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/**
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* Copyright (C) 2009 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.dwca.in;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import com.ibm.lsid.MalformedLSIDException;
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import eu.etaxonomy.cdm.io.dwca.TermUri;
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import eu.etaxonomy.cdm.io.stream.StreamItem;
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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.CdmBase;
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import eu.etaxonomy.cdm.model.common.LSID;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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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.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.IZoologicalName;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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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.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author a.mueller
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* @date 22.11.2011
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*
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*/
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public class GbifReferenceCsv2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>
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implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{
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private static final Logger logger = Logger.getLogger(GbifReferenceCsv2CdmConverter.class);
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private static final String CORE_ID = "coreId";
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/**
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* @param state
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*/
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public GbifReferenceCsv2CdmConverter(DwcaDataImportStateBase state) {
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super(state);
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}
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@Override
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public IReader<MappedCdmBase> map(StreamItem item ){
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List<MappedCdmBase> resultList = new ArrayList<MappedCdmBase>();
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Map<String, String> csv = item.map;
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Reference sourceReference = state.getTransactionalSourceReference();
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String sourceReferecenDetail = null;
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String id = getSourceId(item);
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TaxonBase<?> taxon = getTaxonBase(id, item, TaxonBase.class, state);
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if (isNotBlank(id) && taxon == null){
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String message = "Taxon for id %s could not be found";
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message = String.format(message, id);
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fireWarningEvent(message, item, 8);
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}
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String strCreator = getValue(item, TermUri.DC_CREATOR);
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String strDate = getValue(item, TermUri.DC_DATE);
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String strTitle = getValue(item, TermUri.DC_TITLE);
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String strSource = getValue(item, TermUri.DC_SOURCE);
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String strIdentifier = getValue(item, TermUri.DC_IDENTIFIER);
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String strType = getValue(item, TermUri.DC_TYPE);
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Reference reference = ReferenceFactory.newGeneric();
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resultList.add(new MappedCdmBase<CdmBase>(reference));
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//author
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TeamOrPersonBase<?> author = handleCreator(strCreator);
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reference.setAuthorship(author);
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//date
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TimePeriod publicationDate = handleDate(strDate);
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reference.setDatePublished(publicationDate);
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//title
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reference.setTitle(strTitle);
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//inreference
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Reference inRef = handleInRef(strSource);
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if (inRef != null){
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reference.setInReference(inRef);
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resultList.add(new MappedCdmBase<CdmBase>(inRef));
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}
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//URI
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handleIdentifier(strIdentifier, reference);
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//type
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handleType(reference, strType, taxon, resultList, item);
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return new ListReader<MappedCdmBase>(resultList);
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}
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private void handleType(Reference reference, String strType, TaxonBase<?> taxon, List<MappedCdmBase> resultList, StreamItem item) {
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// TODO handleType not yet implemented
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if (taxon == null){
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String message = "Taxon is null. Reference not imported.";
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fireWarningEvent(message,item, 4);
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//do nothing
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}else{
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boolean isNomRef = false;
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if (isNotBlank(strType)){
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if (strType.matches("Botanical Protologue")){
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if (taxon.getName() != null && reference != null && taxon.getName().isInstanceOf(NonViralName.class)){
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INonViralName nvn = taxon.getName();
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nvn.setNomenclaturalReference(reference);
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isNomRef = true;
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}else{
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//TODO
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}
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}
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}
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//guess a nom ref
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if (isNomRef == false && config.isGuessNomenclaturalReferences()){
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//if reference equals in author and year we assume that it is the nom ref
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//this information is usually only available for ICZN names
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if (taxon.getName() != null && reference != null && taxon.getName().isInstanceOf(NonViralName.class)){
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INonViralName nvn = taxon.getName();
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String taxonAuthor = nvn.getAuthorshipCache();
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String refAuthor = reference.getAuthorship().getNomenclaturalTitle();
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Integer combYear = null;
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Integer origYear = null;
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if (nvn.isInstanceOf(ZoologicalName.class)){
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IZoologicalName zooName = CdmBase.deproxy(nvn, ZoologicalName.class);
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combYear = zooName.getPublicationYear();
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origYear = zooName.getOriginalPublicationYear();
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}
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String refYear = reference.getYear();
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//combination compare
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if (taxonAuthor != null && taxonAuthor.equals(refAuthor)){
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if (combYear != null && String.valueOf(combYear).equals(refYear)){
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//is nom Ref
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isNomRef = true;
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nvn.setNomenclaturalReference(reference);
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}else if (origYear != null && String.valueOf(origYear).equals(refYear)){
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//TODO not yet handled by CDM
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}
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}
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}
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}
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if (config.isHandleAllRefsAsCitation()){
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if (taxon.isInstanceOf(Taxon.class)){
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TaxonDescription desc = getTaxonDescription(CdmBase.deproxy(taxon, Taxon.class), false);
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createCitation(desc, reference, taxon.getName());
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resultList.add(new MappedCdmBase<CdmBase>(desc));
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}else if (taxon.isInstanceOf(Synonym.class)){
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Synonym syn = CdmBase.deproxy(taxon, Synonym.class);
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Taxon tax = syn.getAcceptedTaxon();
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if (tax != null){
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TaxonDescription desc = getTaxonDescription(tax, false);
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createCitation(desc, reference, syn.getName());
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resultList.add(new MappedCdmBase<CdmBase>(desc));
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}
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}
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}
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}
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}
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private void createCitation(TaxonDescription desc, Reference ref, TaxonNameBase nameUsedInSource) {
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Feature feature = Feature.CITATION();
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TextData textData = TextData.NewInstance(feature);
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DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(ref, null, nameUsedInSource, null);
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textData.addSource(source);
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desc.addElement(textData);
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}
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private void handleIdentifier(String strIdentifier, Reference reference) {
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if (StringUtils.isBlank(strIdentifier)){
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return;
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}else if (LSID.isLsid(strIdentifier)){
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LSID lsid;
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try {
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lsid = new LSID(strIdentifier);
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reference.setLsid(lsid);
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} catch (MalformedLSIDException e) {
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//TODO should not happen as we have checked before
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throw new RuntimeException(e);
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}
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}
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try {
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URI uri = URI.create(strIdentifier);
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reference.setUri(uri);
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} catch (Exception e) {
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logger.debug("Reference is not an URI");
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}
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//TODO further identifier types
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}
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private Reference handleInRef(String strSource) {
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if (StringUtils.isBlank(strSource)){
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return null;
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}else{
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Reference inRef = ReferenceFactory.newGeneric();
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return inRef;
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}
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}
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private TimePeriod handleDate(String strDate) {
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TimePeriod tp = TimePeriodParser.parseString(strDate);
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return tp;
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}
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private TeamOrPersonBase handleCreator(String strCreator) {
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Team team = Team.NewTitledInstance(strCreator, strCreator);
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return team;
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}
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@Override
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public String getSourceId(StreamItem item) {
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String id = item.get(CORE_ID);
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return id;
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}
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//********************** PARTITIONABLE **************************************/
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@Override
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protected void makeForeignKeysForItem(StreamItem item, Map<String, Set<String>> fkMap) {
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String value;
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String key;
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if ( hasValue(value = item.get(CORE_ID))){
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key = TermUri.DWC_TAXON.toString();
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Set<String> keySet = getKeySet(key, fkMap);
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keySet.add(value);
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}
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}
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@Override
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public Set<String> requiredSourceNamespaces() {
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Set<String> result = new HashSet<String>();
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result.add(TermUri.DWC_TAXON.toString());
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return result;
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}
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//******************* TO STRING ******************************************/
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@Override
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public String toString(){
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return this.getClass().getName();
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}
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}
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