package eu.etaxonomy.cdm.api.service.portal;
import java.time.LocalDateTime;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
import org.joda.time.DateTime;
+import eu.etaxonomy.cdm.api.dto.portal.CdmBaseDto;
+import eu.etaxonomy.cdm.api.dto.portal.ContainerDto;
+import eu.etaxonomy.cdm.api.dto.portal.FactDto;
+import eu.etaxonomy.cdm.api.dto.portal.FeatureDto;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonBaseDto;
import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.ConceptRelationDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.HomotypicGroupDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.KeyDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.MediaDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.MediaRepresentationDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.SpecimenDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.TaxonNodeAgentsRelDTO;
+import eu.etaxonomy.cdm.api.dto.portal.TaxonPageDto.TaxonNodeDTO;
import eu.etaxonomy.cdm.api.dto.portal.config.TaxonPageDtoConfiguration;
+import eu.etaxonomy.cdm.api.service.exception.TypeDesignationSetException;
+import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetContainer;
+import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetFormatter;
import eu.etaxonomy.cdm.common.CdmUtils;
+import eu.etaxonomy.cdm.compare.taxon.TaxonComparator;
+import eu.etaxonomy.cdm.format.common.TypedLabel;
+import eu.etaxonomy.cdm.format.taxon.TaxonRelationshipFormatter;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.common.LanguageString;
import eu.etaxonomy.cdm.model.common.VersionableEntity;
+import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.description.TextData;
+import eu.etaxonomy.cdm.model.media.ImageFile;
+import eu.etaxonomy.cdm.model.media.Media;
+import eu.etaxonomy.cdm.model.media.MediaRepresentation;
+import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
+import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.TaxonName;
+import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
+import eu.etaxonomy.cdm.model.taxon.TaxonNodeStatus;
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
+import eu.etaxonomy.cdm.strategy.cache.TaggedCacheHelper;
+import eu.etaxonomy.cdm.strategy.cache.TaggedText;
+import eu.etaxonomy.cdm.strategy.cache.taxon.TaxonBaseDefaultCacheStrategy;
/**
* Loads the portal dto from a taxon instance.
*/
public class PortalDtoLoader {
- public TaxonPageDto load(Taxon taxon, TaxonPageDtoConfiguration config) {
- TaxonPageDto result = new TaxonPageDto();
+ public TaxonPageDto load(Taxon taxon, TaxonPageDtoConfiguration config) {
+ TaxonPageDto result = new TaxonPageDto();
- TaxonName name = taxon.getName();
+ TaxonName name = taxon.getName();
- result.id = taxon.getId();
- result.uuid = taxon.getUuid();
- result.lastUpdated = getLastUpdated(null, taxon);
- result.nameLabel = name != null? name.getTitleCache() : "";
- result.taxonLabel = CdmUtils.Nz(taxon.getTitleCache());
+ //load 1:1
+ loadBaseData(taxon, result);
+ result.setLastUpdated(getLastUpdated(null, taxon));
+ result.setNameLabel(name != null? name.getTitleCache() : "");
+ result.setTaxonLabel(CdmUtils.Nz(taxon.getTitleCache()));
+// result.setTypedTaxonLabel(getTypedTaxonLabel(taxon, config));
+ result.setTaggedTaxon(getTaggedTaxon(taxon, config));
- return result;
+ loadTaxonNodes(taxon, result, config);
+ loadSynonyms(taxon, result, config);
+ loadConceptRelations(taxon, result, config);
+ loadFacts(taxon, result, config);
+ loadMedia(taxon, result, config);
+ loadSpecimens(taxon, result, config);
+ loadKeys(taxon, result, config);
+
+ return result;
+ }
+
+ private List<TaggedText> getTaggedTaxon(Taxon taxon, TaxonPageDtoConfiguration config) {
+ List<TypedLabel> result = new ArrayList<>();
+ TaxonBaseDefaultCacheStrategy<TaxonBase<?>> formatter = new TaxonBaseDefaultCacheStrategy<>();
+ List<TaggedText> tags = formatter.getTaggedTitle(taxon);
+ return tags;
+ }
+
+ private void loadKeys(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+ ContainerDto<KeyDTO> container =new ContainerDto<>();
+ //TODO
+
+ if (container.getCount() > 0) {
+ result.setKeys(container);
+ }
+ }
+
+ private void loadSpecimens(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+ //TODO load specimen from multiple places
+
+ ContainerDto<SpecimenDTO> container = new ContainerDto<TaxonPageDto.SpecimenDTO>();
+
+ List<SpecimenOrObservationBase<?>> specimens = new ArrayList<>();
+ for (TaxonDescription taxonDescription : taxon.getDescriptions()) {
+ if (taxonDescription.isImageGallery()) {
+ continue;
+ }
+ for (DescriptionElementBase el : taxonDescription.getElements()) {
+ if (el.isInstanceOf(IndividualsAssociation.class)) {
+ IndividualsAssociation indAss = CdmBase.deproxy(el, IndividualsAssociation.class);
+ SpecimenOrObservationBase<?> specimen = indAss.getAssociatedSpecimenOrObservation();
+ specimens.add(specimen);
+ }
+ }
+ }
+ List<SpecimenOrObservationBase<?>> typeSpecimens = loadTypeSpecimen(taxon.getName(), config);
+ specimens.addAll(typeSpecimens);
+ for (TaxonName syn : taxon.getSynonymNames()) {
+ typeSpecimens = loadTypeSpecimen(syn, config);
+ specimens.addAll(typeSpecimens);
+ }
+
+ for (SpecimenOrObservationBase<?> specimen : specimens) {
+ SpecimenDTO dto = new SpecimenDTO();
+ loadBaseData(specimen, dto);
+ dto.setLabel(specimen.getTitleCache());
+ container.addItem(dto);
+ }
+ if (container.getCount() > 0 ) {
+ result.setSpecimens(container);
+ }
+
+ }
+
+ private List<SpecimenOrObservationBase<?>> loadTypeSpecimen(TaxonName name, TaxonPageDtoConfiguration config) {
+ List<SpecimenOrObservationBase<?>> result = new ArrayList<>();
+ for (SpecimenTypeDesignation desig: name.getSpecimenTypeDesignations()){
+ DerivedUnit specimen = desig.getTypeSpecimen();
+ if (specimen != null) {
+ result.add(specimen);
+ }
+ }
+ return result;
+ }
+
+ private void loadMedia(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+
+ ContainerDto<MediaDTO> container = new ContainerDto<TaxonPageDto.MediaDTO>();
+
+ List<Media> medias = new ArrayList<>();
+ for (TaxonDescription taxonDescription : taxon.getDescriptions()) {
+ if (!taxonDescription.isImageGallery()) {
+ continue;
+ }
+
+ List<Media> newMedia = taxonDescription.getElements().stream()
+ .filter(el->el.isInstanceOf(TextData.class))
+ .map(el->CdmBase.deproxy(el, TextData.class))
+ .filter(td->true)
+ .flatMap(td->td.getMedia().stream())
+ .collect(Collectors.toList())
+ ;
+ medias.addAll(newMedia);
+ }
+ //TODO collect media from elsewhere
+ for (Media media : medias) {
+ MediaDTO dto = new TaxonPageDto.MediaDTO();
+ loadBaseData(media, dto);
+ dto.setLabel(media.getTitleCache());
+ ContainerDto<MediaRepresentationDTO> representations = new ContainerDto<>();
+ for (MediaRepresentation rep : media.getRepresentations()) {
+ MediaRepresentationDTO repDto = new MediaRepresentationDTO();
+ loadBaseData(rep, dto);
+ repDto.setMimeType(rep.getMimeType());
+ repDto.setSuffix(rep.getSuffix());
+ if (!rep.getParts().isEmpty()) {
+ //TODO handle message if n(parts) > 1
+ MediaRepresentationPart part = rep.getParts().get(0);
+ repDto.setUri(part.getUri());
+ repDto.setClazz(part.getClass());
+ repDto.setSize(part.getSize());
+ if (part.isInstanceOf(ImageFile.class)) {
+ ImageFile image = CdmBase.deproxy(part, ImageFile.class);
+ repDto.setHeight(image.getHeight());
+ repDto.setWidth(image.getWidth());
+ }
+ //TODO AudioFile etc.
+ }
+ representations.addItem(repDto);
+ }
+ if (representations.getCount() > 0) {
+ dto.setRepresentations(representations);
+ }
+ //TODO load representation data
+ container.addItem(dto);
+ }
+
+ if (container.getCount() > 0) {
+ result.setMedia(container);
+ }
+
+ }
+
+ private void loadTaxonNodes(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+ ContainerDto<TaxonNodeDTO> container = new ContainerDto<TaxonPageDto.TaxonNodeDTO>();
+ for (TaxonNode node : taxon.getTaxonNodes()) {
+ TaxonNodeDTO dto = new TaxonNodeDTO();
+ loadBaseData(node, dto);
+ //classification
+ Classification classification = node.getClassification();
+ if (classification != null) {
+ dto.setClassificationUuid(node.getClassification().getUuid());
+ dto.setClassificationLabel(classification.getName().getText());
+ }
+ //TODO lang/locale
+ Language language = Language.DEFAULT();
+
+ //status
+ TaxonNodeStatus status = node.getStatus();
+ if (status != null) {
+ dto.setStatus(status.getLabel(language));
+ }
+ //statusNote
+ Map<Language, LanguageString> statusNote = node.getStatusNote();
+ if (statusNote != null) {
+ //TODO handle fallback lang
+ LanguageString statusNoteStr = statusNote.get(language);
+ if (statusNoteStr == null && statusNote.size() > 0) {
+ statusNoteStr = statusNote.entrySet().iterator().next().getValue();
+ }
+ if (statusNoteStr != null) {
+ dto.setStatusNote(statusNoteStr.getText());
+ }
+ }
+ //agent relations
+ Set<TaxonNodeAgentRelation> agents = node.getAgentRelations();
+ if (!agents.isEmpty()) {
+ for (TaxonNodeAgentRelation rel : agents) {
+ TaxonNodeAgentsRelDTO agentDto = new TaxonNodeAgentsRelDTO();
+ loadBaseData(rel, agentDto);
+
+ //TODO laod
+ if (rel.getAgent() != null) {
+ agentDto.setAgent(rel.getAgent().getFullTitle());
+ agentDto.setAgentUuid(rel.getAgent().getUuid());
+ }
+ if (rel.getType() != null) {
+ agentDto.setType(rel.getType().getTitleCache());
+ agentDto.setTypeUuid(rel.getType().getUuid());
+ }
+ dto.addAgent(agentDto);
+ }
+ }
+ container.addItem(dto);
+ }
+ if (container.getCount() > 0) {
+ result.setTaxonNodes(container);
+ }
+
+ }
+
+
+ private void loadSynonyms(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+// List<HomotypicalGroup> homotypicGroups = taxon.getHomotypicSynonymyGroups();
+
+ TaxonComparator comparator = new TaxonComparator();
+
+ TaxonName name = taxon.getName();
+
+ //TODO depending on config add/remove accepted name
+
+ //homotypic synonyms
+ List<Synonym> homotypicSynonmys = taxon.getHomotypicSynonymsByHomotypicGroup(comparator);
+ TaxonPageDto.HomotypicGroupDTO homotypicGroupDto = new TaxonPageDto.HomotypicGroupDTO();
+ if (!homotypicSynonmys.isEmpty()) {
+ loadBaseData(name.getHomotypicalGroup(), homotypicGroupDto);
+
+ for (Synonym syn : homotypicSynonmys) {
+ loadSynonymsInGroup(homotypicGroupDto, syn);
+ }
+ }
+ //TODO NPE
+ handleTypification(name.getHomotypicalGroup(), homotypicGroupDto, config);
+ result.setHomotypicSynonyms(homotypicGroupDto);
+
+ //heterotypic synonyms
+ List<HomotypicalGroup> heteroGroups = taxon.getHeterotypicSynonymyGroups();
+ if (heteroGroups.isEmpty()) {
+ return;
+ }
+ ContainerDto<HomotypicGroupDTO> heteroContainer = new ContainerDto<>();
+ result.setHeterotypicSynonymGroups(heteroContainer);
+
+ for (HomotypicalGroup hg : heteroGroups) {
+ TaxonPageDto.HomotypicGroupDTO hgDto = new TaxonPageDto.HomotypicGroupDTO();
+ loadBaseData(taxon.getName().getHomotypicalGroup(), hgDto);
+ heteroContainer.addItem(hgDto);
+
+ List<Synonym> heteroSyns = taxon.getSynonymsInGroup(hg, comparator);
+ for (Synonym syn : heteroSyns) {
+ loadSynonymsInGroup(hgDto, syn);
+ }
+ handleTypification(hg, hgDto, config);
+ }
+ }
+
+ private void handleTypification(HomotypicalGroup homotypicalGroup, HomotypicGroupDTO hgDto,
+ TaxonPageDtoConfiguration config) {
+
+ boolean withCitation = true;
+ boolean withStartingTypeLabel = true;
+ boolean withNameIfAvailable = false;
+ TypeDesignationSetFormatter formatter = new TypeDesignationSetFormatter(
+ withCitation, withStartingTypeLabel, withNameIfAvailable);
+ Set<TypeDesignationBase<?>> desigs = homotypicalGroup.getTypeDesignations();
+ try {
+ TypeDesignationSetContainer manager = TypeDesignationSetContainer.NewDefaultInstance((Set)desigs);
+ String label = formatter.format(manager);
+ hgDto.setTypes(label);
+
+ } catch (TypeDesignationSetException e) {
+ // TODO type desig error handling
+ e.printStackTrace();
+ }
+ }
+
+ private void loadConceptRelations(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+
+ //concept relations
+ ContainerDto<ConceptRelationDTO> conceptRelContainer = new ContainerDto<>();
+ TaxonRelationshipFormatter taxRelFormatter = TaxonRelationshipFormatter.INSTANCE();
+
+ //... MAN
+ Set<TaxonRelationship> misappliedRels = taxon.getMisappliedNameRelations();
+ for (TaxonRelationship rel : misappliedRels) {
+ boolean inverse = true;
+ boolean withoutName = false;
+ loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
+ }
+
+ //... pro parte Synonyms
+ Set<TaxonRelationship> proParteRels = taxon.getProParteAndPartialSynonymRelations();
+ for (TaxonRelationship rel : proParteRels) {
+ boolean inverse = true;
+ boolean withoutName = false;
+ loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
+ }
+
+ //TODO MAN and pp from this taxon
+
+ //... to-relations
+ Set<TaxonRelationship> toRels = taxon.getRelationsToThisTaxon();
+ for (TaxonRelationship rel : toRels) {
+ boolean inverse = true;
+ boolean withoutName = false;
+ loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
+ }
+
+ //... from-relations
+ Set<TaxonRelationship> fromRels = taxon.getRelationsFromThisTaxon();
+ for (TaxonRelationship rel : fromRels) {
+ boolean inverse = false;
+ boolean withoutName = false;
+ loadConceptRelation(taxRelFormatter, rel, conceptRelContainer, inverse, withoutName);
+ }
+
+ if (conceptRelContainer.getCount() > 0) {
+ result.setConceptRelations(conceptRelContainer);
+ }
+ }
+
+ private void loadConceptRelation(TaxonRelationshipFormatter taxRelFormatter, TaxonRelationship rel, ContainerDto<ConceptRelationDTO> conceptRelContainer, boolean inverse,
+ boolean withoutName) {
+ List<Language> languages = Arrays.asList(new Language[] {Language.DEFAULT()}); // TODO config.locales;
+ List<TaggedText> tags = taxRelFormatter.getTaggedText(rel, inverse, languages, withoutName);
+ String relLabel = TaggedCacheHelper.createString(tags);
+ ConceptRelationDTO dto = new TaxonPageDto.ConceptRelationDTO();
+ loadBaseData(rel, dto);
+ Taxon relTaxon = inverse ? rel.getFromTaxon() : rel.getToTaxon();
+ dto.setRelTaxonId(relTaxon.getId());
+ dto.setRelTaxonUuid(relTaxon.getUuid());
+ dto.setRelTaxonLabel(relTaxon.getTitleCache());
+ dto.setLabel(relLabel);
+ conceptRelContainer.addItem(dto);
+ }
+
+ private void loadSynonymsInGroup(TaxonPageDto.HomotypicGroupDTO hgDto, Synonym syn) {
+ TaxonBaseDto synDto = new TaxonBaseDto();
+ loadBaseData(syn, synDto);
+ synDto.setNameLabel(syn.getName().getTitleCache());
+ synDto.setTaxonLabel(syn.getTitleCache());
+ //TODO
+ hgDto.addSynonym(synDto);
+ }
+
+ private void loadFacts(Taxon taxon, TaxonPageDto result, TaxonPageDtoConfiguration config) {
+
+ //TODO load feature tree
+ Map<Feature,Set<DescriptionElementBase>> featureMap = new HashMap<>();
+
+ //load facts
+ for (TaxonDescription taxonDescription : taxon.getDescriptions()) {
+ if (taxonDescription.isImageGallery()) {
+ continue;
+ }
+ for (DescriptionElementBase deb : taxonDescription.getElements()) {
+ Feature feature = deb.getFeature();
+ if (featureMap.get(feature) == null) {
+ featureMap.put(feature, new HashSet<>());
+ }
+ featureMap.get(feature).add(deb);
+ }
+ }
+
+ //TODO sort
+ if (!featureMap.isEmpty()) {
+ ContainerDto<FeatureDto> features = new ContainerDto<>();
+ result.setFactualData(features);
+ for (Feature feature : featureMap.keySet()) {
+ FeatureDto featureDto = new FeatureDto();
+ featureDto.setId(feature.getId());
+ featureDto.setUuid(feature.getUuid());
+ //TODO locale
+ featureDto.setLabel(feature.getTitleCache());
+ features.addItem(featureDto);
+
+ //
+ for (DescriptionElementBase fact : featureMap.get(feature)){
+ handleFact(featureDto, fact);
+ }
+ }
+ }
}
+ private void handleFact(FeatureDto featureDto, DescriptionElementBase fact) {
+ if (fact.isInstanceOf(TextData.class)) {
+ TextData td = CdmBase.deproxy(fact, TextData.class);
+ //TODO locale
+ Language lang = null;
+ LanguageString ls = td.getPreferredLanguageString(lang);
+ String text = ls == null ? "" : CdmUtils.Nz(ls.getText());
+
+ FactDto factDto = new FactDto();
+ featureDto.getFacts().add(factDto);
+ //TODO do we really need type information for textdata here?
+ TypedLabel typedLabel = new TypedLabel(text);
+ typedLabel.setClassAndId(td);
+ factDto.getTypedLabel().add(typedLabel);
+ }else {
+// TODO
+ }
+
+ }
+
/**
* Compares an existing last date and the last date of an entity
* and returns the resulting last date.
*/
private LocalDateTime getLastUpdated(LocalDateTime existingLastDate, VersionableEntity dateToAddEntity) {
- DateTime dateToAdd = dateToAddEntity.getUpdated() != null ? dateToAddEntity.getUpdated() : dateToAddEntity.getCreated();
+ DateTime dateToAdd = dateToAddEntity.getUpdated() != null ? dateToAddEntity.getUpdated() : dateToAddEntity.getCreated();
LocalDateTime javaLocalDateTimeOfEntity = dateToAdd == null ? null:
LocalDateTime.of(dateToAdd.getYear(), dateToAdd.getMonthOfYear(),
dateToAdd.getDayOfMonth(), dateToAdd.getHourOfDay(),
dateToAdd.getMinuteOfHour(), dateToAdd.getSecondOfMinute());
-
- if (javaLocalDateTimeOfEntity == null || javaLocalDateTimeOfEntity.compareTo(existingLastDate) < 0) {
+ if (existingLastDate == null) {
+ return javaLocalDateTimeOfEntity;
+ }else if (javaLocalDateTimeOfEntity == null || javaLocalDateTimeOfEntity.compareTo(existingLastDate) < 0) {
return existingLastDate;
}else {
return javaLocalDateTimeOfEntity;
}
}
+ private void loadBaseData(CdmBase cdmBase, CdmBaseDto dto) {
+ dto.setId(cdmBase.getId());
+ dto.setUuid(cdmBase.getUuid());
+ }
+
}
BGBM BDI Projects / cdmlib.git / blobdiff