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.UnsupportedEncodingException;

import java.util.ArrayList;

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.beans.factory.annotation.Autowired;

import eu.etaxonomy.cdm.api.service.IClassificationService;

import eu.etaxonomy.cdm.api.service.ITaxonNodeService;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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

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

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

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.persistence.dto.TaxonNodeDto;

/**

 * @author a.mueller

 * @date 18.04.2011

 *

 */

public abstract class DwcaDataExportBase extends DwcaExportBase{

    private static final long serialVersionUID = -5467295551060073610L;

    @SuppressWarnings("unused")

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

    @Autowired

    private IClassificationService classificationService;

    @Autowired

    private ITaxonNodeService taxonNodeService;

    abstract protected void handleTaxonNode(DwcaTaxExportState state, TaxonNode node)throws IOException, FileNotFoundException, UnsupportedEncodingException;

    /**

     * {@inheritDoc}

     */

    @Override

    public int countSteps(DwcaTaxExportState state) {

        //FIXME count without initialization

        List<TaxonNode> allNodes =  allNodes(state);

        return allNodes.size();

    }

    /**

     * Returns the list of {@link TaxonNode taxon nodes} that correspond to the

     * given filter criteria (e.g. subtreeUUids). If no filter is given

     * all taxon nodes of all classifications are returned. If the list has been

     * computed before it is taken from the state cache. Nodes that do not have

     * a taxon attached are not returned. Instead a warning is given that the node is

     * ommitted (empty taxon nodes should not but do exist in CDM databases).

     * <BR>

     * Preliminary implementation. Better implement API method for this.

     */

    //TODO unify with similar methods for other exports

    protected List<TaxonNode> allNodes(DwcaTaxExportState state) {

        Set<UUID> subtreeUuidSet = state.getConfig().getSubtreeUuids();

        if (subtreeUuidSet == null){

            subtreeUuidSet = new HashSet<>();

        }

        //handle empty list as no filter defined

        if (subtreeUuidSet.isEmpty()){

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

            for (Classification classification : classificationList){

                subtreeUuidSet.add(classification.getRootNode().getUuid());

            }

        }

        //TODO memory critical to store ALL node

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

            makeAllNodes(state, subtreeUuidSet);

        }

        List<TaxonNode> allNodes = state.getAllNodes();

        return allNodes;

    }

    private void makeAllNodes(DwcaTaxExportState state, Set<UUID> subtreeSet) {

        try {

            boolean doSynonyms = false;

            boolean recursive = true;

            Set<UUID> uuidSet = new HashSet<>();

            for (UUID subtreeUuid : subtreeSet){

                UUID tnUuuid = taxonNodeUuid(subtreeUuid);

                uuidSet.add(tnUuuid);

                List<TaxonNodeDto> records = getTaxonNodeService().pageChildNodesDTOs(tnUuuid,

                        recursive, doSynonyms, null, null, null).getRecords();

                for (TaxonNodeDto dto : records){

                    uuidSet.add(dto.getUuid());

                }

            }

            List<TaxonNode> allNodes =  getTaxonNodeService().find(uuidSet);

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

            for (TaxonNode node : allNodes){

                if(node.getParent()== null){  //root (or invalid) node

                    continue;

                }

                node = CdmBase.deproxy(node);

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

                if (taxon == null){

                    String message = "There is a taxon node without taxon. id=" + node.getId();

                    state.getResult().addWarning(message);

                    continue;

                }

                result.add(node);

            }

            state.setAllNodes(result);

        } catch (Exception e) {

            String message = "Unexpected exception when trying to compute all taxon nodes";

            state.getResult().addException(e, message);

        }

    }

    /**

     * @param subtreeUuid

     * @return

     */

    private UUID taxonNodeUuid(UUID subtreeUuid) {

        TaxonNode node = taxonNodeService.find(subtreeUuid);

        if (node == null){

            Classification classification = classificationService.find(subtreeUuid);

            if (classification != null){

                node = classification.getRootNode();

            }else{

                throw new IllegalArgumentException("Subtree identifier does not exist: " + subtreeUuid);

            }

        }

        return node.getUuid();

    }

    /**

     * Creates the locationId, locality, countryCode triple

     * @param state

     * @param record

     * @param area

     */

    protected void handleArea(DwcaTaxExportState state, IDwcaAreaRecord record, NamedArea area, TaxonBase<?> taxon, boolean required) {

        if (area != null){

            record.setLocationId(area);

            record.setLocality(area.getLabel());

            if (area.isInstanceOf(Country.class)){

                Country country = CdmBase.deproxy(area, Country.class);

                record.setCountryCode(country.getIso3166_A2());

            }

        }else{

            if (required){

                String message = "Description requires area but area does not exist for taxon " + getTaxonLogString(taxon);

                state.getResult().addWarning(message);

            }

        }

    }

    protected String getTaxonLogString(TaxonBase<?> taxon) {

        return taxon.getTitleCache() + "(" + taxon.getId() + ")";

    }

    protected String getSources(ISourceable<?> sourceable, DwcaTaxExportConfigurator config) {

        String result = "";

        for (IOriginalSource<?> source: sourceable.getSources()){

            if (StringUtils.isBlank(source.getIdInSource())){//idInSource indicates that this source is only data provenance, may be changed in future

                if (source.getCitation() != null){

                    String ref = source.getCitation().getTitleCache();

                    result = CdmUtils.concat(config.getSetSeparator(), result, ref);

                }

            }

        }

        return result;

    }

    protected String getSources3(ISourceable<?> sourceable, DwcaTaxExportConfigurator config) {

        String result = "";

        for (IOriginalSource<?> source: sourceable.getSources()){

                if (source.getCitation() != null){

                    String ref = source.getCitation().getTitleCache();

                    result = CdmUtils.concat(config.getSetSeparator(), result, ref);

                }

        }

        return result;

    }

    protected String getSources2(Set<DescriptionElementSource> set, DwcaTaxExportConfigurator config) {

        String result = "";

        for(DescriptionElementSource source: set){

            if (StringUtils.isBlank(source.getIdInSource())){//idInSource indicates that this source is only data provenance, may be changed in future

                if (source.getCitation() != null){

                    String ref = source.getCitation().getTitleCache();

                    result = CdmUtils.concat(config.getSetSeparator(), result, ref);

                }

            }

        }

        return result;

    }

}