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.cyprus;

import java.util.Arrays;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

import eu.etaxonomy.cdm.io.excel.common.ExcelImportBase;

import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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

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

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

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.strategy.parser.INonViralNameParser;

import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;

/**

 * @author a.babadshanjan

 * @since 08.01.2009

 */

@Component

public class CyprusExcelImport

        extends ExcelImportBase<CyprusImportState, CyprusImportConfigurator, ExcelRowBase> {

    private static final long serialVersionUID = 4449832452730987788L;

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

	public static Set<String> validMarkers = new HashSet<>(Arrays.asList(new String[]{"", "valid", "accepted", "a", "v", "t"}));

	public static Set<String> synonymMarkers = new HashSet<>(Arrays.asList(new String[]{"", "invalid", "synonym", "s", "i"}));

	@Override

	protected boolean isIgnore(CyprusImportState state) {

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

	}

	@Override

	protected boolean doCheck(CyprusImportState state) {

		logger.warn("DoCheck not yet implemented for CyprusExcelImport");

		return true;

	}

//	protected static final String ID_COLUMN = "Id";

	protected static final String SPECIES_COLUMN = "species";

	protected static final String SUBSPECIES_COLUMN = "subspecies";

	protected static final String GENUS_COLUMN = "genus";

	protected static final String FAMILY_COLUMN = "family";

	protected static final String DIVISION_COLUMN = "division";

	protected static final String HOMOTYPIC_SYNONYM_COLUMN = "homotypic synonyms";

	protected static final String HETEROTYPIC_SYNONYMS_COLUMN = "heterotypic synonyms";

	protected static final String ENDEMISM_COLUMN = "endemism";

	protected static final String STATUS_COLUMN = "status";

	protected static final String RED_DATA_BOOK_CATEGORY_COLUMN = "red data book category";

	protected static final String SYSTEMATICS_COLUMN = "systematics";

	// TODO: This enum is for future use (perhaps).

	protected enum Columns {

//		Id("Id"),

		Species("species"),

		Subspecies("subspecies"),

		Genus("genus"),

		Family("family"),

		Division("division"),

		HomotypicSynonyms("homotypic synonyms"),

		HeterotypicSynonyms("heterotypic synonyms"),

		Status("status"),

		Endemism("endemism");

		private final String head;

		private String value;

		private Columns(String head) {

			this.head = head;

		}

		public String head() {

			return this.head;

		}

		public String value() {

			return this.value;

		}

	}

	@Override

    protected void analyzeRecord(Map<String, String> record, CyprusImportState state) {

		Set<String> keys = record.keySet();

    	CyprusRow cyprusRow = new CyprusRow();

    	state.setCyprusRow(cyprusRow);

    	for (String originalKey: keys) {

    		String indexedKey = CdmUtils.removeDuplicateWhitespace(originalKey.trim()).toString();

    		String[] split = indexedKey.split("_");

    		String key = split[0];

    		if (split.length > 1){

    			String indexString = split[1];

    			try {

					Integer.valueOf(indexString);

				} catch (NumberFormatException e) {

					String message = "Index must be integer";

					logger.error(message);

					continue;

				}

    		}

    		String value = record.get(indexedKey);

    		if (! StringUtils.isBlank(value)) {

    			if (logger.isDebugEnabled()) { logger.debug(key + ": " + value); }

        		value = CdmUtils.removeDuplicateWhitespace(value.trim()).toString();

    		}else{

    			continue;

    		}

    		if (key.equalsIgnoreCase(SPECIES_COLUMN)) {

//    			int ivalue = floatString2IntValue(value);

    			cyprusRow.setSpecies(value);

			} else if(key.equalsIgnoreCase(SUBSPECIES_COLUMN)) {

				cyprusRow.setSubspecies(value);

			} else if(key.equalsIgnoreCase(HOMOTYPIC_SYNONYM_COLUMN)) {

				cyprusRow.setHomotypicSynonyms(value);

			} else if(key.equalsIgnoreCase(HETEROTYPIC_SYNONYMS_COLUMN)) {

				cyprusRow.setHeterotypicSynonyms(value);

			} else if(key.equalsIgnoreCase(ENDEMISM_COLUMN)) {

				cyprusRow.setEndemism(value);

			} else if(key.equalsIgnoreCase(STATUS_COLUMN)) {

				cyprusRow.setStatus(value);

			} else if(key.equalsIgnoreCase(RED_DATA_BOOK_CATEGORY_COLUMN)) {

				cyprusRow.setRedDataBookCategory(value);

			} else if(key.equalsIgnoreCase(SYSTEMATICS_COLUMN)) {

				cyprusRow.setSystematics(value);

			} else if(key.equalsIgnoreCase(GENUS_COLUMN)) {

				cyprusRow.setGenus(value);

			} else if(key.equalsIgnoreCase(FAMILY_COLUMN)) {

				cyprusRow.setFamily(value);

			} else if(key.equalsIgnoreCase(DIVISION_COLUMN)) {

				cyprusRow.setDivision(value);

			} else {

				state.setUnsuccessfull();

				logger.error("Unexpected column header " + key);

			}

    	}

    	return;

    }

	private static INonViralNameParser<INonViralName> nameParser = NonViralNameParserImpl.NewInstance();

	private static NomenclaturalCode nc = NomenclaturalCode.ICNAFP;

	private Feature redBookCategory;

	private Feature endemism;

	private PresenceAbsenceTerm indigenous;

	private PresenceAbsenceTerm indigenousDoubtful;

	private PresenceAbsenceTerm cultivatedDoubtful;

	private PresenceAbsenceTerm casual;

	private PresenceAbsenceTerm casualDoubtful;

	private PresenceAbsenceTerm nonInvasive;

	private PresenceAbsenceTerm nonInvasiveDoubtful;

	private PresenceAbsenceTerm invasive;

	private PresenceAbsenceTerm invasiveDoubtful;

	private PresenceAbsenceTerm questionable;

	private PresenceAbsenceTerm questionableDoubtful;

	private boolean termsCreated = false;

	private boolean makeTerms(CyprusImportState state) {

		if (termsCreated == false){

			IInputTransformer transformer = state.getTransformer();

			try {

				//feature

				UUID redBookUuid = transformer.getFeatureUuid("Red book");

				redBookCategory = this.getFeature(state, redBookUuid, "Red book category", "Red data book category", "Red book", null);

				getTermService().save(redBookCategory);

				UUID endemismUuid = transformer.getFeatureUuid("Endemism");

				endemism = this.getFeature(state, endemismUuid, "Endemism", "Endemism", "Endemism", null);

				getTermService().save(endemism);

				//status

				UUID indigenousUuid = transformer.getPresenceTermUuid("IN");

				indigenous = this.getPresenceTerm(state, indigenousUuid, "indigenous", "Indigenous", "IN", false);

				getTermService().save(indigenous);

				UUID indigenousDoubtfulUuid = transformer.getPresenceTermUuid("IN?");

				indigenousDoubtful = this.getPresenceTerm(state, indigenousDoubtfulUuid, "indigenous?", "Indigenous?", "IN?", false);

				getTermService().save(indigenousDoubtful);

				UUID cultivatedDoubtfulUuid = transformer.getPresenceTermUuid("CU?");

				cultivatedDoubtful = this.getPresenceTerm(state, cultivatedDoubtfulUuid, "cultivated?", "Cultivated?", "CU?", false);

				getTermService().save(cultivatedDoubtful);

				UUID casualUuid = transformer.getPresenceTermUuid("CA");

				casual = this.getPresenceTerm(state, casualUuid, "casual", "Casual", "CA", false);

				getTermService().save(casual);

				UUID casualDoubtfulUuid = transformer.getPresenceTermUuid("CA?");

				casualDoubtful = this.getPresenceTerm(state, casualDoubtfulUuid, "casual?", "Casual?", "CA?", false);

				getTermService().save(casualDoubtful);

				UUID nonInvasiveUuid = transformer.getPresenceTermUuid("NN");

				nonInvasive = this.getPresenceTerm(state, nonInvasiveUuid, "naturalized  non-invasive", "Naturalized  non-invasive", "NN", false);

				getTermService().save(nonInvasive);

				UUID nonInvasiveDoubtfulUuid = transformer.getPresenceTermUuid("NN?");

				nonInvasiveDoubtful = this.getPresenceTerm(state, nonInvasiveDoubtfulUuid, "naturalized  non-invasive?", "Naturalized  non-invasive?", "NN?", false);

				getTermService().save(nonInvasiveDoubtful);

				UUID invasiveUuid = transformer.getPresenceTermUuid("NA");

				invasive = this.getPresenceTerm(state, invasiveUuid, "naturalized  invasive", "Naturalized  invasive", "NA", false);

				getTermService().save(invasive);

				UUID invasiveDoubtfulUuid = transformer.getPresenceTermUuid("NA?");

				invasiveDoubtful = this.getPresenceTerm(state, invasiveDoubtfulUuid, "naturalized  invasive?", "Naturalized  invasive?", "NA?", false);

				getTermService().save(invasiveDoubtful);

				UUID questionableUuid = transformer.getPresenceTermUuid("Q");

				questionable = this.getPresenceTerm(state, questionableUuid, "questionable", "Questionable", "Q", false);

				getTermService().save(questionable);

				UUID questionableDoubtfulUuid = transformer.getPresenceTermUuid("Q?");

				questionableDoubtful = this.getPresenceTerm(state, questionableDoubtfulUuid, "questionable?", "Questionable?", "Q?", false);

				getTermService().save(questionableDoubtful);

				termsCreated = true;

				return true;

			} catch (UndefinedTransformerMethodException e) {

				e.printStackTrace();

				return false;

			}

		}

		return true;

	}

	/**

	 *  Stores taxa records in DB

	 */

	@Override

    protected void firstPass(CyprusImportState state) {

		makeTerms(state);

		CyprusRow taxonLight = state.getCyprusRow();

		Reference citation = null;

		String microCitation = null;

		//species name

		String speciesStr = taxonLight.getSpecies();

		String subSpeciesStr = taxonLight.getSubspecies();

		String homotypicSynonymsString = taxonLight.getHomotypicSynonyms();

		List<String> homotypicSynonymList = Arrays.asList(homotypicSynonymsString.split(";"));

		String heterotypicSynonymsString = taxonLight.getHeterotypicSynonyms();

		List<String> heterotypicSynonymList = Arrays.asList(heterotypicSynonymsString.split(";"));

		String systematicsString = taxonLight.getSystematics();

		String endemismString = taxonLight.getEndemism();

		String statusString = taxonLight.getStatus();

		String redBookCategory = taxonLight.getRedDataBookCategory();

		if (StringUtils.isNotBlank(speciesStr)) {

			boolean speciesIsExisting = false;

			Taxon mainTaxon = null;

			//species

			Taxon speciesTaxon = (Taxon)createTaxon(state, Rank.SPECIES(), speciesStr, Taxon.class, nc);

			mainTaxon = speciesTaxon;

			//subspecies

			if (StringUtils.isNotBlank(subSpeciesStr)){

				Taxon existingSpecies = state.getHigherTaxon(speciesStr);

				if (existingSpecies != null){

					speciesIsExisting = true;

					speciesTaxon = existingSpecies;

				}

				Taxon subSpeciesTaxon = (Taxon)createTaxon(state, Rank.SUBSPECIES(), subSpeciesStr, Taxon.class, nc);

				if (subSpeciesTaxon != null){

					makeParent(state, speciesTaxon, subSpeciesTaxon, citation, microCitation);

				}

				mainTaxon = subSpeciesTaxon;

				state.putHigherTaxon(speciesStr, speciesTaxon);

			}

			if (! speciesIsExisting){

				makeHigherTaxa(state, taxonLight, speciesTaxon, citation, microCitation);

			}

			makeHomotypicSynonyms(state, homotypicSynonymList, mainTaxon);

			makeHeterotypicSynonyms(state, heterotypicSynonymList, mainTaxon);

			makeSystematics(systematicsString, mainTaxon);

			makeEndemism(endemismString, mainTaxon);

			makeStatus(statusString, mainTaxon);

			makeRedBookCategory(redBookCategory, mainTaxon);

//			state.putHigherTaxon(higherName, uuid);//(speciesStr, mainTaxon);

			getTaxonService().save(mainTaxon);

		}

		return;

    }

	private void makeHigherTaxa(CyprusImportState state, CyprusRow taxonLight, Taxon speciesTaxon, Reference citation, String microCitation) {

		String divisionStr = taxonLight.getDivision();

		String genusStr = taxonLight.getGenus();

		String familyStr = taxonLight.getFamily();

		Taxon division = getTaxon(state, divisionStr, Rank.DIVISION(), null, citation, microCitation);

		Taxon family = getTaxon(state, familyStr, Rank.FAMILY(), division, citation, microCitation);

		Taxon genus = getTaxon(state, genusStr, Rank.GENUS(), family, citation, microCitation);

		makeParent(state, genus, speciesTaxon, citation, microCitation)	;

	}

	private Taxon getTaxon(CyprusImportState state, String taxonNameStr, Rank rank, Taxon parent, Reference citation, String microCitation) {

		Taxon result;

		if (state.containsHigherTaxon(taxonNameStr)){

			result = state.getHigherTaxon(taxonNameStr);

		}else{

			result = (Taxon)createTaxon(state, rank, taxonNameStr, Taxon.class, nc);

			state.putHigherTaxon(taxonNameStr, result);

			if (parent == null){

				makeParent(state, null,result, citation, microCitation);

			}else{

				makeParent(state, parent, result, citation, microCitation);

			}

		}

		return result;

	}

	private void makeHomotypicSynonyms(CyprusImportState state,

			List<String> homotypicSynonymList, Taxon mainTaxon) {

		for (String homotypicSynonym: homotypicSynonymList){

			if (StringUtils.isNotBlank(homotypicSynonym)){

				Synonym synonym = (Synonym)createTaxon(state, null, homotypicSynonym, Synonym.class, nc);

				mainTaxon.addHomotypicSynonym(synonym);

			}

		}

	}

	private void makeHeterotypicSynonyms(CyprusImportState state, List<String> heterotypicSynonymList, Taxon mainTaxon) {

		for (String heterotypicSynonym: heterotypicSynonymList){

			if (StringUtils.isNotBlank(heterotypicSynonym)){

				Synonym synonym = (Synonym)createTaxon(state, null, heterotypicSynonym, Synonym.class, nc);

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

			}

		}

	}

	private void makeSystematics(String systematicsString, Taxon mainTaxon) {

		//Systematics

		if (StringUtils.isNotBlank(systematicsString)){

			TaxonDescription td = this.getTaxonDescription(mainTaxon, false, true);

			TextData textData = TextData.NewInstance(Feature.SYSTEMATICS());

			textData.putText(Language.UNDETERMINED(), systematicsString);

			td.addElement(textData);

		}

	}

	private void makeEndemism(String endemismString, Taxon mainTaxon) {

		//endemism

		if (StringUtils.isNotBlank(endemismString)){

			//OLD - not wanted as marker

//			boolean flag;

//			if (endemismString.trim().equalsIgnoreCase("not endemic") || endemismString.trim().equalsIgnoreCase("ne?")){

//				flag = false;

//			}else if (endemismString.trim().equalsIgnoreCase("endemic")){

//				flag = true;

//			}else{

//				throw new RuntimeException(endemismString + " is not a valid value for endemism");

//			}

//			Marker marker = Marker.NewInstance(MarkerType.ENDEMIC(), flag);

//			mainTaxon.addMarker(marker);

			//text data

			TaxonDescription td = this.getTaxonDescription(mainTaxon, false, true);

			TextData textData = TextData.NewInstance(endemism);

			textData.putText(Language.ENGLISH(), endemismString);

			td.addElement(textData);

		}

	}

	private void makeStatus(String statusString, Taxon mainTaxon) {

		//status

		if (StringUtils.isNotBlank(statusString)){

			PresenceAbsenceTerm status = null;

			if (statusString.contains("Indigenous?")){

				status = indigenousDoubtful;

			}else if (statusString.contains("Indigenous")){

				status = indigenous;

			}else if (statusString.contains("Casual?") || statusString.contains("Causal?")){

				status = casualDoubtful;

			}else if (statusString.contains("Casual")){

				status = casual;

			}else if (statusString.contains("Cultivated?")){

				status = cultivatedDoubtful;

			}else if (statusString.contains("Cultivated")){

				status = PresenceAbsenceTerm.CULTIVATED();

			}else if (statusString.contains("non-invasive?")){

				status = nonInvasiveDoubtful;

			}else if (statusString.contains("non-invasive")){

				status = nonInvasive;

			}else if (statusString.contains("invasive?")){

				status = invasiveDoubtful;

			}else if (statusString.contains("invasive")){

				status = invasive;

			}else if (statusString.contains("Questionable?")){

				status = questionableDoubtful;

			}else if (statusString.contains("Questionable")){

				status = questionable;

			}else if (statusString.startsWith("F")){

				status = null;

			}else if (statusString.equals("##")){

				status = null;

			}else{

				logger.warn("Unknown status: " + statusString);

				status = null;

			}

			TaxonDescription td = this.getTaxonDescription(mainTaxon, false, true);

			NamedArea area = TdwgAreaProvider.getAreaByTdwgAbbreviation("CYP");

			Distribution distribution = Distribution.NewInstance(area, status);

			td.addElement(distribution);

			//text data

			TextData textData = TextData.NewInstance(Feature.STATUS());

			textData.putText(Language.ENGLISH(), statusString);

			td.addElement(textData);

		}

	}

	private void makeRedBookCategory(String redBookCategory, Taxon mainTaxon) {

		//red data book category

		if (StringUtils.isNotBlank(redBookCategory)){

			TaxonDescription td = this.getTaxonDescription(mainTaxon, false, true);

			TextData textData = TextData.NewInstance(this.redBookCategory);

			textData.putText(Language.ENGLISH(), redBookCategory);

			td.addElement(textData);

		}

	}

	/**

	 *  Stores parent-child, synonym and common name relationships

	 */

	@Override

    protected void secondPass(CyprusImportState state) {

//		CyprusRow cyprusRow = state.getCyprusRow();

		return;

	}

	private TaxonBase<?> createTaxon(CyprusImportState state, Rank rank, String taxonNameStr,

			Class<?> statusClass, NomenclaturalCode nc) {

		TaxonBase<?> taxonBase;

		INonViralName taxonNameBase = null;

		if (nc == NomenclaturalCode.ICVCN){

			logger.warn("ICVCN not yet supported");

		}else{

			taxonNameBase = nc.getNewTaxonNameInstance(rank);

			INonViralNameParser<INonViralName> parser = nameParser;//NonViralNameParserImpl.NewInstance();

			taxonNameBase = parser.parseFullName(taxonNameStr, nc, rank);

			//taxonNameBase.setNameCache(taxonNameStr);

		}

		//Create the taxon

		Reference sec = state.getConfig().getSourceReference();

		// Create the status

		if (statusClass.equals(Taxon.class)){

			taxonBase = Taxon.NewInstance(taxonNameBase, sec);

		}else if (statusClass.equals(Synonym.class)){

			taxonBase = Synonym.NewInstance(taxonNameBase, sec);

		}else {

			Taxon taxon = Taxon.NewInstance(taxonNameBase, sec);

			taxon.setTaxonStatusUnknown(true);

			taxonBase = taxon;

		}

		return taxonBase;

	}

	private boolean makeParent(CyprusImportState state, Taxon parentTaxon, Taxon childTaxon, Reference citation, String microCitation){

		boolean success = true;

		Reference sec = state.getConfig().getSourceReference();

//		Reference sec = parentTaxon.getSec();

		Classification tree = state.getTree(sec);

		if (tree == null){

			tree = makeTree(state, sec);

			tree.setTitleCache(state.getConfig().getSourceReferenceTitle(), true);

		}

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

			success &=  (null !=  tree.addParentChild(parentTaxon, childTaxon, citation, microCitation));

		}else{

			logger.warn("No relationship added for child " + childTaxon.getTitleCache());

		}

		return success;

	}

}