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.tcsrdf;

import java.util.ArrayList;

import java.util.Iterator;

import java.util.List;

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 com.hp.hpl.jena.rdf.model.Model;

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

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.io.common.TdwgAreaProvider;

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

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

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

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

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

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

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

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

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

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

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 29.05.2008

 * @version 1.0

 */

@Component

public class TcsRdfTaxonImport  extends TcsRdfImportBase implements ICdmIO<TcsRdfImportState> {

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

	private static int modCount = 30000;

	public TcsRdfTaxonImport(){

		super();

	}

	@Override

	public boolean doCheck(TcsRdfImportState state){

		boolean result = true;

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

		//result &= checkArticlesWithoutJournal(bmiConfig);

		//result &= checkPartOfJournal(bmiConfig);

		return result;

	}

	protected static CdmSingleAttributeRDFMapperBase[] standardMappers = new CdmSingleAttributeRDFMapperBase[]{

//		new CdmTextElementMapper("genusPart", "genusOrUninomial")

	};

	protected static CdmSingleAttributeRDFMapperBase[] operationalMappers = new CdmSingleAttributeRDFMapperBase[]{

		 new CdmUnclearMapper("hasName")

		,new CdmUnclearMapper("hasName")

		, new CdmUnclearMapper("accordingTo")

		, new CdmUnclearMapper("hasRelationship")

		, new CdmUnclearMapper("code", nsTgeo)	

	};

	protected static CdmSingleAttributeRDFMapperBase[] unclearMappers = new CdmSingleAttributeRDFMapperBase[]{

		new CdmUnclearMapper("primary")

		, new CdmUnclearMapper("note", nsTcom)	

		, new CdmUnclearMapper("taxonStatus", nsTpalm)

		, new CdmUnclearMapper("TaxonName", nsTn)	

		, new CdmUnclearMapper("dateOfEntry", nsTpalm)	

	};

	@Override

	protected void doInvoke(TcsRdfImportState state){

		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);

		MapWrapper<Reference> nomRefMap = (MapWrapper<Reference>)state.getStore(ICdmIO.NOMREF_STORE);

		String xmlElementName;

		String xmlAttributeName;

		String elementNamespace;

		String attributeNamespace;

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

		TcsRdfImportConfigurator config = state.getConfig();

		Model root = config.getSourceRoot();

		String rdfNamespace = config.getRdfNamespaceURIString();

		String idNamespace = "TaxonConcept";

		xmlElementName = "TaxonConcept";

		elementNamespace = config.getTcNamespaceURIString();

		return;

	}

	/**

	 * @param rdfNamespace 

	 * @param elTaxonConcept 

	 * @return

	 */

	private boolean isSynonym(Element elTaxonConcept, Namespace tpalmNamespace) {

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

			return false;

		}

		Element status = elTaxonConcept.getChild("taxonStatus", tpalmNamespace);

		if (status == null){

			return false;

		}else{

			String statusText = status.getTextNormalize();

			if ("S".equalsIgnoreCase(statusText)){

				return true;

			}else if ("A".equalsIgnoreCase(statusText)){

				return false;

			}else if ("C".equalsIgnoreCase(statusText)){

				return false;

			}else if ("V".equalsIgnoreCase(statusText)){

				return false;

			}else if ("O".equalsIgnoreCase(statusText)){

				return false;

			}else if ("U".equalsIgnoreCase(statusText)){

				return false;

			}else{

				logger.warn("Unknown taxon status: " +  statusText);

				return false;

			}

		}

	}

	private boolean hasIsSynonymRelation(Element elTaxonConcept, Namespace rdfNamespace){

		boolean result = false;

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

			return false;

		}

		String elName = "relationshipCategory";

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

		Iterator<Element> relationshipCategories = elTaxonConcept.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;

	}

	private List<DescriptionElementBase> makeGeo(Element elConcept, Namespace geoNamespace, Namespace rdfNamespace){

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

		String xmlElementName = "code";

		List<Element> elGeos = elConcept.getChildren(xmlElementName, geoNamespace);

		int i = 0;

		//for each geoTag

		for (Element elGeo : elGeos){

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

			String strGeoRegion = elGeo.getAttributeValue("resource", rdfNamespace);

			strGeoRegion = strGeoRegion.replace("http://rs.tdwg.org/ontology/voc/GeographicRegion#", "");

			NamedArea namedArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(strGeoRegion);

			PresenceAbsenceTermBase<?> status = PresenceTerm.PRESENT();

			DescriptionElementBase distribution = Distribution.NewInstance(namedArea, status);

			distribution.setFeature(Feature.DISTRIBUTION());

			//System.out.println(namedArea);

			result.add(distribution);

		}

		return result;

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(TcsRdfImportState state){

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

	}

}