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.app.i4life.col;

import java.net.URI;

import java.util.UUID;

import org.apache.log4j.Logger;

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

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

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;

import eu.etaxonomy.cdm.io.dwca.in.DwcaDataImportConfiguratorBase.DatasetUse;

import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;

import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;

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

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

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

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

/**

 * @author a.mueller

 * @created 10.11.2011

 */

public class ColDwcaImportActivator {

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final URI source = dwca_col_All();

	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_dwca();

	static boolean isNoQuotes = true;

	//classification

	static final UUID classificationUuid = UUID.fromString("29d4011f-a6dd-4081-beb8-559ba6b84a6b");

	//default nom code is ICZN as it allows adding publication year 

	static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICZN;

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	static int partitionSize = 5000;

	//config

	static DatasetUse datasetUse = DatasetUse.ORIGINAL_SOURCE;

	static boolean scientificNameIdAsOriginalSourceId = true;

	static boolean guessNomRef = true;

	private boolean handleAllRefsAsCitation = true;

	//validate

	static boolean validateRankConsistency = false;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doDistribution = false;

	//deduplicate

	static final boolean doDeduplicate = false;

	static final MappingType mappingType = MappingType.InMemoryMapping;

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

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

		config.addObserver(new LoggingIoObserver());

		config.setClassificationUuid(classificationUuid);

		config.setCheck(check);

		config.setDbSchemaValidation(hbm2dll);

		config.setMappingType(mappingType);

		config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);

		config.setValidateRankConsistency(validateRankConsistency);

		config.setDefaultPartitionSize(partitionSize);

		config.setNomenclaturalCode(defaultNomCode);

		config.setDatasetUse(datasetUse);

		config.setGuessNomenclaturalReferences(guessNomRef);

		config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);

		config.setNoQuotes(isNoQuotes);

		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){

			ICdmApplicationDefaultConfiguration 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;

	}

	//Dwca

	public static URI dwca_test_in() {

//		URI sourceUrl = URI.create("http://dev.e-taxonomy.eu/trac/export/14463/trunk/cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");

		URI sourceUrl = URI.create("file:///C:/Users/pesiimport/Documents/pesi_cdmlib/cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverterTest-input.zip");

		return sourceUrl;

	}

	//CoL

	public static URI dwca_col_All() {

		URI sourceUrl = URI.create("file:///data/dwca/xylariaceae/added.zip");

		return sourceUrl;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		ColDwcaImportActivator me = new ColDwcaImportActivator();

		me.doImport(cdmDestination);

	}

}