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51264420
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Andreas Müller
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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.dwca.out;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.UnsupportedEncodingException;
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d2f7f487
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Andreas Müller
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import java.util.List;
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51264420
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Andreas Müller
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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 eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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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.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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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.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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/**
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* @author a.mueller
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* @created 18.04.2011
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*/
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public class DwcaTaxonExport extends DwcaDataExportBase {
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private static final long serialVersionUID = -3770976064909193441L;
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private static final Logger logger = Logger.getLogger(DwcaTaxonExport.class);
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private static final String ROW_TYPE = "http://rs.tdwg.org/dwc/terms/Taxon";
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protected static final String fileName = "coreTax.txt";
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private DwcaMetaDataRecord metaRecord;
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/**
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* Constructor
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*/
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public DwcaTaxonExport(DwcaTaxExportState state) {
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super();
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this.ioName = this.getClass().getSimpleName();
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metaRecord = new DwcaMetaDataRecord(IS_CORE, fileName, ROW_TYPE);
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state.addMetaRecord(metaRecord);
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Andreas Müller
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file = DwcaTaxExportFile.TAXON;
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51264420
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Andreas Müller
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}
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@Override
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protected void doInvoke(DwcaTaxExportState state){}
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@Override
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protected void handleTaxonNode(DwcaTaxExportState state, TaxonNode node)
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throws IOException, FileNotFoundException, UnsupportedEncodingException {
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try {
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Taxon taxon = CdmBase.deproxy(node.getTaxon());
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DwcaTaxExportConfigurator config = state.getConfig();
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34b6fc0f
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Andreas Müller
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DwcaTaxonRecord record = new DwcaTaxonRecord(metaRecord, config);
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51264420
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Andreas Müller
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TaxonName name = taxon.getName();
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Taxon parent = node.getParent() == null ? null : node.getParent().getTaxon();
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TaxonName basionym = name.getBasionym();
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Classification classification = node.getClassification();
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if (! state.recordExists(file, taxon)){
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handleTaxonBase(state, record, taxon, name, taxon, parent, basionym, classification, null, false, false);
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecord(file, taxon);
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}
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//synonyms
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3443c007
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Andreas Müller
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if (state.getConfig().isDoSynonyms()){
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handleSynonyms(state, taxon, file, classification, metaRecord);
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}
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51264420
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Andreas Müller
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//misapplied names
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3443c007
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Andreas Müller
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if (state.getConfig().isDoMisappliedNames()){
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handleMisapplication(state, taxon, file, classification, metaRecord);
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}
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51264420
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Andreas Müller
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} catch (Exception e) {
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String message = "Unexpected exception: " + e.getMessage();
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state.getResult().addException(e, message);
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}finally{
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flushWriter(state, file);
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7de8dccc
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Katja Luther
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51264420
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Andreas Müller
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}
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}
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34b6fc0f
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Andreas Müller
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private void handleSynonyms(DwcaTaxExportState state, Taxon taxon, DwcaTaxExportFile file,
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51264420
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Andreas Müller
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Classification classification, DwcaMetaDataRecord metaRecord) throws FileNotFoundException, UnsupportedEncodingException, IOException {
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for (Synonym synonym :taxon.getSynonyms() ){
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8f006e1e
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Andreas Müller
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if (isUnpublished(state.getConfig(), synonym)){
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return;
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}
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DwcaTaxonRecord record = new DwcaTaxonRecord(metaRecord, state.getConfig());
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51264420
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Andreas Müller
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SynonymType type = synonym.getType();
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boolean isProParte = synonym.isProParte();
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boolean isPartial = synonym.isPartial();
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if (type == null){ // should not happen
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type = SynonymType.SYNONYM_OF();
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}
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TaxonName name = synonym.getName();
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//????
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Taxon parent = null;
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TaxonName basionym = name.getBasionym();
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if (! state.recordExists(file, synonym)){
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handleTaxonBase(state, record, synonym, name, taxon, parent, basionym, classification, type, isProParte, isPartial);
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecord(file, synonym);
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}
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}
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}
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private void handleMisapplication(DwcaTaxExportState state, Taxon taxon,
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34b6fc0f
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Andreas Müller
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DwcaTaxExportFile file, Classification classification, DwcaMetaDataRecord metaRecord) throws FileNotFoundException, UnsupportedEncodingException, IOException {
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51264420
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Andreas Müller
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Set<Taxon> misappliedNames = taxon.getMisappliedNames();
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for (Taxon misappliedName : misappliedNames ){
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34b6fc0f
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Andreas Müller
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DwcaTaxonRecord record = new DwcaTaxonRecord(metaRecord, state.getConfig());
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51264420
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Andreas Müller
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TaxonRelationshipType relType = TaxonRelationshipType.MISAPPLIED_NAME_FOR();
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TaxonName name = misappliedName.getName();
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//????
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Taxon parent = null;
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TaxonName basionym = name.getBasionym();
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if (! state.recordExists(file, misappliedName)){
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handleTaxonBase(state, record, misappliedName, name, taxon, parent, basionym, classification,
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relType, false, false);
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecord(file, misappliedName);
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}
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}
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}
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/**
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* @param state
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* @param record
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* @param taxonBase
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* @param name
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* @param acceptedTaxon
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* @param parent
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* @param basionym
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* @param isPartial
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* @param isProParte
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* @param config
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* @param type
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*/
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34b6fc0f
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Andreas Müller
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private void handleTaxonBase(DwcaTaxExportState state, DwcaTaxonRecord record, TaxonBase<?> taxonBase, TaxonName name,
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51264420
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Andreas Müller
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Taxon acceptedTaxon, Taxon parent, TaxonName basionym, Classification classification,
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RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial) {
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record.setId(taxonBase.getId());
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record.setUuid(taxonBase.getUuid());
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//maybe wrong as according to the DwC-A documentation only resolvable ids are allowed, this differs from DwC documentation
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record.setScientificNameId(name);
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record.setScientificName(name.getTitleCache());
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record.setAcceptedNameUsageId(acceptedTaxon.getUuid());
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record.setAcceptedNameUsage(acceptedTaxon.getName() == null? acceptedTaxon.getTitleCache() : acceptedTaxon.getName().getTitleCache());
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//parentNameUsage
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if (parent != null){
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record.setParentNameUsageId(parent.getUuid());
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record.setParentNameUsage(parent.getTitleCache());
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}
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//originalNameUsage
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// ??? - is not a name usage (concept)
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if (basionym != null){
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//FIXME needs to be a coreID otherwise use string only
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// record.setOriginalNameUsageId(basionym.getUuid());
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record.setOriginalNameUsageId(null);
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record.setOriginalNameUsage(basionym.getTitleCache());
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}
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//nameAccordingTo
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Reference sec = taxonBase.getSec();
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if (sec == null){
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801f7c6e
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Andreas Müller
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String message = "There is a taxon without sec " + taxonBase.getTitleCache() + "(" + taxonBase.getId() + ")";
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51264420
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Andreas Müller
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state.getResult().addWarning(message);
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}else{
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record.setNameAccordingToId(taxonBase.getSec().getUuid());
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record.setNameAccordingTo(taxonBase.getSec().getTitleCache());
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}
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//namePublishedIn
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// ??? is not a nameUsage (concept)
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if (name.getNomenclaturalReference() != null){
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record.setNamePublishedInId(name.getNomenclaturalReference().getUuid());
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record.setNamePublishedIn(name.getNomenclaturalReference() == null ? null : name.getNomenclaturalReference().getTitleCache());
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}
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// what is the exact difference to id and acceptedNameUsageId
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record.setTaxonConceptId(taxonBase.getUuid());
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//Classification
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3429c491
|
Andreas Müller
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if (state.getConfig().isWithHigherClassification()){
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d2f7f487
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Andreas Müller
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//all classification and rank specific fields are meant to represent the classification
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3429c491
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Andreas Müller
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handleHigherClassification(state, record, acceptedTaxon, classification);
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d2f7f487
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Andreas Müller
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51264420
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Andreas Müller
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//... higher ranks
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3429c491
|
Andreas Müller
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// handleUninomialOrGenus(record, name);
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// if (name.getRank() != null && name.getRank().equals(Rank.SUBGENUS())){
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// record.setSubgenus(name.getNameCache());
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// }
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51264420
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Andreas Müller
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//record.setSubgenus(name.getInfraGenericEpithet());
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}
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if (name.getRank() != null && (name.getRank().isSupraGeneric() || name.getRank().isGenus())){
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record.setUninomial(name.getGenusOrUninomial());
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}else{
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record.setGenusPart(name.getGenusOrUninomial());
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}
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record.setInfraGenericEpithet(name.getInfraGenericEpithet());
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record.setSpecificEpithet(name.getSpecificEpithet());
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record.setInfraspecificEpithet(name.getInfraSpecificEpithet());
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record.setTaxonRank(name.getRank());
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if (name.getRank() != null){
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record.setVerbatimTaxonRank(name.getRank().getAbbreviation());
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}else{
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String message = "No rank available for " + name.getTitleCache() + "(" + name.getId() + ")";
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state.getResult().addWarning(message);
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}
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record.setScientificNameAuthorship(name.getAuthorshipCache());
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// ??? - use for TextData common names?
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record.setVernacularName(null);
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record.setNomenclaturalCode(name.getNameType());
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// ??? TODO Misapplied Names, inferred synonyms
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handleTaxonomicStatus(record, name, relType, isProParte, isPartial);
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| 258 |
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handleNomStatus(record, taxonBase, name);
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// TODO we need to differentiate technical
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String taxonRemarks = "";
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for (Annotation annotation : taxonBase.getAnnotations()){
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if (AnnotationType.EDITORIAL().equals(annotation.getAnnotationType())){
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taxonRemarks += CdmUtils.Nz(annotation.getText());
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}
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| 266 |
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}
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| 267 |
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for (Annotation annotation : name.getAnnotations()){
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| 268 |
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if (AnnotationType.EDITORIAL().equals(annotation.getAnnotationType())){
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taxonRemarks += CdmUtils.Nz(annotation.getText());
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}
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| 271 |
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}
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| 272 |
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if (StringUtils.isNotBlank(taxonRemarks)){
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record.setTaxonRemarks(taxonRemarks);
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| 274 |
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}
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| 275 |
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| 276 |
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// TODO which date is needed here (taxon, name, sec, ... ?)
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record.setModified(taxonBase.getUpdated());
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// ???
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record.setLanguage(null);
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| 282 |
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record.setRights(taxonBase.getRights());
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//TODO
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record.setRightsHolder(null);
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record.setAccessRights(null);
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| 288 |
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//TODO currently only via default value
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| 289 |
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record.setBibliographicCitation(null);
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record.setInformationWithheld(null);
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| 291 |
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| 292 |
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record.setDatasetId(classification);
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record.setDatasetName(classification.getTitleCache());
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| 294 |
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//TODO
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| 296 |
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record.setSource(null);
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| 297 |
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| 298 |
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return;
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| 299 |
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}
|
| 300 |
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|
| 301 |
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/**
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| 302 |
d2f7f487
|
Andreas Müller
|
* @param state
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| 303 |
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* @param record
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| 304 |
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* @param taxonBase
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| 305 |
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* @param classification
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| 306 |
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*/
|
| 307 |
|
|
private void handleHigherClassification(DwcaTaxExportState state, DwcaTaxonRecord record, Taxon taxon,
|
| 308 |
|
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Classification classification) {
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| 309 |
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TaxonNode node = taxon.getTaxonNode(classification);
|
| 310 |
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|
if (node == null){
|
| 311 |
|
|
return;
|
| 312 |
|
|
}
|
| 313 |
|
|
record.setKingdom(nameOf(node.getAncestorOfRank(Rank.KINGDOM())));
|
| 314 |
|
|
record.setPhylum(nameOf(node.getAncestorOfRank(Rank.PHYLUM())));
|
| 315 |
|
|
record.setClazz(nameOf(node.getAncestorOfRank(Rank.CLASS())));
|
| 316 |
|
|
record.setOrder(nameOf(node.getAncestorOfRank(Rank.ORDER())));
|
| 317 |
|
|
record.setFamily(nameOf(node.getAncestorOfRank(Rank.FAMILY())));
|
| 318 |
|
|
record.setGenus(nameOf(node.getAncestorOfRank(Rank.GENUS())));
|
| 319 |
3429c491
|
Andreas Müller
|
record.setSubgenus(nameOf(node.getAncestorOfRank(Rank.SUBGENUS())));
|
| 320 |
d2f7f487
|
Andreas Müller
|
List<TaxonNode> ancestors = node.getAncestorList();
|
| 321 |
|
|
String higherClassification = higherClassificationString(ancestors);
|
| 322 |
|
|
record.setHigherClassification(higherClassification);
|
| 323 |
|
|
}
|
| 324 |
|
|
|
| 325 |
|
|
/**
|
| 326 |
|
|
* @param ancestors
|
| 327 |
|
|
*/
|
| 328 |
|
|
private String higherClassificationString(List<TaxonNode> ancestors) {
|
| 329 |
|
|
String result = "";
|
| 330 |
|
|
for (TaxonNode node : ancestors){
|
| 331 |
|
|
String nameOfNode = nameOf(node);
|
| 332 |
|
|
if (StringUtils.isBlank(nameOfNode)){
|
| 333 |
|
|
nameOfNode = "-";
|
| 334 |
|
|
}
|
| 335 |
|
|
result = CdmUtils.concat("|", result, nameOfNode);
|
| 336 |
|
|
}
|
| 337 |
|
|
return result;
|
| 338 |
|
|
}
|
| 339 |
|
|
|
| 340 |
|
|
/**
|
| 341 |
|
|
* @param ancestorOfRank
|
| 342 |
|
|
* @return
|
| 343 |
|
|
*/
|
| 344 |
|
|
private String nameOf(TaxonNode node) {
|
| 345 |
|
|
if (node != null && node.getTaxon()!= null){
|
| 346 |
|
|
Taxon taxon = node.getTaxon();
|
| 347 |
3429c491
|
Andreas Müller
|
TaxonName name = taxon.getName();
|
| 348 |
|
|
if (name!= null){
|
| 349 |
|
|
if (isNotBlank(name.getNameCache())){
|
| 350 |
|
|
return name.getNameCache();
|
| 351 |
|
|
}else{
|
| 352 |
|
|
return name.getTitleCache();
|
| 353 |
|
|
}
|
| 354 |
d2f7f487
|
Andreas Müller
|
}else{
|
| 355 |
|
|
return taxon.getTitleCache();
|
| 356 |
|
|
}
|
| 357 |
|
|
}
|
| 358 |
|
|
return null;
|
| 359 |
|
|
}
|
| 360 |
|
|
|
| 361 |
|
|
/**
|
| 362 |
51264420
|
Andreas Müller
|
* @param record
|
| 363 |
|
|
* @param name
|
| 364 |
|
|
* @param type
|
| 365 |
|
|
* @param isPartial
|
| 366 |
|
|
* @param isProParte
|
| 367 |
|
|
*/
|
| 368 |
34b6fc0f
|
Andreas Müller
|
private void handleTaxonomicStatus(DwcaTaxonRecord record,
|
| 369 |
51264420
|
Andreas Müller
|
INonViralName name, RelationshipTermBase<?> type,
|
| 370 |
|
|
boolean isProParte, boolean isPartial) {
|
| 371 |
|
|
if (type == null){
|
| 372 |
|
|
record.setTaxonomicStatus(name.getNomenclaturalCode().acceptedTaxonStatusLabel());
|
| 373 |
|
|
}else{
|
| 374 |
|
|
String status = name.getNomenclaturalCode().synonymStatusLabel();
|
| 375 |
|
|
if (type.equals(SynonymType.HETEROTYPIC_SYNONYM_OF())){
|
| 376 |
|
|
status = "heterotypicSynonym";
|
| 377 |
|
|
}else if(type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
|
| 378 |
|
|
status = "homotypicSynonym";
|
| 379 |
|
|
}else if(type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
| 380 |
|
|
status = "misapplied";
|
| 381 |
|
|
}
|
| 382 |
|
|
if (isProParte){
|
| 383 |
|
|
status = "proParteSynonym";
|
| 384 |
|
|
}else if (isPartial){
|
| 385 |
|
|
String message = "Partial synonym is not part of the gbif toxonomic status vocabulary";
|
| 386 |
|
|
logger.warn(message);
|
| 387 |
|
|
status = "partialSynonym";
|
| 388 |
|
|
}
|
| 389 |
|
|
|
| 390 |
|
|
record.setTaxonomicStatus(status);
|
| 391 |
|
|
}
|
| 392 |
|
|
}
|
| 393 |
|
|
|
| 394 |
3429c491
|
Andreas Müller
|
// /**
|
| 395 |
|
|
// * @param record
|
| 396 |
|
|
// * @param name
|
| 397 |
|
|
// */
|
| 398 |
|
|
// private void handleUninomialOrGenus(DwcaTaxonRecord record, INonViralName name) {
|
| 399 |
|
|
// //epitheta
|
| 400 |
|
|
// String firstEpi = name.getGenusOrUninomial();
|
| 401 |
|
|
// if (StringUtils.isNotBlank(firstEpi)){
|
| 402 |
|
|
// Rank rank = name.getRank();
|
| 403 |
|
|
// if (rank != null){
|
| 404 |
|
|
// if (rank.isLower(Rank.GENUS())){
|
| 405 |
51264420
|
Andreas Müller
|
// record.setGenus(firstEpi);
|
| 406 |
3429c491
|
Andreas Müller
|
// }else if (rank.equals(Rank.GENUS())){
|
| 407 |
|
|
// record.setGenus(firstEpi);
|
| 408 |
|
|
// }else if (rank.equals(Rank.KINGDOM())){
|
| 409 |
|
|
// record.setKingdom(firstEpi);
|
| 410 |
|
|
// }else if (rank.equals(Rank.PHYLUM())){
|
| 411 |
|
|
// record.setPhylum(firstEpi);
|
| 412 |
|
|
// }else if (rank.equals(Rank.CLASS())){
|
| 413 |
|
|
// record.setClazz(firstEpi);
|
| 414 |
|
|
// }else if (rank.equals(Rank.ORDER())){
|
| 415 |
|
|
// record.setOrder(firstEpi);
|
| 416 |
|
|
// }else if (rank.equals(Rank.FAMILY())){
|
| 417 |
|
|
// record.setFamily(firstEpi);
|
| 418 |
|
|
// }else{
|
| 419 |
|
|
// // !!!
|
| 420 |
|
|
// String message = "Rank not covered. Set uninomial as genus instead: " + rank.getLabel();
|
| 421 |
|
|
// logger.warn(message);
|
| 422 |
|
|
//// record.setGenus(firstEpi);
|
| 423 |
|
|
// }
|
| 424 |
|
|
//
|
| 425 |
|
|
// }
|
| 426 |
|
|
// }
|
| 427 |
|
|
// }
|
| 428 |
51264420
|
Andreas Müller
|
|
| 429 |
|
|
|
| 430 |
|
|
/**
|
| 431 |
|
|
* @param record
|
| 432 |
|
|
* @param taxon
|
| 433 |
|
|
* @param name
|
| 434 |
|
|
*/
|
| 435 |
34b6fc0f
|
Andreas Müller
|
private void handleNomStatus(DwcaTaxonRecord record, TaxonBase<?> taxon,
|
| 436 |
51264420
|
Andreas Müller
|
INonViralName name) {
|
| 437 |
|
|
int nStatus = name.getStatus().size();
|
| 438 |
|
|
if (nStatus > 0){
|
| 439 |
|
|
if (name.getStatus().size()> 1){
|
| 440 |
|
|
String warning = "There is more than 1 nomenclatural status ( " + name.getStatus().size()+ "): " + taxon.getTitleCache();
|
| 441 |
|
|
logger.warn(warning);
|
| 442 |
|
|
}
|
| 443 |
|
|
NomenclaturalStatusType status = name.getStatus().iterator().next().getType();
|
| 444 |
|
|
record.setNomenclaturalStatus(status);
|
| 445 |
|
|
}else{
|
| 446 |
|
|
record.setNomenclaturalStatus(null);
|
| 447 |
|
|
}
|
| 448 |
|
|
}
|
| 449 |
|
|
|
| 450 |
|
|
|
| 451 |
|
|
@Override
|
| 452 |
|
|
protected boolean doCheck(DwcaTaxExportState state) {
|
| 453 |
|
|
boolean result = true;
|
| 454 |
|
|
logger.warn("No check implemented for " + this.ioName);
|
| 455 |
|
|
return result;
|
| 456 |
|
|
}
|
| 457 |
|
|
|
| 458 |
|
|
|
| 459 |
|
|
@Override
|
| 460 |
3443c007
|
Andreas Müller
|
public boolean isIgnore(DwcaTaxExportState state) {
|
| 461 |
51264420
|
Andreas Müller
|
return ! state.getConfig().isDoTaxa();
|
| 462 |
|
|
}
|
| 463 |
|
|
|
| 464 |
|
|
}
|