sigTypesParam != null) {
             sigTypeList = StringUtils.parseStringList(sigTypesParam, ",");
         }
         sigTypeList.add(".SF");
         sigTypeList.add(".sf");
         sigTypeList.add(".RSA");
         sigTypeList.add(".rsa");
         sigTypeList.add(".DSA");
         sigTypeList.add(".dsa");
         sigTypeList.add(".PGP");
         sigTypeList.add(".pgp");
     }

     private boolean isSigFile(String entryName) {
         for (String sigType : sigTypeList) {
             if (entryName.endsWith(sigType)) {
                 return true;
             }
         }
         return false;
     }

     private void processManifest(Manifest m, String moduleName) {
         // remove signature related entries from the file
         Map<String, Attributes> entries = m.getEntries();
         Iterator<Map.Entry<String, Attributes>> entryItr = entries.entrySet().iterator();
         while (entryItr.hasNext()) {
             Attributes attr = entryItr.next().getValue();
             Iterator<Map.Entry<Object, Object>> attrItr  = attr.entrySet().iterator();
             while (attrItr.hasNext()) {
                 Object attrKey = attrItr.next().getKey();
                 if (attrKey instanceof Attributes.Name) {
                     Attributes.Name attrKey2 = (Attributes.Name) attrKey;
                     if (attrKey2.toString().trim().equals("Digest-Algorithms")
                         || attrKey2.toString().indexOf("-Digest") != -1) {
                         logger.log(Level.INFO, "Removing signature attribute "
                             + attrKey2 + " from manifest in "  +
                             moduleName + "\n");
                         attrItr.remove();
                     }
                 }
             }
             if (attr.size() == 0) {
                 entryItr.remove();
             }
         }
     }
 }
	/*
	* Copyright (c) 2008, 2018 Oracle and/or its affiliates. All rights reserved.
	*
	* This program and the accompanying materials are made available under the
	* terms of the Eclipse Public License v. 2.0, which is available at
	* http://www.eclipse.org/legal/epl-2.0.
	*
	* This Source Code may also be made available under the following Secondary
	* Licenses when the conditions for such availability set forth in the
	* Eclipse Public License v. 2.0 are satisfied: GNU General Public License,
	* version 2 with the GNU Classpath Exception, which is available at
	* https://www.gnu.org/software/classpath/license.html.
	*
	* SPDX-License-Identifier: EPL-2.0 OR GPL-2.0 WITH Classpath-exception-2.0
	*/

	package com.sun.enterprise.v3.server;

	import com.sun.enterprise.module.bootstrap.ModuleStartup;
	import com.sun.enterprise.module.bootstrap.StartupContext;
	import com.sun.enterprise.v3.common.DoNothingActionReporter;
	import com.sun.enterprise.config.serverbeans.Applications;
	import com.sun.enterprise.config.serverbeans.Application;
	import com.sun.enterprise.config.serverbeans.Server;
	import com.sun.enterprise.config.serverbeans.ServerTags;
	import com.sun.enterprise.config.serverbeans.Domain;
	import com.sun.enterprise.util.io.FileUtils;
	import com.sun.enterprise.util.StringUtils;
	import com.sun.enterprise.deploy.shared.ArchiveFactory;
	import org.glassfish.hk2.api.IterableProvider;
	import org.jvnet.hk2.annotations.Optional;
	import org.jvnet.hk2.annotations.Service;
	import jakarta.inject.Inject;
	import jakarta.inject.Named;

	import org.jvnet.hk2.config.*;
	import org.glassfish.api.admin.CommandRunner;
	import org.glassfish.api.admin.ServerEnvironment;
	import org.glassfish.api.deployment.DeployCommandParameters;
	import org.glassfish.api.deployment.archive.ReadableArchive;
	import org.glassfish.api.deployment.archive.WritableArchive;
	import org.glassfish.api.ActionReport;
	import org.glassfish.deployment.common.DeploymentProperties;
	import org.glassfish.internal.api.*;

	import java.util.*;
	import java.util.jar.*;
	import java.util.logging.Logger;
	import java.util.logging.Level;
	import java.net.URISyntaxException;
	import java.net.URI;
	import java.io.*;
	import java.beans.PropertyVetoException;
	import org.glassfish.kernel.KernelLoggerInfo;

	/**
	* Very simple ModuleStartup that basically force an immediate shutdown.
	* When start() is invoked, the upgrade of the domain.xml has already been
	* performed.
	*
	* @author Jerome Dochez
	*/
	@Service(name="upgrade")
	public class UpgradeStartup implements ModuleStartup {

	@Inject
	CommandRunner runner;

	@Inject
	AppServerStartup appservStartup;

	@Inject
	Applications applications;

	@Inject
	ArchiveFactory archiveFactory;

	@Inject
	ServerEnvironment env;

	@Inject @Named( ServerEnvironment.DEFAULT_INSTANCE_NAME)
	Server server;

	@Inject
	Domain domain;

	@Inject
	CommandRunner commandRunner;

	@Inject @Optional
	IterableProvider<DomainUpgrade> upgrades;

	// we need to refine, a better logger should be used.
	@Inject
	Logger logger;

	@Inject
	private InternalSystemAdministrator kernelIdentity;

	private final static String MODULE_TYPE = "moduleType";

	private final static String J2EE_APPS = "j2ee-apps";
	private final static String J2EE_MODULES = "j2ee-modules";

	private final static String DOMAIN_TARGET = "domain";

	private final static String SIGNATURE_TYPES_PARAM = "-signatureTypes";

	private List<String> sigTypeList = new ArrayList<String>();

	public void setStartupContext(StartupContext startupContext) {
	appservStartup.setStartupContext(startupContext);
	}

	// do nothing, just return, at the time the upgrade service has
	// run correctly.
	public void start() {

	// we need to disable all the applications before starting server
	// so the applications will not get loaded before redeployment
	// store the list of previous enabled applications
	// so we can reset these applications back to enabled after
	// redeployment
	List<Application> enabledApps = new ArrayList<Application>();
	List<String> enabledAppNames = new ArrayList<String>();

	for (Application app : domain.getApplications().getApplications()) {
	logger.log(Level.INFO, "app " + app.getName() + " is " + app.getEnabled() + " resulting in " + Boolean.parseBoolean(app.getEnabled()));
	if (Boolean.parseBoolean(app.getEnabled())) {
	logger.log(Level.INFO, "Disabling application " + app.getName());
	enabledApps.add(app);
	enabledAppNames.add(app.getName());
	}
	}

	if (enabledApps.size()>0) {
	try {
	ConfigSupport.apply(new ConfigCode() {
	public Object run(ConfigBeanProxy... configBeanProxies) throws PropertyVetoException, TransactionFailure {
	for (ConfigBeanProxy proxy : configBeanProxies) {
	Application app = (Application) proxy;
	app.setEnabled(Boolean.FALSE.toString());
	}
	return null;
	}
	}, enabledApps.toArray(new Application[enabledApps.size()]));
	} catch(TransactionFailure tf) {
	logger.log(Level.SEVERE, "Exception while disabling applications", tf);
	return;
	}
	}

	// start the application server
	appservStartup.start();

	initializeSigTypeList();

	// redeploy all existing applications
	for (Application app : applications.getApplications()) {
	// we don't need to redeploy lifecycle modules
	if (Boolean.valueOf(app.getDeployProperties().getProperty
	(ServerTags.IS_LIFECYCLE))) {
	continue;
	}
	logger.log(Level.INFO, "Redeploy application " + app.getName() + " located at " + app.getLocation());
	// we let upgrade proceed even if one application
	// failed to redeploy
	redeployApp(app);
	}

	// re-enables all applications.
	// we need to use the names in the enabledAppNames to find all
	// the application refs that need to be re-enabled
	// as the previous application collected not longer exist
	// after redeployment
	if (enabledAppNames.size()>0) {
	for (Application app : domain.getApplications().getApplications()) {
	if (enabledAppNames.contains(app.getName())) {
	logger.log(Level.INFO, "Enabling application " + app.getName());
	try {
	ConfigSupport.apply(new SingleConfigCode<Application>() {
	public Object run(Application param) throws PropertyVetoException, TransactionFailure {
	if (!Boolean.parseBoolean(param.getEnabled())) {
	param.setEnabled(Boolean.TRUE.toString());
	}
	return null;
	}
	}, app);
	} catch(TransactionFailure tf) {
	logger.log(Level.SEVERE, "Exception while disabling applications", tf);
	return;
	}
	}
	}
	}

	// clean up leftover directories
	cleanupLeftOverDirectories();

	// stop-the server.
	KernelLoggerInfo.getLogger().info(KernelLoggerInfo.exitUpgrade);
	try {
	Thread.sleep(3000);
	if (runner!=null) {
	runner.getCommandInvocation("stop-domain", new DoNothingActionReporter(), kernelIdentity.getSubject()).execute();
	}

	} catch (InterruptedException e) {
	KernelLoggerInfo.getLogger().log(Level.SEVERE, KernelLoggerInfo.exceptionUpgrade, e);
	}

	}

	public void stop() {
	appservStartup.stop();
	}

	private void cleanupLeftOverDirectories() {
	// 1. remove applications/j2ee-apps(modules) directory
	File oldJ2eeAppsRepository = new File(
	env.getApplicationRepositoryPath(), J2EE_APPS);
	FileUtils.whack(oldJ2eeAppsRepository);
	File oldJ2eeModulesRepository = new File(
	env.getApplicationRepositoryPath(), J2EE_MODULES);
	FileUtils.whack(oldJ2eeModulesRepository);

	// 2. remove generated/xml/j2ee-apps(modules) directory
	File oldJ2eeAppsGeneratedXMLDir = new File(
	env.getApplicationGeneratedXMLPath(), J2EE_APPS);
	FileUtils.whack(oldJ2eeAppsGeneratedXMLDir);
	File oldJ2eeModulesGeneratedXMLDir = new File(
	env.getApplicationGeneratedXMLPath(), J2EE_MODULES);
	FileUtils.whack(oldJ2eeModulesGeneratedXMLDir);

	// 3. remove generated/ejb/j2ee-apps(modules) directory
	File oldJ2eeAppsEJBStubDir = new File(
	env.getApplicationEJBStubPath(), J2EE_APPS);
	FileUtils.whack(oldJ2eeAppsEJBStubDir);
	File oldJ2eeModulesEJBStubDir = new File(
	env.getApplicationEJBStubPath(), J2EE_MODULES);
	FileUtils.whack(oldJ2eeModulesEJBStubDir);

	// 4. clean up generated/jsp/j2ee-apps(modules) directory
	File oldJ2eeAppsJSPCompileDir = new File(
	env.getApplicationCompileJspPath(), J2EE_APPS);
	FileUtils.whack(oldJ2eeAppsJSPCompileDir);
	File oldJ2eeModulesJSPCompileDir = new File(
	env.getApplicationCompileJspPath(), J2EE_MODULES);
	FileUtils.whack(oldJ2eeModulesJSPCompileDir);

	// 5. clean up old system apps policy files
	File policyRootDir = env.getApplicationPolicyFilePath();
	File adminapp = new File(policyRootDir, "adminapp");
	FileUtils.whack(adminapp);
	File admingui = new File(policyRootDir, "admingui");
	FileUtils.whack(admingui);
	File ejbtimer = new File(policyRootDir, "__ejb_container_timer_app");
	FileUtils.whack(ejbtimer);
	File mejbapp = new File(policyRootDir, "MEjbApp");
	FileUtils.whack(mejbapp);
	File wstx = new File(policyRootDir, "WSTXServices");
	FileUtils.whack(wstx);
	File jwsappclient = new File(policyRootDir, "__JWSappclients");
	FileUtils.whack(jwsappclient);
	}

	private boolean redeployApp(Application app) {
	// we don't need to redeploy any v3 type application
	if (app.getModule().size() > 0 ) {
	logger.log(Level.INFO, "Skip redeploying v3 type application " +
	app.getName());
	return true;
	}

	// populate the params and properties from application element first
	DeployCommandParameters deployParams = app.getDeployParameters(null);

	// for archive deployment, let's repackage the archive and redeploy
	// that way
	// we cannot just directory redeploy the archive deployed apps in
	// v2->v3 upgrade as the repository layout was different in v2
	// we should not have to repackage for any upgrade from v3
	if (! Boolean.valueOf(app.getDirectoryDeployed())) {
	File repackagedFile = null;
	try {
	repackagedFile = repackageArchive(app);
	} catch (IOException ioe) {
	logger.log(Level.SEVERE, "Repackaging of application " + app.getName() + " failed: " + ioe.getMessage(), ioe);
	return false;
	}
	if (repackagedFile == null) {
	logger.log(Level.SEVERE, "Repackaging of application " + app.getName() + " failed.");
	return false;
	}
	logger.log(Level.INFO, "Repackaged application " + app.getName()
	+ " at " + repackagedFile.getPath());
	deployParams.path = repackagedFile;
	}

	deployParams.properties = app.getDeployProperties();
	// remove the marker properties so they don't get carried over
	// through redeployment
	deployParams.properties.remove(MODULE_TYPE);
	// add the compatibility property so the applications are
	// upgraded/redeployed in a backward compatible way
	deployParams.properties.setProperty(
	DeploymentProperties.COMPATIBILITY, "v2");

	// now override the ones needed for the upgrade
	deployParams.enabled = null;
	deployParams.force = true;
	deployParams.dropandcreatetables = false;
	deployParams.createtables = false;
	deployParams.target = DOMAIN_TARGET;

	ActionReport report = new DoNothingActionReporter();
	commandRunner.getCommandInvocation("deploy", report, kernelIdentity.getSubject()).parameters(deployParams).execute();

	// should we delete the temp file after we are done
	// it seems it might be useful to keep it around for debugging purpose

	if (report.getActionExitCode().equals(ActionReport.ExitCode.FAILURE)) {
	logger.log(Level.SEVERE, "Redeployment of application " + app.getName() + " failed: " + report.getMessage() + "\nPlease redeploy " + app.getName() + " manually.", report.getFailureCause());
	return false;
	}
	return true;
	}

	private File repackageArchive(Application app) throws IOException {
	URI uri = null;
	try {
	uri = new URI(app.getLocation());
	} catch (URISyntaxException e) {
	logger.log(Level.SEVERE, e.getMessage(), e);
	}

	if (uri == null) {
	return null;
	}

	Properties appProperties = app.getDeployProperties();
	String moduleType = appProperties.getProperty(MODULE_TYPE);
	String suffix = getSuffixFromType(moduleType);
	if (suffix == null) {
	suffix = ".jar";
	}
	File repositoryDir = new File(uri);

	// get temporary file directory of the system and set targetDir to it
	File tmp = File.createTempFile("upgrade", null);
	String targetParentDir = tmp.getParent();
	boolean isDeleted = tmp.delete();
	if (!isDeleted) {
	logger.log(Level.WARNING, "Error in deleting file " + tmp.getAbsolutePath());
	}

	if (moduleType.equals(ServerTags.J2EE_APPLICATION)) {
	return repackageApplication(repositoryDir, targetParentDir, suffix);
	} else {
	return repackageStandaloneModule(repositoryDir, targetParentDir, suffix);
	}
	}

	private File repackageApplication(File appDir,
	String targetParentDir, String suffix) throws IOException {
	String appName = appDir.getName();

	ReadableArchive source = archiveFactory.openArchive(appDir);

	File tempEar = new File(targetParentDir, appName + suffix);

	if (tempEar.exists()) {
	boolean isDeleted = tempEar.delete();
	if (!isDeleted) {
	logger.log(Level.WARNING, "Error in deleting file " + tempEar.getAbsolutePath());
	}
	}

	WritableArchive target = archiveFactory.createArchive("jar", tempEar);

	Collection<String> directoryEntries = source.getDirectories();
	List<String> subModuleEntries = new ArrayList<String>();
	List<String> entriesToExclude = new ArrayList<String>();

	// first put all the sub module jars to the target archive
	for (String directoryEntry : directoryEntries) {
	if (directoryEntry.endsWith("_jar") \|\|
	directoryEntry.endsWith("_war") \|\|
	directoryEntry.endsWith("_rar")) {
	subModuleEntries.add(directoryEntry);
	File moduleJar = processModule(new File(
	appDir, directoryEntry), targetParentDir, null);
	OutputStream os = null;
	InputStream is = new BufferedInputStream(
	new FileInputStream(moduleJar));
	try {
	os = target.putNextEntry(moduleJar.getName());
	FileUtils.copy(is, os, moduleJar.length());
	} finally {
	if (os!=null) {
	target.closeEntry();
	}
	is.close();
	}
	}
	}

	// now find all the entries we should exclude to copy to the target
	// basically all sub module entries should be excluded
	for (String subModuleEntry : subModuleEntries) {
	Enumeration<String> ee = source.entries(subModuleEntry);
	while (ee.hasMoreElements()) {
	String eeEntryName = ee.nextElement();
	entriesToExclude.add(eeEntryName);
	}
	}

	// now copy the rest of the entries
	Enumeration<String> e = source.entries();
	while (e.hasMoreElements()) {
	String entryName = e.nextElement();
	if (! entriesToExclude.contains(entryName)) {
	InputStream sis = source.getEntry(entryName);
	if (isSigFile(entryName)) {
	logger.log(Level.INFO, "Excluding signature file: "
	+ entryName + " from repackaged application: " +
	appName + "\n");
	continue;
	}
	if (sis != null) {
	InputStream is = new BufferedInputStream(sis);
	OutputStream os = null;
	try {
	os = target.putNextEntry(entryName);
	FileUtils.copy(is, os, source.getEntrySize(entryName));
	} finally {
	if (os!=null) {
	target.closeEntry();
	}
	is.close();
	}
	}
	}
	}

	// last is manifest if existing.
	Manifest m = source.getManifest();
	if (m!=null) {
	processManifest(m, appName);
	OutputStream os = target.putNextEntry(JarFile.MANIFEST_NAME);
	m.write(os);
	target.closeEntry();
	}

	source.close();
	target.close();

	return tempEar;
	}

	private File repackageStandaloneModule(File moduleDirName,
	String targetParentDir, String suffix) throws IOException {
	return processModule(moduleDirName, targetParentDir, suffix);
	}

	// repackage a module and return it as a jar file
	private File processModule(File moduleDir, String targetParentDir,
	String suffix) throws IOException {

	String moduleName = moduleDir.getName();

	// sub module in ear case
	if (moduleName.endsWith("_jar") \|\| moduleName.endsWith("_war") \|\| moduleName.endsWith("_rar")) {
	suffix = "." + moduleName.substring(moduleName.length() - 3);
	moduleName = moduleName.substring(0, moduleName.lastIndexOf('_'));
	}

	ReadableArchive source = archiveFactory.openArchive(moduleDir);

	File tempJar = new File(targetParentDir, moduleName + suffix);

	if (tempJar.exists()) {
	boolean isDeleted = tempJar.delete();
	if ( !isDeleted) {
	logger.log(Level.WARNING, "Error in deleting file " + tempJar.getAbsolutePath());
	}
	}

	WritableArchive target = archiveFactory.createArchive("jar", tempJar);

	Enumeration<String> e = source.entries();
	while (e.hasMoreElements()) {
	String entryName = e.nextElement();
	if (isSigFile(entryName)) {
	logger.log(Level.INFO, "Excluding signature file: "
	+ entryName + " from repackaged module: " + moduleName +
	"\n");
	continue;
	}
	InputStream sis = source.getEntry(entryName);
	if (sis != null) {
	InputStream is = new BufferedInputStream(sis);
	OutputStream os = null;
	try {
	os = target.putNextEntry(entryName);
	FileUtils.copy(is, os, source.getEntrySize(entryName));
	} finally {
	if (os!=null) {
	target.closeEntry();
	}
	is.close();
	}
	}
	}

	// last is manifest if existing.
	Manifest m = source.getManifest();
	if (m!=null) {
	processManifest(m, moduleName);
	OutputStream os = target.putNextEntry(JarFile.MANIFEST_NAME);
	m.write(os);
	target.closeEntry();
	}

	source.close();
	target.close();

	return tempJar;
	}

	private String getSuffixFromType(String moduleType) {
	if (moduleType == null) {
	return null;
	}
	if (moduleType.equals(ServerTags.CONNECTOR_MODULE)) {
	return ".rar";
	}
	if (moduleType.equals(ServerTags.EJB_MODULE)) {
	return ".jar";
	}
	if (moduleType.equals(ServerTags.WEB_MODULE)) {
	return ".war";
	}
	if (moduleType.equals(ServerTags.APPCLIENT_MODULE)) {
	return ".jar";
	}
	if (moduleType.equals(ServerTags.J2EE_APPLICATION)) {
	return ".ear";
	}
	return null;
	}

	private void initializeSigTypeList() {
	String sigTypesParam = env.getStartupContext().getArguments().getProperty(SIGNATURE_TYPES_PARAM);
	if (sigTypesParam != null) {
	sigTypeList = StringUtils.parseStringList(sigTypesParam, ",");
	}
	sigTypeList.add(".SF");
	sigTypeList.add(".sf");
	sigTypeList.add(".RSA");
	sigTypeList.add(".rsa");
	sigTypeList.add(".DSA");
	sigTypeList.add(".dsa");
	sigTypeList.add(".PGP");
	sigTypeList.add(".pgp");
	}

	private boolean isSigFile(String entryName) {
	for (String sigType : sigTypeList) {
	if (entryName.endsWith(sigType)) {
	return true;
	}
	}
	return false;
	}

	private void processManifest(Manifest m, String moduleName) {
	// remove signature related entries from the file
	Map<String, Attributes> entries = m.getEntries();
	Iterator<Map.Entry<String, Attributes>> entryItr = entries.entrySet().iterator();
	while (entryItr.hasNext()) {
	Attributes attr = entryItr.next().getValue();
	Iterator<Map.Entry<Object, Object>> attrItr = attr.entrySet().iterator();
	while (attrItr.hasNext()) {
	Object attrKey = attrItr.next().getKey();
	if (attrKey instanceof Attributes.Name) {
	Attributes.Name attrKey2 = (Attributes.Name) attrKey;
	if (attrKey2.toString().trim().equals("Digest-Algorithms")
	\|\| attrKey2.toString().indexOf("-Digest") != -1) {
	logger.log(Level.INFO, "Removing signature attribute "
	+ attrKey2 + " from manifest in " +
	moduleName + "\n");
	attrItr.remove();
	}
	}
	}
	if (attr.size() == 0) {
	entryItr.remove();
	}
	}
	}
	}