EDIT

app-import/src/main/java/eu/etaxonomy/cdm/app/i4life/col/ColDwcaExportActivator.java -text

app-import/src/main/java/eu/etaxonomy/cdm/app/i4life/col/ColDwcaImportActivator.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.i4life.col;

import java.io.File;

import java.net.URI;

import java.util.Arrays;

import java.util.List;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

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

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

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

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

import eu.etaxonomy.cdm.io.dwca.out.DwcaEmlRecord;

import eu.etaxonomy.cdm.io.dwca.out.DwcaTaxExportConfigurator;

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

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

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

/**

 *

 * @author a.mueller

 *

 */

public class ColDwcaExportActivator {

	@SuppressWarnings("unused")

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

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

	private static final String fileDestination = "C:\\tmp\\dwcaTmp\\cyprus\\";

//	private static final ICdmDataSource cdmSource = CdmDestinations.cdm_local_cichorieae();

//	private static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql();

//	private static final ICdmDataSource cdmSource = CdmDestinations.cdm_production_cichorieae();

//	private static final ICdmDataSource cdmSource = CdmDestinations.cdm_flora_central_africa_production();

	private static final ICdmDataSource cdmSource = CdmDestinations.cdm_cyprus_production();

	private IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();

	private static DateTime dateTime = new DateTime();

	private static String date = dateTime.getYear() + "-" + dateTime.getMonthOfYear() + "-" + dateTime.getDayOfMonth();

	private static final String defaultBibliographicCitation = "ICN (Hand, R., Kilian, N. & Raab-Straube, E. von; general editors) 2009+ (continuously updated): International Cichorieae Network: Cichorieae Portal. Published on the Internet at http://wp6-cichorieae.e-taxonomy.eu/portal/; " + 

		"accessed ["+date+"].";

	private static final String taxonSourceDefault = "http://wp6-cichorieae.e-taxonomy.eu/portal/?q=cdm_dataportal/taxon/{id}";

	//check - import

	private static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK;

	private static List<UUID> featureExclusions = Arrays.asList(new UUID[]{

			UUID.fromString("5deff505-1a32-4817-9a74-50e6936fd630"),   //occurrences

			UUID.fromString("8075074c-ace8-496b-ac82-47c14553f7fd"),    //Editor_Parenthesis

			UUID.fromString("c0cc5ebe-1f0c-4c31-af53-d486858ea415"),   //Image Sources

			UUID.fromString("9f6c551d-0f19-45ea-a855-4946f6fc1093"),		//Credits

			UUID.fromString("cbf12c6c-94e6-4724-9c48-0f6f10d83e1c"),   //Editor Brackets

			UUID.fromString("0508114d-4158-48b5-9100-369fa75120d3")     //inedited

	});

// ****************** ALL *****************************************

//	private boolean doTaxa = true;

//	private boolean doResourceRelation = true;

//	private boolean doTypesAndSpecimen = true;

//	private boolean doVernacularNames = true;

//	private boolean doReferences = true;

//	private boolean doDescription = true;

//	private boolean doDistributions = true;

//	private boolean doImages = false;

//	private boolean doMetaData = true;

//	private boolean doEml = true;

// ************************ NONE **************************************** //

	private boolean doTaxa = true;

	private boolean doResourceRelation = false;

	private boolean doTypesAndSpecimen = false;

	private boolean doVernacularNames = false;

	private boolean doReferences = false;

	private boolean doDescription = false;

	private boolean doDistributions = false;

	private boolean doImages = false;

	private boolean doMetaData = true;

	private boolean doEml = false;

	public boolean 	doExport(ICdmDataSource source){

		System.out.println("Start export to DWC-A ("+ fileDestination + ") ...");

//		CdmUpdater su = CdmUpdater.NewInstance();

//		IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();

//		

//		try {

//			su.updateToCurrentVersion(source, monitor);

//		} catch (Exception e) {

//			e.printStackTrace();

//		}

//		if (true){

//			return true;

//		}

		//make file destination

		String destination = fileDestination;

		DwcaEmlRecord emlRecord = getEmlRecord();

		DwcaTaxExportConfigurator config = DwcaTaxExportConfigurator.NewInstance(source, new File(destination), emlRecord);

		config.setDoTaxa(doTaxa);

		config.setDoResourceRelation(doResourceRelation);

		config.setDoTypesAndSpecimen(doTypesAndSpecimen);

		config.setDoVernacularNames(doVernacularNames);

		config.setDoReferences(doReferences);

		config.setDoDescription(doDescription);

		config.setDoDistributions(doDistributions);

		config.setDoImages(doImages);

		config.setDoMetaData(doMetaData);

		config.setDoEml(doEml);

		config.setCheck(check);

		config.setProgressMonitor(monitor);

		config.setDefaultBibliographicCitation(defaultBibliographicCitation);

		config.setDefaultTaxonSource(taxonSourceDefault);

		monitor.beginTask("DwcA-Export", 10);

		config.setFeatureExclusions(featureExclusions);

		// invoke import

		CdmDefaultExport<DwcaTaxExportConfigurator> bmExport = new CdmDefaultExport<DwcaTaxExportConfigurator>();

		boolean result = bmExport.invoke(config);

		System.out.println("End export to DWC-A ("+ fileDestination + ")..." + (result? "(successful)":"(with errors)"));

		return result;

	}

	private DwcaEmlRecord getEmlRecord() {

		DwcaEmlRecord emlRecord = new DwcaEmlRecord();

		emlRecord.setIdentifier("My Identifier");

		emlRecord.setTitle("Flora of cyprus");

		emlRecord.setPublicationDate(new DateTime());

		emlRecord.setExpectedCitation("Expected Citation");

		emlRecord.setAbstractInfo("The abstract");

		emlRecord.setAdditionalInformation("Add info");

		emlRecord.setResourceLanguage(null);

		emlRecord.setResourceUrl(URI.create("http://www.flora-of-cyprus.eu//portal/"));

		emlRecord.setMetaDataLanguage(null);

		emlRecord.setResourceLogoUri(null);

		emlRecord.setCreativeCommonsLicensing(null);

		emlRecord.setProjectTitle("Projekt tit");

		emlRecord.setProjectLead("Proj Lead");

		emlRecord.setProjectDescription("Proj Desc");

		Person person = Person.NewInstance();

		Institution institution = Institution.NewInstance();

		InstitutionalMembership m = person.addInstitutionalMembership(institution, null, null, null);

		emlRecord.setResourceCreator(m);

		return emlRecord;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		ColDwcaExportActivator ex = new ColDwcaExportActivator();

		ICdmDataSource source = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmSource;

		ex.doExport(source);

	}

}

/**

* 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.ICdmApplicationConfiguration;

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.DwcaImportConfigurator;

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

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 = 1000;

	//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){

			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;

	}

	//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:////Pesiimport3/col/col_20Nov2012.zip");

		return sourceUrl;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		ColDwcaImportActivator me = new ColDwcaImportActivator();

		me.doImport(cdmDestination);

	}

}