EDIT

/**

* Copyright (C) 2007 EDIT

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.pesi.erms;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.springframework.stereotype.Component;

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

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

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

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

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

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

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

/**

 * @author a.mueller

@Component

        extends ErmsImportBase<TaxonBase<?>>

        implements IMappingImport<TaxonBase<?>, ErmsImportState>{

    private static final long serialVersionUID = -7111568277264140051L;

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

	private static final String dbTableName = "tu";

	public ErmsTaxonImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	protected String getIdQuery() {

	}

    protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {

            //  ExtensionType fuzzyNameExtType = getExtensionType(ErmsTransformer.uuidExtFuzzyName, "fuzzy name", "fuzzy name", "fuzzy name");

            //  mapping.addMapper(DbImportExtensionMapper.NewInstance("tu_fuzzyname", fuzzyNameExtType));

            mapping.addMapper(DbImportExtensionMapper.NewInstance("cache_citation", cacheCitationExtType));

            //flags

			mapping.addMapper(DbImportMarkerMapper.NewInstance("tu_brackish", ErmsTransformer.uuidMarkerBrackish, "brackish", "brackish", "brackish", null));

			mapping.addMapper(DbImportMarkerMapper.NewInstance("tu_fresh", ErmsTransformer.uuidMarkerFreshwater, "freshwater", "fresh", "fresh", null));

			mapping.addMapper(DbImportMarkerMapper.NewInstance("tu_terrestrial", ErmsTransformer.uuidMarkerTerrestrial, "terrestrial", "terrestrial", "terrestrial", null));

			//last action, species expert

			ExtensionType speciesExpertNameExtType = getExtensionType(PesiTransformer.uuidExtSpeciesExpertName, "species expert name", "species expert name", "species expert name");

            mapping.addMapper(DbImportExtensionMapper.NewInstance("ExpertName", speciesExpertNameExtType)); //according to sql script ExpertName maps to SpeciesExpertName in ERMS

            AnnotationType lastActionDateType = getAnnotationType(DbLastActionMapper.uuidAnnotationTypeLastActionDate, "Last action date", "Last action date", null);

            AnnotationType lastActionType = getAnnotationType(DbLastActionMapper.uuidAnnotationTypeLastAction, "Last action", "Last action", null);

            MarkerType hasNoLastActionMarkerType = getMarkerType(DbLastActionMapper.uuidMarkerTypeHasNoLastAction, "has no last action", "No last action information available", "no last action");

            mapping.addMapper(DbImportAnnotationMapper.NewInstance("lastAction", lastActionType, hasNoLastActionMarkerType));

            mapping.addMapper(DbImportMethodMapper.NewDefaultInstance(this, "testTitleCache", ErmsImportState.class));

			mapping.addMapper(DbIgnoreMapper.NewInstance("tu_fossil", "tu_fossil implemented as foreign key"));

		return mapping;

	}

	@Override

	protected String getRecordQuery(ErmsImportConfigurator config) {

		            " status.status_id as status_id, status.status_name, fossil.fossil_name, qualitystatus.qualitystatus_name," +

		            " s.sessiondate lastActionDate, a.action_name lastAction, s.ExpertName ";

				" LEFT OUTER JOIN   tu AS parent2  ON parent2.id = parent1.tu_parent " +

				" LEFT OUTER JOIN tu AS parent3 ON parent2.tu_parent = parent3.id " +

                " LEFT OUTER JOIN status ON tu.tu_status = status.status_id " +

                " LEFT OUTER JOIN [sessions] s ON s.id = ts.session_id " +

                " LEFT OUTER JOIN actions a ON a.id = ts.action_id ";

		String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy;

	}

		return;

    @Override

    protected boolean ignoreRecord(ResultSet rs) throws SQLException {

        Integer id = rs.getInt("id");

        boolean result = id.equals(lastTaxonId);

        lastTaxonId = id;

        return result;

    }

		String vernacularsTable = "vernaculars";

		String distributionTable = "dr";

		        + " UNION  SELECT DISTINCT tu_acctaxon FROM tu "  //fk to accepted taxon (either the accepted taxon or the taxon itself, if accepted)

		        + " UNION  SELECT syn.id FROM tu syn INNER JOIN tu acc ON syn.tu_acctaxon = acc.id WHERE syn.id = acc.tu_parent AND acc.id <> syn.id "  //see also ErmsTaxonRelationImport.isAccepted, there are some autonyms being the accepted taxon of there own parents

                + " UNION  SELECT DISTINCT %s FROM %s " //vernaculars

		        + " UNION  SELECT DISTINCT %s FROM %s ";  //notes

				tuFk, notesTable);

		try {

			while (rs.next()){

				Integer id;

			}

			return result;

		} catch (SQLException e) {

			e.printStackTrace();

			throw new RuntimeException(e);

		}

	}

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, ErmsImportState state) {

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

	}

		fillTaxonName(taxonName, rs, state, meId);

		//add original source for taxon name (taxon original source is added in mapper)

		Reference citation = state.getTransactionalSourceReference();

		addOriginalSource(rs, taxonName, "id", NAME_NAMESPACE, citation);

		TaxonBase<?> result;

		//handle accepted<-> synonym, we create more accepted taxa as we need them within the tree or to attache factual data

		if (state.getAcceptedTaxaKeys().contains(meId)){

			Taxon taxon = Taxon.NewInstance(taxonName, citation);

			if (statusId != 1){

				logger.info("Taxon created as taxon but has status <> 1 ("+statusId+"): " + meId);

				handleNotAcceptedTaxon(taxon, statusId, state, rs);

			}

			result = taxon;

		}else{

			result = Synonym.NewInstance(taxonName, citation);

		}

		handleNameStatus(result.getName(), rs, state);

		return result;

	}

    private void handleNameStatus(TaxonName name, ResultSet rs, ErmsImportState state) throws SQLException {

        NomenclaturalStatusType nomStatus = null;

        int tuStatus = rs.getInt("tu_status");

        if (tuStatus == 8){

            //species inquirenda

            nomStatus = getNomenclaturalStatusType(state, ErmsTransformer.uuidNomStatusSpeciesInquirenda, "species inquirenda", "species inquirenda", null, Language.LATIN(), null);

            //temporary name

            nomStatus = getNomenclaturalStatusType(state, PesiTransformer.uuidNomStatusTemporaryName, "temporary name", "temporary name", null, Language.ENGLISH(), null);

            //nomen dubium

            nomStatus = NomenclaturalStatusType.DOUBTFUL();

        }else if (tuStatus == 5){

            //"alternate representation"

            nomStatus = getNomenclaturalStatusType(state, ErmsTransformer.uuidNomStatusAlternateRepresentation, "alternate representation", "alternate representation", null, Language.ENGLISH(), null);

        }else if (tuStatus == 3){

            //nomen nudum

            nomStatus = NomenclaturalStatusType.NUDUM();

        if (nomStatus == null){

            try {

                nomStatus = state.getTransformer().getNomenclaturalStatusByKey(unacceptReason);

            } catch (UndefinedTransformerMethodException e) {logger.warn("Unhandled method");

            }

        }

        if (nomStatus != null){

            name.addStatus(nomStatus, null, null);

        }

    }

		Integer parent1Rank = rs.getInt("parent1rank");

		Integer parent2Rank = rs.getInt("parent2rank");

	    String parent4Name = rs.getString("parent4name");

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

			taxonName.setGenusOrUninomial(tuName);

		}else if (taxonName.isInfraGeneric()){

			taxonName.setInfraGenericEpithet(tuName);

			taxonName.setGenusOrUninomial(parent1Name);

		}else if (taxonName.isSpecies()){

			taxonName.setSpecificEpithet(tuName);

			getGenusAndInfraGenus(parent1Name, parent2Name, parent1Rank, taxonName);

		}else if (taxonName.isInfraSpecific()){

			if (parent1Rank < 220){

			taxonName.setInfraSpecificEpithet(tuName);

			    taxonName.setSpecificEpithet(parent2Name);

			    getGenusAndInfraGenus(parent3Name, parent4Name, parent3Rank, taxonName);

			}else{

			    //default

			    taxonName.setSpecificEpithet(parent1Name);

			    getGenusAndInfraGenus(parent2Name, parent3Name, parent2Rank, taxonName);

			}

			if ("Biota".equalsIgnoreCase(tuName)){

				Rank rank = Rank.DOMAIN();  //should be Superdomain

				taxonName.setRank(rank);

				taxonName.setGenusOrUninomial(tuName);

			}else{

				String warning = "TaxonName has no rank. Use namecache.";

				logger.warn(warning);

				taxonName.setNameCache(tuName);

			}

		}

		if (containsBrackets(displayName)){

			taxonName.setNameCache(displayName);

            logger.warn("Computed name cache differs at "+pos+".\n Computed   : " + taxonName.getNameCache()+"\n DisplayName: " +displayName);

        }

    }

    private static TaxonBase<?> testTitleCache(ResultSet rs, ErmsImportState state) throws SQLException{

        TaxonBase<?> taxon = (TaxonBase<?>)state.getRelatedObject(DbImportStateBase.CURRENT_OBJECT_NAMESPACE, DbImportStateBase.CURRENT_OBJECT_ID);

        TaxonName taxonName = taxon.getName();

         String displayName = rs.getString("tu_displayname");

         String expectedTitleCache = getExpectedTitleCache(rs);

         //TODO check titleCache, but beware of autonyms

         if (!titleCache.equals(expectedTitleCache)){

             logger.warn("Computed title cache differs at "+pos+".\n Computed             : " + titleCache + "\n DisplayName+Authority: " + expectedTitleCache);

         }

         return taxon;

     }

     //see also PesiErmsValidation.srcFullName()

     private static String getExpectedTitleCache(ResultSet srcRs) throws SQLException {

        String result;

        String epi = srcRs.getString("tu_name");

        epi = " a" + epi;

        String display = srcRs.getString("tu_displayname");

        String sp = srcRs.getString("tu_sp");

        if (display.indexOf(epi) != display.lastIndexOf(epi) && !sp.startsWith("#2#")){ //homonym, animal

            result = srcRs.getString("tu_displayname").replaceFirst(epi+" ", CdmUtils.concat(" ", " "+epi, srcRs.getString("tu_authority")))+" ";

        }else{

            result = CdmUtils.concat(" ", srcRs.getString("tu_displayname"), srcRs.getString("tu_authority"));

        }

		ExtensionType notAccExtensionType = getExtensionType(state, ErmsTransformer.uuidErmsTaxonStatus, "ERMS taxon status", "ERMS taxon status", "status", null);

		String statusName = rs.getString("status_name");

			taxon.addExtension(statusName, notAccExtensionType);

		}

	}

	}

	private boolean containsBrackets(String displayName) {

		int index = displayName.indexOf("[");

		return (index > -1);

	}

			//parent is infrageneric

			taxonName.setInfraGenericEpithet(parentName);

			taxonName.setGenusOrUninomial(grandParentName);

		}else{

			taxonName.setGenusOrUninomial(parentName);

		}

	}

	/**

	    TaxonName result;

		Rank rank = null;

			logger.warn("Rank is null. KingdomId: " + kingdomId + ", rankId: " +  intRank);

		}

		if (nc != null){

		}

	}

	/**

	 * is returned. If the attribute is <code>null</code> the id of the record is returned.

	 * @param rs

	 * @return

	 * @throws SQLException

	 */

	private int parseKingdomId(ResultSet rs) throws SQLException {

		String treeString = rs.getString("tu_sp");

		if (treeString != null){

                    logger.warn(message);

                    throw new RuntimeException(message);

					try {

						logger.warn(message);

						throw new RuntimeException(message);

				}

                String message = "Tree string for kingdom recognition is to short: " + treeString;

                logger.warn(message);

                throw new RuntimeException(message);

		}else{

			return tu_id;

	}

	@Override

	protected boolean doCheck(ErmsImportState state){

		IOValidator<ErmsImportState> validator = new ErmsTaxonImportValidator();

		return validator.validate(state);

	}

	@Override

    protected boolean isIgnore(ErmsImportState state){

	}

}