import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
+import eu.etaxonomy.cdm.api.service.dto.DNASampleDTO;
import eu.etaxonomy.cdm.api.service.dto.DerivateDTO;
import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO;
import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.ContigFile;
private static final String SEPARATOR_STRING = ", ";
+ private static final List<String> DERIVED_UNIT_INIT_STRATEGY = Arrays.asList(new String []{
+ "derivedFrom.derivatives",
+ "derivedFrom.originals",
+ "specimenTypeDesignations.*",
+ "specimenTypeDesignations.citation.*",
+ "specimenTypeDesignations.homotypicalGroup.*",
+ "specimenTypeDesignations.typifiedNames",
+ "collection.$"
+ });
+
public OccurrenceServiceImpl() {
logger.debug("Load OccurrenceService Bean");
}
continue;
}
// collect accession numbers for citation
- String mostSignificantIdentifier = getMostSignificantIdentifier(derivedUnit);
- if (mostSignificantIdentifier != null) {
- preservedSpecimenAccessionNumbers.add(mostSignificantIdentifier);
- }
+ String identifier = getMostSignificantIdentifier(derivedUnit);
// collect collections for herbaria column
- if (derivedUnit.getCollection() != null) {
- Integer herbariumCount = collectionToCountMap.get(derivedUnit.getCollection());
+ eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
+ if (collection != null) {
+ //combine collection with identifier
+ if (identifier != null) {
+ if(collection.getCode()!=null){
+ identifier = (collection.getCode()!=null?collection.getCode():"[no collection]")+" "+identifier;
+ }
+ preservedSpecimenAccessionNumbers.add(identifier);
+ }
+
+ Integer herbariumCount = collectionToCountMap.get(collection);
if (herbariumCount == null) {
herbariumCount = 0;
}
- collectionToCountMap.put(derivedUnit.getCollection(), herbariumCount + 1);
+ collectionToCountMap.put(collection, herbariumCount + 1);
}
if (derivedUnit.getRecordBasis().equals(SpecimenOrObservationType.PreservedSpecimen)) {
PreservedSpecimenDTO preservedSpecimenDTO = assemblePreservedSpecimenDTO(derivedUnit, fieldUnitDTO);
herbariaString += SEPARATOR_STRING;
}
herbariaString = removeTail(herbariaString, SEPARATOR_STRING);
- fieldUnitDTO.setHerbarium(herbariaString);
+ fieldUnitDTO.setCollection(herbariaString);
return fieldUnitDTO;
}
specimenIdentifier = CdmFormatterFactory.format(derivedUnit, new FormatKey[] {
collectionKey, FormatKey.SPACE,
FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE });
+ if(CdmUtils.isBlank(specimenIdentifier)){
+ specimenIdentifier = derivedUnit.getTitleCache();
+ }
if(CdmUtils.isBlank(specimenIdentifier)){
specimenIdentifier = derivedUnit.getUuid().toString();
}
fieldUnitDTO.setHasType(true);
}
TypeDesignationStatusBase<?> typeStatus = specimenTypeDesignation.getTypeStatus();
- if (typeStatus != null) {
- List<String> typedTaxaNames = new ArrayList<>();
- String label = typeStatus.getLabel();
- Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();
- for (TaxonName taxonName : typifiedNames) {
- typedTaxaNames.add(taxonName.getNameCache());
- }
- preservedSpecimenDTO.addTypes(label, typedTaxaNames);
+ Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();
+ List<String> typedTaxaNames = new ArrayList<>();
+ for (TaxonName taxonName : typifiedNames) {
+ typedTaxaNames.add(taxonName.getTitleCache());
}
+ preservedSpecimenDTO.addTypes(typeStatus!=null?typeStatus.getLabel():"", typedTaxaNames);
}
// individuals associations
for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
if (!alreadyCollectedSpecimen.containsKey(specimenDto.getUuid())){
- PreservedSpecimenDTO dto = PreservedSpecimenDTO.newInstance(derivative, null);
+ PreservedSpecimenDTO dto;
+ if (derivative instanceof DnaSample) {
+ dto = new DNASampleDTO(derivative);
+ } else {
+ dto = new PreservedSpecimenDTO(derivative);
+ }
alreadyCollectedSpecimen.put(dto.getUuid(), dto);
dto.addAllDerivates(getDerivedUnitDTOsFor(dto, derivative, alreadyCollectedSpecimen));
derivedUnits.add(dto);
taxa.add(associatedTaxon);
for (Taxon taxon : taxa) {
- List<SpecimenOrObservationBase> perTaxonOccurrences = dao.listByAssociatedTaxon(null,taxon, null, null, null, null);
+ List<SpecimenOrObservationBase> perTaxonOccurrences = dao.listByAssociatedTaxon(null,taxon, null, null, null, DERIVED_UNIT_INIT_STRATEGY);
for (SpecimenOrObservationBase<?> o : perTaxonOccurrences) {
if (o.isInstanceOf(DerivedUnit.class)){
- DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(o, DerivedUnit.class);
- DerivateDTO derivedUnitDTO = PreservedSpecimenDTO.newInstance(derivedUnit, taxon.getName());
+ DerivedUnit derivedUnit;
+ DerivateDTO derivedUnitDTO;
+ if (o.isInstanceOf(DnaSample.class)) {
+ derivedUnit = HibernateProxyHelper.deproxy(o, DnaSample.class);
+ derivedUnitDTO = new DNASampleDTO(derivedUnit);
+ } else {
+ derivedUnit = HibernateProxyHelper.deproxy(o, DerivedUnit.class);
+ derivedUnitDTO = new PreservedSpecimenDTO(derivedUnit);
+ }
if (alreadyCollectedSpecimen.get(derivedUnitDTO.getUuid()) == null){
alreadyCollectedSpecimen.put(derivedUnitDTO.getUuid(), derivedUnitDTO);
}
}
-//=======
-//<<<<<<< Updated upstream
-//=======
-// @SuppressWarnings("unchecked")
-// @Override
-// public List<FieldUnitDTO> findFieldUnitDTOByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships,
-// UUID associatedTaxonUuid) {
-//
-// Set<Taxon> taxa = new HashSet<>();
-// Set<Integer> occurrenceIds = new HashSet<>();
-// List<FieldUnitDTO> fieldUnitDTOs = new ArrayList<>();
-// HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen = new HashMap<>();
-// List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
-// boolean includeUnpublished = INCLUDE_UNPUBLISHED;
-//
-// // Integer limit = PagerUtils.limitFor(pageSize);
-// // Integer start = PagerUtils.startFor(pageSize, pageNumber);
-//
-// Taxon associatedTaxon = (Taxon) taxonService.load(associatedTaxonUuid);
-//
-//
-// if (includedRelationships != null) {
-// taxa = taxonService.listRelatedTaxa(associatedTaxon, includedRelationships, null, includeUnpublished, null, null, null);
-// }
-//
-// taxa.add(associatedTaxon);
-//
-// for (Taxon taxon : taxa) {
-// List<SpecimenOrObservationBase> perTaxonOccurrences = dao.listByAssociatedTaxon(null,taxon, null, null, null, null);
-// for (SpecimenOrObservationBase<?> o : perTaxonOccurrences) {
-// if (o.isInstanceOf(DerivedUnit.class)){
-// DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(o, DerivedUnit.class);
-// DerivateDTO derivedUnitDTO;
-// //DNASampleDTO dnaDto;
-// if (derivedUnit instanceof DnaSample){
-// derivedUnitDTO = DNASampleDTO.newInstance((DnaSample)derivedUnit);
-// }else{
-// derivedUnitDTO = PreservedSpecimenDTO.newInstance(derivedUnit);
-// }
-// if (alreadyCollectedSpecimen.get(derivedUnitDTO.getUuid()) == null){
-// alreadyCollectedSpecimen.put(derivedUnitDTO.getUuid(), derivedUnitDTO);
-// }
-// derivedUnitDTO.addAllDerivates(getDerivedUnitDTOsFor(derivedUnitDTO, derivedUnit, alreadyCollectedSpecimen));
-// FieldUnitDTO dto = this.findFieldUnitDTO(derivedUnitDTO, fieldUnitDTOs, alreadyCollectedSpecimen);
-// if (dto != null){
-// dto.addTaxonRelatedDerivedUnits(derivedUnitDTO);
-// }
-// }
-// }
-//
-// }
-//
-// return fieldUnitDTOs;
-//
-// }
-//
-//>>>>>>> Stashed changes
-//>>>>>>> Stashed changes
+
+
@Override
public List<DerivedUnit> findByAccessionNumber(
String accessionNumberString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
fieldUnitDto.addDerivate(derivedUnitDTO);
fieldUnits.add(fieldUnitDto);
}else{
- DerivateDTO originalDTO = PreservedSpecimenDTO.newInstance((DerivedUnit)specimen, null);
+ DerivateDTO originalDTO;
+ if (specimen instanceof DnaSample){
+ originalDTO = new DNASampleDTO((DnaSample)specimen);
+ } else {
+ originalDTO = new PreservedSpecimenDTO((DerivedUnit)specimen);
+ }
originalDTO.addDerivate(derivedUnitDTO);
fieldUnitDto = findFieldUnitDTO(originalDTO, fieldUnits, alreadyCollectedSpecimen);
}
}
@Override
-//=======
-//<<<<<<< Updated upstream
-//=======
-//
-// public FieldUnitDTO findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits, HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen) {
-// //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
-// //from which this DerivedUnit was derived until all FieldUnits are found.
-// List<SpecimenOrObservationBase> specimens = new ArrayList<>();
-// List<String> propertyPaths = new ArrayList<>();
-// propertyPaths.add("descriptions.elements.media.title");
-//
-// specimens = dao.findOriginalsForDerivedUnit(derivedUnitDTO.getUuid(), propertyPaths);
-//
-// if (specimens.size() > 1){
-// logger.debug("The derived unit with uuid " + derivedUnitDTO.getUuid() + "has more than one orginal");
-// }
-// // for (SpecimenOrObservationBase specimen: specimens){
-// SpecimenOrObservationBase specimen = null;
-// if (specimens.size() > 0){
-// specimen = specimens.get(0);
-// }else{
-// return null;
-// }
-// FieldUnitDTO fieldUnitDto = null;
-// if (alreadyCollectedSpecimen.get(specimen.getUuid()) != null){
-// alreadyCollectedSpecimen.get(specimen.getUuid()).addDerivate(derivedUnitDTO);
-// if (specimen instanceof FieldUnit){
-// return (FieldUnitDTO)alreadyCollectedSpecimen.get(specimen.getUuid());
-// }else{
-// fieldUnitDto = findFieldUnitDTO(alreadyCollectedSpecimen.get(specimen.getUuid()), fieldUnits, alreadyCollectedSpecimen);
-// }
-//
-//// if ( alreadyCollectedSpecimen.get(specimen.getUuid()) instanceof FieldUnitDTO){
-//// ((FieldUnitDTO)alreadyCollectedSpecimen.get(specimen.getUuid())).getTaxonRelatedDerivedUnits().add(derivedUnitDTO.getUuid());
-//// }
-// }else{
-// if (specimen.isInstanceOf(FieldUnit.class)){
-// fieldUnitDto = FieldUnitDTO.newInstance((FieldUnit)specimen);
-//
-// fieldUnitDto.addPreservedSpecimenDTO((PreservedSpecimenDTO)derivedUnitDTO);
-// fieldUnits.add(fieldUnitDto);
-// }else{
-// DerivateDTO originalDTO = PreservedSpecimenDTO.newInstance((DerivedUnit)specimen);
-// originalDTO.addDerivate(derivedUnitDTO);
-// fieldUnitDto = findFieldUnitDTO(originalDTO, fieldUnits, alreadyCollectedSpecimen);
-// }
-//
-// }
-// // }
-// alreadyCollectedSpecimen.put(derivedUnitDTO.getUuid(), derivedUnitDTO);
-//
-// return fieldUnitDto;
-//
-// }
-//
-// @Override
-//>>>>>>> Stashed changes
-//>>>>>>> Stashed changes
@Transactional(readOnly = false)
public UpdateResult moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
return moveSequence(from.getUuid(), to.getUuid(), sequence.getUuid());
}
@Override
- public Pager<SpecimenOrObservationBase> findByTitle(
- IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config) {
+ public <S extends SpecimenOrObservationBase> Pager<S> findByTitle(
+ IIdentifiableEntityServiceConfigurator<S> config) {
if (config instanceof FindOccurrencesConfigurator) {
FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
}
- occurrences.addAll(dao.findOccurrences(occurrenceConfig.getClazz(),
+ List<? extends SpecimenOrObservationBase> foundOccurrences = dao.findOccurrences(occurrenceConfig.getClazz(),
occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
- occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
+ occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
+ occurrences.addAll(foundOccurrences);
occurrences = filterOccurencesByAssignmentAndHierarchy(occurrenceConfig, occurrences, taxon, taxonName);
- return new DefaultPagerImpl<>(config.getPageNumber(), occurrences.size(), config.getPageSize(), occurrences);
+ return new DefaultPagerImpl<>(config.getPageNumber(), occurrences.size(), config.getPageSize(), (List<S>)occurrences);
}
return super.findByTitle(config);
}
//filter out (un-)assigned specimens
if(taxon==null && taxonName==null){
AssignmentStatus assignmentStatus = occurrenceConfig.getAssignmentStatus();
- List<SpecimenOrObservationBase<?>> specimenWithAssociations = new ArrayList<>();
+ List<SpecimenOrObservationBase> specimenWithAssociations = new ArrayList<>();
if(!assignmentStatus.equals(AssignmentStatus.ALL_SPECIMENS)){
- for (SpecimenOrObservationBase<?> specimenOrObservationBase : occurrences) {
+ for (SpecimenOrObservationBase specimenOrObservationBase : occurrences) {
boolean includeUnpublished = true; //TODO not sure if this is correct, maybe we have to propagate publish flag to higher methods.
Collection<TaxonBase<?>> associatedTaxa = listAssociatedTaxa(specimenOrObservationBase,
includeUnpublished, null, null, null, null);
BGBM BDI Projects / cdmlib.git / blobdiff