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.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 18.04.2011

 */

@Component

public class DwcaTaxExport extends DwcaExportBase {

    private static final long serialVersionUID = -3770976064909193441L;

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

	private static final String ROW_TYPE = "http://rs.tdwg.org/dwc/terms/Taxon";

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

	/**

	 *

	 */

	public DwcaTaxExport() {

		super();

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

		this.exportData = ExportDataWrapper.NewByteArrayInstance();

	}

	/** Retrieves data from a CDM DB and serializes the 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);

		DwcaMetaDataRecord metaRecord = new DwcaMetaDataRecord(true, 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);

		PrintWriter writer = null;

		try {

			writer = createPrintWriter(fileName, state);

			List<TaxonNode> allNodes;

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

			    getAllNodes(state, classificationSet);

			}

			allNodes = state.getAllNodes();

			int i = 0;

			for (TaxonNode node : allNodes){

				i++;

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

				DwcaTaxRecord record = new DwcaTaxRecord(metaRecord, config);

				TaxonName name = taxon.getName();

				Taxon parent = node.getParent() == null ? null : node.getParent().getTaxon();

				TaxonName basionym = name.getBasionym();

				Classification classification = node.getClassification();

				if (! this.recordExists(taxon)){

					handleTaxonBase(record, taxon, name, taxon, parent, basionym, classification, null, false, false, config);

					record.write(writer);

					this.addExistingRecord(taxon);

				}

				node.getClassification().getName();

				//synonyms

				handleSynonyms(taxon, writer, classification, metaRecord, config);

				//misapplied names

				handleMisapplication(taxon, writer, classification, metaRecord, config);

				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;

	}

	private void handleSynonyms(Taxon taxon, PrintWriter writer, Classification classification, DwcaMetaDataRecord metaRecord, DwcaTaxExportConfigurator config) {

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

			DwcaTaxRecord record = new DwcaTaxRecord(metaRecord, config);

			SynonymType type = synonym.getType();

			boolean isProParte = synonym.isProParte();

			boolean isPartial = synonym.isPartial();

			if (type == null){ // should not happen

				type = SynonymType.SYNONYM_OF();

			}

			TaxonName name = synonym.getName();

			//????

			Taxon parent = null;

			TaxonName basionym = name.getBasionym();

			if (! this.recordExists(synonym)){

				handleTaxonBase(record, synonym, name, taxon, parent, basionym, classification, type, isProParte, isPartial, config);

				record.write(writer);

				this.addExistingRecord(synonym);

			}

		}

	}

	private void handleMisapplication(Taxon taxon, PrintWriter writer, Classification classification, DwcaMetaDataRecord metaRecord, DwcaTaxExportConfigurator config) {

		Set<Taxon> misappliedNames = taxon.getMisappliedNames();

		for (Taxon misappliedName : misappliedNames ){

			DwcaTaxRecord record = new DwcaTaxRecord(metaRecord, config);

			TaxonRelationshipType relType = TaxonRelationshipType.MISAPPLIED_NAME_FOR();

			TaxonName name = misappliedName.getName();

			//????

			Taxon parent = null;

			TaxonName basionym = name.getBasionym();

			if (! this.recordExists(misappliedName)){

				handleTaxonBase(record, misappliedName, name, taxon, parent, basionym, classification, relType, false, false, config);

				record.write(writer);

				this.addExistingRecord(misappliedName);

			}

		}

	}

	/**

	 * @param record

	 * @param taxonBase

	 * @param name

	 * @param acceptedTaxon

	 * @param parent

	 * @param basionym

	 * @param isPartial

	 * @param isProParte

	 * @param config

	 * @param type

	 */

	private void handleTaxonBase(DwcaTaxRecord record, TaxonBase<?> taxonBase, TaxonName name,

			Taxon acceptedTaxon, Taxon parent, TaxonName basionym, Classification classification,

			RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial, DwcaTaxExportConfigurator config) {

		record.setId(taxonBase.getId());

		record.setUuid(taxonBase.getUuid());

		//maybe wrong as according to the DwC-A documentation only resolvable ids are allowed, this differs from DwC documentation

		record.setScientificNameId(name);

		record.setScientificName(name.getTitleCache());

		record.setAcceptedNameUsageId(acceptedTaxon.getUuid());

		record.setAcceptedNameUsage(acceptedTaxon.getName() == null? acceptedTaxon.getTitleCache() : acceptedTaxon.getName().getTitleCache());

		//parentNameUsage

		if (parent != null){

			record.setParentNameUsageId(parent.getUuid());

			record.setParentNameUsage(parent.getTitleCache());

		}

		//originalNameUsage

		// ??? - is not a name usage (concept)

		if (basionym != null){

			//FIXME needs to be a coreID otherwise use string only

//			record.setOriginalNameUsageId(basionym.getUuid());

			record.setOriginalNameUsageId(null);

			record.setOriginalNameUsage(basionym.getTitleCache());

		}

		//nameAccordingTo

		Reference sec = taxonBase.getSec();

		if (sec == null){

			String message = "There is a taxon without sec " + taxonBase.getTitleCache() + "( " + taxonBase.getId() + ")";

			logger.warn(message);

		}else{

			record.setNameAccordingToId(taxonBase.getSec().getUuid());

			record.setNameAccordingTo(taxonBase.getSec().getTitleCache());

		}

		//namePublishedIn

		// ??? is not a nameUsage (concept)

		if (name.getNomenclaturalReference() != null){

			record.setNamePublishedInId(name.getNomenclaturalReference().getUuid());

			record.setNamePublishedIn(name.getNomenclaturalReference() == null ? null : name.getNomenclaturalReference().getTitleCache());

		}

		// what is the exact difference to id and acceptedNameUsageId

		record.setTaxonConceptId(taxonBase.getUuid());

		//Classification

		if (config.isWithHigherClassification()){

			//FIXME all classification and rank specific fields are meant to represent the classification

			//currently the information is only compiled for the exact same range but it should be compiled

			//for all ranks above the rank of this taxon

			//TODO we do not support this yet

			record.setHigherClassification(null);

			//... higher ranks

			handleUninomialOrGenus(record, name);

			if (name.getRank() != null &&  name.getRank().equals(Rank.SUBGENUS())){

				record.setSubgenus(name.getNameCache());

			}

			//record.setSubgenus(name.getInfraGenericEpithet());

		}

		if (name.getRank() != null &&  (name.getRank().isSupraGeneric() || name.getRank().isGenus())){

			record.setUninomial(name.getGenusOrUninomial());

		}else{

			record.setGenusPart(name.getGenusOrUninomial());

		}

		record.setInfraGenericEpithet(name.getInfraGenericEpithet());

		record.setSpecificEpithet(name.getSpecificEpithet());

		record.setInfraspecificEpithet(name.getInfraSpecificEpithet());

		record.setTaxonRank(name.getRank());

		if (name.getRank() != null){

			record.setVerbatimTaxonRank(name.getRank().getAbbreviation());

		}else{

			String message = "No rank available for " + name.getTitleCache() + "(" + name.getId() + ")";

			logger.warn(message);

		}

		record.setScientificNameAuthorship(name.getAuthorshipCache());

		// ??? - use for TextData common names?

		record.setVernacularName(null);

		record.setNomenclaturalCode(name.getNomenclaturalCode());

		// ??? TODO Misapplied Names, inferred synonyms

		handleTaxonomicStatus(record, name, relType, isProParte, isPartial);

		handleNomStatus(record, taxonBase, name);

		// TODO we need to differentiate technical

		String taxonRemarks = "";

		for (Annotation annotation : taxonBase.getAnnotations()){

			if (AnnotationType.EDITORIAL().equals(annotation.getAnnotationType())){

				taxonRemarks += CdmUtils.Nz(annotation.getText());

			}

		}

		for (Annotation annotation : name.getAnnotations()){

			if (AnnotationType.EDITORIAL().equals(annotation.getAnnotationType())){

				taxonRemarks += CdmUtils.Nz(annotation.getText());

			}

		}

		if (StringUtils.isNotBlank(taxonRemarks)){

			record.setTaxonRemarks(taxonRemarks);

		}

		// TODO which date is needed here (taxon, name, sec, ... ?)

		record.setModified(taxonBase.getUpdated());

		// ???

		record.setLanguage(null);

		record.setRights(taxonBase.getRights());

		//TODO

		record.setRightsHolder(null);

		record.setAccessRights(null);

		//TODO currently only via default value

		record.setBibliographicCitation(null);

		record.setInformationWithheld(null);

		record.setDatasetId(classification);

		record.setDatasetName(classification.getTitleCache());

		//TODO

		record.setSource(null);

		return;

	}

	/**

	 * @param record

	 * @param name

	 * @param type

	 * @param isPartial

	 * @param isProParte

	 */

	private void handleTaxonomicStatus(DwcaTaxRecord record,

			INonViralName name, RelationshipTermBase<?> type,

			boolean isProParte, boolean isPartial) {

		if (type == null){

			record.setTaxonomicStatus(name.getNomenclaturalCode().acceptedTaxonStatusLabel());

		}else{

			String status = name.getNomenclaturalCode().synonymStatusLabel();

			if (type.equals(SynonymType.HETEROTYPIC_SYNONYM_OF())){

				status = "heterotypicSynonym";

			}else if(type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){

				status = "homotypicSynonym";

			}else if(type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){

				status = "misapplied";

			}

			if (isProParte){

				status = "proParteSynonym";

			}else if (isPartial){

				String message = "Partial synonym is not part of the gbif toxonomic status vocabulary";

				logger.warn(message);

				status = "partialSynonym";

			}

			record.setTaxonomicStatus(status);

		}

	}

	/**

	 * @param record

	 * @param name

	 */

	private void handleUninomialOrGenus(DwcaTaxRecord record, INonViralName name) {

		//epethita

		String firstEpi = name.getGenusOrUninomial();

		if (!StringUtils.isBlank(firstEpi)){

			Rank rank = name.getRank();

			if (rank != null){

				if (rank.isLower(Rank.GENUS())){

					record.setGenus(firstEpi);

				}else if (rank.equals(Rank.GENUS())){

					record.setGenus(firstEpi);

				}else if (rank.equals(Rank.KINGDOM())){

					record.setKingdom(firstEpi);

				}else if (rank.equals(Rank.PHYLUM())){

					record.setPhylum(firstEpi);

				}else if (rank.equals(Rank.CLASS())){

					record.setClazz(firstEpi);

				}else if (rank.equals(Rank.ORDER())){

					record.setOrder(firstEpi);

				}else if (rank.equals(Rank.FAMILY())){

					record.setFamily(firstEpi);

				}else{

					// !!!

					String message = "Rank not covered. Set uninomial as genus instead: " + rank.getLabel();

					logger.warn(message);

//					record.setGenus(firstEpi);

				}

			}

		}

	}

	/**

	 * @param record

	 * @param taxon

	 * @param name

	 */

	private void handleNomStatus(DwcaTaxRecord record, TaxonBase<?> taxon,

			INonViralName name) {

		int nStatus = name.getStatus().size();

		if (nStatus > 0){

			if (name.getStatus().size()> 1){

				String warning = "There is more than 1 nomenclatural status ( " + name.getStatus().size()+ "): " + taxon.getTitleCache();

				logger.warn(warning);

			}

			NomenclaturalStatusType status = name.getStatus().iterator().next().getType();

			record.setNomenclaturalStatus(status);

		}else{

			record.setNomenclaturalStatus(null);

		}

	}

	@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().isDoTaxa();

	}

}