cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/portal/TaxonPageDtoLoaderBase.java

   1 /**
   2 * Copyright (C) 2024 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.api.service.portal;
  10
  11 import java.util.ArrayList;
  12 import java.util.List;
  13 import java.util.Set;
  14 import java.util.UUID;
  15 import java.util.stream.Collectors;
  16
  17 import org.apache.commons.lang3.StringUtils;
  18
  19 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  20 import eu.etaxonomy.cdm.api.dto.portal.AnnotatableDto;
  21 import eu.etaxonomy.cdm.api.dto.portal.AnnotationDto;
  22 import eu.etaxonomy.cdm.api.dto.portal.CdmBaseDto;
  23 import eu.etaxonomy.cdm.api.dto.portal.ContainerDto;
  24 import eu.etaxonomy.cdm.api.dto.portal.MarkerDto;
  25 import eu.etaxonomy.cdm.api.dto.portal.MediaDto2;
  26 import eu.etaxonomy.cdm.api.dto.portal.SingleSourcedDto;
  27 import eu.etaxonomy.cdm.api.dto.portal.SourceDto;
  28 import eu.etaxonomy.cdm.api.dto.portal.SourcedDto;
  29 import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto;
  30 import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.MediaRepresentationDTO;
  31 import eu.etaxonomy.cdm.api.dto.portal.config.IAnnotatableLoaderConfiguration;
  32 import eu.etaxonomy.cdm.format.common.TypedLabel;
  33 import eu.etaxonomy.cdm.format.reference.OriginalSourceFormatter;
  34 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  35 import eu.etaxonomy.cdm.model.common.Annotation;
  36 import eu.etaxonomy.cdm.model.common.AnnotationType;
  37 import eu.etaxonomy.cdm.model.common.CdmBase;
  38 import eu.etaxonomy.cdm.model.common.ICdmBase;
  39 import eu.etaxonomy.cdm.model.common.IPublishable;
  40 import eu.etaxonomy.cdm.model.common.Language;
  41 import eu.etaxonomy.cdm.model.common.LanguageString;
  42 import eu.etaxonomy.cdm.model.common.Marker;
  43 import eu.etaxonomy.cdm.model.common.MultilanguageTextHelper;
  44 import eu.etaxonomy.cdm.model.common.SingleSourcedEntityBase;
  45 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  46 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  47 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  48 import eu.etaxonomy.cdm.model.media.ExternalLink;
  49 import eu.etaxonomy.cdm.model.media.ImageFile;
  50 import eu.etaxonomy.cdm.model.media.Media;
  51 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  52 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  53 import eu.etaxonomy.cdm.model.name.TaxonName;
  54 import eu.etaxonomy.cdm.model.reference.ISourceable;
  55 import eu.etaxonomy.cdm.model.reference.NamedSource;
  56 import eu.etaxonomy.cdm.model.reference.NamedSourceBase;
  57 import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
  58 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  59 import eu.etaxonomy.cdm.model.reference.Reference;
  60 import eu.etaxonomy.cdm.model.term.Representation;
  61 import eu.etaxonomy.cdm.model.term.TermBase;
  62 import eu.etaxonomy.cdm.persistence.dao.common.ICdmGenericDao;
  63 import eu.etaxonomy.cdm.strategy.cache.TaggedText;
  64
  65 /**
  66  * @author muellera
  67  * @since 27.02.2024
  68  */
  69 public abstract class TaxonPageDtoLoaderBase {
  70
  71     protected ICdmRepository repository;
  72     protected ICdmGenericDao dao;
  73
  74     public TaxonPageDtoLoaderBase(ICdmRepository repository, ICdmGenericDao dao) {
  75         this.repository = repository;
  76         this.dao = dao;
  77     }
  78
  79     //currently only used by fact loader
  80     protected String getTermLabel(TermBase term, Language localeLang) {
  81         if (term == null) {
  82             return null;
  83         }
  84         Representation rep = term.getPreferredRepresentation(localeLang);
  85         String label = rep == null ? null : rep.getLabel();
  86         label = label == null ? term.getLabel() : label;
  87         return label;
  88     }
  89
  90     protected <P extends IPublishable> List<P> filterPublished(List<P> listToPublish) {
  91         if (listToPublish == null) {
  92             return null;
  93         }else {
  94             return listToPublish.stream().filter(s->s.isPublish()).collect(Collectors.toList());
  95         }
  96     }
  97
  98     protected <P extends IPublishable> Set<P> filterPublished(Set<P> setToPublish) {
  99         if (setToPublish == null) {
 100             return null;
 101         }else {
 102             return setToPublish.stream().filter(s->s.isPublish()).collect(Collectors.toSet());
 103         }
 104     }
 105
 106     public static void loadBaseData(IAnnotatableLoaderConfiguration config, CdmBase cdmBase, CdmBaseDto dto) {
 107         dto.setId(cdmBase.getId());
 108         dto.setUuid(cdmBase.getUuid());
 109
 110         loadAnnotatable(config, cdmBase, dto);
 111         loadSources(config, cdmBase, dto);
 112         //loadIdentifiable(cdmBase, dto);
 113     }
 114
 115     static void loadAnnotatable(IAnnotatableLoaderConfiguration config, CdmBase cdmBase, CdmBaseDto dto) {
 116         if (dto instanceof AnnotatableDto && cdmBase.isInstanceOf(AnnotatableEntity.class)) {
 117             AnnotatableEntity annotatable = CdmBase.deproxy(cdmBase, AnnotatableEntity.class);
 118             AnnotatableDto annotatableDto = (AnnotatableDto)dto;
 119             //annotation
 120             for (Annotation annotation : annotatable.getAnnotations()) {
 121                 if ((annotation.getAnnotationType() != null
 122                         //config == null currently needs to be allowed as it is also used by DistributionInfoBuilder an
 123                         //also for now empty annotation types needs to be interpreted as "no filter" as we do not distinguish
 124                         //null and empty yet, this may change in future
 125                         && (config == null || config.getAnnotationTypes().isEmpty()
 126                             || config.getAnnotationTypes().contains(annotation.getAnnotationType().getUuid())))
 127                         || (annotation.getAnnotationType() == null && config != null && config.getAnnotationTypes().contains(AnnotationType.uuidUntyped))
 128                                 && StringUtils.isNotBlank(annotation.getText())) {
 129
 130                     AnnotationDto annotationDto = new AnnotationDto();
 131                     annotatableDto.addAnnotation(annotationDto);
 132                     //TODO id needed? but need to adapt dto and container then
 133                     loadBaseData(config, annotation, annotationDto);
 134                     annotationDto.setText(annotation.getText());
 135                     UUID uuidAnnotationType = annotation.getAnnotationType() == null ? null :annotation.getAnnotationType().getUuid();
 136                     annotationDto.setTypeUuid(uuidAnnotationType);
 137                     //language etc. currently not yet used
 138                 }else if (config != null && !config.getAnnotationTypes().isEmpty() && config.getAnnotationTypes().contains(AnnotationType.uuidUntyped) &&  (annotation.getAnnotationType() == null)){
 139                     AnnotationDto annotationDto = new AnnotationDto();
 140                     annotatableDto.addAnnotation(annotationDto);
 141                     //TODO id needed? but need to adapt dto and container then
 142                     loadBaseData(config, annotation, annotationDto);
 143                     annotationDto.setText(annotation.getText());
 144                     UUID uuidAnnotationType = null;
 145                     annotationDto.setTypeUuid(uuidAnnotationType);
 146
 147                 }
 148             }
 149
 150             //marker
 151             for (Marker marker : annotatable.getMarkers()) {
 152                 if (marker.getMarkerType() != null
 153                         //TODO markertype filter
 154 //                        && marker.getMarkerType().getUuid().equals(AnnotationType.uuidEditorial)
 155                            ){
 156
 157                     MarkerDto markerDto = new MarkerDto();
 158                     annotatableDto.addMarker(markerDto);
 159                     //TODO id needed? but need to adapt dto and container then
 160                     loadBaseData(config, marker, markerDto);
 161                     if (marker.getMarkerType() != null) {
 162                         markerDto.setTypeUuid(marker.getMarkerType().getUuid());
 163                         //TODO locale
 164                         markerDto.setType(marker.getMarkerType().getTitleCache());
 165                     }
 166                     markerDto.setValue(marker.getValue());
 167                 }
 168             }
 169         }
 170     }
 171
 172     static void loadSources(IAnnotatableLoaderConfiguration config, CdmBase cdmBase, CdmBaseDto dto) {
 173         if (dto instanceof SingleSourcedDto && cdmBase.isInstanceOf(SingleSourcedEntityBase.class)) {
 174             //TODO other sourced
 175             SingleSourcedEntityBase sourced = CdmBase.deproxy(cdmBase, SingleSourcedEntityBase.class);
 176             SingleSourcedDto sourcedDto = (SingleSourcedDto)dto;
 177             NamedSource source = sourced.getSource();
 178             if (source != null && isPublicSource(source) && !source.checkEmpty()) {
 179                 SourceDto sourceDto = makeSource(config, source);
 180                 sourcedDto.setSource(sourceDto);
 181             }
 182         } else if (dto instanceof SourcedDto && cdmBase instanceof ISourceable) {
 183             @SuppressWarnings("unchecked")
 184             ISourceable<OriginalSourceBase> sourced = (ISourceable<OriginalSourceBase>)cdmBase;
 185             SourcedDto sourcedDto = (SourcedDto)dto;
 186             for (OriginalSourceBase source : sourced.getSources()) {
 187                 if (isPublicSource(source)) {
 188                     SourceDto sourceDto = makeSource(config, source);
 189                     sourcedDto.addSource(sourceDto);
 190                 }
 191             }
 192         }
 193         //load description sources for facts
 194         if (cdmBase.isInstanceOf(DescriptionElementBase.class)){
 195             DescriptionBase<?> db = CdmBase.deproxy(cdmBase, DescriptionElementBase.class).getInDescription();
 196             if (db != null) {  //test sometime do not have a description for facts
 197                 SourcedDto sourcedDto = (SourcedDto)dto;
 198                 for (OriginalSourceBase source : db.getSources()) {
 199                     if (isPublicSource(source)) {
 200                         SourceDto sourceDto = new SourceDto();
 201                         loadSource(config, source, sourceDto);
 202                         sourcedDto.addSource(sourceDto);
 203                     }
 204                 }
 205             }
 206         }
 207     }
 208
 209     private static void loadSource(IAnnotatableLoaderConfiguration config, OriginalSourceBase source, SourceDto sourceDto) {
 210
 211         source = CdmBase.deproxy(source);
 212         //base data
 213         loadBaseData(config, source, sourceDto);
 214
 215         ICdmBase linkedObject = source.getCitation();
 216         if (linkedObject == null) {
 217             //cdmsource
 218             linkedObject = source.getCdmSource();
 219         }
 220
 221         //citation doi & uri & links
 222         Reference ref = source.getCitation();
 223         if (ref != null) {
 224             sourceDto.setDoi(ref.getDoiString());
 225             sourceDto.setUri(ref.getUri());
 226             sourceDto.setUuid(ref.getUuid());
 227             sourceDto.setOriginalInfo(source.getOriginalInfo());
 228             Set<ExternalLink> links = ref.getLinks();
 229
 230             if(source.getAccessed() != null) {
 231                 sourceDto.setAccessed(source.getAccessed().toString());
 232             }
 233             for (ExternalLink link : links) {
 234                 if (link.getUri() != null) {
 235                     sourceDto.addLink(link.getUri());
 236                 }
 237             }
 238         }
 239
 240         //label
 241         //TODO this probably does not use specimen or cdmSource if necessary,
 242         //     also long citation is still preliminary
 243         String label = OriginalSourceFormatter.INSTANCE_LONG_CITATION.format(source);
 244         TypedLabel typedLabel = new TypedLabel(source, label);
 245         sourceDto.addLabel(typedLabel);
 246         sourceDto.setType(source.getType() != null ? source.getType().toString() : null);
 247
 248         if (source.isInstanceOf(NamedSourceBase.class)) {
 249             NamedSourceBase ns = CdmBase.deproxy(source, NamedSourceBase.class);
 250
 251             //nameUsedInSource
 252             TaxonName name =  ns.getNameUsedInSource();
 253             if (name != null) {
 254                 List<TaggedText> taggedName = name.cacheStrategy().getTaggedTitle(name);
 255                 //TODO nom status?
 256                 sourceDto.setNameInSource(taggedName);
 257                 sourceDto.setNameInSourceUuid(name.getUuid());
 258             }
 259
 260             //specimen uuid
 261             if (source.isInstanceOf(DescriptionElementSource.class)) {
 262                 DescriptionElementSource des = CdmBase.deproxy(source, DescriptionElementSource.class);
 263                 if (linkedObject == null) {
 264                     linkedObject = des.getSpecimen();
 265                 }
 266             }
 267         }
 268
 269         sourceDto.setLinkedUuid(getUuid(linkedObject));
 270         String linkedObjectStr = linkedObject == null ? null : CdmBase.deproxy(linkedObject).getClass().getSimpleName();
 271         sourceDto.setLinkedClass(linkedObjectStr);
 272     }
 273
 274     protected static SourceDto makeSource(IAnnotatableLoaderConfiguration config, OriginalSourceBase source) {
 275         if (source == null) {
 276             return null;
 277         }
 278         SourceDto sourceDto = new SourceDto();
 279         loadSource(config, source, sourceDto);
 280         return sourceDto;
 281     }
 282
 283     protected static UUID getUuid(ICdmBase cdmBase) {
 284         return cdmBase == null ? null : cdmBase.getUuid();
 285     }
 286
 287     protected static boolean isPublicSource(OriginalSourceBase source) {
 288         if (source.getType() == null) {
 289             return false; //should not happen
 290         }else {
 291             OriginalSourceType type = source.getType();
 292             //TODO 3 make source type configurable
 293             return type.isPublicSource();
 294         }
 295     }
 296
 297     protected void makeMediaContainer(IAnnotatableLoaderConfiguration config, TaxonPageDto result, List<Media> medias) {
 298         ContainerDto<MediaDto2> container = new ContainerDto<>();
 299
 300         for (Media media : medias) {
 301             handleSingleMedia(config, container, media);
 302         }
 303
 304         if (container.getCount() > 0) {
 305             result.setMedia(container);
 306         }
 307     }
 308
 309     protected void handleSingleMedia(IAnnotatableLoaderConfiguration config, ContainerDto<MediaDto2> container, Media media) {
 310
 311         MediaDto2 dto = new MediaDto2();
 312         loadBaseData(config, media, dto);
 313
 314         //media
 315         dto.setLabel(media.getTitleCache());
 316         //TODO i18n
 317         List<Language> languages = new ArrayList<>();
 318         LanguageString description = MultilanguageTextHelper.getPreferredLanguageString(media.getAllDescriptions(), languages);
 319         dto.setDescription(description == null ? null : description.getText());
 320
 321         //representations
 322         ContainerDto<MediaRepresentationDTO> representations = new ContainerDto<>();
 323         for (MediaRepresentation rep : media.getRepresentations()) {
 324             MediaRepresentationDTO repDto = new MediaRepresentationDTO();
 325             loadBaseData(config, rep, repDto);
 326             repDto.setMimeType(rep.getMimeType());
 327             repDto.setSuffix(rep.getSuffix());
 328             if (!rep.getParts().isEmpty()) {
 329                 //TODO handle message if n(parts) > 1
 330                 MediaRepresentationPart part = rep.getParts().get(0);
 331                 repDto.setUri(part.getUri());
 332                 repDto.setClazz(part.getClass().getSimpleName());
 333                 repDto.setSize(part.getSize());
 334                 if (part.isInstanceOf(ImageFile.class)) {
 335                     ImageFile image = CdmBase.deproxy(part, ImageFile.class);
 336                     repDto.setHeight(image.getHeight());
 337                     repDto.setWidth(image.getWidth());
 338                 }
 339                 //TODO AudioFile etc.
 340             }
 341             representations.addItem(repDto);
 342         }
 343         if (representations.getCount() > 0) {
 344             dto.setRepresentations(representations);
 345         }
 346         //TODO load representation data
 347         container.addItem(dto);
 348     }
 349 }