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/**
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* Copyright (C) 2017 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.cdmLight;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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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 java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang3.StringUtils;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.CdmExportBase;
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import eu.etaxonomy.cdm.io.common.ExportResult.ExportResultState;
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import eu.etaxonomy.cdm.io.common.ICdmExport;
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import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.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.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.ICdmBase;
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import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroupNameComparator;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeComparator;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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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.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author k.luther
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* @date 15.03.2017
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*/
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@Component
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public class CdmLightClassificationExport
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extends CdmExportBase<CdmLightExportConfigurator, CdmLightExportState, IExportTransformer, File>
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implements ICdmExport<CdmLightExportConfigurator, CdmLightExportState>{
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private static final long serialVersionUID = 2518643632756927053L;
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private static final String STD_TEAM_CONCATINATION = ", ";
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private static final String FINAL_TEAM_CONCATINATION = " & ";
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private static final String IPNI_NAME_IDENTIFIER = "Ipni Name Identifier";
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private static final String TROPICOS_NAME_IDENTIFIER = "Tropicos Name Identifier";
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private static final String WFO_NAME_IDENTIFIER = "WFO Name Identifier";
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public CdmLightClassificationExport() {
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super();
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this.ioName = this.getClass().getSimpleName();
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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protected void doInvoke(CdmLightExportState state) {
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try {
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CdmLightExportConfigurator config = state.getConfig();
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config.setFieldsTerminatedBy(",");
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if (config.getClassificationUuids().isEmpty()){
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//TODO
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state.setEmptyData();
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return;
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}
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//TODO MetaData
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for (UUID classificationUuid : config.getClassificationUuids()){
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handleSingleClassification(state, classificationUuid);
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}
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state.getProcessor().createFinalResult(state);
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} catch (Exception e) {
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state.getResult().addException(e, "An unexpected error occurred in main method doInvoke() " +
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e.getMessage());
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}
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}
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/**
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* @param state
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* @param classificationUuid
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*/
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private void handleSingleClassification(CdmLightExportState state, UUID classificationUuid) {
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try {
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Classification classification = getClassificationService().find(classificationUuid);
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if (classification == null){
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String message = String.format("Classification for given classification UUID not found. No data imported for %s", classificationUuid.toString());
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//TODO
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state.getResult().addWarning(message);
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}else{
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TaxonNode root = classification.getRootNode();
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UUID uuid = root.getUuid();
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root = getTaxonNodeService().load(uuid);
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for (TaxonNode child : root.getChildNodes()){
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handleTaxon(state, child);
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//TODO progress monitor
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}
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}
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} catch (Exception e) {
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state.getResult().addException(e, "An unexpected error occurred when handling classification " +
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classificationUuid + ": " + e.getMessage() + e.getStackTrace());
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}
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}
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/**
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* @param state
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* @param taxon
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*/
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private void handleTaxon(CdmLightExportState state, TaxonNode taxonNode) {
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// Taxon taxon = taxonNode.getTaxon();
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if (taxonNode == null){
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state.getResult().addError ("The taxonNode was null.", "handleTaxon");
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state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
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return;
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}
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if (taxonNode.getTaxon() == null){
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state.getResult().addError ("There was a taxon node without a taxon: " + taxonNode.getUuid(), "handleTaxon");
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state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
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}else{
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Taxon taxon = taxonNode.getTaxon();
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try{
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TaxonName name = taxon.getName();
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handleName(state, name);
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for (Synonym syn : taxon.getSynonyms()){
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handleSynonym(state, syn);
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}
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CdmLightExportTable table = CdmLightExportTable.TAXON;
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String[] csvLine = new String[table.getSize()];
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csvLine[table.getIndex(CdmLightExportTable.TAXON_ID)] = getId(state, taxon);
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csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
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Taxon parent = (taxonNode.getParent()==null) ? null : taxonNode.getParent().getTaxon();
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csvLine[table.getIndex(CdmLightExportTable.PARENT_FK)] = getId(state, parent);
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csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
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csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(taxon.getSec());
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csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_ID)] = getId(state, taxonNode.getClassification());
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csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification().getTitleCache();
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state.getProcessor().put(table, taxon, csvLine);
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handleDescriptions(state, taxon);
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}catch(Exception e){
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state.getResult().addException (e, "An unexpected problem occurred when trying to export "
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+ "taxon with id " + taxon.getId());
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state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
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}
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}
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taxonNode.removeNullValueFromChildren();
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for (TaxonNode child: taxonNode.getChildNodes()){
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handleTaxon(state, child);
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}
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}
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/**
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* @param state
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* @param taxon
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*/
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private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
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if (cdmBase instanceof Taxon){
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Taxon taxon = HibernateProxyHelper.deproxy(cdmBase, Taxon.class);
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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List<DescriptionElementBase> simpleFacts = new ArrayList<>();
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List<DescriptionElementBase> specimenFacts = new ArrayList<>();
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List<DescriptionElementBase> distributionFacts = new ArrayList<>();
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List<DescriptionElementBase> commonNameFacts = new ArrayList<>();
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List<DescriptionElementBase> usageFacts = new ArrayList<>();
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for (TaxonDescription description: descriptions){
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if (description.getElements() != null){
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for (DescriptionElementBase element: description.getElements()){
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element = CdmBase.deproxy(element);
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if (element.getFeature().equals(Feature.COMMON_NAME())){
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commonNameFacts.add(element);
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}else if (element.getFeature().equals(Feature.DISTRIBUTION())){
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distributionFacts.add(element);
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}else if (element instanceof IndividualsAssociation || isSpecimenFeature(element.getFeature())){
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specimenFacts.add(element);
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}else{
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simpleFacts.add(element);
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}
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}
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}
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}
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if (!commonNameFacts.isEmpty()){
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handleCommonNameFacts(state, taxon, commonNameFacts);
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}
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if (!distributionFacts.isEmpty()){
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handleDistributionFacts(state, taxon, distributionFacts);
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}
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if (!specimenFacts.isEmpty()){
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handleSpecimenFacts(state, taxon, specimenFacts);
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}
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if (!simpleFacts.isEmpty()){
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handleSimpleFacts(state, taxon, simpleFacts);
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}
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} else if (cdmBase instanceof TaxonName){
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TaxonName name = CdmBase.deproxy(cdmBase, TaxonName.class);
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Set<TaxonNameDescription> descriptions = name.getDescriptions();
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List<DescriptionElementBase> simpleFacts = new ArrayList<>();
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for (TaxonNameDescription description: descriptions){
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if (description.getElements() != null){
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for (DescriptionElementBase element: description.getElements()){
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if (!element.getFeature().equals(Feature.PROTOLOGUE())){
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simpleFacts.add(element);
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}
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}
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}
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}
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if (!simpleFacts.isEmpty()){
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handleSimpleFacts(state, name, simpleFacts);
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}
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}
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}
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/**
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* @param feature
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* @return
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*/
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private boolean isSpecimenFeature(Feature feature) {
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//TODO allow user defined specimen features
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if (feature == null){
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return false;
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}else if (feature.isSupportsIndividualAssociation()){
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return true;
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}else{
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return feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.INDIVIDUALS_ASSOCIATION())
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|| feature.equals(Feature.MATERIALS_EXAMINED()) || feature.equals(Feature.OBSERVATION())
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|| feature.equals(Feature.OCCURRENCE())
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;
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}
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}
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289
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/**
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* @param state
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291
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* @param taxon
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292
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* @param simpleFacts
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*/
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294
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private void handleSimpleFacts(CdmLightExportState state, CdmBase cdmBase,
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List<DescriptionElementBase> simpleFacts) {
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try {
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297
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CdmLightExportTable table = CdmLightExportTable.SIMPLE_FACT;
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298
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299
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for (DescriptionElementBase element: simpleFacts){
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300
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handleSingleSimpleFact(state, cdmBase, table, element);
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}
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302
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} catch (Exception e) {
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state.getResult().addException(e, "An unexpected error occurred when handling simple facts for " +
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cdmBaseStr(cdmBase) + ": " + e.getMessage());
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305
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}
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306
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}
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307
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308
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/**
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309
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* @param state
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310
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* @param cdmBase
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311
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* @param table
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312
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* @param element
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313
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*/
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314
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private void handleSingleSimpleFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
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315
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DescriptionElementBase element) {
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316
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try {
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317
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String[] csvLine;
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318
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handleSource(state, element, CdmLightExportTable.SIMPLE_FACT);
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319
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320
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if (element instanceof TextData){
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321
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TextData textData = (TextData)element;
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322
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csvLine = new String[table.getSize()];
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323
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csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
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324
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if (cdmBase instanceof Taxon){
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325
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csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
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326
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csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
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327
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}else if (cdmBase instanceof TaxonName){
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328
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csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
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csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
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330
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}
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331
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csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = textData.getFeature().getLabel();
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332
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333
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String mediaUris = "";
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334
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for (Media media: textData.getMedia()){
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335
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String mediaString = extractMediaUris(media.getRepresentations().iterator());
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336
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if (!StringUtils.isBlank(mediaString)){
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337
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mediaUris += mediaString + ";";
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338
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}
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|
339
|
else{
|
|
340
|
state.getResult().addWarning("Empty Media object for uuid: " +
|
|
341
|
cdmBase.getUuid() + " uuid of media: " + media.getUuid());
|
|
342
|
}
|
|
343
|
}
|
|
344
|
csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
|
|
345
|
if (textData.getFeature().equals(Feature.CITATION())){
|
|
346
|
// csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
|
|
347
|
state.getProcessor().put(table, textData, csvLine);
|
|
348
|
}else if (!textData.getMultilanguageText().isEmpty()){
|
|
349
|
for (Language language: textData.getMultilanguageText().keySet()){
|
|
350
|
String[] csvLineLanguage = csvLine.clone();
|
|
351
|
LanguageString langString = textData.getLanguageText(language);
|
|
352
|
|
|
353
|
csvLineLanguage[table.getIndex(CdmLightExportTable.FACT_TEXT)] = langString.getText();
|
|
354
|
csvLineLanguage[table.getIndex(CdmLightExportTable.LANGUAGE)] = language.getLabel();
|
|
355
|
state.getProcessor().put(table, textData, csvLineLanguage);
|
|
356
|
}
|
|
357
|
} else{
|
|
358
|
state.getProcessor().put(table, textData, csvLine);
|
|
359
|
}
|
|
360
|
}
|
|
361
|
} catch (Exception e) {
|
|
362
|
state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
|
|
363
|
cdmBaseStr(element) + ": " + e.getMessage());
|
|
364
|
}
|
|
365
|
}
|
|
366
|
|
|
367
|
|
|
368
|
/**
|
|
369
|
* @param state
|
|
370
|
* @param specimenFacts
|
|
371
|
*/
|
|
372
|
private void handleSpecimenFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> specimenFacts) {
|
|
373
|
CdmLightExportTable table = CdmLightExportTable.SPECIMEN_FACT;
|
|
374
|
|
|
375
|
for (DescriptionElementBase element: specimenFacts){
|
|
376
|
try {
|
|
377
|
String[] csvLine = new String[table.getSize()];
|
|
378
|
csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
|
|
379
|
csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
|
|
380
|
handleSource(state, element, table);
|
|
381
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_NOTES)] = createAnnotationsString(element.getAnnotations());
|
|
382
|
|
|
383
|
if (element instanceof IndividualsAssociation){
|
|
384
|
|
|
385
|
IndividualsAssociation indAssociation = (IndividualsAssociation)element;
|
|
386
|
if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
|
|
387
|
SpecimenOrObservationBase<?> specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation());
|
|
388
|
|
|
389
|
if (specimenBase instanceof SpecimenOrObservationBase){
|
|
390
|
SpecimenOrObservationBase derivedUnit = specimenBase;
|
|
391
|
handleSpecimen(state, derivedUnit);
|
|
392
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
|
|
393
|
}else{
|
|
394
|
//field units are not supported
|
|
395
|
state.getResult().addError("The associated Specimen of taxon " + taxon.getUuid() + " is not an DerivedUnit. Could not be exported.");
|
|
396
|
}
|
|
397
|
}
|
|
398
|
} else if (element instanceof TextData){
|
|
399
|
TextData textData = HibernateProxyHelper.deproxy(element, TextData.class);
|
|
400
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_DESCRIPTION)] = createMultilanguageString(textData.getMultilanguageText());
|
|
401
|
}
|
|
402
|
state.getProcessor().put(table, element, csvLine);
|
|
403
|
} catch (Exception e) {
|
|
404
|
state.getResult().addException(e, "An unexpected error occurred when handling single specimen fact " +
|
|
405
|
cdmBaseStr(element) + ": " + e.getMessage());
|
|
406
|
}
|
|
407
|
}
|
|
408
|
}
|
|
409
|
|
|
410
|
/**
|
|
411
|
* @param multilanguageText
|
|
412
|
* @return
|
|
413
|
*/
|
|
414
|
private String createMultilanguageString(Map<Language, LanguageString> multilanguageText) {
|
|
415
|
String text = "";
|
|
416
|
int index = multilanguageText.size();
|
|
417
|
for(LanguageString langString: multilanguageText.values()){
|
|
418
|
text += langString.getText();
|
|
419
|
if (index > 1){
|
|
420
|
text += "; ";
|
|
421
|
}
|
|
422
|
index --;
|
|
423
|
}
|
|
424
|
|
|
425
|
return text;
|
|
426
|
}
|
|
427
|
|
|
428
|
/**
|
|
429
|
* @param annotations
|
|
430
|
* @return
|
|
431
|
*/
|
|
432
|
private String createAnnotationsString(Set<Annotation> annotations) {
|
|
433
|
StringBuffer strBuff = new StringBuffer();
|
|
434
|
|
|
435
|
for (Annotation ann:annotations){
|
|
436
|
if (ann.getAnnotationType() == null ||!ann.getAnnotationType().equals(AnnotationType.TECHNICAL())){
|
|
437
|
strBuff.append(ann.getText());
|
|
438
|
strBuff.append("; ");
|
|
439
|
}
|
|
440
|
}
|
|
441
|
|
|
442
|
if (strBuff.length() > 2){
|
|
443
|
return strBuff.substring(0, strBuff.length()-2);
|
|
444
|
}else{
|
|
445
|
return null;
|
|
446
|
}
|
|
447
|
}
|
|
448
|
|
|
449
|
/**
|
|
450
|
* @param state
|
|
451
|
* @param taxon
|
|
452
|
* @param element
|
|
453
|
*/
|
|
454
|
private void handleSource(CdmLightExportState state, DescriptionElementBase element, CdmLightExportTable factsTable) {
|
|
455
|
CdmLightExportTable table = CdmLightExportTable.FACT_SOURCES;
|
|
456
|
Set<DescriptionElementSource> sources = element.getSources();
|
|
457
|
for (DescriptionElementSource source: sources){
|
|
458
|
try {
|
|
459
|
String[] csvLine = new String[table.getSize()];
|
|
460
|
Reference ref = source.getCitation();
|
|
461
|
if ((ref == null) && (source.getNameUsedInSource() == null)){
|
|
462
|
continue;
|
|
463
|
}
|
|
464
|
if (ref != null){
|
|
465
|
if (state.getReferenceFromStore(ref.getId()) == null){
|
|
466
|
handleReference(state, ref);
|
|
467
|
csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, ref);
|
|
468
|
}
|
|
469
|
}
|
|
470
|
csvLine[table.getIndex(CdmLightExportTable.FACT_FK)] = getId(state, element);
|
|
471
|
|
|
472
|
csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)] = getId(state, source.getNameUsedInSource());
|
|
473
|
csvLine[table.getIndex(CdmLightExportTable.FACT_TYPE)] = factsTable.getTableName();
|
|
474
|
if ( StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)]) && StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)])){
|
|
475
|
continue;
|
|
476
|
}
|
|
477
|
state.getProcessor().put(table, source, csvLine);
|
|
478
|
} catch (Exception e) {
|
|
479
|
state.getResult().addException(e, "An unexpected error occurred when handling single source " +
|
|
480
|
cdmBaseStr(element) + ": " + e.getMessage());
|
|
481
|
}
|
|
482
|
}
|
|
483
|
|
|
484
|
}
|
|
485
|
|
|
486
|
/**
|
|
487
|
* @param state
|
|
488
|
* @param distributionFacts
|
|
489
|
*/
|
|
490
|
private void handleDistributionFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> distributionFacts) {
|
|
491
|
CdmLightExportTable table = CdmLightExportTable.GEOGRAPHIC_AREA_FACT;
|
|
492
|
|
|
493
|
for (DescriptionElementBase element: distributionFacts){
|
|
494
|
try {
|
|
495
|
if (element instanceof Distribution){
|
|
496
|
String[] csvLine = new String[table.getSize()];
|
|
497
|
Distribution distribution = (Distribution)element;
|
|
498
|
csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
|
|
499
|
handleSource(state, element, table);
|
|
500
|
csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
|
|
501
|
if (distribution.getArea() != null){
|
|
502
|
csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = distribution.getArea().getLabel();
|
|
503
|
}
|
|
504
|
if (distribution.getStatus() != null){
|
|
505
|
csvLine[table.getIndex(CdmLightExportTable.STATUS_LABEL)] = distribution.getStatus().getLabel();
|
|
506
|
}
|
|
507
|
state.getProcessor().put(table, distribution, csvLine);
|
|
508
|
} else{
|
|
509
|
state.getResult().addError("The distribution description for the taxon " + taxon.getUuid() + " is not of type distribution. Could not be exported. UUID of the description element: " + element.getUuid());
|
|
510
|
}
|
|
511
|
} catch (Exception e) {
|
|
512
|
state.getResult().addException(e, "An unexpected error occurred when handling single distribution " +
|
|
513
|
cdmBaseStr(element) + ": " + e.getMessage());
|
|
514
|
}
|
|
515
|
}
|
|
516
|
}
|
|
517
|
|
|
518
|
/**
|
|
519
|
* @param state
|
|
520
|
* @param commonNameFacts
|
|
521
|
*/
|
|
522
|
private void handleCommonNameFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> commonNameFacts) {
|
|
523
|
CdmLightExportTable table = CdmLightExportTable.COMMON_NAME_FACT;
|
|
524
|
|
|
525
|
for (DescriptionElementBase element: commonNameFacts){
|
|
526
|
try {
|
|
527
|
if (element instanceof CommonTaxonName){
|
|
528
|
String[] csvLine = new String[table.getSize()];
|
|
529
|
CommonTaxonName commonName = (CommonTaxonName)element;
|
|
530
|
csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
|
|
531
|
handleSource(state, element, table);
|
|
532
|
csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
|
|
533
|
if (commonName.getName() != null){csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = commonName.getName();}
|
|
534
|
if (commonName.getLanguage() != null){csvLine[table.getIndex(CdmLightExportTable.LANGUAGE)] = commonName.getLanguage().getLabel();}
|
|
535
|
if (commonName.getArea() != null){ csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = commonName.getArea().getLabel();}
|
|
536
|
state.getProcessor().put(table, commonName, csvLine);
|
|
537
|
} else{
|
|
538
|
state.getResult().addError("The distribution description for the taxon " + taxon.getUuid() + " is not of type distribution. Could not be exported. UUID of the description element: " + element.getUuid());
|
|
539
|
}
|
|
540
|
} catch (Exception e) {
|
|
541
|
state.getResult().addException(e, "An unexpected error occurred when handling single common name " +
|
|
542
|
cdmBaseStr(element) + ": " + e.getMessage());
|
|
543
|
}
|
|
544
|
}
|
|
545
|
}
|
|
546
|
|
|
547
|
/**
|
|
548
|
* @param sec
|
|
549
|
* @return
|
|
550
|
*/
|
|
551
|
private String getTitleCache(IIdentifiableEntity identEntity) {
|
|
552
|
if (identEntity == null){
|
|
553
|
return "";
|
|
554
|
}
|
|
555
|
//TODO refresh?
|
|
556
|
return identEntity.getTitleCache();
|
|
557
|
}
|
|
558
|
|
|
559
|
/**
|
|
560
|
* @param state
|
|
561
|
* @param taxon
|
|
562
|
* @return
|
|
563
|
*/
|
|
564
|
private String getId(CdmLightExportState state, ICdmBase cdmBase) {
|
|
565
|
if (cdmBase == null){
|
|
566
|
return "";
|
|
567
|
}
|
|
568
|
//TODO make configurable
|
|
569
|
return cdmBase.getUuid().toString();
|
|
570
|
}
|
|
571
|
|
|
572
|
/**
|
|
573
|
* @param state
|
|
574
|
* @param syn
|
|
575
|
*/
|
|
576
|
private void handleSynonym(CdmLightExportState state, Synonym syn) {
|
|
577
|
try {
|
|
578
|
TaxonName name = syn.getName();
|
|
579
|
handleName(state, name);
|
|
580
|
|
|
581
|
CdmLightExportTable table = CdmLightExportTable.SYNONYM;
|
|
582
|
String[] csvLine = new String[table.getSize()];
|
|
583
|
|
|
584
|
csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, syn);
|
|
585
|
csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, syn.getAcceptedTaxon());
|
|
586
|
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
|
|
587
|
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, syn.getSec());
|
|
588
|
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(syn.getSec());
|
|
589
|
|
|
590
|
state.getProcessor().put(table, syn, csvLine);
|
|
591
|
} catch (Exception e) {
|
|
592
|
state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
|
|
593
|
cdmBaseStr(syn) + ": " + e.getMessage());
|
|
594
|
}
|
|
595
|
}
|
|
596
|
|
|
597
|
/**
|
|
598
|
* @param state
|
|
599
|
* @param name
|
|
600
|
*/
|
|
601
|
private void handleName(CdmLightExportState state, TaxonName name) {
|
|
602
|
if (name == null){
|
|
603
|
return;
|
|
604
|
}
|
|
605
|
try {
|
|
606
|
Rank rank = name.getRank();
|
|
607
|
CdmLightExportTable table = CdmLightExportTable.SCIENTIFIC_NAME;
|
|
608
|
name = HibernateProxyHelper.deproxy(name);
|
|
609
|
String[] csvLine = new String[table.getSize()];
|
|
610
|
|
|
611
|
csvLine[table.getIndex(CdmLightExportTable.NAME_ID)] = getId(state, name);
|
|
612
|
if (name.getLsid() != null){
|
|
613
|
csvLine[table.getIndex(CdmLightExportTable.LSID)] = name.getLsid().getLsid();
|
|
614
|
}else{
|
|
615
|
csvLine[table.getIndex(CdmLightExportTable.LSID)] = "";
|
|
616
|
}
|
|
617
|
|
|
618
|
handleIdentifier(state, name);
|
|
619
|
handleDescriptions(state, name);
|
|
620
|
|
|
621
|
csvLine[table.getIndex(CdmLightExportTable.RANK)] = getTitleCache(rank);
|
|
622
|
if (rank != null){
|
|
623
|
csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
|
|
624
|
if (rank.isInfraGeneric()){
|
|
625
|
try {
|
|
626
|
csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
|
|
627
|
} catch (UnknownCdmTypeException e) {
|
|
628
|
state.getResult().addError("Infrageneric marker expected but not available for rank " + name.getRank().getTitleCache());
|
|
629
|
}
|
|
630
|
}
|
|
631
|
if (rank.isInfraSpecific()){
|
|
632
|
csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
|
|
633
|
}
|
|
634
|
}else{
|
|
635
|
csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = "";
|
|
636
|
}
|
|
637
|
if (name.isProtectedTitleCache()){
|
|
638
|
csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] =name.getTitleCache();
|
|
639
|
}else{
|
|
640
|
//TODO: adapt the tropicos titlecache creation
|
|
641
|
csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
|
|
642
|
}
|
|
643
|
csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
|
|
644
|
csvLine[table.getIndex(CdmLightExportTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
|
|
645
|
|
|
646
|
csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
|
|
647
|
csvLine[table.getIndex(CdmLightExportTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
|
|
648
|
|
|
649
|
csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
|
|
650
|
csvLine[table.getIndex(CdmLightExportTable.BAS_AUTHORTEAM_FK)] = getId(state,name.getBasionymAuthorship());
|
|
651
|
if (name.getBasionymAuthorship() != null){
|
|
652
|
if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
|
|
653
|
handleAuthor(state, name.getBasionymAuthorship());
|
|
654
|
}
|
|
655
|
}
|
|
656
|
csvLine[table.getIndex(CdmLightExportTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
|
|
657
|
if (name.getExBasionymAuthorship() != null){
|
|
658
|
if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
|
|
659
|
handleAuthor(state, name.getExBasionymAuthorship());
|
|
660
|
}
|
|
661
|
|
|
662
|
}
|
|
663
|
csvLine[table.getIndex(CdmLightExportTable.COMB_AUTHORTEAM_FK)] = getId(state,name.getCombinationAuthorship());
|
|
664
|
if (name.getCombinationAuthorship() != null){
|
|
665
|
if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
|
|
666
|
handleAuthor(state, name.getCombinationAuthorship());
|
|
667
|
}
|
|
668
|
}
|
|
669
|
csvLine[table.getIndex(CdmLightExportTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
|
|
670
|
if (name.getExCombinationAuthorship() != null){
|
|
671
|
if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
|
|
672
|
handleAuthor(state, name.getExCombinationAuthorship());
|
|
673
|
}
|
|
674
|
|
|
675
|
}
|
|
676
|
|
|
677
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
|
|
678
|
|
|
679
|
Reference nomRef = (Reference)name.getNomenclaturalReference();
|
|
680
|
|
|
681
|
if (nomRef != null){
|
|
682
|
if (state.getReferenceFromStore(nomRef.getId()) == null){
|
|
683
|
handleReference(state, nomRef);
|
|
684
|
}
|
|
685
|
csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, nomRef);
|
|
686
|
csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = nomRef.getType().name();
|
|
687
|
if (nomRef.getVolume() != null){
|
|
688
|
csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = nomRef.getVolume();
|
|
689
|
csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
|
|
690
|
}
|
|
691
|
if (nomRef.getDatePublished() != null){
|
|
692
|
csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = nomRef.getTimePeriodPublishedString();
|
|
693
|
csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
|
|
694
|
csvLine[table.getIndex(CdmLightExportTable.VERBATIM_DATE)] = null;
|
|
695
|
}
|
|
696
|
if (name.getNomenclaturalMicroReference() != null){
|
|
697
|
csvLine[table.getIndex(CdmLightExportTable.DETAIL)] = name.getNomenclaturalMicroReference();
|
|
698
|
}
|
|
699
|
nomRef = HibernateProxyHelper.deproxy(nomRef);
|
|
700
|
if (nomRef.getInReference() != null){
|
|
701
|
Reference inReference = nomRef.getInReference();
|
|
702
|
if (inReference.getDatePublished() != null && nomRef.getDatePublished() == null){
|
|
703
|
csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = inReference.getDatePublishedString();
|
|
704
|
csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = inReference.getDatePublished().getYear();
|
|
705
|
}
|
|
706
|
if (nomRef.getVolume() == null && inReference.getVolume() != null){
|
|
707
|
csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = inReference.getVolume();
|
|
708
|
csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
|
|
709
|
}
|
|
710
|
if (inReference.getInReference() != null){
|
|
711
|
inReference = inReference.getInReference();
|
|
712
|
}
|
|
713
|
if (inReference.getAbbrevTitle() == null){
|
|
714
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitleCache());
|
|
715
|
}else{
|
|
716
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
|
|
717
|
}
|
|
718
|
if (inReference.getTitle() == null){
|
|
719
|
csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitleCache());
|
|
720
|
}else{
|
|
721
|
csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
|
|
722
|
}
|
|
723
|
|
|
724
|
|
|
725
|
TeamOrPersonBase<?> author = inReference.getAuthorship();
|
|
726
|
if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))){
|
|
727
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
|
|
728
|
csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
|
|
729
|
}else{
|
|
730
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
|
|
731
|
csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
|
|
732
|
}
|
|
733
|
}else{
|
|
734
|
if (nomRef.getAbbrevTitle() == null){
|
|
735
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitleCache());
|
|
736
|
}else{
|
|
737
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle());
|
|
738
|
}
|
|
739
|
if (nomRef.getTitle() == null){
|
|
740
|
csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitleCache());
|
|
741
|
}else{
|
|
742
|
csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitle());
|
|
743
|
}
|
|
744
|
TeamOrPersonBase<?> author = nomRef.getAuthorship();
|
|
745
|
if (author != null ){
|
|
746
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
|
|
747
|
csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
|
|
748
|
}else{
|
|
749
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
|
|
750
|
csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
|
|
751
|
}
|
|
752
|
|
|
753
|
}
|
|
754
|
}else{
|
|
755
|
csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = "";
|
|
756
|
}
|
|
757
|
|
|
758
|
|
|
759
|
|
|
760
|
/*
|
|
761
|
* Collation
|
|
762
|
|
|
763
|
Detail
|
|
764
|
|
|
765
|
|
|
766
|
TitlePageYear
|
|
767
|
*/
|
|
768
|
Set<TaxonNameDescription> descriptions = name.getDescriptions();
|
|
769
|
String protologueUriString = extractURIs(state, descriptions, Feature.PROTOLOGUE());
|
|
770
|
|
|
771
|
csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_URI)] = protologueUriString;
|
|
772
|
|
|
773
|
if (name.getStatus() == null || name.getStatus().isEmpty()){
|
|
774
|
csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = "";
|
|
775
|
csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = "";
|
|
776
|
}else{
|
|
777
|
|
|
778
|
String statusStringAbbrev = extractStatusString(state, name, true);
|
|
779
|
String statusString = extractStatusString(state, name, false);
|
|
780
|
|
|
781
|
csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = statusString.trim();
|
|
782
|
csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
|
|
783
|
}
|
|
784
|
|
|
785
|
HomotypicalGroup group =name.getHomotypicalGroup();
|
|
786
|
|
|
787
|
if (state.getHomotypicalGroupFromStore(group.getId()) == null){
|
|
788
|
handleHomotypicalGroup(state, group);
|
|
789
|
}
|
|
790
|
csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
|
|
791
|
List<TaxonName> typifiedNames = new ArrayList<>();
|
|
792
|
typifiedNames.addAll(group.getTypifiedNames());
|
|
793
|
Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
|
|
794
|
Integer seqNumber= typifiedNames.indexOf(name);
|
|
795
|
csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
|
|
796
|
state.getProcessor().put(table, name, csvLine);
|
|
797
|
|
|
798
|
/*
|
|
799
|
*
|
|
800
|
Tropicos_ID
|
|
801
|
IPNI_ID
|
|
802
|
|
|
803
|
|
|
804
|
InfragenericRank
|
|
805
|
|
|
806
|
|
|
807
|
InfraspecificRank
|
|
808
|
Collation
|
|
809
|
Volume (Issue)
|
|
810
|
Detail
|
|
811
|
DatePublished
|
|
812
|
YearPublished
|
|
813
|
TitlePageYear
|
|
814
|
|
|
815
|
|
|
816
|
|
|
817
|
HomotypicGroupSequenceNumber
|
|
818
|
|
|
819
|
|
|
820
|
*
|
|
821
|
*/
|
|
822
|
} catch (Exception e) {
|
|
823
|
state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
|
|
824
|
cdmBaseStr(name) + ": " + e.getMessage());
|
|
825
|
}
|
|
826
|
}
|
|
827
|
|
|
828
|
/**
|
|
829
|
* @return
|
|
830
|
*/
|
|
831
|
private String createCollatation(TaxonName name) {
|
|
832
|
String collation = "";
|
|
833
|
if (name.getNomenclaturalReference() != null){
|
|
834
|
Reference ref = (Reference) name.getNomenclaturalReference();
|
|
835
|
collation = getVolume(ref);
|
|
836
|
}
|
|
837
|
if (name.getNomenclaturalMicroReference() != null){
|
|
838
|
if (!StringUtils.isBlank(collation)){
|
|
839
|
collation += ":";
|
|
840
|
}
|
|
841
|
collation +=name.getNomenclaturalMicroReference();
|
|
842
|
}
|
|
843
|
|
|
844
|
return collation;
|
|
845
|
}
|
|
846
|
|
|
847
|
/**
|
|
848
|
* @param nomenclaturalReference
|
|
849
|
* @return
|
|
850
|
*/
|
|
851
|
private String getVolume(Reference reference) {
|
|
852
|
if (reference.getVolume() != null){
|
|
853
|
return reference.getVolume();
|
|
854
|
}else if (reference.getInReference() != null){
|
|
855
|
if (reference.getInReference().getVolume() != null){
|
|
856
|
return reference.getInReference().getVolume();
|
|
857
|
}
|
|
858
|
}
|
|
859
|
return null;
|
|
860
|
}
|
|
861
|
|
|
862
|
/**
|
|
863
|
* @param state
|
|
864
|
* @param name
|
|
865
|
*/
|
|
866
|
private void handleIdentifier(CdmLightExportState state, TaxonName name) {
|
|
867
|
CdmLightExportTable table = CdmLightExportTable.IDENTIFIER;
|
|
868
|
String[] csvLine;
|
|
869
|
try {
|
|
870
|
Set<String> IPNIidentifiers = name.getIdentifiers(DefinedTerm.IPNI_NAME_IDENTIFIER());
|
|
871
|
Set<String> tropicosIdentifiers = name.getIdentifiers(DefinedTerm.TROPICOS_NAME_IDENTIFIER());
|
|
872
|
Set<String> WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
|
|
873
|
if (!IPNIidentifiers.isEmpty()){
|
|
874
|
csvLine = new String[table.getSize()];
|
|
875
|
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
|
|
876
|
csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
|
|
877
|
csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(IPNIidentifiers);
|
|
878
|
state.getProcessor().put(table, name, csvLine);
|
|
879
|
}
|
|
880
|
if (!tropicosIdentifiers.isEmpty()){
|
|
881
|
csvLine = new String[table.getSize()];
|
|
882
|
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
|
|
883
|
csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = TROPICOS_NAME_IDENTIFIER;
|
|
884
|
csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(tropicosIdentifiers);
|
|
885
|
state.getProcessor().put(table, name, csvLine);
|
|
886
|
}
|
|
887
|
if (!WFOIdentifiers.isEmpty()){
|
|
888
|
csvLine = new String[table.getSize()];
|
|
889
|
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
|
|
890
|
csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
|
|
891
|
csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(WFOIdentifiers);
|
|
892
|
state.getProcessor().put(table, name, csvLine);
|
|
893
|
}
|
|
894
|
} catch (Exception e) {
|
|
895
|
state.getResult().addException(e, "An unexpected error occurred when handling identifiers for " +
|
|
896
|
cdmBaseStr(name) + ": " + e.getMessage());
|
|
897
|
|
|
898
|
}
|
|
899
|
}
|
|
900
|
|
|
901
|
/**
|
|
902
|
* @param tropicosIdentifiers
|
|
903
|
*/
|
|
904
|
private String extractIdentifier(Set<String> identifierSet) {
|
|
905
|
|
|
906
|
String identifierString = "";
|
|
907
|
for (String identifier: identifierSet){
|
|
908
|
if (!StringUtils.isBlank(identifierString)){
|
|
909
|
identifierString += ", ";
|
|
910
|
}
|
|
911
|
identifierString += identifier;
|
|
912
|
}
|
|
913
|
|
|
914
|
return identifierString;
|
|
915
|
}
|
|
916
|
|
|
917
|
/**
|
|
918
|
* @param state
|
|
919
|
* @param descriptions
|
|
920
|
* @return
|
|
921
|
*/
|
|
922
|
private String extractURIs(CdmLightExportState state,
|
|
923
|
Set<? extends DescriptionBase<?>> descriptionsSet, Feature feature) {
|
|
924
|
String mediaUriString = "";
|
|
925
|
SpecimenDescription specimenDescription;
|
|
926
|
TaxonDescription taxonDescription;
|
|
927
|
TaxonNameDescription nameDescription;
|
|
928
|
Set<DescriptionElementBase> elements = new HashSet<>();
|
|
929
|
for (DescriptionBase<?> description : descriptionsSet){
|
|
930
|
try {
|
|
931
|
if (!description.getElements().isEmpty()){
|
|
932
|
if (description instanceof SpecimenDescription){
|
|
933
|
specimenDescription = (SpecimenDescription)description;
|
|
934
|
elements = specimenDescription.getElements();
|
|
935
|
}else if (description instanceof TaxonDescription){
|
|
936
|
taxonDescription = (TaxonDescription) description;
|
|
937
|
elements = taxonDescription.getElements();
|
|
938
|
} else if (description instanceof TaxonNameDescription){
|
|
939
|
nameDescription = (TaxonNameDescription) description;
|
|
940
|
elements = nameDescription.getElements();
|
|
941
|
}
|
|
942
|
|
|
943
|
for (DescriptionElementBase element : elements){
|
|
944
|
Feature entityFeature = HibernateProxyHelper.deproxy(element.getFeature());
|
|
945
|
if (entityFeature.equals(feature)){
|
|
946
|
if (!element.getMedia().isEmpty()){
|
|
947
|
List<Media> media = element.getMedia();
|
|
948
|
for (Media mediaElement: media){
|
|
949
|
Iterator<MediaRepresentation> it = mediaElement.getRepresentations().iterator();
|
|
950
|
mediaUriString = extractMediaUris(it);
|
|
951
|
}
|
|
952
|
}
|
|
953
|
}
|
|
954
|
}
|
|
955
|
}
|
|
956
|
} catch (Exception e) {
|
|
957
|
state.getResult().addException(e, "An unexpected error occurred when extracting media URIs for " +
|
|
958
|
cdmBaseStr(description) + ": " + e.getMessage());
|
|
959
|
}
|
|
960
|
}
|
|
961
|
return mediaUriString;
|
|
962
|
}
|
|
963
|
|
|
964
|
/**
|
|
965
|
* @param state
|
|
966
|
* @param basionymAuthorship
|
|
967
|
*/
|
|
968
|
private void handleAuthor(CdmLightExportState state, TeamOrPersonBase<?> author) {
|
|
969
|
try {
|
|
970
|
if (state.getAuthorFromStore(author.getId()) != null){
|
|
971
|
return;
|
|
972
|
}
|
|
973
|
state.addAuthorToStore(author);
|
|
974
|
CdmLightExportTable table = CdmLightExportTable.NOMENCLATURAL_AUTHOR;
|
|
975
|
String[] csvLine = new String[table.getSize()];
|
|
976
|
CdmLightExportTable tableAuthorRel = CdmLightExportTable.NOMENCLATURAL_AUTHOR_TEAM_RELATION;
|
|
977
|
String[] csvLineRel = new String[tableAuthorRel.getSize()];
|
|
978
|
String[] csvLineMember = new String[table.getSize()];
|
|
979
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, author);
|
|
980
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = author.getNomenclaturalTitle();
|
|
981
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = author.getTitleCache();
|
|
982
|
author = HibernateProxyHelper.deproxy(author);
|
|
983
|
if (author instanceof Person){
|
|
984
|
Person authorPerson = (Person)author;
|
|
985
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FIRST_NAME)] = authorPerson.getFirstname();
|
|
986
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_LASTNAME)] = authorPerson.getLastname();
|
|
987
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = authorPerson.getPrefix();
|
|
988
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = authorPerson.getSuffix();
|
|
989
|
} else{
|
|
990
|
// create an entry in rel table and all members in author table, check whether the team members already in author table
|
|
991
|
|
|
992
|
Team authorTeam = (Team)author;
|
|
993
|
int index = 0;
|
|
994
|
for (Person member: authorTeam.getTeamMembers()){
|
|
995
|
csvLineRel = new String[tableAuthorRel.getSize()];
|
|
996
|
csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_FK)] = getId(state, authorTeam);
|
|
997
|
csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state, member);
|
|
998
|
csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_SEQ_NUMBER)] = String.valueOf(index);
|
|
999
|
state.getProcessor().put(tableAuthorRel, authorTeam.getId() +":" +member.getId(), csvLineRel);
|
|
1000
|
|
|
1001
|
if (state.getAuthorFromStore(member.getId()) == null){
|
|
1002
|
state.addAuthorToStore(member);
|
|
1003
|
csvLineMember = new String[table.getSize()];
|
|
1004
|
csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, member);
|
|
1005
|
csvLineMember[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = member.getNomenclaturalTitle();
|
|
1006
|
csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = member.getTitleCache();
|
|
1007
|
csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_FIRST_NAME)] = member.getFirstname();
|
|
1008
|
csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_LASTNAME)] = member.getLastname();
|
|
1009
|
csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = member.getPrefix();
|
|
1010
|
csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = member.getSuffix();
|
|
1011
|
state.getProcessor().put(table, member, csvLineMember);
|
|
1012
|
}
|
|
1013
|
index++;
|
|
1014
|
|
|
1015
|
}
|
|
1016
|
}
|
|
1017
|
state.getProcessor().put(table, author, csvLine);
|
|
1018
|
} catch (Exception e) {
|
|
1019
|
state.getResult().addException(e, "An unexpected error occurred when handling author " +
|
|
1020
|
cdmBaseStr(author) + ": " + e.getMessage());
|
|
1021
|
}
|
|
1022
|
}
|
|
1023
|
|
|
1024
|
/**
|
|
1025
|
* @param state
|
|
1026
|
* @param name
|
|
1027
|
* @param statusString
|
|
1028
|
* @return
|
|
1029
|
*/
|
|
1030
|
private String extractStatusString(CdmLightExportState state, TaxonName name, boolean abbrev) {
|
|
1031
|
try {
|
|
1032
|
Set<NomenclaturalStatus> status = name.getStatus();
|
|
1033
|
if (status.isEmpty()){
|
|
1034
|
return "";
|
|
1035
|
}
|
|
1036
|
String statusString = "";
|
|
1037
|
for (NomenclaturalStatus nameStatus: status){
|
|
1038
|
if (nameStatus != null){
|
|
1039
|
if (abbrev){
|
|
1040
|
if (nameStatus.getType() != null){
|
|
1041
|
statusString += nameStatus.getType().getIdInVocabulary();
|
|
1042
|
}
|
|
1043
|
}else{
|
|
1044
|
if (nameStatus.getType() != null){
|
|
1045
|
statusString += nameStatus.getType().getTitleCache();
|
|
1046
|
}
|
|
1047
|
}
|
|
1048
|
if (!abbrev){
|
|
1049
|
|
|
1050
|
if (nameStatus.getRuleConsidered() != null && !StringUtils.isBlank(nameStatus.getRuleConsidered())){
|
|
1051
|
statusString += " " + nameStatus.getRuleConsidered();
|
|
1052
|
}
|
|
1053
|
if (nameStatus.getCitation() != null){
|
|
1054
|
statusString += " " + nameStatus.getCitation().getTitleCache();
|
|
1055
|
}
|
|
1056
|
if (nameStatus.getCitationMicroReference() != null && !StringUtils.isBlank(nameStatus.getCitationMicroReference())){
|
|
1057
|
statusString += " " + nameStatus.getCitationMicroReference();
|
|
1058
|
}
|
|
1059
|
}
|
|
1060
|
statusString += " ";
|
|
1061
|
}
|
|
1062
|
}
|
|
1063
|
return statusString;
|
|
1064
|
} catch (Exception e) {
|
|
1065
|
state.getResult().addException(e, "An unexpected error occurred when extracting status string for " +
|
|
1066
|
cdmBaseStr(name) + ": " + e.getMessage());
|
|
1067
|
return "";
|
|
1068
|
}
|
|
1069
|
}
|
|
1070
|
|
|
1071
|
/**
|
|
1072
|
* @param group
|
|
1073
|
*/
|
|
1074
|
private void handleHomotypicalGroup(CdmLightExportState state, HomotypicalGroup group) {
|
|
1075
|
try {
|
|
1076
|
state.addHomotypicalGroupToStore(group);
|
|
1077
|
CdmLightExportTable table = CdmLightExportTable.HOMOTYPIC_GROUP;
|
|
1078
|
String[] csvLine = new String[table.getSize()];
|
|
1079
|
|
|
1080
|
csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_ID)] = getId(state, group);
|
|
1081
|
List<TaxonName> typifiedNames = new ArrayList<>();
|
|
1082
|
typifiedNames.addAll(group.getTypifiedNames());
|
|
1083
|
Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
|
|
1084
|
String typifiedNamesString = "";
|
|
1085
|
for (TaxonName name: typifiedNames){
|
|
1086
|
//Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)
|
|
1087
|
//TODO: nameRelations, which and how to display
|
|
1088
|
|
|
1089
|
|
|
1090
|
typifiedNamesString += name.getTitleCache()+ extractStatusString(state, name, true) + "; ";
|
|
1091
|
}
|
|
1092
|
typifiedNamesString = typifiedNamesString.substring(0, typifiedNamesString.length()-2);
|
|
1093
|
if (typifiedNamesString != null){
|
|
1094
|
csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = typifiedNamesString.trim();
|
|
1095
|
}else{
|
|
1096
|
csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = "";
|
|
1097
|
}
|
|
1098
|
Set<TypeDesignationBase> typeDesigantions = group.getTypeDesignations();
|
|
1099
|
List<TypeDesignationBase> designationList = new ArrayList<>();
|
|
1100
|
designationList.addAll(typeDesigantions);
|
|
1101
|
Collections.sort(designationList, new TypeComparator());
|
|
1102
|
StringBuffer typeDesignationString = new StringBuffer();
|
|
1103
|
for (TypeDesignationBase typeDesignation: typeDesigantions){
|
|
1104
|
if (typeDesignation != null && typeDesignation.getTypeStatus() != null){
|
|
1105
|
typeDesignationString.append(typeDesignation.getTypeStatus().getTitleCache() + ": ");
|
|
1106
|
}
|
|
1107
|
if (typeDesignation instanceof SpecimenTypeDesignation){
|
|
1108
|
if (((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen() != null){
|
|
1109
|
typeDesignationString.append(((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen().getTitleCache());
|
|
1110
|
handleSpecimen(state, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
|
|
1111
|
}
|
|
1112
|
}else{
|
|
1113
|
if (((NameTypeDesignation)typeDesignation).getTypeName() != null){
|
|
1114
|
typeDesignationString.append(((NameTypeDesignation)typeDesignation).getTypeName().getTitleCache());
|
|
1115
|
}
|
|
1116
|
}
|
|
1117
|
if(typeDesignation.getCitation() != null ){
|
|
1118
|
typeDesignationString.append(", "+typeDesignation.getCitation().getTitleCache());
|
|
1119
|
}
|
|
1120
|
//TODO...
|
|
1121
|
/*
|
|
1122
|
* Sortierung:
|
|
1123
|
1. Status der Typen: a) holo, lecto, neo, syn, b) epi, paralecto, c) para (wenn überhaupt) – die jeweiligen iso immer direct mit dazu
|
|
1124
|
2. Land
|
|
1125
|
3. Sammler
|
|
1126
|
4. Nummer
|
|
1127
|
|
|
1128
|
Aufbau der Typusinformationen:
|
|
1129
|
Land: Lokalität mit Höhe und Koordinaten; Datum; Sammler Nummer (Herbar/Barcode, Typusart; Herbar/Barcode, Typusart …)
|
|
1130
|
|
|
1131
|
*/
|
|
1132
|
}
|
|
1133
|
String typeDesignations = typeDesignationString.toString();
|
|
1134
|
if (typeDesignations != null){
|
|
1135
|
csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = typeDesignations;
|
|
1136
|
}else{
|
|
1137
|
csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = "";
|
|
1138
|
}
|
|
1139
|
state.getProcessor().put(table, String.valueOf(group.getId()), csvLine);
|
|
1140
|
} catch (Exception e) {
|
|
1141
|
state.getResult().addException(e, "An unexpected error occurred when handling homotypic group " +
|
|
1142
|
cdmBaseStr(group) + ": " + e.getMessage());
|
|
1143
|
}
|
|
1144
|
}
|
|
1145
|
|
|
1146
|
/**
|
|
1147
|
* @param name
|
|
1148
|
* @return
|
|
1149
|
*/
|
|
1150
|
private String getTropicosTitleCache(CdmLightExportState state, TaxonName name) {
|
|
1151
|
try {
|
|
1152
|
String basionymStart = "(";
|
|
1153
|
String basionymEnd = ") ";
|
|
1154
|
String exAuthorSeperator = " ex ";
|
|
1155
|
TeamOrPersonBase<?> combinationAuthor = name.getCombinationAuthorship();
|
|
1156
|
TeamOrPersonBase<?> exCombinationAuthor = name.getExCombinationAuthorship();
|
|
1157
|
TeamOrPersonBase<?> basionymAuthor = name.getBasionymAuthorship();
|
|
1158
|
TeamOrPersonBase<?> exBasionymAuthor = name.getExBasionymAuthorship();
|
|
1159
|
|
|
1160
|
String combinationAuthorString = "";
|
|
1161
|
if (combinationAuthor != null){
|
|
1162
|
combinationAuthor = HibernateProxyHelper.deproxy(combinationAuthor);
|
|
1163
|
if (combinationAuthor instanceof Team){
|
|
1164
|
combinationAuthorString = createTropicosTeamTitle(combinationAuthor);
|
|
1165
|
}else{
|
|
1166
|
Person person = HibernateProxyHelper.deproxy(combinationAuthor, Person.class);
|
|
1167
|
combinationAuthorString = createTropicosAuthorString(person);
|
|
1168
|
}
|
|
1169
|
}
|
|
1170
|
String exCombinationAuthorString = "";
|
|
1171
|
if (exCombinationAuthor != null){
|
|
1172
|
exCombinationAuthor = HibernateProxyHelper.deproxy(exCombinationAuthor);
|
|
1173
|
if (exCombinationAuthor instanceof Team){
|
|
1174
|
exCombinationAuthorString = createTropicosTeamTitle(exCombinationAuthor);
|
|
1175
|
}else{
|
|
1176
|
Person person = HibernateProxyHelper.deproxy(exCombinationAuthor, Person.class);
|
|
1177
|
exCombinationAuthorString = createTropicosAuthorString(person);
|
|
1178
|
}
|
|
1179
|
}
|
|
1180
|
|
|
1181
|
String basionymAuthorString = "";
|
|
1182
|
if (basionymAuthor != null){
|
|
1183
|
basionymAuthor = HibernateProxyHelper.deproxy(basionymAuthor);
|
|
1184
|
if (basionymAuthor instanceof Team){
|
|
1185
|
basionymAuthorString = createTropicosTeamTitle(basionymAuthor);
|
|
1186
|
}else{
|
|
1187
|
Person person = HibernateProxyHelper.deproxy(basionymAuthor, Person.class);
|
|
1188
|
basionymAuthorString = createTropicosAuthorString(person);
|
|
1189
|
}
|
|
1190
|
}
|
|
1191
|
|
|
1192
|
String exBasionymAuthorString = "";
|
|
1193
|
|
|
1194
|
if (exBasionymAuthor != null){
|
|
1195
|
exBasionymAuthor = HibernateProxyHelper.deproxy(exBasionymAuthor);
|
|
1196
|
if (exBasionymAuthor instanceof Team){
|
|
1197
|
exBasionymAuthorString = createTropicosTeamTitle(exBasionymAuthor);
|
|
1198
|
|
|
1199
|
}else{
|
|
1200
|
Person person = HibernateProxyHelper.deproxy(exBasionymAuthor, Person.class);
|
|
1201
|
exBasionymAuthorString = createTropicosAuthorString(person);
|
|
1202
|
}
|
|
1203
|
}
|
|
1204
|
String completeAuthorString = name.getNameCache() + " ";
|
|
1205
|
|
|
1206
|
completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymStart: "";
|
|
1207
|
completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString)) ? (CdmUtils.Nz(exBasionymAuthorString) + exAuthorSeperator): "" ;
|
|
1208
|
completeAuthorString += (!CdmUtils.isBlank(basionymAuthorString))? CdmUtils.Nz(basionymAuthorString):"";
|
|
1209
|
completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymEnd:"";
|
|
1210
|
completeAuthorString += (!CdmUtils.isBlank(exCombinationAuthorString)) ? (CdmUtils.Nz(exCombinationAuthorString) + exAuthorSeperator): "" ;
|
|
1211
|
completeAuthorString += (!CdmUtils.isBlank(combinationAuthorString))? CdmUtils.Nz(combinationAuthorString):"";
|
|
1212
|
|
|
1213
|
|
|
1214
|
return completeAuthorString;
|
|
1215
|
} catch (Exception e) {
|
|
1216
|
state.getResult().addException(e, "An unexpected error occurred when handling tropicos title cache for " +
|
|
1217
|
cdmBaseStr(name) + ": " + e.getMessage());
|
|
1218
|
return null;
|
|
1219
|
}
|
|
1220
|
}
|
|
1221
|
|
|
1222
|
/**
|
|
1223
|
* @param combinationAuthor
|
|
1224
|
* @return
|
|
1225
|
*/
|
|
1226
|
private String createTropicosTeamTitle(TeamOrPersonBase<?> combinationAuthor) {
|
|
1227
|
String combinationAuthorString;
|
|
1228
|
Team team = HibernateProxyHelper.deproxy(combinationAuthor, Team.class);
|
|
1229
|
Team tempTeam = Team.NewInstance();
|
|
1230
|
for (Person teamMember:team.getTeamMembers()){
|
|
1231
|
combinationAuthorString = createTropicosAuthorString(teamMember);
|
|
1232
|
Person tempPerson = Person.NewTitledInstance(combinationAuthorString);
|
|
1233
|
tempTeam.addTeamMember(tempPerson);
|
|
1234
|
}
|
|
1235
|
combinationAuthorString = tempTeam.generateTitle();
|
|
1236
|
return combinationAuthorString;
|
|
1237
|
}
|
|
1238
|
|
|
1239
|
/**
|
|
1240
|
* @param teamMember
|
|
1241
|
*/
|
|
1242
|
private String createTropicosAuthorString(Person teamMember) {
|
|
1243
|
String nomAuthorString = "";
|
|
1244
|
String[] splittedAuthorString = null;
|
|
1245
|
if (teamMember == null){
|
|
1246
|
return nomAuthorString;
|
|
1247
|
}
|
|
1248
|
|
|
1249
|
if (teamMember.getFirstname() != null){
|
|
1250
|
String firstNameString = teamMember.getFirstname().replaceAll("\\.", "\\. ");
|
|
1251
|
splittedAuthorString = firstNameString.split("\\s");
|
|
1252
|
for (String split: splittedAuthorString){
|
|
1253
|
if (!StringUtils.isBlank(split)){
|
|
1254
|
nomAuthorString += split.substring(0, 1);
|
|
1255
|
nomAuthorString += ".";
|
|
1256
|
}
|
|
1257
|
}
|
|
1258
|
}
|
|
1259
|
if (teamMember.getLastname() != null){
|
|
1260
|
String lastNameString = teamMember.getLastname().replaceAll("\\.", "\\. ");
|
|
1261
|
splittedAuthorString = lastNameString.split("\\s");
|
|
1262
|
for (String split: splittedAuthorString){
|
|
1263
|
nomAuthorString += " " +split;
|
|
1264
|
}
|
|
1265
|
}
|
|
1266
|
if (StringUtils.isBlank(nomAuthorString.trim())){
|
|
1267
|
if (teamMember.getTitleCache() != null) {
|
|
1268
|
String titleCacheString = teamMember.getTitleCache().replaceAll("\\.", "\\. ");
|
|
1269
|
splittedAuthorString = titleCacheString.split("\\s");
|
|
1270
|
}
|
|
1271
|
|
|
1272
|
|
|
1273
|
int index = 0;
|
|
1274
|
for (String split: splittedAuthorString){
|
|
1275
|
if ( index < splittedAuthorString.length-1 && (split.length()==1 || split.endsWith("."))){
|
|
1276
|
nomAuthorString += split;
|
|
1277
|
}else{
|
|
1278
|
nomAuthorString = nomAuthorString +" "+ split;
|
|
1279
|
}
|
|
1280
|
index++;
|
|
1281
|
}
|
|
1282
|
}
|
|
1283
|
return nomAuthorString.trim();
|
|
1284
|
}
|
|
1285
|
|
|
1286
|
/**
|
|
1287
|
* @param state
|
|
1288
|
* @param name
|
|
1289
|
*/
|
|
1290
|
private void handleReference(CdmLightExportState state, Reference reference) {
|
|
1291
|
try {
|
|
1292
|
state.addReferenceToStore(reference);
|
|
1293
|
CdmLightExportTable table = CdmLightExportTable.REFERENCE;
|
|
1294
|
|
|
1295
|
String[] csvLine = new String[table.getSize()];
|
|
1296
|
csvLine[table.getIndex(CdmLightExportTable.REFERENCE_ID)] = getId(state, reference);
|
|
1297
|
//TODO short citations correctly
|
|
1298
|
String shortCitation = createShortCitation(reference); //Should be Author(year) like in Taxon.sec
|
|
1299
|
csvLine[table.getIndex(CdmLightExportTable.BIBLIO_SHORT_CITATION)] = shortCitation;
|
|
1300
|
//TODO get preferred title
|
|
1301
|
csvLine[table.getIndex(CdmLightExportTable.REF_TITLE)] = reference.getTitle();
|
|
1302
|
csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_TITLE)] = reference.getAbbrevTitle();
|
|
1303
|
csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = reference.getDatePublishedString();
|
|
1304
|
//TBC
|
|
1305
|
csvLine[table.getIndex(CdmLightExportTable.EDITION)] = reference.getEdition();
|
|
1306
|
csvLine[table.getIndex(CdmLightExportTable.EDITOR)] = reference.getEditor();
|
|
1307
|
csvLine[table.getIndex(CdmLightExportTable.ISBN)] = reference.getIsbn();
|
|
1308
|
csvLine[table.getIndex(CdmLightExportTable.ISSN)] = reference.getIssn();
|
|
1309
|
csvLine[table.getIndex(CdmLightExportTable.ORGANISATION)] = reference.getOrganization();
|
|
1310
|
csvLine[table.getIndex(CdmLightExportTable.PAGES)] = reference.getPages();
|
|
1311
|
csvLine[table.getIndex(CdmLightExportTable.PLACE_PUBLISHED)] = reference.getPlacePublished();
|
|
1312
|
csvLine[table.getIndex(CdmLightExportTable.PUBLISHER)] = reference.getPublisher();
|
|
1313
|
csvLine[table.getIndex(CdmLightExportTable.REF_ABSTRACT)] = reference.getReferenceAbstract();
|
|
1314
|
csvLine[table.getIndex(CdmLightExportTable.SERIES_PART)] = reference.getSeriesPart();
|
|
1315
|
csvLine[table.getIndex(CdmLightExportTable.VOLUME)] = reference.getVolume();
|
|
1316
|
csvLine[table.getIndex(CdmLightExportTable.YEAR)] = reference.getYear();
|
|
1317
|
if ( reference.getAuthorship() != null){
|
|
1318
|
csvLine[table.getIndex(CdmLightExportTable.AUTHORSHIP_TITLE)] = reference.getAuthorship().getTitleCache();
|
|
1319
|
csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state,reference.getAuthorship());
|
|
1320
|
}
|
|
1321
|
|
|
1322
|
csvLine[table.getIndex(CdmLightExportTable.IN_REFERENCE)] = getId(state, reference.getInReference());
|
|
1323
|
if (reference.getInReference() != null && state.getReferenceFromStore(reference.getInReference().getId()) == null){
|
|
1324
|
handleReference(state, reference.getInReference());
|
|
1325
|
}
|
|
1326
|
if ( reference.getInstitution() != null){ csvLine[table.getIndex(CdmLightExportTable.INSTITUTION)] = reference.getInstitution().getTitleCache();}
|
|
1327
|
if ( reference.getLsid() != null){ csvLine[table.getIndex(CdmLightExportTable.LSID)] = reference.getLsid().getLsid();}
|
|
1328
|
if ( reference.getSchool() != null){ csvLine[table.getIndex(CdmLightExportTable.SCHOOL)] = reference.getSchool().getTitleCache();}
|
|
1329
|
if ( reference.getUri() != null){ csvLine[table.getIndex(CdmLightExportTable.URI)] = reference.getUri().toString();}
|
|
1330
|
csvLine[table.getIndex(CdmLightExportTable.REF_TYPE)] = reference.getType().getKey();
|
|
1331
|
|
|
1332
|
state.getProcessor().put(table, reference, csvLine);
|
|
1333
|
} catch (Exception e) {
|
|
1334
|
state.getResult().addException(e, "An unexpected error occurred when handling reference " +
|
|
1335
|
cdmBaseStr(reference) + ": " + e.getMessage());
|
|
1336
|
}
|
|
1337
|
|
|
1338
|
}
|
|
1339
|
|
|
1340
|
|
|
1341
|
/**
|
|
1342
|
* @param reference
|
|
1343
|
* @return
|
|
1344
|
*/
|
|
1345
|
private String createShortCitation(Reference reference) {
|
|
1346
|
TeamOrPersonBase<?> authorship = reference.getAuthorship();
|
|
1347
|
String shortCitation = "";
|
|
1348
|
if (authorship == null) {
|
|
1349
|
return null;
|
|
1350
|
}
|
|
1351
|
authorship = HibernateProxyHelper.deproxy(authorship);
|
|
1352
|
if (authorship instanceof Person){ shortCitation = ((Person)authorship).getLastname();}
|
|
1353
|
else if (authorship instanceof Team){
|
|
1354
|
|
|
1355
|
Team authorTeam = HibernateProxyHelper.deproxy(authorship, Team.class);
|
|
1356
|
int index = 0;
|
|
1357
|
|
|
1358
|
for (Person teamMember : authorTeam.getTeamMembers()){
|
|
1359
|
index++;
|
|
1360
|
String concat = concatString(authorTeam, authorTeam.getTeamMembers(), index);
|
|
1361
|
shortCitation += concat + teamMember.getLastname();
|
|
1362
|
}
|
|
1363
|
|
|
1364
|
}
|
|
1365
|
if (reference.getYear() != null){
|
|
1366
|
shortCitation = shortCitation + " (" + reference.getYear() + ")";
|
|
1367
|
}
|
|
1368
|
return shortCitation;
|
|
1369
|
}
|
|
1370
|
|
|
1371
|
private static String concatString(Team team, List<Person> teamMembers, int i) {
|
|
1372
|
String concat;
|
|
1373
|
if (i <= 1){
|
|
1374
|
concat = "";
|
|
1375
|
}else if (i < teamMembers.size() || ( team.isHasMoreMembers() && i == teamMembers.size())){
|
|
1376
|
concat = STD_TEAM_CONCATINATION;
|
|
1377
|
}else{
|
|
1378
|
concat = FINAL_TEAM_CONCATINATION;
|
|
1379
|
}
|
|
1380
|
return concat;
|
|
1381
|
}
|
|
1382
|
|
|
1383
|
/*
|
|
1384
|
* TypeDesignation table
|
|
1385
|
* Specimen_Fk
|
|
1386
|
* EditName_Fk
|
|
1387
|
* TypeVerbatimCitation
|
|
1388
|
* TypeCategory
|
|
1389
|
* TypeDesignatedByString
|
|
1390
|
* TypeDesignatedByRef_Fk
|
|
1391
|
*/
|
|
1392
|
|
|
1393
|
private void handleSpecimenTypeDesignations(CdmLightExportState state, TaxonName name){
|
|
1394
|
try {
|
|
1395
|
Set<SpecimenTypeDesignation> typeDesignations = name.getSpecimenTypeDesignations();
|
|
1396
|
CdmLightExportTable table = CdmLightExportTable.TYPE_DESIGNATION;
|
|
1397
|
String nameId = getId(state, name);
|
|
1398
|
String[] csvLine = new String[table.getSize()];
|
|
1399
|
for (SpecimenTypeDesignation specimenType: typeDesignations){
|
|
1400
|
csvLine = new String[table.getSize()];
|
|
1401
|
DerivedUnit specimen = specimenType.getTypeSpecimen();
|
|
1402
|
if (state.getSpecimenFromStore(specimen.getId()) == null){
|
|
1403
|
handleSpecimen(state, specimen);
|
|
1404
|
}
|
|
1405
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
|
|
1406
|
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = nameId;
|
|
1407
|
csvLine[table.getIndex(CdmLightExportTable.TYPE_VERBATIM_CITATION)] = specimenType.getTypeSpecimen().generateTitle();
|
|
1408
|
//TODO: add link to existing Vorcabulary
|
|
1409
|
csvLine[table.getIndex(CdmLightExportTable.TYPE_CATEGORY)] = "";
|
|
1410
|
csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_STRING)] = specimenType.getCitation().getTitleCache();
|
|
1411
|
csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_REF_FK)] = getId(state, specimenType.getCitation());
|
|
1412
|
}
|
|
1413
|
} catch (Exception e) {
|
|
1414
|
state.getResult().addException(e, "An unexpected error occurred when handling specimen type designations for " +
|
|
1415
|
cdmBaseStr(name) + ": " + e.getMessage());
|
|
1416
|
}
|
|
1417
|
}
|
|
1418
|
|
|
1419
|
/**
|
|
1420
|
* @param state
|
|
1421
|
* @param specimen
|
|
1422
|
*/
|
|
1423
|
private void handleSpecimen(CdmLightExportState state, SpecimenOrObservationBase specimen) {
|
|
1424
|
try {
|
|
1425
|
state.addSpecimenToStore(specimen);
|
|
1426
|
CdmLightExportTable table = CdmLightExportTable.SPECIMEN;
|
|
1427
|
String specimenId = getId(state, specimen);
|
|
1428
|
String[] csvLine = new String[table.getSize()];
|
|
1429
|
|
|
1430
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_ID)] = specimenId;
|
|
1431
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
|
|
1432
|
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractURIs(state, specimen.getDescriptions(), Feature.IMAGE());
|
|
1433
|
if (specimen instanceof DerivedUnit){
|
|
1434
|
DerivedUnit derivedUnit = (DerivedUnit)specimen;
|
|
1435
|
if (derivedUnit.getCollection() != null){ csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection().getCode();}
|
|
1436
|
|
|
1437
|
if (specimen instanceof MediaSpecimen){
|
|
1438
|
MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
|
|
1439
|
Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
|
|
1440
|
String mediaUris = extractMediaUris(it);
|
|
1441
|
csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
|
|
1442
|
|
|
1443
|
}
|
|
1444
|
|
|
1445
|
if (derivedUnit.getDerivedFrom() != null){
|
|
1446
|
for (SpecimenOrObservationBase<?> original: derivedUnit.getDerivedFrom().getOriginals()){
|
|
1447
|
//TODO: What to do if there are more then one FieldUnit??
|
|
1448
|
if (original instanceof FieldUnit){
|
|
1449
|
FieldUnit fieldUnit = (FieldUnit)original;
|
|
1450
|
csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
|
|
1451
|
|
|
1452
|
GatheringEvent gathering = fieldUnit.getGatheringEvent();
|
|
1453
|
if (gathering != null){
|
|
1454
|
if (gathering.getLocality() != null){ csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();}
|
|
1455
|
if (gathering.getCountry() != null){csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();}
|
|
1456
|
csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
|
|
1457
|
addCollectingAreas(state, gathering);
|
|
1458
|
if (gathering.getGatheringDate() != null){csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
|
|
1459
|
if (!gathering.getCollectingAreas().isEmpty()){
|
|
1460
|
int index = 0;
|
|
1461
|
csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
|
|
1462
|
for (NamedArea area: gathering.getCollectingAreas()){
|
|
1463
|
if (index == 0){
|
|
1464
|
csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getTermType().getKey();
|
|
1465
|
csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
|
|
1466
|
}
|
|
1467
|
if (index == 1){
|
|
1468
|
csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getTermType().getKey();
|
|
1469
|
csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
|
|
1470
|
}
|
|
1471
|
if (index == 2){
|
|
1472
|
csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getTermType().getKey();
|
|
1473
|
csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
|
|
1474
|
}
|
|
1475
|
if (index == 3){
|
|
1476
|
csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
|
|
1477
|
break;
|
|
1478
|
}
|
|
1479
|
index++;
|
|
1480
|
}
|
|
1481
|
}
|
|
1482
|
}
|
|
1483
|
}
|
|
1484
|
}
|
|
1485
|
}
|
|
1486
|
}
|
|
1487
|
|
|
1488
|
state.getProcessor().put(table, specimen, csvLine);
|
|
1489
|
} catch (Exception e) {
|
|
1490
|
state.getResult().addException(e, "An unexpected error occurred when handling specimen " +
|
|
1491
|
cdmBaseStr(specimen) + ": " + e.getMessage());
|
|
1492
|
}
|
|
1493
|
}
|
|
1494
|
|
|
1495
|
/**
|
|
1496
|
* @param it
|
|
1497
|
*/
|
|
1498
|
private String extractMediaUris(Iterator<MediaRepresentation> it) {
|
|
1499
|
String mediaUriString = "";
|
|
1500
|
boolean first = true;
|
|
1501
|
while(it.hasNext()){
|
|
1502
|
MediaRepresentation rep = it.next();
|
|
1503
|
List<MediaRepresentationPart> parts = rep.getParts();
|
|
1504
|
for (MediaRepresentationPart part: parts){
|
|
1505
|
if (first){
|
|
1506
|
if (part.getUri() != null){
|
|
1507
|
mediaUriString += part.getUri().toString();
|
|
1508
|
first = false;
|
|
1509
|
}
|
|
1510
|
}else{
|
|
1511
|
if (part.getUri() != null){
|
|
1512
|
mediaUriString += ", " +part.getUri().toString();
|
|
1513
|
}
|
|
1514
|
}
|
|
1515
|
}
|
|
1516
|
}
|
|
1517
|
return mediaUriString;
|
|
1518
|
}
|
|
1519
|
|
|
1520
|
/**
|
|
1521
|
* @param state
|
|
1522
|
* @param gathering
|
|
1523
|
*/
|
|
1524
|
private void addCollectingAreas(CdmLightExportState state, GatheringEvent gathering) {
|
|
1525
|
// TODO implement !!!
|
|
1526
|
|
|
1527
|
if (!gathering.getCollectingAreas().isEmpty()){
|
|
1528
|
state.getResult().addWarning("Collecting areas not yet implemented but gathering " +
|
|
1529
|
cdmBaseStr(gathering) + " has collecting areas.");
|
|
1530
|
}
|
|
1531
|
|
|
1532
|
}
|
|
1533
|
|
|
1534
|
/**
|
|
1535
|
* @param gathering
|
|
1536
|
* @return
|
|
1537
|
*/
|
|
1538
|
private String createCollectorString(CdmLightExportState state, GatheringEvent gathering, FieldUnit fieldUnit) {
|
|
1539
|
try {
|
|
1540
|
String collectorString = "";
|
|
1541
|
AgentBase<?> collectorA = CdmBase.deproxy(gathering.getCollector());
|
|
1542
|
if (gathering.getCollector() != null){
|
|
1543
|
if (collectorA instanceof TeamOrPersonBase
|
|
1544
|
&& state.getConfig().isHighLightPrimaryCollector()){
|
|
1545
|
|
|
1546
|
Person primaryCollector = fieldUnit.getPrimaryCollector();
|
|
1547
|
if (collectorA instanceof Team){
|
|
1548
|
Team collectorTeam = (Team)collectorA;
|
|
1549
|
boolean isFirst = true;
|
|
1550
|
for (Person member: collectorTeam.getTeamMembers()){
|
|
1551
|
if (!isFirst){
|
|
1552
|
collectorString += "; ";
|
|
1553
|
}
|
|
1554
|
if (member.equals(primaryCollector)){
|
|
1555
|
//highlight
|
|
1556
|
collectorString += "<b>" + member.getTitleCache() + "</b>";
|
|
1557
|
}else{
|
|
1558
|
collectorString += member.getTitleCache();
|
|
1559
|
}
|
|
1560
|
}
|
|
1561
|
}
|
|
1562
|
} else{
|
|
1563
|
collectorString = collectorA.getTitleCache();
|
|
1564
|
}
|
|
1565
|
}
|
|
1566
|
return collectorString;
|
|
1567
|
} catch (Exception e) {
|
|
1568
|
state.getResult().addException(e, "An unexpected error occurred when creating collector string for " +
|
|
1569
|
cdmBaseStr(fieldUnit) + ": " + e.getMessage());
|
|
1570
|
return "";
|
|
1571
|
}
|
|
1572
|
}
|
|
1573
|
|
|
1574
|
|
|
1575
|
/**
|
|
1576
|
* Returns a string representation of the {@link CdmBase cdmBase} object
|
|
1577
|
* for result messages.
|
|
1578
|
*/
|
|
1579
|
private String cdmBaseStr(CdmBase cdmBase) {
|
|
1580
|
if (cdmBase == null){
|
|
1581
|
return "-no object available-";
|
|
1582
|
}else{
|
|
1583
|
return cdmBase.getClass().getSimpleName() + ": " + cdmBase.getUuid();
|
|
1584
|
}
|
|
1585
|
}
|
|
1586
|
|
|
1587
|
/**
|
|
1588
|
* {@inheritDoc}
|
|
1589
|
*/
|
|
1590
|
@Override
|
|
1591
|
protected boolean doCheck(CdmLightExportState state) {
|
|
1592
|
return false;
|
|
1593
|
}
|
|
1594
|
|
|
1595
|
/**
|
|
1596
|
* {@inheritDoc}
|
|
1597
|
*/
|
|
1598
|
@Override
|
|
1599
|
protected boolean isIgnore(CdmLightExportState state) {
|
|
1600
|
return false;
|
|
1601
|
}
|
|
1602
|
|
|
1603
|
}
|