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.phycobank;

import java.util.ArrayList;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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.Classification;

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

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

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

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

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

/**

 * @author a.mueller

 * @since 2018-08-09

 */

@Component

public class PhycobankHigherClassificationExcelImport<CONFIG extends PhycobankHigherClassificationImportConfigurator>

        extends SimpleExcelTaxonImport<CONFIG> {

    private static final long serialVersionUID = -77504409820284052L;

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

    private static final String GENUS = "genus";

    private static final String FAMILIA = "familia";

    private static final String SUBORDO = "subordo";

    private static final String ORDO = "ordo";

    private static final String SUBCLASSIS = "subclassis";

    private static final String CLASSIS = "classis";

    private static final String PHYLUM = "phylum";

    private static final List<String> propertyPaths = null;

    private static TaxonRelationshipType relType;

    private Reference secReference;

    private Reference phycobankReference;

    @Override

    protected String getWorksheetName(CONFIG config) {

        return config.getWorksheetName();

    }

    private class RankedUninomial{

        public RankedUninomial(String uninomial, Rank rank) {

            this.uninomial = uninomial;

            this.rank = rank;

        }

        String uninomial;

        Rank rank;

        @Override

        public String toString() {

            return "RankedUninomial [uninomial=" + uninomial + ", rank=" + rank + "]";

        }

    }

    /**

	 *  Creates higher taxonomy

	 */

	@Override

    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {

	    @SuppressWarnings("deprecation")

        TaxonRelationshipType type = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();

	    relType = type;

	    String line = "line " + state.getCurrentLine();

	    System.out.println(line);

        Map<String, String> record = state.getOriginalRecord();

        List<RankedUninomial> rankedUninomials = makeRankedUninomials(state, record);

        createOrVerifyRankedUninomials(state, rankedUninomials, line);

		return;

    }

    /**

     * For the given list of {@link RankedUninomial}s names and taxa are created

     * if they do not yet exist. Parent child relationships as well as concept

     * relationships are created if they do not yet exists.

     * If the data is inconsistent to existing data inconsistency is logged and

     * no higher classification is created.

     * @param state

     * @param rankedUninomials

     * @param line

     */

    private TaxonNode createOrVerifyRankedUninomials(SimpleExcelTaxonImportState<CONFIG> state,

            List<RankedUninomial> rankedUninomials, String line) {

        if (rankedUninomials.isEmpty()){

            return getClassification(state).getRootNode();

        }else{

            RankedUninomial rankedUninomial = rankedUninomials.get(0);

            rankedUninomials.remove(0);

            Taxon taxon = getOrMakeTaxon(state, rankedUninomial, line);

            TaxonNode existingNode = taxon.getTaxonNode(getClassification(state));

            TaxonNode existingHigherNode = existingNode == null? null : existingNode.getParent();

            //recursive call

            TaxonNode createdHigher = createOrVerifyRankedUninomials(state, rankedUninomials, line);

//            boolean exists = verifyNextHigher(state, rankedUninomials, existingHigher);

            if (existingNode != null){

                if (existingHigherNode == null){

                    logger.warn(line + ": Higher node does not exist. This should not happen. Please check classification.");

                }else if (existingHigherNode.equals(createdHigher)){

                    //nothing to do;

                }else{

                    logger.warn(line + ": Inconsistency in data. Higher taxon for rank " + rankedUninomial.rank + "/" + rankedUninomial.uninomial +

                            " differs from existing higher taxon. Higher taxonomy not created. Please check classification.");

                }

            }else { //existingNode == null

                if (createdHigher == null){

                    logger.warn(line + ": Created higher node is null. This should not happen. Please check classification and concept relationships.");

                    return null;

                }else{

                    existingNode = createdHigher.addChildTaxon(taxon, getSecReference(state), line);

                    getTaxonNodeService().saveOrUpdate(existingNode);

                }

            }

            makeConceptRelation(state, existingNode, line);

            return existingNode;

        }

    }

//

//

//    /**

//     *

//     * @param state

//     * @param rankedUninomials

//     * @param nextHigher

//     * @return

//     */

//    private boolean verifyNextHigher(SimpleExcelTaxonImportState<CONFIG> state,

//            List<RankedUninomial> rankedUninomials,

//            TaxonNode nextHigher) {

//        if (nextHigher == null){

//            return false;

//        }else{

//            boolean result = true;

//            RankedUninomial rankedUninomial = rankedUninomials.get(0);

//            TaxonName name = nextHigher.getTaxon().getName();

//            if (!rankedUninomial.rank.equals(name.getRank())){

//                result = false;

//            }

//            if (!rankedUninomial.uninomial.equals(name.getNameCache())){

//                result = false;

//            }

//            return result;

//        }

//    }

    /**

     * Creates a list of {@link RankedUninomial}s for the given record.

     * Empty fields are not listed.

     * @param state

     * @param record

     * @return

     */

    private List<RankedUninomial> makeRankedUninomials(

            SimpleExcelTaxonImportState<CONFIG> state, Map<String, String> record) {

        List<RankedUninomial> result = new ArrayList<>();

        addRankedUninomial(result, record, GENUS, Rank.GENUS());

        addRankedUninomial(result, record, FAMILIA, Rank.FAMILY());

        addRankedUninomial(result, record, SUBORDO, Rank.SUBORDER());

        addRankedUninomial(result, record, ORDO, Rank.ORDER());

        addRankedUninomial(result, record, SUBCLASSIS, Rank.SUBCLASS());

        addRankedUninomial(result, record, CLASSIS, Rank.CLASS());

        addRankedUninomial(result, record, PHYLUM, Rank.PHYLUM());

        return result;

    }

    /**

     * Creates a {@link RankedUninomial} for a given record field and

     * adds it to the list. If the field is empty no {@link RankedUninomial} is

     * created.

     * @param list

     * @param record

     * @param fieldName

     * @param rank

     */

    private void addRankedUninomial(List<RankedUninomial> list, Map<String, String> record,

            String fieldName, Rank rank) {

        String uninomial = record.get(fieldName);

        if (isNotBlank(uninomial)){

            list.add(new RankedUninomial(uninomial.trim(), rank));

        }

    }

    /**

     * @param state

     * @param uninomial

     * @param rank

     * @param sec

     * @return

     */

    protected Taxon getOrMakeTaxon(SimpleExcelTaxonImportState<CONFIG> state,

            RankedUninomial rankedUninomial, String line) {

        Reference phycobankRef = getPhycobankReference(state);

        List<TaxonName> nameCandidates = getNameService().findNamesByNameCache(

                rankedUninomial.uninomial, MatchMode.EXACT, propertyPaths);

        List<TaxonName> names = rankedNames(state, nameCandidates, rankedUninomial.rank);

        Taxon taxon;

        if (names.isEmpty()){

            taxon = createTaxonAndName(state, rankedUninomial.uninomial,

                    rankedUninomial.rank, line);

        }else{

            if (names.size() > 1){

                List<Taxon> taxa = new ArrayList<>();

                for (TaxonName name : names){

                    taxa.addAll(getReferencedTaxa(name, state.getConfig().getPhycobankReference()));

                }

                if (taxa.isEmpty()){

                    logger.warn(line + ": More than 1 name matches, but no matching taxon exists. Create new taxon with arbitrary name.");

                    TaxonName name = names.get(0);

                    taxon = getOrCreateTaxon(state, name, phycobankRef, line);

                }else if (taxa.size() == 1){

                    taxon = taxa.get(0);

                }else{

                    logger.warn(line + ": More than 1 taxon matches, take arbitrary one. This is unexpected and could be improved in code by "

                            + "also checking parent relationships.");

                    taxon = taxa.get(0);

                }

            }else{

                TaxonName name = names.get(0);

                taxon = getOrCreateTaxon(state, name, phycobankRef, line);

            }

        }

        return taxon;

    }

    /**

     * @param state

     * @return

     */

    private Classification getClassification(SimpleExcelTaxonImportState<CONFIG> state) {

        Classification result = null;

        List<Classification> classifications = getClassificationService().list(null, null, null, null, null);

        Reference sec = getSecReference(state);

        for (Classification classification: classifications){

            if (classification.getCitation() != null && classification.getCitation().equals(sec)){

                result = classification;

            }

        }

        if (result == null){

            result = Classification.NewInstance(sec.getTitleCache());

            result.setReference(sec);

            getClassificationService().save(result);

        }

        return result;

    }

    /**

     * @param state

     */

    private Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state) {

        UUID uuid = state.getConfig().getSecReference().getUuid();

        if (secReference == null || !secReference.getUuid().equals(uuid)){

            secReference = getReferenceService().find(uuid);

            if (secReference == null){

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

                getReferenceService().save(secReference);

            }

        }

        return secReference;

    }

    private Reference getPhycobankReference(SimpleExcelTaxonImportState<CONFIG> state) {

        UUID uuid = state.getConfig().getPhycobankReference().getUuid();

        if (phycobankReference == null || !phycobankReference.getUuid().equals(uuid)){

            phycobankReference = getReferenceService().find(uuid);

            if (phycobankReference == null){

                phycobankReference = state.getConfig().getPhycobankReference();

                getReferenceService().save(phycobankReference);

            }

        }

        return phycobankReference;

    }

    /**

     * @param state

     * @param uninomial

     * @param rank

     * @param line

     * @return

     */

    private Taxon createTaxonAndName(SimpleExcelTaxonImportState<CONFIG> state, String uninomial,

            Rank rank, String line) {

        TaxonName newName = TaxonNameFactory.NewBotanicalInstance(rank);

        newName.setGenusOrUninomial(uninomial);

        newName.addPrimaryTaxonomicSource(getSourceReference(state));

        newName.addImportSource(null, null, getSourceReference(state), line);

        Taxon taxon = createTaxon(state, newName, line);

        return taxon;

    }

    /**

     * @param state

     * @param name

     * @param sec

     * @param line

     * @return

     */

    private Taxon getOrCreateTaxon(SimpleExcelTaxonImportState<CONFIG> state, TaxonName name,

            Reference phycobankRef, String line) {

        List<Taxon> taxa = getReferencedTaxa(name, phycobankRef);

        Taxon result;

        if (taxa.isEmpty()){

            return createTaxon(state, name, line);

        }else{

            if (taxa.size()> 1){

                logger.warn(line + ": More then 1 taxon matches for given name. Take arbitrary one.");

            }

            result = taxa.get(0);

        }

        return result;

    }

    /**

     * @param name

     * @param sec

     * @return

     */

    protected List<Taxon> getReferencedTaxa(TaxonName name, Reference sec) {

        List<Taxon> taxa = new ArrayList<>();

        for (Taxon taxon : name.getTaxa()){

            if (sec.equals(taxon.getSec())){

                taxa.add(taxon);

            }

        }

        return taxa;

    }

    /**

     * @param state

     * @param name

     * @param line

     * @return

     */

    private Taxon createTaxon(SimpleExcelTaxonImportState<CONFIG> state,

            TaxonName name, String line) {

        Taxon taxon = Taxon.NewInstance(name, getPhycobankReference(state));

        taxon.addImportSource(null, null, getSourceReference(state), line);

        return taxon;

    }

    /**

     * Returns those names that match in rank

     * @return

     */

    private List<TaxonName> rankedNames(SimpleExcelTaxonImportState<CONFIG> state,

            List<TaxonName> nameCandidates,

            Rank rank) {

        List<TaxonName> result = new ArrayList<>();

        for (TaxonName name : nameCandidates) {

            if (rank.equals(name.getRank())){

                result.add(name);

            }

        }

        return result;

    }

    /**

     * @param state

     * @param childNode

     * @param microCitation

     */

    private void makeConceptRelation(SimpleExcelTaxonImportState<CONFIG> state,

            TaxonNode childNode, String microCitation) {

        Taxon child = childNode.getTaxon();

        Taxon parent = childNode.getParent().getTaxon();

        if (parent == null){

            return;

        }

        Reference sec = getSecReference(state);

        Set<TaxonRelationship> rels = child.getRelationsFromThisTaxon();

        boolean hasRelation = false;

        for (TaxonRelationship rel : rels){

            if (rel.getType().equals(relType)

                    && rel.getToTaxon().equals(parent)

                    && rel.getCitation().equals(sec)){

                hasRelation = true;

            }

        }

        if (!hasRelation){

            child.addTaxonRelation(parent, relType, sec, microCitation);

        }

    }

}