EDIT

/**

* Copyright (C) 2009 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.test.function;

import java.io.IOException;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.EnumSet;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.hibernate.Query;

import org.hibernate.Session;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

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

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

import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.api.service.search.SearchResult;

import eu.etaxonomy.cdm.common.AccountStore;

import eu.etaxonomy.cdm.database.CdmDataSource;

import eu.etaxonomy.cdm.database.CdmPersistentDataSource;

import eu.etaxonomy.cdm.database.DataSourceNotFoundException;

import eu.etaxonomy.cdm.database.DatabaseTypeEnum;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.model.agent.Person;

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * This class is purely for function testing. Not used in production or testing frameworks.

 *

 * @author a.mueller

 */

public class Datasource {

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

	private void testNewConfigControler(){

		List<CdmPersistentDataSource> lsDataSources = CdmPersistentDataSource.getAllDataSources();

		DbSchemaValidation schema = DbSchemaValidation.VALIDATE;

		String server;

		String database;

		String username;

		System.out.println(lsDataSources);

		ICdmDataSource dataSource;

		dataSource = lsDataSources.get(1);

//		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;

//		server = "localhost";

////		database = "cdm36";

//		database = "cdm_edaphobase";

//		username = "edit";

//		dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));

       server = "160.45.63.175";

       database = "cdm_cyprus";

       username = "edit";

       dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));

//		server = "160.45.63.171";

//		database = "cdm_production_cichorieae";

//		username = "edit";

//		dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));

//		server = "test.e-taxonomy.eu";

//		database = "cdm_test1";

////		String database = "cdm_edit_flora_malesiana";

//		username = "edit";

//		dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));

//		server = "localhost";

//		database = "testCDM";

//		username = "postgres";

//		dataSource = CdmDataSource.NewInstance(DatabaseTypeEnum.PostgreSQL, server, database, DatabaseTypeEnum.PostgreSQL.getDefaultPort(), username, AccountStore.readOrStorePassword(server, database, username, null));

//		//SQLServer

//		server = "BGBM-PESISQL";

//		database = "cdm36";

//		int port = 1433;

//		username = "cdmupdater";

//		dataSource = CdmDataSource.NewSqlServer2012Instance(server, database, port, username, AccountStore.readOrStorePassword(server, database, username, null));

////

//		//H2

//        String path = "C:\\Users\\a.mueller\\.cdmLibrary\\writableResources\\h2\\LocalH2";

////		String path = "C:\\Users\\pesiimport\\.cdmLibrary\\writableResources\\h2\\LocalH2";

////      String path = "C:\\Users\\a.mueller\\eclipse\\svn\\cdmlib-trunk\\cdmlib-remote-webapp\\src\\test\\resources\\h2";

//		username = "sa";

//    	dataSource = CdmDataSource.NewH2EmbeddedInstance("cdm", username, "", path);

//    	dataSource = CdmDataSource.NewH2EmbeddedInstance(database, username, "sa");

//       server = "160.45.63.201";

//       database = "cdm_integration_cichorieae";

//       username = "edit";

//       dataSource = CdmDataSource.NewMySqlInstance(server, database, username, AccountStore.readOrStorePassword(server, database, username, null));

// 		try {

//			CdmUpdater updater = new CdmUpdater();

//			if (schema == DbSchemaValidation.VALIDATE){

//				updater.updateToCurrentVersion(dataSource, DefaultProgressMonitor.NewInstance());

//			}

//		} catch (Exception e) {

//			e.printStackTrace();

//		}

		//CdmPersistentDataSource.save(dataSource.getName(), dataSource);

		CdmApplicationController appCtr;

		appCtr = CdmApplicationController.NewInstance(dataSource, schema);

		EnumSet<TaxaAndNamesSearchMode> searchModes = EnumSet.noneOf(TaxaAndNamesSearchMode.class);

        searchModes.add(TaxaAndNamesSearchMode.doTaxa);

        searchModes.add(TaxaAndNamesSearchMode.doSynonyms);

        UUID classificationUUID = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");

        Classification classification = appCtr.getClassificationService().find(classificationUUID);

        UUID subtreeUUID = UUID.fromString("e993df74-671c-4a03-9c4c-be4a6447a0f2");

        TaxonNode subtree = appCtr.getTaxonNodeService().find(subtreeUUID);

        NamedArea area = (NamedArea)appCtr.getTermService().find(UUID.fromString("fbf21230-4a42-4f4c-9af8-5da52123c264"));

        Set<NamedArea> namedAreas = new HashSet<>();

        namedAreas.add(area);

        Set<PresenceAbsenceTerm> distributionStatus = null;

        int pageSize = 25;

        int pageNumber = 0;

        try {

            Pager<SearchResult<TaxonBase>> result = appCtr.getTaxonService().findTaxaAndNamesByFullText(searchModes, "Phyla can*",

                    classification, subtree,

                    namedAreas, distributionStatus, null, false, pageSize, pageNumber, null, null);

            result = appCtr.getTaxonService().findTaxaAndNamesByFullText(searchModes, "Phyla can*",

                    classification, subtree,

                    namedAreas, distributionStatus, null, false, pageSize, pageNumber, null, null);

            result = appCtr.getTaxonService().findTaxaAndNamesByFullText(searchModes, "Phyla can*",

                    classification, subtree,

                    namedAreas, distributionStatus, null, false, pageSize, pageNumber, null, null);

            result = appCtr.getTaxonService().findTaxaAndNamesByFullText(searchModes, "Phyla can*",

                    classification, subtree,

                    namedAreas, distributionStatus, null, false, pageSize, pageNumber, null, null);

        } catch (Exception e) {

            // TODO Auto-generated catch block

            e.printStackTrace();

        }

//	    List<String> DEFAULT_INIT_STRATEGY = Arrays.asList(new String []{

//	            "$"

//	    });

//		IFindTaxaAndNamesConfigurator config = FindTaxaAndNamesConfiguratorImpl.NewInstance();

//        config.setIncludeUnpublished(false);

//        config.setPageNumber(0);

//        config.setPageSize(25);

//        config.setTitleSearchString("Lapsana communis");

//        config.setDoTaxa(true );

//        config.setDoSynonyms(true);

//        config.setDoMisappliedNames(true);

//        config.setDoTaxaByCommonNames(true);

//        config.setMatchMode(MatchMode.BEGINNING);

//        config.setTaxonPropertyPath(DEFAULT_INIT_STRATEGY);

//        config.setNamedAreas(null);

//        config.setDoIncludeAuthors(false);

//        config.setOrder(null);

//        UUID treeUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e");

//        Classification classification = appCtr.getClassificationService().find(treeUuid);

//        config.setClassification(classification);

//

//		Pager<IdentifiableEntity> result = appCtr.getTaxonService().findTaxaAndNames(config);

//		Classification classification = appCtr.getClassificationService().list(null, null, null, null, null).get(0);

//		logger.warn(classification.getMicroReference());

//        logger.warn(classification.getName());

//		TransactionStatus tx = appCtr.startTransaction();

//		testGroupedTaxa(appCtr);

//		int n = appCtr.getAgentService().count(null);

//		logger.warn("End adding " + n + " persons");

//		appCtr.getCommonService().createFullSampleData();

//		ValidationManager valMan = (ValidationManager)appCtr.getBean("validationManager");

//		valMan.registerValidationListeners();

//		State state = State.NewInstance();

//		Taxon taxon = Taxon.NewInstance(null, null);

//		TaxonDescription desc = TaxonDescription.NewInstance(taxon);

////		CategoricalData catData = CategoricalData.NewInstance(state, Feature.HABITAT());

//		QuantitativeData quantData = QuantitativeData.NewInstance(Feature.ANATOMY());

//		StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.AVERAGE(), 2);

//		quantData.addStatisticalValue(statisticalValue);

//		desc.addElement(quantData);

//		appCtr.getTermService().saveOrUpdate(state);

//

//		appCtr.getTaxonService().save(taxon);

		//		insertSomeData(appCtr);

//		deleteHighLevelNode(appCtr);   //->problem with Duplicate Key in Classification_TaxonNode

		appCtr.close();

		System.exit(0);

	}

    /**

     * @param appCtr

     */

    private void testGroupedTaxa(CdmApplicationController appCtr) {

        UUID classificationUuid = UUID.fromString("91231ebf-1c7a-47b9-a56c-b45b33137244");

		UUID taxonUuid1 = UUID.fromString("3bae1c86-1235-4e2e-be63-c7f8c4410527");

		UUID taxonUuid2 = UUID.fromString("235d3872-defe-4b92-bf2f-75a7c91510de");

		List<UUID> taxonUuids = Arrays.asList(new UUID[]{taxonUuid1, taxonUuid2});

		Rank maxRank = DefinedTermBase.getTermByClassAndUUID(Rank.class, UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6"));

		Rank minRank = DefinedTermBase.getTermByClassAndUUID(Rank.class, UUID.fromString("78786e16-2a70-48af-a608-494023b91904"));

        List<GroupedTaxonDTO> groupedTaxa = appCtr.getClassificationService().groupTaxaByHigherTaxon(taxonUuids, classificationUuid, minRank, maxRank);

        System.out.println(groupedTaxa);

    }

    private void addPerson(CdmApplicationController appCtr) {

        TransactionStatus tx = appCtr.startTransaction();

		appCtr.getAgentService().save(Person.NewInstance());

		appCtr.commitTransaction(tx);

    }

	private void deleteHighLevelNode(CdmApplicationController appCtr) {

		TransactionStatus tx = appCtr.startTransaction();

		ITaxonNodeService service = appCtr.getTaxonNodeService();

		TaxonNode node = service.find(60554);

//		service.delete(node);

		ITaxonService taxonService = appCtr.getTaxonService();

		Taxon taxon = node.getTaxon();

		//try {

			taxonService.deleteTaxon(taxon.getUuid(), new TaxonDeletionConfigurator(), node.getClassification().getUuid());

		/*} catch (DataChangeNoRollbackException e) {

			e.printStackTrace();

		}*/

		try {

			appCtr.commitTransaction(tx);

		} catch (Exception e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		TaxonNode node2 = service.find(60554);

	}

	private void insertSomeData(CdmApplicationController appCtr) {

		Classification cl = Classification.NewInstance("myClass");

		TaxonNode node1 = cl.addChildTaxon(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(null), null), null, null);

		appCtr.getClassificationService().save(cl);

		Taxon t2 = Taxon.NewInstance(null, null);

		t2.setTitleCache("Taxon2", true);

		TaxonNode node2 = node1.addChildTaxon(t2, null, null);

		Taxon t3 = Taxon.NewInstance(null, null);

		t3.setTitleCache("Taxon3", true);

		TaxonNode node3 = node1.addChildTaxon(t3, 0, null, null);

		appCtr.getTaxonNodeService().saveOrUpdate(node1);

		cl.addChildNode(node3, 0, null, null);

		appCtr.getTaxonNodeService().saveOrUpdate(node3);

		appCtr.getClassificationService().saveOrUpdate(cl);

		FeatureTree ft1 = FeatureTree.NewInstance();

		FeatureNode fn1 = FeatureNode.NewInstance(null);

		ft1.getRoot().addChild(fn1);

		appCtr.getFeatureNodeService().save(fn1);

		FeatureNode fn2 = FeatureNode.NewInstance(null);

		fn1.addChild(fn2);

		FeatureNode fn3 = FeatureNode.NewInstance(null);

		fn1.addChild(fn2, 0);

		appCtr.getFeatureNodeService().saveOrUpdate(fn1);

		ft1.getRoot().addChild(fn3, 0);

		appCtr.getFeatureNodeService().saveOrUpdate(fn3);

		appCtr.getFeatureTreeService().saveOrUpdate(ft1);

	}

	private void testDatabaseChange() throws DataSourceNotFoundException{

		CdmApplicationController appCtr;

		appCtr = CdmApplicationController.NewInstance();

//		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;

//		String server = "192.168.2.10";

//		String database = "cdm_test_andreas";

//		String user = "edit";

//		String pwd = "wp5";

//

		DatabaseTypeEnum dbType = DatabaseTypeEnum.SqlServer2005;

		String server = "LAPTOPHP";

		String database = "cdmTest";

		String username = "edit";

		String password = "";

		ICdmDataSource dataSource = CdmDataSource.NewInstance(DatabaseTypeEnum.SqlServer2005, "LAPTOPHP", "cdmTest", DatabaseTypeEnum.SqlServer2005.getDefaultPort(), "edit", "");

		appCtr.getDatabaseService().saveDataSource("testSqlServer", dataSource);

		try {

			appCtr.getDatabaseService().connectToDatabase(dbType, server, database, username, password);

		} catch (TermNotFoundException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		appCtr.close();

	}

	private void testSqlServer2005(){

		DatabaseTypeEnum databaseTypeEnum = DatabaseTypeEnum.SqlServer2005;

		String server = "LAPTOPHP";

		String database = "cdmTest";

		String username = "edit";

		String password = "";

		ICdmDataSource dataSource = CdmDataSource.NewInstance(databaseTypeEnum, server, database, databaseTypeEnum.getDefaultPort(), username, password);

		CdmPersistentDataSource ds = CdmPersistentDataSource.save("testSqlServer", dataSource);

		CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds);

		Person agent = Person.NewInstance();

		appCtr.getAgentService().save(agent);

		TaxonName tn = TaxonNameFactory.NewBotanicalInstance(null);

		appCtr.getNameService().save(tn);

		appCtr.close();

	}

	private void testLocalHsql(){

		CdmApplicationController appCtr = null;

		try {

			CdmPersistentDataSource ds = CdmPersistentDataSource.NewLocalHsqlInstance();

			appCtr = CdmApplicationController.NewInstance(ds);

			List<?> l = appCtr.getNameService().list(null,5, 1,null,null);

			System.out.println(l);

			//Agent agent = new Agent();

			//appCtr.getAgentService().saveAgent(agent);

			appCtr.close();

		} catch (RuntimeException e) {

			logger.error("Runtime Exception");

			e.printStackTrace();

			if (appCtr != null){

			    appCtr.close();

			}

		} catch (DataSourceNotFoundException e) {

			logger.error("Runtime Exception");

			e.printStackTrace();

		}

	}

	private void testLocalH2(){

		DbSchemaValidation validation = DbSchemaValidation.CREATE;

		ICdmDataSource ds =

			CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);

//			ds =

//				 CdmPersistentDataSource.NewInstance("localH2");

		CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation);

		boolean exists = appCtr.getUserService().userExists("admin");

		try {

			IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(null);

			String nameCache = "testName";

			name.setNameCache(nameCache);

			name.setTitleCache(nameCache, true);

			Reference ref = ReferenceFactory.newGeneric();

			ref.setTitleCache("mySec", true);

			Taxon taxon = Taxon.NewInstance(name, ref);

			TaxonDescription description = TaxonDescription.NewInstance();

			taxon.addDescription(description);

			NamedArea area1 = appCtr.getTermService().getAreaByTdwgAbbreviation("GER");

			Distribution distribution = Distribution.NewInstance(area1, PresenceAbsenceTerm.PRESENT());

			description.addElement(distribution);

			List<Distribution> distrList = new ArrayList<Distribution>();

			distrList.add(distribution);

			List<NamedArea> areaList = new ArrayList<NamedArea>();

			areaList.add(area1);

		//	distribution.getInDescription().get

			appCtr.getTaxonService().save(taxon);

			System.out.println(taxon.getDescriptions().size());

			TransactionStatus txStatus = appCtr.startTransaction();

			Session session = appCtr.getSessionFactory().getCurrentSession();

			//String hqlQuery = "from DescriptionBase d join d.elements  as e "

//				String hqlQuery = "from Taxon t join t.descriptions  as d "+

//				 " inner join d.elements e on e member of d "

//				+

//				"";//" where e.area = :namedArea " ;

			String hqlQuery = "Select t from Distribution e join e.inDescription d join d.taxon t join t.name n "+

				" WHERE e.area in (:namedArea) AND n.nameCache = :nameCache ";

			Query query = session.createQuery(hqlQuery);

			//query.setEntity("namedArea", area1);

			query.setParameter("nameCache", nameCache);

			query.setParameterList("namedArea", areaList);

			List resultList = query.list();

			//List list = appCtr.getCommonService().getHqlResult(hqlQuery);

			for (Object o:resultList){

				System.out.println(o);

			}

			appCtr.commitTransaction(txStatus);

			//System.out.println(l);

			//Agent agent = new Agent();

			//appCtr.getAgentService().saveAgent(agent);

			appCtr.close();

		} catch (RuntimeException e) {

			logger.error("Runtime Exception");

			e.printStackTrace();

			appCtr.close();

		}

	}

	private boolean testWritableResourceDirectory() throws IOException{

		CdmApplicationUtils.getWritableResourceDir();

		return true;

	}

	private boolean testH2(){

//		testLocalH2();

//		if (true)return true;

		DbSchemaValidation validation = DbSchemaValidation.CREATE;

		ICdmDataSource ds =

			CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);

			//CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");

//		ds =

//			 CdmPersistentDataSource.NewInstance("localH2");

		CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation);

		try {

		    TaxonName botName1 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

			TaxonName botName2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

			IBotanicalName hybridName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

			botName1.addRelationshipToName(botName2, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), null);

			UUID uuid1 = botName1.getUuid();

			UUID uuid2 = botName2.getUuid();

			try {

				Logger loggerTrace = Logger.getLogger("org.hibernate.type");

				//loggerTrace.setLevel(Level.TRACE);

				System.out.println(logger.getName());

				appCtr.getNameService().save(botName1);

				ResultSet rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");

				rs.next();

				int c = rs.getInt("n");

				System.out.println("Begin :" + c);

				botName1.removeRelationToTaxonName(botName2);

				botName1.setSpecificEpithet("DELETED");

				botName2.addHybridParent(hybridName, HybridRelationshipType.FIRST_PARENT(), null);

				TransactionStatus tx = appCtr.startTransaction();

				appCtr.getNameService().saveOrUpdate(botName2);

				rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");

				rs.next();

				c = rs.getInt("n");

				System.out.println("End: " + c);

				appCtr.commitTransaction(tx);

				appCtr.getNameService().saveOrUpdate(botName1);

				rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");

				rs.next();

				c = rs.getInt("n");

				System.out.println("End: " + c);

			} catch (SQLException e) {

				// TODO Auto-generated catch block

				e.printStackTrace();

			}

			//Agent agent = new Agent();

			//appCtr.getAgentService().saveAgent(agent);

			appCtr.close();

			return true;

		} catch (RuntimeException e) {

			logger.error("Runtime Exception");

			e.printStackTrace();

			appCtr.close();

		}

		return false;

	}

	private void test(){

		System.out.println("Start Datasource");

		testNewConfigControler();

    	//testDatabaseChange();

		//testSqlServer();

		//CdmUtils.findLibrary(au.com.bytecode.opencsv.CSVReader.class);

		//testPostgreServer();

		//testLocalHsql();

		//testLocalH2();

		//testWritableResourceDirectory();

//		testH2();

		System.out.println("\nEnd Datasource");

	}

	/**

	 * @param args

	 */

	public static void  main(String[] args) {

		Datasource cc = new Datasource();

    	cc.test();

	}

}