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.taxeditor.store;

import java.util.ArrayList;

import java.util.List;

import java.util.Set;

import java.util.SortedSet;

import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

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

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

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

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

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

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

import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;

import eu.etaxonomy.cdm.api.service.config.impl.TaxonServiceConfiguratorImpl;

import eu.etaxonomy.cdm.database.DataSourceNotFoundException;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

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

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

import eu.etaxonomy.cdm.model.common.init.TermNotFoundException;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.name.NameRelationshipType;

import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;

import eu.etaxonomy.cdm.model.name.TaxonNameBase;

import eu.etaxonomy.cdm.model.reference.ReferenceBase;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

import eu.etaxonomy.taxeditor.store.datasource.CdmDataSourceRepository;

/**

 * This implementation of ICdmDataRepository depends on hibernate sessions to store the data correctly 

 * for the current session. No state is held in this class.

 * 

 * Only methods that either get or manipulate data are exposed here. So this class acts as a facade 

 * for the methods in cdmlib-service. 

 * 

 * 

 * @author n.hoffmann

 * @created 17.03.2009

 * @version 1.0

 */

public class CdmStore{

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

	// FIXME change this to ClassPathResources as soon as it is included into the plugin

	private static String DEFAULT_APPLICATION_CONTEXT = null;

	private static DbSchemaValidation DEFAULT_DB_SCHEMA_VALIDATION = DbSchemaValidation.UPDATE;

	private static CdmStore instance;

	private CdmApplicationController applicationController;

	private ConversationHolder globalReadOnlyConversation;

	private static DbSchemaValidation dbSchemaValidation;

	/**

	 * 

	 * @return

	 */

	public static CdmStore getDefault(){

		return getDefault(DEFAULT_APPLICATION_CONTEXT);

	}

	/**

	 * 

	 * @param applicationContextBean

	 * @return

	 */

	public static CdmStore getDefault(String applicationContextBean){

		if(instance == null){

			logger.info("Initializing application context ...");

			ICdmDataSource cdmDatasource = CdmDataSourceRepository.getDefault().

					getCurrentDataSource();

			instance = new CdmStore(cdmDatasource, getDbSchemaValidation(), applicationContextBean);

			logger.info("Application context initialized.");

		}

		return instance;

	}

	/**

	 * @return

	 */

	private static DbSchemaValidation getDbSchemaValidation() {

		return (dbSchemaValidation == null) ? DEFAULT_DB_SCHEMA_VALIDATION : dbSchemaValidation;

	}

	/**

	 * 

	 */

	private CdmStore(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, String applicationContextBean) {

		// TODO application context bean is not honored by application controller at the moment. 

		// cdmDefaultApplicationController bean gets loaded per default always.

		try {

			CdmStore.DEFAULT_APPLICATION_CONTEXT = applicationContextBean;

//			applicationController = CdmApplicationController.NewInstance(applicationContextBean, dataSource, dbSchemaValidation, false);

//			logger.warn("OMITTING TERM LOADING FOR DEBUGGING");

//			applicationController = CdmApplicationController.NewInstance(dataSource, dbSchemaValidation, true);

			applicationController = CdmApplicationController.NewInstance(dataSource, dbSchemaValidation);

		} catch (Exception e) {

			throw new RuntimeException(e);

		}

	}

	public Set<TaxonRelationshipType> getConceptRelationshipTypes() {

		Set<TaxonRelationshipType> conceptRelationshipTypes = getTaxonRelationshipTypes().getTerms();

		// remove these two relations as they are considered standard taxon relations

		conceptRelationshipTypes.remove(TaxonRelationshipType.MISAPPLIED_NAME_FOR());

		conceptRelationshipTypes.remove(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN());

		return conceptRelationshipTypes;

	}

	public ReferenceBase getDefaultSec() {

		// TODO why is this returning null? and of course, replace w the real deal

		return applicationController.getReferenceService().getReferenceByUuid(

				UUID.fromString("f3593c18-a8d2-4e51-bdad-0befbf8fb2d1"));

	}

	private TermVocabulary<Feature> getFeaturesInternal() {

		return applicationController.getDescriptionService().getDefaultFeatureVocabulary();

	}

	public static TermVocabulary<Feature> getFeatures() {

		return getDefault().getFeaturesInternal();

	}

	public SortedSet<NameRelationshipType> getNameRelationshipTypes() {

//		if (nameRelationshipTypes == null)

		return applicationController.getNameService().getNameRelationshipTypeVocabulary()

						.getTermsOrderedByLabels(Language.DEFAULT());

	}

	public TermVocabulary<NomenclaturalStatusType> getNomStatus() {

		return applicationController.getNameService().getStatusTypeVocabulary();

	}

	private SortedSet<Rank> getRanksInternal() {

		return applicationController.getNameService().getRankVocabulary().getOrderedTerms(null);

	}

	public static SortedSet<Rank> getRanks() {

		return getDefault().getRanksInternal();

	}

	public List<Taxon> getRootTaxa() {

		boolean onlyWithChildren = false;

		boolean withMisapplications = true;

		return applicationController.getTaxonService().getRootTaxa(

				getDefaultSec(), onlyWithChildren, withMisapplications);

	}

	public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypes() {

		return applicationController.getTaxonService().getTaxonRelationshipTypeVocabulary();

	}

	public Set<Taxon> getTaxonomicChildren(Taxon parentTaxon) {

		new Throwable("Not implemented.");

		return null;

	}

	public TermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationStatus() {

		return applicationController.getNameService().getSpecimenTypeDesignationVocabulary();

	}

	public void removeAllTaxa() {

		new Throwable("Not implemented.");

	}

	public void removeTaxon(Taxon taxon) {

		new Throwable("Not implemented.");

	}

	public UUID saveTaxon(Taxon taxon) {

		return applicationController.getTaxonService().save(taxon);

	}

	public void setApplicationController(

			CdmApplicationController applicationController) {

		this.applicationController = applicationController;

	}

	public CdmApplicationController getApplicationController(){

		return applicationController;

	}

	public void setTaxonomicParent(Taxon taxon, Taxon newParentTaxon) {

		new Throwable("Not implemented.");

	}

	/**

	 * Create a new conversation and bind resources to it

	 * 

	 * @return

	 */

	public static ConversationHolder NewConversation(){

		CdmStore store = getDefault();

		CdmApplicationController controller = store.getApplicationController();

		ConversationHolder conversation = controller.NewConversation();

		return conversation;

	}

	/**

	 * Creates a new conversation, binds resources to the conversation and 

	 * start a transaction for this conversation.

	 * 

	 * @return

	 */

	public static ConversationHolder NewTransactionalConversation() {

		ConversationHolder conversation = NewConversation();

		conversation.startTransaction();

		return conversation;

	}

	private ConversationHolder getGlobalReadOnlyConversation() {

		ConversationHolder conversation = globalReadOnlyConversation == null 

				? NewConversation() 

				: globalReadOnlyConversation;

		conversation.bind();

		return conversation;

	}

	public static ConversationHolder getGlobalConversation(){

		return getDefault().getGlobalReadOnlyConversation();

	}

	public static ITaxonService getTaxonService(){

		return getDefault().getApplicationController().getTaxonService();

	}

	public static INameService getNameService(){

		return getDefault().getApplicationController().getNameService();

	}

	public static IReferenceService getReferenceService(){

		return getDefault().getApplicationController().getReferenceService();

	}

	public static ILocationService getLocationService(){

		return getDefault().getApplicationController().getLocationService();

	}

	/**

	 * @param searchText

	 * @return

	 */

	@SuppressWarnings("unchecked")

	public static List<TaxonNameBase> searchNameString(String searchText) {

		List<TaxonNameBase> resultSet = new ArrayList<TaxonNameBase>();

		resultSet.addAll(getNameService()

				.getNamesByName(searchText.replace("*", "%")));

		return resultSet;

	}

	private List findTaxaByName(String queryString, boolean restrictToTaxonObjs) {

		ITaxonServiceConfigurator configurator = new TaxonServiceConfiguratorImpl();

		configurator.setSearchString(queryString);

		configurator.setDoTaxa(true);

		configurator.setMatchMode(MatchMode.BEGINNING);

		if (restrictToTaxonObjs) {

			configurator.setDoNamesWithoutTaxa(false);

			configurator.setDoSynonyms(false);			

		} else {

			configurator.setDoNamesWithoutTaxa(true);

			configurator.setDoSynonyms(true);

		}

		configurator.setReferenceBase(null);

		configurator.setPageNumber(0);

		// TODO currently limit results to 1000 for now

		configurator.setPageSize(1000);

		List<IdentifiableEntity> result = getTaxonService().findTaxaAndNames(configurator).getRecords();

		return result;

	}

	public static List searchTaxaByName(String queryString){

		return getDefault().findTaxaByName(queryString, false);

	}

	public static List searchTaxaByName(String queryString, boolean restrictToTaxonObjs){

		return getDefault().findTaxaByName(queryString, restrictToTaxonObjs);

	}

	/**

	 * Searches for references by string. "%" is used as a wildcard.

	 * 

	 * @param text

	 * @return 

	 */

	public static List<ReferenceBase> getReferencesByTitle(String reference) {

		reference = reference.replace("*", "%");

		List<ReferenceBase> resultsList = null;

		try {

			resultsList = getReferenceService().getReferencesByTitle(reference);

		} catch (RuntimeException e) {

//			MessageDialog.openError(GlobalController.getShell(), "Search reference error", 

//					"Reference search returned an error. This could be a Hibernate concurrency problem. " +

//					"Please try saving your work, then searching again.");

			e.printStackTrace();

		}

		return resultsList;

	}

	public static List<Language> getLanguages() {

		ITermService termService = getDefault().getApplicationController().getTermService();

		ArrayList<Language> languages = new ArrayList<Language>();

		for (Language language : termService.getLanguageVocabulary()) {

			languages.add(language);

		}

//		languages.add(Language.ENGLISH());

//		languages.add(Language.GERMAN());

		return languages;

	}

	/**

	 * FIXME mock

	 * 

	 * @return

	 */

	public static Language getDefaultLanguage(){

		return Language.ENGLISH();

	}

	public static boolean changeDataSource(ICdmDataSource dataSource){

		// some more things have to happen here

		instance = new CdmStore(dataSource, getDbSchemaValidation(), getApplicationContextBean());

		return true;

	}

	/**

	 * @return

	 */

	private static String getApplicationContextBean() {

		return DEFAULT_APPLICATION_CONTEXT;

	}

}