EDIT

/**

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 *

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See LICENSE.TXT at the top of this package for the full license terms.

 */

package eu.etaxonomy.cdm.api.application;

import java.util.EnumSet;

import java.util.List;

import java.util.Properties;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.hibernate.SessionFactory;

import org.springframework.beans.MutablePropertyValues;

import org.springframework.beans.factory.config.BeanDefinition;

import org.springframework.beans.factory.xml.XmlBeanDefinitionReader;

import org.springframework.context.ApplicationListener;

import org.springframework.context.support.AbstractApplicationContext;

import org.springframework.core.io.ClassPathResource;

import org.springframework.core.io.Resource;

import org.springframework.security.authentication.ProviderManager;

import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;

import org.springframework.security.core.Authentication;

import org.springframework.security.core.context.SecurityContext;

import org.springframework.security.core.context.SecurityContextHolder;

import org.springframework.transaction.PlatformTransactionManager;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.conversation.ConversationHolder;

import eu.etaxonomy.cdm.api.service.IAgentService;

import eu.etaxonomy.cdm.api.service.IAnnotationService;

import eu.etaxonomy.cdm.api.service.IClassificationService;

import eu.etaxonomy.cdm.api.service.ICollectionService;

import eu.etaxonomy.cdm.api.service.ICommonService;

import eu.etaxonomy.cdm.api.service.IDatabaseService;

import eu.etaxonomy.cdm.api.service.IDescriptionService;

import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;

import eu.etaxonomy.cdm.api.service.IEntityConstraintViolationService;

import eu.etaxonomy.cdm.api.service.IEntityValidationService;

import eu.etaxonomy.cdm.api.service.IEventBaseService;

import eu.etaxonomy.cdm.api.service.IFeatureNodeService;

import eu.etaxonomy.cdm.api.service.IFeatureTreeService;

import eu.etaxonomy.cdm.api.service.IGrantedAuthorityService;

import eu.etaxonomy.cdm.api.service.IGroupService;

import eu.etaxonomy.cdm.api.service.IIdentificationKeyService;

import eu.etaxonomy.cdm.api.service.ILocationService;

import eu.etaxonomy.cdm.api.service.IMediaService;

import eu.etaxonomy.cdm.api.service.IMetadataService;

import eu.etaxonomy.cdm.api.service.INameService;

import eu.etaxonomy.cdm.api.service.IOccurrenceService;

import eu.etaxonomy.cdm.api.service.IPolytomousKeyNodeService;

import eu.etaxonomy.cdm.api.service.IPolytomousKeyService;

import eu.etaxonomy.cdm.api.service.IPreferenceService;

import eu.etaxonomy.cdm.api.service.IProgressMonitorService;

import eu.etaxonomy.cdm.api.service.IReferenceService;

import eu.etaxonomy.cdm.api.service.IRegistrationService;

import eu.etaxonomy.cdm.api.service.IRightsService;

import eu.etaxonomy.cdm.api.service.ITaxonNodeService;

import eu.etaxonomy.cdm.api.service.ITaxonService;

import eu.etaxonomy.cdm.api.service.ITermService;

import eu.etaxonomy.cdm.api.service.IUserService;

import eu.etaxonomy.cdm.api.service.IVocabularyService;

import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;

import eu.etaxonomy.cdm.api.service.molecular.IPrimerService;

import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;

import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;

import eu.etaxonomy.cdm.common.monitor.NullProgressMonitor;

import eu.etaxonomy.cdm.common.monitor.SubProgressMonitor;

import eu.etaxonomy.cdm.database.CdmPersistentDataSource;

import eu.etaxonomy.cdm.database.DataSourceNotFoundException;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.term.DefinedTermBase;

import eu.etaxonomy.cdm.persistence.hibernate.HibernateConfiguration;

import eu.etaxonomy.cdm.persistence.hibernate.permission.CRUD;

import eu.etaxonomy.cdm.persistence.hibernate.permission.ICdmPermissionEvaluator;

/**

 * @author a.mueller

 */

public class CdmApplicationController implements ICdmRepository {

	private static final Logger logger = Logger.getLogger(CdmApplicationController.class);

	public static final String DEFAULT_APPLICATION_CONTEXT_RESOURCE = "/eu/etaxonomy/cdm/defaultApplicationContext.xml";

	public AbstractApplicationContext applicationContext;

	protected ICdmRepository configuration;

	private final Resource applicationContextResource;

	private final IProgressMonitor progressMonitor;

	final protected static DbSchemaValidation defaultDbSchemaValidation = DbSchemaValidation.VALIDATE;

	/**

	 * Constructor, opens a spring ApplicationContext by using the default data source

	 *

	 * @throws DataSourceNotFoundException

	 */

	public static CdmApplicationController NewInstance() throws DataSourceNotFoundException{

		logger.info("Start CdmApplicationController with default data source");

		CdmPersistentDataSource dataSource = getDefaultDatasource();

		DbSchemaValidation dbSchemaValidation = defaultDbSchemaValidation;

		return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, false);

	}

	/**

	 * Constructor, opens a spring ApplicationContext by using the default data source

	 *

	 * @param dbSchemaValidation

	 *            validation type for database schema

	 * @throws DataSourceNotFoundException

	 */

	public static CdmApplicationController NewInstance(DbSchemaValidation dbSchemaValidation) throws DataSourceNotFoundException{

		logger.info("Start CdmApplicationController with default data source");

		CdmPersistentDataSource dataSource = getDefaultDatasource();

		return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, false);

	}

	/**

	 * Constructor, opens an spring ApplicationContext by using the according data source

	 * and the default database schema validation type

	 *

	 * @param dataSource

	 */

	public static CdmApplicationController NewInstance(ICdmDataSource dataSource){

		return CdmApplicationController.NewInstance(null, dataSource, defaultDbSchemaValidation, false);

	}

	public static CdmApplicationController NewInstance(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation){

		return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, false);

	}

	public static CdmApplicationController NewInstance(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading){

		return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, omitTermLoading);

	}

	public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource,

			DbSchemaValidation dbSchemaValidation, boolean omitTermLoading){

		return CdmApplicationController.NewInstance(applicationContextResource, dataSource, dbSchemaValidation,

		        null, omitTermLoading, null);

	}

    public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource,

            DbSchemaValidation dbSchemaValidation, boolean omitTermLoading, IProgressMonitor progressMonitor){

        return new CdmApplicationController(applicationContextResource, dataSource, dbSchemaValidation,

                null, omitTermLoading, progressMonitor, null);

    }

	public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource,

			DbSchemaValidation dbSchemaValidation, HibernateConfiguration hibernateConfig,

			boolean omitTermLoading, IProgressMonitor progressMonitor){

		return new CdmApplicationController(applicationContextResource, dataSource, dbSchemaValidation,

		        hibernateConfig, omitTermLoading, progressMonitor, null);

	}

	//TODO discuss need for listeners before commit to trunk

	//	public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading, IProgressMonitor progressMonitor, List<ApplicationListener> listeners) {

	//		return new CdmApplicationController(applicationContextResource, dataSource, dbSchemaValidation, omitTermLoading, progressMonitor,listeners);

	//	}

	/**

	 * @return

	 */

	protected static ClassPathResource getClasspathResource(){

		return new ClassPathResource(DEFAULT_APPLICATION_CONTEXT_RESOURCE);

	}

	/**

	 * @return

	 * @throws DataSourceNotFoundException

	 */

	protected static CdmPersistentDataSource getDefaultDatasource() throws DataSourceNotFoundException{

		CdmPersistentDataSource dataSource = CdmPersistentDataSource.NewDefaultInstance();

		return dataSource;

	}

	/**

	 *

	 * FIXME:Remoting this constructor is added only to allow extension of this cntroller

	 * class. and should be removed after refactoring

	 */

	protected CdmApplicationController(){

		applicationContextResource = null;

		progressMonitor = null;

	}

	/**

	 * Constructor, opens an spring 2.5 ApplicationContext by using the according data

	 * source

	 *

	 * @param dataSource

	 * @param dbSchemaValidation

	 * @param omitTermLoading

	 */

	protected CdmApplicationController(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation,

	        HibernateConfiguration hibernateConfig,

	        boolean omitTermLoading, IProgressMonitor progressMonitor, List<ApplicationListener> listeners){

		logger.info("Start CdmApplicationController with datasource: " + dataSource.getName());

		if (dbSchemaValidation == null) {

			dbSchemaValidation = defaultDbSchemaValidation;

		}

		this.applicationContextResource = applicationContextResource != null ? applicationContextResource : getClasspathResource();

		this.progressMonitor = progressMonitor != null ? progressMonitor : new NullProgressMonitor();

		setNewDataSource(dataSource, dbSchemaValidation, hibernateConfig, omitTermLoading, listeners);

	}

	/**

	 * Sets the application context to a new spring ApplicationContext by using the

	 * according data source and initializes the Controller.

	 *

	 * @param dataSource

	 */

	private boolean setNewDataSource(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation,

	        HibernateConfiguration hibernateConfig,

	        boolean omitTermLoading, List<ApplicationListener> listeners){

		if (dbSchemaValidation == null) {

			dbSchemaValidation = defaultDbSchemaValidation;

		}

		logger.info("Connecting to '" + dataSource.getName() + "'");

		MonitoredGenericApplicationContext applicationContext = new MonitoredGenericApplicationContext();

		int refreshTasks = 45;

		int nTasks = 5 + refreshTasks;

		//		nTasks += applicationContext.countTasks();

		progressMonitor.beginTask("Connecting to '" + dataSource.getName() + "'", nTasks);

		//		progressMonitor.worked(1);

		BeanDefinition datasourceBean = dataSource.getDatasourceBean();

		datasourceBean.setAttribute("isLazy", false);

		progressMonitor.subTask("Registering datasource.");

		applicationContext.registerBeanDefinition("dataSource", datasourceBean);

		progressMonitor.worked(1);

		BeanDefinition hibernatePropBean = dataSource.getHibernatePropertiesBean(dbSchemaValidation, hibernateConfig);

		applicationContext.registerBeanDefinition("hibernateProperties", hibernatePropBean);

		XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(applicationContext);

		progressMonitor.subTask("Registering resources.");

		xmlReader.loadBeanDefinitions(applicationContextResource);

		progressMonitor.worked(1);

		//omitTerms

		if (omitTermLoading == true) {

			String initializerName = "persistentTermInitializer";

			BeanDefinition beanDef = applicationContext.getBeanDefinition(initializerName);

			MutablePropertyValues values = beanDef.getPropertyValues();

			values.addPropertyValue("omit", omitTermLoading);

		}

		if (listeners != null) {

			for (ApplicationListener<?> listener : listeners) {

				applicationContext.addApplicationListener(listener);

			}

		}

		//		String message = "Start application context. This might take a while ...";

		////		progressMonitor.subTask(message);

		//		SubProgressMonitor subMonitor= new SubProgressMonitor(progressMonitor, 10);

		//		subMonitor.beginTask(message, 2);

		//		applicationContext.setProgressMonitor(subMonitor);

		applicationContext.refresh(new SubProgressMonitor(progressMonitor, refreshTasks));

		applicationContext.start();

		//		progressMonitor.worked(1);

		progressMonitor.subTask("Cleaning up.");

		setApplicationContext(applicationContext);

		progressMonitor.worked(1);

		progressMonitor.done();

		return true;

	}

	/**

     * Overrides all default with values in hibernate config, if defined

     * @param hibernatePropBean

     * @param hibernateConfig

     */

    private void registerHibernateConfig(BeanDefinition hibernatePropBean, HibernateConfiguration hibernateConfig) {

        setHibernateProperty(hibernatePropBean, HibernateConfiguration.REGISTER_ENVERS,

                hibernateConfig.getRegisterEnvers());

        setHibernateProperty(hibernatePropBean, HibernateConfiguration.REGISTER_SEARCH,

                hibernateConfig.getRegisterSearch());

        setHibernateProperty(hibernatePropBean, HibernateConfiguration.SHOW_SQL,

                hibernateConfig.getShowSql());

        setHibernateProperty(hibernatePropBean, HibernateConfiguration.FORMAT_SQL,

                hibernateConfig.getFormatSql());

    }

    private void setHibernateProperty(BeanDefinition hibernatePropBean, String key, Boolean value) {

	    if (value != null){

	        setHibernateProperty(hibernatePropBean, key, String.valueOf(value));

	    }

	}

    private void setHibernateProperty(BeanDefinition hibernatePropBean, String key, String value) {

        if (value != null){

            Properties props = (Properties)hibernatePropBean.getPropertyValues().get("properties");

            props.setProperty(key, value);

        }

    }

	/**

	 * Tests if some DefinedTermsAreMissing.

	 *

	 * @return true, if at least one is missing, else false

	 */

	public boolean testDefinedTermsAreMissing(){

		UUID englishUuid = UUID.fromString("e9f8cdb7-6819-44e8-95d3-e2d0690c3523");

		DefinedTermBase<?> english = this.getTermService().load(englishUuid);

		if (english == null || !english.getUuid().equals(englishUuid)) {

			return true;

		}

		else {

			return false;

		}

	}

	/**

	 * Changes the ApplicationContext to the new dataSource

	 *

	 * @param dataSource

	 */

	public boolean changeDataSource(ICdmDataSource dataSource){

		//logger.info("Change datasource to : " + dataSource);

		return setNewDataSource(dataSource, DbSchemaValidation.VALIDATE, null, false, null);

	}

	/**

	 * Changes the ApplicationContext to the new dataSource

	 *

	 * @param dataSource

	 * @param dbSchemaValidation

	 */

	public boolean changeDataSource(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation){

		//logger.info("Change datasource to : " + dataSource);

		return setNewDataSource(dataSource, dbSchemaValidation, null, false, null);

	}

	/**

	 * Changes the ApplicationContext to the new dataSource

	 *

	 * @param dataSource

	 * @param dbSchemaValidation

	 * @param omitTermLoading

	 */

	public boolean changeDataSource(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading){

		logger.info("Change datasource to : " + dataSource);

		return setNewDataSource(dataSource, dbSchemaValidation, null, omitTermLoading, null);

	}

	/**

	 * Changes the ApplicationContext to the new dataSource

	 *

	 * @param dataSource

	 * @param dbSchemaValidation

	 * @param omitTermLoading

	 */

	public boolean changeDataSource(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading,

			List<ApplicationListener> listeners){

		logger.info("Change datasource to : " + dataSource);

		return setNewDataSource(dataSource, dbSchemaValidation, null, omitTermLoading, listeners);

	}

	/**

	 * Sets a new application Context.

	 *

	 * @param ac

	 */

	public void setApplicationContext(AbstractApplicationContext ac){

		closeApplicationContext(); //closes old application context if necessary

		applicationContext = ac;

		applicationContext.registerShutdownHook();

		init();

	}

	@Override

	public void finalize(){

		close();

	}

	/**

	 * closes the application

	 */

	public void close(){

		closeApplicationContext();

	}

	/**

	 * closes the application context

	 */

	protected void closeApplicationContext(){

		if (applicationContext != null) {

			logger.info("Close ApplicationContext");

			applicationContext.close();

		}

	}

	protected void init(){

		logger.debug("Init " + this.getClass().getName() + " ... ");

		if (logger.isDebugEnabled()) {

			for (String beanName : applicationContext.getBeanDefinitionNames()) {

				logger.debug(beanName);

			}

		}

		//TODO delete next row (was just for testing)

		if (logger.isInfoEnabled()) {

			logger.info("Registered Beans: ");

			String[] beanNames = applicationContext.getBeanDefinitionNames();

			for (String beanName : beanNames) {

				logger.info(beanName);

			}

		}

		configuration = (ICdmRepository) applicationContext.getBean("cdmRepository");

		try {

			//FIXME:Remoting catching exection to allow for remoting

			getDatabaseService().setApplicationController(this);

		}

		catch (UnsupportedOperationException uoe) {

			logger.warn("getDatabaseService() is not implmented for current application context");

		}

	}

	/* ****** Services ******** */

	@Override

	public final IAnnotationService getAnnotationService(){

	    return configuration.getAnnotationService();

	}

	@Override

	public final INameService getNameService(){

	    return configuration.getNameService();

	}

	@Override

	public final ITaxonService getTaxonService(){

		return configuration.getTaxonService();

	}

	@Override

	public final IClassificationService getClassificationService(){

		return configuration.getClassificationService();

	}

	@Override

	public final ITaxonNodeService getTaxonNodeService(){

	    try{

	        return configuration.getTaxonNodeService();

	    } catch (Exception e){

	        e.printStackTrace();

	    }

	    return null;

	}

	@Override

	public final IReferenceService getReferenceService(){

		return configuration.getReferenceService();

	}

	@Override

	public final IAgentService getAgentService(){

		return configuration.getAgentService();

	}

	@Override

	public final IDatabaseService getDatabaseService(){

		return configuration.getDatabaseService();

	}

	@Override

	public final ITermService getTermService(){

		return configuration.getTermService();

	}

	@Override

	public final IDescriptionService getDescriptionService(){

		return configuration.getDescriptionService();

	}

	@Override

	public final IOccurrenceService getOccurrenceService(){

		return configuration.getOccurrenceService();

	}

	@Override

	public IAmplificationService getAmplificationService(){

		return configuration.getAmplificationService();

	}

	@Override

	public ISequenceService getSequenceService(){

		return configuration.getSequenceService();

	}

	@Override

	public IEventBaseService getEventBaseService() {

	    return configuration.getEventBaseService();

	}

	@Override

	public final IPrimerService getPrimerService(){

		return configuration.getPrimerService();

	}

	@Override

	public final IMediaService getMediaService(){

		return configuration.getMediaService();

	}

    @Override

    public final IMetadataService getMetadataService(){

        return configuration.getMetadataService();

    }

	@Override

	public final ICommonService getCommonService(){

		return configuration.getCommonService();

	}

	@Override

	public final ILocationService getLocationService(){

		return configuration.getLocationService();

	}

	@Override

	public final IUserService getUserService(){

		return configuration.getUserService();

	}

	@Override

	public final IGrantedAuthorityService getGrantedAuthorityService(){

		return configuration.getGrantedAuthorityService();

	}

	@Override

	public IGroupService getGroupService(){

		return configuration.getGroupService();

	}

	@Override

	public final ICollectionService getCollectionService(){

		return configuration.getCollectionService();

	}

	@Override

	public final IFeatureTreeService getFeatureTreeService(){

		return configuration.getFeatureTreeService();

	}

	@Override

	public final IPreferenceService getPreferenceService(){

	    return configuration.getPreferenceService();

	}

	@Override

	public final IFeatureNodeService getFeatureNodeService(){

		return configuration.getFeatureNodeService();

	}

	@Override

	public final IVocabularyService getVocabularyService(){

		return configuration.getVocabularyService();

	}

	@Override

	public final IIdentificationKeyService getIdentificationKeyService(){

		return configuration.getIdentificationKeyService();

	}

	@Override

	public final IPolytomousKeyService getPolytomousKeyService(){

		return configuration.getPolytomousKeyService();

	}

	@Override

	public final IPolytomousKeyNodeService getPolytomousKeyNodeService(){

		return configuration.getPolytomousKeyNodeService();

	}

    /**

     * {@inheritDoc}

     */

    @Override

    public IProgressMonitorService getProgressMonitorService() {

        return configuration.getProgressMonitorService();

    }

	@Override

	public IEntityValidationService getEntityValidationService(){

		return configuration.getEntityValidationService();

	}

	@Override

	public IEntityConstraintViolationService getEntityConstraintViolationService(){

		return configuration.getEntityConstraintViolationService();

	}

	@Override

	public final IDescriptiveDataSetService getDescriptiveDataSetService(){

		return configuration.getDescriptiveDataSetService();

	}

	@Override

	public final ConversationHolder NewConversation(){

		//return (ConversationHolder)applicationContext.getBean("conversationHolder");

		return configuration.NewConversation();

	}

	/* **** Security ***** */

	@Override

	public void authenticate(String username, String password){

		UsernamePasswordAuthenticationToken tokenForUser = new UsernamePasswordAuthenticationToken(username, password);

		Authentication authentication = this.getAuthenticationManager().authenticate(tokenForUser);

		SecurityContext context = SecurityContextHolder.getContext();

		context.setAuthentication(authentication);

	}

	@Override

	public final ProviderManager getAuthenticationManager(){

		return configuration.getAuthenticationManager();

	}

	@Override

	public ICdmPermissionEvaluator getPermissionEvaluator(){

		return configuration.getPermissionEvaluator();

	}

	/**

	 * @see org.springframework.security.access.PermissionEvaluator#hasPermission(org.springframework.security.core.Authentication,

	 *      java.lang.Object, java.lang.Object)

	 *

	 * @param targetDomainObject

	 * @param permission

	 * @return

	 */

	public boolean currentAuthentiationHasPermissions(CdmBase targetDomainObject, EnumSet<CRUD> permission){

		SecurityContext context = SecurityContextHolder.getContext();

		return getPermissionEvaluator().hasPermission(context.getAuthentication(), targetDomainObject, permission);

	}

	@Override

	public final PlatformTransactionManager getTransactionManager(){

		return configuration.getTransactionManager();

	}

	@Override

	public final Object getBean(String name){

		return this.applicationContext.getBean(name);

	}

	/*

	 * OLD TRANSACTION STUFF

	 */

	/* **** flush ********** */

	public void flush(){

		SessionFactory sf = (SessionFactory) applicationContext.getBean("sessionFactory");

		sf.getCurrentSession().flush();

	}

	public SessionFactory getSessionFactory(){

		return (SessionFactory) applicationContext.getBean("sessionFactory");

	}

	@Override

	public TransactionStatus startTransaction(){

		return startTransaction(false);

	}

	@Override

	public TransactionStatus startTransaction(Boolean readOnly){

		return configuration.startTransaction(readOnly);

	}

	@Override

	public void commitTransaction(TransactionStatus txStatus){

		PlatformTransactionManager txManager = configuration.getTransactionManager();

		txManager.commit(txStatus);

		return;

	}

    /**

     * {@inheritDoc}

     */

    @Override

    public IRightsService getRightsService() {

        return configuration.getRightsService();

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public IRegistrationService getRegistrationService() {

        return configuration.getRegistrationService();

    }

}