EDIT

/**

* Copyright (C) 2015 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.edaphobase;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.codehaus.plexus.util.StringUtils;

import org.springframework.stereotype.Component;

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

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

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

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @date 18.12.2015

 *

 */

@Component

public class EdaphobaseTaxonImport extends EdaphobaseImportBase {

    private static final long serialVersionUID = -9138378836474086070L;

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

    private static final String tableName = "tax_taxon";

    private static final String pluralString = "taxa";

    private static final Object AUTHOR_NAMESPACE = "tax_author_name";

    /**

     * @param tableName

     * @param pluralString

     */

    public EdaphobaseTaxonImport() {

        super(tableName, pluralString);

    }

    @Override

    protected String getIdQuery(EdaphobaseImportState state) {

        return "SELECT DISTINCT taxon_id FROM tax_taxon t "

                + " ORDER BY taxon_id";

    }

    @Override

    protected String getRecordQuery(EdaphobaseImportConfigurator config) {

        String result = " SELECT DISTINCT t.*, r.value_summary as rankStr, pr.value_summary as parentRankStr, ppr.value_summary as grandParentRankStr, pppr.value_summary as grandGrandParentRankStr, "

                    + " pt.name as parentName, ppt.name as grandParentName, pppt.name as grandGrandParentName "

                + " FROM tax_taxon t "

                    + " LEFT JOIN tax_taxon pt ON t.parent_taxon_fk = pt.taxon_id "

                    + " LEFT JOIN tax_taxon ppt ON pt.parent_taxon_fk = ppt.taxon_id "

                    + " LEFT JOIN tax_taxon pppt ON ppt.parent_taxon_fk = pppt.taxon_id "

                    + " LEFT OUTER JOIN selective_list.element r ON r.element_id = t.tax_rank_fk "

                    + " LEFT OUTER JOIN selective_list.element pr ON pr.element_id = pt.tax_rank_fk "

                    + " LEFT OUTER JOIN selective_list.element ppr ON ppr.element_id = ppt.tax_rank_fk "

                    + " LEFT OUTER JOIN selective_list.element pppr ON pppr.element_id = pppt.tax_rank_fk "

                + " WHERE t.taxon_id IN (@IDSET)";

        result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);

        return result;

    }

    @Override

    protected void doInvoke(EdaphobaseImportState state) {

        super.doInvoke(state);

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, EdaphobaseImportState state) {

        ResultSet rs = partitioner.getResultSet();

        Set<TaxonBase> taxaToSave = new HashSet<>();

        try {

            while (rs.next()){

                makeSingleTaxon(state, rs, taxaToSave);

            }

        } catch (SQLException | UndefinedTransformerMethodException e) {

             e.printStackTrace();

        }

        getTaxonService().saveOrUpdate(taxaToSave);

        return true;

    }

    /**

     * @param state

     * @param rs

     * @param taxaToSave

     * @throws SQLException

     * @throws UndefinedTransformerMethodException

     */

    private void makeSingleTaxon(EdaphobaseImportState state, ResultSet rs, Set<TaxonBase> taxaToSave)

            throws SQLException, UndefinedTransformerMethodException {

        Integer id = nullSafeInt(rs, "taxon_id");

        Integer year = nullSafeInt(rs, "tax_year");

        boolean isBrackets = rs.getBoolean("tax_brackets");

        String remark = rs.getString("remark");

        String nameStr = rs.getString("name");

        String authorName = rs.getString("tax_author_name");

        //parentTaxonFk

        //rankFk

        Integer nomRefId = nullSafeInt(rs, "tax_document");

        boolean isValid = rs.getBoolean("valid");

        boolean idDeleted = rs.getBoolean("deleted");

        String displayString = rs.getString("display_string");

        Integer version = nullSafeInt(rs, "versionfield");

        String pages = rs.getString("pages");

        String treeIndex = rs.getString("path_to_root");

//      Integer rankFk = nullSafeInt(rs, "tax_rank_fk");

        String nameAddition = rs.getString("name_addition");

        String officialRemark = rs.getString("official_remark");

        boolean isGroup = rs.getBoolean("taxonomic_group");

        String rankStr = rs.getString("rankStr");

        String parentRankStr = rs.getString("parentRankStr");

        String grandParentRankStr = rs.getString("grandParentRankStr");

        String grandGrandParentRankStr = rs.getString("grandGrandParentRankStr");

        String parentNameStr = rs.getString("parentName");

        String grandParentNameStr = rs.getString("grandParentName");

        String grandGrandParentNameStr = rs.getString("grandGrandParentName");

        TaxonBase<?> taxonBase;

        rankStr= extractEnglish(rankStr);

        parentRankStr= extractEnglish(parentRankStr);

        grandParentRankStr= extractEnglish(grandParentRankStr);

        grandGrandParentRankStr= extractEnglish(grandGrandParentRankStr);

        //Name etc.

        Rank rank = makeRank(state, rankStr);

        checkRankMarker(state, rank);

        IZoologicalName name = TaxonNameFactory.NewZoologicalInstance(rank);

        setNamePart(nameStr, rank, name);

        Rank parentRank = makeRank(state, parentRankStr);

        setNamePart(parentNameStr, parentRank, name);

        Rank parentParentRank = makeRank(state, grandParentRankStr);

        setNamePart(grandParentNameStr, parentParentRank, name);

        Rank grandParentParentRank = makeRank(state, grandGrandParentRankStr);

        setNamePart(grandGrandParentNameStr, grandParentParentRank, name);

        if (grandParentParentRank != null && grandParentParentRank.isLower(Rank.GENUS()) || isBlank(name.getGenusOrUninomial()) ){

            logger.warn("Grand-Grandparent rank is lower than genus for " +

                    name.getTitleCache() + " (edapho-id: " + id + "; cdm-id: " + name.getId() + ")");

        }

        //Authors

        if (StringUtils.isNotBlank(authorName)){

            TeamOrPersonBase<?> author = state.getRelatedObject(AUTHOR_NAMESPACE, authorName, TeamOrPersonBase.class);

            if (author == null){

                logger.warn("Author not found in state: "  + authorName);

            }else{

                if (isBrackets){

                    name.setBasionymAuthorship(author);

                    name.setOriginalPublicationYear(year);

                }else{

                    name.setCombinationAuthorship(author);

                    name.setPublicationYear(year);

                }

            }

        }

        //nomRef

        if (nomRefId != null){

            Reference nomRef = state.getRelatedObject(REFERENCE_NAMESPACE, String.valueOf(nomRefId), Reference.class);

            if (nomRef == null){

                logger.warn("Reference " + nomRefId + " could not be found");

            }

            name.setNomenclaturalReference(nomRef);

        }

        name.setNomenclaturalMicroReference(StringUtils.isBlank(pages)? null : pages);

        //taxon

        Reference secRef = state.getRelatedObject(REFERENCE_NAMESPACE, state.getConfig().getSecUuid().toString(), Reference.class);

        if (secRef == null){

            secRef = makeSecRef(state);

        }

        if (isValid){

            taxonBase = Taxon.NewInstance(name, secRef);

        }else{

            taxonBase = Synonym.NewInstance(name, secRef);

        }

        handleTaxonomicGroupMarker(state, taxonBase, isGroup);

        taxaToSave.add(taxonBase);

        //remarks

        doNotes(taxonBase, remark);

        //id

        ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, TAXON_NAMESPACE);

        ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, TAXON_NAMESPACE);

        handleExampleIdentifiers(taxonBase, id);

    }

    /**

     * @param rankStr

     * @return

     */

    private String extractEnglish(String rankStr) {

        if (rankStr == null){

            return null;

        }

        String[] splits = rankStr.split(", ");

        if (splits.length != 3){

            String message = "Wrong rank format: "+  rankStr;

            logger.error(message);

            return null;

        }

        return splits[1].trim();

    }

    static Map<Integer,UUID> idMap = new HashMap<>();

    static{

        idMap.put(86594, UUID.fromString("715c2370-45a4-450c-99f7-e196758979ca"));  //Aporrectodea caliginosa

        idMap.put(86593, UUID.fromString("230f1a69-5dcd-4829-a01c-17490a2fdf34"));  //Aporrectodea

        idMap.put(86684, UUID.fromString("0982dc0e-1a79-45a0-8abc-8166625b94b8"));  //Achaeta

        idMap.put(104328, UUID.fromString("15f0b5f8-44e4-4ae1-8b40-f36f0a049b27")); //Chamaedrilus

        idMap.put(97537, UUID.fromString("899c62e3-a116-4c5b-b22a-c76e761cc32e"));  //Araeolaimoides caecus

    }

    /**

     * @param taxonBase

     * @param id

     */

    private void handleExampleIdentifiers(TaxonBase<?> taxonBase, Integer id) {

        if (idMap.get(id) != null){

            taxonBase.setUuid(idMap.get(id));

        }

    }

    /**

     * @param state

     * @param rank

     * @throws UndefinedTransformerMethodException

     */

    private void checkRankMarker(EdaphobaseImportState state, Rank rank) throws UndefinedTransformerMethodException {

        if (rank != null){

            Set<Marker> markers = rank.getMarkers();

            if ( markers.size() == 0){  //we assume that no markers exist, at least not for markers of unused ranks

                UUID edaphoRankMarkerTypeUuid = state.getTransformer().getMarkerTypeUuid("EdaphoRankMarker");

                MarkerType marker = getMarkerType(state, edaphoRankMarkerTypeUuid, "Edaphobase rank", "Rank used in Edaphobase", "EdaRk" );

                Representation rep = Representation.NewInstance("Rang, verwendet in Edaphobase", "Edaphobase Rang", "EdaRg", Language.GERMAN());

                marker.addRepresentation(rep);

                rank.addMarker(Marker.NewInstance(marker, true));

                getTermService().saveOrUpdate(rank);

            }

        }else{

            logger.info("Rank is null and marker can not be set");

        }

    }

    /**

     * @param state

     * @param isGroup

     * @param taxonBase

     */

    private void handleTaxonomicGroupMarker(EdaphobaseImportState state, TaxonBase<?> taxonBase, boolean isGroup) {

        if (! isGroup){

            return;

        }else{

            try {

                MarkerType markerType = getMarkerType(state, state.getTransformer().getMarkerTypeUuid("TaxGrossgruppe"), "Tax. Gruppe", "Taxonomische Grossgruppe", "TGG", null, Language.GERMAN());

                if (taxonBase.isInstanceOf(Synonym.class)){

                    logger.warn("Syonym is marked as 'taxonomische Grossgruppe'");

                }

                taxonBase.addMarker(Marker.NewInstance(markerType, true));

            } catch (UndefinedTransformerMethodException e) {

            }

        }

    }

    /**

     * @param state

     * @return

     */

    private Reference makeSecRef(EdaphobaseImportState state) {

        Reference ref = ReferenceFactory.newDatabase();

        ref.setTitle(state.getConfig().getEdaphobaseSecundumTitle());

        ref.setUuid(state.getConfig().getSecUuid());

        state.addRelatedObject(REFERENCE_NAMESPACE, ref.getUuid().toString(), ref);

        getReferenceService().save(ref);

        return ref;

    }

    @Override

    public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,

            EdaphobaseImportState state) {

        Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();

        Map<String, TeamOrPersonBase<?>> authorMap = new HashMap<>();

        Set<String> authorSet = new HashSet<>();

        Set<String> referenceIdSet = new HashSet<>();

        try {

            while (rs.next()){

                String authorStr = rs.getString("tax_author_name");

                authorSet.add(authorStr);

                handleForeignKey(rs, referenceIdSet, "tax_document");

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        //Authors

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

        for (String authorStr : authorSet){

            UUID uuid = state.getAuthorUuid(authorStr);

            uuidSet.add(uuid);

        }

        List<TeamOrPersonBase<?>> authors = (List)getAgentService().find(uuidSet);

        Map<UUID, TeamOrPersonBase<?>> authorUuidMap = new HashMap<>();

        for (TeamOrPersonBase<?> author : authors){

            authorUuidMap.put(author.getUuid(), author);

        }

        for (String authorStr : authorSet){

            UUID uuid = state.getAuthorUuid(authorStr);

            TeamOrPersonBase<?> author = authorUuidMap.get(uuid);

            authorMap.put(authorStr, author);

        }

        result.put(AUTHOR_NAMESPACE, authorMap);

        //reference map

        String nameSpace = REFERENCE_NAMESPACE;

        Class<?> cdmClass = Reference.class;

        Set<String> idSet = referenceIdSet;

        Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

        result.put(nameSpace, referenceMap);

        //secundum

        UUID secUuid = state.getConfig().getSecUuid();

        Reference secRef = getReferenceService().find(secUuid);

        referenceMap.put(secUuid.toString(), secRef);

        return result;

    }

    private void setNamePart(String nameStr, Rank rank, IZoologicalName name) {

        if (rank != null){

            if (rank.isSupraGeneric() || rank.isGenus()){

                if (isBlank(name.getGenusOrUninomial())){

                    name.setGenusOrUninomial(nameStr);

                }

            }else if (rank.isInfraGenericButNotSpeciesGroup()){

                if (isBlank(name.getInfraGenericEpithet())){

                    name.setInfraGenericEpithet(nameStr);

                }

            }else if (rank.isSpeciesAggregate() || rank.isSpecies()){

                if (isBlank(name.getSpecificEpithet())){

                    name.setSpecificEpithet(nameStr);

                }

            }else if (rank.isInfraSpecific()){

                if (isBlank(name.getInfraSpecificEpithet())){

                    name.setInfraSpecificEpithet(nameStr);

                }

            }

        }

    }

    private Rank makeRank(EdaphobaseImportState state, String rankStr) {

        Rank rank = null;

        try {

            rank = state.getTransformer().getRankByKey(rankStr);

            if (rank == null && rankStr != null){

                if (rankStr.equals("Cohort")){

                    //position not really clear #7285

                    Rank lowerRank = Rank.SUPERORDER();

                    rank = this.getRank(state, Rank.uuidCohort, "Cohort", "Cohort", null,

                            (OrderedTermVocabulary<Rank>)Rank.GENUS().getVocabulary(),

                            lowerRank, RankClass.Suprageneric);

                }else if (rankStr.equals("Hyporder")){

                    rank = this.getRank(state, Rank.uuidHyporder, "Hyporder", "Hyporder", null,

                            (OrderedTermVocabulary<Rank>)Rank.GENUS().getVocabulary(),

                            Rank.SUBORDER(), RankClass.Suprageneric);

                }

            }

        } catch (UndefinedTransformerMethodException e) {

            e.printStackTrace();

        }

        return rank;

    }

    @Override

    protected boolean doCheck(EdaphobaseImportState state) {

        return true;

    }

    @Override

    protected boolean isIgnore(EdaphobaseImportState state) {

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

    }

}