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.redlist.gefaesspflanzen;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.Arrays;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Map.Entry;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author pplitzner

 * @since Mar 1, 2016

 */

@Component

@SuppressWarnings("serial")

public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {

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

    private static final String tableName = "Rote Liste Gefäßpflanzen";

    private static final String pluralString = "classifications";

    public RedListGefaesspflanzenImportClassification() {

        super(tableName, pluralString);

    }

    @Override

    protected String getIdQuery(RedListGefaesspflanzenImportState state) {

        return "SELECT SEQNUM "

                + "FROM V_TAXATLAS_D20_EXPORT t "

                + " ORDER BY SEQNUM";

    }

    @Override

    protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {

        String result = "select distinct e.*, f.FAMILIE "

                + "from V_TAXATLAS_D20_EXPORT e, GATTUNG_FAMILIE f "

                + "where e.EPI1 = f.GATTUNG and e.SEQNUM IN (@IDSET)";

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

        return result;

    }

    @Override

    protected void doInvoke(RedListGefaesspflanzenImportState state) {

        Classification gesamtListe = makeClassification("Gesamtliste", state.getConfig().getClassificationUuid(), "Gesamtliste", null, RedListUtil.gesamtListeReferenceUuid, state);

        Classification checkliste = makeClassification("Checkliste", RedListUtil.checkListClassificationUuid, "Checkliste", null, RedListUtil.checkListReferenceUuid, state);

        makeClassification("Ehrendorfer", RedListUtil.uuidClassificationE, "Ehrendorfer", null, RedListUtil.uuidClassificationReferenceE, state);

        makeClassification("Wisskirchen (Standardliste)", RedListUtil.uuidClassificationW, "Wisskirchen (Standardliste)", 1998, RedListUtil.uuidClassificationReferenceW, state);

        makeClassification("Korneck (Rote Liste)", RedListUtil.uuidClassificationK, "Korneck (Rote Liste)", 1996, RedListUtil.uuidClassificationReferenceK, state);

        makeClassification("Atlas (Westdeutschland)", RedListUtil.uuidClassificationAW, "Atlas (Westdeutschland)", 1988, RedListUtil.uuidClassificationReferenceAW, state);

        makeClassification("Atlas (Ostdeutschland)", RedListUtil.uuidClassificationAO, "Atlas (Ostdeutschland)", 1996, RedListUtil.uuidClassificationReferenceAO, state);

        makeClassification("Rothmaler", RedListUtil.uuidClassificationR, "Rothmaler", 2011, RedListUtil.uuidClassificationReferenceR, state);

        makeClassification("Oberdorfer", RedListUtil.uuidClassificationO, "Oberdorfer", 2001, RedListUtil.uuidClassificationReferenceO, state);

        makeClassification("Schmeil-Fitschen", RedListUtil.uuidClassificationS, "Schmeil-Fitschen", 2011, RedListUtil.uuidClassificationReferenceS, state);

        importFamilies(gesamtListe, checkliste, state);

        super.doInvoke(state);

    }

    private void importFamilies(Classification gesamtListe, Classification checkliste, RedListGefaesspflanzenImportState state) {

        for(UUID uuid:state.getFamilyMap().values()){

            Taxon family = HibernateProxyHelper.deproxy(getTaxonService().load(uuid, true, Arrays.asList(new String[]{"*"})), Taxon.class);

            gesamtListe.addParentChild(null, family, null, null);

            checkliste.addParentChild(null, family, null, null);

            family.setSec(gesamtListe.getReference());

            family.setTitleCache(null);

            getClassificationService().saveOrUpdate(gesamtListe);

            getClassificationService().saveOrUpdate(checkliste);

        }

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {

        ResultSet rs = partitioner.getResultSet();

        Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());

        Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);

        Classification classificationE = getClassificationService().load(RedListUtil.uuidClassificationE);

        Classification classificationW = getClassificationService().load(RedListUtil.uuidClassificationW);

        Classification classificationK = getClassificationService().load(RedListUtil.uuidClassificationK);

        Classification classificationAW = getClassificationService().load(RedListUtil.uuidClassificationAW);

        Classification classificationAO = getClassificationService().load(RedListUtil.uuidClassificationAO);

        Classification classificationR = getClassificationService().load(RedListUtil.uuidClassificationR);

        Classification classificationO = getClassificationService().load(RedListUtil.uuidClassificationO);

        Classification classificationS = getClassificationService().load(RedListUtil.uuidClassificationS);

        try {

            while (rs.next()){

                makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification,

                        classificationE, classificationW, classificationK, classificationAW

                        , classificationAO, classificationR, classificationO, classificationS);

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        logger.info("Update classification (1000 nodes)");

        getClassificationService().saveOrUpdate(gesamtListeClassification);

        getClassificationService().saveOrUpdate(checklistClassification);

        getClassificationService().saveOrUpdate(classificationE);

        getClassificationService().saveOrUpdate(classificationW);

        getClassificationService().saveOrUpdate(classificationK);

        getClassificationService().saveOrUpdate(classificationAW);

        getClassificationService().saveOrUpdate(classificationAO);

        getClassificationService().saveOrUpdate(classificationR);

        getClassificationService().saveOrUpdate(classificationO);

        getClassificationService().saveOrUpdate(classificationS);

        return true;

    }

    private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs,

            Classification gesamtListeClassification, Classification checklistClassification,

            Classification classificationE, Classification classificationW, Classification classificationK,

            Classification classificationAW, Classification classificationAO, Classification classificationR,

            Classification classificationO, Classification classificationS)

            throws SQLException {

        long id = rs.getLong(RedListUtil.NAMNR);

        String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));

        String gueltString = rs.getString(RedListUtil.GUELT);

        String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);

        String familieString = rs.getString(RedListUtil.FAMILIE);

        String clTaxonString = rs.getString(RedListUtil.CL_TAXON);

        String relationE = rs.getString(RedListUtil.E);

        String relationW = rs.getString(RedListUtil.W);

        String relationK = rs.getString(RedListUtil.K);

        String relationAW = rs.getString(RedListUtil.AW);

        String relationAO = rs.getString(RedListUtil.AO);

        String relationR = rs.getString(RedListUtil.R);

        String relationO = rs.getString(RedListUtil.O);

        String relationS = rs.getString(RedListUtil.S);

        //Gesamtliste

        TaxonBase<?> taxonBase = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);

        taxonBase.setSec(gesamtListeClassification.getReference());

        Taxon parent = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, Taxon.class);

        if(parent!=null && !parent.isInstanceOf(Taxon.class)){

            RedListUtil.logMessage(id, parent+" is no taxon but is a parent of "+taxonBase+" (Gesamtliste)", logger);

        }

        //add to family if no parent found

        if(parent==null){

            if(!taxonBase.isInstanceOf(Taxon.class)){

                RedListUtil.logMessage(id, taxonBase+" has no parent but is not a taxon.", logger);

            }

            else{

                Taxon family = (Taxon) state.getRelatedObject(RedListUtil.FAMILY_NAMESPACE_GESAMTLISTE, familieString);

                gesamtListeClassification.addParentChild(family, HibernateProxyHelper.deproxy(taxonBase, Taxon.class), null, null);

                //Buttler/Checklist taxon

                if(CdmUtils.isNotBlank(clTaxonString) && clTaxonString.equals(RedListUtil.CL_TAXON_B)){

                    checklistClassification.addParentChild(family, HibernateProxyHelper.deproxy(taxonBase, Taxon.class), null, null);

                    taxonBase.setSec(checklistClassification.getReference());

                }

                if(family.getTaxonNodes().isEmpty()){

                    gesamtListeClassification.addChildTaxon(family, null, null);

                    //do not add empty families to checklist classification

                    if(!getClassificationService().listChildNodesOfTaxon(family.getUuid(), RedListUtil.checkListClassificationUuid,

                            true, null, null, null).isEmpty()){

                        checklistClassification.addChildTaxon(family, null, null);

                    }

                }

            }

        }

        //add to higher taxon

        else{

            createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBase, parent);

            //Buttler/Checklist taxon

            if(CdmUtils.isNotBlank(clTaxonString) && clTaxonString.equals(RedListUtil.CL_TAXON_B)){

                if(!checklistClassification.isTaxonInTree(parent)){

                    RedListUtil.logInfoMessage(id, parent+" is parent taxon but is not in checklist. Skipping child "+taxonBase, logger);

                }

                else{

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

                        createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBase, parent);

                    }

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

                        //if it is a synonym it is already added to the accepted taxon

                        //so we just change the sec reference

                        taxonBase.setSec(checklistClassification.getReference());

                        taxonBase.setTitleCache(null);

                    }

                }

            }

        }

        taxonBase.setTitleCache(null, false);//refresh title cache

        //add taxa for concept relationships to E, W, K, AW, AO, R, O, S

        addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, relationE, taxonBase, id, state);

        addTaxonToClassification(classificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, relationW, taxonBase, id, state);

        addTaxonToClassification(classificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, relationK, taxonBase, id, state);

        addTaxonToClassification(classificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, relationAW, taxonBase, id, state);

        addTaxonToClassification(classificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, relationAO, taxonBase, id, state);

        addTaxonToClassification(classificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, relationR, taxonBase, id, state);

        addTaxonToClassification(classificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, relationO, taxonBase, id, state);

        addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, relationS, taxonBase, id, state);

    }

    private void addTaxonToClassification(Classification classification, String classificationNamespace, String relationString, final TaxonBase<?> gesamtListeTaxon, long id, RedListGefaesspflanzenImportState state){

        Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class);

        //add concept relation to gesamtliste/checkliste

        if(taxon!=null && isNotBlank(relationString) && !relationString.equals(".")){

            //if the related concept in gesamtliste/checkliste is a synonym then we

            //create a relation to the accepted taxon

            Taxon acceptedGesamtListeTaxon = getAcceptedTaxon(gesamtListeTaxon);

            String relationSubstring = relationString.substring(relationString.length()-1, relationString.length());

            TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(relationSubstring);

            if(taxonRelationshipTypeByKey==null){

                RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+gesamtListeTaxon.generateTitle(), logger);

            }

            //there is no type "included in" so we have to reverse the direction

            if(relationSubstring.equals("<")){

                if(acceptedGesamtListeTaxon!=null){

                    acceptedGesamtListeTaxon.addTaxonRelation(taxon, taxonRelationshipTypeByKey, null, null);

                }

            }

            else{

                if(acceptedGesamtListeTaxon!=null){

                    taxon.addTaxonRelation(acceptedGesamtListeTaxon, taxonRelationshipTypeByKey, null, null);

                }

            }

            taxon.setSec(classification.getReference());

            classification.addChildTaxon(taxon, null, null);

            taxon.setTitleCache(null);//Reset title cache to see sec ref in title

        }

    }

    private void createParentChildNodes(Classification classification, long id, String gueltString,

            String taxZusatzString, TaxonBase<?> taxonBase, Taxon parent) {

        if(taxonBase==null){

            RedListUtil.logMessage(id, "child taxon/synonym of "+parent+"  is null. ("+classification.generateTitle()+")" , logger);

            return;

        }

        //taxon

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

            //misapplied name

            String appendedPhrase = taxonBase.getAppendedPhrase();

            if(appendedPhrase!=null && appendedPhrase.equals(RedListUtil.AUCT)){

                if(parent==null){

                    RedListUtil.logMessage(id, "parent taxon of misapplied name "+taxonBase+"  is null. ("+classification.getTitleCache()+")" , logger);

                    return;

                }

                parent.addMisappliedName((Taxon) taxonBase, null, null);

                //return because misapplied names do not have sec references

                return;

            }

            else{

                classification.addParentChild(parent, (Taxon)taxonBase, null, null);

            }

            if(isNotBlank(taxZusatzString)){

                if(taxZusatzString.trim().equals("p. p.")){

                    RedListUtil.logMessage(id, "pro parte for accepted taxon "+taxonBase, logger);

                }

            }

        }

        //synonym

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

            if(parent==null){

                RedListUtil.logMessage(id, "parent taxon of synonym "+taxonBase+"  is null. ("+classification.getTitleCache()+")" , logger);

                return;

            }

            //basionym

            if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){

                parent.addHomotypicSynonym((Synonym) taxonBase);

                parent.getName().addBasionym(taxonBase.getName());

            }

            //regular synonym

            else{

                Synonym synonym = (Synonym) taxonBase;

                parent.addSynonym(synonym, SynonymType.HETEROTYPIC_SYNONYM_OF());

                //TAX_ZUSATZ

                if(isNotBlank(taxZusatzString)){

                    if(taxZusatzString.trim().equals("p. p.")){

                        synonym.setProParte(true);

                    }

                    else if(taxZusatzString.trim().equals("s. l. p. p.")){

                        synonym.setProParte(true);

                        taxonBase.setAppendedPhrase("s. l.");

                    }

                    else if(taxZusatzString.trim().equals("s. str. p. p.")){

                        synonym.setProParte(true);

                        taxonBase.setAppendedPhrase("s. str.");

                    }

                    else if(taxZusatzString.trim().equals("s. l.")

                            || taxZusatzString.trim().equals("s. str.")){

                        taxonBase.setAppendedPhrase(taxZusatzString);

                    }

                    else{

                        RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);

                    }

                }

            }

        }

        //set sec reference

        taxonBase.setSec(classification.getReference());

    }

    @Override

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

            RedListGefaesspflanzenImportState state) {

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

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

        try {

            while (rs.next()){

                idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));

                idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        //add taxa and their parent taxa

        result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_E, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_E));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_W, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_W));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_K, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_K));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AW, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AW));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AO, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AO));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_R, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_R));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_O, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_O));

        result.put(RedListUtil.CLASSIFICATION_NAMESPACE_S, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_S));

        //add families

        //gesamtliste

        Map<String, Taxon> familyMapGL = new HashMap<String, Taxon>();

        for (Entry<String, UUID> entry: state.getFamilyMap().entrySet()) {

            familyMapGL.put(entry.getKey(), HibernateProxyHelper.deproxy(getTaxonService().load(entry.getValue()), Taxon.class));

        }

        result.put(RedListUtil.FAMILY_NAMESPACE_GESAMTLISTE, familyMapGL);

        return result;

    }

    private Classification makeClassification(String classificationName, UUID classificationUuid, String referenceName, Integer yearPublished, UUID referenceUuid, RedListGefaesspflanzenImportState state) {

        Classification classification = Classification.NewInstance(classificationName, Language.DEFAULT());

        classification.setUuid(classificationUuid);

        Reference reference = ReferenceFactory.newGeneric();

        reference.setTitle(referenceName);

        reference.setUuid(referenceUuid);

        classification.setReference(reference);

        if(yearPublished!=null){

            reference.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(yearPublished));

        }

        return getClassificationService().save(classification);

    }

    @Override

    protected boolean doCheck(RedListGefaesspflanzenImportState state) {

        return false;

    }

    @Override

    protected boolean isIgnore(RedListGefaesspflanzenImportState state) {

        return false;

    }

}