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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.taxonx;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import org.jdom.Attribute;
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import org.jdom.Content;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.jdom.Text;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.ICommonService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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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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* @since 29.07.2008
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*/
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@Component
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public class TaxonXDescriptionImport
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extends CdmImportBase<TaxonXImportConfigurator, TaxonXImportState> {
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private static final long serialVersionUID = 1957356490206741364L;
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private static final Logger logger = Logger.getLogger(TaxonXDescriptionImport.class);
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public TaxonXDescriptionImport(){
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super();
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}
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@Override
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public boolean doCheck(TaxonXImportState state){
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boolean result = true;
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logger.warn("Checking for Facts not yet implemented");
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//result &= checkArticlesWithoutJournal(bmiConfig);
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return result;
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}
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public Map<Integer, Feature> fillFactCategories(IImportConfigurator config, CdmApplicationController cdmApp){
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logger.warn("not yet implemented");
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Map<Integer, Feature> featureMap = new HashMap<Integer, Feature>();
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// IDescriptionService descriptionService = cdmApp.getDescriptionService();
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// ITermService termService = cdmApp.getTermService();
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//
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// Object source = config.getSource();
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return featureMap;
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}
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private String getDescriptionTitle(TaxonXImportState state){
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String result = "Untitled";
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Reference ref = state.getModsReference();
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if (ref != null){
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result = ref.getTitle();
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if ( CdmUtils.isEmpty(result)){
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result = ref.getTitleCache();
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}
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}
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return result;
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}
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@Override
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public void doInvoke(TaxonXImportState state){
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logger.debug("not yet fully implemented");
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TaxonXImportConfigurator txConfig = state.getConfig();
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Element root = txConfig.getSourceRoot();
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Namespace nsTaxonx = root.getNamespace();
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//Object source = config.getSource();
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logger.info("start make Descriptions ...");
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//for testing only
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Taxon taxon = getTaxon(txConfig);
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if (taxon == null){
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logger.warn("Taxon could not be found");
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state.setUnsuccessfull();
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}
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Reference modsReference = state.getModsReference();
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if (modsReference == null){
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modsReference = state.getConfig().getSourceReference();
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}
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//unlazyDescription(txConfig, taxon);
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TaxonDescription description = TaxonDescription.NewInstance();
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description.setTitleCache(getDescriptionTitle(state), true);
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if (modsReference != null){
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description.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, modsReference, null);
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}
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Element elTaxonBody = root.getChild("taxonxBody", nsTaxonx);
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Element elTreatment = elTaxonBody.getChild("treatment", nsTaxonx);
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List<Element> elDivs = elTreatment.getChildren("div", nsTaxonx);
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for (Element div : elDivs){
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Attribute attrType = div.getAttribute("type", nsTaxonx);
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String strType = attrType.getValue();
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Feature feature = null;
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try {
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feature = TaxonXTransformer.descriptionType2feature(strType);
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} catch (UnknownCdmTypeException e) {
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feature = handleFeatureException(strType, e, txConfig);
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}
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String text = getText(div);
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if (!"".equals(CdmUtils.Nz(text).trim())){
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// hibernate throws an exception when a string is longer than approx. 65500 chars.
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// for now we truncate any description text to 65500 characters.
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if(text.length() > 65500){
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text = text.substring(0, 65500) + "... [text truncated]";
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logger.warn("Truncation of text: description for taxon " + taxon.getTitleCache() + " was longer than 65500 characters.");
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}
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DescriptionElementBase descriptionElement = TextData.NewInstance(text, Language.ENGLISH(), null);
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descriptionElement.setFeature(feature);
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description.addElement(descriptionElement);
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//add reference
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if (modsReference != null){
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descriptionElement.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, modsReference, null, null, null);
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}
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}
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}
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if (description.size() >0){
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taxon.addDescription(description);
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getTaxonService().save(taxon);
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}
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return;
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}
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private Feature handleFeatureException(String strType, UnknownCdmTypeException e, TaxonXImportConfigurator txConfig){
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Feature feature = null;
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TermVocabulary<Feature> featureVoc = Feature.BIOLOGY_ECOLOGY().getVocabulary();
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for (Feature oneFeature : featureVoc.getTerms()){
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if (strType.equals(oneFeature.getLabel()) || strType.equals(oneFeature.getRepresentation(Language.DEFAULT() ).getText() )){
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feature = oneFeature;
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}
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}
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if (feature == null){
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feature = Feature.NewInstance(strType, strType, null);
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featureVoc.addTerm(feature);
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getTermService().save(feature);
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logger.warn(e.getMessage() + ". Feature was added to the feature vocabulary. " + getBracketSourceName(txConfig));
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}
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return feature;
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}
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private String getText(Element div){
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String result = "";
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Iterator<Content> it =div.getDescendants();
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while (it.hasNext()){
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Content next = it.next();
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if (next instanceof Text){
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result += ((Text)next).getText();
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}
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}
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return result;
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}
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private Taxon getTaxon(TaxonXImportConfigurator config){
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Taxon result;
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// result = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(null), null);
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ICommonService commonService = getCommonService();
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String originalSourceId = config.getOriginalSourceId();
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String namespace = config.getOriginalSourceTaxonNamespace();
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result = commonService.getSourcedObjectByIdInSource(Taxon.class, originalSourceId , namespace);
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if (result == null){
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logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found");
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}
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return result;
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}
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private void unlazyDescription(TaxonXImportConfigurator config, Taxon taxon){
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// logger.warn("Preliminary commented"); //used single Transaction for all import instead !
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// TransactionStatus txStatus = config.getCdmAppController().startTransaction();
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// ITaxonService taxonService = config.getCdmAppController().getTaxonService();
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// taxonService.saveTaxon(taxon);
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// taxon.getDescriptions().size();
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// config.getCdmAppController().commitTransaction(txStatus);
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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(TaxonXImportState state){
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return ! state.getConfig().isDoFacts();
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}
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private String getBracketSourceName(TaxonXImportConfigurator config){
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return "(" + config.getSourceNameString() + ")";
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}
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}
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