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/**
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* Copyright (C) 2017 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.vaadin.model.registration;
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import java.util.UUID;
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import org.apache.commons.collections.CollectionUtils;
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import eu.etaxonomy.cdm.api.util.DerivedUnitConversionException;
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import eu.etaxonomy.cdm.api.util.DerivedUnitConverter;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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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.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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/**
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* A DTO which is use in the context of the {@link SpecimenTypeDesignationSetDTO} which is backed up
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* <code>SpecimenTypeDesignation.typeSpecimen.derivedFrom.type</code> object graph.
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* <p>
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* The contained {@link DerivedUnit} either is a {@link MediaSpecimen} with or a {@link DerivedUnit}, depending on the
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* "kind of unit" which is defined by the associated <code>DerivationEvent.type</code>:
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*
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* <ul>
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* <li>{@link DerivationEventType#GATHERING_IN_SITU()} -> {@link DerivedUnit}</li>
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* <li>{@link DerivationEventTypes#CULTURE_METABOLIC_INACTIVE()} -> {@link DerivedUnit}</li>
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* <li>{@link DerivationEventTypes#UNPUBLISHED_IMAGE()} -> {@link MediaSpecimen}</li>
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* <li>{@link DerivationEventTypes#PUBLISHED_IMAGE()} -> {@link MediaSpecimen}</li>
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* </ul>
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*
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* @author a.kohlbecker
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* @since Jun 22, 2017
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*
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*/
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public class SpecimenTypeDesignationDTO {
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SpecimenTypeDesignation std;
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private DerivedUnit replacedTypeSpecimen;
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/**
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* @return the std
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*/
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public SpecimenTypeDesignation asSpecimenTypeDesignation() {
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return std;
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}
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public DerivedUnit replacedTypeSpecimen(){
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return replacedTypeSpecimen;
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}
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/**
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* Creates an new new instance of SpecimenTypeDesignationDTO which is backed up
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* by an newly instantiated <code>SpecimenTypeDesignation.typeSpecimen.derivedFrom.type</code> object graph.
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*/
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public SpecimenTypeDesignationDTO(){
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this(SpecimenTypeDesignation.NewInstance());
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}
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/**
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* Creates a new instance of SpecimenTypeDesignationDTO.
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*
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* The constructor assures that <code>SpecimenTypeDesignation.typeSpecimen.derivedFrom.type</code> are never null.
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* That is in case the supplied std parameter or if any of the above listed properties is null the missing instances
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* are created and added to the object graph.
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*
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* @param std
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*/
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public SpecimenTypeDesignationDTO(SpecimenTypeDesignation std) {
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this.std = std;
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if(std.getTypeSpecimen() == null){
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DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
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std.setTypeSpecimen(derivedUnit);
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}
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if(std.getTypeSpecimen().getDerivedFrom() == null){
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DerivationEvent derivedFrom = DerivationEvent.NewInstance(DerivationEventType.GATHERING_IN_SITU());
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std.getTypeSpecimen().setDerivedFrom(derivedFrom);
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}
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}
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public DefinedTerm getKindOfUnit(){
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return std.getTypeSpecimen().getKindOfUnit();
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}
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public void setKindOfUnit(DefinedTerm kindOfUnit) throws DerivedUnitConversionException{
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std.getTypeSpecimen().setKindOfUnit(kindOfUnit);
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DerivedUnit typeSpecimen = HibernateProxyHelper.deproxy(std.getTypeSpecimen());
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Class<? extends DerivedUnit> requiredSpecimenType = specimenTypeFor(kindOfUnit);
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Class<? extends DerivedUnit> currentType = typeSpecimen.getClass();
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if(!requiredSpecimenType.equals(currentType)){
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SpecimenOrObservationType convertToType = specimenOrObservationTypeFor(kindOfUnit);
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if(requiredSpecimenType.equals(MediaSpecimen.class)){
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DerivedUnitConverter<MediaSpecimen> converter = new DerivedUnitConverter<MediaSpecimen>(std);
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std = converter.convertTo((Class<MediaSpecimen>)requiredSpecimenType, convertToType);
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} else {
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if(currentType == MediaSpecimen.class){
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MediaSpecimen mediaSpecimen = (MediaSpecimen)typeSpecimen;
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// set null to allow conversion
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mediaSpecimen.setMediaSpecimen(null);
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}
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DerivedUnitConverter<DerivedUnit> converter = new DerivedUnitConverter<DerivedUnit>(std);
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std = converter.convertTo((Class<DerivedUnit>)requiredSpecimenType, convertToType);
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}
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if(typeSpecimen.getId() != 0){
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replacedTypeSpecimen = typeSpecimen;
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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 the total count of typeDesignations associated with the type specimen
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*/
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public int getAssociatedTypeDesignationCount() {
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return std.getTypeSpecimen().getSpecimenTypeDesignations().size();
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}
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/**
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* See constructor doc.
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*
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* @param kindOfUnit
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* @return
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* either <code>DerivedUnit</code> or <code>MediaSpecimen</code> never null.
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* <code>DerivedUnit</code> is the fall back return value.
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*/
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private Class<? extends DerivedUnit> specimenTypeFor(DefinedTerm derivationEventType) {
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UUID detUuid = derivationEventType.getUuid();
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if(detUuid.equals(KindOfUnitTerms.SPECIMEN().getUuid())) {
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return DerivedUnit.class;
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}
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if(detUuid.equals(KindOfUnitTerms.CULTURE_METABOLIC_INACTIVE().getUuid())) {
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return DerivedUnit.class;
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}
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if(detUuid.equals(KindOfUnitTerms.PUBLISHED_IMAGE().getUuid())) {
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return MediaSpecimen.class;
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}
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if(detUuid.equals(KindOfUnitTerms.UNPUBLISHED_IMAGE().getUuid())) {
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return MediaSpecimen.class;
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}
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return DerivedUnit.class;
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}
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private SpecimenOrObservationType specimenOrObservationTypeFor(DefinedTerm derivationEventType) {
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UUID detUuid = derivationEventType.getUuid();
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if(detUuid.equals(KindOfUnitTerms.SPECIMEN().getUuid())) {
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return SpecimenOrObservationType.PreservedSpecimen;
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}
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if(detUuid.equals(KindOfUnitTerms.CULTURE_METABOLIC_INACTIVE().getUuid())) {
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return SpecimenOrObservationType.LivingSpecimen;
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}
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if(detUuid.equals(KindOfUnitTerms.PUBLISHED_IMAGE().getUuid())) {
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return SpecimenOrObservationType.StillImage;
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}
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if(detUuid.equals(KindOfUnitTerms.UNPUBLISHED_IMAGE().getUuid())) {
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return SpecimenOrObservationType.StillImage;
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}
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return SpecimenOrObservationType.PreservedSpecimen;
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}
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public SpecimenTypeDesignationStatus getTypeStatus(){
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return HibernateProxyHelper.deproxy(std.getTypeStatus(), SpecimenTypeDesignationStatus.class);
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}
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public void setTypeStatus(SpecimenTypeDesignationStatus typeStatus){
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std.setTypeStatus(typeStatus);
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}
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public Collection getCollection(){
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return std.getTypeSpecimen().getCollection();
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}
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public void setCollection(Collection collection){
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std.getTypeSpecimen().setCollection(collection);
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}
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public String getAccessionNumber(){
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return std.getTypeSpecimen().getAccessionNumber();
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}
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public void setAccessionNumber(String accessionNumber){
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std.getTypeSpecimen().setAccessionNumber(accessionNumber);
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}
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public URI getPreferredStableUri(){
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return std.getTypeSpecimen().getPreferredStableUri();
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}
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public void setPreferredStableUri(URI uri){
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std.getTypeSpecimen().setPreferredStableUri(uri);
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}
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public Reference getDesignationReference() {
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return std.getCitation();
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}
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public void setDesignationReference(Reference citation) {
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std.setCitation(citation);
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}
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public String getDesignationReferenceDetail() {
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return std.getCitationMicroReference();
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}
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public void setDesignationReferenceDetail(String detail) {
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std.setCitationMicroReference(detail);
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}
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public URI getMediaUri(){
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if(checkMediaSpecimen()){
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MediaRepresentationPart part = findMediaRepresentationPart();
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if(part != null){
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return part.getUri();
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}
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}
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return null;
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}
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public void setMediaUri(URI mediaUri){
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if(checkMediaSpecimen()){
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MediaRepresentationPart part = findOrMakeMediaRepresentationPart();
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part.setUri(mediaUri);
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}
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}
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public Reference getMediaSpecimenReference(){
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if(checkMediaSpecimen()){
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IdentifiableSource source = findMediaSpecimenIdentifieableSource();
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if(source != null){
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return source.getCitation();
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}
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}
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return null;
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}
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public void setMediaSpecimenReference(Reference reference){
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if(checkMediaSpecimen()){
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IdentifiableSource source = findOrMakeMediaSpecimenIdentifieableSource();
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source.setCitation(reference);
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}
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}
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public String getMediaSpecimenReferenceDetail(){
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if(checkMediaSpecimen()){
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IdentifiableSource source = findMediaSpecimenIdentifieableSource();
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if(source != null){
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return source.getCitationMicroReference();
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}
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}
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return null;
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}
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public void setMediaSpecimenReferenceDetail(String referenceDetail){
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if(checkMediaSpecimen()){
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IdentifiableSource source = findOrMakeMediaSpecimenIdentifieableSource();
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source.setCitationMicroReference(referenceDetail);
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}
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}
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/**
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* @return
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*/
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private IdentifiableSource findMediaSpecimenIdentifieableSource() {
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IdentifiableSource source = null;
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Media media = findMediaSpecimen().getMediaSpecimen();
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if(media != null){
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// FIXME use marker type to tag the MediaSpecimenReference and make sure that there is always only one.
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if(!CollectionUtils.isEmpty(media.getSources())){
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source = media.getSources().iterator().next();
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}
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}
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return source;
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}
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/**
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*
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*/
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private MediaRepresentationPart findMediaRepresentationPart() {
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Media media = findMediaSpecimen().getMediaSpecimen();
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if(media != null){
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if(!CollectionUtils.isEmpty(media.getRepresentations())){
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MediaRepresentation repr = media.getRepresentations().iterator().next();
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if(!CollectionUtils.isEmpty(repr.getParts())) {
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MediaRepresentationPart part = repr.getParts().iterator().next();
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return part;
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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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private MediaRepresentationPart findOrMakeMediaRepresentationPart() {
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if(findMediaSpecimen().getMediaSpecimen() == null){
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findMediaSpecimen().setMediaSpecimen(Media.NewInstance());
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}
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Media media = findMediaSpecimen().getMediaSpecimen();
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if(CollectionUtils.isEmpty(media.getRepresentations())){
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media.addRepresentation(MediaRepresentation.NewInstance());
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}
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MediaRepresentation repr = media.getRepresentations().iterator().next();
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if(CollectionUtils.isEmpty(repr.getParts())) {
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repr.addRepresentationPart(MediaRepresentationPart.NewInstance(null, null));
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}
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MediaRepresentationPart part = repr.getParts().iterator().next();
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return part;
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}
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/**
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* @return
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*/
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private IdentifiableSource findOrMakeMediaSpecimenIdentifieableSource() {
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IdentifiableSource source ;
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Media media = findMediaSpecimen().getMediaSpecimen();
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if(media == null){
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media = Media.NewInstance();
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findMediaSpecimen().setMediaSpecimen(Media.NewInstance());
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}
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if(CollectionUtils.isEmpty(media.getSources())){
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source = IdentifiableSource.NewPrimaryMediaSourceInstance(null, null);
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media.addSource(source);
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} else {
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source = media.getSources().iterator().next();
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}
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return source;
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}
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/**
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* @return
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*/
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public boolean checkMediaSpecimen() {
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return findMediaSpecimen() != null;
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}
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/**
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* @return
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*/
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private MediaSpecimen findMediaSpecimen() {
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DerivedUnit sp = HibernateProxyHelper.deproxy(std.getTypeSpecimen());
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if(MediaSpecimen.class.isAssignableFrom(sp.getClass())){
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return (MediaSpecimen) sp;
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}
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return null;
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}
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}
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