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/**
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* Copyright (C) 2015 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.dto;
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import java.io.Serializable;
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import java.util.AbstractMap;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Comparator;
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import java.util.EnumSet;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.TreeSet;
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import java.util.stream.Collectors;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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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.Feature;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.TermBase;
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import eu.etaxonomy.cdm.ref.TypedEntityReference;
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public abstract class SpecimenOrObservationBaseDTO extends TypedEntityReference<SpecimenOrObservationBase<?>>{
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private static final long serialVersionUID = -7597690654462090732L;
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private int id;
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private TreeSet<AbstractMap.SimpleEntry<String, String>> characterData;
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private DerivationTreeSummaryDTO derivationTreeSummary;
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protected String taxonName;
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protected String summaryLabel;
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protected boolean hasDetailImage;
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private boolean hasCharacterData;
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private boolean hasDna;
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private boolean hasSpecimenScan;
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private SpecimenOrObservationType recordBase;
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private TermBase kindOfUnit;
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private String collectorsString;
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private String individualCount;
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private Set<DerivedUnitDTO> derivatives;
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private Set<AnnotationDTO> annotations = new HashSet<>();
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private Set<SpecimenTypeDesignationDTO> specimenTypeDesignations;
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private EventDTO<DerivationEvent> derivationEvent;
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// TODO use DTO !!!
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private Set<IdentifiableSource> sources;
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private List<MediaDTO> listOfMedia = new ArrayList<>();
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private DefinedTerm sex;
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private DefinedTerm lifeStage;
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private List<DeterminationEventDTO>determinations;
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protected SpecimenOrObservationBaseDTO(SpecimenOrObservationBase<?> specimenOrObservation) {
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super(HibernateProxyHelper.getClassWithoutInitializingProxy(specimenOrObservation), specimenOrObservation.getUuid(), specimenOrObservation.getTitleCache());
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this.id = specimenOrObservation.getId();
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Set<Media> collectedMedia = collectMedia(specimenOrObservation);
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addMediaAsDTO(collectedMedia);
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setKindOfUnit(specimenOrObservation.getKindOfUnit());
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setSex(specimenOrObservation.getSex());
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setIndividualCount(specimenOrObservation.getIndividualCount());
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lifeStage = specimenOrObservation.getLifeStage();
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FieldUnit fieldUnit = null;
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if (specimenOrObservation instanceof FieldUnit){
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fieldUnit = (FieldUnit)specimenOrObservation;
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}else{
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fieldUnit = getFieldUnit((DerivedUnit)specimenOrObservation);
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}
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if (fieldUnit != null){
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AgentBase<?> collector = null;
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if (fieldUnit.getGatheringEvent() != null){
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collector = fieldUnit.getGatheringEvent().getCollector();
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}
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String fieldNumberString = CdmUtils.Nz(fieldUnit.getFieldNumber());
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if (collector != null){
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if (collector.isInstanceOf(TeamOrPersonBase.class)){
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collectorsString = CdmBase.deproxy(collector, TeamOrPersonBase.class).getCollectorTitleCache();
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}else{
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collectorsString = collector.getTitleCache(); //institutions
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}
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}
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collectorsString = CdmUtils.concat(" - ", collectorsString, fieldNumberString);
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}
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setDeterminations(specimenOrObservation.getDeterminations().stream()
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.map(det -> DeterminationEventDTO.from(det))
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.collect(Collectors.toList())
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);
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if (specimenOrObservation instanceof DerivedUnit){
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DerivedUnit derivedUnit = (DerivedUnit)specimenOrObservation;
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if (derivedUnit.getSpecimenTypeDesignations() != null){
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setSpecimenTypeDesignations(derivedUnit.getSpecimenTypeDesignations());
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}
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}
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}
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/**
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* finds the field unit of the derived unit or null if no field unit exist
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* @param specimenOrObservation
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* @return
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*/
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private FieldUnit getFieldUnit(DerivedUnit specimenOrObservation) {
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if (specimenOrObservation.getDerivedFrom() != null && !specimenOrObservation.getDerivedFrom().getOriginals().isEmpty()){
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for (SpecimenOrObservationBase<?> specimen: specimenOrObservation.getDerivedFrom().getOriginals()){
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if (specimen instanceof FieldUnit){
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return (FieldUnit)specimen;
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}else if (specimen instanceof DerivedUnit){
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getFieldUnit(HibernateProxyHelper.deproxy(specimen,DerivedUnit.class));
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}
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}
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}
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return null;
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}
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public String getCollectorsString() {
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return collectorsString;
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}
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public void setCollectorsString(String collectorsString) {
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this.collectorsString = collectorsString;
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}
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public Set<SpecimenTypeDesignationDTO> getSpecimenTypeDesignations() {
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return specimenTypeDesignations;
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}
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public void setSpecimenTypeDesignations(Set<SpecimenTypeDesignation> specimenTypeDesignations) {
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this.specimenTypeDesignations = new HashSet<>();
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for (SpecimenTypeDesignation typeDes: specimenTypeDesignations){
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if (typeDes != null){
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this.specimenTypeDesignations.add(new SpecimenTypeDesignationDTO(typeDes));
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}
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}
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}
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public Set<IdentifiableSource> getSources() {
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return sources;
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}
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public void setSources(Set<IdentifiableSource> sources) {
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this.sources = sources;
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}
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public DerivationTreeSummaryDTO getDerivationTreeSummary() {
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return derivationTreeSummary;
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}
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public void setDerivationTreeSummary(DerivationTreeSummaryDTO derivationTreeSummary) {
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this.derivationTreeSummary = derivationTreeSummary;
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if(derivationTreeSummary != null) {
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setHasSpecimenScan(isHasSpecimenScan() || !derivationTreeSummary.getSpecimenScans().isEmpty());
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setHasDetailImage(isHasDetailImage() || !derivationTreeSummary.getDetailImages().isEmpty());
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setHasDna(isHasDna() || !derivationTreeSummary.getMolecularDataList().isEmpty());
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}
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}
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public TreeSet<AbstractMap.SimpleEntry<String, String>> getCharacterData() {
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return characterData;
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}
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public void addCharacterData(String character, String state){
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if(characterData==null){
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characterData = new TreeSet<>(new PairComparator());
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}
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characterData.add(new AbstractMap.SimpleEntry<>(character, state));
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this.setHasCharacterData(!this.characterData.isEmpty());
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}
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private class PairComparator implements Comparator<AbstractMap.SimpleEntry<String,String>>, Serializable {
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private static final long serialVersionUID = -8589392050761963540L;
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@Override
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public int compare(AbstractMap.SimpleEntry<String, String> o1, AbstractMap.SimpleEntry<String, String> o2) {
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if(o1==null && o2!=null){
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return -1;
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}
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if(o1!=null && o2==null){
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return 1;
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}
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if(o1!=null && o2!=null){
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return o1.getKey().compareTo(o2.getKey());
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}
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return 0;
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}
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}
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public boolean isHasCharacterData() {
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return hasCharacterData;
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}
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public void setHasCharacterData(boolean hasCharacterData) {
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this.hasCharacterData = hasCharacterData;
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}
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public boolean isHasDna() {
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return hasDna;
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}
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public void setHasDna(boolean hasDna) {
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this.hasDna = hasDna;
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}
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public boolean isHasDetailImage() {
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return hasDetailImage;
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}
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public void setHasDetailImage(boolean hasDetailImage) {
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this.hasDetailImage = hasDetailImage;
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}
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public boolean isHasSpecimenScan() {
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return hasSpecimenScan;
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}
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public void setHasSpecimenScan(boolean hasSpecimenScan) {
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this.hasSpecimenScan = hasSpecimenScan;
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}
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/**
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* @return The summary of all DerivedUnit identifiers with the label of
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* this SpecimenOrObservationBase.
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* This label is usually being user for citing the unit in publications.
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*/
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public String getSummaryLabel() {
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return summaryLabel;
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}
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/**
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* Summary of all DerivedUnit identifiers with the label of this SpecimenOrObservationBase.
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* This label is usually being user for citing the unit in publications.
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*/
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public void setSummaryLabel(String summaryLabel) {
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this.summaryLabel = summaryLabel;
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}
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public SpecimenOrObservationType getRecordBase() {
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return recordBase;
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}
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public void setRecordBase(SpecimenOrObservationType specimenOrObservationType) {
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this.recordBase = specimenOrObservationType;
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}
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public Set<DerivedUnitDTO> getDerivatives() {
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if (this.derivatives == null){
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this.derivatives = new HashSet<>();
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}
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return derivatives;
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}
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public void setDerivatives(Set<DerivedUnitDTO> derivatives) {
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this.derivatives = derivatives;
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updateTreeDependantData(derivatives);
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}
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public void addDerivative(DerivedUnitDTO derivate){
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if (this.derivatives == null){
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this.derivatives = new HashSet<>();
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}
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this.derivatives.add(derivate);
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Set<DerivedUnitDTO> derivatives = new HashSet<>();
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derivatives.add(derivate);
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updateTreeDependantData(derivatives);
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}
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public void addAllDerivatives(Set<DerivedUnitDTO> derivatives){
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if (this.derivatives == null){
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this.derivatives = new HashSet<>();
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}
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this.derivatives.addAll(derivatives);
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updateTreeDependantData(derivatives);
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}
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/**
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* To be overwritten by implementing classes to
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* update data which depends on the derivation tree
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*/
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protected abstract void updateTreeDependantData(Set<DerivedUnitDTO> derivatives) ;
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/**
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* Recursively collects all derivatives from this.
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*/
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public Collection<DerivedUnitDTO> collectDerivatives() {
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return collectDerivatives(new HashSet<>());
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}
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/**
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* private partner method to {@link #collectDerivatives()} for recursive calls.
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*
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* @param dtos
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*/
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private Collection<DerivedUnitDTO> collectDerivatives(Set<DerivedUnitDTO> dtos) {
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dtos.addAll(getDerivatives());
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if(derivatives != null) {
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for(SpecimenOrObservationBaseDTO subDto : derivatives) {
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dtos.addAll(subDto.collectDerivatives(dtos));
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}
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}
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return dtos;
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}
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public EventDTO<DerivationEvent> getDerivationEvent() {
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return derivationEvent;
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}
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public void setDerivationEvent(EventDTO<DerivationEvent> derivationEvent) {
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this.derivationEvent = derivationEvent;
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}
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public List<MediaDTO> getListOfMedia() {
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return listOfMedia;
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}
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public void setListOfMedia(List<MediaDTO> listOfMedia) {
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this.listOfMedia = listOfMedia;
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}
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protected Set<Media> collectMedia(SpecimenOrObservationBase<?> specimenOrObservation){
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Set<Media> collectedMedia = new HashSet<>();
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Set<SpecimenDescription> descriptions = specimenOrObservation.getSpecimenDescriptionImageGallery();
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for (DescriptionBase<?> desc : descriptions){
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if (desc instanceof SpecimenDescription){
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SpecimenDescription specimenDesc = (SpecimenDescription)desc;
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for (DescriptionElementBase element : specimenDesc.getElements()){
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if (element.isInstanceOf(TextData.class)&& element.getFeature().equals(Feature.IMAGE())) {
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for (Media media :element.getMedia()){
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collectedMedia.add(media);
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}
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}
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}
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}
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}
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return collectedMedia;
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}
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private void addMediaAsDTO(Set<Media> media) {
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for(Media m : media) {
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List<MediaDTO> dtos = MediaDTO.fromEntity(m);
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getListOfMedia().addAll(dtos);
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}
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}
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/**
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* @param sob
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* The Unit to assemble the derivatives information for
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* @param maxDepth
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* The maximum number of derivation events levels up to which derivatives are to be assembled.
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* <code>NULL</code> means infinitely.
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* @param includeTypes
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* Allows for positive filtering by {@link SpecimenOrObservationType}.
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* Filter is disabled when <code>NULL</code>. This only affects the derivatives assembled in the
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* {@link #derivatives} list. The <code>unitLabelsByCollection</code> are always collected for the
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* whole bouquet of derivatives.
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* @param unitLabelsByCollection
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* A map to record the unit labels (most significant identifier + collection code) per collection.
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* Optional parameter, may be <code>NULL</code>.
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* @return
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*/
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protected Set<DerivedUnitDTO> assembleDerivatives(SpecimenOrObservationBase<?> sob,
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Integer maxDepth, EnumSet<SpecimenOrObservationType> includeTypes) {
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boolean doDescend = maxDepth == null || maxDepth > 0;
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Integer nextLevelMaxDepth = maxDepth != null ? maxDepth - 1 : null;
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Set<DerivedUnitDTO> derivateDTOs = new HashSet<>();
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// collectDerivedUnitsMaxdepth => 0 to avoid aggregation of sub ordinate
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// derivatives at each level
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Integer collectDerivedUnitsMaxdepth = 0;
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for (DerivedUnit derivedUnit : sob.collectDerivedUnits(collectDerivedUnitsMaxdepth)) {
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if(!derivedUnit.isPublish()){
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continue;
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}
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if (doDescend && (includeTypes == null || includeTypes.contains(derivedUnit.getRecordBasis()))) {
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SpecimenOrObservationBaseDTO derivedUnitDTO = SpecimenOrObservationDTOFactory.fromEntity(derivedUnit, nextLevelMaxDepth);
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if (derivedUnitDTO instanceof DerivedUnitDTO) {
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derivateDTOs.add((DerivedUnitDTO)derivedUnitDTO);
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}
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setHasCharacterData(isHasCharacterData() || derivedUnitDTO.isHasCharacterData());
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// NOTE! the flags setHasDetailImage, setHasDna, setHasSpecimenScan are also set in
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// setDerivateDataDTO(), see below
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setHasDetailImage(isHasDetailImage() || derivedUnitDTO.isHasDetailImage());
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setHasDna(isHasDna() || derivedUnitDTO.isHasDna());
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setHasSpecimenScan(isHasSpecimenScan() || derivedUnitDTO.isHasSpecimenScan());
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setHasCharacterData(isHasCharacterData() || derivedUnitDTO.isHasCharacterData());
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}
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}
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return derivateDTOs;
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}
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public TermBase getKindOfUnit() {
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return kindOfUnit;
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}
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public void setKindOfUnit(TermBase kindOfUnit) {
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this.kindOfUnit = HibernateProxyHelper.deproxy(kindOfUnit);
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}
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public DefinedTerm getSex() {
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return sex;
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}
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public void setSex(DefinedTerm sex) {
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this.sex = sex;
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}
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public DefinedTerm getLifeStage() {
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return lifeStage;
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425
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}
|
426
|
public void setLifeStage(DefinedTerm lifeStage) {
|
427
|
this.lifeStage = lifeStage;
|
428
|
}
|
429
|
|
430
|
public int getId() {
|
431
|
return id;
|
432
|
}
|
433
|
|
434
|
public String getIndividualCount() {
|
435
|
return individualCount;
|
436
|
}
|
437
|
public void setIndividualCount(String individualCount) {
|
438
|
this.individualCount = individualCount;
|
439
|
}
|
440
|
|
441
|
public List<DeterminationEventDTO> getDeterminations() {
|
442
|
return determinations;
|
443
|
}
|
444
|
|
445
|
public void setDeterminations(List<DeterminationEventDTO> determinations) {
|
446
|
this.determinations = determinations;
|
447
|
}
|
448
|
|
449
|
public Set<AnnotationDTO> getAnnotations() {
|
450
|
return annotations;
|
451
|
}
|
452
|
|
453
|
protected void addAnnotation(AnnotationDTO annotation) {
|
454
|
this.annotations.add(annotation);
|
455
|
}
|
456
|
}
|