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.FileNotFoundException;

import java.io.IOException;

import java.io.PrintWriter;

import java.io.UnsupportedEncodingException;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

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.io.common.ExportDataWrapper;

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.INonViralName;

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

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

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.DerivedUnit;

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

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

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

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);

	private static final String ROW_TYPE = "http://rs.gbif.org/terms/1.0/TypesAndSpecimen";

	private static final String fileName = "typesAndSpecimen.txt";

	/**

	 * Constructor

	 */

	public DwcaTypesExport() {

		super();

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

		this.exportData = ExportDataWrapper.NewByteArrayInstance();

	}

	/** 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 void doInvoke(DwcaTaxExportState state){

		DwcaTaxExportConfigurator config = state.getConfig();

		TransactionStatus txStatus = startTransaction(true);

		PrintWriter writer = null;

		try {

			writer = createPrintWriter(fileName, state);

			DwcaMetaDataRecord metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE);

			state.addMetaRecord(metaRecord);

			Set<UUID> classificationUuidSet = config.getClassificationUuids();

            List<Classification> classificationList;

            if (classificationUuidSet.isEmpty()){

                classificationList = getClassificationService().list(Classification.class, null, 0, null, null);

            }else{

                classificationList = getClassificationService().find(classificationUuidSet);

            }

            Set<Classification> classificationSet = new HashSet<Classification>();

            classificationSet.addAll(classificationList);

            List<TaxonNode> allNodes;

            if (state.getAllNodes().isEmpty()){

                getAllNodes(state, classificationSet);

            }

            allNodes = state.getAllNodes();

			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(metaRecord, config);

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

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

								record.write(writer);

								this.addExistingRecordUuid(individualAssociation);

							}

						}

					}

				}

				//type specimen

				INonViralName nvn = taxon.getName();

				handleTypeName(writer, taxon, nvn, metaRecord, config);

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

					handleTypeName(writer, synonym, nvn, metaRecord, config);

				}

				//FIXME

				//Determinations

				writer.flush();

			}

		} catch (FileNotFoundException e) {

			e.printStackTrace();

		} catch (UnsupportedEncodingException e) {

			e.printStackTrace();

		} catch (ClassCastException e) {

			e.printStackTrace();

		} catch (IOException e) {

			e.printStackTrace();

		} finally{

			closeWriter(writer, state);

		}

		commitTransaction(txStatus);

		return;

	}

	/**

	 * @param writer

	 * @param taxon

	 * @param nvn

	 * @param config

	 * @return

	 */

	private Set<TypeDesignationBase> handleTypeName(PrintWriter writer, TaxonBase<?> taxonBase,

	        INonViralName nvn, DwcaMetaDataRecord metaRecord, DwcaTaxExportConfigurator config) {

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

		for (TypeDesignationBase<?> designation:designations){

			DwcaTypesRecord record = new DwcaTypesRecord(metaRecord, config);

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

				record.write(writer);

				addExistingRecordUuid(designation);

			}

		}

		return designations;

	}

	private boolean handleSpecimen(DwcaTypesRecord record, IndividualsAssociation individualsAssociation, TypeDesignationBase<?> designation, TaxonBase<?> taxonBase, DwcaTaxExportConfigurator config) {

		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.setId(taxonBase.getId());

		record.setUuid(taxonBase.getUuid());

		record.setBibliographicCitation(facade.getTitleCache());

		record.setTypeStatus(status);

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

		TaxonName scientificName = getScientificName(facade);

		if (scientificName != null){

			record.setScientificName(scientificName.getTitleCache());

			record.setTaxonRank(scientificName.getRank());

		}

		record.setOccurrenceId(facade.innerDerivedUnit());

		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 ???

		String source2 = "";

		if (individualsAssociation!=null) {

            source2 = getSources2(individualsAssociation.getSources(), config);

        }

		record.setSource(getSources3(facade.innerDerivedUnit(), config));

		record.setDescriptionSource(source2);

		record.setEventDate(facade.getGatheringPeriod());

		//TODO missing

		record.setVerbatimLabel(null);

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

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

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

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

			}

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

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

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

			}

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

                record.setCoordinatesPrecisionOrError(facade.getExactLocation().getErrorRadius().toString());

            }

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

                record.setCoordinatesSystem(facade.getExactLocation().getReferenceSystem().toString());

            }

		}

		return true;

	}

	private TaxonName<?,?> getScientificName(DerivedUnitFacade facade) {

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

		for (DeterminationEvent detEvent : detEvents){

			if (detEvent.getPreferredFlag()== true || detEvents.size()==1){

				return detEvent.getTaxon().getName();

			}

		}

		return null;

	}

	private DerivedUnitFacade getFacadeFromDesignation(TypeDesignationBase<?> designation) {

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

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

			try {

				DerivedUnit 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(DerivedUnit.class)){

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

			logger.warn(message);

			//TODO handle empty records

			return null;

		}else{

			DerivedUnit derivedUnit = CdmBase.deproxy(specimen, DerivedUnit.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();

	}

}