EDIT

app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/CaryoActivator.java -text

app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoImportConfigurator.java -text

app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoImportState.java -text

app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTaxonImport.java -text

app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoTransformer.java -text

/**

* 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.app.caryophyllales;

import java.net.URI;

import java.net.URISyntaxException;

import java.util.UUID;

import org.apache.log4j.Logger;

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

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

import eu.etaxonomy.cdm.app.berlinModelImport.SourceBase;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.caryo.CaryoImportConfigurator;

import eu.etaxonomy.cdm.io.common.CdmDefaultImport;

import eu.etaxonomy.cdm.io.common.Source;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;

import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.io.cyprus.CyprusImportConfigurator;

import eu.etaxonomy.cdm.io.cyprus.CyprusTransformer;

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 16.12.2010

 * @version 1.0

 */

public class CaryoActivator extends SourceBase{

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

	//database validation status (create, update, validate ...)

	static final DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final Source source = caryo_len61();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();

	//classification

	static final UUID classificationUuid = UUID.fromString("125d7812-065b-46a2-88ee-06d6115e105e");

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doDeduplicate = false;

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

		CaryoImportConfigurator config= CaryoImportConfigurator.NewInstance(source, cdmDestination);

		config.setClassificationUuid(classificationUuid);

		config.setCheck(check);

		config.setDoTaxa(doTaxa);

		config.setDbSchemaValidation(hbm2dll);

		CdmDefaultImport myImport = new CdmDefaultImport();

		//...

		if (true){

			System.out.println("Start import from ("+ source.toString() + ") ...");

			config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));

			myImport.invoke(config);

			System.out.println("End import from ("+ source.toString() + ")...");

		}

		//deduplicate

		if (doDeduplicate){

			ICdmApplicationConfiguration app = myImport.getCdmAppController();

			int count = app.getAgentService().deduplicate(Person.class, null, null);

			logger.warn("Deduplicated " + count + " persons.");

//			count = app.getAgentService().deduplicate(Team.class, null, null);

//			logger.warn("Deduplicated " + count + " teams.");

			count = app.getReferenceService().deduplicate(Reference.class, null, null);

			logger.warn("Deduplicated " + count + " references.");

		}

	}

	private Reference getSourceReference(String string) {

		Reference result = ReferenceFactory.newGeneric();

		result.setTitleCache(string);

		return result;

	}

	//Cyprus

	public static URI caryo_local() {

		URI sourceUrl;

		try {

			sourceUrl = new URI("file:/C:/localCopy/Data/zypern/Zypern.xls");

			return sourceUrl;

		} catch (URISyntaxException e) {

			e.printStackTrace();

			return null;

		}

	}

	public static Source caryo_len61(){

		//	Cyryophyllales source

		String dbms = Source.SQL_SERVER_2008;

		String strServer = "Lenovo-T61";

		String strDB = "CARYOPHYLLALES";

		int port = 1433;

		String userName = "WebUser";

		return  makeSource(dbms, strServer, strDB, port, userName, null);

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		CaryoActivator me = new CaryoActivator();

		me.doImport(cdmDestination);

	}

}

/**

* 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.io.caryo;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase;

import eu.etaxonomy.cdm.io.common.IImportConfigurator;

import eu.etaxonomy.cdm.io.common.Source;

import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;

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

/**

 * @author a.mueller

 * @created 20.03.2008

 * @version 1.0

 */

public class CaryoImportConfigurator extends DbImportConfiguratorBase<CaryoImportState> implements IImportConfigurator{

	@SuppressWarnings("unused")

	private static Logger logger = Logger.getLogger(CaryoImportConfigurator.class);

	private boolean isDoTaxa;

	private static IInputTransformer defaultTransformer = new CaryoTransformer();

	public static CaryoImportConfigurator NewInstance(Source source, ICdmDataSource destination){

		return new CaryoImportConfigurator(source, destination);

}

	protected void makeIoClassList(){

		ioClassList = new Class[]{

				CaryoTaxonImport.class ,

		};	

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()

	 */

	public CaryoImportState getNewState() {

		return new CaryoImportState(this);

	}

	private CaryoImportConfigurator(Source source, ICdmDataSource destination) {

	   super(source, destination, NomenclaturalCode.ICBN, defaultTransformer);

	}

	public boolean isDoTaxa() {

		return this.isDoTaxa;

	}

	public void setDoTaxa(boolean isDoTaxa) {

		this.isDoTaxa = isDoTaxa;

	}

}

// $Id$

/**

* 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.io.caryo;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.common.DbImportStateBase;

/**

 * @author a.mueller

 * @created 11.05.2009

 * @version 1.0

 */

public class CaryoImportState extends DbImportStateBase<CaryoImportConfigurator, CaryoImportState>{

	@SuppressWarnings("unused")

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

	public CaryoImportState(CaryoImportConfigurator config) {

		super(config);

	}

}

/**

* 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.io.caryo;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.io.common.DbImportBase;

import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;

import eu.etaxonomy.cdm.io.common.Source;

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class CaryoTaxonImport  extends DbImportBase<CaryoImportState, CaryoImportConfigurator> {

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

	private int modCount = 10000;

	private static final String pluralString = "taxa";

	private static final String dbTableName = "CARYOPHYLLALES";

	private static final String FAMILY = "Family";

	private static final String PERSON = "Person";

	private static final String TEAM = "Team";

	private static final String JOURNAL = "Journal";

	private static final String BOOK = "Book";

	private Map<String, Taxon> familyMap = new HashMap<String, Taxon>();

	private Map<String, TeamOrPersonBase> personMap = new HashMap<String, TeamOrPersonBase>();

	private Map<String, TeamOrPersonBase> teamMap = new HashMap<String, TeamOrPersonBase>();

	private Map<String, Reference> journalMap = new HashMap<String, Reference>();

	private Map<String, Reference> bookMap = new HashMap<String, Reference>();

	private Classification classification;

	public CaryoTaxonImport(){

		super(pluralString, dbTableName);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.DbImportBase#getIdQuery(eu.etaxonomy.cdm.io.common.DbImportStateBase)

	 */

	@Override

	protected String getIdQuery(CaryoImportState state) {

		String strRecordQuery = 

			" SELECT ID " + 

			" FROM " + dbTableName; 

		return strRecordQuery;	

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.DbImportBase#getRecordQuery(eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase)

	 */

	@Override

	protected String getRecordQuery(CaryoImportConfigurator config) {

		String strRecordQuery = 

			" SELECT cs.* " + 

			" FROM " + getTableName() + " t " +

			" WHERE ( t.ID IN (" + ID_LIST_TOKEN + ") )";

		return strRecordQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)

	 */

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, CaryoImportState state) {

		boolean success = true;

		Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>();

//		Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);

		classification = getClassification(state);

		try {

			doFamilies(state);

			doAuthors(state);

			doJournals(state);

			doBooks(state);

			ResultSet rs = partitioner.getResultSet();

			int i = 0;

			//for each reference

            while (rs.next()){

        		if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}

        		Integer taxonId = rs.getInt("IDcurrentspec");

        		//String dtSpcJahr -> ignore !

        		//empty: fiSpcLiteratur

        		//TODO

        		//fiSpcspcgrptax

				try {

//					classification.addParentChild(nextHigherTaxon, species, sourceRef, null);

//					

//					

//					this.doIdCreatedUpdatedNotes(state, species, rs, taxonId, TAXON_NAMESPACE);

//					

//					objectsToSave.add(species); 

				} catch (Exception e) {

					logger.warn("Exception in current_species: IDcurrentspec " + taxonId + ". " + e.getMessage());

//					e.printStackTrace();

				} 

            }

//            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );

			logger.warn(pluralString + " to save: " + objectsToSave.size());

			getTaxonService().save(objectsToSave);	

			return success;

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

	}

	private void doAuthors(CaryoImportState state) {

		// TODO Auto-generated method stub

	}

	private void doBooks(CaryoImportState state) {

		// TODO Auto-generated method stub

	}

	private void doJournals(CaryoImportState state) {

		// TODO Auto-generated method stub

	}

	private void doFamilies(CaryoImportState state) throws SQLException {

		Source source = state.getConfig().getSource();

		String sqlFamily = "SELECT DISTINCT family FROM table WHERE family IS NOT NULL";

		ResultSet rs = source.getResultSet(sqlFamily);

		while (rs.next()){

			String family = rs.getString("family");

			BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());

			name.setGenusOrUninomial(family);

			Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());

			classification.addChildTaxon(taxon, null, null, null);

//			taxon.addSource(id, idNamespace, citation, null);

			familyMap.put(family, taxon);

		}

	}

	private Classification getClassification(CaryoImportState state) {

		if (this.classification == null){

			String name = state.getConfig().getClassificationName();

			Reference<?> reference = state.getTransactionalSourceReference();

			this.classification = Classification.NewInstance(name, reference, Language.DEFAULT());

			if (state.getConfig().getClassificationUuid() != null){

				classification.setUuid(state.getConfig().getClassificationUuid());

			}

			getClassificationService().save(classification);

		}

		return this.classification;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)

	 */

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {

//		String nameSpace;

//		Class cdmClass;

//		Set<String> idSet;

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();

//		try{

//			Set<String> taxonIdSet = new HashSet<String>();

//			

//			while (rs.next()){

////				handleForeignKey(rs, taxonIdSet, "taxonId");

//			}

//			

//			//taxon map

//			nameSpace = TAXON_NAMESPACE;

//			cdmClass = Taxon.class;

//			idSet = taxonIdSet;

//			Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

//			result.put(nameSpace, objectMap);

//

//			

//		} catch (SQLException e) {

//			throw new RuntimeException(e);

//		}

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	@Override

	protected boolean doCheck(CaryoImportState state){

		return true;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	protected boolean isIgnore(CaryoImportState state){

		return ! state.getConfig().isDoTaxa();

	}

}

// $Id$

/**

* 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.io.caryo;

import java.util.UUID;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

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

/**

 * @author a.mueller

 * @created 01.03.2010

 * @version 1.0

 */

public final class CaryoTransformer extends InputTransformerBase {

	@SuppressWarnings("unused")

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

	//feature

//	public static final UUID endemismUuid =  UUID.fromString("dd343c31-1916-4786-a530-536ea995dce4");

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getMarkerTypeByKey(java.lang.String)

	 */

	@Override

	public MarkerType getMarkerTypeByKey(String key) throws UndefinedTransformerMethodException {

		if (StringUtils.isBlank(key)){return null;

//		}else if (key.equalsIgnoreCase("distribution")){return MarkerType.;

//		}else if (key.equalsIgnoreCase("habitatecology")){return Feature.ECOLOGY();

		}else{

			return null;

		}

	}

	@Override

	public UUID getMarkerTypeUuid(String key) throws UndefinedTransformerMethodException {

		if (StringUtils.isBlank(key)){return null;

//		}else if (key.equalsIgnoreCase("IMPERFECTLY KNOWN SPECIES")){return uuidIncompleteTaxon;

		}else{

			return null;

		}

	}

	@Override

	public UUID getFeatureUuid(String key) throws UndefinedTransformerMethodException {

		if (StringUtils.isBlank(key)){return null;

//		}else if (key.equalsIgnoreCase("Endemism")){return endemismUuid;

		}else{

			return null;

		}

	}

}