EDIT

package eu.etaxonomy.cdm.io.csv.caryophyllales.out;

import java.io.ByteArrayOutputStream;

import java.io.FileOutputStream;

import java.io.OutputStream;

import java.io.OutputStreamWriter;

import java.io.PrintWriter;

import java.util.ArrayList;

import java.util.Collections;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Set;

import java.util.TreeMap;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.ext.geo.CondensedDistributionRecipe;

import eu.etaxonomy.cdm.ext.geo.EditGeoService;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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

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

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.TextData;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.persistence.query.MatchMode;

@Component

public class CsvNameExport extends CsvNameExportBase {

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

    public CsvNameExport() {

        super();

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

    }

    @Override

    protected void doInvoke(CsvNameExportState state) {

        CsvNameExportConfigurator config = state.getConfig();

        PrintWriter writer = null;

        try {

            switch(config.getTarget()) {

            case FILE :

                OutputStream os = new FileOutputStream(config.getDestination());

                os.write(239);

                os.write(187);

                os.write(191);

                writer = new PrintWriter(new OutputStreamWriter(os, "UTF-8"));

                break;

            case EXPORT_DATA :

                exportStream = new ByteArrayOutputStream();

                writer = new PrintWriter(exportStream);

                break;

            default:

                break;

            }

            List<HashMap<String, String>> result;

            if (config.isNamesOnly()){

                txStatus = startTransaction();

                result = getNameService().getNameRecords();

            } else {

                result = getRecordsForPrintPub(state);

            }

            NameRecord nameRecord;

            int count = 0;

            boolean isFirst = true;

            for (HashMap<String,String> record:result){

                if (count > 0){

                    isFirst = false;

                }

                count++;

                nameRecord = new NameRecord(record, isFirst);

                nameRecord.print(writer, config);

            }

            writer.flush();

            writer.close();

        } catch (Exception e) {

            // TODO Auto-generated catch block

            e.printStackTrace();

        }

        if (txStatus != null  ){

            commitTransaction(txStatus);

        }

        return;

    }

    @Override

    protected boolean doCheck(CsvNameExportState state) {

        boolean result = true;

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

        return result;

    }

    @Override

    protected boolean isIgnore(CsvNameExportState state) {

        return false;

    }

    public List<HashMap<String,String>> getRecordsForPrintPub(CsvNameExportState state){

        List<String> propertyPaths = new ArrayList<String>();

        propertyPaths.add("childNodes");

        txStatus = startTransaction();

        Classification classification = getClassificationService().load(state.getConfig().getClassificationUUID());

        TaxonNode rootNode = classification.getRootNode();

        rootNode = getTaxonNodeService().load(rootNode.getUuid(), propertyPaths);

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

        for (TaxonNode child: rootNode.getChildNodes()){

            child = HibernateProxyHelper.deproxy(child, TaxonNode.class);

            childrenUuids.add(child.getUuid());

        }

        Set<UUID> parentsNodesUUID = new HashSet<UUID>(childrenUuids);

        childrenUuids.clear();

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

        TaxonNameBase name;

        findChildren(state, childrenUuids, parentsNodesUUID);

        List<HashMap<String,String>> nameRecords = new ArrayList<HashMap<String,String>>();

        HashMap<String,String> nameRecord = new HashMap<String,String>();

        childrenNodes = getTaxonNodeService().find(childrenUuids);

        for(TaxonNode genusNode : childrenNodes)   {

            nameRecords.add(createNewRecord(genusNode, state));

            refreshTransaction();

        }

        return nameRecords;

    }

    /**

     * @param state

     * @param childrenUuids

     * @param parentsNodesUUID

     * @param familyNode

     */

    private void findChildren(CsvNameExportState state, Set<UUID> childrenUuids, Set<UUID> parentsNodesUUID) {

        TaxonNameBase name;

        List<TaxonNode> familyNodes = getTaxonNodeService().find(parentsNodesUUID);

        parentsNodesUUID =new HashSet<UUID>();

        for (TaxonNode familyNode: familyNodes){

            familyNode = HibernateProxyHelper.deproxy(familyNode, TaxonNode.class);

            for (TaxonNode child: familyNode.getChildNodes()){

                child = HibernateProxyHelper.deproxy(child, TaxonNode.class);

                name = HibernateProxyHelper.deproxy(child.getTaxon().getName(), TaxonNameBase.class);

                if (child.getTaxon().getName().getRank().isLower(Rank.GENUS())) {

                    childrenUuids.add(child.getUuid());

                    if (child.hasChildNodes()){

                        parentsNodesUUID.add(child.getUuid());

                    }

                }else{

                    parentsNodesUUID.add(child.getUuid());

                }

            }

            //refreshTransaction();

            if (!parentsNodesUUID.isEmpty()){

                findChildren(state, childrenUuids, parentsNodesUUID);

            }

        }

    }

    private String createSynonymNameString(BotanicalName synonymName) {

        String synonymString = null;

        synonymString = synonymName.generateFullTitle();

        if (synonymName.getNameCache() != null){

        synonymString = synonymString.replaceAll(synonymName.getNameCache(), "<i>"+ synonymName.getNameCache() + "</i>");

        } else{

            if (synonymName.getGenusOrUninomial() != null){

                synonymString = synonymString.replaceAll(synonymName.getGenusOrUninomial(), "<i>"+ synonymName.getGenusOrUninomial() + "</i>");

            }

            if (synonymName.getInfraGenericEpithet() != null){

                synonymString = synonymString.replaceAll(synonymName.getInfraGenericEpithet(),  "<i>"+ synonymName.getInfraGenericEpithet() + "</i>");

            }

            if (synonymName.getSpecificEpithet() != null){

                synonymString = synonymString.replaceAll(synonymName.getSpecificEpithet(),  "<i>"+ synonymName.getSpecificEpithet() + "</i>");

            }

            if (synonymName.getInfraSpecificEpithet() != null){

                synonymString = synonymString.replaceAll(synonymName.getInfraSpecificEpithet(),  "<i>"+ synonymName.getInfraSpecificEpithet() + "</i>");

            }

        }

        return synonymString;

    }

    private List<TaxonNode> getGenusNodes (UUID classificationUUID){

        Classification classification = getClassificationService().load(classificationUUID);

        TaxonNode rootNode = classification.getRootNode();

        rootNode = getTaxonNodeService().load(rootNode.getUuid());

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

        for (TaxonNode child: rootNode.getChildNodes()){

            child = HibernateProxyHelper.deproxy(child, TaxonNode.class);

            childrenUuids.add(child.getUuid());

        }

        List<TaxonNode> familyNodes = getTaxonNodeService().find(childrenUuids);

        childrenUuids.clear();

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

        for (TaxonNode familyNode: familyNodes){

            for (TaxonNode child: familyNode.getChildNodes()){

                child = HibernateProxyHelper.deproxy(child, TaxonNode.class);

                childrenUuids.add(child.getUuid());

            }

            genusNodes = getTaxonNodeService().find(childrenUuids);

        }

        return genusNodes;

    }

    private TaxonNode getHigherNode(TaxonNode node, Rank rank){

        Rank nodeRank = node.getTaxon().getName().getRank();

        if (nodeRank.isKindOf(rank)){

            return node;

        }else if (nodeRank.isHigher(rank)){

            return null;

        } else {

            return node.getAncestorOfRank(rank);

        }

    }

    private void extractDescriptions(HashMap<String, String> nameRecord, Taxon taxon, Feature feature, String columnName){

        StringBuffer descriptionsString = new StringBuffer();

        TextData textElement;

        List<Distribution> distributions = new ArrayList<Distribution>();

        for (DescriptionBase<?> descriptionBase: taxon.getDescriptions()){

            Set<DescriptionElementBase> elements = descriptionBase.getElements();

            for (DescriptionElementBase element: elements){

                if (element.getFeature().equals(feature)){

                    if (element instanceof TextData){

                        textElement = HibernateProxyHelper.deproxy(element, TextData.class);

                        descriptionsString.append(textElement.getText(Language.ENGLISH()));

                    }else if (element instanceof Distribution){

                        Distribution distribution = HibernateProxyHelper.deproxy(element, Distribution.class);

                        distributions.add(distribution);

                    }

                }

            }

        }

     //   Collections.sort(distributions, new DistributionNodeByAreaLabelComparator());

        EditGeoService.getCondensedDistribution(distributions, true,

                Set<MarkerType> hideMarkedAreas,

                MarkerType fallbackAreaMarkerType,

                CondensedDistributionRecipe recipe,

                List<Language> langs);

        for (Distribution distribution:distributions){

            if (descriptionsString.length()> 0 ){

                descriptionsString.append(", ");

            }

            descriptionsString.append(distribution.getArea().getIdInVocabulary());

        }

        nameRecord.put(columnName, descriptionsString.toString());

    }

    private Feature getNotesFeature(CsvNameExportState state){

        if (state.getNotesFeature() != null){

            return state.getNotesFeature();

        } else{

            Pager<DefinedTermBase> notesFeature = getTermService().findByTitle(Feature.class, "Notes" ,MatchMode.EXACT, null, null, null, null, null);

            if (notesFeature.getRecords().size() == 0){

                return null;

            }else{

                DefinedTermBase feature=  notesFeature.getRecords().iterator().next();

                if (feature instanceof Feature){

                    state.setNotesFeature((Feature)feature);

                    return (Feature) feature;

                } else{

                    return null;

                }

            }

        }

    }

    private HashMap<String, String> createNewRecord(TaxonNode childNode, CsvNameExportState state){

        HashMap<String, String> nameRecord = new HashMap<String,String>();

        nameRecord.put("classification", childNode.getClassification().getTitleCache());

        TaxonNode familyNode = getHigherNode(childNode, Rank.FAMILY());

        familyNode = HibernateProxyHelper.deproxy(familyNode, TaxonNode.class);

        familyNode.getTaxon().setProtectedTitleCache(true);

        nameRecord.put("familyTaxon", familyNode.getTaxon().getTitleCache());

        Taxon taxon = (Taxon)getTaxonService().load(familyNode.getTaxon().getUuid());

        taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);

        //if publish flag is set

        //  if (taxon.isPublish()){

        BotanicalName name = HibernateProxyHelper.deproxy(taxon.getName(), BotanicalName.class);

        nameRecord.put("familyName", name.getNameCache());

        extractDescriptions(nameRecord, taxon, Feature.INTRODUCTION(), "descriptionsFam");

        TaxonNode genusNode = getHigherNode(childNode, Rank.GENUS());

        if (genusNode!= null){

            genusNode = HibernateProxyHelper.deproxy(genusNode, TaxonNode.class);

            genusNode.getTaxon().setProtectedTitleCache(true);

            nameRecord.put("genusTaxon", genusNode.getTaxon().getTitleCache());

            taxon = (Taxon)getTaxonService().load(genusNode.getTaxon().getUuid());

            taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);

            //if publish flag is set

            //  if (taxon.isPublish()){

            name = HibernateProxyHelper.deproxy(taxon.getName(), BotanicalName.class);

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

                nameRecord.put("genusName", name.getNameCache());

            }else{

                nameRecord.put("genusName", name.getGenusOrUninomial());

            }

            extractDescriptions(nameRecord, taxon, Feature.INTRODUCTION(), "descriptionsGen");

        }

        taxon = (Taxon) getTaxonService().load(childNode.getTaxon().getUuid());

        taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);

        //  if (taxon.isPublish()){

        nameRecord.put("childTaxon", taxon.getTitleCache());

        if (taxon.getSec()!= null){

            nameRecord.put("secRef", taxon.getSec().getTitleCache());

        }else{

            nameRecord.put("secRef", null);

        }

        name = HibernateProxyHelper.deproxy(getNameService().load(taxon.getName().getUuid()), BotanicalName.class);

        nameRecord.put("childName",name.getTitleCache());

        nameRecord.put("nameId", String.valueOf(name.getId()));

        nameRecord.put("nameCache", name.getNameCache());

        nameRecord.put("titleName", name.getTitleCache());

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

            nameRecord.put("NomRefTitleCache", name.getNomenclaturalReference().getTitleCache());

        } else{

            nameRecord.put("NomRefTitleCache",null);

        }

        nameRecord.put("fullName", name.getNameCache());

        nameRecord.put("fullTitleCache",  name.getFullTitleCache());

        Set<TypeDesignationBase> typeDesSet =  name.getTypeDesignations();

        Iterator<TypeDesignationBase> it = typeDesSet.iterator();

        String typeNameString = NOT_DESIGNATED;

        String statusString = null;

        if (it.hasNext()){

            NameTypeDesignation typeDes = HibernateProxyHelper.deproxy(it.next(), NameTypeDesignation.class);

            BotanicalName typeName =  HibernateProxyHelper.deproxy(typeDes.getTypeName(), BotanicalName.class);

            if (typeName != null){

                typeNameString = "<i>" + typeName.getNameCache() +"</i> "  + typeName.getAuthorshipCache();

                if (typeDes.getTypeStatus() != null){

                    NameTypeDesignationStatus status = HibernateProxyHelper.deproxy(typeDes.getTypeStatus(), NameTypeDesignationStatus.class);

                    statusString = status.getTitleCache();

                }

            }

        }

        nameRecord.put("typeName", typeNameString);

        StringBuffer homotypicalSynonyms = new StringBuffer();

        TreeMap<HomotypicalGroup,List<Synonym>> heterotypicSynonymsList = new TreeMap<HomotypicalGroup,List<Synonym>>(new HomotypicalGroupComparator());

        List<Synonym> homotypicSynonymsList = new ArrayList<Synonym>();

        StringBuffer heterotypicalSynonyms = new StringBuffer();

        List<Synonym> homotypicSynonyms;

        HomotypicalGroup group;

        BotanicalName synonymName;

        String doubtfulTitleCache;

        for (SynonymRelationship synRel: taxon.getSynonymRelations()){

            synonymName = HibernateProxyHelper.deproxy(synRel.getSynonym().getName(), BotanicalName.class);

            if (synRel.getType().equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())){

                group = HibernateProxyHelper.deproxy(synonymName.getHomotypicalGroup(), HomotypicalGroup.class);

                synonymName.generateFullTitle();

                if (synRel.getSynonym().isDoubtful()){

                    doubtfulTitleCache = "?" + synonymName.getFullTitleCache();

                    synonymName.setFullTitleCache(doubtfulTitleCache, true);

                }

                if (heterotypicSynonymsList.containsKey(group)){

                    heterotypicSynonymsList.get(group).add(synRel.getSynonym());

                }else{

                    homotypicSynonyms = new ArrayList<Synonym>();

                    homotypicSynonyms.add(synRel.getSynonym());

                    heterotypicSynonymsList.put(group, homotypicSynonyms);

                    homotypicSynonyms= null;

                }

            } else{

                synonymName.generateFullTitle();

                homotypicSynonymsList.add(synRel.getSynonym());

            }

        }

        String synonymString;

        boolean first = true;

        for (List<Synonym> list: heterotypicSynonymsList.values()){

            Collections.sort(list, new HomotypicGroupTaxonComparator(null));

            first = true;

            for (TaxonBase<?> synonym : list){

                if (first){

                    heterotypicalSynonyms.append(" <heterotypic> ");

                }else{

                    heterotypicalSynonyms.append(" <homonym> ");

                }

                first = false;

                synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);

                synonymString = createSynonymNameString(synonymName);

                heterotypicalSynonyms.append(synonymString);

            }

        }

        first = true;

        Collections.sort(homotypicSynonymsList, new TaxonComparator());

        for (TaxonBase<?> synonym : homotypicSynonymsList){

            if (!first){

                homotypicalSynonyms.append(" <homonym> ");

            }

            first = false;

            synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);

            synonymString = createSynonymNameString(synonymName);

            homotypicalSynonyms.append(synonymString);

        }

        nameRecord.put("synonyms_homotypic", homotypicalSynonyms.toString());

        nameRecord.put("synonyms_heterotypic", heterotypicalSynonyms.toString());

        nameRecord.put("status", statusString);

        Set<NameRelationship> nameRelations = name.getNameRelations();

        String relatedName = null;

        String nameRelType = null;

        if (nameRelations.size()>0){

            NameRelationship nameRel = nameRelations.iterator().next();

            BotanicalName fromName = HibernateProxyHelper.deproxy(nameRel.getFromName(), BotanicalName.class);

            if (fromName.equals(taxon.getName())){

                relatedName = nameRel.getToName().getTitleCache();

            }else{

                relatedName = nameRel.getFromName().getTitleCache();

            }

            nameRel = HibernateProxyHelper.deproxy(nameRel, NameRelationship.class);

            nameRelType = nameRel.getType().getTitleCache();

        }

        nameRecord.put("relatedName", relatedName);

        nameRecord.put("nameRelType", nameRelType);

        extractDescriptions(nameRecord, taxon, Feature.DISTRIBUTION(), "description");

        return nameRecord;

    }

}