Revision cb9801c1
Added by Katja Luther over 5 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/UnitsGatheringEvent.java | ||
|---|---|---|
| 172 | 172 |
if (latitude != 0.0) {
|
| 173 | 173 |
coordinates.setLatitude(latitude); |
| 174 | 174 |
} |
| 175 |
if (errorRadius != 0) {
|
|
| 175 |
if (errorRadius != null && errorRadius != 0) {
|
|
| 176 | 176 |
coordinates.setErrorRadius(errorRadius); |
| 177 | 177 |
} |
| 178 | 178 |
coordinates.setReferenceSystem(referenceSystem); |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImpl.java | ||
|---|---|---|
| 884 | 884 |
} |
| 885 | 885 |
|
| 886 | 886 |
/** |
| 887 |
* |
|
| 887 | 888 |
* {@inheritDoc}
|
| 888 | 889 |
*/ |
| 889 | 890 |
@Override |
| ... | ... | |
| 892 | 893 |
Query query = getSession().createQuery(queryString); |
| 893 | 894 |
query.setParameter("accessionNumberString", accessionNumberString);
|
| 894 | 895 |
@SuppressWarnings("unchecked")
|
| 895 |
List<DerivedUnit> results = query.list(); |
|
| 896 |
defaultBeanInitializer.initializeAll(results, propertyPaths); |
|
| 896 |
List<DerivedUnit> dnaSamples = query.list(); |
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| 897 |
defaultBeanInitializer.initializeAll(dnaSamples, propertyPaths); |
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| 898 |
List<DerivedUnit> results = new ArrayList<>(); |
|
| 899 |
for (DerivedUnit sample:dnaSamples){
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|
| 900 |
extractDeterminedOriginals(sample, results); |
|
| 901 |
} |
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| 902 |
|
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| 897 | 903 |
return results; |
| 898 | 904 |
} |
| 899 | 905 |
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| 906 |
/** |
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| 907 |
* @param dnaSamples |
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| 908 |
* @param results |
|
| 909 |
*/ |
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private void extractDeterminedOriginals(DerivedUnit sample, List<DerivedUnit> results) {
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|
| 911 |
|
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| 912 |
if (sample.getDeterminations() != null){
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| 913 |
results.add(sample); |
|
| 914 |
}else{
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| 915 |
extractDeterminedOriginals(sample, results); |
|
| 916 |
} |
|
| 917 |
} |
|
| 918 |
|
|
| 900 | 919 |
/** |
| 901 | 920 |
* {@inheritDoc}
|
| 902 | 921 |
*/ |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/occurrence/IOccurrenceDao.java | ||
|---|---|---|
| 407 | 407 |
|
| 408 | 408 |
/** |
| 409 | 409 |
* |
| 410 |
* Returns {@link DerivedUNit} that has the accession number
|
|
| 410 |
* Returns {@link DerivedUnit} that has the accession number and is determined to a taxon
|
|
| 411 | 411 |
* @param accessionNumber |
| 412 | 412 |
* @param propertyPaths |
| 413 | 413 |
* @return a derived unit |
| cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/DerivedUnitFacadeController.java | ||
|---|---|---|
| 109 | 109 |
ModelAndView mv = new ModelAndView(); |
| 110 | 110 |
// DerivedUnitFacade duf = newFacadeFrom(occurrenceUuid, response,Arrays.asList(new String []{
|
| 111 | 111 |
// "fieldObjectMedia", "fieldObjectMedia.title"})); |
| 112 |
SpecimenOrObservationBase sob = service.load(occurrenceUuid, Arrays.asList(new String []{"descriptions", "kindOfUnit"}));
|
|
| 112 |
SpecimenOrObservationBase sob = service.load(occurrenceUuid, Arrays.asList(new String []{"descriptions", "descriptions.descriptionElements.$", "descriptions.descriptionElements.media", "kindOfUnit","gatheringEvent.*"}));
|
|
| 113 | 113 |
FieldUnitDTO dto; |
| 114 | 114 |
if (sob instanceof FieldUnit){
|
| 115 | 115 |
dto = FieldUnitDTO.newInstance((FieldUnit)sob); |
| cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/OccurrencePortalController.java | ||
|---|---|---|
| 57 | 57 |
"derivedFrom.originals.determinations.taxon", |
| 58 | 58 |
"derivedFrom.originals.gatheringEvent.exactLocation.$", |
| 59 | 59 |
"derivedFrom.gatheringEvent.exactLocation.$", |
| 60 |
"derivationEvents.derivatives.$", |
|
| 60 | 61 |
"specimenTypeDesignations.*", |
| 61 | 62 |
"specimenTypeDesignations.citation.*", |
| 62 | 63 |
"specimenTypeDesignations.homotypicalGroup.*", |
| ... | ... | |
| 66 | 67 |
"gatheringEvent.$", |
| 67 | 68 |
"gatheringEvent.exactLocation.referenceSystem", // TODO implement auto initializer? |
| 68 | 69 |
"gatheringEvent.collectingAreas", |
| 69 |
"descriptions" |
|
| 70 |
"annotations", |
|
| 71 |
"descriptions", |
|
| 72 |
"collection.institute.$" |
|
| 70 | 73 |
}); |
| 71 | 74 |
|
| 72 | 75 |
@Autowired |
| ... | ... | |
| 125 | 128 |
if(sob instanceof DerivedUnit){
|
| 126 | 129 |
DerivedUnit derivedUnit = (DerivedUnit) sob; |
| 127 | 130 |
if(derivedUnit.isPublish()){
|
| 128 |
return service.assemblePreservedSpecimenDTO(derivedUnit); |
|
| 131 |
PreservedSpecimenDTO dto = service.assemblePreservedSpecimenDTO(derivedUnit); |
|
| 132 |
return dto; |
|
| 129 | 133 |
} |
| 130 | 134 |
} |
| 131 | 135 |
return null; |
| cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonListController.java | ||
|---|---|---|
| 294 | 294 |
config.setNamedAreas(areas); |
| 295 | 295 |
config.setDoIncludeAuthors(includeAuthors != null ? includeAuthors : Boolean.FALSE); |
| 296 | 296 |
config.setOrder(order); |
| 297 |
|
|
| 297 | 298 |
if(classificationUuid != null){
|
| 298 | 299 |
Classification classification = classificationService.find(classificationUuid); |
| 299 | 300 |
config.setClassification(classification); |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java | ||
|---|---|---|
| 506 | 506 |
herbariaString += SEPARATOR_STRING; |
| 507 | 507 |
} |
| 508 | 508 |
herbariaString = removeTail(herbariaString, SEPARATOR_STRING); |
| 509 |
fieldUnitDTO.setHerbarium(herbariaString);
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|
| 509 |
fieldUnitDTO.setCollection(herbariaString);
|
|
| 510 | 510 |
|
| 511 | 511 |
return fieldUnitDTO; |
| 512 | 512 |
} |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DNASampleDTO.java | ||
|---|---|---|
| 43 | 43 |
} |
| 44 | 44 |
this.setSequences(seqDtos); |
| 45 | 45 |
this.amplificationResults = dnaSample.getAmplificationResults(); |
| 46 |
this.dnaQuality = dnaSample.getDnaQuality();
|
|
| 46 |
this.dnaQuality = HibernateProxyHelper.deproxy(dnaSample.getDnaQuality(), DnaQuality.class);
|
|
| 47 | 47 |
} |
| 48 | 48 |
|
| 49 | 49 |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DerivateDTO.java | ||
|---|---|---|
| 81 | 81 |
setSpecimenTypeDesignations(derivedUnit.getSpecimenTypeDesignations()); |
| 82 | 82 |
} |
| 83 | 83 |
} |
| 84 |
|
|
| 85 |
|
|
| 84 | 86 |
} |
| 85 | 87 |
public String getTitleCache() {
|
| 86 | 88 |
return getLabel(); |
| ... | ... | |
| 135 | 137 |
} |
| 136 | 138 |
|
| 137 | 139 |
public void setSpecimenTypeDesignations(Set<SpecimenTypeDesignation> specimenTypeDesignations) {
|
| 138 |
this.specimenTypeDesignations = specimenTypeDesignations; |
|
| 140 |
this.specimenTypeDesignations = new HashSet(); |
|
| 141 |
for (SpecimenTypeDesignation typeDes: specimenTypeDesignations){
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|
| 142 |
this.specimenTypeDesignations.add(typeDes); |
|
| 143 |
} |
|
| 144 |
|
|
| 139 | 145 |
} |
| 140 | 146 |
|
| 141 | 147 |
|
| ... | ... | |
| 270 | 276 |
/** |
| 271 | 277 |
* @return the collection |
| 272 | 278 |
*/ |
| 273 |
public String getHerbarium() {
|
|
| 279 |
public String getCollection() {
|
|
| 274 | 280 |
if (collection != null){
|
| 275 | 281 |
return collection.getCode(); |
| 276 | 282 |
} else {
|
| ... | ... | |
| 280 | 286 |
/** |
| 281 | 287 |
* @param collection the collection to set |
| 282 | 288 |
*/ |
| 283 |
public void setHerbarium(String herbarium) {
|
|
| 289 |
public void setCollection(String herbarium) {
|
|
| 284 | 290 |
if (collection == null){
|
| 285 | 291 |
collection = new CollectionDTO(herbarium, null, null, null); |
| 286 | 292 |
}else{
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/IdentifiedEntityDTO.java | ||
|---|---|---|
| 32 | 32 |
String typeLabel; |
| 33 | 33 |
String identifier; |
| 34 | 34 |
public AlternativeIdentifier(DefinedTerm identifierType, String identifier) {
|
| 35 |
|
|
| 35 | 36 |
if (identifierType != null){
|
| 36 | 37 |
this.typeUuid = identifierType.getUuid(); |
| 37 | 38 |
this.typeLabel = identifierType.getTitleCache(); |
| 38 | 39 |
} |
| 40 |
|
|
| 39 | 41 |
this.identifier = identifier; |
| 40 | 42 |
} |
| 41 | 43 |
public UUID getTypeUuid() {return typeUuid;}
|
| ... | ... | |
| 54 | 56 |
public IdentifiedEntityDTO(DefinedTerm identifierType, String identifier, |
| 55 | 57 |
UUID entityUuid, String titleCache, String abbrevTitleCache){
|
| 56 | 58 |
super(entityUuid, titleCache, abbrevTitleCache); |
| 57 |
this.identifier = new AlternativeIdentifier(identifierType, identifier); |
|
| 59 |
if (identifier != null){
|
|
| 60 |
this.identifier = new AlternativeIdentifier(identifierType, identifier); |
|
| 61 |
} |
|
| 62 |
|
|
| 58 | 63 |
} |
| 59 | 64 |
|
| 60 | 65 |
public AlternativeIdentifier getIdentifier() {
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/PreservedSpecimenDTO.java | ||
|---|---|---|
| 18 | 18 |
import org.hibernate.envers.tools.Pair; |
| 19 | 19 |
|
| 20 | 20 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
| 21 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
|
| 21 | 22 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 22 | 23 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 23 | 24 |
|
| ... | ... | |
| 84 | 85 |
listLabel = derivedUnit.getCatalogNumber(); |
| 85 | 86 |
setCollectorsNumber(derivedUnit.getCollectorsNumber()); |
| 86 | 87 |
if (derivedUnit.getDerivedFrom() != null){
|
| 87 |
setDerivationEvent(new DerivationEventDTO(derivedUnit.getDerivedFrom() ));
|
|
| 88 |
setDerivationEvent(new DerivationEventDTO(HibernateProxyHelper.deproxy(derivedUnit.getDerivedFrom(), DerivationEvent.class )));
|
|
| 88 | 89 |
} |
| 89 | 90 |
if (derivedUnit.getPreservation()!= null){
|
| 90 | 91 |
setPreservationMethod(derivedUnit.getPreservation().getMaterialMethodText()); |
Also available in: Unified diff
ref #7755: provide all data for specimen pages