Revision a9527b12
Added by Andreas Kohlbecker over 3 years ago
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/format/occurrences/MediaSpecimenFormatter.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.format.occurrences; |
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|
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
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import eu.etaxonomy.cdm.model.media.Media; |
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen; |
| 13 | 14 |
|
| ... | ... | |
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@Override |
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protected void initFormatKeys(Object object) {
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super.initFormatKeys(object); |
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MediaSpecimen mediaSpecimen = (MediaSpecimen)object;
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MediaSpecimen mediaSpecimen = HibernateProxyHelper.deproxy(object, MediaSpecimen.class);
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|
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Media media = mediaSpecimen.getMediaSpecimen(); |
| 29 | 30 |
if(media!=null){
|
| 30 | 31 |
if(media.getArtist()!=null){
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IOccurrenceService.java | ||
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| 689 | 689 |
List<FieldUnitDTO> findFieldUnitDTOByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships, |
| 690 | 690 |
UUID associatedTaxonUuid, List<String> propertyPaths); |
| 691 | 691 |
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FieldUnitDTO findFieldUnitDTO(SpecimenOrObservationBaseDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits,
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FieldUnitDTO findFieldUnitDTO(DerivedUnitDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits,
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HashMap<UUID, SpecimenOrObservationBaseDTO> alreadyCollectedSpecimen); |
| 694 | 694 |
|
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| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java | ||
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| 399 | 399 |
return derivedUnitDTO; |
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} |
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|
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private Set<SpecimenOrObservationBaseDTO> getDerivedUnitDTOsFor(SpecimenOrObservationBaseDTO specimenDto, DerivedUnit specimen, HashMap<UUID, SpecimenOrObservationBaseDTO> alreadyCollectedSpecimen) {
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Set<SpecimenOrObservationBaseDTO> derivedUnits = new HashSet<>();
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// load |
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private Set<DerivedUnitDTO> getDerivedUnitDTOsFor(SpecimenOrObservationBaseDTO specimenDto, DerivedUnit specimen, HashMap<UUID, SpecimenOrObservationBaseDTO> alreadyCollectedSpecimen) {
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Set<DerivedUnitDTO> derivedUnits = new HashSet<>();
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for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
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for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
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if (!alreadyCollectedSpecimen.containsKey(specimenDto.getUuid())){
|
| ... | ... | |
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for (SpecimenOrObservationBase<?> o : perTaxonOccurrences) {
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| 518 | 518 |
if (o.isInstanceOf(DerivedUnit.class)){
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| 519 | 519 |
DerivedUnit derivedUnit; |
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SpecimenOrObservationBaseDTO derivedUnitDTO;
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DerivedUnitDTO derivedUnitDTO;
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if (o.isInstanceOf(DnaSample.class)) {
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derivedUnit = HibernateProxyHelper.deproxy(o, DnaSample.class); |
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derivedUnitDTO = new DNASampleDTO(derivedUnit); |
| ... | ... | |
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List<String> propertyPaths) {
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| 549 | 549 |
|
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DnaSample dnaSample = dao.findByGeneticAccessionNumber(accessionNumberString, propertyPaths); |
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SpecimenOrObservationBaseDTO derivedUnitDTO;
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DerivedUnitDTO derivedUnitDTO;
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HashMap<UUID, SpecimenOrObservationBaseDTO> alreadyCollectedSpecimen = new HashMap<>(); |
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List<FieldUnitDTO> fieldUnitDTOs = new ArrayList<>(); |
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if (dnaSample != null){
|
| ... | ... | |
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|
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@Override |
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@Transactional(readOnly=true) |
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public FieldUnitDTO findFieldUnitDTO(SpecimenOrObservationBaseDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits,
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public FieldUnitDTO findFieldUnitDTO(DerivedUnitDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits,
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HashMap<UUID, SpecimenOrObservationBaseDTO> alreadyCollectedSpecimen) {
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//It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
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//from which this DerivedUnit was derived until all FieldUnits are found. |
| ... | ... | |
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fieldUnitDto.addDerivate(derivedUnitDTO); |
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fieldUnits.add(fieldUnitDto); |
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}else{
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SpecimenOrObservationBaseDTO originalDTO;
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DerivedUnitDTO originalDTO;
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if (specimen instanceof DnaSample){
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originalDTO = new DNASampleDTO((DnaSample)specimen); |
| 701 | 701 |
} else {
|
| ... | ... | |
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public FieldUnitDTO loadFieldUnitDTO(UUID derivedUnitUuid) {
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FieldUnitDTO fieldUnitDTO = null; |
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SpecimenOrObservationBaseDTO derivedUnitDTO = null;
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DerivedUnitDTO derivedUnitDTO = null;
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Map<UUID, SpecimenOrObservationBaseDTO> cycleDetectionMap = new HashMap<>(); |
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SpecimenOrObservationBase derivative = dao.load(derivedUnitUuid); |
| ... | ... | |
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} |
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break; |
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}else{
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// So this must be a DerivedUnitDTO |
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if (derivedUnitDTO == null){
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derivedUnitDTO = originalDTO; |
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derivedUnitDTO = (DerivedUnitDTO)originalDTO;
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} else {
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originalDTO.addDerivate(derivedUnitDTO); |
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derivedUnitDTO = originalDTO; |
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derivedUnitDTO = (DerivedUnitDTO)originalDTO;
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} |
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} |
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} |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/FieldUnitDTO.java | ||
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| 39 | 39 |
private String date; |
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private String collectionsStatistics; |
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private boolean hasType; |
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|
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private GatheringEventDTO gatheringEvent; |
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|
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public static FieldUnitDTO fromEntity(FieldUnit entity){
|
| ... | ... | |
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*/ |
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private FieldUnitDTO(FieldUnit fieldUnit, EnumSet<SpecimenOrObservationType> specimenOrObservationTypeFilter ) {
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super(fieldUnit); |
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if(specimenOrObservationTypeFilter == null) {
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specimenOrObservationTypeFilter = EnumSet.allOf(SpecimenOrObservationType.class); |
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} |
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if (fieldUnit.getGatheringEvent() != null){
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gatheringEvent = GatheringEventDTO.newInstance(fieldUnit.getGatheringEvent()); |
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} |
| ... | ... | |
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} |
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|
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public boolean isHasType() {
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boolean hasType = collectDerivatives() |
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.stream() |
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.anyMatch(derivedUnitDTO -> derivedUnitDTO.getSpecimenTypeDesignations() != null && !derivedUnitDTO.getSpecimenTypeDesignations().isEmpty()); |
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return hasType; |
| 239 | 244 |
} |
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public void setHasType(boolean hasType) {
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this.hasType = hasType; |
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} |
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|
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public GatheringEventDTO getGatheringEvent() {
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return gatheringEvent; |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/SpecimenOrObservationBaseDTO.java | ||
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| 11 | 11 |
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.HashSet; |
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import java.util.List; |
| ... | ... | |
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private String collectorsNumber; |
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private String barcode; |
| 60 | 61 |
private String preservationMethod; |
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private Set<SpecimenOrObservationBaseDTO> derivates;
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private Set<DerivedUnitDTO> derivates;
|
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|
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private Set<SpecimenTypeDesignationDTO> specimenTypeDesignations; |
| 64 | 65 |
|
| ... | ... | |
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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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} |
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// @Override |
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// public String getTitleCache() {
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// return getLabel(); |
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// } |
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|
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|
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public String getListLabel() {
|
| ... | ... | |
| 312 | 307 |
|
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|
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public Set<SpecimenOrObservationBaseDTO> getDerivates() {
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public Set<DerivedUnitDTO> getDerivates() {
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if (this.derivates == null){
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this.derivates = new HashSet<>(); |
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} |
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return derivates; |
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} |
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public void setDerivates(Set<SpecimenOrObservationBaseDTO> derivates) {
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public void setDerivates(Set<DerivedUnitDTO> derivates) {
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this.derivates = derivates; |
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} |
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public void addDerivate(SpecimenOrObservationBaseDTO derivate){
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public void addDerivate(DerivedUnitDTO derivate){
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if (this.derivates == null){
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this.derivates = new HashSet<>(); |
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} |
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this.derivates.add(derivate); |
| 328 | 326 |
} |
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public void addAllDerivates(Set<SpecimenOrObservationBaseDTO> derivates){
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public void addAllDerivates(Set<DerivedUnitDTO> derivates){
|
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if (this.derivates == null){
|
| 331 | 329 |
this.derivates = new HashSet<>(); |
| 332 | 330 |
} |
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this.derivates.addAll(derivates); |
| 334 | 332 |
} |
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|
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/** |
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* collects all derivatives from this an derivatives of 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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/** |
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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(getDerivates()); |
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if(derivates != null) {
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for(SpecimenOrObservationBaseDTO subDto : derivates) {
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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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|
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public DerivationEventDTO getDerivationEvent() {
|
| 337 | 357 |
return derivationEvent; |
| 338 | 358 |
} |
Also available in: Unified diff
ref #9252 determinig hasTypes from actual data and fixing type probelms in methods