EDIT

/**

* Copyright (C) 2009 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.tcsxml.in;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.jdom.Attribute;

import org.jdom.Element;

import org.jdom.Namespace;

import org.jdom.filter.ElementFilter;

import org.jdom.filter.Filter;

import org.springframework.stereotype.Component;

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

import eu.etaxonomy.cdm.common.ResultWrapper;

import eu.etaxonomy.cdm.common.XmlHelp;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 *

 */

@Component

public class TcsXmlTaxonImport  extends TcsXmlImportBase implements ICdmIO<TcsXmlImportState> {

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

	private static int modCount = 30000;

	public TcsXmlTaxonImport(){

		super();

	}

	@Override

	public boolean doCheck(TcsXmlImportState state){

		boolean result = true;

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

		//result &= checkArticlesWithoutJournal(bmiConfig);

		//result &= checkPartOfJournal(bmiConfig);

		return result;

	}

	/**

	 * Computes a list of all TaxonConcept ids (ref-attribute) that are related as synonyms

	 * @param elTaxonConceptList

	 * @param success

	 * @return

	 */

	private Set<String> makeSynonymIds(List<Element> elTaxonConceptList, ResultWrapper<Boolean> success){

		//TODO use XPath

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

		Namespace tcsNamespace;

		//for each taxonConcept

		for (Element elTaxonConcept : elTaxonConceptList){

			tcsNamespace = elTaxonConcept.getNamespace();

			String childName = "TaxonRelationships";

			boolean obligatory = false;

			Element elTaxonRelationships = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

			if (elTaxonRelationships == null){

				continue;

			}

			String tcsElementName = "TaxonRelationship";

			List<Element> elTaxonRelationshipList = elTaxonRelationships.getChildren(tcsElementName, tcsNamespace);

			for (Element elTaxonRelationship : elTaxonRelationshipList){

				String relationshipType = elTaxonRelationship.getAttributeValue("type");

				if ("has synonym".equalsIgnoreCase(relationshipType)){

					childName = "ToTaxonConcept";

					obligatory = true;

					Element elToTaxonConcept = XmlHelp.getSingleChildElement(success, elTaxonRelationship, childName, tcsNamespace, obligatory);

					String linkType = elToTaxonConcept.getAttributeValue("linkType");

					if (linkType == null || linkType.equals("local")){

						String ref = elToTaxonConcept.getAttributeValue("ref");

						result.add(ref);

					}else{

						logger.warn("External link types for synonym not yet implemented");

					}		

				}

			}

		}

		return result;

	}

	protected static final Reference unknownSec(){

		ReferenceFactory refFactory = ReferenceFactory.newInstance();

		Reference result = refFactory.newGeneric();

		result.setTitleCache("UNKNOWN", true);

		return result;

	}

	@Override

	public void doInvoke(TcsXmlImportState state){

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

		MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE);

		MapWrapper<TaxonNameBase<?,?>> taxonNameMap = (MapWrapper<TaxonNameBase<?,?>>)state.getStore(ICdmIO.TAXONNAME_STORE);

		MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);

		Map<String, CommonTaxonName> commonNameMap = new HashMap<String, CommonTaxonName>();

		ITaxonService taxonService = getTaxonService();

		ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);

		String childName;

		boolean obligatory;

		String idNamespace = "TaxonConcept";

		TcsXmlImportConfigurator config = state.getConfig();

		Element elDataSet = getDataSetElement(config);

		Namespace tcsNamespace = config.getTcsXmlNamespace();

		childName = "TaxonConcepts";

		obligatory = false;

		Element elTaxonConcepts = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);

		String tcsElementName = "TaxonConcept";

		List<Element> elTaxonConceptList = elTaxonConcepts.getChildren(tcsElementName, tcsNamespace);

		Set<String> synonymIdSet = makeSynonymIds(elTaxonConceptList, success);

		//TODO make the same for the Assertions

		int i = 0;

		//for each taxonConcept

		for (Element elTaxonConcept : elTaxonConceptList){

			if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}

			List<String> elementList = new ArrayList<String>();

			//create TaxonName element

			String strId = elTaxonConcept.getAttributeValue("id");

			//TODO

			String strConceptType = elTaxonConcept.getAttributeValue("type"); //original, revision, incomplete, aggregate, nominal

			String strPrimary = elTaxonConcept.getAttributeValue("primary"); //If primary='true' the concept is the first level response to a query. If 'false' the concept may be a secondary concept linked directly or indirectly to the definition of a primary concept.

			String strForm = elTaxonConcept.getAttributeValue("form");  //anamorph, teleomorph, hybrid

			childName = "Name";

			obligatory = true;

			Element elName = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

			if (isVernacular(success, elName)){

				handleVernacularName(success, strId, elName, commonNameMap);

			}else{

				TaxonNameBase<?,?> taxonName = makeScientificName(elName, null, taxonNameMap, success);

				elementList.add(childName.toString());

				//TODO how to handle

				childName = "Rank";

				obligatory = false;

				Element elRank = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				Rank rank = TcsXmlTaxonNameImport.makeRank(elRank);

				if (rank != null){

					logger.warn("Rank in TaxonIO not yet implemented");

				}

				elementList.add(childName.toString());

				childName = "AccordingTo";

				obligatory = false;

				Element elAccordingTo = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				Reference sec = makeAccordingTo(elAccordingTo, referenceMap, success);

				elementList.add(childName.toString());

				// TODO may sec be null?

				if (sec == null){

					sec = unknownSec();

				}

				TaxonBase taxonBase;

				if (synonymIdSet.contains(strId)){

					taxonBase = Synonym.NewInstance(taxonName, sec);

				}else{

					taxonBase = Taxon.NewInstance(taxonName, sec);	

				}

				childName = "TaxonRelationships";

				obligatory = false;

				Element elTaxonRelationships = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				makeTaxonRelationships(taxonBase, elTaxonRelationships, success);

				elementList.add(childName.toString());

				childName = "SpecimenCircumscription";

				obligatory = false;

				Element elSpecimenCircumscription = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				makeSpecimenCircumscription(taxonBase, elSpecimenCircumscription, success);

				elementList.add(childName.toString());

				childName = "CharacterCircumscription";

				obligatory = false;

				Element elCharacterCircumscription = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				makeCharacterCircumscription(taxonBase, elCharacterCircumscription, success);

				elementList.add(childName.toString());

				childName = "ProviderLink";

				obligatory = false;

				Element elProviderLink = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				makeProviderLink(taxonBase, elProviderLink, success);

				elementList.add(childName.toString());

				childName = "ProviderSpecificData";

				obligatory = false;

				Element elProviderSpecificData = XmlHelp.getSingleChildElement(success, elTaxonConcept, childName, tcsNamespace, obligatory);

				makeProviderSpecificData(taxonBase, elProviderSpecificData, success);

				elementList.add(childName.toString());

				testAdditionalElements(elTaxonConcept, elementList);

				ImportHelper.setOriginalSource(taxonBase, config.getSourceReference(), strId, idNamespace);

				taxonMap.put(strId, taxonBase);

			}

		}

		state.setCommonNameMap(commonNameMap);

		//invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap);

		logger.info(i + " taxa handled. Saving ...");

		taxonService.save(taxonMap.objects());

		logger.info("end makeTaxa ...");

		if (!success.getValue()){

			state.setUnsuccessfull();

		}

		return;

	}

	private void handleVernacularName(ResultWrapper<Boolean> success, String taxonId, Element elName, Map<String, CommonTaxonName> commonNameMap) {

		String name = elName.getTextNormalize();

		//TODO ref

		Language language = null;

		String strLanguage = elName.getAttributeValue("language");

		//TODO

		//Language

		if (strLanguage != null){

			language = Language.getLanguageByLabel(strLanguage);

			if (language == null){

				language = Language.getLanguageByDescription(strLanguage);

			}

			if (language == null){

				logger.warn("language ("+strLanguage+") not found for name " + name);	

			}

		}

		CommonTaxonName commonName = CommonTaxonName.NewInstance(name, language);

		commonNameMap.put(taxonId, commonName);

		//TODO check other elements

	}

	private boolean isVernacular(ResultWrapper<Boolean> success, Element elName) {

		try{

			String strScientific = elName.getAttributeValue("scientific");

			boolean scientific = Boolean.valueOf(strScientific);

			return ! scientific;

		} catch (Exception e) {

			logger.warn("Value for scientific is not boolean");

			success.setValue(false);

			return false;

		}

	}

	private boolean hasIsSynonymRelation(Element taxonConcept, Namespace rdfNamespace){

		boolean result = false;

		if (taxonConcept == null || ! "TaxonConcept".equalsIgnoreCase(taxonConcept.getName()) ){

			return false;

		}

		String elName = "relationshipCategory";

		Filter filter = new ElementFilter(elName, taxonConcept.getNamespace());

		Iterator<Element> relationshipCategories = taxonConcept.getDescendants(filter);

		while (relationshipCategories.hasNext()){

			Element relationshipCategory = relationshipCategories.next();

			Attribute resource = relationshipCategory.getAttribute("resource", rdfNamespace);

			String isSynonymFor = "http://rs.tdwg.org/ontology/voc/TaxonConcept#IsSynonymFor";

			if (resource != null && isSynonymFor.equalsIgnoreCase(resource.getValue()) ){

				return true;

			}

		}

		return result;

	}

	/**

	 * @param elTaxonRelationships

	 * @param success

	 */

	private TaxonNameBase<?, ?> makeScientificName(Element elName, NomenclaturalCode code, MapWrapper<? extends TaxonNameBase<?,?>> objectMap, ResultWrapper<Boolean> success){

		TaxonNameBase<?, ?> result = null;

		if (elName != null){

			String language = elName.getAttributeValue("language");

			//Language

			if (language != null){

				logger.warn("language for name not yet implemented. Language for scientific name should always be Latin");	

			}

			Class<? extends IdentifiableEntity> clazz = (Class<? extends IdentifiableEntity>)NonViralName.class;

			if (code != null){

				clazz = code.getCdmClass();

			}

			result = (TaxonNameBase<?,?>)makeReferenceType (elName, clazz , objectMap, success);

			if(result == null){

				logger.warn("Name not found");

				success.setValue(false);

			}

		}else{

			logger.warn("Name element is null");

		}

		return result;

	}

	/**

	 * @param elTaxonRelationships

	 * @param success

	 */

	private void makeTaxonRelationships(TaxonBase name, Element elTaxonRelationships, ResultWrapper<Boolean> success){

		//TaxonRelationships are handled in TcsXmlTaxonRelationsImport

		return;

	}

	private void makeSpecimenCircumscription(TaxonBase name, Element elSpecimenCircumscription, ResultWrapper<Boolean> success){

		if (elSpecimenCircumscription != null){

			logger.warn("makeProviderLink not yet implemented");

			success.setValue(false);

		}

	}

	private void makeCharacterCircumscription(TaxonBase name, Element elCharacterCircumscription, ResultWrapper<Boolean> success){

		if (elCharacterCircumscription != null){

			logger.warn("makeProviderLink not yet implemented");

			success.setValue(false);

		}

	}

	private void makeProviderLink(TaxonBase name, Element elProviderLink, ResultWrapper<Boolean> success){

		if (elProviderLink != null){

			logger.warn("makeProviderLink not yet implemented");

			success.setValue(false);

		}

	}

	private void makeProviderSpecificData(TaxonBase name, Element elProviderSpecificData, ResultWrapper<Boolean> success){

		if (elProviderSpecificData != null){

			logger.warn("makeProviderLink not yet implemented");

			success.setValue(false);

		}

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(TcsXmlImportState state){

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

	}

}