EDIT

/**

* Copyright (C) 2016 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.greece;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;

import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;

import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @since 14.12.2016

 */

public abstract class FloraHellenicaImportBase<CONFIG extends FloraHellenicaImportConfigurator>

            extends SimpleExcelTaxonImport<CONFIG>{

    private static final long serialVersionUID = 2593130403213346396L;

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

    private Map<UUID, Taxon> acceptedTaxonMap = new HashMap<>();

    private Reference sourceReference;

    private Reference secReference;

    private Reference secReference2;

    @SuppressWarnings("unchecked")

    private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(this);

    /**

     * @param taxon

     * @return

     */

    protected TaxonDescription getTaxonDescription(Taxon taxon) {

        if (!taxon.getDescriptions().isEmpty()){

            return taxon.getDescriptions().iterator().next();

        }else{

            TaxonDescription desc = TaxonDescription.NewInstance(taxon);

            desc.setDefault(true);

            return desc;

        }

    }

    /**

     * @param state

     * @return

     */

    protected Reference getSourceCitation(SimpleExcelTaxonImportState<CONFIG> state) {

        if (this.sourceReference == null){

            this.sourceReference = getPersistentReference(state.getConfig().getSourceReference());

        }

        return this.sourceReference;

    }

    protected Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state) {

        if (this.secReference == null){

            this.secReference = getPersistentReference(state.getConfig().getSecReference());

        }

        return this.secReference;

    }

    protected Reference getSecReference2(SimpleExcelTaxonImportState<CONFIG> state) {

        if (this.secReference2 == null){

            this.secReference2 = getPersistentReference(state.getConfig().getSecReference2());

        }

        return this.secReference2;

    }

    /**

     * @param reference

     * @return

     */

    private Reference getPersistentReference(Reference reference) {

        Reference result = getReferenceService().find(reference.getUuid());

        if (result == null){

            result = reference;

        }

        return result;

    }

    /**

     * @param record

     * @param state

     * @return

     */

    protected Taxon getAcceptedTaxon(Map<String, String> record,

            SimpleExcelTaxonImportState<CONFIG> state, String key) {

        String accStr = getValue(record, key);

        if (accStr == null){

            return null;

        }

        accStr = accStr.trim();

        Taxon accTaxon = state.getTaxon(accStr);

        if (accTaxon == null){

            String message = state.getCurrentLine()+  ": Accepted taxon could not be found: " + accStr;

            logger.warn(message);

            return null;

        }else{

            initAcceptedTaxonMap();

//            accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());

            accTaxon = acceptedTaxonMap.get(accTaxon.getUuid());

        }

        return accTaxon;

    }

    private void initAcceptedTaxonMap() {

        if (acceptedTaxonMap.isEmpty()){

            List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null);

            for (Taxon taxon : list){

                acceptedTaxonMap.put(taxon.getUuid(), taxon);

            }

        }

    }

    /**

     * @param record

     * @param state

     * @return

     */

    protected Taxon getHigherTaxon(Map<String, String> record,

            SimpleExcelTaxonImportState<CONFIG> state, String key) {

        String accStr = getValue(record, key);

        if (accStr == null){

            return null;

        }

        accStr = accStr.trim();

        Taxon accTaxon = state.getHigherTaxon(accStr);

        if (accTaxon == null){

            String message = state.getCurrentLine()+  ": Higher taxon could not be found: " + accStr;

            logger.info(message); //not critical

            return null;

        }else{

            initAcceptedTaxonMap();

//            accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());

            accTaxon = acceptedTaxonMap.get(accTaxon.getUuid());

        }

        return accTaxon;

    }

    protected IBotanicalName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,

            String famStr) {

        TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());

        famStr = famStr.substring(0,1).toUpperCase() + famStr.substring(1).toLowerCase();

        name.setGenusOrUninomial(famStr);

        name.addSource(makeOriginalSource(state));

        return name;

    }

    /**

     * @param state

     * @param name

     * @return

     */

    protected <NAME extends INonViralName> NAME replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, NAME name) {

        NAME result = deduplicationHelper.getExistingName(state, name);

        deduplicationHelper.replaceAuthorNamesAndNomRef(state, result);

        return result;

    }

    /**

     * @param state

     * @return

     */

    @Override

    protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {

        return IdentifiableSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, getSourceCitation(state));

    }

}