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.taxonx;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.jdom.Element;

import org.jdom.Namespace;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.service.ICommonService;

import eu.etaxonomy.cdm.api.service.INameService;

import eu.etaxonomy.cdm.api.service.ITaxonService;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

import eu.etaxonomy.cdm.model.agent.AgentBase;

import eu.etaxonomy.cdm.model.agent.Person;

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

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

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

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

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

/**

 * @author a.mueller

 * @created 29.07.2008

 * @version 1.0

 */

@Component

public class TaxonXNomenclatureImport extends CdmIoBase<TaxonXImportState> implements ICdmIO<TaxonXImportState> {

    private static final long serialVersionUID = 796115831082828758L;

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

	@SuppressWarnings("unused")

	private static int modCount = 10000;

	public TaxonXNomenclatureImport(){

		super();

	}

	@Override

    public boolean doCheck(TaxonXImportState state){

		boolean result = true;

		logger.warn("Checking for Types not yet implemented");

		//result &= checkArticlesWithoutJournal(bmiConfig);

		//result &= checkPartOfJournal(bmiConfig);

		return result;

	}

	@Override

    public void doInvoke(TaxonXImportState state){

		logger.info("start make Nomenclature ...");

		TransactionStatus tx = startTransaction();

		TaxonXImportConfigurator config = state.getConfig();

		Element root = config.getSourceRoot();

		Namespace nsTaxonx = root.getNamespace();

		//for testing only

		Taxon taxon = getTaxon(config);

		boolean isChanged = false;

		Element elTaxonBody = root.getChild("taxonxBody", nsTaxonx);

		Element elTreatment = elTaxonBody.getChild("treatment", nsTaxonx);

		Element elNomenclature = elTreatment.getChild("nomenclature", nsTaxonx);

		//isChanged |= doCollectionEvent(txConfig, elNomenclature, nsTaxonx, taxon);

		if (taxon != null && taxon.getName() != null && elNomenclature != null){

			isChanged |= doNomenclaturalType(config, elNomenclature, nsTaxonx, taxon.getName());

			List<Element> elSynonymyList = new ArrayList<Element>();

			elSynonymyList.addAll(elNomenclature.getChildren("synonomy", nsTaxonx));

			elSynonymyList.addAll(elNomenclature.getChildren("synonymy", nsTaxonx)); //wrong spelling in TaxonX-Schema

			for (Element elSynonymy : elSynonymyList){

				String synonymName = elSynonymy.getChildTextTrim("name");

				if (elSynonymy.getChild("type", nsTaxonx) != null || elSynonymy.getChild("type_loc", nsTaxonx) != null){

					Synonym synonym = getSynonym(config, taxon, synonymName);

					if (synonym != null){

						isChanged |= doNomenclaturalType(config, elSynonymy, nsTaxonx, synonym.getName());

					}

				}

			}

		}

		if (isChanged){

			getTaxonService().save(taxon);

		}

		commitTransaction(tx);

		return;

	}

	private Synonym getSynonym(TaxonXImportConfigurator config, Taxon taxon, String synName){

		Synonym result = null;

		unlazySynonym(config, taxon);

		Set<Synonym> synList = taxon.getSynonyms();

		for (Synonym syn : synList){

			TaxonNameBase<?,?> nameBase = syn.getName();

			if (nameBase != null){

				if (nameBase.isInstanceOf(NonViralName.class)){

					if (nameBase.getNameCache().equals(synName)){

						return syn;  //only first synonym is returned

					}

				}

			}

		}

		logger.warn("Synonym ("+synName+ ")not found for taxon " + taxon.getTitleCache() + getBracketSourceName(config));

		return result;

	}

	private Taxon getTaxon(TaxonXImportConfigurator config){

		Taxon result;

//		result =  Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(null), null);

		//ICommonService commonService =config.getCdmAppController().getCommonService();

		ICommonService commonService = getCommonService();

		String originalSourceId = config.getOriginalSourceId();

		String namespace = config.getOriginalSourceTaxonNamespace();

		result = (Taxon)commonService.getSourcedObjectByIdInSource(Taxon.class, originalSourceId , namespace);

		if (result == null){

			logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found");

		}

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	@Override

    protected boolean isIgnore(TaxonXImportState state){

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

	}

	/**

	 *

	 * Reads the collection_event tag, creates the according data and stores it.

	 * TODO under work

	 * @param elNomenclature

	 * @param nsTaxonx

	 * @param taxonBase

	 * @return

	 */

	private boolean doNomenclaturalType(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonNameBase taxonName){

		boolean success = true;

		if (taxonName == null){

			logger.warn("taxonName is null");

			return false;

		}

		if (elNomenclature == null){

			logger.warn("elNomenclature is null");

			return false;

		}

		Element elType = elNomenclature.getChild("type", nsTaxonx);

		Element elTypeLoc = elNomenclature.getChild("type_loc", nsTaxonx);

		if (elType != null || elTypeLoc != null){

			unlazyTypeDesignation(config, taxonName);

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

				success &= doNameType(elType, taxonName, config);

			}else{

				success &= doSpecimenType(config, elType, elTypeLoc, taxonName);

			}

			return success;

		}

		return false;

	}

	private boolean doSpecimenType(TaxonXImportConfigurator config, Element elType, Element elTypeLoc, TaxonNameBase taxonName){

		Reference citation = null;

		String citationMicroReference = null;

		String originalNameString = null;

		boolean isNotDesignated = true;

		boolean addToAllHomotypicNames = true;

		SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance();

		//elType

		if (elType != null){

			doElType(elType, simpleSpecimen, config);

		}//elType

		//typeLoc

		HashMap<DerivedUnit, SpecimenTypeDesignationStatus> typeLocMap = null;

		if (elTypeLoc != null){

			typeLocMap = doElTypeLoc(elTypeLoc, simpleSpecimen, taxonName, config);

		}

		if (typeLocMap != null && typeLocMap.size() >0){

			for (DerivedUnit specimen : typeLocMap.keySet()){

				SpecimenTypeDesignationStatus status = typeLocMap.get(specimen);

				taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames);

			}

		}else{ // no type_loc

			SpecimenTypeDesignationStatus status = null;

			taxonName.addSpecimenTypeDesignation(simpleSpecimen.getSpecimen(), status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames);

		}

		return true;

	}

	private boolean doElType(Element elType, SimpleSpecimen simpleSpecimen, TaxonXImportConfigurator config){

		//type

		String text = elType.getTextNormalize();

		if (text.endsWith(";")){

			text = text + " ";

		}

		String[] type = text.split(";");

		if (type.length != 3 ){

			if (text.equals("")){

				logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config));

			}else{

				logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));

			}

			simpleSpecimen.setTitleCache(elType.getTextNormalize());

		}else{

			String strLocality = type[0].trim();

			if (! "".equals(strLocality)){

//				simpleSpecimen.setLocality(strLocality);

			}

			String strCollector = type[1].trim();

			if (! "".equals(strCollector)){

				AgentBase collector = Person.NewTitledInstance(strCollector);

//				simpleSpecimen.setCollector(collector);

			}

			String strCollectorNumber = type[2].trim();

			if (! "".equals(strCollectorNumber)){

//				simpleSpecimen.setCollectorsNumber(strCollectorNumber);

			}

			String title = CdmUtils.concat(" ", new String[]{strLocality, strCollector, strCollectorNumber});

			simpleSpecimen.setTitleCache(title);

		}

		return true;

	}

	private boolean doNameType(Element elType, TaxonNameBase taxonName, TaxonXImportConfigurator config){

		boolean success = true;

		//type

		String text = elType.getTextNormalize();

		logger.info("Type: " + text);

		if (text.endsWith(";")){

			text = text + " ";

		}

		String[] type = text.split(";");

		if (type.length != 3 ){

			if (text.equals("")){

				logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config));

			}else{

				logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));

			}

			success = false;

		}else{

			String statusStr = type[0].trim();

			String taxonNameStr = type[1].trim();

			String authorStr = type[2].trim();

			NameTypeDesignationStatus status = getNameTypeStatus(statusStr);

			/*boolean isLectoType = getIsLectoType(statusStr);*/

//			if (status == null){

//				logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));

//				success = false;

//			}else{

//				TaxonNameBase childType = getChildrenNameType(taxonName, taxonNameStr, authorStr);

//				if (childType != null){

//					return doNameTypeDesignation(taxonName, childType, status);

//				}else{

					String[] epis = taxonNameStr.split(" ");

					String uninomial = epis[0].trim();

					String specEpi = epis[1].trim();

					Pager<TaxonNameBase> nameTypes = getNameService().searchNames(uninomial, null, specEpi, null, Rank.SPECIES(), null, null, null, null);

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

					for (TaxonNameBase nt : nameTypes.getRecords()){

						if (compareAuthorship(nt, authorStr)){

							result.add(nt);

							success &= doNameTypeDesignation(taxonName, nt, status/*, isLectoType*/);

						}else{

							//TODO ?

						}

					}

					if (result.size() > 1){

						logger.warn("More than 1 name matches: " + text);

						success = false;

					}else if (result.size() == 0){

						logger.warn("No name matches: " + text + "(" + config.getSourceNameString() + ")");

						success = false;

					}

//				}

//			}

		}

		return success;

	}

//	private TaxonNameBase getChildrenNameType(TaxonNameBase name, String typeStr, String authorStr){

//		TaxonNameBase result = null;

//		Set<TaxonBase> list = name.getTaxonBases();

//		for (TaxonBase taxonBase : list){

//			Taxon taxon;

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

//				taxon = CdmBase.deproxy(taxonBase, Taxon.class);

//			}else{

//				Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);

//				taxon = syn.getAcceptedTaxa().iterator().next();

//			}

//			Set<Taxon> children = taxon.getTaxonomicChildren();

//			for (Taxon child: children){

//				INonViralName childName = child.getName();

//				if (childName.getNameCache().equals(typeStr)){

//					if (compareAuthorship(childName, authorStr)){

//						return childName;

//					}

//				}

//			}

//		}

//		return result;

//	}

	private boolean compareAuthorship(INonViralName typeName, String authorStr){

		 boolean result = false;

		 authorStr = authorStr.replaceAll("\\s+and\\s+", "&");

		 authorStr = authorStr.replaceAll("\\s*", "");

		 authorStr = authorStr.replaceAll("\\.$", "");

		 String typeCache = typeName.getAuthorshipCache().replaceAll("\\s*", "");

		 typeCache = typeCache.replaceAll("\\.$", "");

		 if (authorStr.equals(typeCache)){

			 return true;

		 }else{

			 logger.info("   Authors different: " + authorStr + " <-> " + typeCache);

		 }

		 return result;

	}

	private NameTypeDesignationStatus getNameTypeStatus(String statusString){

		//FIXME some types (not further defined types) do not exist yet

		if (true){

			return null;

		}

		if (statusString.trim().equalsIgnoreCase("Type")){

			return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();

		}else if (statusString.trim().equalsIgnoreCase("Lectotype")){

			return NameTypeDesignationStatus.LECTOTYPE();

		}else if (statusString.trim().equalsIgnoreCase("Holotype")){

			logger.warn("Holotype does not yet exist in CDM");

			return NameTypeDesignationStatus.NOT_APPLICABLE();

		}else if (statusString.trim().equalsIgnoreCase("paratype")){

			logger.warn("paratype does not yet exist in CDM");

			return NameTypeDesignationStatus.NOT_APPLICABLE();

		}

		else{

			logger.warn("Status not recognized: " + statusString);

			return null;

		}

	}

	private boolean getIsLectoType(String statusString){

		//FIXME may be deleted once getNameTypeStatus works finde

		if (statusString.trim().equals("Lectotype")){

			return true;

		}else{

			return false;

		}

	}

	private boolean doNameTypeDesignation(TaxonNameBase name, TaxonNameBase type, NameTypeDesignationStatus status/*, boolean isLectoType*/){

		Reference citation = null;

		String citationMicroReference = null;

		String originalNameString = null;

		boolean addToAllHomotypicNames = true;

//		name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString, status, addToAllHomotypicNames);

		name.addNameTypeDesignation(type, citation, citationMicroReference, originalNameString,status, false, false, /*isLectoType, */false, addToAllHomotypicNames);

		return true;

	}

	/**

	 * Reads the typeLoc element split in parts for eacht type (holo, iso,...)

	 * @param elTypeLoc

	 * @param simpleSpecimen

	 * @param taxonName

	 * @param config

	 * @return

	 */

	private HashMap<DerivedUnit, SpecimenTypeDesignationStatus> doElTypeLoc(Element elTypeLoc,

			SimpleSpecimen simpleSpecimen,

			TaxonNameBase<?,?> taxonName,

			TaxonXImportConfigurator config){

		HashMap<DerivedUnit, SpecimenTypeDesignationStatus> result = new HashMap<DerivedUnit, SpecimenTypeDesignationStatus>();

		String typeLocFullString = elTypeLoc.getTextTrim();

		typeLocFullString = typeLocFullString.replace("(", "").replace(")", "");

		String[] typeLocStatusList = typeLocFullString.split(";");

		DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen();

		for (String typeLocStatus : typeLocStatusList){

			typeLocStatus = typeLocStatus.trim();

			int pos = typeLocStatus.indexOf(" ");

			if (pos == -1){

				logger.warn("Unknown format or empty type_loc : '" +typeLocStatus + "'" + getBracketSourceName(config));

				result.put(originalSpecimen, null);

			}else{

				String statusString = typeLocStatus.substring(0,pos);

				SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config);

				//TODO

				//String[] collectionStrings = typeLocStatus.substring(pos).split(",");

				String tmpCollString = typeLocStatus.substring(pos).trim();

				//for(String collectionString : collectionStrings){

					if (tmpCollString.contains("typ")){

						logger.warn("Is this really only a collection string? : "  + tmpCollString + getBracketSourceName(config));

					}

					DerivedUnit specimen;

					specimen = (DerivedUnit)originalSpecimen.clone();

					String title = originalSpecimen.getTitleCache();

					title = title + "(" + tmpCollString + ")";

					specimen.setTitleCache(title, true );

					result.put(specimen, status);

				//}

			}

		}

		return result;

	}

	/**

	 *

	 * Reads the collection_event tag, creates the according data and stores it.

	 * TODO under work

	 * @param elNomenclature

	 * @param nsTaxonx

	 * @param taxonBase

	 * @return

	 */

	private boolean doCollectionEvent(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonBase taxonBase){

		boolean result = false;

		if (elNomenclature == null){

			return false;

		}

		Element elCollectionEvent = elNomenclature.getChild("collection_event", nsTaxonx);

		if (elCollectionEvent == null){

			return result;

		}

		Element elLocality = elCollectionEvent.getChild("locality", nsTaxonx);

		Element elType = elCollectionEvent.getChild("type", nsTaxonx);

		Element elTypeLoc = elCollectionEvent.getChild("type_loc", nsTaxonx);

		//locality

		SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance();

		String locality = elLocality.getTextNormalize();

		if (! "".equals(locality)){

			simpleSpecimen.setLocality(locality);

		}

		//type

		String[] type = elType.getTextNormalize().split(" ");

		if (type.length != 2 ){

			logger.warn("<collecion_even><type> is of unsupported format: " + elType.getTextNormalize());

		}else{

			AgentBase collector = Person.NewTitledInstance(type[0]);

			simpleSpecimen.setCollector(collector);

			String collectorNumber = type[1];

			simpleSpecimen.setCollectorsNumber(collectorNumber);

		}

		//typeLoc

		String typeLocFullString = elTypeLoc.getTextTrim();

		typeLocFullString = typeLocFullString.replace("(", "").replace(")", "");

		String[] typeLocStatusList = typeLocFullString.split(";");

		DerivedUnit originalSpecimen = simpleSpecimen.getSpecimen();

		//TODO special character ?, �, !

		for (String typeLocStatus : typeLocStatusList){

			typeLocStatus = typeLocStatus.trim();

			int pos = typeLocStatus.indexOf(" ");

			if (pos == -1){

				logger.warn("Unknown format: " + typeLocStatus);

			}else{

				String statusString = typeLocStatus.substring(0,pos);

				SpecimenTypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config);

				String[] collectionStrings = typeLocStatus.substring(pos).split(",");

				for(String collectionString : collectionStrings){

					if (taxonBase != null){

						TaxonNameBase<?, ?> taxonName = taxonBase.getName();

						if (taxonName != null){

							Reference citation = null;

							String citationMicroReference = null;

							String originalNameString = null;

							boolean isNotDesignated = true;

							boolean addToAllHomotypicNames = true;

							DerivedUnit specimen = (DerivedUnit)originalSpecimen.clone();

							unlazyTypeDesignation(config, taxonName);

							taxonName.addSpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString, isNotDesignated, addToAllHomotypicNames);

							result = true;

						}

					}

				}

			}

		}

		return result;

	}

	private static Map<String, SpecimenTypeDesignationStatus> statusMap;

	private static void fillTypeStatusMap(){

		statusMap = new HashMap<String, SpecimenTypeDesignationStatus>();

		statusMap.put("epitype", SpecimenTypeDesignationStatus.EPITYPE());

		statusMap.put("holotype", SpecimenTypeDesignationStatus.HOLOTYPE());

		statusMap.put("iconotype", SpecimenTypeDesignationStatus.ICONOTYPE());

		statusMap.put("isotype", SpecimenTypeDesignationStatus.ISOTYPE());

		statusMap.put("isoneotype", SpecimenTypeDesignationStatus.ISONEOTYPE());

		statusMap.put("isosyntype", SpecimenTypeDesignationStatus.ISOSYNTYPE());

		statusMap.put("isolectotype", SpecimenTypeDesignationStatus.ISOLECTOTYPE());

		statusMap.put("lectotype", SpecimenTypeDesignationStatus.LECTOTYPE());

		statusMap.put("syntype", SpecimenTypeDesignationStatus.SYNTYPE());

		statusMap.put("paratype", SpecimenTypeDesignationStatus.PARATYPE());

		statusMap.put("neotype", SpecimenTypeDesignationStatus.NEOTYPE());

		statusMap.put("isoepitype", SpecimenTypeDesignationStatus.ISOEPITYPE());

		statusMap.put("originalmaterial", SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL());

		statusMap.put("paralectotype", SpecimenTypeDesignationStatus.PARALECTOTYPE());

		statusMap.put("paraneotype", SpecimenTypeDesignationStatus.PARANEOTYPE());

		statusMap.put("phototype", SpecimenTypeDesignationStatus.PHOTOTYPE());

		statusMap.put("secondsteplectotype", SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE());

		statusMap.put("secondstepneotype", SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE());

		statusMap.put("type", null);

	}

	//TODO move to TypeDesignation class

	/**

	 * Returns the typeDesignationStatus according to a type designation status string

	 * @param statusString

	 * @return TypeDesignationStatus

	 */

	private static SpecimenTypeDesignationStatus getStatusByStatusString(String statusString, TaxonXImportConfigurator config){

		SpecimenTypeDesignationStatus result = null;

		if (statusString == null || "".equals(statusString.trim())){

			return null;

		}

		statusString = statusString.trim().toLowerCase();

		statusString = statusString.replace("typi", "typus");

		statusString = statusString.replace("typus", "type");

		statusString = statusString.replace("types", "type");

		statusString = statusString.toLowerCase();

		if (statusMap == null){

			fillTypeStatusMap();

		}

		result = statusMap.get(statusString);

		if (statusString.equals("type")){

			logger.info("No type designation type" + getBracketSourceName(config));

		}else if (result == null){

			logger.warn("Unknown type status string: " + statusString + getBracketSourceName(config));

		}

		return result;

	}

	/**

	 * TODO Preliminary to avoid laizy loading errors

	 */

	private void unlazyTypeDesignation(TaxonXImportConfigurator config, TaxonNameBase taxonNameBase){

		TransactionStatus txStatus = startTransaction();

		//INameService taxonNameService = config.getCdmAppController().getNameService();

		INameService taxonNameService = getNameService();

		taxonNameService.save(taxonNameBase);

		Set<TaxonNameBase> typifiedNames = taxonNameBase.getHomotypicalGroup().getTypifiedNames();

		for(TaxonNameBase typifiedName: typifiedNames){

			typifiedName.getTypeDesignations().size();

		}

		//taxonNameService.saveTaxonName(taxonNameBase);

		commitTransaction(txStatus);

	}

	/**

	 * TODO Preliminary to avoid laizy loading errors

	 */

	private void unlazySynonym(IImportConfigurator config, Taxon taxon){

		TransactionStatus txStatus = startTransaction();

		ITaxonService taxonService = getTaxonService();

		taxonService.save(taxon);

		Set<Synonym> synonyms = taxon.getSynonyms();

		logger.debug(synonyms.size());

		//taxonService.saveTaxon(taxon);

		commitTransaction(txStatus);

	}

	private static String getBracketSourceName(TaxonXImportConfigurator config){

		return "(" + config.getSourceNameString() + ")";

	}

}