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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.outputmodel;
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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.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.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.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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*/
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@Component
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public class OutputModelClassificationExport
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extends CdmExportBase<OutputModelConfigurator, OutputModelExportState, IExportTransformer>
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implements ICdmExport<OutputModelConfigurator, OutputModelExportState>{
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private static final long serialVersionUID = 2518643632756927053L;
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public OutputModelClassificationExport() {
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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(OutputModelExportState state) {
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OutputModelConfigurator config = state.getConfig();
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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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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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// gtTaxonNodeService().
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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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}
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state.getProcessor().createFinalResult(state);
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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(OutputModelExportState state, TaxonNode taxonNode) {
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Taxon taxon = taxonNode.getTaxon();
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if (taxon == null){
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state.getResult().addError("There was a taxon node without a taxon: " + taxonNode.getUuid());
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state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
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System.err.println("There was a taxon node without a taxon: " + taxonNode.getUuid());
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}else{
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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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OutputModelTable table = OutputModelTable.TAXON;
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String[] csvLine = new String[table.getSize()];
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csvLine[table.getIndex(OutputModelTable.TAXON_ID)] = getId(state, taxon);
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csvLine[table.getIndex(OutputModelTable.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(OutputModelTable.PARENT_FK)] = getId(state, parent);
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csvLine[table.getIndex(OutputModelTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
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csvLine[table.getIndex(OutputModelTable.SEC_REFERENCE)] = getTitleCache(taxon.getSec());
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csvLine[table.getIndex(OutputModelTable.CLASSIFICATION_ID)] = getId(state, taxonNode.getClassification());
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csvLine[table.getIndex(OutputModelTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification().getTitleCache();
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state.getProcessor().put(table, taxon, csvLine, state);
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handleDescriptions(state, taxon);
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}catch(Exception e){
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state.getResult().addError("An unexpected problems trying to export taxon with id " + taxon.getId() + e.getStackTrace());
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e.printStackTrace();
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state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
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}
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}
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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(OutputModelExportState 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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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.getFeature().equals(Feature.SPECIMEN())){
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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()){ handleCommonNameFacts(state, taxon, commonNameFacts);}
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if (!distributionFacts.isEmpty()){ handleDistributionFacts(state, taxon, distributionFacts);}
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if (!specimenFacts.isEmpty()){ handleSpecimenFacts(state, taxon, specimenFacts);}
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if (!simpleFacts.isEmpty()){ handleSimpleFacts(state, taxon, simpleFacts);}
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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()){ handleSimpleFacts(state, cdmBase, simpleFacts);}
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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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* @param simpleFacts
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*/
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private void handleSimpleFacts(OutputModelExportState state, CdmBase cdmBase,
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List<DescriptionElementBase> simpleFacts) {
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OutputModelTable table = OutputModelTable.SIMPLE_FACT;
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String[] csvLine = new String[table.getSize()];
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for (DescriptionElementBase element: simpleFacts){
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handleSource(state, element, OutputModelTable.SIMPLE_FACT);
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if (element instanceof TextData){
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TextData textData = (TextData)element;
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csvLine = new String[table.getSize()];
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csvLine[table.getIndex(OutputModelTable.FACT_ID)] = getId(state, element);
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if (cdmBase instanceof Taxon){
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csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, cdmBase);
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csvLine[table.getIndex(OutputModelTable.NAME_FK)] = "";
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}else if (cdmBase instanceof TaxonName){
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csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = "";
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csvLine[table.getIndex(OutputModelTable.NAME_FK)] = getId(state, cdmBase);
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}
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csvLine[table.getIndex(OutputModelTable.FACT_CATEGORY)] = textData.getFeature().getLabel();
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String mediaUris = "";
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for (Media media: textData.getMedia()){
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String mediaString = extractMediaUris(media.getRepresentations().iterator());
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if (!StringUtils.isBlank(mediaString)){ mediaUris += mediaString + ";";}
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else{state.getResult().addWarning("Empty Media object for uuid: " + cdmBase.getUuid() + " uuid of media: " + media.getUuid());}
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}
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csvLine[table.getIndex(OutputModelTable.MEDIA_URI)] = mediaUris;
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if (textData.getFeature().equals(Feature.CITATION())){
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// csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, cdmBase);
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state.getProcessor().put(table, textData, csvLine, state);
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}else if (!textData.getMultilanguageText().isEmpty()){
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for (Language language: textData.getMultilanguageText().keySet()){
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String[] csvLineLanguage = csvLine.clone();
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LanguageString langString = textData.getLanguageText(language);
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csvLineLanguage[table.getIndex(OutputModelTable.FACT_TEXT)] = langString.getText();
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csvLineLanguage[table.getIndex(OutputModelTable.LANGUAGE)] = language.getLabel();
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state.getProcessor().put(table, textData, csvLineLanguage, state);
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}
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} else{
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state.getProcessor().put(table, textData, csvLine, state);
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}
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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 specimenFacts
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*/
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private void handleSpecimenFacts(OutputModelExportState state, Taxon taxon, List<DescriptionElementBase> specimenFacts) {
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OutputModelTable table = OutputModelTable.SPECIMEN_FACT;
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String[] csvLine = new String[table.getSize()];
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for (DescriptionElementBase element: specimenFacts){
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if (element instanceof IndividualsAssociation){
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IndividualsAssociation indAssociation = (IndividualsAssociation)element;
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csvLine[table.getIndex(OutputModelTable.FACT_ID)] = getId(state, element);
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handleSource(state, element, table);
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if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
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SpecimenOrObservationBase specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation());
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if (specimenBase instanceof DerivedUnit){
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DerivedUnit derivedUnit = (DerivedUnit)specimenBase;
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handleSpecimen(state, derivedUnit);
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csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, taxon);
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csvLine[table.getIndex(OutputModelTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
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state.getProcessor().put(table, indAssociation, csvLine, state);
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}else{
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state.getResult().addError("The associated Specimen of taxon " + taxon.getUuid() + " is not an DerivedUnit. Could not be exported.");
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}
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}
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} else{
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state.getResult().addError("The specimen description for the taxon " + taxon.getUuid() + " is not of type individual association. Could not be exported. UUID of the description element: " + element.getUuid());
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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 taxon
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* @param element
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*/
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private void handleSource(OutputModelExportState state, DescriptionElementBase element, OutputModelTable factsTable) {
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OutputModelTable table = OutputModelTable.FACT_SOURCES;
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String[] csvLine = new String[table.getSize()];
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Set<DescriptionElementSource> sources = element.getSources();
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for (DescriptionElementSource source: sources){
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csvLine = new String[table.getSize()];
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Reference ref = source.getCitation();
|
|
331
|
if ((ref == null) && (source.getNameUsedInSource() == null)){
|
|
332
|
continue;
|
|
333
|
}
|
|
334
|
if (ref != null){
|
|
335
|
if (state.getReferenceFromStore(ref.getId()) == null){
|
|
336
|
handleReference(state, ref);
|
|
337
|
csvLine[table.getIndex(OutputModelTable.REFERENCE_FK)] = getId(state, ref);
|
|
338
|
}
|
|
339
|
}
|
|
340
|
csvLine[table.getIndex(OutputModelTable.FACT_FK)] = getId(state, element);
|
|
341
|
|
|
342
|
csvLine[table.getIndex(OutputModelTable.NAME_IN_SOURCE_FK)] = getId(state, source.getNameUsedInSource());
|
|
343
|
csvLine[table.getIndex(OutputModelTable.FACT_TYPE)] = factsTable.getTableName();
|
|
344
|
if ( StringUtils.isBlank(csvLine[table.getIndex(OutputModelTable.REFERENCE_FK)]) && StringUtils.isBlank(csvLine[table.getIndex(OutputModelTable.NAME_IN_SOURCE_FK)])){
|
|
345
|
continue;
|
|
346
|
}
|
|
347
|
state.getProcessor().put(table, source, csvLine, state);
|
|
348
|
}
|
|
349
|
|
|
350
|
}
|
|
351
|
|
|
352
|
/**
|
|
353
|
* @param state
|
|
354
|
* @param distributionFacts
|
|
355
|
*/
|
|
356
|
private void handleDistributionFacts(OutputModelExportState state, Taxon taxon, List<DescriptionElementBase> distributionFacts) {
|
|
357
|
OutputModelTable table = OutputModelTable.GEOGRAPHIC_AREA_FACT;
|
|
358
|
String[] csvLine = new String[table.getSize()];
|
|
359
|
|
|
360
|
for (DescriptionElementBase element: distributionFacts){
|
|
361
|
if (element instanceof Distribution){
|
|
362
|
Distribution distribution = (Distribution)element;
|
|
363
|
csvLine[table.getIndex(OutputModelTable.FACT_ID)] = getId(state, element);
|
|
364
|
handleSource(state, element, table);
|
|
365
|
csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, taxon);
|
|
366
|
if (distribution.getArea() != null){ csvLine[table.getIndex(OutputModelTable.AREA_LABEL)] = distribution.getArea().getLabel();}
|
|
367
|
if (distribution.getStatus() != null){ csvLine[table.getIndex(OutputModelTable.STATUS_LABEL)] = distribution.getStatus().getLabel();}
|
|
368
|
state.getProcessor().put(table, distribution, csvLine, state);
|
|
369
|
} else{
|
|
370
|
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());
|
|
371
|
}
|
|
372
|
}
|
|
373
|
}
|
|
374
|
|
|
375
|
/**
|
|
376
|
* @param state
|
|
377
|
* @param commonNameFacts
|
|
378
|
*/
|
|
379
|
private void handleCommonNameFacts(OutputModelExportState state, Taxon taxon, List<DescriptionElementBase> commonNameFacts) {
|
|
380
|
OutputModelTable table = OutputModelTable.COMMON_NAME_FACT;
|
|
381
|
String[] csvLine = new String[table.getSize()];
|
|
382
|
|
|
383
|
for (DescriptionElementBase element: commonNameFacts){
|
|
384
|
if (element instanceof CommonTaxonName){
|
|
385
|
CommonTaxonName commonName = (CommonTaxonName)element;
|
|
386
|
csvLine[table.getIndex(OutputModelTable.FACT_ID)] = getId(state, element);
|
|
387
|
handleSource(state, element, table);
|
|
388
|
csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, taxon);
|
|
389
|
if (commonName.getName() != null){csvLine[table.getIndex(OutputModelTable.FACT_TEXT)] = commonName.getName();}
|
|
390
|
if (commonName.getLanguage() != null){csvLine[table.getIndex(OutputModelTable.LANGUAGE)] = commonName.getLanguage().getLabel();}
|
|
391
|
if (commonName.getArea() != null){ csvLine[table.getIndex(OutputModelTable.AREA_LABEL)] = commonName.getArea().getLabel();}
|
|
392
|
state.getProcessor().put(table, commonName, csvLine, state);
|
|
393
|
} else{
|
|
394
|
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());
|
|
395
|
}
|
|
396
|
}
|
|
397
|
|
|
398
|
}
|
|
399
|
|
|
400
|
/**
|
|
401
|
* @param sec
|
|
402
|
* @return
|
|
403
|
*/
|
|
404
|
private String getTitleCache(IIdentifiableEntity identEntity) {
|
|
405
|
if (identEntity == null){
|
|
406
|
return "";
|
|
407
|
}
|
|
408
|
//TODO refresh?
|
|
409
|
return identEntity.getTitleCache();
|
|
410
|
}
|
|
411
|
|
|
412
|
/**
|
|
413
|
* @param state
|
|
414
|
* @param taxon
|
|
415
|
* @return
|
|
416
|
*/
|
|
417
|
private String getId(OutputModelExportState state, ICdmBase cdmBase) {
|
|
418
|
if (cdmBase == null){
|
|
419
|
return "";
|
|
420
|
}
|
|
421
|
//TODO make configurable
|
|
422
|
return cdmBase.getUuid().toString();
|
|
423
|
}
|
|
424
|
|
|
425
|
/**
|
|
426
|
* @param state
|
|
427
|
* @param syn
|
|
428
|
*/
|
|
429
|
private void handleSynonym(OutputModelExportState state, Synonym syn) {
|
|
430
|
TaxonName name = syn.getName();
|
|
431
|
handleName(state, name);
|
|
432
|
|
|
433
|
OutputModelTable table = OutputModelTable.SYNONYM;
|
|
434
|
String[] csvLine = new String[table.getSize()];
|
|
435
|
|
|
436
|
csvLine[table.getIndex(OutputModelTable.SYNONYM_ID)] = getId(state, syn);
|
|
437
|
csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, syn.getAcceptedTaxon());
|
|
438
|
csvLine[table.getIndex(OutputModelTable.NAME_FK)] = getId(state, name);
|
|
439
|
csvLine[table.getIndex(OutputModelTable.SEC_REFERENCE_FK)] = getId(state, syn.getSec());
|
|
440
|
csvLine[table.getIndex(OutputModelTable.SEC_REFERENCE)] = getTitleCache(syn.getSec());
|
|
441
|
|
|
442
|
state.getProcessor().put(table, syn, csvLine, state);
|
|
443
|
}
|
|
444
|
|
|
445
|
/**
|
|
446
|
* @param state
|
|
447
|
* @param name
|
|
448
|
*/
|
|
449
|
private void handleName(OutputModelExportState state, TaxonName name) {
|
|
450
|
Rank rank = name.getRank();
|
|
451
|
OutputModelTable table = OutputModelTable.SCIENTIFIC_NAME;
|
|
452
|
name = HibernateProxyHelper.deproxy(name);
|
|
453
|
String[] csvLine = new String[table.getSize()];
|
|
454
|
|
|
455
|
csvLine[table.getIndex(OutputModelTable.NAME_ID)] = getId(state, name);
|
|
456
|
if (name.getLsid() != null){
|
|
457
|
csvLine[table.getIndex(OutputModelTable.LSID)] = name.getLsid().getLsid();
|
|
458
|
}else{
|
|
459
|
csvLine[table.getIndex(OutputModelTable.LSID)] = "";
|
|
460
|
}
|
|
461
|
|
|
462
|
handleIdentifier(state, name, csvLine, table);
|
|
463
|
handleDescriptions(state, name);
|
|
464
|
|
|
465
|
csvLine[table.getIndex(OutputModelTable.RANK)] = getTitleCache(rank);
|
|
466
|
if (rank != null){
|
|
467
|
csvLine[table.getIndex(OutputModelTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
|
|
468
|
if (rank.isInfraGeneric()){
|
|
469
|
try {
|
|
470
|
csvLine[table.getIndex(OutputModelTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
|
|
471
|
} catch (UnknownCdmTypeException e) {
|
|
472
|
// TODO Auto-generated catch block
|
|
473
|
e.printStackTrace();
|
|
474
|
}
|
|
475
|
}
|
|
476
|
if (rank.isInfraSpecific()){
|
|
477
|
csvLine[table.getIndex(OutputModelTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
|
|
478
|
}
|
|
479
|
}else{
|
|
480
|
csvLine[table.getIndex(OutputModelTable.RANK_SEQUENCE)] = "";
|
|
481
|
}
|
|
482
|
if (name.isProtectedTitleCache()){
|
|
483
|
csvLine[table.getIndex(OutputModelTable.FULL_NAME_WITH_AUTHORS)] =name.getTitleCache();
|
|
484
|
}else{
|
|
485
|
csvLine[table.getIndex(OutputModelTable.FULL_NAME_WITH_AUTHORS)] = getTropicosTitleCache(name);
|
|
486
|
}
|
|
487
|
csvLine[table.getIndex(OutputModelTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
|
|
488
|
csvLine[table.getIndex(OutputModelTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
|
|
489
|
|
|
490
|
csvLine[table.getIndex(OutputModelTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
|
|
491
|
csvLine[table.getIndex(OutputModelTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
|
|
492
|
|
|
493
|
csvLine[table.getIndex(OutputModelTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
|
|
494
|
csvLine[table.getIndex(OutputModelTable.BAS_AUTHORTEAM_FK)] = getId(state,name.getBasionymAuthorship());
|
|
495
|
if (name.getBasionymAuthorship() != null){
|
|
496
|
if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
|
|
497
|
handleAuthor(state, name.getBasionymAuthorship());
|
|
498
|
}
|
|
499
|
}
|
|
500
|
csvLine[table.getIndex(OutputModelTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
|
|
501
|
if (name.getExBasionymAuthorship() != null){
|
|
502
|
if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
|
|
503
|
handleAuthor(state, name.getExBasionymAuthorship());
|
|
504
|
}
|
|
505
|
|
|
506
|
}
|
|
507
|
csvLine[table.getIndex(OutputModelTable.COMB_AUTHORTEAM_FK)] = getId(state,name.getCombinationAuthorship());
|
|
508
|
if (name.getCombinationAuthorship() != null){
|
|
509
|
if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
|
|
510
|
handleAuthor(state, name.getCombinationAuthorship());
|
|
511
|
}
|
|
512
|
}
|
|
513
|
csvLine[table.getIndex(OutputModelTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
|
|
514
|
if (name.getExCombinationAuthorship() != null){
|
|
515
|
if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
|
|
516
|
handleAuthor(state, name.getExCombinationAuthorship());
|
|
517
|
}
|
|
518
|
|
|
519
|
}
|
|
520
|
|
|
521
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
|
|
522
|
|
|
523
|
Reference nomRef = (Reference)name.getNomenclaturalReference();
|
|
524
|
|
|
525
|
if (nomRef != null){
|
|
526
|
if (state.getReferenceFromStore(nomRef.getId()) == null){
|
|
527
|
handleReference(state, nomRef);
|
|
528
|
}
|
|
529
|
csvLine[table.getIndex(OutputModelTable.REFERENCE_FK)] = getId(state, nomRef);
|
|
530
|
csvLine[table.getIndex(OutputModelTable.PUBLICATION_TYPE)] = nomRef.getType().name();
|
|
531
|
if (nomRef.getVolume() != null){
|
|
532
|
csvLine[table.getIndex(OutputModelTable.VOLUME_ISSUE)] = nomRef.getVolume();
|
|
533
|
}
|
|
534
|
if (nomRef.getDatePublished() != null){
|
|
535
|
csvLine[table.getIndex(OutputModelTable.DATE_PUBLISHED)] = nomRef.getDatePublishedString();
|
|
536
|
csvLine[table.getIndex(OutputModelTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
|
|
537
|
}
|
|
538
|
if (name.getNomenclaturalMicroReference() != null){
|
|
539
|
csvLine[table.getIndex(OutputModelTable.DETAIL)] = name.getNomenclaturalMicroReference();
|
|
540
|
}
|
|
541
|
nomRef = HibernateProxyHelper.deproxy(nomRef);
|
|
542
|
if (nomRef.getInReference() != null){
|
|
543
|
Reference inReference = nomRef.getInReference();
|
|
544
|
if (inReference.getInReference() != null){
|
|
545
|
inReference = inReference.getInReference();
|
|
546
|
}
|
|
547
|
if (inReference.getAbbrevTitle() == null){
|
|
548
|
csvLine[table.getIndex(OutputModelTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitleCache());
|
|
549
|
}else{
|
|
550
|
csvLine[table.getIndex(OutputModelTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
|
|
551
|
}
|
|
552
|
if (inReference.getTitle() == null){
|
|
553
|
csvLine[table.getIndex(OutputModelTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitleCache());
|
|
554
|
}else{
|
|
555
|
csvLine[table.getIndex(OutputModelTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
|
|
556
|
}
|
|
557
|
|
|
558
|
|
|
559
|
TeamOrPersonBase author = inReference.getAuthorship();
|
|
560
|
if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))){
|
|
561
|
csvLine[table.getIndex(OutputModelTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
|
|
562
|
csvLine[table.getIndex(OutputModelTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
|
|
563
|
}else{
|
|
564
|
csvLine[table.getIndex(OutputModelTable.ABBREV_REF_AUTHOR)] = "";
|
|
565
|
csvLine[table.getIndex(OutputModelTable.FULL_REF_AUTHOR)] = "";
|
|
566
|
}
|
|
567
|
}else{
|
|
568
|
csvLine[table.getIndex(OutputModelTable.ABBREV_TITLE)] = "";
|
|
569
|
csvLine[table.getIndex(OutputModelTable.FULL_TITLE)] = "";
|
|
570
|
csvLine[table.getIndex(OutputModelTable.ABBREV_REF_AUTHOR)]= "";
|
|
571
|
csvLine[table.getIndex(OutputModelTable.FULL_REF_AUTHOR)] = "";
|
|
572
|
|
|
573
|
}
|
|
574
|
}else{
|
|
575
|
csvLine[table.getIndex(OutputModelTable.PUBLICATION_TYPE)] = "";
|
|
576
|
}
|
|
577
|
|
|
578
|
|
|
579
|
|
|
580
|
/*
|
|
581
|
* Collation
|
|
582
|
|
|
583
|
Detail
|
|
584
|
|
|
585
|
|
|
586
|
TitlePageYear
|
|
587
|
*/
|
|
588
|
Set<TaxonNameDescription> descriptions = name.getDescriptions();
|
|
589
|
String protologueUriString = extractURIs(descriptions, Feature.PROTOLOGUE());
|
|
590
|
|
|
591
|
csvLine[table.getIndex(OutputModelTable.PROTOLOGUE_URI)] = protologueUriString;
|
|
592
|
|
|
593
|
if (name.getStatus() == null || name.getStatus().isEmpty()){
|
|
594
|
csvLine[table.getIndex(OutputModelTable.NOM_STATUS)] = "";
|
|
595
|
csvLine[table.getIndex(OutputModelTable.NOM_STATUS_ABBREV)] = "";
|
|
596
|
}else{
|
|
597
|
|
|
598
|
String statusStringAbbrev = extractStatusString(name, true);
|
|
599
|
String statusString = extractStatusString(name, false);
|
|
600
|
|
|
601
|
csvLine[table.getIndex(OutputModelTable.NOM_STATUS)] = statusString.trim();
|
|
602
|
csvLine[table.getIndex(OutputModelTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
|
|
603
|
}
|
|
604
|
|
|
605
|
HomotypicalGroup group =name.getHomotypicalGroup();
|
|
606
|
|
|
607
|
if (state.getHomotypicalGroupFromStore(group.getId()) == null){
|
|
608
|
handleHomotypicalGroup(state, group);
|
|
609
|
}
|
|
610
|
csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
|
|
611
|
List<TaxonName> typifiedNames = new ArrayList<>();
|
|
612
|
typifiedNames.addAll(group.getTypifiedNames());
|
|
613
|
Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
|
|
614
|
Integer seqNumber= typifiedNames.indexOf(name);
|
|
615
|
csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
|
|
616
|
state.getProcessor().put(table, name, csvLine, state);
|
|
617
|
|
|
618
|
/*
|
|
619
|
*
|
|
620
|
Tropicos_ID
|
|
621
|
IPNI_ID
|
|
622
|
|
|
623
|
|
|
624
|
InfragenericRank
|
|
625
|
|
|
626
|
|
|
627
|
InfraspecificRank
|
|
628
|
Collation
|
|
629
|
Volume (Issue)
|
|
630
|
Detail
|
|
631
|
DatePublished
|
|
632
|
YearPublished
|
|
633
|
TitlePageYear
|
|
634
|
|
|
635
|
|
|
636
|
|
|
637
|
HomotypicGroupSequenceNumber
|
|
638
|
|
|
639
|
|
|
640
|
*
|
|
641
|
*/
|
|
642
|
}
|
|
643
|
|
|
644
|
/**
|
|
645
|
* @param state
|
|
646
|
* @param name
|
|
647
|
*/
|
|
648
|
private void handleIdentifier(OutputModelExportState state, TaxonName name, String[] csvLine, OutputModelTable table) {
|
|
649
|
Set<String> IPNIidentifiers = name.getIdentifiers(DefinedTerm.IPNI_NAME_IDENTIFIER());
|
|
650
|
Set<String> tropicosIdentifiers = name.getIdentifiers(DefinedTerm.TROPICOS_NAME_IDENTIFIER());
|
|
651
|
Set<String> WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
|
|
652
|
if (!IPNIidentifiers.isEmpty()){ extractIdentifier(IPNIidentifiers, csvLine, table.getIndex(OutputModelTable.IPNI_ID));}
|
|
653
|
if (!tropicosIdentifiers.isEmpty()){extractIdentifier(tropicosIdentifiers, csvLine, table.getIndex(OutputModelTable.TROPICOS_ID));}
|
|
654
|
if (!WFOIdentifiers.isEmpty()){extractIdentifier(WFOIdentifiers, csvLine, table.getIndex(OutputModelTable.WFO_ID));}
|
|
655
|
}
|
|
656
|
|
|
657
|
/**
|
|
658
|
* @param tropicosIdentifiers
|
|
659
|
*/
|
|
660
|
private void extractIdentifier(Set<String> identifierSet, String[] csvLine, int index) {
|
|
661
|
String identifierString = "";
|
|
662
|
for (String identifier: identifierSet){
|
|
663
|
if (!StringUtils.isBlank(identifierString)){
|
|
664
|
identifierString += ", ";
|
|
665
|
}
|
|
666
|
identifierString += identifier;
|
|
667
|
}
|
|
668
|
|
|
669
|
csvLine[index] = identifierString;
|
|
670
|
}
|
|
671
|
|
|
672
|
/**
|
|
673
|
* @param descriptions
|
|
674
|
* @return
|
|
675
|
*/
|
|
676
|
private String extractURIs(Set<?> descriptions, Feature feature) {
|
|
677
|
String mediaUriString = "";
|
|
678
|
boolean first = true;
|
|
679
|
SpecimenDescription specimenDescription;
|
|
680
|
TaxonDescription taxonDescription;
|
|
681
|
TaxonNameDescription nameDescription;
|
|
682
|
Set<DescriptionElementBase> elements = new HashSet();
|
|
683
|
Set<DescriptionBase> descriptionsSet = (Set<DescriptionBase>)descriptions;
|
|
684
|
for (DescriptionBase description : descriptionsSet){
|
|
685
|
if (!description.getElements().isEmpty()){
|
|
686
|
if (description instanceof SpecimenDescription){
|
|
687
|
specimenDescription = (SpecimenDescription)description;
|
|
688
|
elements = specimenDescription.getElements();
|
|
689
|
}else if (description instanceof TaxonDescription){
|
|
690
|
taxonDescription = (TaxonDescription) description;
|
|
691
|
elements = taxonDescription.getElements();
|
|
692
|
} else if (description instanceof TaxonNameDescription){
|
|
693
|
nameDescription = (TaxonNameDescription) description;
|
|
694
|
elements = nameDescription.getElements();
|
|
695
|
}
|
|
696
|
|
|
697
|
for (DescriptionElementBase element : elements){
|
|
698
|
Feature entityFeature = HibernateProxyHelper.deproxy(element.getFeature());
|
|
699
|
if (entityFeature.equals(feature)){
|
|
700
|
if (!element.getMedia().isEmpty()){
|
|
701
|
List<Media> media = element.getMedia();
|
|
702
|
for (Media mediaElement: media){
|
|
703
|
Iterator<MediaRepresentation> it = mediaElement.getRepresentations().iterator();
|
|
704
|
mediaUriString = extractMediaUris(it);
|
|
705
|
}
|
|
706
|
}
|
|
707
|
}
|
|
708
|
}
|
|
709
|
}
|
|
710
|
}
|
|
711
|
return mediaUriString;
|
|
712
|
}
|
|
713
|
|
|
714
|
/**
|
|
715
|
* @param state
|
|
716
|
* @param basionymAuthorship
|
|
717
|
*/
|
|
718
|
private void handleAuthor(OutputModelExportState state, TeamOrPersonBase author) {
|
|
719
|
if (state.getAuthorFromStore(author.getId()) != null){
|
|
720
|
return;
|
|
721
|
}
|
|
722
|
state.addAuthorToStore(author);
|
|
723
|
OutputModelTable table = OutputModelTable.NOMENCLATURAL_AUTHOR;
|
|
724
|
String[] csvLine = new String[table.getSize()];
|
|
725
|
OutputModelTable tableAuthorRel = OutputModelTable.NOMENCLATURAL_AUTHOR_TEAM_RELATION;
|
|
726
|
String[] csvLineRel = new String[tableAuthorRel.getSize()];
|
|
727
|
String[] csvLineMember = new String[table.getSize()];
|
|
728
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_ID)] = getId(state, author);
|
|
729
|
csvLine[table.getIndex(OutputModelTable.ABBREV_AUTHOR)] = author.getNomenclaturalTitle();
|
|
730
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_TITLE)] = author.getTitleCache();
|
|
731
|
author = HibernateProxyHelper.deproxy(author);
|
|
732
|
if (author instanceof Person){
|
|
733
|
Person authorPerson = (Person)author;
|
|
734
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_FIRST_NAME)] = authorPerson.getFirstname();
|
|
735
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_LASTNAME)] = authorPerson.getLastname();
|
|
736
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_PREFIX)] = authorPerson.getPrefix();
|
|
737
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_SUFFIX)] = authorPerson.getSuffix();
|
|
738
|
} else{
|
|
739
|
// create an entry in rel table and all members in author table, check whether the team members already in author table
|
|
740
|
|
|
741
|
Team authorTeam = (Team)author;
|
|
742
|
int index = 0;
|
|
743
|
for (Person member: authorTeam.getTeamMembers()){
|
|
744
|
csvLineRel = new String[tableAuthorRel.getSize()];
|
|
745
|
csvLineRel[tableAuthorRel.getIndex(OutputModelTable.AUTHOR_TEAM_FK)] = getId(state, authorTeam);
|
|
746
|
csvLineRel[tableAuthorRel.getIndex(OutputModelTable.AUTHOR_FK)] = getId(state, member);
|
|
747
|
csvLineRel[tableAuthorRel.getIndex(OutputModelTable.AUTHOR_TEAM_SEQ_NUMBER)] = String.valueOf(index);
|
|
748
|
state.getProcessor().put(tableAuthorRel, authorTeam.getId() +":" +member.getId(), csvLineRel, state);
|
|
749
|
|
|
750
|
if (state.getAuthorFromStore(member.getId()) == null){
|
|
751
|
state.addAuthorToStore(member);
|
|
752
|
csvLineMember = new String[table.getSize()];
|
|
753
|
csvLineMember[table.getIndex(OutputModelTable.AUTHOR_ID)] = getId(state, member);
|
|
754
|
csvLineMember[table.getIndex(OutputModelTable.ABBREV_AUTHOR)] = member.getNomenclaturalTitle();
|
|
755
|
csvLineMember[table.getIndex(OutputModelTable.AUTHOR_TITLE)] = member.getTitleCache();
|
|
756
|
csvLineMember[table.getIndex(OutputModelTable.AUTHOR_FIRST_NAME)] = member.getFirstname();
|
|
757
|
csvLineMember[table.getIndex(OutputModelTable.AUTHOR_LASTNAME)] = member.getLastname();
|
|
758
|
csvLineMember[table.getIndex(OutputModelTable.AUTHOR_PREFIX)] = member.getPrefix();
|
|
759
|
csvLineMember[table.getIndex(OutputModelTable.AUTHOR_SUFFIX)] = member.getSuffix();
|
|
760
|
state.getProcessor().put(table, member, csvLineMember, state);
|
|
761
|
}
|
|
762
|
index++;
|
|
763
|
|
|
764
|
}
|
|
765
|
}
|
|
766
|
state.getProcessor().put(table, author, csvLine, state);
|
|
767
|
|
|
768
|
|
|
769
|
|
|
770
|
|
|
771
|
}
|
|
772
|
|
|
773
|
/**
|
|
774
|
* @param name
|
|
775
|
* @param statusString
|
|
776
|
* @return
|
|
777
|
*/
|
|
778
|
private String extractStatusString(TaxonName name, boolean abbrev) {
|
|
779
|
Set<NomenclaturalStatus> status = name.getStatus();
|
|
780
|
if (status.isEmpty()){
|
|
781
|
return "";
|
|
782
|
}
|
|
783
|
String statusString = "";
|
|
784
|
for (NomenclaturalStatus nameStatus: status){
|
|
785
|
if (nameStatus != null){
|
|
786
|
if (abbrev){
|
|
787
|
if (nameStatus.getType() != null){
|
|
788
|
statusString += nameStatus.getType().getIdInVocabulary();
|
|
789
|
}
|
|
790
|
}else{
|
|
791
|
if (nameStatus.getType() != null){
|
|
792
|
statusString += nameStatus.getType().getTitleCache();
|
|
793
|
}
|
|
794
|
}
|
|
795
|
if (!abbrev){
|
|
796
|
|
|
797
|
if (nameStatus.getRuleConsidered() != null && !StringUtils.isBlank(nameStatus.getRuleConsidered())){
|
|
798
|
statusString += " " + nameStatus.getRuleConsidered();
|
|
799
|
}
|
|
800
|
if (nameStatus.getCitation() != null){
|
|
801
|
statusString += " " + nameStatus.getCitation().getTitleCache();
|
|
802
|
}
|
|
803
|
if (nameStatus.getCitationMicroReference() != null && !StringUtils.isBlank(nameStatus.getCitationMicroReference())){
|
|
804
|
statusString += " " + nameStatus.getCitationMicroReference();
|
|
805
|
}
|
|
806
|
}
|
|
807
|
statusString += " ";
|
|
808
|
}
|
|
809
|
}
|
|
810
|
return statusString;
|
|
811
|
}
|
|
812
|
|
|
813
|
/**
|
|
814
|
* @param group
|
|
815
|
*/
|
|
816
|
private void handleHomotypicalGroup(OutputModelExportState state, HomotypicalGroup group) {
|
|
817
|
state.addHomotypicalGroupToStore(group);
|
|
818
|
OutputModelTable table = OutputModelTable.HOMOTYPIC_GROUP;
|
|
819
|
String[] csvLine = new String[table.getSize()];
|
|
820
|
|
|
821
|
csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_ID)] = getId(state, group);
|
|
822
|
List<TaxonName> typifiedNames = new ArrayList<>();
|
|
823
|
typifiedNames.addAll(group.getTypifiedNames());
|
|
824
|
Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
|
|
825
|
String typifiedNamesString = "";
|
|
826
|
for (TaxonName name: typifiedNames){
|
|
827
|
//Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)
|
|
828
|
//TODO: nameRelations, which and how to display
|
|
829
|
|
|
830
|
|
|
831
|
typifiedNamesString += name.getTitleCache()+ extractStatusString(name, true) + "; ";
|
|
832
|
}
|
|
833
|
typifiedNamesString = typifiedNamesString.substring(0, typifiedNamesString.length()-2);
|
|
834
|
if (typifiedNamesString != null){
|
|
835
|
csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_STRING)] = typifiedNamesString.trim();
|
|
836
|
}else{
|
|
837
|
csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_STRING)] = "";
|
|
838
|
}
|
|
839
|
Set<TypeDesignationBase> typeDesigantions = group.getTypeDesignations();
|
|
840
|
List<TypeDesignationBase> designationList = new ArrayList<>();
|
|
841
|
designationList.addAll(typeDesigantions);
|
|
842
|
Collections.sort(designationList, new TypeComparator());
|
|
843
|
StringBuffer typeDesignationString = new StringBuffer();
|
|
844
|
for (TypeDesignationBase typeDesignation: typeDesigantions){
|
|
845
|
if (typeDesignation != null && typeDesignation.getTypeStatus() != null){
|
|
846
|
typeDesignationString.append(typeDesignation.getTypeStatus().getTitleCache() + ": ");
|
|
847
|
}
|
|
848
|
if (typeDesignation instanceof SpecimenTypeDesignation){
|
|
849
|
if (((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen() != null){
|
|
850
|
typeDesignationString.append(((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen().getTitleCache());
|
|
851
|
handleSpecimen(state, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
|
|
852
|
}
|
|
853
|
}else{
|
|
854
|
if (((NameTypeDesignation)typeDesignation).getTypeName() != null){
|
|
855
|
typeDesignationString.append(((NameTypeDesignation)typeDesignation).getTypeName().getTitleCache());
|
|
856
|
}
|
|
857
|
}
|
|
858
|
if(typeDesignation.getCitation() != null ){
|
|
859
|
typeDesignationString.append(", "+typeDesignation.getCitation().getTitleCache());
|
|
860
|
}
|
|
861
|
//TODO...
|
|
862
|
/*
|
|
863
|
* Sortierung:
|
|
864
|
1. Status der Typen: a) holo, lecto, neo, syn, b) epi, paralecto, c) para (wenn überhaupt) – die jeweiligen iso immer direct mit dazu
|
|
865
|
2. Land
|
|
866
|
3. Sammler
|
|
867
|
4. Nummer
|
|
868
|
|
|
869
|
Aufbau der Typusinformationen:
|
|
870
|
Land: Lokalität mit Höhe und Koordinaten; Datum; Sammler Nummer (Herbar/Barcode, Typusart; Herbar/Barcode, Typusart …)
|
|
871
|
|
|
872
|
*/
|
|
873
|
}
|
|
874
|
String typeDesignations = typeDesignationString.toString();
|
|
875
|
if (typeDesignations != null){
|
|
876
|
csvLine[table.getIndex(OutputModelTable.TYPE_STRING)] = typeDesignations;
|
|
877
|
}else{
|
|
878
|
csvLine[table.getIndex(OutputModelTable.TYPE_STRING)] = "";
|
|
879
|
}
|
|
880
|
state.getProcessor().put(table, String.valueOf(group.getId()), csvLine, state);
|
|
881
|
|
|
882
|
}
|
|
883
|
|
|
884
|
/**
|
|
885
|
* @param name
|
|
886
|
* @return
|
|
887
|
*/
|
|
888
|
private String getTropicosTitleCache(TaxonName name) {
|
|
889
|
String basionymStart = "(";
|
|
890
|
String basionymEnd = ") ";
|
|
891
|
String exAuthorSeperator = " ex ";
|
|
892
|
TeamOrPersonBase combinationAuthor = name.getCombinationAuthorship();
|
|
893
|
TeamOrPersonBase exCombinationAuthor = name.getExCombinationAuthorship();
|
|
894
|
TeamOrPersonBase basionymAuthor = name.getBasionymAuthorship();
|
|
895
|
TeamOrPersonBase exBasionymAuthor = name.getExBasionymAuthorship();
|
|
896
|
|
|
897
|
String combinationAuthorString = "";
|
|
898
|
if (combinationAuthor != null){
|
|
899
|
combinationAuthor = HibernateProxyHelper.deproxy(combinationAuthor);
|
|
900
|
if (combinationAuthor instanceof Team){
|
|
901
|
combinationAuthorString = createTropicosTeamTitle(combinationAuthor);
|
|
902
|
}else{
|
|
903
|
Person person = HibernateProxyHelper.deproxy(combinationAuthor, Person.class);
|
|
904
|
combinationAuthorString = createTropicosAuthorString(person);
|
|
905
|
}
|
|
906
|
}
|
|
907
|
String exCombinationAuthorString = "";
|
|
908
|
if (exCombinationAuthor != null){
|
|
909
|
exCombinationAuthor = HibernateProxyHelper.deproxy(exCombinationAuthor);
|
|
910
|
if (exCombinationAuthor instanceof Team){
|
|
911
|
exCombinationAuthorString = createTropicosTeamTitle(exCombinationAuthor);
|
|
912
|
}else{
|
|
913
|
Person person = HibernateProxyHelper.deproxy(exCombinationAuthor, Person.class);
|
|
914
|
exCombinationAuthorString = createTropicosAuthorString(person);
|
|
915
|
}
|
|
916
|
}
|
|
917
|
|
|
918
|
String basionymAuthorString = "";
|
|
919
|
if (basionymAuthor != null){
|
|
920
|
basionymAuthor = HibernateProxyHelper.deproxy(basionymAuthor);
|
|
921
|
if (basionymAuthor instanceof Team){
|
|
922
|
basionymAuthorString = createTropicosTeamTitle(basionymAuthor);
|
|
923
|
}else{
|
|
924
|
Person person = HibernateProxyHelper.deproxy(basionymAuthor, Person.class);
|
|
925
|
basionymAuthorString = createTropicosAuthorString(person);
|
|
926
|
}
|
|
927
|
}
|
|
928
|
|
|
929
|
String exBasionymAuthorString = "";
|
|
930
|
|
|
931
|
if (exBasionymAuthor != null){
|
|
932
|
; exBasionymAuthor = HibernateProxyHelper.deproxy(exBasionymAuthor);
|
|
933
|
if (exBasionymAuthor instanceof Team){
|
|
934
|
exBasionymAuthorString = createTropicosTeamTitle(exBasionymAuthor);
|
|
935
|
|
|
936
|
}else{
|
|
937
|
Person person = HibernateProxyHelper.deproxy(exBasionymAuthor, Person.class);
|
|
938
|
exBasionymAuthorString = createTropicosAuthorString(person);
|
|
939
|
}
|
|
940
|
}
|
|
941
|
String completeAuthorString = name.getNameCache() + " ";
|
|
942
|
|
|
943
|
completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymStart: "";
|
|
944
|
completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString)) ? (CdmUtils.Nz(exBasionymAuthorString) + exAuthorSeperator): "" ;
|
|
945
|
completeAuthorString += (!CdmUtils.isBlank(basionymAuthorString))? CdmUtils.Nz(basionymAuthorString):"";
|
|
946
|
completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymEnd:"";
|
|
947
|
completeAuthorString += (!CdmUtils.isBlank(exCombinationAuthorString)) ? (CdmUtils.Nz(exCombinationAuthorString) + exAuthorSeperator): "" ;
|
|
948
|
completeAuthorString += (!CdmUtils.isBlank(combinationAuthorString))? CdmUtils.Nz(combinationAuthorString):"";
|
|
949
|
|
|
950
|
|
|
951
|
return completeAuthorString;
|
|
952
|
}
|
|
953
|
|
|
954
|
/**
|
|
955
|
* @param combinationAuthor
|
|
956
|
* @return
|
|
957
|
*/
|
|
958
|
private String createTropicosTeamTitle(TeamOrPersonBase combinationAuthor) {
|
|
959
|
String combinationAuthorString;
|
|
960
|
Team team = HibernateProxyHelper.deproxy(combinationAuthor, Team.class);
|
|
961
|
Team tempTeam = Team.NewInstance();
|
|
962
|
for (Person teamMember:team.getTeamMembers()){
|
|
963
|
combinationAuthorString = createTropicosAuthorString(teamMember);
|
|
964
|
Person tempPerson = Person.NewTitledInstance(combinationAuthorString);
|
|
965
|
tempTeam.addTeamMember(tempPerson);
|
|
966
|
}
|
|
967
|
combinationAuthorString = tempTeam.generateTitle();
|
|
968
|
return combinationAuthorString;
|
|
969
|
}
|
|
970
|
|
|
971
|
/**
|
|
972
|
* @param teamMember
|
|
973
|
*/
|
|
974
|
private String createTropicosAuthorString(Person teamMember) {
|
|
975
|
String nomAuthorString = "";
|
|
976
|
String[] splittedAuthorString = null;
|
|
977
|
if (teamMember == null){
|
|
978
|
return nomAuthorString;
|
|
979
|
}
|
|
980
|
|
|
981
|
if (teamMember.getFirstname() != null){
|
|
982
|
String firstNameString = teamMember.getFirstname().replaceAll("\\.", "\\. ");
|
|
983
|
splittedAuthorString = firstNameString.split("\\s");
|
|
984
|
for (String split: splittedAuthorString){
|
|
985
|
if (!StringUtils.isBlank(split)){
|
|
986
|
nomAuthorString += split.substring(0, 1);
|
|
987
|
nomAuthorString += ".";
|
|
988
|
}
|
|
989
|
}
|
|
990
|
}
|
|
991
|
if (teamMember.getLastname() != null){
|
|
992
|
String lastNameString = teamMember.getLastname().replaceAll("\\.", "\\. ");
|
|
993
|
splittedAuthorString = lastNameString.split("\\s");
|
|
994
|
for (String split: splittedAuthorString){
|
|
995
|
nomAuthorString += " " +split;
|
|
996
|
}
|
|
997
|
}
|
|
998
|
if (StringUtils.isBlank(nomAuthorString.trim())){
|
|
999
|
if (teamMember.getTitleCache() != null) {
|
|
1000
|
String titleCacheString = teamMember.getTitleCache().replaceAll("\\.", "\\. ");
|
|
1001
|
splittedAuthorString = titleCacheString.split("\\s");
|
|
1002
|
}
|
|
1003
|
|
|
1004
|
|
|
1005
|
int index = 0;
|
|
1006
|
for (String split: splittedAuthorString){
|
|
1007
|
if ( index < splittedAuthorString.length-1 && (split.length()==1 || split.endsWith("."))){
|
|
1008
|
nomAuthorString += split;
|
|
1009
|
}else{
|
|
1010
|
nomAuthorString = nomAuthorString +" "+ split;
|
|
1011
|
}
|
|
1012
|
index++;
|
|
1013
|
}
|
|
1014
|
}
|
|
1015
|
return nomAuthorString.trim();
|
|
1016
|
}
|
|
1017
|
|
|
1018
|
/**
|
|
1019
|
* @param state
|
|
1020
|
* @param name
|
|
1021
|
*/
|
|
1022
|
private void handleReference(OutputModelExportState state, Reference reference) {
|
|
1023
|
state.addReferenceToStore(reference);
|
|
1024
|
OutputModelTable table = OutputModelTable.REFERENCE;
|
|
1025
|
|
|
1026
|
String[] csvLine = new String[table.getSize()];
|
|
1027
|
csvLine[table.getIndex(OutputModelTable.REFERENCE_ID)] = getId(state, reference);
|
|
1028
|
//TODO short citations correctly
|
|
1029
|
String shortCitation = reference.getAbbrevTitleCache(); //Should be Author(year) like in Taxon.sec
|
|
1030
|
csvLine[table.getIndex(OutputModelTable.BIBLIO_SHORT_CITATION)] = shortCitation;
|
|
1031
|
//TODO get preferred title
|
|
1032
|
csvLine[table.getIndex(OutputModelTable.REF_TITLE)] = reference.getTitle();
|
|
1033
|
csvLine[table.getIndex(OutputModelTable.DATE_PUBLISHED)] = reference.getDatePublishedString();
|
|
1034
|
//TBC
|
|
1035
|
csvLine[table.getIndex(OutputModelTable.EDITION)] = reference.getEdition();
|
|
1036
|
csvLine[table.getIndex(OutputModelTable.EDITOR)] = reference.getEditor();
|
|
1037
|
csvLine[table.getIndex(OutputModelTable.ISBN)] = reference.getIsbn();
|
|
1038
|
csvLine[table.getIndex(OutputModelTable.ISSN)] = reference.getIssn();
|
|
1039
|
csvLine[table.getIndex(OutputModelTable.ORGANISATION)] = reference.getOrganization();
|
|
1040
|
csvLine[table.getIndex(OutputModelTable.PAGES)] = reference.getPages();
|
|
1041
|
csvLine[table.getIndex(OutputModelTable.PLACE_PUBLISHED)] = reference.getPlacePublished();
|
|
1042
|
csvLine[table.getIndex(OutputModelTable.PUBLISHER)] = reference.getPublisher();
|
|
1043
|
csvLine[table.getIndex(OutputModelTable.REF_ABSTRACT)] = reference.getReferenceAbstract();
|
|
1044
|
csvLine[table.getIndex(OutputModelTable.SERIES_PART)] = reference.getSeriesPart();
|
|
1045
|
csvLine[table.getIndex(OutputModelTable.VOLUME)] = reference.getVolume();
|
|
1046
|
csvLine[table.getIndex(OutputModelTable.YEAR)] = reference.getYear();
|
|
1047
|
if ( reference.getAuthorship() != null){
|
|
1048
|
csvLine[table.getIndex(OutputModelTable.AUTHORSHIP_TITLE)] = reference.getAuthorship().getTitleCache();
|
|
1049
|
csvLine[table.getIndex(OutputModelTable.AUTHOR_FK)] = getId(state,reference.getAuthorship());
|
|
1050
|
}
|
|
1051
|
|
|
1052
|
csvLine[table.getIndex(OutputModelTable.IN_REFERENCE)] = getId(state, reference.getInReference());
|
|
1053
|
if (reference.getInReference() != null && state.getReferenceFromStore(reference.getInReference().getId()) == null){
|
|
1054
|
handleReference(state, reference.getInReference());
|
|
1055
|
}
|
|
1056
|
if ( reference.getInstitution() != null){ csvLine[table.getIndex(OutputModelTable.INSTITUTION)] = reference.getInstitution().getTitleCache();}
|
|
1057
|
if ( reference.getLsid() != null){ csvLine[table.getIndex(OutputModelTable.LSID)] = reference.getLsid().getLsid();}
|
|
1058
|
if ( reference.getSchool() != null){ csvLine[table.getIndex(OutputModelTable.SCHOOL)] = reference.getSchool().getTitleCache();}
|
|
1059
|
if ( reference.getUri() != null){ csvLine[table.getIndex(OutputModelTable.URI)] = reference.getUri().toString();}
|
|
1060
|
csvLine[table.getIndex(OutputModelTable.REF_TYPE)] = reference.getType().getKey();
|
|
1061
|
|
|
1062
|
state.getProcessor().put(table, reference, csvLine, state);
|
|
1063
|
|
|
1064
|
}
|
|
1065
|
|
|
1066
|
|
|
1067
|
/*
|
|
1068
|
* TypeDesignation table
|
|
1069
|
* Specimen_Fk
|
|
1070
|
* EditName_Fk
|
|
1071
|
* TypeVerbatimCitation
|
|
1072
|
* TypeCategory
|
|
1073
|
* TypeDesignatedByString
|
|
1074
|
* TypeDesignatedByRef_Fk
|
|
1075
|
*/
|
|
1076
|
|
|
1077
|
private void handleSpecimenTypeDesignations(OutputModelExportState state, TaxonName name){
|
|
1078
|
Set<SpecimenTypeDesignation> typeDesignations = name.getSpecimenTypeDesignations();
|
|
1079
|
OutputModelTable table = OutputModelTable.TYPE_DESIGNATION;
|
|
1080
|
String nameId = getId(state, name);
|
|
1081
|
String[] csvLine = new String[table.getSize()];
|
|
1082
|
for (SpecimenTypeDesignation specimenType: typeDesignations){
|
|
1083
|
DerivedUnit specimen = specimenType.getTypeSpecimen();
|
|
1084
|
if (state.getSpecimenFromStore(specimen.getId()) == null){
|
|
1085
|
handleSpecimen(state, specimen);
|
|
1086
|
}
|
|
1087
|
csvLine[table.getIndex(OutputModelTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
|
|
1088
|
csvLine[table.getIndex(OutputModelTable.NAME_FK)] = nameId;
|
|
1089
|
csvLine[table.getIndex(OutputModelTable.TYPE_VERBATIM_CITATION)] = specimenType.getTypeSpecimen().generateTitle();
|
|
1090
|
//TODO: add link to existing Vorcabulary
|
|
1091
|
csvLine[table.getIndex(OutputModelTable.TYPE_CATEGORY)] = "";
|
|
1092
|
csvLine[table.getIndex(OutputModelTable.TYPE_DESIGNATED_BY_STRING)] = specimenType.getCitation().getTitleCache();
|
|
1093
|
csvLine[table.getIndex(OutputModelTable.TYPE_DESIGNATED_BY_REF_FK)] = getId(state, specimenType.getCitation());
|
|
1094
|
}
|
|
1095
|
}
|
|
1096
|
|
|
1097
|
/**
|
|
1098
|
* @param state
|
|
1099
|
* @param specimen
|
|
1100
|
*/
|
|
1101
|
private void handleSpecimen(OutputModelExportState state, DerivedUnit specimen) {
|
|
1102
|
state.addSpecimenToStore(specimen);
|
|
1103
|
OutputModelTable table = OutputModelTable.SPECIMEN;
|
|
1104
|
String specimenId = getId(state, specimen);
|
|
1105
|
String[] csvLine = new String[table.getSize()];
|
|
1106
|
|
|
1107
|
csvLine[table.getIndex(OutputModelTable.SPECIMEN_ID)] = specimenId;
|
|
1108
|
csvLine[table.getIndex(OutputModelTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
|
|
1109
|
csvLine[table.getIndex(OutputModelTable.SPECIMEN_IMAGE_URIS)] = extractURIs(specimen.getDescriptions(), Feature.IMAGE());
|
|
1110
|
if (specimen.getCollection() != null){ csvLine[table.getIndex(OutputModelTable.HERBARIUM_ABBREV)] = specimen.getCollection().getCode();}
|
|
1111
|
if (specimen instanceof MediaSpecimen){
|
|
1112
|
MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
|
|
1113
|
Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
|
|
1114
|
String mediaUris = extractMediaUris(it);
|
|
1115
|
csvLine[table.getIndex(OutputModelTable.MEDIA_SPECIMEN_URL)] = mediaUris;
|
|
1116
|
|
|
1117
|
}
|
|
1118
|
|
|
1119
|
if (specimen.getDerivedFrom() != null){
|
|
1120
|
for (SpecimenOrObservationBase original: specimen.getDerivedFrom().getOriginals()){
|
|
1121
|
//TODO: What to do if there are more then one FieldUnit??
|
|
1122
|
if (original instanceof FieldUnit){
|
|
1123
|
FieldUnit fieldUnit = (FieldUnit)original;
|
|
1124
|
csvLine[table.getIndex(OutputModelTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
|
|
1125
|
|
|
1126
|
GatheringEvent gathering = fieldUnit.getGatheringEvent();
|
|
1127
|
if (gathering != null){
|
|
1128
|
if (gathering.getLocality() != null){ csvLine[table.getIndex(OutputModelTable.LOCALITY)] = gathering.getLocality().getLanguageLabel();}
|
|
1129
|
if (gathering.getCountry() != null){csvLine[table.getIndex(OutputModelTable.COUNTRY)] = gathering.getCountry().getLabel();}
|
|
1130
|
csvLine[table.getIndex(OutputModelTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
|
|
1131
|
addCollectingAreas(gathering);
|
|
1132
|
if (gathering.getGatheringDate() != null){csvLine[table.getIndex(OutputModelTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
|
|
1133
|
if (!gathering.getCollectingAreas().isEmpty()){
|
|
1134
|
int index = 0;
|
|
1135
|
csvLine[table.getIndex(OutputModelTable.FURTHER_AREAS)] = "0";
|
|
1136
|
for (NamedArea area: gathering.getCollectingAreas()){
|
|
1137
|
if (index == 0){
|
|
1138
|
csvLine[table.getIndex(OutputModelTable.AREA_CATEGORY1)] = area.getTermType().getKey();
|
|
1139
|
csvLine[table.getIndex(OutputModelTable.AREA_NAME1)] = area.getLabel();
|
|
1140
|
}
|
|
1141
|
if (index == 1){
|
|
1142
|
csvLine[table.getIndex(OutputModelTable.AREA_CATEGORY2)] = area.getTermType().getKey();
|
|
1143
|
csvLine[table.getIndex(OutputModelTable.AREA_NAME2)] = area.getLabel();
|
|
1144
|
}
|
|
1145
|
if (index == 2){
|
|
1146
|
csvLine[table.getIndex(OutputModelTable.AREA_CATEGORY3)] = area.getTermType().getKey();
|
|
1147
|
csvLine[table.getIndex(OutputModelTable.AREA_NAME3)] = area.getLabel();
|
|
1148
|
}
|
|
1149
|
if (index == 3){
|
|
1150
|
csvLine[table.getIndex(OutputModelTable.FURTHER_AREAS)] = "1";
|
|
1151
|
break;
|
|
1152
|
}
|
|
1153
|
index++;
|
|
1154
|
}
|
|
1155
|
}
|
|
1156
|
}
|
|
1157
|
}
|
|
1158
|
}
|
|
1159
|
}
|
|
1160
|
|
|
1161
|
state.getProcessor().put(table, specimen, csvLine, state);
|
|
1162
|
|
|
1163
|
|
|
1164
|
|
|
1165
|
|
|
1166
|
}
|
|
1167
|
|
|
1168
|
/**
|
|
1169
|
* @param it
|
|
1170
|
*/
|
|
1171
|
private String extractMediaUris(Iterator<MediaRepresentation> it) {
|
|
1172
|
String mediaUriString = "";
|
|
1173
|
boolean first = true;
|
|
1174
|
while(it.hasNext()){
|
|
1175
|
MediaRepresentation rep = it.next();
|
|
1176
|
List<MediaRepresentationPart> parts = rep.getParts();
|
|
1177
|
for (MediaRepresentationPart part: parts){
|
|
1178
|
if (first){
|
|
1179
|
if (part.getUri() != null){
|
|
1180
|
mediaUriString += part.getUri().toString();
|
|
1181
|
first = false;
|
|
1182
|
}
|
|
1183
|
}else{
|
|
1184
|
if (part.getUri() != null){mediaUriString += ", " +part.getUri().toString();}
|
|
1185
|
}
|
|
1186
|
}
|
|
1187
|
}
|
|
1188
|
return mediaUriString;
|
|
1189
|
}
|
|
1190
|
|
|
1191
|
/**
|
|
1192
|
* @param gathering
|
|
1193
|
*/
|
|
1194
|
private void addCollectingAreas(GatheringEvent gathering) {
|
|
1195
|
// TODO Auto-generated method stub
|
|
1196
|
|
|
1197
|
}
|
|
1198
|
|
|
1199
|
/**
|
|
1200
|
* @param gathering
|
|
1201
|
* @return
|
|
1202
|
*/
|
|
1203
|
private String createCollectorString(OutputModelExportState state, GatheringEvent gathering, FieldUnit fieldUnit) {
|
|
1204
|
String collectorString = "";
|
|
1205
|
if (gathering.getCollector() != null){
|
|
1206
|
TeamOrPersonBase collector = (TeamOrPersonBase) HibernateProxyHelper.deproxy(gathering.getCollector());
|
|
1207
|
Person primaryCollector = fieldUnit.getPrimaryCollector();
|
|
1208
|
|
|
1209
|
if (state.getConfig().isHighLightPrimaryCollector()){
|
|
1210
|
if (collector instanceof Team){
|
|
1211
|
Team collectorTeam = (Team)collector;
|
|
1212
|
boolean isFirst = true;
|
|
1213
|
for (Person member: collectorTeam.getTeamMembers()){
|
|
1214
|
if (!isFirst){
|
|
1215
|
collectorString += "; ";
|
|
1216
|
}
|
|
1217
|
if (member.equals(primaryCollector)){
|
|
1218
|
//highlight
|
|
1219
|
collectorString += "<b>" + member.getTitleCache() + "</b>";
|
|
1220
|
}else{
|
|
1221
|
collectorString += member.getTitleCache();
|
|
1222
|
}
|
|
1223
|
}
|
|
1224
|
}
|
|
1225
|
|
|
1226
|
} else{
|
|
1227
|
collectorString = collector.getTitleCache();
|
|
1228
|
}
|
|
1229
|
}
|
|
1230
|
return collectorString;
|
|
1231
|
}
|
|
1232
|
|
|
1233
|
/**
|
|
1234
|
* {@inheritDoc}
|
|
1235
|
*/
|
|
1236
|
@Override
|
|
1237
|
protected boolean doCheck(OutputModelExportState state) {
|
|
1238
|
return false;
|
|
1239
|
}
|
|
1240
|
|
|
1241
|
/**
|
|
1242
|
* {@inheritDoc}
|
|
1243
|
*/
|
|
1244
|
@Override
|
|
1245
|
protected boolean isIgnore(OutputModelExportState state) {
|
|
1246
|
return false;
|
|
1247
|
}
|
|
1248
|
|
|
1249
|
|
|
1250
|
|
|
1251
|
|
|
1252
|
|
|
1253
|
}
|