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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.tcsrdf;
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import java.io.InputStream;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.jdom.Attribute;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.springframework.stereotype.Component;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import eu.etaxonomy.cdm.common.XmlHelp;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.IGeneric;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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* @created 29.05.2008
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* @version 1.0
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*/
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@Component
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public class TcsRdfTaxonNameImport extends TcsRdfImportBase implements ICdmIO<TcsRdfImportState> {
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private static final Logger logger = Logger.getLogger(TcsRdfTaxonNameImport.class);
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private static int modCount = 5000;
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public TcsRdfTaxonNameImport(){
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super();
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}
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@Override
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public boolean doCheck(TcsRdfImportState config){
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boolean result = true;
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logger.warn("BasionymRelations not yet implemented");
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logger.warn("Checking for TaxonNames not yet implemented");
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//result &= checkArticlesWithoutJournal(tcsConfig);
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//result &= checkPartOfJournal(tcsConfig);
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return result;
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}
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protected static CdmSingleAttributeRDFMapperBase[] standardMappers = new CdmSingleAttributeRDFMapperBase[]{
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new CdmTextElementMapper("genusPart", "genusOrUninomial")
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, new CdmTextElementMapper("uninomial", "genusOrUninomial") //TODO make it a more specific Mapper for both attributes
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, new CdmTextElementMapper("specificEpithet", "specificEpithet")
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, new CdmTextElementMapper("infraspecificEpithet", "infraSpecificEpithet")
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, new CdmTextElementMapper("infragenericEpithet", "infraGenericEpithet")
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, new CdmTextElementMapper("microReference", nsTcom, "nomenclaturalMicroReference")
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};
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protected static CdmSingleAttributeRDFMapperBase[] operationalMappers = new CdmSingleAttributeRDFMapperBase[]{
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new CdmUnclearMapper("basionymAuthorship")
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, new CdmUnclearMapper("combinationAuthorship")
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, new CdmUnclearMapper("hasAnnotation")
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, new CdmUnclearMapper("rank")
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, new CdmUnclearMapper("nomenclaturalCode")
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, new CdmUnclearMapper("publishedIn", nsTcom)
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, new CdmUnclearMapper("year")
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};
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protected static CdmSingleAttributeRDFMapperBase[] unclearMappers = new CdmSingleAttributeRDFMapperBase[]{
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new CdmUnclearMapper("authorship")
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, new CdmUnclearMapper("rankString")
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, new CdmUnclearMapper("nameComplete")
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, new CdmUnclearMapper("hasBasionym")
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, new CdmUnclearMapper("dateOfEntry", nsTpalm)
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};
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@Override
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protected void doInvoke(TcsRdfImportState state){
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MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE);
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MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);
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MapWrapper<TeamOrPersonBase> authorMap = (MapWrapper<TeamOrPersonBase>)state.getStore(ICdmIO.TEAM_STORE);
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String tcsElementName;
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Namespace tcsNamespace;
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String value;
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logger.info("start makeTaxonNames ...");
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TcsRdfImportConfigurator config = state.getConfig();
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Model root = config.getSourceRoot();
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String rdfNamespace = config.getRdfNamespaceURIString();
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String taxonNameNamespace = config.getTnNamespaceURIString();
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String idNamespace = "TaxonName";
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Resource elTaxonName = root.getResource(taxonNameNamespace);
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int i = 0;
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TaxonNameBase name;
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Property property = root.getProperty(taxonNameNamespace+"authorship");
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ResIterator iterator = root.listSubjectsWithProperty(property, (RDFNode) null);
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String id ;
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while (iterator.hasNext()){
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Resource resource = iterator.next();
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name = handleNameResource(resource, config);
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id = resource.getNameSpace();
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taxonNameMap.put(id, name);
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}
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logger.info(i + " names handled");
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getNameService().save(taxonNameMap.objects());
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// makeNameSpecificData(nameMap);
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logger.info("end makeTaxonNames ...");
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return;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean isIgnore(TcsRdfImportState state){
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return ! state.getConfig().isDoTaxonNames();
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}
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protected TaxonNameBase handleNameModel(Model model, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap, String uri){
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Resource nameAbout = model.getResource(uri);
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TaxonNameBase result = handleNameResource(nameAbout, config);
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taxonNameMap.put(uri, result);
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return result;
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}
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private TaxonNameBase handleNameResource(Resource nameAbout, TcsRdfImportConfigurator config){
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String idNamespace = "TaxonName";
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StmtIterator stmts = nameAbout.listProperties();
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while(stmts.hasNext()){
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System.out.println(stmts.next().getPredicate().toString());
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}
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Property prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nomenclaturalCode");
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Statement stateNomenclaturalCode = nameAbout.getProperty(prop);
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String strNomenclaturalCode = stateNomenclaturalCode.getObject().toString();
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//Rank
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"rankString");
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String strRank = nameAbout.getProperty(prop).getString();
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try {
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Rank rank = TcsRdfTransformer.rankString2Rank(strRank);
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NomenclaturalCode nomCode;
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if (strNomenclaturalCode != null){
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nomCode = TcsRdfTransformer.nomCodeString2NomCode(strNomenclaturalCode);
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}else{
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nomCode = NomenclaturalCode.ICNAFP;
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}
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TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank);
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Set<String> omitAttributes = null;
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//makeStandardMapper(nameAbout, nameBase, omitAttributes, standardMappers);
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"nameComplete");
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String strNameComplete = nameAbout.getProperty(prop).getString();
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nameBase.setTitleCache(strNameComplete, true);
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prop = nameAbout.getModel().getProperty(config.getCommonNamespaceURIString()+"publishedIn");
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String strPublishedIn = nameAbout.getProperty(prop).getString();
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if (strPublishedIn != null && strPublishedIn != ""){
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IGeneric nomRef = ReferenceFactory.newGeneric(); //TODO
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nomRef.setTitleCache(strPublishedIn, true);
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nameBase.setNomenclaturalReference(nomRef);
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try{
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"year");
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String strYear = nameAbout.getProperty(prop).getString();
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Integer year = null;
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if (strYear != null){
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try {
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year = Integer.valueOf(strYear);
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TimePeriod timeP = TimePeriod.NewInstance(year);
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nomRef.setDatePublished(timeP);
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} catch (RuntimeException e) {
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logger.warn("year could not be parsed");
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}
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}
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}catch(NullPointerException e){
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}
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if (config.isPublishReferences()){
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((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
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}
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}
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if (nameBase instanceof NonViralName){
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NonViralName<?> nonViralName = (NonViralName<?>)nameBase;
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"genusPart");
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String strGenusPart;
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try{
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strGenusPart = nameAbout.getProperty(prop).getString();
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}catch(NullPointerException e){
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"uninomial");
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strGenusPart = nameAbout.getProperty(prop).getString();
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}
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nonViralName.setGenusOrUninomial(strGenusPart);
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infragenericEpithet");
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try{
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String strInfragenericEpithet = nameAbout.getProperty(prop).getString();
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nonViralName.setInfraGenericEpithet(strInfragenericEpithet);
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}catch(NullPointerException e){
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}
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try {
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"specificEpithet");
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String strSpecificEpithet = nameAbout.getProperty(prop).getString();
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nonViralName.setSpecificEpithet(strSpecificEpithet);
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}catch(NullPointerException e){
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}
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try{
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"infraspecificEpithet");
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String strInfraspecificEpithet = nameAbout.getProperty(prop).getString();
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nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet);
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}catch(NullPointerException e){
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}
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//Authorships
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//TODO
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/*
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* <tn:authorteam>
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<tm:Team>
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<tm:name>(Raf.) Fernald</tm:name>
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<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:2691-1"
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tm:index="1"
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tm:role="Combination Author"/>
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<tm:hasMember rdf:resource="urn:lsid:ipni.org:authors:8096-1"
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tm:index="1"
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tm:role="Basionym Author"/>
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</tm:Team>
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</tn:authorteam>
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*/
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"authorship");
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Statement stateAuthorship = nameAbout.getProperty(prop);
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prop = nameAbout.getModel().getProperty(config.getTnNamespaceURIString()+"authorteam");
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Statement stateAuthorTeam = nameAbout.getProperty(prop);
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Team authorTeam = new Team();
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authorTeam.setTitleCache(stateAuthorship.getObject().toString(), true);
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Statement stateAutorTeamTeam = null;
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Statement stateAutorTeamName = null;
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StmtIterator stateTeamMember = null;
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if (stateAuthorTeam != null){
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prop = stateAuthorTeam.getModel().getProperty(config.getTeamNamespaceURIString()+"Team");
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try{
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stateAutorTeamTeam = stateAuthorTeam.getProperty(prop);
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}catch(Exception e){
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}
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try{
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prop = stateAuthorTeam.getModel().getProperty(config.getTeamNamespaceURIString()+"name");
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stateAutorTeamName = stateAuthorTeam.getProperty(prop);
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}catch(Exception e){
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}
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try{
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prop = nameAbout.getModel().getProperty(config.getTeamNamespaceURIString()+"hasMember");
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stateTeamMember = ((Resource)stateAuthorTeam.getObject()).listProperties(prop);
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String memberString = null;
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Person person;
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for (Statement statement :stateTeamMember.toList()){
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memberString =statement.getObject().toString();
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if (memberString != null){
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person = Person.NewTitledInstance(memberString);
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authorTeam.addTeamMember(person);
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}
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}
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}catch(Exception e){
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System.err.println(e.getMessage());
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}
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}
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nonViralName.setCombinationAuthorship(authorTeam);
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//Annotations:
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/*
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* <tn:hasAnnotation>
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<tn:NomenclaturalNote>
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<tn:noteType rdf:resource="http://rs.tdwg.org/ontology/voc/TaxonName#replacementNameFor"/>
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<tn:objectTaxonName rdf:resource="urn:lsid:ipni.org:names:151538-1"/>
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</tn:NomenclaturalNote>
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</tn:hasAnnotation>
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*/
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/*
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String strInfraspecificEpithet = nameAbout.getProperty(prop).getString();
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tcsElementName = "basionymAuthorship";
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String basionymAuthorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
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if (basionymAuthorValue != null){
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TeamOrPersonBase<?> basionymAuthor = Team.NewInstance();
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basionymAuthor.setNomenclaturalTitle(basionymAuthorValue);
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nonViralName.setBasionymAuthorship(basionymAuthor);
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}
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//TODO
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tcsElementName = "combinationAuthorship";
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String combinationAuthorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
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if (combinationAuthorValue != null){
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TeamOrPersonBase<?> combinationAuthor = Team.NewInstance();
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combinationAuthor.setNomenclaturalTitle(combinationAuthorValue);
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nonViralName.setCombinationAuthorship(combinationAuthor);
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}
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//set the authorshipCache
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346
|
tcsElementName = "authorship";
|
|
347
|
String authorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
348
|
String cache = nonViralName.getAuthorshipCache();
|
|
349
|
if ( authorValue != null){
|
|
350
|
//compare existing authorship cache with new one and check if it is necessary to
|
|
351
|
//make cache protected //TODO refinement
|
|
352
|
if (cache == null){
|
|
353
|
nonViralName.setAuthorshipCache(authorValue);
|
|
354
|
}else{
|
|
355
|
cache = basionymAuthorValue == null ? cache : cache.replace(basionymAuthorValue, "");
|
|
356
|
cache = combinationAuthorValue == null ? cache : cache.replace(combinationAuthorValue, "");
|
|
357
|
cache = cache.replace("\\(|\\)", "");
|
|
358
|
cache = cache.trim();
|
|
359
|
if (! cache.equals("")){
|
|
360
|
nonViralName.setAuthorshipCache(authorValue);
|
|
361
|
}
|
|
362
|
}
|
|
363
|
}*/
|
|
364
|
}
|
|
365
|
//ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), nameAbout, idNamespace);
|
|
366
|
|
|
367
|
//checkAdditionalContents(elTaxonName, standardMappers, operationalMappers, unclearMappers);
|
|
368
|
|
|
369
|
return nameBase;
|
|
370
|
|
|
371
|
}catch(Exception e){
|
|
372
|
e.printStackTrace();
|
|
373
|
return null;
|
|
374
|
}
|
|
375
|
/*
|
|
376
|
//name
|
|
377
|
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace);
|
|
378
|
nameBase.setTitleCache(strNameComplete, true);
|
|
379
|
|
|
380
|
//Reference
|
|
381
|
//TODO
|
|
382
|
String tcsElementName = "publishedIn";
|
|
383
|
Namespace tcsNamespace = config.getCommonNamespaceURIString();
|
|
384
|
String value = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, tcsNamespace);
|
|
385
|
if (value != null && value != ""){
|
|
386
|
IGeneric nomRef = ReferenceFactory.newGeneric(); //TODO
|
|
387
|
nomRef.setTitleCache(value, true);
|
|
388
|
nameBase.setNomenclaturalReference(nomRef);
|
|
389
|
|
|
390
|
//TODO
|
|
391
|
tcsElementName = "year";
|
|
392
|
tcsNamespace = taxonNameNamespace;
|
|
393
|
Integer year = null;
|
|
394
|
value = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, tcsNamespace);
|
|
395
|
if (value != null){
|
|
396
|
try {
|
|
397
|
year = Integer.valueOf(value);
|
|
398
|
TimePeriod timeP = TimePeriod.NewInstance(year);
|
|
399
|
nomRef.setDatePublished(timeP);
|
|
400
|
} catch (RuntimeException e) {
|
|
401
|
logger.warn("year could not be parsed");
|
|
402
|
}
|
|
403
|
}
|
|
404
|
if (config.isPublishReferences()){
|
|
405
|
((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
|
|
406
|
}
|
|
407
|
}
|
|
408
|
|
|
409
|
//Status
|
|
410
|
tcsNamespace = taxonNameNamespace;
|
|
411
|
Element elAnnotation = elTaxonName.getChild("hasAnnotation", tcsNamespace);
|
|
412
|
if (elAnnotation != null){
|
|
413
|
Element elNomenclaturalNote = elAnnotation.getChild("NomenclaturalNote", tcsNamespace);
|
|
414
|
if (elNomenclaturalNote != null){
|
|
415
|
String statusValue = (String)ImportHelper.getXmlInputValue(elNomenclaturalNote, "note", tcsNamespace);
|
|
416
|
String type = XmlHelp.getChildAttributeValue(elNomenclaturalNote, "type", tcsNamespace, "resource", rdfNamespace);
|
|
417
|
String tdwgType = "http://rs.tdwg.org/ontology/voc/TaxonName#PublicationStatus";
|
|
418
|
if (tdwgType.equalsIgnoreCase(type)){
|
|
419
|
try {
|
|
420
|
NomenclaturalStatusType statusType = TcsRdfTransformer.nomStatusString2NomStatus(statusValue);
|
|
421
|
//NomenclaturalStatusType statusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusValue);
|
|
422
|
if (statusType != null){
|
|
423
|
nameBase.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
424
|
}
|
|
425
|
} catch (UnknownCdmTypeException e) {
|
|
426
|
if (! statusValue.equals("valid")){
|
|
427
|
logger.warn("Unknown NomenclaturalStatusType: " + statusValue);
|
|
428
|
}
|
|
429
|
}
|
|
430
|
}
|
|
431
|
}
|
|
432
|
}
|
|
433
|
|
|
434
|
if (nameBase instanceof NonViralName){
|
|
435
|
NonViralName<?> nonViralName = (NonViralName<?>)nameBase;
|
|
436
|
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace);
|
|
437
|
|
|
438
|
//for names of rank genus the uninomial property should be used
|
|
439
|
if (strGenusPart == null){
|
|
440
|
strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace);
|
|
441
|
}
|
|
442
|
nonViralName.setGenusOrUninomial(strGenusPart);
|
|
443
|
|
|
444
|
String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace);
|
|
445
|
nonViralName.setGenusOrUninomial(strInfragenericEpithet);
|
|
446
|
|
|
447
|
|
|
448
|
|
|
449
|
String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace);
|
|
450
|
nonViralName.setSpecificEpithet(strSpecificEpithet);
|
|
451
|
|
|
452
|
String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace);
|
|
453
|
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet);
|
|
454
|
//AuthorTeams
|
|
455
|
//TODO
|
|
456
|
tcsElementName = "basionymAuthorship";
|
|
457
|
String basionymAuthorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
458
|
if (basionymAuthorValue != null){
|
|
459
|
TeamOrPersonBase<?> basionymAuthor = Team.NewInstance();
|
|
460
|
basionymAuthor.setNomenclaturalTitle(basionymAuthorValue);
|
|
461
|
nonViralName.setBasionymAuthorship(basionymAuthor);
|
|
462
|
}
|
|
463
|
|
|
464
|
//TODO
|
|
465
|
tcsElementName = "combinationAuthorship";
|
|
466
|
String combinationAuthorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
467
|
if (combinationAuthorValue != null){
|
|
468
|
TeamOrPersonBase<?> combinationAuthor = Team.NewInstance();
|
|
469
|
combinationAuthor.setNomenclaturalTitle(combinationAuthorValue);
|
|
470
|
nonViralName.setCombinationAuthorship(combinationAuthor);
|
|
471
|
}
|
|
472
|
|
|
473
|
//set the authorshipCache
|
|
474
|
tcsElementName = "authorship";
|
|
475
|
String authorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
476
|
String cache = nonViralName.getAuthorshipCache();
|
|
477
|
if ( authorValue != null){
|
|
478
|
//compare existing authorship cache with new one and check if it is necessary to
|
|
479
|
//make cache protected //TODO refinement
|
|
480
|
if (cache == null){
|
|
481
|
nonViralName.setAuthorshipCache(authorValue);
|
|
482
|
}else{
|
|
483
|
cache = basionymAuthorValue == null ? cache : cache.replace(basionymAuthorValue, "");
|
|
484
|
cache = combinationAuthorValue == null ? cache : cache.replace(combinationAuthorValue, "");
|
|
485
|
cache = cache.replace("\\(|\\)", "");
|
|
486
|
cache = cache.trim();
|
|
487
|
if (! cache.equals("")){
|
|
488
|
nonViralName.setAuthorshipCache(authorValue);
|
|
489
|
}
|
|
490
|
}
|
|
491
|
}
|
|
492
|
}
|
|
493
|
ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), nameAbout, idNamespace);
|
|
494
|
|
|
495
|
checkAdditionalContents(elTaxonName, standardMappers, operationalMappers, unclearMappers);
|
|
496
|
|
|
497
|
//nameId
|
|
498
|
//TODO
|
|
499
|
//ImportHelper.setOriginalSource(nameBase, tcsConfig.getSourceReference(), nameId);
|
|
500
|
//taxonNameMap.put(nameAbout, nameBase);
|
|
501
|
return nameBase;
|
|
502
|
}catch(UnknownCdmTypeException e){
|
|
503
|
e.printStackTrace();
|
|
504
|
}
|
|
505
|
return null;*/
|
|
506
|
}
|
|
507
|
|
|
508
|
protected TaxonNameBase handleNameElement(Element elTaxonName, Namespace rdfNamespace, Namespace taxonNameNamespace, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap){
|
|
509
|
String idNamespace = "TaxonName";
|
|
510
|
Attribute about = elTaxonName.getAttribute("about", rdfNamespace);
|
|
511
|
|
|
512
|
//create TaxonName element
|
|
513
|
|
|
514
|
|
|
515
|
String nameAbout = elTaxonName.getAttributeValue("about", rdfNamespace);
|
|
516
|
if (nameAbout == null){
|
|
517
|
nameAbout = XmlHelp.getChildAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "about", rdfNamespace);
|
|
518
|
}
|
|
519
|
|
|
520
|
|
|
521
|
String strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rankString", taxonNameNamespace, "rankString", rdfNamespace);
|
|
522
|
if (strRank == null){
|
|
523
|
strRank = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "rankString", rdfNamespace);
|
|
524
|
|
|
525
|
}
|
|
526
|
|
|
527
|
if (strRank == null){
|
|
528
|
strRank = XmlHelp.getChildAttributeValue(elTaxonName, "rank", taxonNameNamespace, "resource", rdfNamespace);
|
|
529
|
|
|
530
|
}
|
|
531
|
|
|
532
|
String strNomenclaturalCode = XmlHelp.getChildContentAttributeValue(elTaxonName, "TaxonName", taxonNameNamespace, "nomenclaturalCode", rdfNamespace);
|
|
533
|
if (strNomenclaturalCode == null){
|
|
534
|
strNomenclaturalCode = XmlHelp.getChildAttributeValue(elTaxonName, "nomenclaturalCode", taxonNameNamespace, "resource", rdfNamespace);
|
|
535
|
|
|
536
|
}
|
|
537
|
try {
|
|
538
|
|
|
539
|
Rank rank = TcsRdfTransformer.rankString2Rank(strRank);
|
|
540
|
NomenclaturalCode nomCode;
|
|
541
|
if (strNomenclaturalCode != null){
|
|
542
|
nomCode = TcsRdfTransformer.nomCodeString2NomCode(strNomenclaturalCode);
|
|
543
|
}else{
|
|
544
|
nomCode = NomenclaturalCode.ICNAFP;
|
|
545
|
}
|
|
546
|
|
|
547
|
TaxonNameBase<?,?> nameBase = nomCode.getNewTaxonNameInstance(rank);
|
|
548
|
|
|
549
|
Set<String> omitAttributes = null;
|
|
550
|
//makeStandardMapper(elTaxonName, nameBase, omitAttributes, standardMappers);
|
|
551
|
|
|
552
|
//name
|
|
553
|
String strNameComplete = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "nameComplete", rdfNamespace);
|
|
554
|
nameBase.setTitleCache(strNameComplete, true);
|
|
555
|
|
|
556
|
//Reference
|
|
557
|
//TODO
|
|
558
|
String tcsElementName = "publishedIn";
|
|
559
|
String tcsNamespace = config.getCommonNamespaceURIString();
|
|
560
|
/*String value = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, tcsNamespace);
|
|
561
|
if (value != null && value != ""){
|
|
562
|
IGeneric nomRef = ReferenceFactory.newGeneric(); //TODO
|
|
563
|
nomRef.setTitleCache(value, true);
|
|
564
|
nameBase.setNomenclaturalReference(nomRef);
|
|
565
|
|
|
566
|
//TODO
|
|
567
|
tcsElementName = "year";
|
|
568
|
tcsNamespace = taxonNameNamespace;
|
|
569
|
Integer year = null;
|
|
570
|
value = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, tcsNamespace);
|
|
571
|
if (value != null){
|
|
572
|
try {
|
|
573
|
year = Integer.valueOf(value);
|
|
574
|
TimePeriod timeP = TimePeriod.NewInstance(year);
|
|
575
|
nomRef.setDatePublished(timeP);
|
|
576
|
} catch (RuntimeException e) {
|
|
577
|
logger.warn("year could not be parsed");
|
|
578
|
}
|
|
579
|
}
|
|
580
|
if (config.isPublishReferences()){
|
|
581
|
((Reference)nomRef).addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
|
|
582
|
}
|
|
583
|
}
|
|
584
|
|
|
585
|
//Status
|
|
586
|
tcsNamespace = taxonNameNamespace;
|
|
587
|
Element elAnnotation = elTaxonName.getChild("hasAnnotation", tcsNamespace);
|
|
588
|
if (elAnnotation != null){
|
|
589
|
Element elNomenclaturalNote = elAnnotation.getChild("NomenclaturalNote", tcsNamespace);
|
|
590
|
if (elNomenclaturalNote != null){
|
|
591
|
String statusValue = (String)ImportHelper.getXmlInputValue(elNomenclaturalNote, "note", tcsNamespace);
|
|
592
|
String type = XmlHelp.getChildAttributeValue(elNomenclaturalNote, "type", tcsNamespace, "resource", rdfNamespace);
|
|
593
|
String tdwgType = "http://rs.tdwg.org/ontology/voc/TaxonName#PublicationStatus";
|
|
594
|
if (tdwgType.equalsIgnoreCase(type)){
|
|
595
|
try {
|
|
596
|
NomenclaturalStatusType statusType = TcsRdfTransformer.nomStatusString2NomStatus(statusValue);
|
|
597
|
//NomenclaturalStatusType statusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusValue);
|
|
598
|
if (statusType != null){
|
|
599
|
nameBase.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
600
|
}
|
|
601
|
} catch (UnknownCdmTypeException e) {
|
|
602
|
if (! statusValue.equals("valid")){
|
|
603
|
logger.warn("Unknown NomenclaturalStatusType: " + statusValue);
|
|
604
|
}
|
|
605
|
}
|
|
606
|
}
|
|
607
|
}
|
|
608
|
}
|
|
609
|
|
|
610
|
if (nameBase instanceof NonViralName){
|
|
611
|
NonViralName<?> nonViralName = (NonViralName<?>)nameBase;
|
|
612
|
String strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "genusPart", rdfNamespace);
|
|
613
|
|
|
614
|
//for names of rank genus the uninomial property should be used
|
|
615
|
if (strGenusPart == null){
|
|
616
|
strGenusPart = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "uninomial", rdfNamespace);
|
|
617
|
}
|
|
618
|
nonViralName.setGenusOrUninomial(strGenusPart);
|
|
619
|
|
|
620
|
String strInfragenericEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infragenericEpithet", rdfNamespace);
|
|
621
|
nonViralName.setGenusOrUninomial(strInfragenericEpithet);
|
|
622
|
|
|
623
|
|
|
624
|
|
|
625
|
String strSpecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "specificEpithet", rdfNamespace);
|
|
626
|
nonViralName.setSpecificEpithet(strSpecificEpithet);
|
|
627
|
|
|
628
|
String strInfraspecificEpithet = XmlHelp.getChildContent(elTaxonName, "TaxonName", taxonNameNamespace, "infraspecificEpithet", rdfNamespace);
|
|
629
|
nonViralName.setInfraSpecificEpithet(strInfraspecificEpithet);
|
|
630
|
//AuthorTeams
|
|
631
|
//TODO
|
|
632
|
tcsElementName = "basionymAuthorship";
|
|
633
|
String basionymAuthorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
634
|
if (basionymAuthorValue != null){
|
|
635
|
TeamOrPersonBase<?> basionymAuthor = Team.NewInstance();
|
|
636
|
basionymAuthor.setNomenclaturalTitle(basionymAuthorValue);
|
|
637
|
nonViralName.setBasionymAuthorship(basionymAuthor);
|
|
638
|
}
|
|
639
|
|
|
640
|
//TODO
|
|
641
|
tcsElementName = "combinationAuthorship";
|
|
642
|
String combinationAuthorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
643
|
if (combinationAuthorValue != null){
|
|
644
|
TeamOrPersonBase<?> combinationAuthor = Team.NewInstance();
|
|
645
|
combinationAuthor.setNomenclaturalTitle(combinationAuthorValue);
|
|
646
|
nonViralName.setCombinationAuthorship(combinationAuthor);
|
|
647
|
}
|
|
648
|
|
|
649
|
//set the authorshipCache
|
|
650
|
tcsElementName = "authorship";
|
|
651
|
String authorValue = (String)ImportHelper.getXmlInputValue(elTaxonName, tcsElementName, taxonNameNamespace);
|
|
652
|
String cache = nonViralName.getAuthorshipCache();
|
|
653
|
if ( authorValue != null){
|
|
654
|
//compare existing authorship cache with new one and check if it is necessary to
|
|
655
|
//make cache protected //TODO refinement
|
|
656
|
if (cache == null){
|
|
657
|
nonViralName.setAuthorshipCache(authorValue);
|
|
658
|
}else{
|
|
659
|
cache = basionymAuthorValue == null ? cache : cache.replace(basionymAuthorValue, "");
|
|
660
|
cache = combinationAuthorValue == null ? cache : cache.replace(combinationAuthorValue, "");
|
|
661
|
cache = cache.replace("\\(|\\)", "");
|
|
662
|
cache = cache.trim();
|
|
663
|
if (! cache.equals("")){
|
|
664
|
nonViralName.setAuthorshipCache(authorValue);
|
|
665
|
}
|
|
666
|
}
|
|
667
|
}
|
|
668
|
}
|
|
669
|
ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), nameAbout, idNamespace);
|
|
670
|
|
|
671
|
checkAdditionalContents(elTaxonName, standardMappers, operationalMappers, unclearMappers);
|
|
672
|
|
|
673
|
//nameId
|
|
674
|
//TODO
|
|
675
|
//ImportHelper.setOriginalSource(nameBase, tcsConfig.getSourceReference(), nameId);
|
|
676
|
//taxonNameMap.put(nameAbout, nameBase);
|
|
677
|
return nameBase;
|
|
678
|
*/}catch(UnknownCdmTypeException e){
|
|
679
|
e.printStackTrace();
|
|
680
|
}
|
|
681
|
return null;
|
|
682
|
}
|
|
683
|
|
|
684
|
public TaxonNameBase handleRdfElementFromStream(InputStream is, TcsRdfImportConfigurator config, MapWrapper<TaxonNameBase> taxonNameMap, String uri){
|
|
685
|
Model model = ModelFactory.createDefaultModel();
|
|
686
|
try{
|
|
687
|
model.read(is, null);
|
|
688
|
|
|
689
|
config.makeNamespaces(model);
|
|
690
|
|
|
691
|
String rdfNamespace = config.getRdfNamespaceURIString();
|
|
692
|
String taxonNameNamespace = config.getTnNamespaceURIString();
|
|
693
|
return handleNameModel(model, config, taxonNameMap, uri);
|
|
694
|
|
|
695
|
|
|
696
|
}catch(Exception e){
|
|
697
|
logger.debug("The file was no valid rdf file");
|
|
698
|
}
|
|
699
|
|
|
700
|
|
|
701
|
|
|
702
|
return null;
|
|
703
|
}
|
|
704
|
|
|
705
|
}
|