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/**
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* Copyright (C) 2023 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.api.service.portal;
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import java.awt.Color;
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import java.time.LocalDateTime;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.joda.time.DateTime;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.api.dto.portal.AnnotatableDto;
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import eu.etaxonomy.cdm.api.dto.portal.AnnotationDto;
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import eu.etaxonomy.cdm.api.dto.portal.CdmBaseDto;
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import eu.etaxonomy.cdm.api.dto.portal.CommonNameDto;
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import eu.etaxonomy.cdm.api.dto.portal.ContainerDto;
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import eu.etaxonomy.cdm.api.dto.portal.DistributionInfoDto;
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import eu.etaxonomy.cdm.api.dto.portal.FactDto;
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import eu.etaxonomy.cdm.api.dto.portal.FactDtoBase;
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import eu.etaxonomy.cdm.api.dto.portal.FeatureDto;
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import eu.etaxonomy.cdm.api.dto.portal.IFactDto;
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import eu.etaxonomy.cdm.api.dto.portal.IndividualsAssociationDto;
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import eu.etaxonomy.cdm.api.dto.portal.MarkerDto;
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import eu.etaxonomy.cdm.api.dto.portal.MessagesDto;
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import eu.etaxonomy.cdm.api.dto.portal.SingleSourcedDto;
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import eu.etaxonomy.cdm.api.dto.portal.SourceDto;
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import eu.etaxonomy.cdm.api.dto.portal.SourcedDto;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonBaseDto;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonBaseDto.TaxonNameDto;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonInteractionDto;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.ConceptRelationDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.HomotypicGroupDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.KeyDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.MediaDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.MediaRepresentationDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.NameRelationDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.SpecimenDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.TaxonNodeAgentsRelDTO;
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import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.TaxonNodeDTO;
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import eu.etaxonomy.cdm.api.dto.portal.config.DistributionInfoConfiguration;
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import eu.etaxonomy.cdm.api.dto.portal.config.TaxonPageDtoConfiguration;
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import eu.etaxonomy.cdm.api.service.geo.DistributionServiceUtilities;
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import eu.etaxonomy.cdm.api.service.geo.IDistributionService;
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import eu.etaxonomy.cdm.api.service.l10n.LocaleContext;
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import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetContainer;
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import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetFormatter;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.TreeNode;
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import eu.etaxonomy.cdm.compare.taxon.TaxonComparator;
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import eu.etaxonomy.cdm.format.common.TypedLabel;
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import eu.etaxonomy.cdm.format.description.CategoricalDataFormatter;
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import eu.etaxonomy.cdm.format.description.QuantitativeDataFormatter;
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import eu.etaxonomy.cdm.format.description.distribution.CondensedDistributionConfiguration;
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import eu.etaxonomy.cdm.format.reference.OriginalSourceFormatter;
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import eu.etaxonomy.cdm.format.taxon.TaxonRelationshipFormatter;
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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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.ICdmBase;
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import eu.etaxonomy.cdm.model.common.IPublishable;
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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.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.MultilanguageTextHelper;
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import eu.etaxonomy.cdm.model.common.SingleSourcedEntityBase;
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import eu.etaxonomy.cdm.model.common.VersionableEntity;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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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.IDescribable;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonInteraction;
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import eu.etaxonomy.cdm.model.description.TemporalData;
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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.ExternalLink;
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import eu.etaxonomy.cdm.model.media.ImageFile;
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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.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalSource;
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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.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.ISourceable;
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import eu.etaxonomy.cdm.model.reference.NamedSource;
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import eu.etaxonomy.cdm.model.reference.NamedSourceBase;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeStatus;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.model.term.TermBase;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.strategy.cache.TaggedCacheHelper;
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import eu.etaxonomy.cdm.strategy.cache.TaggedText;
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import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.taxon.TaxonBaseDefaultCacheStrategy;
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/**
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* Loads the portal dto from a taxon instance.
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* Maybe later also supports loading from persistence.
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*
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* @author a.mueller
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* @date 09.01.2023
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*/
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public class PortalDtoLoader {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger();
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private ICdmRepository repository;
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public PortalDtoLoader(ICdmRepository repository) {
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this.repository = repository;
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}
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public TaxonPageDto load(Taxon taxon, TaxonPageDtoConfiguration config) {
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TaxonPageDto result = new TaxonPageDto();
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loadAcceptedTaxon(taxon, config, result);
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loadTaxonNodes(taxon, result, config);
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loadSynonyms(taxon, result, config);
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loadConceptRelations(taxon, result, config);
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loadFacts(taxon, result, config);
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loadMedia(taxon, result, config);
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loadSpecimens(taxon, result, config);
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loadKeys(taxon, result, config);
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return result;
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}
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private void loadAcceptedTaxon(Taxon taxon, TaxonPageDtoConfiguration config, TaxonPageDto result) {
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try {
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TaxonName name = taxon.getName();
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//load 1:1
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//TODO supplementalData for name
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loadBaseData(taxon, result);
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result.setLastUpdated(getLastUpdated(null, taxon));
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result.setLabel(CdmUtils.Nz(taxon.getTitleCache()));
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// result.setTypedTaxonLabel(getTypedTaxonLabel(taxon, config));
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result.setTaggedLabel(getTaggedTaxon(taxon, config));
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if (name != null) {
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handleName(config, result, name, result);
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}
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if (taxon.getSec() != null) {
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result.setSecTitleCache(taxon.getSec().getTitleCache());
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}
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} catch (Exception e) {
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//e.printStackTrace();
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result.addMessage(MessagesDto.NewErrorInstance("Error when loading accepted name data.", e));
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}
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}
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private void handleName(TaxonPageDtoConfiguration config, TaxonBaseDto taxonDto, TaxonName name, TaxonPageDto pageDto) {
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TaxonNameDto nameDto = taxonDto.new TaxonNameDto();
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loadBaseData(name, nameDto);
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INameCacheStrategy formatter = name.cacheStrategy();
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formatter.setEtAlPosition(config.getEtAlPosition());
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taxonDto.setName(nameDto);
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taxonDto.setNameLabel(formatter.getTitleCache(name));
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handleRelatedNames(name, taxonDto, config);
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loadProtologues(name, taxonDto);
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taxonDto.setNameUuid(name.getUuid());
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taxonDto.setNameType(name.getNameType().toString());
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loadNameFacts(name, taxonDto, config, pageDto);
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nameDto.setTaggedName(formatter.getTaggedFullTitle(name));
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}
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private List<TaggedText> getTaggedTaxon(TaxonBase<?> taxon, TaxonPageDtoConfiguration config) {
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// List<TypedLabel> result = new ArrayList<>();
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TaxonBaseDefaultCacheStrategy<TaxonBase<?>> formatter = new TaxonBaseDefaultCacheStrategy<>();
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List<TaggedText> tags = formatter.getTaggedTitle(taxon);
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return tags;
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}
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private void loadKeys(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
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try {
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ContainerDto<KeyDTO> container = new ContainerDto<>();
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//TODO other key types, but type must not be null, otherwise NPE
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Pager<PolytomousKey> keys = repository.getIdentificationKeyService().findKeysConvering(taxon, PolytomousKey.class, null, null, null);
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for (PolytomousKey key : keys.getRecords()) {
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KeyDTO dto = new KeyDTO();
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loadBaseData(key, dto);
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dto.setLabel(key.getTitleCache());
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dto.setKeyClass(key.getClass().getSimpleName());
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container.addItem(dto);
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}
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if (container.getCount() > 0) {
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result.setKeys(container);
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}
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} catch (Exception e) {
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//e.printStackTrace();
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result.addMessage(MessagesDto.NewErrorInstance("Error when loading identification key data.", e));
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}
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}
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private void loadSpecimens(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
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//TODO load specimen from multiple places
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try {
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ContainerDto<SpecimenDTO> container = new ContainerDto<>();
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List<SpecimenOrObservationBase<?>> specimens = new ArrayList<>();
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for (TaxonDescription taxonDescription : taxon.getDescriptions()) {
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if (taxonDescription.isImageGallery()) {
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continue;
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}
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for (DescriptionElementBase el : taxonDescription.getElements()) {
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if (el.isInstanceOf(IndividualsAssociation.class)) {
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IndividualsAssociation indAss = CdmBase.deproxy(el, IndividualsAssociation.class);
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SpecimenOrObservationBase<?> specimen = indAss.getAssociatedSpecimenOrObservation();
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specimens.add(specimen);
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}
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}
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}
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List<SpecimenOrObservationBase<?>> typeSpecimens = loadTypeSpecimen(taxon.getName(), config);
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specimens.addAll(typeSpecimens);
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for (TaxonName syn : taxon.getSynonymNames()) {
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typeSpecimens = loadTypeSpecimen(syn, config);
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specimens.addAll(typeSpecimens);
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}
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//TODO maybe still need to check full derivate path #4484, #8424, #9559
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for (SpecimenOrObservationBase<?> specimen : filterPublished(specimens)) {
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SpecimenDTO dto = new SpecimenDTO();
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loadBaseData(specimen, dto);
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dto.setLabel(specimen.getTitleCache());
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container.addItem(dto);
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}
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if (container.getCount() > 0 ) {
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result.setSpecimens(container);
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}
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} catch (Exception e) {
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//e.printStackTrace();
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result.addMessage(MessagesDto.NewErrorInstance("Error when loading specimen data.", e));
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}
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}
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private List<SpecimenOrObservationBase<?>> loadTypeSpecimen(TaxonName name, TaxonPageDtoConfiguration config) {
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List<SpecimenOrObservationBase<?>> result = new ArrayList<>();
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for (SpecimenTypeDesignation desig: name.getSpecimenTypeDesignations()){
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DerivedUnit specimen = desig.getTypeSpecimen();
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if (specimen != null) {
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result.add(specimen);
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}
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}
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return result;
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}
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300
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private void loadMedia(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
|
|
301
|
|
|
302
|
try {
|
|
303
|
ContainerDto<MediaDTO> container = new ContainerDto<TaxonPageDto.MediaDTO>();
|
|
304
|
|
|
305
|
List<Media> medias = new ArrayList<>();
|
|
306
|
for (TaxonDescription taxonDescription : taxon.getDescriptions()) {
|
|
307
|
if (!taxonDescription.isImageGallery()) {
|
|
308
|
continue;
|
|
309
|
}
|
|
310
|
|
|
311
|
List<Media> newMedia = taxonDescription.getElements().stream()
|
|
312
|
.filter(el->el.isInstanceOf(TextData.class))
|
|
313
|
.map(el->CdmBase.deproxy(el, TextData.class))
|
|
314
|
.filter(td->true)
|
|
315
|
.flatMap(td->td.getMedia().stream())
|
|
316
|
.collect(Collectors.toList())
|
|
317
|
;
|
|
318
|
medias.addAll(newMedia);
|
|
319
|
}
|
|
320
|
//TODO collect media from elsewhere
|
|
321
|
for (Media media : medias) {
|
|
322
|
MediaDTO dto = new TaxonPageDto.MediaDTO();
|
|
323
|
loadBaseData(media, dto);
|
|
324
|
dto.setLabel(media.getTitleCache());
|
|
325
|
ContainerDto<MediaRepresentationDTO> representations = new ContainerDto<>();
|
|
326
|
for (MediaRepresentation rep : media.getRepresentations()) {
|
|
327
|
MediaRepresentationDTO repDto = new MediaRepresentationDTO();
|
|
328
|
loadBaseData(rep, dto);
|
|
329
|
repDto.setMimeType(rep.getMimeType());
|
|
330
|
repDto.setSuffix(rep.getSuffix());
|
|
331
|
if (!rep.getParts().isEmpty()) {
|
|
332
|
//TODO handle message if n(parts) > 1
|
|
333
|
MediaRepresentationPart part = rep.getParts().get(0);
|
|
334
|
repDto.setUri(part.getUri());
|
|
335
|
repDto.setClazz(part.getClass());
|
|
336
|
repDto.setSize(part.getSize());
|
|
337
|
if (part.isInstanceOf(ImageFile.class)) {
|
|
338
|
ImageFile image = CdmBase.deproxy(part, ImageFile.class);
|
|
339
|
repDto.setHeight(image.getHeight());
|
|
340
|
repDto.setWidth(image.getWidth());
|
|
341
|
}
|
|
342
|
//TODO AudioFile etc.
|
|
343
|
}
|
|
344
|
representations.addItem(repDto);
|
|
345
|
}
|
|
346
|
if (representations.getCount() > 0) {
|
|
347
|
dto.setRepresentations(representations);
|
|
348
|
}
|
|
349
|
//TODO load representation data
|
|
350
|
container.addItem(dto);
|
|
351
|
}
|
|
352
|
|
|
353
|
if (container.getCount() > 0) {
|
|
354
|
result.setMedia(container);
|
|
355
|
}
|
|
356
|
} catch (Exception e) {
|
|
357
|
//e.printStackTrace();
|
|
358
|
result.addMessage(MessagesDto.NewErrorInstance("Error when loading media data.", e));
|
|
359
|
}
|
|
360
|
}
|
|
361
|
|
|
362
|
private void loadTaxonNodes(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
|
|
363
|
try {
|
|
364
|
ContainerDto<TaxonNodeDTO> container = new ContainerDto<TaxonPageDto.TaxonNodeDTO>();
|
|
365
|
for (TaxonNode node : taxon.getTaxonNodes()) {
|
|
366
|
TaxonNodeDTO dto = new TaxonNodeDTO();
|
|
367
|
loadBaseData(node, dto);
|
|
368
|
//classification
|
|
369
|
Classification classification = node.getClassification();
|
|
370
|
if (classification != null) {
|
|
371
|
dto.setClassificationUuid(node.getClassification().getUuid());
|
|
372
|
dto.setClassificationLabel(classification.getName().getText());
|
|
373
|
}
|
|
374
|
//TODO lang/locale
|
|
375
|
Language language = Language.DEFAULT();
|
|
376
|
|
|
377
|
//status
|
|
378
|
TaxonNodeStatus status = node.getStatus();
|
|
379
|
if (status != null) {
|
|
380
|
dto.setStatus(status.getLabel(language));
|
|
381
|
}
|
|
382
|
//statusNote
|
|
383
|
Map<Language, LanguageString> statusNote = node.getStatusNote();
|
|
384
|
if (statusNote != null) {
|
|
385
|
//TODO handle fallback lang
|
|
386
|
LanguageString statusNoteStr = statusNote.get(language);
|
|
387
|
if (statusNoteStr == null && statusNote.size() > 0) {
|
|
388
|
statusNoteStr = statusNote.entrySet().iterator().next().getValue();
|
|
389
|
}
|
|
390
|
if (statusNoteStr != null) {
|
|
391
|
dto.setStatusNote(statusNoteStr.getText());
|
|
392
|
}
|
|
393
|
}
|
|
394
|
//agent relations
|
|
395
|
Set<TaxonNodeAgentRelation> agents = node.getAgentRelations();
|
|
396
|
if (!agents.isEmpty()) {
|
|
397
|
for (TaxonNodeAgentRelation rel : agents) {
|
|
398
|
TaxonNodeAgentsRelDTO agentDto = new TaxonNodeAgentsRelDTO();
|
|
399
|
loadBaseData(rel, agentDto);
|
|
400
|
|
|
401
|
//TODO laod
|
|
402
|
if (rel.getAgent() != null) {
|
|
403
|
agentDto.setAgent(rel.getAgent().getFullTitle());
|
|
404
|
agentDto.setAgentUuid(rel.getAgent().getUuid());
|
|
405
|
//TODO compute preferred external link
|
|
406
|
agentDto.setAgentLink(null);
|
|
407
|
}
|
|
408
|
if (rel.getType() != null) {
|
|
409
|
agentDto.setType(rel.getType().getTitleCache());
|
|
410
|
agentDto.setTypeUuid(rel.getType().getUuid());
|
|
411
|
}
|
|
412
|
dto.addAgent(agentDto);
|
|
413
|
}
|
|
414
|
}
|
|
415
|
container.addItem(dto);
|
|
416
|
}
|
|
417
|
if (container.getCount() > 0) {
|
|
418
|
result.setTaxonNodes(container);
|
|
419
|
}
|
|
420
|
} catch (Exception e) {
|
|
421
|
// e.printStackTrace();
|
|
422
|
result.addMessage(MessagesDto.NewErrorInstance("Error when loading taxon node data.", e));
|
|
423
|
}
|
|
424
|
}
|
|
425
|
|
|
426
|
private void loadSynonyms(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
|
|
427
|
|
|
428
|
try {
|
|
429
|
// List<HomotypicalGroup> homotypicGroups = taxon.getHomotypicSynonymyGroups();
|
|
430
|
|
|
431
|
TaxonComparator comparator = new TaxonComparator();
|
|
432
|
|
|
433
|
TaxonName name = taxon.getName();
|
|
434
|
|
|
435
|
//TODO depending on config add/remove accepted name
|
|
436
|
|
|
437
|
//homotypic synonyms
|
|
438
|
List<Synonym> homotypicSynonmys = filterPublished(taxon.getHomotypicSynonymsByHomotypicGroup(comparator));
|
|
439
|
|
|
440
|
TaxonPageDto.HomotypicGroupDTO homotypicGroupDto = new TaxonPageDto.HomotypicGroupDTO();
|
|
441
|
if (homotypicSynonmys != null && !homotypicSynonmys.isEmpty()) {
|
|
442
|
loadBaseData(name.getHomotypicalGroup(), homotypicGroupDto);
|
|
443
|
|
|
444
|
for (Synonym syn : homotypicSynonmys) {
|
|
445
|
loadSynonymsInGroup(homotypicGroupDto, syn, config, result);
|
|
446
|
}
|
|
447
|
}
|
|
448
|
if (name != null) {
|
|
449
|
handleTypification(name.getHomotypicalGroup(), homotypicGroupDto, result, config);
|
|
450
|
}
|
|
451
|
result.setHomotypicSynonyms(homotypicGroupDto);
|
|
452
|
|
|
453
|
//heterotypic synonyms
|
|
454
|
List<HomotypicalGroup> heteroGroups = taxon.getHeterotypicSynonymyGroups();
|
|
455
|
if (heteroGroups.isEmpty()) {
|
|
456
|
return;
|
|
457
|
}
|
|
458
|
ContainerDto<HomotypicGroupDTO> heteroContainer = new ContainerDto<>();
|
|
459
|
result.setHeterotypicSynonymGroups(heteroContainer);
|
|
460
|
|
|
461
|
for (HomotypicalGroup hg : heteroGroups) {
|
|
462
|
TaxonPageDto.HomotypicGroupDTO hgDto = new TaxonPageDto.HomotypicGroupDTO();
|
|
463
|
loadBaseData(taxon.getName().getHomotypicalGroup(), hgDto);
|
|
464
|
heteroContainer.addItem(hgDto);
|
|
465
|
|
|
466
|
List<Synonym> heteroSyns = filterPublished(taxon.getSynonymsInGroup(hg, comparator));
|
|
467
|
for (Synonym syn : heteroSyns) {
|
|
468
|
loadSynonymsInGroup(hgDto, syn, config, result);
|
|
469
|
}
|
|
470
|
handleTypification(hg, hgDto, result, config);
|
|
471
|
}
|
|
472
|
} catch (Exception e) {
|
|
473
|
//e.printStackTrace();
|
|
474
|
result.addMessage(MessagesDto.NewErrorInstance("Error when loading synonym data.", e));
|
|
475
|
}
|
|
476
|
}
|
|
477
|
|
|
478
|
private <P extends IPublishable> List<P> filterPublished(List<P> listToPublish) {
|
|
479
|
if (listToPublish == null) {
|
|
480
|
return null;
|
|
481
|
}else {
|
|
482
|
return listToPublish.stream().filter(s->s.isPublish()).collect(Collectors.toList());
|
|
483
|
}
|
|
484
|
}
|
|
485
|
private <P extends IPublishable> Set<P> filterPublished(Set<P> setToPublish) {
|
|
486
|
if (setToPublish == null) {
|
|
487
|
return null;
|
|
488
|
}else {
|
|
489
|
return setToPublish.stream().filter(s->s.isPublish()).collect(Collectors.toSet());
|
|
490
|
}
|
|
491
|
}
|
|
492
|
|
|
493
|
private void handleTypification(HomotypicalGroup homotypicalGroup, HomotypicGroupDTO hgDto,
|
|
494
|
TaxonPageDto result, TaxonPageDtoConfiguration config) {
|
|
495
|
|
|
496
|
boolean withCitation = true;
|
|
497
|
boolean withStartingTypeLabel = true;
|
|
498
|
boolean withNameIfAvailable = false;
|
|
499
|
TypeDesignationSetFormatter formatter = new TypeDesignationSetFormatter(
|
|
500
|
withCitation, withStartingTypeLabel, withNameIfAvailable);
|
|
501
|
Set<TypeDesignationBase<?>> desigs = homotypicalGroup.getTypeDesignations();
|
|
502
|
try {
|
|
503
|
TypeDesignationSetContainer manager = TypeDesignationSetContainer.NewDefaultInstance((Set)desigs);
|
|
504
|
List<TaggedText> tags = formatter.toTaggedText(manager);
|
|
505
|
String label = TaggedCacheHelper.createString(tags);
|
|
506
|
hgDto.setTypes(label);
|
|
507
|
hgDto.setTaggedTypes(tags);
|
|
508
|
// hgDto.setTypedTypes(null);
|
|
509
|
|
|
510
|
} catch (Exception e) {
|
|
511
|
// e.printStackTrace();
|
|
512
|
result.addMessage(MessagesDto.NewErrorInstance("Error when creating type designation information", e));
|
|
513
|
}
|
|
514
|
}
|
|
515
|
|
|
516
|
private void loadConceptRelations(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
|
|
517
|
|
|
518
|
try {
|
|
519
|
//concept relations
|
|
520
|
ContainerDto<ConceptRelationDTO> conceptRelContainer = new ContainerDto<>();
|
|
521
|
TaxonRelationshipFormatter taxRelFormatter = TaxonRelationshipFormatter.INSTANCE();
|
|
522
|
|
|
523
|
//... MAN
|
|
524
|
Set<TaxonRelationship> misappliedRels = taxon.getMisappliedNameRelations();
|
|
525
|
for (TaxonRelationship rel : misappliedRels) {
|
|
526
|
boolean inverse = true;
|
|
527
|
boolean withoutName = false;
|
|
528
|
loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
|
|
529
|
}
|
|
530
|
|
|
531
|
//... pro parte Synonyms
|
|
532
|
Set<TaxonRelationship> proParteRels = taxon.getProParteAndPartialSynonymRelations();
|
|
533
|
for (TaxonRelationship rel : proParteRels) {
|
|
534
|
boolean inverse = true;
|
|
535
|
boolean withoutName = false;
|
|
536
|
loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
|
|
537
|
}
|
|
538
|
|
|
539
|
//TODO MAN and pp from this taxon
|
|
540
|
|
|
541
|
//... to-relations
|
|
542
|
Set<TaxonRelationship> toRels = taxon.getRelationsToThisTaxon();
|
|
543
|
toRels.removeAll(misappliedRels);
|
|
544
|
toRels.removeAll(proParteRels);
|
|
545
|
for (TaxonRelationship rel : toRels) {
|
|
546
|
boolean inverse = true;
|
|
547
|
boolean withoutName = false;
|
|
548
|
loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
|
|
549
|
}
|
|
550
|
|
|
551
|
//... from-relations
|
|
552
|
Set<TaxonRelationship> fromRels = taxon.getRelationsFromThisTaxon();
|
|
553
|
for (TaxonRelationship rel : fromRels) {
|
|
554
|
boolean inverse = false;
|
|
555
|
boolean withoutName = false;
|
|
556
|
loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
|
|
557
|
}
|
|
558
|
|
|
559
|
if (conceptRelContainer.getCount() > 0) {
|
|
560
|
result.setConceptRelations(conceptRelContainer);
|
|
561
|
}
|
|
562
|
} catch (Exception e) {
|
|
563
|
//e.printStackTrace();
|
|
564
|
result.addMessage(MessagesDto.NewErrorInstance("Error when loading concept relation data.", e));
|
|
565
|
}
|
|
566
|
}
|
|
567
|
|
|
568
|
private void loadConceptRelation(TaxonRelationshipFormatter taxRelFormatter, TaxonRelationship rel, ContainerDto<ConceptRelationDTO> conceptRelContainer, boolean inverse,
|
|
569
|
boolean withoutName) {
|
|
570
|
|
|
571
|
List<Language> languages = Arrays.asList(new Language[] {Language.DEFAULT()}); // TODO config.locales;
|
|
572
|
List<TaggedText> tags = taxRelFormatter.getTaggedText(rel, inverse, languages, withoutName);
|
|
573
|
String relLabel = TaggedCacheHelper.createString(tags);
|
|
574
|
ConceptRelationDTO dto = new TaxonPageDto.ConceptRelationDTO();
|
|
575
|
loadBaseData(rel, dto);
|
|
576
|
dto.setRelSource(makeSource(rel.getSource()));
|
|
577
|
Taxon relTaxon = inverse ? rel.getFromTaxon() : rel.getToTaxon();
|
|
578
|
dto.setRelTaxonId(relTaxon.getId());
|
|
579
|
dto.setRelTaxonUuid(relTaxon.getUuid());
|
|
580
|
dto.setRelTaxonLabel(relTaxon.getTitleCache());
|
|
581
|
dto.setSecSource(makeSource(relTaxon.getSecSource()));
|
|
582
|
dto.setLabel(relLabel);
|
|
583
|
dto.setTaggedLabel(tags);
|
|
584
|
dto.setNameUuid(relTaxon.getName() != null ? relTaxon.getName().getUuid() : null);
|
|
585
|
|
|
586
|
if (rel.getType() != null) {
|
|
587
|
dto.setRelTypeUuid(rel.getType().getUuid());
|
|
588
|
}
|
|
589
|
for (TaxonNode node : relTaxon.getTaxonNodes()) {
|
|
590
|
Classification classification = node.getClassification();
|
|
591
|
if (classification != null) {
|
|
592
|
dto.addClassificationUuids(classification.getUuid());
|
|
593
|
}
|
|
594
|
}
|
|
595
|
conceptRelContainer.addItem(dto);
|
|
596
|
}
|
|
597
|
|
|
598
|
private void loadSynonymsInGroup(TaxonPageDto.HomotypicGroupDTO hgDto, Synonym syn,
|
|
599
|
TaxonPageDtoConfiguration config, TaxonPageDto pageDto) {
|
|
600
|
|
|
601
|
TaxonBaseDto synDto = new TaxonBaseDto();
|
|
602
|
loadBaseData(syn, synDto);
|
|
603
|
synDto.setLabel(syn.getTitleCache());
|
|
604
|
synDto.setTaggedLabel(getTaggedTaxon(syn, config));
|
|
605
|
|
|
606
|
if (syn.getName() != null) {
|
|
607
|
handleName(config, synDto, syn.getName(), pageDto);
|
|
608
|
}
|
|
609
|
|
|
610
|
//TODO
|
|
611
|
hgDto.addSynonym(synDto);
|
|
612
|
}
|
|
613
|
|
|
614
|
private void loadProtologues(TaxonName name, TaxonBaseDto taxonBaseDto) {
|
|
615
|
NomenclaturalSource nomSource = name.getNomenclaturalSource();
|
|
616
|
if (nomSource != null) {
|
|
617
|
Set<ExternalLink> links = nomSource.getLinks();
|
|
618
|
for (ExternalLink link : links) {
|
|
619
|
if (link.getUri() != null) {
|
|
620
|
taxonBaseDto.addProtologue(link.getUri());
|
|
621
|
}
|
|
622
|
}
|
|
623
|
}
|
|
624
|
}
|
|
625
|
|
|
626
|
private void handleRelatedNames(TaxonName name, TaxonBaseDto taxonDto, TaxonPageDtoConfiguration config) {
|
|
627
|
//exclusions TODO handle via config
|
|
628
|
Set<UUID> excludedTypes = new HashSet<>(); //both directions
|
|
629
|
excludedTypes.add(NameRelationshipType.uuidBasionym);
|
|
630
|
excludedTypes.add(NameRelationshipType.uuidReplacedSynonym);
|
|
631
|
Set<UUID> excludedFromTypes = new HashSet<>(excludedTypes);
|
|
632
|
Set<UUID> excludedToTypes = new HashSet<>(excludedTypes);
|
|
633
|
//TODO non-types
|
|
634
|
|
|
635
|
//TODO config.getLocales();
|
|
636
|
Language locale = Language.DEFAULT();
|
|
637
|
|
|
638
|
for (NameRelationship rel : name.getRelationsFromThisName()) {
|
|
639
|
TaxonName relatedName = rel.getToName();
|
|
640
|
if (relatedName == null || rel.getType() == null || excludedFromTypes.contains(rel.getType().getUuid())) {
|
|
641
|
continue;
|
|
642
|
}
|
|
643
|
NameRelationDTO dto = new NameRelationDTO();
|
|
644
|
loadBaseData(rel, dto);
|
|
645
|
//name
|
|
646
|
dto.setNameUuid(relatedName.getUuid());
|
|
647
|
dto.setNameLabel(relatedName.getTaggedName());
|
|
648
|
//type
|
|
649
|
dto.setRelTypeUuid(rel.getType().getUuid());
|
|
650
|
Representation rep = rel.getType().getPreferredRepresentation(locale);
|
|
651
|
dto.setRelType(rep == null ? rel.getType().toString() : rep.getLabel());
|
|
652
|
//inverse
|
|
653
|
dto.setInverse(false);
|
|
654
|
//ruleConsidered
|
|
655
|
dto.setRuleConsidered(rel.getRuleConsidered());
|
|
656
|
taxonDto.addRelatedName(dto);
|
|
657
|
}
|
|
658
|
|
|
659
|
//to relations
|
|
660
|
for (NameRelationship rel : name.getRelationsToThisName()) {
|
|
661
|
TaxonName relatedName = rel.getFromName();
|
|
662
|
if (relatedName == null || rel.getType() == null || excludedFromTypes.contains(rel.getType().getUuid())) {
|
|
663
|
continue;
|
|
664
|
}
|
|
665
|
NameRelationDTO dto = new NameRelationDTO();
|
|
666
|
loadBaseData(rel, dto);
|
|
667
|
//name
|
|
668
|
dto.setNameUuid(relatedName.getUuid());
|
|
669
|
dto.setNameLabel(relatedName.getTaggedName());
|
|
670
|
//type
|
|
671
|
dto.setRelTypeUuid(rel.getType().getUuid());
|
|
672
|
Representation rep = rel.getType().getPreferredInverseRepresentation(Arrays.asList(new Language[] {locale}));
|
|
673
|
dto.setRelType(rep == null ? rel.getType().toString() : rep.getLabel());
|
|
674
|
//inverse
|
|
675
|
dto.setInverse(true);
|
|
676
|
taxonDto.addRelatedName(dto);
|
|
677
|
}
|
|
678
|
}
|
|
679
|
|
|
680
|
private void loadFacts(Taxon taxon, TaxonPageDto taxonPageDto, TaxonPageDtoConfiguration config) {
|
|
681
|
|
|
682
|
try {
|
|
683
|
//compute the features that do exist for this taxon
|
|
684
|
Map<UUID, Feature> existingFeatureUuids = getExistingFeatureUuids(taxon);
|
|
685
|
|
|
686
|
//filter, sort and structure according to feature tree
|
|
687
|
TreeNode<Feature, UUID> filteredRootNode;
|
|
688
|
if (config.getFeatureTree() != null) {
|
|
689
|
|
|
690
|
@SuppressWarnings({ "unchecked"})
|
|
691
|
TermTree<Feature> featureTree = repository.getTermTreeService().find(config.getFeatureTree());
|
|
692
|
filteredRootNode = filterFeatureNode(featureTree.getRoot(), existingFeatureUuids.keySet());
|
|
693
|
} else {
|
|
694
|
filteredRootNode = createDefaultFeatureNode(taxon);
|
|
695
|
}
|
|
696
|
|
|
697
|
//load facts per feature
|
|
698
|
Map<UUID,Set<DescriptionElementBase>> featureMap = loadFeatureMap(taxon);
|
|
699
|
|
|
700
|
//load final result
|
|
701
|
if (filteredRootNode != null && !filteredRootNode.getChildren().isEmpty()) {
|
|
702
|
ContainerDto<FeatureDto> features = new ContainerDto<>();
|
|
703
|
for (TreeNode<Feature,UUID> node : filteredRootNode.getChildren()) {
|
|
704
|
handleFeatureNode(config, featureMap, features, node, taxonPageDto);
|
|
705
|
}
|
|
706
|
taxonPageDto.setTaxonFacts(features);
|
|
707
|
}
|
|
708
|
} catch (Exception e) {
|
|
709
|
//e.printStackTrace();
|
|
710
|
taxonPageDto.addMessage(MessagesDto.NewErrorInstance("Error when loading factual data.", e));
|
|
711
|
}
|
|
712
|
}
|
|
713
|
|
|
714
|
//TODO merge with loadFacts, it is almost the same, see //DIFFERENT
|
|
715
|
private void loadNameFacts(TaxonName name, TaxonBaseDto nameDto, TaxonPageDtoConfiguration config, TaxonPageDto pageDto) {
|
|
716
|
|
|
717
|
try {
|
|
718
|
//compute the features that do exist for this taxon
|
|
719
|
Map<UUID, Feature> existingFeatureUuids = getExistingFeatureUuids(name);
|
|
720
|
|
|
721
|
//filter, sort and structure according to feature tree
|
|
722
|
TreeNode<Feature, UUID> filteredRootNode;
|
|
723
|
//DIFFERENT
|
|
724
|
// if (config.getFeatureTree() != null) {
|
|
725
|
//
|
|
726
|
// @SuppressWarnings({ "unchecked"})
|
|
727
|
// TermTree<Feature> featureTree = repository.getTermTreeService().find(config.getFeatureTree());
|
|
728
|
// filteredRootNode = filterFeatureNode(featureTree.getRoot(), existingFeatureUuids.keySet());
|
|
729
|
// } else {
|
|
730
|
filteredRootNode = createDefaultFeatureNode(name);
|
|
731
|
// } //DIFFERENT END
|
|
732
|
|
|
733
|
//load facts per feature
|
|
734
|
Map<UUID,Set<DescriptionElementBase>> featureMap = loadFeatureMap(name);
|
|
735
|
|
|
736
|
//load final result
|
|
737
|
if (!filteredRootNode.getChildren().isEmpty()) {
|
|
738
|
ContainerDto<FeatureDto> features = new ContainerDto<>();
|
|
739
|
for (TreeNode<Feature,UUID> node : filteredRootNode.getChildren()) {
|
|
740
|
handleFeatureNode(config, featureMap, features, node, pageDto);
|
|
741
|
}
|
|
742
|
//DIFFERENT
|
|
743
|
nameDto.setNameFacts(features);
|
|
744
|
}
|
|
745
|
} catch (Exception e) {
|
|
746
|
//e.printStackTrace();
|
|
747
|
//DIFFERENT
|
|
748
|
pageDto.addMessage(MessagesDto.NewErrorInstance("Error when loading factual data.", e));
|
|
749
|
}
|
|
750
|
}
|
|
751
|
|
|
752
|
private void handleFeatureNode(TaxonPageDtoConfiguration config,
|
|
753
|
Map<UUID, Set<DescriptionElementBase>> featureMap, ContainerDto<FeatureDto> features,
|
|
754
|
TreeNode<Feature, UUID> node, TaxonPageDto pageDto) {
|
|
755
|
|
|
756
|
Feature feature = node.getData();
|
|
757
|
//TODO locale
|
|
758
|
FeatureDto featureDto = new FeatureDto(feature.getUuid(), feature.getId(), feature.getLabel());
|
|
759
|
features.addItem(featureDto);
|
|
760
|
|
|
761
|
List<Distribution> distributions = new ArrayList<>();
|
|
762
|
|
|
763
|
//
|
|
764
|
for (DescriptionElementBase fact : featureMap.get(feature.getUuid())){
|
|
765
|
if (fact.isInstanceOf(Distribution.class)) {
|
|
766
|
distributions.add(CdmBase.deproxy(fact, Distribution.class));
|
|
767
|
}else {
|
|
768
|
//TODO how to handle CommonNames, do we also want to have a data structure
|
|
769
|
//with Language|
|
|
770
|
// -- Area|
|
|
771
|
// --name
|
|
772
|
// a bit like for distribution??
|
|
773
|
handleFact(featureDto, fact, pageDto);
|
|
774
|
}
|
|
775
|
}
|
|
776
|
|
|
777
|
handleDistributions(config, featureDto, distributions, pageDto);
|
|
778
|
//TODO really needed?
|
|
779
|
orderFacts(featureDto);
|
|
780
|
|
|
781
|
//children
|
|
782
|
ContainerDto<FeatureDto> childFeatures = new ContainerDto<>();
|
|
783
|
for (TreeNode<Feature,UUID> child : node.getChildren()) {
|
|
784
|
handleFeatureNode(config, featureMap, childFeatures, child, pageDto);
|
|
785
|
}
|
|
786
|
if (childFeatures.getCount() > 0) {
|
|
787
|
featureDto.setSubFeatures(childFeatures);
|
|
788
|
}
|
|
789
|
}
|
|
790
|
|
|
791
|
//TODO not really used yet, only for distinguishing fact classes,
|
|
792
|
//needs discussion if needed and how to implement.
|
|
793
|
//we could also move compareTo methods to DTO classes but with this
|
|
794
|
//remove from having only data in the DTO, no logic
|
|
795
|
private void orderFacts(FeatureDto featureDto) {
|
|
796
|
List<IFactDto> list = featureDto.getFacts().getItems();
|
|
797
|
Collections.sort(list, (f1,f2)->{
|
|
798
|
if (!f1.getClass().equals(f2.getClass())) {
|
|
799
|
return f1.getClass().getSimpleName().compareTo(f2.getClass().getSimpleName());
|
|
800
|
}else {
|
|
801
|
if (f1 instanceof FactDto) {
|
|
802
|
FactDto fact1 = (FactDto)f1;
|
|
803
|
FactDto fact2 = (FactDto)f2;
|
|
804
|
|
|
805
|
// return fact1.getTypedLabel().toString().compareTo(fact2.getTypedLabel().toString());
|
|
806
|
return 0; //FIXME;
|
|
807
|
} else if (f1 instanceof CommonNameDto) {
|
|
808
|
int result = 0;
|
|
809
|
CommonNameDto fact1 = (CommonNameDto)f1;
|
|
810
|
CommonNameDto fact2 = (CommonNameDto)f2;
|
|
811
|
return 0; //FIXME
|
|
812
|
}
|
|
813
|
}
|
|
814
|
return 0; //FIXME
|
|
815
|
});
|
|
816
|
|
|
817
|
}
|
|
818
|
|
|
819
|
private Map<UUID, Set<DescriptionElementBase>> loadFeatureMap(IDescribable<?> describable) {
|
|
820
|
Map<UUID, Set<DescriptionElementBase>> featureMap = new HashMap<>();
|
|
821
|
|
|
822
|
//... load facts
|
|
823
|
for (DescriptionBase<?> description : filterPublished(describable.getDescriptions())) {
|
|
824
|
if (description.isImageGallery()) {
|
|
825
|
continue;
|
|
826
|
}
|
|
827
|
for (DescriptionElementBase deb : description.getElements()) {
|
|
828
|
Feature feature = deb.getFeature();
|
|
829
|
if (featureMap.get(feature.getUuid()) == null) {
|
|
830
|
featureMap.put(feature.getUuid(), new HashSet<>());
|
|
831
|
}
|
|
832
|
featureMap.get(feature.getUuid()).add(deb);
|
|
833
|
}
|
|
834
|
}
|
|
835
|
return featureMap;
|
|
836
|
}
|
|
837
|
|
|
838
|
private TreeNode<Feature, UUID> createDefaultFeatureNode(IDescribable<?> describable) {
|
|
839
|
TreeNode<Feature, UUID> root = new TreeNode<>();
|
|
840
|
Set<Feature> requiredFeatures = new HashSet<>();
|
|
841
|
|
|
842
|
for (DescriptionBase<?> description : describable.getDescriptions()) {
|
|
843
|
if (description.isImageGallery()) {
|
|
844
|
continue;
|
|
845
|
}
|
|
846
|
for (DescriptionElementBase deb : description.getElements()) {
|
|
847
|
Feature feature = deb.getFeature();
|
|
848
|
if (feature != null) { //null should not happen
|
|
849
|
requiredFeatures.add(feature);
|
|
850
|
}
|
|
851
|
}
|
|
852
|
}
|
|
853
|
List<Feature> sortedChildren = new ArrayList<>(requiredFeatures);
|
|
854
|
Collections.sort(sortedChildren, (f1,f2) -> f1.getTitleCache().compareTo(f2.getTitleCache()));
|
|
855
|
sortedChildren.stream().forEachOrdered(f->root.addChild(new TreeNode<>(f.getUuid(), f)));
|
|
856
|
return root;
|
|
857
|
}
|
|
858
|
|
|
859
|
/**
|
|
860
|
* Recursive call to a feature tree's feature node in order to creates a tree structure
|
|
861
|
* ordered in the same way as the according feature tree but only containing features
|
|
862
|
* that do really exist for the given taxon. If only a child node is required the parent
|
|
863
|
* node/feature is also considered to be required.<BR>
|
|
864
|
*/
|
|
865
|
private TreeNode<Feature, UUID> filterFeatureNode(TermNode<Feature> featureNode,
|
|
866
|
Set<UUID> existingFeatureUuids) {
|
|
867
|
|
|
868
|
//first filter children
|
|
869
|
List<TreeNode<Feature, UUID>> requiredChildNodes = new ArrayList<>();
|
|
870
|
for (TermNode<Feature> childNode : featureNode.getChildNodes()) {
|
|
871
|
TreeNode<Feature, UUID> child = filterFeatureNode(childNode, existingFeatureUuids);
|
|
872
|
if (child != null) {
|
|
873
|
requiredChildNodes.add(child);
|
|
874
|
}
|
|
875
|
}
|
|
876
|
|
|
877
|
//if any child is required or this node is required ....
|
|
878
|
if (!requiredChildNodes.isEmpty() ||
|
|
879
|
featureNode.getTerm() != null && existingFeatureUuids.contains(featureNode.getTerm().getUuid())) {
|
|
880
|
|
|
881
|
TreeNode<Feature,UUID> result = new TreeNode<>();
|
|
882
|
//add this nodes data
|
|
883
|
Feature feature = featureNode.getTerm() == null ? null : featureNode.getTerm();
|
|
884
|
if (feature != null) {
|
|
885
|
result.setNodeId(feature.getUuid());
|
|
886
|
result.setData(feature);
|
|
887
|
}
|
|
888
|
//add child data
|
|
889
|
requiredChildNodes.stream().forEachOrdered(c->result.addChild(c));
|
|
890
|
return result;
|
|
891
|
}else {
|
|
892
|
return null;
|
|
893
|
}
|
|
894
|
}
|
|
895
|
|
|
896
|
/**
|
|
897
|
* Computes the (unsorted) set of features for which facts exist
|
|
898
|
* for the given taxon.
|
|
899
|
*/
|
|
900
|
private Map<UUID, Feature> getExistingFeatureUuids(IDescribable<?> describable) {
|
|
901
|
Map<UUID, Feature> result = new HashMap<>();
|
|
902
|
for (DescriptionBase<?> description : filterPublished(describable.getDescriptions())) {
|
|
903
|
if (description.isImageGallery()) {
|
|
904
|
continue;
|
|
905
|
}
|
|
906
|
for (DescriptionElementBase deb : description.getElements()) {
|
|
907
|
Feature feature = deb.getFeature();
|
|
908
|
if (feature != null) { //null should not happen
|
|
909
|
result.put(feature.getUuid(), feature);
|
|
910
|
}
|
|
911
|
}
|
|
912
|
}
|
|
913
|
return result;
|
|
914
|
}
|
|
915
|
|
|
916
|
private void handleDistributions(TaxonPageDtoConfiguration config, FeatureDto featureDto,
|
|
917
|
List<Distribution> distributions, TaxonPageDto pageDto) {
|
|
918
|
|
|
919
|
if (distributions.isEmpty()) {
|
|
920
|
return;
|
|
921
|
}
|
|
922
|
IDistributionService distributionService = repository.getDistributionService();
|
|
923
|
|
|
924
|
//configs
|
|
925
|
DistributionInfoConfiguration distributionConfig = config.getDistributionInfoConfiguration(featureDto.getUuid());
|
|
926
|
CondensedDistributionConfiguration condensedConfig = distributionConfig.getCondensedDistributionConfiguration();
|
|
927
|
|
|
928
|
String statusColorsString = distributionConfig.getStatusColorsString();
|
|
929
|
|
|
930
|
|
|
931
|
//copied from DescriptionListController
|
|
932
|
|
|
933
|
boolean ignoreDistributionStatusUndefined = true; //workaround until #9500 is fully implemented
|
|
934
|
distributionConfig.setIgnoreDistributionStatusUndefined(ignoreDistributionStatusUndefined);
|
|
935
|
boolean neverUseFallbackAreaAsParent = true; //may become a service parameter in future
|
|
936
|
|
|
937
|
//fallbackArea markers include markers for fully hidden areas and fallback areas.
|
|
938
|
//The later are hidden markers on areas that have non-hidden subareas (#4408)
|
|
939
|
Set<MarkerType> fallbackAreaMarkerTypes = distributionConfig.getFallbackAreaMarkerTypeList();
|
|
940
|
if(!CdmUtils.isNullSafeEmpty(fallbackAreaMarkerTypes)){
|
|
941
|
condensedConfig.fallbackAreaMarkers = fallbackAreaMarkerTypes.stream().map(mt->mt.getUuid()).collect(Collectors.toSet());
|
|
942
|
}
|
|
943
|
|
|
944
|
Map<PresenceAbsenceTerm, Color> distributionStatusColors;
|
|
945
|
try {
|
|
946
|
distributionStatusColors = DistributionServiceUtilities.buildStatusColorMap(
|
|
947
|
statusColorsString, repository.getTermService(), repository.getVocabularyService());
|
|
948
|
} catch (JsonProcessingException e) {
|
|
949
|
pageDto.addMessage(MessagesDto.NewErrorInstance("JsonProcessingException when reading distribution status colors", e));
|
|
950
|
//TODO is null allowed?
|
|
951
|
distributionStatusColors = null;
|
|
952
|
}
|
|
953
|
|
|
954
|
DistributionInfoDto dto = distributionService.composeDistributionInfoFor(distributionConfig, distributions,
|
|
955
|
neverUseFallbackAreaAsParent,
|
|
956
|
distributionStatusColors, LocaleContext.getLanguages());
|
|
957
|
|
|
958
|
//should not be necessary anymore as distribution data is now loaded directly in DIstributionServiceImpl
|
|
959
|
//by calling PortalDtoLoader.loadBaseData() directly
|
|
960
|
// if (distributionConfig.isUseTreeDto() && dto.getTree() != null) {
|
|
961
|
// DistributionTreeDto tree = (DistributionTreeDto)dto.getTree();
|
|
962
|
// TreeNode<Set<DistributionDto>, NamedAreaDto> root = tree.getRootElement();
|
|
963
|
// //fill uuid->distribution map
|
|
964
|
// Map<UUID,Distribution> distributionMap = new HashMap<>();
|
|
965
|
// distributions.stream().forEach(d->distributionMap.put(d.getUuid(), d));
|
|
966
|
// handleDistributionDtoNode(distributionMap, root);
|
|
967
|
// }
|
|
968
|
|
|
969
|
featureDto.addFact(dto);
|
|
970
|
}
|
|
971
|
|
|
972
|
//should not be necessary anymore as distribution data is now loaded directly in DIstributionServiceImpl
|
|
973
|
//by calling PortalDtoLoader.loadBaseData() directly
|
|
974
|
// private static void handleDistributionDtoNode(Map<UUID, Distribution> map,
|
|
975
|
// TreeNode<Set<DistributionDto>, NamedAreaDto> root) {
|
|
976
|
// if (root.getData() != null) {
|
|
977
|
// root.getData().stream().forEach(dto->{
|
|
978
|
// Distribution distr = map.get(dto.getUuid());
|
|
979
|
// loadBaseData(distr, dto);
|
|
980
|
// dto.setTimeperiod(distr.getTimeperiod() == null ? null : distr.getTimeperiod().toString());
|
|
981
|
// });
|
|
982
|
// }
|
|
983
|
//
|
|
984
|
// //handle children
|
|
985
|
// if (root.getChildren() != null) {
|
|
986
|
// root.getChildren().stream().forEach(c->handleDistributionDtoNode(map, c));
|
|
987
|
// }
|
|
988
|
// }
|
|
989
|
|
|
990
|
private FactDtoBase handleFact(FeatureDto featureDto, DescriptionElementBase fact, TaxonPageDto pageDto) {
|
|
991
|
//TODO locale
|
|
992
|
Language localeLang = null;
|
|
993
|
|
|
994
|
FactDtoBase result;
|
|
995
|
if (fact.isInstanceOf(TextData.class)) {
|
|
996
|
TextData td = CdmBase.deproxy(fact, TextData.class);
|
|
997
|
LanguageString ls = td.getPreferredLanguageString(localeLang);
|
|
998
|
String text = ls == null ? "" : CdmUtils.Nz(ls.getText());
|
|
999
|
|
|
1000
|
FactDto factDto = new FactDto();
|
|
1001
|
featureDto.addFact(factDto);
|
|
1002
|
//TODO do we really need type information for textdata here?
|
|
1003
|
TypedLabel typedLabel = new TypedLabel(text);
|
|
1004
|
typedLabel.setClassAndId(td);
|
|
1005
|
factDto.getTypedLabel().add(typedLabel);
|
|
1006
|
loadBaseData(td, factDto);
|
|
1007
|
//TODO
|
|
1008
|
result = factDto;
|
|
1009
|
}else if (fact.isInstanceOf(CommonTaxonName.class)) {
|
|
1010
|
CommonTaxonName ctn = CdmBase.deproxy(fact, CommonTaxonName.class);
|
|
1011
|
CommonNameDto dto = new CommonNameDto();
|
|
1012
|
featureDto.addFact(dto);
|
|
1013
|
|
|
1014
|
Language lang = ctn.getLanguage();
|
|
1015
|
if (lang != null) {
|
|
1016
|
String langLabel = getTermLabel(lang, localeLang);
|
|
1017
|
dto.setLanguage(langLabel);
|
|
1018
|
dto.setLanguageUuid(lang.getUuid());
|
|
1019
|
}else {
|
|
1020
|
//TODO
|
|
1021
|
dto.setLanguage("-");
|
|
1022
|
}
|
|
1023
|
//area
|
|
1024
|
NamedArea area = ctn.getArea();
|
|
1025
|
if (area != null) {
|
|
1026
|
String areaLabel = getTermLabel(area, localeLang);
|
|
1027
|
dto.setArea(areaLabel);
|
|
1028
|
dto.setAreaUUID(area.getUuid());
|
|
1029
|
}
|
|
1030
|
dto.setName(ctn.getName());
|
|
1031
|
dto.setTransliteration(ctn.getTransliteration());
|
|
1032
|
loadBaseData(ctn, dto);
|
|
1033
|
//TODO sort all common names (not urgent as this is done by portal code)
|
|
1034
|
result = dto;
|
|
1035
|
} else if (fact.isInstanceOf(IndividualsAssociation.class)) {
|
|
1036
|
IndividualsAssociation ia = CdmBase.deproxy(fact, IndividualsAssociation.class);
|
|
1037
|
IndividualsAssociationDto dto = new IndividualsAssociationDto ();
|
|
1038
|
|
|
1039
|
LanguageString description = MultilanguageTextHelper.getPreferredLanguageString(ia.getDescription(), Arrays.asList(localeLang));
|
|
1040
|
if (description != null) {
|
|
1041
|
dto.setDescritpion(description.getText());
|
|
1042
|
}
|
|
1043
|
SpecimenOrObservationBase<?> specimen = ia.getAssociatedSpecimenOrObservation();
|
|
1044
|
if (specimen != null) {
|
|
1045
|
//TODO what to use here??
|
|
1046
|
dto.setOccurrence(specimen.getTitleCache());
|
|
1047
|
dto.setOccurrenceUuid(specimen.getUuid());
|
|
1048
|
}
|
|
1049
|
|
|
1050
|
featureDto.addFact(dto);
|
|
1051
|
loadBaseData(ia, dto);
|
|
1052
|
result = dto;
|
|
1053
|
} else if (fact.isInstanceOf(TaxonInteraction.class)) {
|
|
1054
|
TaxonInteraction ti = CdmBase.deproxy(fact, TaxonInteraction.class);
|
|
1055
|
TaxonInteractionDto dto = new TaxonInteractionDto ();
|
|
1056
|
|
|
1057
|
LanguageString description = MultilanguageTextHelper.getPreferredLanguageString(
|
|
1058
|
ti.getDescription(), Arrays.asList(localeLang));
|
|
1059
|
if (description != null) {
|
|
1060
|
dto.setDescritpion(description.getText());
|
|
1061
|
}
|
|
1062
|
Taxon taxon = ti.getTaxon2();
|
|
1063
|
if (taxon != null) {
|
|
1064
|
//TODO what to use here??
|
|
1065
|
dto.setTaxon(taxon.cacheStrategy().getTaggedTitle(taxon));
|
|
1066
|
dto.setTaxonUuid(taxon.getUuid());
|
|
1067
|
}
|
|
1068
|
featureDto.addFact(dto);
|
|
1069
|
loadBaseData(ti, dto);
|
|
1070
|
result = dto;
|
|
1071
|
}else if (fact.isInstanceOf(CategoricalData.class)) {
|
|
1072
|
CategoricalData cd = CdmBase.deproxy(fact, CategoricalData.class);
|
|
1073
|
FactDto factDto = new FactDto();
|
|
1074
|
featureDto.addFact(factDto);
|
|
1075
|
//TODO do we really need type information for textdata here?
|
|
1076
|
String label = CategoricalDataFormatter.NewInstance(null).format(cd, localeLang);
|
|
1077
|
TypedLabel typedLabel = new TypedLabel(label);
|
|
1078
|
typedLabel.setClassAndId(cd);
|
|
1079
|
factDto.getTypedLabel().add(typedLabel);
|
|
1080
|
//TODO
|
|
1081
|
loadBaseData(cd, factDto);
|
|
1082
|
result = factDto;
|
|
1083
|
}else if (fact.isInstanceOf(QuantitativeData.class)) {
|
|
1084
|
QuantitativeData qd = CdmBase.deproxy(fact, QuantitativeData.class);
|
|
1085
|
FactDto factDto = new FactDto();
|
|
1086
|
featureDto.addFact(factDto);
|
|
1087
|
//TODO do we really need type information for textdata here?
|
|
1088
|
String label = QuantitativeDataFormatter.NewInstance(null).format(qd, localeLang);
|
|
1089
|
TypedLabel typedLabel = new TypedLabel(label);
|
|
1090
|
typedLabel.setClassAndId(qd);
|
|
1091
|
factDto.getTypedLabel().add(typedLabel);
|
|
1092
|
//TODO
|
|
1093
|
loadBaseData(qd, factDto);
|
|
1094
|
result = factDto;
|
|
1095
|
}else if (fact.isInstanceOf(TemporalData.class)) {
|
|
1096
|
TemporalData td = CdmBase.deproxy(fact, TemporalData.class);
|
|
1097
|
FactDto factDto = new FactDto();
|
|
1098
|
featureDto.addFact(factDto);
|
|
1099
|
//TODO do we really need type information for textdata here?
|
|
1100
|
String label = td.toString();
|
|
1101
|
TypedLabel typedLabel = new TypedLabel(label);
|
|
1102
|
typedLabel.setClassAndId(td);
|
|
1103
|
factDto.getTypedLabel().add(typedLabel);
|
|
1104
|
//TODO
|
|
1105
|
loadBaseData(td, factDto);
|
|
1106
|
result = factDto;
|
|
1107
|
}else {
|
|
1108
|
pageDto.addMessage(MessagesDto.NewWarnInstance("DescriptionElement type not yet handled: " + fact.getClass().getSimpleName()));
|
|
1109
|
return null;
|
|
1110
|
}
|
|
1111
|
result.setTimeperiod(fact.getTimeperiod() == null ? null : fact.getTimeperiod().toString());
|
|
1112
|
return result;
|
|
1113
|
}
|
|
1114
|
|
|
1115
|
private String getTermLabel(TermBase term, Language localeLang) {
|
|
1116
|
if (term == null) {
|
|
1117
|
return null;
|
|
1118
|
}
|
|
1119
|
Representation rep = term.getPreferredRepresentation(localeLang);
|
|
1120
|
String label = rep == null ? null : rep.getLabel();
|
|
1121
|
label = label == null ? term.getLabel() : label;
|
|
1122
|
return label;
|
|
1123
|
}
|
|
1124
|
|
|
1125
|
/**
|
|
1126
|
* Compares an existing last date and the last date of an entity
|
|
1127
|
* and returns the resulting last date.
|
|
1128
|
*/
|
|
1129
|
private LocalDateTime getLastUpdated(LocalDateTime existingLastDate, VersionableEntity dateToAddEntity) {
|
|
1130
|
|
|
1131
|
DateTime dateToAdd = dateToAddEntity.getUpdated() != null ? dateToAddEntity.getUpdated() : dateToAddEntity.getCreated();
|
|
1132
|
|
|
1133
|
LocalDateTime javaLocalDateTimeOfEntity = dateToAdd == null ? null:
|
|
1134
|
LocalDateTime.of(dateToAdd.getYear(), dateToAdd.getMonthOfYear(),
|
|
1135
|
dateToAdd.getDayOfMonth(), dateToAdd.getHourOfDay(),
|
|
1136
|
dateToAdd.getMinuteOfHour(), dateToAdd.getSecondOfMinute());
|
|
1137
|
|
|
1138
|
if (existingLastDate == null) {
|
|
1139
|
return javaLocalDateTimeOfEntity;
|
|
1140
|
}else if (javaLocalDateTimeOfEntity == null || javaLocalDateTimeOfEntity.compareTo(existingLastDate) < 0) {
|
|
1141
|
return existingLastDate;
|
|
1142
|
}else {
|
|
1143
|
return javaLocalDateTimeOfEntity;
|
|
1144
|
}
|
|
1145
|
}
|
|
1146
|
|
|
1147
|
public static void loadBaseData(CdmBase cdmBase, CdmBaseDto dto) {
|
|
1148
|
dto.setId(cdmBase.getId());
|
|
1149
|
dto.setUuid(cdmBase.getUuid());
|
|
1150
|
|
|
1151
|
loadAnnotatable(cdmBase, dto);
|
|
1152
|
loadSources(cdmBase, dto);
|
|
1153
|
//loadIdentifiable(cdmBase, dto);
|
|
1154
|
}
|
|
1155
|
|
|
1156
|
private static void loadSources(CdmBase cdmBase, CdmBaseDto dto) {
|
|
1157
|
if (dto instanceof SingleSourcedDto && cdmBase.isInstanceOf(SingleSourcedEntityBase.class)) {
|
|
1158
|
//TODO other sourced
|
|
1159
|
SingleSourcedEntityBase sourced = CdmBase.deproxy(cdmBase, SingleSourcedEntityBase.class);
|
|
1160
|
SingleSourcedDto sourcedDto = (SingleSourcedDto)dto;
|
|
1161
|
NamedSource source = sourced.getSource();
|
|
1162
|
if (source != null) { //TODO && !source.isEmpty() - does not exist yet
|
|
1163
|
SourceDto sourceDto = makeSource(source);
|
|
1164
|
sourcedDto.setSource(sourceDto);
|
|
1165
|
}
|
|
1166
|
} else if (dto instanceof SourcedDto && cdmBase instanceof ISourceable) {
|
|
1167
|
@SuppressWarnings("unchecked")
|
|
1168
|
ISourceable<OriginalSourceBase> sourced = (ISourceable<OriginalSourceBase>)cdmBase;
|
|
1169
|
SourcedDto sourcedDto = (SourcedDto)dto;
|
|
1170
|
for (OriginalSourceBase source : sourced.getSources()) {
|
|
1171
|
SourceDto sourceDto = makeSource(source);
|
|
1172
|
sourcedDto.addSource(sourceDto);
|
|
1173
|
}
|
|
1174
|
}
|
|
1175
|
//load description sources for facts
|
|
1176
|
if (cdmBase.isInstanceOf(DescriptionElementBase.class)){
|
|
1177
|
DescriptionBase<?> db = CdmBase.deproxy(cdmBase, DescriptionElementBase.class).getInDescription();
|
|
1178
|
if (db != null) { //test sometime do not have a description for facts
|
|
1179
|
SourcedDto sourcedDto = (SourcedDto)dto;
|
|
1180
|
for (OriginalSourceBase source : db.getSources()) {
|
|
1181
|
SourceDto sourceDto = new SourceDto();
|
|
1182
|
loadSource(source, sourceDto);
|
|
1183
|
sourcedDto.addSource(sourceDto);
|
|
1184
|
}
|
|
1185
|
}
|
|
1186
|
}
|
|
1187
|
}
|
|
1188
|
|
|
1189
|
private static SourceDto makeSource(OriginalSourceBase source) {
|
|
1190
|
if (source == null) {
|
|
1191
|
return null;
|
|
1192
|
}
|
|
1193
|
SourceDto sourceDto = new SourceDto();
|
|
1194
|
loadSource(source, sourceDto);
|
|
1195
|
return sourceDto;
|
|
1196
|
}
|
|
1197
|
|
|
1198
|
private static void loadSource(OriginalSourceBase source, SourceDto sourceDto) {
|
|
1199
|
|
|
1200
|
source = CdmBase.deproxy(source);
|
|
1201
|
//base data
|
|
1202
|
loadBaseData(source, sourceDto);
|
|
1203
|
|
|
1204
|
ICdmBase linkedObject = source.getCitation();
|
|
1205
|
if (linkedObject == null) {
|
|
1206
|
//cdmsource
|
|
1207
|
linkedObject = source.getCdmSource();
|
|
1208
|
}
|
|
1209
|
|
|
1210
|
//citation doi & uri & links
|
|
1211
|
Reference ref = source.getCitation();
|
|
1212
|
if (ref != null) {
|
|
1213
|
sourceDto.setDoi(ref.getDoiString());
|
|
1214
|
sourceDto.setUri(ref.getUri());
|
|
1215
|
sourceDto.setUuid(ref.getUuid());
|
|
1216
|
sourceDto.setOriginalInfo(source.getOriginalInfo());
|
|
1217
|
Set<ExternalLink> links = ref.getLinks();
|
|
1218
|
for (ExternalLink link : links) {
|
|
1219
|
if (link.getUri() != null) {
|
|
1220
|
sourceDto.addLink(link.getUri());
|
|
1221
|
}
|
|
1222
|
}
|
|
1223
|
}
|
|
1224
|
|
|
1225
|
//label
|
|
1226
|
//TODO this probably does not use specimen or cdmSource if necessary,
|
|
1227
|
// also long citation is still preliminary
|
|
1228
|
String label = OriginalSourceFormatter.INSTANCE_LONG_CITATION.format(source);
|
|
1229
|
TypedLabel typedLabel = new TypedLabel(source, label);
|
|
1230
|
sourceDto.addLabel(typedLabel);
|
|
1231
|
sourceDto.setType(source.getType() != null ? source.getType().toString() : null);
|
|
1232
|
|
|
1233
|
if (source.isInstanceOf(NamedSourceBase.class)) {
|
|
1234
|
NamedSourceBase ns = CdmBase.deproxy(source, NamedSourceBase.class);
|
|
1235
|
|
|
1236
|
//nameUsedInSource
|
|
1237
|
TaxonName name = ns.getNameUsedInSource();
|
|
1238
|
if (name != null) {
|
|
1239
|
List<TaggedText> taggedName = name.cacheStrategy().getTaggedTitle(name);
|
|
1240
|
//TODO nom status?
|
|
1241
|
sourceDto.setNameInSource(taggedName);
|
|
1242
|
sourceDto.setNameInSourceUuid(name.getUuid());
|
|
1243
|
}
|
|
1244
|
|
|
1245
|
//specimen uuid
|
|
1246
|
if (source.isInstanceOf(DescriptionElementSource.class)) {
|
|
1247
|
DescriptionElementSource des = CdmBase.deproxy(source, DescriptionElementSource.class);
|
|
1248
|
if (linkedObject == null) {
|
|
1249
|
linkedObject = des.getSpecimen();
|
|
1250
|
}
|
|
1251
|
}
|
|
1252
|
}
|
|
1253
|
|
|
1254
|
sourceDto.setLinkedUuid(getUuid(linkedObject));
|
|
1255
|
String linkedObjectStr = linkedObject == null ? null : CdmBase.deproxy(linkedObject).getClass().getSimpleName();
|
|
1256
|
sourceDto.setLinkedClass(linkedObjectStr);
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
private static UUID getUuid(ICdmBase cdmBase) {
|
|
1260
|
return cdmBase == null ? null : cdmBase.getUuid();
|
|
1261
|
}
|
|
1262
|
|
|
1263
|
private static void loadAnnotatable(CdmBase cdmBase, CdmBaseDto dto) {
|
|
1264
|
if (dto instanceof AnnotatableDto && cdmBase.isInstanceOf(AnnotatableEntity.class)) {
|
|
1265
|
AnnotatableEntity annotatable = CdmBase.deproxy(cdmBase, AnnotatableEntity.class);
|
|
1266
|
AnnotatableDto annotatableDto = (AnnotatableDto)dto;
|
|
1267
|
//annotation
|
|
1268
|
for (Annotation annotation : annotatable.getAnnotations()) {
|
|
1269
|
if (annotation.getAnnotationType() != null
|
|
1270
|
//TODO annotation type filter
|
|
1271
|
&& annotation.getAnnotationType().getUuid().equals(AnnotationType.uuidEditorial)
|
|
1272
|
&& StringUtils.isNotBlank(annotation.getText())) {
|
|
1273
|
|
|
1274
|
AnnotationDto annotationDto = new AnnotationDto();
|
|
1275
|
annotatableDto.addAnnotation(annotationDto);
|
|
1276
|
//TODO id needed? but need to adapt dto and container then
|
|
1277
|
loadBaseData(annotation, annotationDto);
|
|
1278
|
annotationDto.setText(annotation.getText());
|
|
1279
|
UUID uuidAnnotationType = annotation.getAnnotationType() == null ? null :annotation.getAnnotationType().getUuid();
|
|
1280
|
annotationDto.setTypeUuid(uuidAnnotationType);
|
|
1281
|
//language etc. currently not yet used
|
|
1282
|
}
|
|
1283
|
}
|
|
1284
|
|
|
1285
|
//marker
|
|
1286
|
for (Marker marker : annotatable.getMarkers()) {
|
|
1287
|
if (marker.getMarkerType() != null
|
|
1288
|
//TODO markertype filter
|
|
1289
|
// && marker.getMarkerType().getUuid().equals(AnnotationType.uuidEditorial)
|
|
1290
|
){
|
|
1291
|
|
|
1292
|
MarkerDto markerDto = new MarkerDto();
|
|
1293
|
annotatableDto.addMarker(markerDto);
|
|
1294
|
//TODO id needed? but need to adapt dto and container then
|
|
1295
|
loadBaseData(marker, markerDto);
|
|
1296
|
if (marker.getMarkerType() != null) {
|
|
1297
|
markerDto.setTypeUuid(marker.getMarkerType().getUuid());
|
|
1298
|
//TODO locale
|
|
1299
|
markerDto.setType(marker.getMarkerType().getTitleCache());
|
|
1300
|
}
|
|
1301
|
markerDto.setValue(marker.getValue());
|
|
1302
|
}
|
|
1303
|
}
|
|
1304
|
}
|
|
1305
|
}
|
|
1306
|
}
|