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.csv.redlist.out;

import java.io.ByteArrayOutputStream;

import java.io.PrintWriter;

import java.util.ArrayList;

import java.util.Collections;

import java.util.Comparator;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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.TaxonRelationship;

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

/**

 * @author a.oppermann

 * @since 18.10.2012

 */

@Component

public class CsvTaxExportRedlist extends CsvExportBaseRedlist {

    private static final long serialVersionUID = 841703025922543361L;

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

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

	private static final String fileName = "RedlistCoreTax.csv";

	public CsvTaxExportRedlist() {

		super();

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

	}

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

	 * Starts with root taxa and traverses the classification to retrieve

	 * children taxa, synonyms, relationships, descriptive data, red list

	 * status (features).

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

	 *

	 * @param exImpConfig

	 * @param dbname

	 * @param filename

	 */

	@Override

	protected void doInvoke(CsvTaxExportStateRedlist state){

		CsvTaxExportConfiguratorRedlist config = state.getConfig();

		TransactionStatus txStatus = startTransaction(true);

		List<NamedArea> selectedAreas = config.getNamedAreas();

		Set<TaxonNode> taxonNodes = assembleTaxonNodeSet(config);

		PrintWriter writer = null;

		ByteArrayOutputStream byteArrayOutputStream;

		try {

			byteArrayOutputStream = config.getByteArrayOutputStream();

			writer = new PrintWriter(byteArrayOutputStream);

			//geographical Filter

			List<TaxonNode> filteredNodes = handleGeographicalFilter(state, selectedAreas, taxonNodes);

			//sorting List

			Collections.sort(filteredNodes, new Comparator<TaxonNode>() {

				@Override

				public int compare(TaxonNode tn1, TaxonNode tn2) {

					Taxon taxon1 = tn1.getTaxon();

					Taxon taxon2 = tn2.getTaxon();

					if(taxon1 != null && taxon2 != null){

						return taxon1.getTitleCache().compareTo(taxon2.getTitleCache());

					}

					else{

						return 0;

					}

				}

			});

			for (TaxonNode node : filteredNodes){

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

				CsvTaxRecordRedlist record = assembleRecord(state);

				INonViralName name = taxon.getName();

				Classification classification = node.getClassification();

				config.setClassificationTitleCache(classification.getTitleCache());

				if (! this.recordExists(taxon)){

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

					record.write(writer);

					this.addExistingRecord(taxon);

				}

				//misapplied names

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

				writer.flush();

			}

		} catch (ClassCastException e) {

			e.printStackTrace();

		}

		finally{

		    if(writer!=null){

		        writer.close();

		    }

			this.clearExistingRecordIds();

		}

		commitTransaction(txStatus);

		return;

	}

	//TODO: Exception handling

	protected Set<TaxonNode> assembleTaxonNodeSet(CsvTaxExportConfiguratorRedlist config){

		Set<TaxonNode> taxonNodes = new HashSet<>();

		if(config != null){

			List<UUID> taxonNodeUuidSet = new ArrayList<>(config.getTaxonNodeUuids());

			List<TaxonNode> loadedNodes = getTaxonNodeService().load(taxonNodeUuidSet, null);

			taxonNodes.addAll(loadedNodes);

		}

		return taxonNodes;

	}

	//TODO: Exception handling

	private CsvTaxRecordRedlist assembleRecord(CsvTaxExportStateRedlist state) {

		if(state!=null){

			CsvTaxExportConfiguratorRedlist config = state.getConfig();

			CsvMetaDataRecordRedlist metaRecord = new CsvMetaDataRecordRedlist(true, fileName, ROW_TYPE);

			state.addMetaRecord(metaRecord);

			CsvTaxRecordRedlist record = new CsvTaxRecordRedlist(metaRecord, config);

			return record;

		}

		return null;

	}

	/**

	 * Takes positive List of areas and iterates over a given taxon node

	 * and their {@link Taxon} to return all {@link Taxon} with the desired

	 * geographical attribute.

	 *

	 * <p><p>

	 *

	 * If selectedAreas is null all child {@link TaxonNode}s of the given taxon node will be returned.

	 * @param state

	 *

	 * @param selectedAreas

	 * @param taxonNodes

	 * @return

	 */

	protected List<TaxonNode> handleGeographicalFilter(CsvTaxExportStateRedlist state, List<NamedArea> selectedAreas,

	        Set<TaxonNode> taxonNodes) {

	    List<TaxonNode> filteredNodes = new ArrayList<>();

	    List<TaxonNode> allNodes = new ArrayList<>();

	    for (TaxonNode node : taxonNodes){

	        if(node.getTaxon()!=null){

	            allNodes.add(node);

	        }

	        allNodes.addAll(getTaxonNodeService().loadChildNodesOfTaxonNode(node, null, true,

	                state.getConfig().isIncludeUnpublished(), null));

	    }

	    //Geographical filter

	    if(selectedAreas != null && !selectedAreas.isEmpty() && selectedAreas.size() < 16){

	        for (TaxonNode node : allNodes){

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

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

	            for (TaxonDescription description : descriptions){

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

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

	                        Distribution distribution = CdmBase.deproxy(el, Distribution.class);

	                        NamedArea area = distribution.getArea();

	                        for(NamedArea selectedArea:selectedAreas){

	                            if(selectedArea.getUuid().equals(area.getUuid())){

	                                filteredNodes.add(node);

	                            }

	                        }

	                    }

	                }

	            }

	        }

	    }else{

	        filteredNodes = allNodes;

	    }

	    return filteredNodes;

	}

	/**

	 * handles misapplied {@link Taxon}

	 * @param taxon

	 * @param writer

	 * @param classification

	 * @param metaRecord

	 * @param config

	 */

	private void handleMisapplication(Taxon taxon, PrintWriter writer, Classification classification, CsvTaxRecordRedlist record, CsvTaxExportConfiguratorRedlist config) {

		Set<TaxonRelationship> misappliedNameRels = taxon.getMisappliedNameRelations();

		for (TaxonRelationship misappliedNameRel : misappliedNameRels ){

//			CsvTaxRecordRedlist record = new CsvTaxRecordRedlist(metaRecord, config);

			Taxon misappliedName = misappliedNameRel.getFromTaxon();

			INonViralName name = misappliedName.getName();

			if (! this.recordExists(misappliedName)){

				handleTaxonBase(record, misappliedName, name, taxon, classification,

				        misappliedNameRel.getType(), false, false, config);

				record.write(writer);

				this.addExistingRecord(misappliedName);

			}

		}

	}

	/**

	 * handles the information record for the actual {@link Taxon} including {@link Classification classification}, Taxon Name, Taxon ID,

	 * Taxon Status, Synonyms, {@link Feature features} data

	 * @param record the concrete information record

	 * @param taxonBase {@link Taxon}

	 * @param name

	 * @param acceptedTaxon

	 * @param parent

	 * @param basionym

	 * @param isPartial

	 * @param isProParte

	 * @param config

	 * @param type

	 */

	private void handleTaxonBase(CsvTaxRecordRedlist record,TaxonBase<?> taxonBase,

			INonViralName name, Taxon acceptedTaxon, Classification classification,

			RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial,

			CsvTaxExportConfiguratorRedlist config) {

		List<Feature> features = config.getFeatures();

		record.setHeadLinePrinted(config.isHasHeaderLines());

		if(features != null) {

            record.setPrintFeatures(features);

        }

		config.setHasHeaderLines(false);

		record.setDatasetName(classification.getTitleCache());

		record.setScientificName(name.getTitleCache());

		record.setScientificNameId(name.getUuid().toString());

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

		//synonyms

		handleSynonyms(record,(Taxon) taxonBase);

		//distribution

		handleDiscriptionData(record, (Taxon) taxonBase);

		if(features!= null) {

			List<List<String>> featureCells = new ArrayList<List<String>>(features.size());

			for(int i = 0; i < features.size(); i++) {

				featureCells.add(new ArrayList<String>());

			}

			handleRelatedRedlistStatus(record, (Taxon)taxonBase, false, featureCells, features);

			handleRelatedRedlistStatus(record, (Taxon)taxonBase, true, featureCells, features);

		}

		return;

	}

	private void handleTaxonomicStatus(

			CsvTaxRecordRedlist record,

			INonViralName name,

			RelationshipTermBase<?> type,

			boolean isProParte,

			boolean isPartial) {

		if (type == null){

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

		}else{

			String status = name.getNameType().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";

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

                status = "proParteMisapplied";

            }

			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);

		}

	}

	private void handleSynonyms(CsvTaxRecordRedlist record, Taxon taxon) {

		Set<Synonym> synonyms = taxon.getSynonyms();

		ArrayList<String> synonymLabels = new ArrayList<>();

		for (Synonym synonym :synonyms ){

			SynonymType type = synonym.getType();

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

				type = SynonymType.SYNONYM_OF();

			}

			INonViralName name = synonym.getName();

			synonymLabels.add(name.getTitleCache());

		}

		record.setSynonyms(synonymLabels);

	}

	private void handleDiscriptionData(CsvTaxRecordRedlist record, Taxon taxon) {

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

		ArrayList<String> distributions = new ArrayList<String>();

		for (TaxonDescription description : descriptions){

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

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

						Distribution distribution = CdmBase.deproxy(el, Distribution.class);

						NamedArea area = distribution.getArea();

						distributions.add(area.getTitleCache());

				}

			}

		}

		record.setCountryCode(distributions);

	}

	private void handleRedlistStatus(CsvTaxRecordRedlist record, Taxon taxon, List<List<String>> featureCells, List<Feature> features){

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

		for (TaxonDescription description : descriptions){

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

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

					CategoricalData categoricalData = CdmBase.deproxy(el, CategoricalData.class);

					for(State state:categoricalData.getStatesOnly()){

						Feature stateFeature = categoricalData.getFeature();

						// find matching feature and put data into according cell

						for(int i = 0; i < features.size(); i++) {

							if(features.get(i).equals(stateFeature)){

								List<String> cell = featureCells.get(i);

								cell.add(state.toString());

							}

						}

					}

				}else if(el.isInstanceOf(TextData.class)){

					TextData textData = CdmBase.deproxy(el, TextData.class);

					Feature textFeature = textData.getFeature();

					// find matching feature and put data into according cell

					for(int i = 0; i < features.size(); i++) {

						if(features.get(i).equals(textFeature)){

							List<String> cell = featureCells.get(i);

							String text = textData.getText(Language.GERMAN());

							text = text.replaceAll(System.getProperty("line.separator"), "");

							text = text.replaceAll("                            ", " ");

							cell.add(text);

						}

					}

				}

			}

		}

		record.setFeatures(featureCells);

	}

	private void handleRelatedRedlistStatus(CsvTaxRecordRedlist record, Taxon taxon, boolean relationFrom, List<List<String>> featureCells, List<Feature> features) {

		if (relationFrom) {

            handleRedlistStatus(record, taxon, featureCells, features);

        }

		Set<TaxonRelationship> taxRels;

		if(relationFrom){

			taxRels = taxon.getRelationsFromThisTaxon();

		}else{

			taxRels = taxon.getRelationsToThisTaxon();

		}

		for (TaxonRelationship taxRel:taxRels){

			if(taxRel.getType().equals(TaxonRelationshipType.CONGRUENT_TO())){

				Taxon relatedTaxon;

				if(relationFrom){

					relatedTaxon = taxRel.getToTaxon();

				}else{

					relatedTaxon = taxRel.getFromTaxon();

				}

				handleRedlistStatus(record, relatedTaxon, featureCells, features);

			}

		}

	}

	@Override

	protected boolean doCheck(CsvTaxExportStateRedlist state) {

		boolean result = true;

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

		return result;

	}

	@Override

	protected boolean isIgnore(CsvTaxExportStateRedlist state) {

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

	}

}