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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.tcsxml.in;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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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 eu.etaxonomy.cdm.common.ResultWrapper;
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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.io.tcsxml.TcsXmlTransformer;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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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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@Component("tcsXmlTaxonNameIO")
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public class TcsXmlTaxonNameImport extends TcsXmlImportBase implements ICdmIO<TcsXmlImportState> {
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private static final long serialVersionUID = -1978871518114999061L;
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private static final Logger logger = Logger.getLogger(TcsXmlTaxonNameImport.class);
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private static int modCount = 5000;
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public TcsXmlTaxonNameImport(){
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super();
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}
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@Override
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public boolean doCheck(TcsXmlImportState state){
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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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//@SuppressWarnings("unchecked")
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@Override
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public void doInvoke(TcsXmlImportState state){
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logger.info("start make TaxonNames ...");
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MapWrapper<Person> authorMap = (MapWrapper<Person>)state.getStore(ICdmIO.TEAM_STORE);
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MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);
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MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);
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ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
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String childName;
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boolean obligatory;
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String idNamespace = "TaxonName";
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TcsXmlImportConfigurator config = state.getConfig();
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Element elDataSet = getDataSetElement(config);
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Namespace tcsNamespace = config.getTcsXmlNamespace();
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childName = "TaxonNames";
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obligatory = false;
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Element elTaxonNames = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);
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String tcsElementName = "TaxonName";
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List<Element> elTaxonNameList = elTaxonNames == null ? new ArrayList<Element>() : (List<Element>)elTaxonNames.getChildren(tcsElementName, tcsNamespace);
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int i = 0;
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//for each taxonName
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for (Element elTaxonName : elTaxonNameList){
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if ((++i % modCount) == 0){ logger.info("Names handled: " + (i-1));}
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String strId = elTaxonName.getAttributeValue("id");
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/*List<String> elementList = new ArrayList<String>();
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//create TaxonName element
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String strId = elTaxonName.getAttributeValue("id");
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String strNomenclaturalCode = elTaxonName.getAttributeValue("nomenclaturalCode");
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childName = "Rank";
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obligatory = false;
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Element elRank = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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Rank rank = null;
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if (elRank != null){
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rank = makeRank(elRank);
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if (rank == null){
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logger.warn("Unknown rank for" + strId);
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}
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}
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elementList.add(childName.toString());
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try {
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TaxonName nameBase;
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NomenclaturalCode nomCode = TcsXmlTransformer.nomCodeString2NomCode(strNomenclaturalCode);
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if (nomCode != null){
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nameBase = nomCode.getNewTaxonNameInstance(rank);
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}else{
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nameBase = TaxonNameFactory.NewNonViralInstance(rank);
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}
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childName = "Simple";
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obligatory = true;
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Element elSimple = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
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nameBase.setTitleCache(simple, false);
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elementList.add(childName.toString());
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childName = "CanonicalName";
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obligatory = false;
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Element elCanonicalName = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeCanonicalName(nameBase, elCanonicalName, taxonNameMap, success);
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elementList.add(childName.toString());
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childName = "CanonicalAuthorship";
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obligatory = false;
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Element elCanonicalAuthorship = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeCanonicalAuthorship(nameBase, elCanonicalAuthorship, authorMap, success);
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elementList.add(childName.toString());
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childName = "PublishedIn";
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obligatory = false;
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Element elPublishedIn = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makePublishedIn(nameBase, elPublishedIn, referenceMap, success);
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elementList.add(childName.toString());
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childName = "Year";
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obligatory = false;
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Element elYear = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeYear(nameBase, elYear, success);
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elementList.add(childName.toString());
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childName = "MicroReference";
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obligatory = false;
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Element elMicroReference = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeMicroReference(nameBase, elMicroReference, success);
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elementList.add(childName.toString());
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childName = "Typification";
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obligatory = false;
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Element elTypification = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeTypification(nameBase, elTypification, success);
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elementList.add(childName.toString());
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childName = "PublicationStatus";
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obligatory = false;
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Element elPublicationStatus = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makePublicationStatus(nameBase, elPublicationStatus, success);
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elementList.add(childName.toString());
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childName = "ProviderLink";
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obligatory = false;
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Element elProviderLink = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeProviderLink(nameBase, elProviderLink, success);
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elementList.add(childName.toString());
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childName = "ProviderSpecificData";
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obligatory = false;
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Element elProviderSpecificData = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeProviderSpecificData(nameBase, elProviderSpecificData, success);
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elementList.add(childName.toString());
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ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), strId, idNamespace);
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if (strId != null){
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if (strId.matches("urn:lsid:ipni.org:.*:.*:.*")){
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strId = strId.substring(0,strId.lastIndexOf(":"));
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}
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}
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taxonNameMap.put(strId, nameBase);
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} catch (UnknownCdmTypeException e) {
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logger.warn("Name with id " + strId + " has unknown nomenclatural code.");
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success.setValue(false);
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}*/
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taxonNameMap.put(removeVersionOfRef(strId), handleTaxonNameElement(elTaxonName, success, state));
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}
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logger.info(i + " names handled");
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Collection<TaxonName> col = taxonNameMap.objects();
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getNameService().save(col);
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logger.info("end makeTaxonNames ...");
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if (!success.getValue()){
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state.setUnsuccessfull();
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}
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return;
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}
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/**
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* Returns the rank represented by the rank element.<br>
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* Returns <code>null</code> if the element is null.<br>
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* Returns <code>null</code> if the code and the text are both either empty or do not exists.<br>
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* Returns the rank represented by the code attribute, if the code attribute is not empty and could be resolved.<br>
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* If the code could not be resolved it returns the rank represented most likely by the elements text.<br>
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* Returns UNKNOWN_RANK if code attribute and element text could not be resolved.
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* @param elRank tcs rank element
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* @return
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*/
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protected static Rank makeRank(Element elRank){
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Rank result;
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if (elRank == null){
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return null;
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}
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String strRankCode = elRank.getAttributeValue("code");
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String strRankString = elRank.getTextNormalize();
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if ( StringUtils.isBlank(strRankCode) && StringUtils.isBlank(strRankString)){
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return null;
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}
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Rank codeRank = null;
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try {
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codeRank = TcsXmlTransformer.rankCode2Rank(strRankCode);
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} catch (UnknownCdmTypeException e1) {
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codeRank = Rank.UNKNOWN_RANK();
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}
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Rank stringRank = null;
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try {
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boolean useUnknown = true;
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stringRank = TcsXmlTransformer.rankString2Rank(strRankString);
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//stringRank = Rank.getRankByNameOrIdInVoc(strRankString, useUnknown);
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} catch (UnknownCdmTypeException e1) {
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//does not happen because of useUnknown = true
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}
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//codeRank exists
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if ( (codeRank != null) && ! codeRank.equals(Rank.UNKNOWN_RANK())){
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result = codeRank;
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if (! codeRank.equals(stringRank) && ! stringRank.equals(Rank.UNKNOWN_RANK())){
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logger.warn("code rank and string rank are unequal. code: " + codeRank.getLabel() + " <-> string: " + stringRank.getLabel());
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}
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}
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//codeRank does not exist
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else{
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result = stringRank;
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logger.warn("string rank used, because code rank does not exist or was not recognized: " + strRankString );
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}
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return result;
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}
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public TaxonName handleTaxonNameElement(Element elTaxonName, ResultWrapper<Boolean> success, TcsXmlImportState state){
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Namespace tcsNamespace = state.getConfig().getTcsXmlNamespace();
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MapWrapper<Person> authorMap = (MapWrapper<Person>)state.getStore(ICdmIO.TEAM_STORE);
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MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);
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MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);
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266
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267
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268
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List<String> elementList = new ArrayList<>();
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String idNamespace = "TaxonName";
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//create TaxonName element
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String strId = elTaxonName.getAttributeValue("id");
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String strNomenclaturalCode = elTaxonName.getAttributeValue("nomenclaturalCode");
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//Content elTaxName = elTaxonName.getChild(name, ns);
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String childName = "Rank";
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275
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boolean obligatory = false;
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Element elRank = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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Rank rank = null;
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278
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if (elRank != null){
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rank = TcsXmlTaxonNameImport.makeRank(elRank);
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if (rank == null){
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logger.warn("Unknown rank for" + strId);
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}
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283
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}
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284
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elementList.add(childName.toString());
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285
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286
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287
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try {
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TaxonName nameBase;
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NomenclaturalCode nomCode = TcsXmlTransformer.nomCodeString2NomCode(strNomenclaturalCode);
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if (nomCode != null){
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nameBase = nomCode.getNewTaxonNameInstance(rank);
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}else{
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nameBase = TaxonNameFactory.NewNonViralInstance(rank);
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}
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childName = "Simple";
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obligatory = true;
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297
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Element elSimple = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
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nameBase.setTitleCache(simple, false);
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300
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elementList.add(childName.toString());
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301
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302
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childName = "CanonicalName";
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obligatory = false;
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Element elCanonicalName = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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makeCanonicalName(nameBase, elCanonicalName, taxonNameMap, success);
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elementList.add(childName.toString());
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307
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308
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childName = "CanonicalAuthorship";
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obligatory = false;
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310
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Element elCanonicalAuthorship = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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311
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makeCanonicalAuthorship(nameBase, elCanonicalAuthorship, authorMap, success);
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elementList.add(childName.toString());
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313
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314
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childName = "PublishedIn";
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obligatory = false;
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316
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Element elPublishedIn = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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317
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makePublishedIn(nameBase, elPublishedIn, referenceMap, success);
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elementList.add(childName.toString());
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319
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320
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childName = "Year";
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obligatory = false;
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Element elYear = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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323
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makeYear(nameBase, elYear, success);
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elementList.add(childName.toString());
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325
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326
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childName = "MicroReference";
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obligatory = false;
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328
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Element elMicroReference = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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329
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makeMicroReference(nameBase, elMicroReference, success);
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elementList.add(childName.toString());
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331
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332
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childName = "Typification";
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obligatory = false;
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334
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Element elTypification = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
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335
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makeTypification(nameBase, elTypification, success);
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elementList.add(childName.toString());
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337
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338
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childName = "PublicationStatus";
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339
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obligatory = false;
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340
|
Element elPublicationStatus = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
|
|
341
|
makePublicationStatus(nameBase, elPublicationStatus, success);
|
|
342
|
elementList.add(childName.toString());
|
|
343
|
|
|
344
|
childName = "ProviderLink";
|
|
345
|
obligatory = false;
|
|
346
|
Element elProviderLink = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
|
|
347
|
makeProviderLink(nameBase, elProviderLink, success);
|
|
348
|
elementList.add(childName.toString());
|
|
349
|
|
|
350
|
childName = "ProviderSpecificData";
|
|
351
|
obligatory = false;
|
|
352
|
Element elProviderSpecificData = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
|
|
353
|
makeProviderSpecificData(nameBase, elProviderSpecificData, success, state);
|
|
354
|
elementList.add(childName.toString());
|
|
355
|
|
|
356
|
return nameBase;
|
|
357
|
|
|
358
|
} catch (UnknownCdmTypeException e) {
|
|
359
|
logger.warn("Name with id " + strId + " has unknown nomenclatural code.");
|
|
360
|
success.setValue(false);
|
|
361
|
}
|
|
362
|
return null;
|
|
363
|
}
|
|
364
|
|
|
365
|
|
|
366
|
|
|
367
|
private void makeCanonicalAuthorship(TaxonName name, Element elCanonicalAuthorship, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success){
|
|
368
|
if (elCanonicalAuthorship != null){
|
|
369
|
Namespace ns = elCanonicalAuthorship.getNamespace();
|
|
370
|
|
|
371
|
if (name.isNonViral()){
|
|
372
|
INonViralName nonViralName = name;
|
|
373
|
|
|
374
|
String childName = "Simple";
|
|
375
|
boolean obligatory = true;
|
|
376
|
Element elSimple = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
|
|
377
|
String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
|
|
378
|
//TODO
|
|
379
|
//logger.warn("authorship cache cache protected not yet implemented");
|
|
380
|
//nonViralName.setAuthorshipCache(simple, cacheProtected);
|
|
381
|
|
|
382
|
childName = "Authorship";
|
|
383
|
obligatory = false;
|
|
384
|
Element elAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
|
|
385
|
TeamOrPersonBase author = makeNameCitation(elAuthorship, authorMap, success);
|
|
386
|
nonViralName.setCombinationAuthorship(author);
|
|
387
|
//setCombinationAuthorship(author);
|
|
388
|
testNoMoreElements();
|
|
389
|
|
|
390
|
childName = "BasionymAuthorship";
|
|
391
|
obligatory = false;
|
|
392
|
Element elBasionymAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
|
|
393
|
TeamOrPersonBase<?> basionymAuthor = makeNameCitation(elBasionymAuthorship, authorMap, success);
|
|
394
|
nonViralName.setBasionymAuthorship(basionymAuthor);
|
|
395
|
testNoMoreElements();
|
|
396
|
|
|
397
|
childName = "CombinationAuthorship";
|
|
398
|
obligatory = false;
|
|
399
|
Element elCombinationAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
|
|
400
|
TeamOrPersonBase<?> combinationAuthor = makeNameCitation(elCombinationAuthorship, authorMap ,success);
|
|
401
|
if (combinationAuthor != null){
|
|
402
|
nonViralName.setCombinationAuthorship(combinationAuthor);
|
|
403
|
}
|
|
404
|
testNoMoreElements();
|
|
405
|
|
|
406
|
if (elAuthorship != null && (elBasionymAuthorship != null || elCombinationAuthorship != null) ){
|
|
407
|
logger.warn("Authorship and (BasionymAuthorship or CombinationAuthorship) must not exist at the same time in CanonicalAuthorship");
|
|
408
|
success.setValue(false);
|
|
409
|
}
|
|
410
|
}
|
|
411
|
}
|
|
412
|
}
|
|
413
|
|
|
414
|
private void makeMicroReference(TaxonName name, Element elMicroReference, ResultWrapper<Boolean> success){
|
|
415
|
if (elMicroReference != null){
|
|
416
|
String microReference = elMicroReference.getTextNormalize();
|
|
417
|
name.setNomenclaturalMicroReference(microReference);
|
|
418
|
}
|
|
419
|
}
|
|
420
|
|
|
421
|
private void makeCanonicalName(TaxonName name, Element elCanonicalName, MapWrapper<TaxonName> taxonNameMap, ResultWrapper<Boolean> success){
|
|
422
|
boolean cacheProtected = false;
|
|
423
|
|
|
424
|
if (elCanonicalName == null){
|
|
425
|
return;
|
|
426
|
}
|
|
427
|
Namespace ns = elCanonicalName.getNamespace();
|
|
428
|
|
|
429
|
String childName = "Simple";
|
|
430
|
boolean obligatory = true;
|
|
431
|
Element elSimple = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
432
|
String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
|
|
433
|
name.setFullTitleCache(simple, cacheProtected);
|
|
434
|
|
|
435
|
if (name.isNonViral()){
|
|
436
|
INonViralName nonViralName = name;
|
|
437
|
childName = "Uninomial";
|
|
438
|
obligatory = false;
|
|
439
|
Element elUninomial = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
440
|
String uninomial = (elUninomial == null)? "" : elUninomial.getTextNormalize();
|
|
441
|
if (StringUtils.isNotBlank(uninomial)){
|
|
442
|
nonViralName.setGenusOrUninomial(uninomial);
|
|
443
|
if (nonViralName.getRank() != null && nonViralName.getRank().isLower(Rank.GENUS())){ // TODO check
|
|
444
|
logger.warn("Name " + simple + " lower then 'genus' but has a canonical name part 'Uninomial'.");
|
|
445
|
}
|
|
446
|
}
|
|
447
|
testNoMoreElements();
|
|
448
|
|
|
449
|
childName = "Genus";
|
|
450
|
obligatory = false;
|
|
451
|
Element elGenus = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
452
|
if (elGenus != null){
|
|
453
|
//TODO do Attributes reference
|
|
454
|
makeGenusReferenceType(name, elGenus, taxonNameMap, success);
|
|
455
|
String genus = elGenus.getTextNormalize();
|
|
456
|
if (StringUtils.isNotBlank(genus)){
|
|
457
|
nonViralName.setGenusOrUninomial(genus);
|
|
458
|
if (nonViralName.getRank() != null && ! nonViralName.getRank().isLower(Rank.GENUS() )){ // TODO check
|
|
459
|
logger.warn("Name " + simple + " is not lower then 'genus' but has canonical name part 'Genus'.");
|
|
460
|
}
|
|
461
|
}
|
|
462
|
}
|
|
463
|
|
|
464
|
childName = "InfragenericEpithet";
|
|
465
|
obligatory = false;
|
|
466
|
Element elInfrageneric = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
467
|
String infraGenericEpithet = (elInfrageneric == null)? "" : elInfrageneric.getTextNormalize();
|
|
468
|
if (! infraGenericEpithet.trim().equals("")){
|
|
469
|
nonViralName.setInfraGenericEpithet(infraGenericEpithet);
|
|
470
|
if (nonViralName.getRank() != null && ! name.getRank().isInfraGeneric()){
|
|
471
|
logger.warn("Name " + simple + " is not infra generic but has canonical name part 'InfragenericEpithet'.");
|
|
472
|
}
|
|
473
|
}
|
|
474
|
testNoMoreElements();
|
|
475
|
|
|
476
|
childName = "SpecificEpithet";
|
|
477
|
obligatory = false;
|
|
478
|
Element elSpecificEpithet = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
479
|
String specificEpithet = (elSpecificEpithet == null)? "" : elSpecificEpithet.getTextNormalize();
|
|
480
|
if (! specificEpithet.trim().equals("")){
|
|
481
|
nonViralName.setSpecificEpithet(specificEpithet);
|
|
482
|
if (nonViralName.getRank() != null && name.getRank().isHigher(Rank.SPECIES()) ){
|
|
483
|
logger.warn("Name " + simple + " is not species or below but has canonical name part 'SpecificEpithet'.");
|
|
484
|
}
|
|
485
|
}
|
|
486
|
testNoMoreElements();
|
|
487
|
|
|
488
|
childName = "InfraspecificEpithet";
|
|
489
|
obligatory = false;
|
|
490
|
Element elInfraspecificEpithet = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
491
|
String infraspecificEpithet = (elInfraspecificEpithet == null)? "" : elInfraspecificEpithet.getTextNormalize();
|
|
492
|
if (! infraspecificEpithet.trim().equals("")){
|
|
493
|
nonViralName.setInfraSpecificEpithet(infraspecificEpithet);
|
|
494
|
if (nonViralName.getRank() != null && ! name.isInfraSpecific() ){
|
|
495
|
logger.warn("Name " + simple + " is not infraspecific but has canonical name part 'InfraspecificEpithet'.");
|
|
496
|
}
|
|
497
|
}
|
|
498
|
testNoMoreElements();
|
|
499
|
|
|
500
|
|
|
501
|
}else{ //ViralName
|
|
502
|
//logger.warn("Non NonViralNames not yet supported by makeCanonicalName");
|
|
503
|
}
|
|
504
|
|
|
505
|
|
|
506
|
childName = "CultivarNameGroup";
|
|
507
|
obligatory = false;
|
|
508
|
Element elCultivarNameGroup = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
|
|
509
|
String cultivarNameGroup = (elCultivarNameGroup == null)? "" : elCultivarNameGroup.getTextNormalize();
|
|
510
|
if (! "".equals(cultivarNameGroup.trim())){
|
|
511
|
if (name.isCultivar()){
|
|
512
|
makeCultivarEpithet();
|
|
513
|
}else{
|
|
514
|
logger.warn("Non cultivar name has 'cultivar name group' element. Omitted");
|
|
515
|
}
|
|
516
|
}
|
|
517
|
return;
|
|
518
|
}
|
|
519
|
|
|
520
|
private void makeCultivarEpithet(){
|
|
521
|
//TODO
|
|
522
|
//logger.warn("'makeCultivarName' Not yet implemented");
|
|
523
|
}
|
|
524
|
|
|
525
|
private void makeGenusReferenceType(TaxonName name, Element elGenus, MapWrapper<TaxonName> taxonNameMap, ResultWrapper<Boolean> success){
|
|
526
|
if(name.isNonViral()){
|
|
527
|
INonViralName nonViralName = name;
|
|
528
|
if (elGenus != null){
|
|
529
|
INonViralName genusReferenceName;
|
|
530
|
//TODO code
|
|
531
|
Class<TaxonName> clazz = TaxonName.class;
|
|
532
|
genusReferenceName = makeReferenceType(elGenus, clazz, taxonNameMap, success);
|
|
533
|
genusReferenceName.setNameType(NomenclaturalCode.NonViral);
|
|
534
|
//Genus is stored either in Genus part (if ref) or in titleCache (if plain text)
|
|
535
|
String genus = genusReferenceName.getGenusOrUninomial()!= null ? genusReferenceName.getGenusOrUninomial(): genusReferenceName.getTitleCache();
|
|
536
|
nonViralName.setGenusOrUninomial(genus);
|
|
537
|
}else{
|
|
538
|
logger.warn("Missing Genus information");
|
|
539
|
}
|
|
540
|
}else{
|
|
541
|
//TODO (can be changed if Viral Name also has Genus in future
|
|
542
|
//logger.warn("Genus ref type for Viral Name not implemented yet");
|
|
543
|
}
|
|
544
|
|
|
545
|
}
|
|
546
|
|
|
547
|
private void makePublishedIn(TaxonName name, Element elPublishedIn, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
|
|
548
|
if (elPublishedIn != null && name != null){
|
|
549
|
Class<Reference> clazz = Reference.class;
|
|
550
|
Reference ref = makeReferenceType(elPublishedIn, clazz, referenceMap, success);
|
|
551
|
if (ref instanceof Reference){
|
|
552
|
name.setNomenclaturalReference(ref);
|
|
553
|
}else if (ref == null){
|
|
554
|
logger.warn("Nomecl. reference could not be created for '" + name.getTitleCache() + "'");
|
|
555
|
}else{
|
|
556
|
logger.warn("Reference is not of type INomenclaturalReference and could not be added to the name " + name.getTitleCache());
|
|
557
|
}
|
|
558
|
}else if (name == null){
|
|
559
|
logger.warn("TaxonName must not be 'null'");
|
|
560
|
success.setValue(false);
|
|
561
|
}
|
|
562
|
}
|
|
563
|
|
|
564
|
private void makeYear(TaxonName name, Element elYear, ResultWrapper<Boolean> success){
|
|
565
|
if (elYear != null){
|
|
566
|
String year = elYear.getTextNormalize();
|
|
567
|
if (year != null){
|
|
568
|
if (name.isZoological()){
|
|
569
|
name.setPublicationYear(getIntegerYear(year));
|
|
570
|
}else{
|
|
571
|
VerbatimTimePeriod period = VerbatimTimePeriod.NewVerbatimInstance(getIntegerYear(year));
|
|
572
|
if (name.getNomenclaturalReference()!= null){
|
|
573
|
name.getNomenclaturalReference().setDatePublished(period);
|
|
574
|
} else{
|
|
575
|
Reference nomRef = ReferenceFactory.newGeneric();
|
|
576
|
nomRef.setDatePublished(period);
|
|
577
|
}
|
|
578
|
logger.debug("Year can be set only for a zoological name, add the year to the nomenclatural reference.");
|
|
579
|
}
|
|
580
|
}
|
|
581
|
}
|
|
582
|
}
|
|
583
|
|
|
584
|
}
|