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.io.dwca.out;

import java.io.File;

import java.io.FileNotFoundException;

import java.io.FileOutputStream;

import java.io.IOException;

import java.io.OutputStreamWriter;

import java.io.PrintWriter;

import java.io.UnsupportedEncodingException;

import java.util.List;

import java.util.Set;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.occurrence.Collection;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;

import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

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

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

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

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

/**

 * @author a.mueller

 * @created 20.04.2011

 */

@Component

public class DwcaTypesExport extends DwcaExportBase {

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

	/**

	 * Constructor

	 */

	public DwcaTypesExport() {

		super();

		this.ioName = this.getClass().getSimpleName();

	}

	/** Retrieves data from a CDM DB and serializes them CDM to XML.

	 * Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships.

	 * Taxa that are not part of the classification are not found.

	 * 

	 * @param exImpConfig

	 * @param dbname

	 * @param filename

	 */

	@Override

	protected boolean doInvoke(DwcaTaxExportState state){

		DwcaTaxExportConfigurator config = state.getConfig();

		String dbname = config.getSource() != null ? config.getSource().getName() : "unknown";

    	String fileName = config.getDestinationNameString();

		logger.info("Serializing DB " + dbname + " to file " + fileName);

		TransactionStatus txStatus = startTransaction(true);

		try {

			final String coreTaxFileName = "typesAndSpecimen.txt";

			fileName = fileName + File.separatorChar + coreTaxFileName;

			File f = new File(fileName);

			if (!f.exists()){

				f.createNewFile();

			}

			FileOutputStream fos = new FileOutputStream(f);

			PrintWriter writer = new PrintWriter(new OutputStreamWriter(fos, "UTF8"), true);

			List<TaxonNode> allNodes =  getAllNodes(null);

			for (TaxonNode node : allNodes){

				Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);

				//TODO use API methods to retrieve all related specimen

				//individual associations

				Set<TaxonDescription> descriptions = taxon.getDescriptions();

				for (TaxonDescription description : descriptions){

					for (DescriptionElementBase el : description.getElements()){

						if (el.isInstanceOf(IndividualsAssociation.class)){

							DwcaTypesRecord record = new DwcaTypesRecord();

							IndividualsAssociation individualAssociation = CdmBase.deproxy(el,IndividualsAssociation.class);

							if (! this.recordExistsUuid(individualAssociation) && handleSpecimen(record, individualAssociation, null, taxon)){

								record.write(writer);

								this.addExistingRecordUuid(individualAssociation);

							}

						}

					}

				}

				//type specimen 

				NonViralName<?> nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);

				handleTypeName(writer, taxon, nvn);

				for (Synonym synonym : taxon.getSynonyms()){

					handleTypeName(writer, synonym, nvn);

				}

				//FIXME

				//Determinations

				writer.flush();

			}

		} catch (FileNotFoundException e) {

			e.printStackTrace();

		} catch (UnsupportedEncodingException e) {

			e.printStackTrace();

		} catch (ClassCastException e) {

			e.printStackTrace();

		} catch (IOException e) {

			e.printStackTrace();

		}

		commitTransaction(txStatus);

		return true;

	}

	/**

	 * @param writer

	 * @param taxon

	 * @param nvn

	 * @return

	 */

	private Set<TypeDesignationBase<?>> handleTypeName(PrintWriter writer, TaxonBase taxonBase, NonViralName<?> nvn) {

		Set<TypeDesignationBase<?>> designations = nvn.getTypeDesignations();

		for (TypeDesignationBase designation:designations){

			DwcaTypesRecord record = new DwcaTypesRecord();

			if (! this.recordExistsUuid(designation) && handleSpecimen(record, null, designation, taxonBase)){

				record.write(writer);

				addExistingRecordUuid(designation);

			}

		}

		return designations;

	}

	private boolean handleSpecimen(DwcaTypesRecord record, IndividualsAssociation individualsAssociation, TypeDesignationBase designation, TaxonBase taxonBase) {

		TypeDesignationStatusBase status = null;

		DerivedUnitFacade facade = null;

		if (individualsAssociation != null){

			facade = getFacadeFromAssociation(individualsAssociation);

		}else if (designation != null){

			facade = getFacadeFromDesignation(designation);

			status = designation.getTypeStatus();

		}

		if (facade == null){

			return false;

		}

		record.setCoreid(taxonBase.getId());

		record.setBibliographicCitation(facade.getTitleCache());

		record.setTypeStatus(status);

		record.setTypeDesignatedBy( (designation == null || designation.getCitation()==null)? null: designation.getCitation().getTitleCache());

		TaxonNameBase scientificName = getScientificName(facade);

		if (scientificName != null){

			record.setScientificName(scientificName.getTitleCache());

			record.setTaxonRank(scientificName.getRank());

		}

		record.setOccurrenceId(facade.innerDerivedUnit().getUuid().toString());

		Collection collection = facade.getCollection();

		if (collection != null){

			record.setCollectionCode(collection.getCode());

			if (collection.getInstitute() != null){

				record.setInstitutionCode(collection.getInstitute().getCode());

			}

		}

		record.setCatalogNumber(facade.getCatalogNumber());

		record.setLocality(facade.getLocalityText());

		record.setSex(facade.getSex());

		record.setRecordedBy(facade.getCollector());

		//TODO ???

		record.setSource(null);

		record.setEventDate(facade.getGatheringPeriod());

		//TODO missing

		record.setVerbatimLabel(null);

		if (facade.getExactLocation() != null){

			if (facade.getExactLocation().getLongitude() != null){

				record.setVerbatimLongitude(facade.getExactLocation().getLongitudeSexagesimal().toString());

			}

			if (facade.getExactLocation().getLatitude() != null){

				record.setVerbatimLatitude(facade.getExactLocation().getLatitudeSexagesimal().toString());

			}

		}

		return true;

	}

	private TaxonNameBase getScientificName(DerivedUnitFacade facade) {

		Set<DeterminationEvent> detEvents = facade.getDeterminations();

		for (DeterminationEvent detEvent : detEvents){

			if (detEvent.getPreferredFlag()== true){

				return detEvent.getTaxon().getName();

			}

		}

		return null;

	}

	private DerivedUnitFacade getFacadeFromDesignation(TypeDesignationBase designation) {

		if (designation.isInstanceOf(SpecimenTypeDesignation.class)){

			SpecimenTypeDesignation specDesig = CdmBase.deproxy(designation, SpecimenTypeDesignation.class);

			try {

				DerivedUnitBase derivedUnit = specDesig.getTypeSpecimen();

				if (derivedUnit == null){

					return null;

				}else{

					DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(derivedUnit);

					return facade;

				}

			} catch (DerivedUnitFacadeNotSupportedException e) {

				String message = "DerivedUnit is too complex to be handled by facade based darwin core archive export";

				logger.warn(message);

				//TODO handle empty records

				return null; 

			}

		}else{

			return null;

		}

	}

	private DerivedUnitFacade getFacadeFromAssociation(IndividualsAssociation individualsAssociation) {

		SpecimenOrObservationBase specimen = individualsAssociation.getAssociatedSpecimenOrObservation();

		DerivedUnitFacade facade;

		if (! specimen.isInstanceOf(DerivedUnitBase.class)){

			String message = "Non DerivedUnit specimen can not yet be handled by this export";

			logger.warn(message);

			//TODO handle empty records

			return null; 

		}else{

			DerivedUnitBase<?> derivedUnit = CdmBase.deproxy(specimen, DerivedUnitBase.class);

			try {

				facade = DerivedUnitFacade.NewInstance(derivedUnit);

			} catch (DerivedUnitFacadeNotSupportedException e) {

				String message = "DerivedUnit is too complex to be handled by facade based darwin core archive export";

				logger.warn(message);

				//TODO handle empty records

				return null; 

			}

		}

		return facade;

	}

	@Override

	protected boolean doCheck(DwcaTaxExportState state) {

		boolean result = true;

		logger.warn("No check implemented for " + this.ioName);

		return result;

	}

	@Override

	protected boolean isIgnore(DwcaTaxExportState state) {

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

	}

}