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/*
 * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 *
 * Copyright (c) 1997-2012 Oracle 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://glassfish.dev.java.net/public/CDDL+GPL_1_1.html
 * or packager/legal/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 packager/legal/LICENSE.txt.
 *
 * GPL Classpath Exception:
 * Oracle designates this particular file as subject to the "Classpath"
 * exception as provided by Oracle 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.
 */
// Portions Copyright [2016-2017] [Payara Foundation and/or its affiliates]

package com.sun.enterprise.deployment;

import com.google.common.base.Function;
import com.google.common.collect.FluentIterable;
import com.google.common.collect.ImmutableSet;
import com.sun.enterprise.deployment.node.ApplicationNode;
import com.sun.enterprise.deployment.runtime.application.wls.ApplicationParam;
import com.sun.enterprise.deployment.runtime.common.SecurityRoleMapping;
import com.sun.enterprise.deployment.runtime.common.wls.SecurityRoleAssignment;
import com.sun.enterprise.deployment.types.EjbReference;
import com.sun.enterprise.deployment.types.EjbReferenceContainer;
import com.sun.enterprise.deployment.types.MessageDestinationReferenceContainer;
import com.sun.enterprise.deployment.types.ResourceEnvReferenceContainer;
import com.sun.enterprise.deployment.types.ResourceReferenceContainer;
import com.sun.enterprise.deployment.types.RoleMappingContainer;
import com.sun.enterprise.deployment.types.ServiceReferenceContainer;
import com.sun.enterprise.deployment.util.ApplicationVisitor;
import com.sun.enterprise.deployment.util.ComponentVisitor;
import com.sun.enterprise.deployment.util.DOLUtils;
import com.sun.enterprise.util.LocalStringManagerImpl;
import com.sun.enterprise.util.StringUtils;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.TreeSet;
import java.util.UUID;
import java.util.Vector;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
import javax.inject.Inject;
import javax.persistence.EntityManagerFactory;
import org.glassfish.api.deployment.archive.ArchiveType;
import org.glassfish.deployment.common.DeploymentUtils;
import org.glassfish.deployment.common.Descriptor;
import org.glassfish.deployment.common.DescriptorVisitor;
import org.glassfish.deployment.common.ModuleDescriptor;
import org.glassfish.deployment.common.RootDeploymentDescriptor;
import org.glassfish.deployment.common.SecurityRoleMapper;
import org.glassfish.deployment.common.SecurityRoleMapperFactory;
import org.glassfish.deployment.versioning.VersioningUtils;
import org.glassfish.hk2.api.ServiceLocator;
import org.glassfish.internal.api.Globals;
import org.glassfish.security.common.Role;

/**
 * Objects of this type encapsulate the data and behaviour of a J2EE
 * application.
 *
 * @author Danny Coward
 */

public class Application extends CommonResourceBundleDescriptor
        implements RoleMappingContainer, WritableJndiNameEnvironment, 
            EjbReferenceContainer, ResourceEnvReferenceContainer,
            ResourceReferenceContainer, ServiceReferenceContainer,
            MessageDestinationReferenceContainer {

    /**
     * default value for the library-directory element
     */
    private static final String LIBRARY_DIRECTORY_DEFAULT_VALUE = "lib";

    private static final String PERSISTENCE_UNIT_NAME_SEPARATOR = "#";
    private static final String ROLLING_UPGRADES_ID_DELIMITER = System.getProperty("org.jboss.weld.clustering.rollingUpgradesIdDelimiter", "..");

    /**
     * Store generated XML dir to be able to get the generated WSDL
     */
    private String generatedXMLDir;

    // Set of modules in this application
    private Set> modules = new OrderedSet>();

    // True if unique id has been set.  Allows callers to avoid
    // applying unique ids to subcomponents multiple times.
    private boolean uniqueIdSet = false;

    // IASRI 4645310
    /**
     * unique id for this application
     */
    private long uniqueId;

    // IASRI 4645310
    /**
     * represents the virtual status of this application object
     */
    private boolean virtual = false;

    // IASRI 4662001, 4720955
    /**
     * represents whether all ejb modules in an application will be pass by
     * value or pass by reference
     */
    private Boolean passByReference = null;

    // use a String object as lock so it can be serialized as part
    // of the Application object
    private String cmpDescriptorsLock = "cmp descriptors lock";

    // flag to indicate that the memory representation of this application 
    // is not in sync with the disk representation
    private boolean isDirty;

    // data structure to map roles to users and groups
    private transient SecurityRoleMapper roleMapper;

    // IASRI 4648645 - application registration name
    /**
     * name used to register this application
     */
    private String registrationName;

    private String appName;
   
    private String archiveName;

    private String compatValue;
    
    private String classLoadingDelegate;
    private final List scanningInclusions = new ArrayList<>();
    private final List scanningExclusions = new ArrayList<>();
    private final Set whitelistPackages = new HashSet<>();


    private boolean initializeInOrder = false;

    // realm associated with this application
    private String realm;
    
    @Inject
    private transient SecurityRoleMapperFactory securityRoleMapperFactory;

    /**
     * A flag to store the resolved keepstate value for the current application.
     * See org.glassfish.ejb.startup.EjbApplication for details.  This value
     * may be different from super.keepState.
     */
    private boolean keepStateResolved;

    // Physical entity manager factory corresponding to the unit name of 
    // each application-level persistence unit.  Only available at runtime.
    private transient Map entityManagerFactories =
            new HashMap();

    private Set entityManagerFactoryUnitNames =
            new HashSet();

    // the jndi environment entries
    private Set environmentProperties =
            new HashSet();
    private Set ejbReferences =
            new HashSet();
    private Set resourceEnvReferences =
            new HashSet();
    private Set messageDestReferences =
            new HashSet();
    private Set resourceReferences =
            new HashSet();
    private Set serviceReferences =
            new HashSet();
    private Set
            entityManagerFactoryReferences =
            new HashSet();
    private Set
            entityManagerReferences =
            new HashSet();

    // for i18N
    private static LocalStringManagerImpl localStrings =
            new LocalStringManagerImpl(Application.class);

    private Set appRoles;

    private String libraryDirectory;

    private List roleMaps = new ArrayList();
    private List wlRoleAssignments = new ArrayList();

    private boolean loadedFromApplicationXml = true;

    private Set resourceAdapters = new HashSet();

    private Set applicationParams = 
            new HashSet();

    private static final ServiceLocator habitat = Globals.getDefaultHabitat();
    
    private Application() {
        super("", localStrings.getLocalString(
                "enterprise.deployment.application.description",
                "Application description"));
    }

    // Create logger object per Java SDK 1.4 to log messages
    // introduced Santanu De, Sun Microsystems, March 2002

    static Logger _logger = DOLUtils.getDefaultLogger();


    /**
     * @return the default version of the deployment descriptor
     *         loaded by this descriptor
     */
    @Override
    public String getDefaultSpecVersion() {
        return ApplicationNode.SPEC_VERSION;
    }

    @Override
    public boolean isEmpty() {
        return modules.isEmpty();
    }

	/**
     * Creates a new application to hold a standalone module
     *
     * @param name      the application name
     * @param newModule the standalone module descriptor
     * @return the application
     */
    public static Application createVirtualApplication(String name, ModuleDescriptor newModule) {
    	
        // create a new empty application
        Application application = createApplication();
        
        application.setVirtual(true);
        if (name == null && newModule != null && newModule.getDescriptor() != null) {
            name = newModule.getDescriptor().getDisplayName();

        }
        String untaggedName = VersioningUtils.getUntaggedName(name);
        if (name != null) {
            application.setDisplayName(untaggedName);
            application.setName(untaggedName);
            application.setAppName(untaggedName);
        }

        // add the module to it
		if (newModule != null) {
			newModule.setStandalone(true);
			newModule.setArchiveUri(untaggedName);
			if (newModule.getDescriptor() != null) {
				newModule.getDescriptor().setApplication(application);
			}
			application.addModule(newModule);
		}
        
        return application;
    }
    
    public static Application createApplication() {
        // create a new empty application
        Application retVal = habitat.create(Application.class);
        habitat.inject(retVal);
        habitat.postConstruct(retVal);
        
        return retVal; // new Application();
    }

    /**
     * Returns the generated XML directory feturn the set of ejb references this ejb declares.
     */
    @Override
    public Set getEjbReferenceDescriptors() {
        return ejbReferences;
    }

    /**
     * Adds a reference to another ejb to me.
     */
    @Override
    public void addEjbReferenceDescriptor(EjbReference ejbReference) {
        ejbReferences.add(ejbReference);
        ejbReference.setReferringBundleDescriptor(this);
    }

    @Override
    public void removeEjbReferenceDescriptor(EjbReference ejbReference) {
        ejbReferences.remove(ejbReference);
    }

    /**
     * Return a reference to another ejb by the same name or throw an IllegalArgumentException.
     * @param name
     * @return 
     */
    public EjbReference getEjbReferenceByName(String name) {
        return (EjbReferenceDescriptor) getEjbReference(name);
    }

    @Override
    public EjbReference getEjbReference(String name) {
        for (EjbReference er : getEjbReferenceDescriptors()) {
            if (er.getName().equals(name)) {
                return er;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoejbrefbyname",
                "This app [{0}] has no ejb reference by the name of [{1}] ", new Object[]{getName(), name}));
    }

    @Override
    public Set getServiceReferenceDescriptors() {
        return serviceReferences;
    }

    @Override
    public void addServiceReferenceDescriptor(ServiceReferenceDescriptor
            serviceRef) {
        serviceRef.setBundleDescriptor(this);
        serviceReferences.add(serviceRef);
    }

    @Override
    public void removeServiceReferenceDescriptor(ServiceReferenceDescriptor
            serviceRef) {
        serviceReferences.remove(serviceRef);
    }

    /**
     * Looks up an service reference with the given name.
     * Throws an IllegalArgumentException if it is not found.
     * @param name
     */
    @Override
    public ServiceReferenceDescriptor getServiceReferenceByName(String name) {
        for (ServiceReferenceDescriptor srd : this.getServiceReferenceDescriptors()) {
            if (srd.getName().equals(name)) {
                return srd;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoservicerefbyname",
                "This app [{0}] has no service reference by the name of [{1}]",
                new Object[]{getRegistrationName(), name}));
    }

    @Override
    public Set getMessageDestinationReferenceDescriptors() {
        return messageDestReferences;
    }

    @Override
    public void addMessageDestinationReferenceDescriptor
            (MessageDestinationReferenceDescriptor messageDestRef) {
        messageDestRef.setReferringBundleDescriptor(this);
        messageDestReferences.add(messageDestRef);
    }

    @Override
    public void removeMessageDestinationReferenceDescriptor
            (MessageDestinationReferenceDescriptor msgDestRef) {
        messageDestReferences.remove(msgDestRef);
    }

    /**
     * Looks up an message destination reference with the given name.
     * Throws an IllegalArgumentException if it is not found.
     * @param name
     */
    @Override
    public MessageDestinationReferenceDescriptor
        getMessageDestinationReferenceByName(String name) {

        for (MessageDestinationReferenceDescriptor mdr : messageDestReferences) {
            if (mdr.getName().equals(name)) {
                return mdr;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "exceptionapphasnomsgdestrefbyname",

                "This app [{0}] has no message destination reference by the name of [{1}]",
                new Object[]{getRegistrationName(), name}));
    }

    /**
     * Return the set of resource environment references this application declares.
     */
    @Override
    public Set getResourceEnvReferenceDescriptors() {
        return resourceEnvReferences;
    }

    @Override
    public void addResourceEnvReferenceDescriptor(ResourceEnvReferenceDescriptor resourceEnvReference) {
        resourceEnvReferences.add(resourceEnvReference);
    }

    @Override
    public void removeResourceEnvReferenceDescriptor(ResourceEnvReferenceDescriptor resourceEnvReference) {
        resourceEnvReferences.remove(resourceEnvReference);
    }

    /**
     * Return a reference to another ejb by the same name or throw an IllegalArgumentException.
     * @param name
     */
    @Override
    public ResourceEnvReferenceDescriptor getResourceEnvReferenceByName(String name) {
        for (ResourceEnvReferenceDescriptor jdr : this.getResourceEnvReferenceDescriptors()) {
            if (jdr.getName().equals(name)) {
                return jdr;

            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoresourceenvrefbyname",
                "This app {0} has no resource environment reference by the name of {1}",
                new Object[] {getRegistrationName(), name}));
    }


    /**
     * Return the set of resource references this ejb declares.
     */
    @Override
    public Set getResourceReferenceDescriptors() {
        return resourceReferences;
    }
    /**
     * Adds a resource reference to me.
     */
    @Override
    public void addResourceReferenceDescriptor(ResourceReferenceDescriptor resourceReference) {
        resourceReferences.add(resourceReference);
    }

    /**
     * Removes the given resource reference from me.
     */
    @Override
    public void removeResourceReferenceDescriptor(ResourceReferenceDescriptor resourceReference) {
        resourceReferences.remove(resourceReference);
    }

    /**
     * Return the resource object corresponding to the supplied name or throw an illegal argument exception.
     * @param name
     * @return 
     */
    @Override
    public ResourceReferenceDescriptor getResourceReferenceByName(String name) {
        for (ResourceReferenceDescriptor next : this.getResourceReferenceDescriptors()) {
            if (next.getName().equals(name)) {
                return next;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoresourcerefbyname",
                "This app {0} has no resource reference by the name of {1}",
                new Object[]{getRegistrationName(), name}));
    }

    /**
     * Returns the environment property object searching on the supplied key.
     * throws an illegal argument exception if no such environment property exists.
     * @param name
     */
    @Override
    public EnvironmentProperty getEnvironmentPropertyByName(String name) {
        for (EnvironmentProperty ev : this.getEnvironmentProperties()) {
            if (ev.getName().equals(name)) {
                return ev;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoenvpropertybyname",
                "This app {0} has no environment property by the name of {1}",
                new Object[]{getRegistrationName(), name}));
    }

    /**
     * Return a copy of the structure holding the environment properties.
     */
    @Override
    public Set getEnvironmentProperties() {
        return environmentProperties;
    }

    @Override
    public void addEnvironmentProperty(EnvironmentProperty environmentProperty) {
        this.environmentProperties.add(environmentProperty);
    }

    /**
     * Removes the given environment property from me.
     */
    @Override
    public void removeEnvironmentProperty(EnvironmentProperty environmentProperty) {
        this.getEnvironmentProperties().remove(environmentProperty);

    }

    @Override
    public Set
        getEntityManagerFactoryReferenceDescriptors() {

        return entityManagerFactoryReferences;
    }

    /**
     * Return the entity manager factory reference descriptor corresponding to
     * the given name.
     * @param name
     * @return 
     */
    @Override
    public EntityManagerFactoryReferenceDescriptor
        getEntityManagerFactoryReferenceByName(String name) {
        for (EntityManagerFactoryReferenceDescriptor next :
                getEntityManagerFactoryReferenceDescriptors()) {
            if (next.getName().equals(name)) {
                return next;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoentitymgrfactoryrefbyname",
                "This app {0} has no entity manager factory reference by the name of {1}",
                new Object[]{getRegistrationName(), name}));
    }

    @Override
    public void addEntityManagerFactoryReferenceDescriptor
            (EntityManagerFactoryReferenceDescriptor reference) {
        reference.setReferringBundleDescriptor(this);
        this.entityManagerFactoryReferences.add(reference);
    }

    @Override
    public Set
        getEntityManagerReferenceDescriptors() {

        return entityManagerReferences;
    }

    /**
     * Return the entity manager factory reference descriptor corresponding to
     * the given name.
     * @param name
     * @return 
     */
    @Override
    public EntityManagerReferenceDescriptor
        getEntityManagerReferenceByName(String name) {
        for (EntityManagerReferenceDescriptor next :
                getEntityManagerReferenceDescriptors()) {

            if (next.getName().equals(name)) {
                return next;
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnoentitymgrrefbyname",
                "This app {0} has no entity manager reference by the name of {1}",

                new Object[]{getRegistrationName(), name}));
    }

    @Override
    public void addEntityManagerReferenceDescriptor
            (EntityManagerReferenceDescriptor reference) {
        reference.setReferringBundleDescriptor(this);
        this.getEntityManagerReferenceDescriptors().add(reference);
    }

    @Override
    public Set
        getPostConstructDescriptors() {
        throw new UnsupportedOperationException();
    }

    @Override
    public void addPostConstructDescriptor(LifecycleCallbackDescriptor
        postConstructDesc) {
        throw new UnsupportedOperationException();
    }

    @Override
    public LifecycleCallbackDescriptor
        getPostConstructDescriptorByClass(String className) {
        throw new UnsupportedOperationException();
    }

    @Override
    public Set getPreDestroyDescriptors() {
        throw new UnsupportedOperationException();
    }

    @Override
    public void addPreDestroyDescriptor(LifecycleCallbackDescriptor preDestroyDesc) {
        throw new UnsupportedOperationException();
    }

    @Override
    public LifecycleCallbackDescriptor getPreDestroyDescriptorByClass(String className) {
        throw new UnsupportedOperationException();
    }

    @Override
    public List getInjectableResourcesByClass(String className) {
        return (getInjectableResourcesByClass(className, this));
    }

    @Override
    public InjectionInfo getInjectionInfoByClass(Class clazz) {
        return (getInjectionInfoByClass(clazz, this));
    }

    public void setGeneratedXMLDirectory(String xmlDir) {
        generatedXMLDir = xmlDir;
    }

   /**
     * @return 
     */
    public String getGeneratedXMLDirectory() {
        return generatedXMLDir;
    }

    // START OF IASRI 4648645 - application registration name
    /**
     * Sets the registration name for this application. This name is used
     * while deploying the application. The deployment process gurantees
     * that this name is unique.
     *
     * @param appId the registration name used for this application
     */
    public void setRegistrationName(String appId) {

        // at his point we need to swap our RoleMapper, if we have one... 
        SecurityRoleMapper roleMapper = null;
        try {
            roleMapper = getRoleMapper();
        } catch (IllegalArgumentException ignore) {
        }

        if (roleMapper != null) {
            if (securityRoleMapperFactory == null) {
                throw new IllegalArgumentException(localStrings.getLocalString(
                        "enterprise.deployment.norolemapperfactorydefine",
                        "This application has no role mapper factory defined"));
            }
            securityRoleMapperFactory.removeRoleMapper(getName());
            roleMapper.setName(appId);
            securityRoleMapperFactory.setRoleMapper(appId, roleMapper);
        }

        this.registrationName = appId;
    }

    /**
     * Returns the registration name of this application.
     *
     * @return the registration name of this application
     */
    public String getRegistrationName() {
        if (registrationName != null) {
            return registrationName;
        } else {
            return getName();
        }
    }
    // END OF IASRI 4648645


    /**
     * Returns the value of the app-name element in the application.xml if 
     * it's defined. The default EE app name is the unqualified name of 
     * the .ear or stand-alone module, minus the file extension. 
     *
     * @return the EE app name of this application
     */
    public String getAppName() {
        return VersioningUtils.getUntaggedName(appName);
    }

    /**
     * Sets the EE app name
     * @param appName the EE app name of this application
     */
    public void setAppName(String appName) {
        this.appName = VersioningUtils.getUntaggedName(appName);
    }

    /**
     * Returns the value of the archive-name element in the sun-application.xml
     * When the app-name is not present in application.xml and archive-name is
     * present in sun-application.xml, the value of archive-name minus file 
     * extension will be used as the default name of the app-name.
     *
     * @return the EE app name of this application
     */
    public String getArchiveName() {
        return archiveName;
    }

    /**
     * Sets the archive name using the archive-name element defined 
     * in sun-application.xml
     * @param archiveName archiveName to calculate default EE6 app-name
     */
    public void setArchiveName(String archiveName) {
        this.archiveName = archiveName;
        if (appName == null && archiveName != null) {
            appName = DeploymentUtils.getDefaultEEName(archiveName);
        }
    }

    @Override
    public String getCompatibility() {
        return compatValue;
    }

    @Override
    public void setCompatibility(String compatValue) {
        this.compatValue = compatValue;
    }

    public String getClassLoadingDelegate() {
        return classLoadingDelegate;
    }

    public void setClassLoadingDelegate(String classLoadingDelegate) {
        this.classLoadingDelegate = classLoadingDelegate;
    }

    public List getScanningExclusions() {
        return scanningExclusions;
    }

    public List getScanningInclusions() {
        return scanningInclusions;
    }

    public void addScanningInclusions(List inclusions) {
        addScanningInclusions(inclusions, getLibraryDirectory());
    }

    public void addScanningInclusions(List inclusions, String libDir) {
        this.scanningInclusions.addAll(FluentIterable.from(inclusions)
                .transform(new WildcardToRegex(libDir)).toList());
    }

    public void addScanningExclusions(List exclusions) {
        addScanningExclusions(exclusions, getLibraryDirectory());
    }

    public void addScanningExclusions(List exclusions, String libDir) {
        this.scanningExclusions.addAll(FluentIterable.from(exclusions)
                .transform(new WildcardToRegex(libDir)).toList());
    }

    public boolean isWhitelistEnabled() {
        return !whitelistPackages.isEmpty();
    }

    public Set getWhitelistPackages() {
        return ImmutableSet.copyOf(whitelistPackages);
    }

    public void addWhitelistPackage(String aPackage) {
        whitelistPackages.add(aPackage);
    }

    /**
     * @return the initializeInOrder flag
     * when the return value is true, the modules inside ear will be loaded
     * by their declaration order in application.xml
     */
    public boolean isInitializeInOrder() {
        return initializeInOrder;
    }

    /**
     * Sets the initializeInOrder flag
     * @param initializeInOrder
     */
    public void setInitializeInOrder(boolean initializeInOrder) {
        this.initializeInOrder = initializeInOrder;   
    } 

    /**
     * Set the physical entity manager factory for a persistence unit
     * within this application.
     * This method takes a parameter called persistenceRootUri to support for
     * fully-qualified persistence-unit-name syntax within
     * persistence-unit-refs and persistence-context-refs. The syntax is similar
     * to ejb-link and messge-destination-link. See (EJB 3 core spec: 15.10.2)
     *
     * @param unitName:           Name of the persistence-unit
     * @param persistenceRootUri: uri of the root of the persistence.xml
     *                            (excluding META-INF) in which the persistence unit was defined.
     *                            This uri is relative to the top of the .ear.
     * @param emf:                an entity manager factory.
     */
    public void addEntityManagerFactory(
            String unitName,
            String persistenceRootUri,
            EntityManagerFactory emf) {

        String fullyQualifiedUnitName = persistenceRootUri +
                PERSISTENCE_UNIT_NAME_SEPARATOR + unitName;

        // Always allow fully qualified lookup.
        entityManagerFactories.put(fullyQualifiedUnitName, emf);

        // Allow unqualified lookup, unless there are multiple .ear level
        // persistence units declaring the same persistence unit name. In that
        // case, only a fully-qualified lookup will work.  Note that even
        // though the entity manager factory map might contain more than one
        // key pointing to the same entity manager factory, the behavior
        // of getEntityManagerFactories() is not affected since it returns a Set.
        if (entityManagerFactoryUnitNames.contains(unitName)) {
            entityManagerFactories.remove(unitName);
        } else {
            entityManagerFactories.put(unitName, emf);
            entityManagerFactoryUnitNames.add(unitName);
        }
    }

    /**
     * Retrieve the physical entity manager factory associated with the
     * unitName of an application-level persistence unit.   Returns null if
     * no matching entry is found.
     * @param unitName
     * @param declaringModule
     * @return 
     */
    public EntityManagerFactory getEntityManagerFactory
            (String unitName, BundleDescriptor declaringModule) {

        String lookupString = unitName;

        int separatorIndex =
                unitName.lastIndexOf(PERSISTENCE_UNIT_NAME_SEPARATOR);

        if (separatorIndex != -1) {
            String unqualifiedUnitName =
                    unitName.substring(separatorIndex + 1);
            String path = unitName.substring(0, separatorIndex);

            String persistenceRootUri = getTargetUri(declaringModule, path);

            lookupString = persistenceRootUri +
                    PERSISTENCE_UNIT_NAME_SEPARATOR + unqualifiedUnitName;
        }

        return entityManagerFactories.get(lookupString);
    }

    /**
     * Returns the set of physical entity manager factories associated with
     * persistence units in this application.
     * @return 
     */
    @Override
    public Set getEntityManagerFactories() {

        return new HashSet
                (entityManagerFactories.values());

    }

    /**
     * Return the set of roles used in this application. Currently, for release 1.0, it is an
     * * aggregation of all the roles in the sub-modules of the application.
     *
     * @return the Set of roles in the application.
     */
    @Override
    public Set getRoles() {
        Set roles = new HashSet();
        for (BundleDescriptor bd : getBundleDescriptors()) {
            if (bd != null) {
                roles.addAll(bd.getRoles());
            }
        }
        return roles;
    }

    /**
     * Return the set of {@link org.glassfish.security.common.Role} objects
     * I have (the ones defined in application xml).
     * @return 
     */
    public Set getAppRoles() {
        if (this.appRoles == null) {
            this.appRoles = new HashSet();
        }
        return this.appRoles;
    }

    /**
     * Adds a new {@link org.glassfish.security.common.Role} to the application based on the descriptor
     * @param descriptor 
     */
    public void addAppRole(SecurityRoleDescriptor descriptor) {
        Role role = new Role(descriptor.getName());
        role.setDescription(descriptor.getDescription());
        getAppRoles().add(role);
    }


    /**
     * Adds a new abstract role
     * @param role
     */
    @Override
    public void addRole(Role role) {
        for (BundleDescriptor bd : getBundleDescriptors()) {
            bd.addRole(role);
        }
    }

    /**
     * Removes the given role.
     * @param role
     */
    @Override
    public void removeRole(Role role) {
        getAppRoles().remove(role);
        for (BundleDescriptor bd : getBundleDescriptors()) {
            bd.removeRole(role);
        }
    }

    /**
     * Reset the display name of this application.
     *
     * @param name the display name of the application.
     */
    @Override
    public void setName(String name) {
        name = name.replace('/', '-');
        name = name.replace('\\', '-'); // for deploying from NT to solaris & vice versa. This will
        // need to be cleaned when we clean up the backend for registering apps
        super.setName(name);
        if (this.getRoleMapper() != null) {
            this.getRoleMapper().setName(name);
        }
    }

    public void setLibraryDirectory(String value) {
        libraryDirectory = value;
    }

    /**
     * Returns an "intelligent" value for the library directory setting, meaning
     * the current value if it has been set to a non-null, non-empty value;
     * the default value if the value has never been set, and null if the value
     * has been set to empty.
     *
     * @return String value of the library directory setting
     */
    public String getLibraryDirectory() {
        if (libraryDirectory != null) {
            return (libraryDirectory.length() == 0) ? null : libraryDirectory;
        } else {
            return LIBRARY_DIRECTORY_DEFAULT_VALUE;
        }
    }

    public String getLibraryDirectoryRawValue() {
        return libraryDirectory;
    }

    public void removeModule(ModuleDescriptor descriptor) {
        if (modules.contains(descriptor)) {
            if (descriptor.getDescriptor() != null) {
                descriptor.getDescriptor().setApplication(null);
            }
            modules.remove(descriptor);
        }
    }

    public void addModule(ModuleDescriptor descriptor) {
        modules.add(descriptor);
        if (descriptor.getDescriptor() != null) {
            descriptor.getDescriptor().setApplication(this);
        }
    }

    /**
     * Obtain a full set of module descriptors
     *
     * @return the set of bundle descriptors
     */
    public Set> getModules() {
        return modules;
    }

    /**
     * Get the uri of a target based on a source module and a
     * a relative uri from the perspective of that source module.
     *
     * @param origin            bundle descriptor within this application
     * @param relativeTargetUri relative uri from the given bundle descriptor
     * @return target uri
     */
    public String getTargetUri(BundleDescriptor origin,
                               String relativeTargetUri) {
        String targetUri = null;

        try {
            String archiveUri = origin.getModuleDescriptor().getArchiveUri();
            URI originUri = new URI(archiveUri);
            URI resolvedUri = originUri.resolve(relativeTargetUri);
            targetUri = resolvedUri.getPath();
        } catch (URISyntaxException use) {
            _logger.log(Level.FINE, "origin " + origin + " has invalid syntax",
                    use);
        }

        return targetUri;
    }

    /**
     * Get a target bundle descriptor based on an input bundle descriptor and
     * a relative uri from the perspective of the input bundle descriptor.
     *
     * @param origin            bundle descriptor within this application
     * @param relativeTargetUri relative uri from the given bundle descriptor
     *                          to another bundle within the application.
     * @return target BundleDescriptor or null if not found.
     */
    public BundleDescriptor getRelativeBundle(BundleDescriptor origin,
                                              String relativeTargetUri) {
        String targetBundleUri = getTargetUri(origin, relativeTargetUri);

        BundleDescriptor targetBundle = null;

        if (targetBundleUri != null) {
            targetBundle = getModuleByUri(targetBundleUri);
        }

        return targetBundle;
    }

    /**
     * Return the relative uri between two modules, from the perspective
     * of the first bundle.
     *
     * @param origin
     * @param target
     * @return relative uri or empty string if the two bundles are the same
     */
    public String getRelativeUri(BundleDescriptor origin,
                                 BundleDescriptor target) {

        String originUri = origin.getModuleDescriptor().getArchiveUri();
        String targetUri = target.getModuleDescriptor().getArchiveUri();

        StringTokenizer tokenizer = new StringTokenizer(originUri, "/");
        int numTokens = tokenizer.countTokens();
        int numSeparators = (numTokens > 0) ? (numTokens - 1) : 0;

        StringBuffer relativeUri = new StringBuffer();

        // The simplest way to compute a relative uri is to add one "../"
        // for each sub-path in the origin URI, then add the target URI.
        // It's possible for the result to not be normalized if the origin
        // and target have at least one common root, but that shouldn't
        // matter as long as when the relative URI is resolved against the
        // origin it produces the target.
        for (int i = 0; i < numSeparators; i++) {
            relativeUri.append("../");
        }

        relativeUri.append(targetUri);

        return relativeUri.toString();
    }

    /**
     * Lookup module by uri.
     *
     * @param uri the module path in the application archive
     * @return a bundle descriptor in this application identified by uri
     *         or null if not found.
     */
    public ModuleDescriptor getModuleDescriptorByUri(String uri) {
        for (ModuleDescriptor aModule : getModules()) {
            if (aModule.getArchiveUri().equals(uri)) {
                return aModule;
            }
        }
        return null;
    }


    /**
     * Lookup module by uri.
     *
     * @return a bundle descriptor in this application identified by uri
     *         or null if not found.
     */
    public Collection> getModuleDescriptorsByType(ArchiveType type) {
        if (type==null) {
            throw new IllegalArgumentException("type cannot be null");
        }
        LinkedList> results = new LinkedList>();
        for (ModuleDescriptor aModule : getModules()) {
            if (type.equals(aModule.getModuleType())) {
                results.add(aModule);
            }
        }
        return results;
    }

    /**
     * Lookup module by uri.
     *
     * @param uri the module path in the application archive
     * @return a bundle descriptor in this application identified by uri
     *         or null if not found.
     */
    public BundleDescriptor getModuleByUri(String uri) {
        ModuleDescriptor md = getModuleDescriptorByUri(uri);
        if (md != null) {
            return md.getDescriptor();
        }
        return null;
    }

    /**
     * @param type the module type
     * @param uri  the module path in the application archive
     * @return a bundle descriptor in this application identified by
     *         its type and uri
     */
    public  T getModuleByTypeAndUri(Class type, String uri) {
        for (ModuleDescriptor aModule : getModules()) {
            try {
                T descriptor = type.cast(aModule.getDescriptor());
                if (descriptor.getModuleDescriptor().getArchiveUri().equals(uri)) {
                    return descriptor;
                }
            } catch(ClassCastException e) {
                // ignore
            }
        }
        return null;
    }

    /**
     * Obtain the EJB in this application of the given display name. If the EJB is not
     * present, throw an IllegalArgumentException.
     *
     * @param ejbName the name of the bean
     * @return the EjbDescriptor object with the given display name
     */
    public EjbDescriptor getEjbByName(String ejbName) {
        for (EjbBundleDescriptor ejbd : getBundleDescriptors(EjbBundleDescriptor.class)) {
            if (ejbd.hasEjbByName(ejbName)) {
                return ejbd.getEjbByName(ejbName);
            }
        }
        throw new IllegalArgumentException(localStrings.getLocalString(
                "enterprise.deployment.exceptionapphasnobeannamed",
                "This application has no beans of name {0}", ejbName));
    }

    /**
     * Return whether the application contains the given ejb by name..
     *
     * @param ejbName the name of the bean
     * @return true if there is a bean matching the given name
     */
    public boolean hasEjbByName(String ejbName) {
        for (EjbBundleDescriptor ebd : getBundleDescriptors(EjbBundleDescriptor.class)) {
            if (ebd.hasEjbByName(ejbName)) {
                return true;
            }
        }
        return false;
    }

    /**
     * if this application object is virtual, return the standalone
     * bundle descriptor it is wrapping otherwise return null
     *
     * @return the wrapped standalone bundle descriptor
     */
    public BundleDescriptor getStandaloneBundleDescriptor() {
        if (isVirtual()) {
            if (getModules().size()>1) {
                // this is an error, the application is virtual,
                // which mean a wrapper for a standalone module and
                // it seems I have more than one module in my list...
                throw new IllegalStateException("Virtual application contains more than one module");
            }
            return getModules().iterator().next().getDescriptor();
        } else {
            return null;
        }
    }


    /**
     * Obtain a full set of bundle descriptors for a particular type
     *
     * @param type the bundle descriptor type requested
     * @return the set of bundle descriptors
     */
    public  Set getBundleDescriptors(Class type) {
        if (type == null) {
            return null;
        }
        Set bundleSet = new OrderedSet();
        for (ModuleDescriptor aModule : getModules()) {
            try {
                T descriptor = type.cast(aModule.getDescriptor());
                bundleSet.add(descriptor);
            } catch(ClassCastException e) {
                // ignore
            }
            // any children, this need to happen outside of the casting as the parent
            // type has nothing to do with the children extensions.
            if (aModule.getDescriptor() != null) {
                bundleSet.addAll(aModule.getDescriptor().getExtensionsDescriptors(type));
            }
        }
        return bundleSet;
    }

    /**
     * Obtain a full set of bundle descriptors for a particular type
     *
     * @param bundleType the bundle descriptor type requested
     * @return the set of bundle descriptors
     */
    public Set getBundleDescriptorsOfType(ArchiveType bundleType) {
        if (bundleType == null) {
            return Collections.emptySet();
        }
        Set bundleSet = new OrderedSet();
        for (ModuleDescriptor aModule : getModules()) {
            if (aModule.getDescriptor().getModuleType()== bundleType) {
                bundleSet.add((BundleDescriptor)aModule.getDescriptor());
            }
            for (RootDeploymentDescriptor rd : aModule.getDescriptor().getExtensionsDescriptors()) {
                if (rd instanceof BundleDescriptor) {
                     if (((BundleDescriptor)rd).getModuleType()== bundleType){
                         bundleSet.add((BundleDescriptor)rd); 
                     }
                }
            }
        }
        return bundleSet;
    }

    /**
     * Obtain a set of all bundle descriptors, regardless of type
     *
     * @return the set of bundle descriptors
     */
    public Set getBundleDescriptors() {
        Set bundleSet = new OrderedSet();
        for (ModuleDescriptor aModule :  getModules()) {
            BundleDescriptor bundleDesc = aModule.getDescriptor();
            if (bundleDesc != null) {
                bundleSet.add(bundleDesc);
                for (RootDeploymentDescriptor rd : 
                    bundleDesc.getExtensionsDescriptors()) {
                    if (rd instanceof BundleDescriptor) {
                        bundleSet.add((BundleDescriptor)rd);
                    }
                }
            } else {
                DOLUtils.getDefaultLogger().fine("Null descriptor for module " + aModule.getArchiveUri());
            }
        }
        return bundleSet;
    }

    /**
     * Add a bundle descriptor to this application.
     *
     * @param bundleDescriptor the bundle descriptor to add
     */
    @Override
    public void addBundleDescriptor(BundleDescriptor bundleDescriptor) {
        ModuleDescriptor newModule = bundleDescriptor.getModuleDescriptor();
        addModule(newModule);
    }

    /**
     * Remove a web bundle descriptor from this application.
     *
     * @param bundleDescriptor the web bundle descriptor to remove
     */
    public void removeBundleDescriptor(BundleDescriptor bundleDescriptor) {
        bundleDescriptor.setApplication(null);
        getBundleDescriptors().remove(bundleDescriptor);
    }

    /**
     * Return the Vector of ejb deployment objects.
     */
    public Vector getEjbDescriptors() {
        Vector ejbDescriptors = new Vector();
        for (EjbBundleDescriptor ejbBundleDescriptor : getBundleDescriptors(EjbBundleDescriptor.class)) {
            ejbDescriptors.addAll(ejbBundleDescriptor.getEjbs());
        }

        return ejbDescriptors;
    }

    // START OF IASRI 4718761 - pass-by-ref need to compare DD from previous
    // deployment when reusing the old bits

    /**
     * Returns all the ejb descriptor in this application in ordered form.
     * The comparison is done based on the descriptor's name.
     *
     * @return all ejb descriptors in ordered form
     */
    public EjbDescriptor[] getSortedEjbDescriptors() {
        Vector ejbDesc = getEjbDescriptors();
        EjbDescriptor[] descs = (EjbDescriptor[]) ejbDesc.toArray(
                new EjbDescriptor[ejbDesc.size()]);

        // The sorting algorithm used by this api is a modified mergesort.
        // This algorithm offers guaranteed n*log(n) performance, and 
        // can approach linear performance on nearly sorted lists. 

        // since ejb name is only unique within a module, add the module uri
        // as the additional piece of information for comparison
        Arrays.sort(descs,
                new Comparator() {
                    public int compare(Object o1, Object o2) {
                        EjbDescriptor desc1 = (EjbDescriptor) o1;
                        EjbDescriptor desc2 = (EjbDescriptor) o2;
                        String moduleUri1 = desc1.getEjbBundleDescriptor().getModuleDescriptor().getArchiveUri();
                        String moduleUri2 = desc2.getEjbBundleDescriptor().getModuleDescriptor().getArchiveUri();
                        return (moduleUri1 + desc1.getName()).compareTo(
                                moduleUri2 + desc2.getName());
                    }
                }
        );

        return descs;
    }

    // END OF IASRI 4718761

    // START OF IASRI 4645310

    /**
     * Sets the virtual status of this application.
     * If this application object represents a stand alone module,
     * virtaul status should be true; else false.
     *
     * @param virtual new value of this application's virtaul status
     */
    public void setVirtual(boolean virtual) {
        this.virtual = virtual;
    }

    /**
     * Returns the virtual status of this application.
     *
     * @return true if this application obj represents a stand alone module
     */
    public boolean isVirtual() {
        return this.virtual;
    }

    public boolean isUniqueIdSet() {
        return uniqueIdSet;
    }

    /**
     * Sets the unique id for this application.  It traverses through all
     * the  ejbs in the application and sets the unique id for each of them.
     * The traversal is done in ascending element order.
     *
     * NOTE : assumption is that the id has already been left shifted 16
     *        bits to allow space for the component ids.
     *
     * @param id unique id for this application
     */
    public void setUniqueId(long id) {
        _logger.log(Level.FINE, "[Application] " + getName() + " , uid: " + id);
        this.uniqueId = id;

        EjbDescriptor[] descs = getSortedEjbDescriptors();

        Set uniqueIds = new TreeSet<>();
        for (int i = 0; i < descs.length; i++) {
            // Maximum of 2^16 beans max per application
            String module = descs[i].getEjbBundleDescriptor().getModuleDescriptor().getArchiveUri();
            long uid = Math.abs(UUID.nameUUIDFromBytes((module.replaceFirst(Pattern.quote(ROLLING_UPGRADES_ID_DELIMITER) + ".*$", "")
                    + descs[i].getName()).getBytes()).getLeastSignificantBits() % 65536);
            // in case of an id collision, increment until find empty slot
            while(uniqueIds.contains(uid)) {
                uid = ++uid % 65536;
            }
            uniqueIds.add(uid);
            descs[i].setUniqueId((id | uid));
            if (_logger.isLoggable(Level.FINE)) {
                _logger.log(Level.FINE, "Ejb  " + module + ":" + descs[i].getName() + " id = " +
                        descs[i].getUniqueId());
            }
        }

        uniqueIdSet = true;
    }

    /**
     * Returns the unique id used for this application.
     *
     * @return unique id used for this application
     */
    public long getUniqueId() {
        return this.uniqueId;
    }
    // END OF IASRI 4645310

    // START IASRI 4662001, 4720955

    /**
     * Sets the pass-by-reference property for this application.
     * EJB spec requires pass-by-value (false) which is the default.
     * This can be set to true for non-compliant operation and possibly
     * higher performance.  For a stand-alone  server, this can be used.
     * By setting pass-by-reference in sun-application.xml, it can apply to
     * all the enclosed ejb modules.
     *
     * @param passByReference boolean true or false - pass-by-reference property of application.
     *                        true - application is pass-by-reference
     *                        false - application is pass-by-value
     */
    public void setPassByReference(boolean passByReference) {
        this.passByReference = Boolean.valueOf(passByReference);
    }

    /**
     * Gets the value of pass-by-reference property for this application
     * Checks to see if the pass-by-reference property is defined.  If
     * this application's pass-by-reference property is defined, this method
     * returns the value of the application's pass-by-reference property.
     * Otherwise, if the application's pass-by-reference property is undefined,
     * this method returns a default value of false.
     *
     * @return boolean pass-by-reference property for this application
     */
    public boolean getPassByReference() {
        boolean passByReference = false;

        if (this.isPassByReferenceDefined()) {
            passByReference = this.passByReference.booleanValue();
        }
        return passByReference;
    }
    // END OF IASRI 4662001, 4720955

    // START OF IASRI 4720955
    /* *
     * Determines if the application's pass-by-reference property has been
     * defined or undefined in sun-application.xml
     *
     * @return true - pass-by-reference is defined in sun-application.xml
     *         false - pass-by-reference is undefined in sun-application.xml
     */

    public boolean isPassByReferenceDefined() {
        boolean passByReferenceDefined = false;
        if (this.passByReference != null) {
            passByReferenceDefined = true;
        }
        return passByReferenceDefined;
    }
    // END OF IASRI 4720955

    /**
     * Add all the deployment information about the given application to me.
     * @param application
     */
    public void addApplication(Application application) {
        for (ModuleDescriptor md : application.getModules()) {
            addModule(md);
        }
    }

    /**
     * Return all my subcomponents that have a file format (EJB, WAR and
     * AppCLient JAR).
     * @return 
     */
    public Set getArchivableDescriptors() {
        Set archivableDescriptors = new OrderedSet();
        archivableDescriptors.addAll(getBundleDescriptors());
        return archivableDescriptors;
    }

    /**
     * Sets the mapping of rolename to users and groups on a particular server.
     * @param roleMapper
     */
    public void setRoleMapper(SecurityRoleMapper roleMapper) {
        // should verify against the roles
        this.roleMapper = roleMapper;
    }

    /**
     * Return true if I have information to do with deployment on a
     * particular operational environment.
     * @return 
     */
    public boolean hasRuntimeInformation() {
        return true;
    }

    /**
     * Return my mapping of rolename to users and groups on a particular
     * server.
     * @return 
     */
    @Override
    public SecurityRoleMapper getRoleMapper() {
        if (this.roleMapper == null) {
            if (securityRoleMapperFactory == null) {
                _logger.log(Level.FINE, "SecurityRoleMapperFactory NOT set.");
            } else {
                this.roleMapper = securityRoleMapperFactory.getRoleMapper(this.getName());
            }
        }
        return this.roleMapper;
    }

    /**
     * Sets the realm for this application
     * @param realm
     */
    public void setRealm(String realm) {
        this.realm = realm;
    }

    /**
     * @return the realm for this application
     */
    public String getRealm() {
        return realm;
    }

    /**
     * A flag to indicate that my data has changed since the last save.
     * @return 
     */
    public boolean isDirty() {
        return this.isDirty;
    }

    /**
     * @return the class loader associated with this application
     */
    @Override
    public ClassLoader getClassLoader() {
        return classLoader;
    }

    /**
     * A formatted String representing my state.
     */
    public void print(StringBuffer toStringBuffer) {
        toStringBuffer.append("Application");
        toStringBuffer.append("\n");
        super.print(toStringBuffer);
        toStringBuffer.append("\n smallIcon ").append(super.getSmallIconUri());
        for (ModuleDescriptor aModule : getModules()) {
            toStringBuffer.append("\n  Module : ");
            aModule.print(toStringBuffer);
        }
        toStringBuffer.append("\n Bundles: \n");
        if (this.getBundleDescriptors() != null) {
            printDescriptorSet(this.getBundleDescriptors(), toStringBuffer);
        }
        toStringBuffer.append("\n roles ").append(getRoles());
        toStringBuffer.append("\n RoleMapper ").append(this.getRoleMapper());
        toStringBuffer.append("\n Realm ").append(realm);
    }

    private void printDescriptorSet(Set descSet, StringBuffer sbuf) {
        for (Iterator itr = descSet.iterator(); itr.hasNext();) {
            Object obj = itr.next();
            if (obj instanceof Descriptor)
                ((Descriptor) obj).print(sbuf);
            else
                sbuf.append(obj);
        }
    }

    /**
     * visit the descriptor and all sub descriptors with a DOL visitor implementation
     *
     * @param aVisitor visitor to traverse the descriptors
     */
    public void visit(DescriptorVisitor aVisitor) {
        if (aVisitor instanceof ApplicationVisitor) {
            visit((ComponentVisitor) aVisitor);
        } else {
            super.visit(aVisitor);
        }
    }

    /**
     * @return the module ID for this module descriptor
     */
    @Override
    public String getModuleID() {
        if (appName != null) {
            return appName;
        }
        return moduleID;
    }

    /**
     * @return true if this module is an application object
     */
    @Override
    public boolean isApplication() {
        return true;
    }

    /**
     * @return the module type for this bundle descriptor
     */
    @Override
    public ArchiveType getModuleType() {
        return DOLUtils.earType();
    }

    public void addSecurityRoleMapping(SecurityRoleMapping roleMapping) {
        roleMaps.add(roleMapping);
    }

    public List getSecurityRoleMappings() {
        return roleMaps;
    }

    public List getWlRoleAssignments() {
        return wlRoleAssignments;
    }

    public void addWLRoleAssignments(SecurityRoleAssignment wlRoleAssignment) {
        wlRoleAssignments.add(wlRoleAssignment);
    }

    /**
     * This method records how this Application object is constructed.  We
     * keep this information to avoid additional disk access in
     * DescriptorArchivist.write() when deciding if the application.xml
     * should be copied or written to the generated/xml directory.
     * @param bool
     */
    public void setLoadedFromApplicationXml(boolean bool) {
        loadedFromApplicationXml = bool;
    }

    /**
     * @return true if this Application is from reading application.xml from
     *         disk;  false if this Application object is derived from the content
     *         of the ear file.
     */
    public boolean isLoadedFromApplicationXml() {
        return loadedFromApplicationXml;
    }

/*
    // getter and setter of in-memory object of sun-configuration.xml
    public void setResourceList(List rList) {
        resourceList = rList;
    }

    public List getResourceList() {
        return resourceList;
    }
*/

    //resource-adapters referred by application via :
    //resource-ref, resource-env-ref, ra-mid
    /**
     * add a resource-adapter to referred resource-adapters list
     * @param raName resource-adapter name
     */
    public void addResourceAdapter(String raName){
        resourceAdapters.add(raName);
    }

    /**
     * get the list of resource-adapters referred by the application
     * @return resource-adapters list
     */
    public Set getResourceAdapters(){
        return resourceAdapters;
    }

    /**
     * @return the Set of application paramaters.
     */
    public Set getApplicationParams() {
        return applicationParams; 
    }

   /**
     * Adds a new context parameter to my list.
     * @param appParam
     */
    public void addApplicationParam(ApplicationParam appParam) {
        applicationParams.add(appParam);
    }

    @Override
    public boolean getKeepState() {
        // for standalone module, get the keep-state value specified in
        // module glassfish-*.xml
        if (isVirtual()) {
            BundleDescriptor bundleDesc = getStandaloneBundleDescriptor();
            if (bundleDesc != null) {
                return bundleDesc.getKeepState();
            }
        }
        return super.getKeepState();
    }

    /**
     * Returns the resolved keepstate value. 
     * @return keepStateResolved
     */
    public boolean getKeepStateResolved() {
        return keepStateResolved;
    }

    /**
     * Sets the resolved keepstate value.  
     * @param keepStateResolved
     */
    public void setKeepStateResolved(String keepStateResolved) {
        this.keepStateResolved = Boolean.valueOf(keepStateResolved);
    }


    private static class WildcardToRegex implements Function {
        public WildcardToRegex(String libDir) {
            this.libDir = libDir;
        }

        @Override
        public Pattern apply(String input) {
            input = input.replaceAll("(\\?|\\*)", ".$1");
            input = input.replaceFirst("\\.jar$", "");
            if(StringUtils.ok(libDir)) {
                input = String.format("^%s/%s(-.*)?\\.jar$", libDir, input);
            }
            return Pattern.compile(input, Pattern.CASE_INSENSITIVE);
        }

        private final String libDir;
    }
}




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