-// $Id$
/**
* Copyright (C) 2007 EDIT
* European Distributed Institute of Taxonomy
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.UUID;
import org.apache.log4j.Logger;
-import org.apache.lucene.index.CorruptIndexException;
import org.apache.lucene.queryparser.classic.ParseException;
import org.apache.lucene.search.BooleanClause.Occur;
import org.apache.lucene.search.BooleanQuery.Builder;
import eu.etaxonomy.cdm.api.service.UpdateResult.Status;
import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
+import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator.AssignmentStatus;
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
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;
+import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.Link;
import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.MolecularData;
import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
+import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
import eu.etaxonomy.cdm.api.service.search.QueryFactory;
import eu.etaxonomy.cdm.api.service.search.SearchResult;
import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
+import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
+import eu.etaxonomy.cdm.format.CdmFormatterFactory;
+import eu.etaxonomy.cdm.format.ICdmFormatter.FormatKey;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.CdmBaseType;
import eu.etaxonomy.cdm.model.agent.AgentBase;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
+import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
/**
* @author a.babadshanjan
@Autowired
private INameService nameService;
+ @Autowired
+ private IEventBaseService eventService;
+
@Autowired
private ITaxonService taxonService;
@Override
public List<Country> getCountryByName(String name) {
List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null);
- List<Country> countries = new ArrayList<Country>();
+ List<Country> countries = new ArrayList<>();
for (int i = 0; i < terms.size(); i++) {
countries.add((Country) terms.get(i));
}
public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = dao.countDerivationEvents(occurence);
- List<DerivationEvent> results = new ArrayList<DerivationEvent>();
+ List<DerivationEvent> results = new ArrayList<>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
results = dao.getDerivationEvents(occurence, pageSize, pageNumber, propertyPaths);
}
public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
- List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
+ List<DeterminationEvent> results = new ArrayList<>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
results = dao.getDeterminations(occurrence, taxonBase, pageSize, pageNumber, propertyPaths);
}
public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = dao.countMedia(occurence);
- List<Media> results = new ArrayList<Media>();
+ List<Media> results = new ArrayList<>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
}
@Override
public Pager<Media> getMediainHierarchy(SpecimenOrObservationBase rootOccurence, Integer pageSize,
Integer pageNumber, List<String> propertyPaths) {
- List<Media> media = new ArrayList<Media>();
+ List<Media> media = new ArrayList<>();
//media specimens
if(rootOccurence.isInstanceOf(MediaSpecimen.class)){
MediaSpecimen mediaSpecimen = HibernateProxyHelper.deproxy(rootOccurence, MediaSpecimen.class);
Set<Sequence> sequences = dnaSample.getSequences();
//we do show only those gelPhotos which lead to a consensus sequence
for (Sequence sequence : sequences) {
- Set<Media> dnaRelatedMedia = new HashSet<Media>();
+ Set<Media> dnaRelatedMedia = new HashSet<>();
for (SingleRead singleRead : sequence.getSingleReads()){
AmplificationResult amplification = singleRead.getAmplificationResult();
dnaRelatedMedia.add(amplification.getGelPhoto());
}
@Override
- public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonNameBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+ public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
Integer numberOfResults = dao.count(type, determinedAs);
- List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
+ List<SpecimenOrObservationBase> results = new ArrayList<>();
pageNumber = pageNumber == null ? 0 : pageNumber;
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
Integer start = pageSize == null ? 0 : pageSize * pageNumber;
@Override
public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
Integer numberOfResults = dao.count(type, determinedAs);
- List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
+ List<SpecimenOrObservationBase> results = new ArrayList<>();
pageNumber = pageNumber == null ? 0 : pageNumber;
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
Integer start = pageSize == null ? 0 : pageSize * pageNumber;
}
@Override
- public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
- return dao.getDerivedUnitUuidAndTitleCache();
+ public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {
+ return dao.getDerivedUnitUuidAndTitleCache(limit, pattern);
}
@Override
public List<DerivedUnitFacade> listDerivedUnitFacades(
DescriptionBase description, List<String> propertyPaths) {
- List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
+ List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<>();
IndividualsAssociation tempIndividualsAssociation;
SpecimenOrObservationBase tempSpecimenOrObservationBase;
- List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
- for (DescriptionElementBase element : elements) {
- if (element.isInstanceOf(IndividualsAssociation.class)) {
- tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
- if (tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null) {
- tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
- if (tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)) {
- try {
- derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
- } catch (DerivedUnitFacadeNotSupportedException e) {
- logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " + e.getMessage());
- }
+ List<IndividualsAssociation> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
+ for (IndividualsAssociation element : elements) {
+ tempIndividualsAssociation = HibernateProxyHelper.deproxy(element, IndividualsAssociation.class);
+ if (tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null) {
+ tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
+ if (tempSpecimenOrObservationBase.isInstanceOf(DerivedUnit.class)) {
+ try {
+ derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance(HibernateProxyHelper.deproxy(tempSpecimenOrObservationBase, DerivedUnit.class)));
+ } catch (DerivedUnitFacadeNotSupportedException e) {
+ logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " + e.getMessage());
}
}
-
}
}
}
// gather the IDs of all relevant field units
- Set<Integer> fieldUnitIds = new HashSet<Integer>();
+ Set<UUID> fieldUnitUuids = new HashSet<>();
List<SpecimenOrObservationBase> records = listByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, null, null, orderHints, propertyPaths);
for (SpecimenOrObservationBase<?> specimen : records) {
for (FieldUnit fieldUnit : getFieldUnits(specimen.getUuid())) {
- fieldUnitIds.add(fieldUnit.getId());
+ fieldUnitUuids.add(fieldUnit.getUuid());
}
}
- //dao.listByIds() does the paging of the field units. Passing the field units directly to the Pager would not work
- List<SpecimenOrObservationBase> fieldUnits = dao.listByIds(fieldUnitIds, pageSize, pageNumber, orderHints, propertyPaths);
- return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, fieldUnitIds.size(), pageSize, fieldUnits);
+ //dao.list() does the paging of the field units. Passing the field units directly to the Pager would not work
+ List<SpecimenOrObservationBase> fieldUnits = dao.list(fieldUnitUuids, pageSize, pageNumber, orderHints, propertyPaths);
+ return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, fieldUnitUuids.size(), pageSize, fieldUnits);
}
@Override
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
// Country
NamedArea country = gatheringEvent.getCountry();
- fieldUnitDTO.setCountry(country != null ? country.getDescription() : null);
+ fieldUnitDTO.setCountry(country != null ? country.getLabel() : null);
// Collection
AgentBase collector = gatheringEvent.getCollector();
String fieldNumber = fieldUnit.getFieldNumber();
Partial gatheringDate = gatheringEvent.getGatheringDate();
String dateString = null;
if (gatheringDate != null) {
- gatheringDate.toString();
+ dateString = gatheringDate.toString();
}
else if(gatheringEvent.getTimeperiod()!=null && gatheringEvent.getTimeperiod().getFreeText()!=null){
dateString = gatheringEvent.getTimeperiod().getFreeText();
fieldUnitDTO.setTaxonName(associatedTaxon.getName().getTitleCache());
// Herbaria map
- Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
+ Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<>();
// List of accession numbers for citation
- List<String> preservedSpecimenAccessionNumbers = new ArrayList<String>();
+ List<String> preservedSpecimenAccessionNumbers = new ArrayList<>();
// assemble preserved specimen DTOs
Set<DerivationEvent> derivationEvents = fieldUnit.getDerivationEvents();
// assemble citation
String citation = fieldUnit.getTitleCache();
+ if((CdmUtils.isBlank(citation) || citation.equals(IdentifiableEntityDefaultCacheStrategy.TITLE_CACHE_GENERATION_NOT_IMPLEMENTED))
+ && !fieldUnit.isProtectedTitleCache()){
+ fieldUnit.setTitleCache(null);
+ citation = fieldUnit.getTitleCache();
+ }
if (!preservedSpecimenAccessionNumbers.isEmpty()) {
citation += " (";
for (String accessionNumber : preservedSpecimenAccessionNumbers) {
}
PreservedSpecimenDTO preservedSpecimenDTO = new PreservedSpecimenDTO();
- // check identifiers in priority order accNo>barCode>catalogNumber
- if (derivedUnit.getAccessionNumber() != null && !derivedUnit.getAccessionNumber().isEmpty()) {
- preservedSpecimenDTO.setAccessionNumber(derivedUnit.getAccessionNumber());
+ //specimen identifier
+ FormatKey collectionKey = FormatKey.COLLECTION_CODE;
+ String specimenIdentifier = CdmFormatterFactory.format(derivedUnit, collectionKey);
+ if (CdmUtils.isBlank(specimenIdentifier)) {
+ collectionKey = FormatKey.COLLECTION_NAME;
}
- else if(derivedUnit.getBarcode()!=null && !derivedUnit.getBarcode().isEmpty()){
- preservedSpecimenDTO.setAccessionNumber(derivedUnit.getBarcode());
- }
- else if(derivedUnit.getCatalogNumber()!=null && !derivedUnit.getCatalogNumber().isEmpty()){
- preservedSpecimenDTO.setAccessionNumber(derivedUnit.getCatalogNumber());
+ specimenIdentifier = CdmFormatterFactory.format(derivedUnit, new FormatKey[] {
+ collectionKey, FormatKey.SPACE,
+ FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE });
+ if(CdmUtils.isBlank(specimenIdentifier)){
+ specimenIdentifier = derivedUnit.getUuid().toString();
}
+ preservedSpecimenDTO.setAccessionNumber(specimenIdentifier);
preservedSpecimenDTO.setUuid(derivedUnit.getUuid().toString());
+ //preferred stable URI
+ preservedSpecimenDTO.setPreferredStableUri(derivedUnit.getPreferredStableUri());
+
// citation
Collection<FieldUnit> fieldUnits = getFieldUnits(derivedUnit);
if (fieldUnits.size() == 1) {
}
for (DescriptionElementBase descriptionElementBase : characterDataForSpecimen) {
String character = descriptionElementBase.getFeature().getLabel();
- ArrayList<Language> languages = new ArrayList<Language>(Collections.singleton(Language.DEFAULT()));
+ ArrayList<Language> languages = new ArrayList<>(Collections.singleton(Language.DEFAULT()));
if (descriptionElementBase instanceof QuantitativeData) {
QuantitativeData quantitativeData = (QuantitativeData) descriptionElementBase;
DefaultQuantitativeDescriptionBuilder builder = new DefaultQuantitativeDescriptionBuilder();
}
TypeDesignationStatusBase<?> typeStatus = specimenTypeDesignation.getTypeStatus();
if (typeStatus != null) {
- List<String> typedTaxaNames = new ArrayList<String>();
+ List<String> typedTaxaNames = new ArrayList<>();
String label = typeStatus.getLabel();
- Set<TaxonNameBase> typifiedNames = specimenTypeDesignation.getTypifiedNames();
- for (TaxonNameBase taxonNameBase : typifiedNames) {
- typedTaxaNames.add(taxonNameBase.getFullTitleCache());
+ Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();
+ for (TaxonName taxonName : typifiedNames) {
+ typedTaxaNames.add(taxonName.getFullTitleCache());
}
preservedSpecimenDTO.addTypes(label, typedTaxaNames);
}
if (individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)) {
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
Taxon taxon = taxonDescription.getTaxon();
- if (taxon != null && taxon.getName() != null) {
- preservedSpecimenDTO.addAssociatedTaxon(taxon.getName().getTitleCache());
+ if (taxon != null) {
+ preservedSpecimenDTO.addAssociatedTaxon(taxon);
}
}
}
logger.error("Could not create BOLD URI", e1);
}
final DefinedTerm dnaMarker = sequence.getDnaMarker();
- MolecularData molecularData = derivateDataDTO.addProviderLink(boldUri != null ? boldUri : null, dnaMarker != null ? dnaMarker.getLabel() : "[no marker]");
+ Link providerLink = null;
+ if(boldUri!=null && dnaMarker!=null){
+ providerLink = new DerivateDataDTO.Link(boldUri, dnaMarker.getLabel());
+ }
+ MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
//contig file
ContigFile contigFile = null;
if (sequence.getContigFile() != null) {
MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
if (contigMediaRepresentationPart != null) {
- contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
+ contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
}
}
- if(contigFile==null){
- contigFile = molecularData.addContigFile(null, "[no contig]");
+ else{
+ contigFile = molecularData.addContigFile(null);
}
// primer files
if (sequence.getSingleReads() != null) {
else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
- String mediaUriString = getMediaUriString(media);
+ URI mediaUri = getMediaUri(media);
if (media.getKindOfUnit() != null) {
// specimen scan
- if (media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))) {
+ if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
derivateDTO.setHasSpecimenScan(true);
String imageLinkText = "scan";
if (derivateDTO instanceof PreservedSpecimenDTO && ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber() != null) {
imageLinkText = ((PreservedSpecimenDTO) derivateDTO).getAccessionNumber();
}
- derivateDataDTO.addSpecimenScan(mediaUriString == null ? "" : mediaUriString, imageLinkText);
+ derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText);
}
// detail image
- else if (media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))) {
+ else if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
derivateDTO.setHasDetailImage(true);
- String motif = "";
- if (media.getMediaSpecimen() != null && media.getMediaSpecimen().getTitle() != null) {
- motif = media.getMediaSpecimen().getTitle().getText();
+ String motif = "detail image";
+ if (media.getMediaSpecimen()!=null){
+ if(CdmUtils.isNotBlank(media.getMediaSpecimen().getTitleCache())) {
+ motif = media.getMediaSpecimen().getTitleCache();
+ }
}
- derivateDataDTO.addDetailImage(mediaUriString == null ? "" : mediaUriString, motif != null ? motif : "[no motif]");
+ derivateDataDTO.addDetailImage(mediaUri, motif);
}
}
}
return string;
}
- private String getMediaUriString(MediaSpecimen mediaSpecimen) {
- String mediaUri = null;
+ private URI getMediaUri(MediaSpecimen mediaSpecimen) {
+ URI mediaUri = null;
Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
if (part.getUri() != null) {
- mediaUri = part.getUri().toASCIIString();
+ mediaUri = part.getUri();
}
}
}
}
private Collection<DerivedUnit> getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen) {
- Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
+ Collection<DerivedUnit> derivedUnits = new ArrayList<>();
for (DerivationEvent derivationEvent : specimen.getDerivationEvents()) {
for (DerivedUnit derivative : derivationEvent.getDerivatives()) {
derivedUnits.add(derivative);
public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
- Set<Taxon> taxa = new HashSet<Taxon>();
- Set<Integer> occurrenceIds = new HashSet<Integer>();
- List<T> occurrences = new ArrayList<T>();
+ Set<Taxon> taxa = new HashSet<>();
+ Set<Integer> occurrenceIds = new HashSet<>();
+ List<T> occurrences = new ArrayList<>();
// Integer limit = PagerUtils.limitFor(pageSize);
// Integer start = PagerUtils.startFor(pageSize, pageNumber);
occurrenceIds.add(o.getId());
}
}
- occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
+ occurrences = (List<T>) dao.loadList(occurrenceIds, propertyPaths);
return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
- List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
+ List<String> propertyPaths) throws IOException, LuceneParseException {
LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
// --- execute search
- TopGroups<BytesRef> topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
+ TopGroups<BytesRef> topDocsResultSet;
+ try {
+ topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
+ } catch (ParseException e) {
+ LuceneParseException parseException = new LuceneParseException(e.getMessage());
+ parseException.setStackTrace(e.getStackTrace());
+ throw parseException;
+ }
- Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
+ Map<CdmBaseType, String> idFieldMap = new HashMap<>();
idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
// --- initialize taxa, highlight matches ....
// FIXME: use HQL queries to increase performance
SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
// specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
- Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
+ Collection<FieldUnit> fieldUnits = new ArrayList<>();
if (specimen.isInstanceOf(FieldUnit.class)) {
fieldUnits.add(HibernateProxyHelper.deproxy(specimen, FieldUnit.class));
}
private Collection<FieldUnit> getFieldUnits(DerivedUnit derivedUnit) {
- Collection<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
+ Collection<FieldUnit> fieldUnits = new HashSet<>();
Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
if (originals != null && !originals.isEmpty()) {
for (SpecimenOrObservationBase<?> original : originals) {
---types TERM
-preservationMethod
--medium TERM
- -storedUnder CDM TaxonNameBase
+ -storedUnder CDM TaxonName
*/
- Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
+ Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<>();
//Choose the correct entry point to traverse the graph (FieldUnit or DerivedUnit)
private Collection<ICdmBase> getSpecimenOrObservationNonCascadedAssociatedElements(
SpecimenOrObservationBase<?> specimen) {
- Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<ICdmBase>();
+ Collection<ICdmBase> nonCascadedCdmEntities = new HashSet<>();
// scan SpecimenOrObservationBase
for (DeterminationEvent determinationEvent : specimen.getDeterminations()) {
// modifier
}
@Override
- public DeleteResult isDeletable(SpecimenOrObservationBase specimen, DeleteConfiguratorBase config) {
+ public DeleteResult isDeletable(UUID specimenUuid, DeleteConfiguratorBase config) {
DeleteResult deleteResult = new DeleteResult();
+ SpecimenOrObservationBase specimen = this.load(specimenUuid);
SpecimenDeleteConfigurator specimenDeleteConfigurator = (SpecimenDeleteConfigurator) config;
// check elements found by super method
- Set<CdmBase> relatedObjects = super.isDeletable(specimen, config).getRelatedObjects();
+ Set<CdmBase> relatedObjects = super.isDeletable(specimenUuid, config).getRelatedObjects();
for (CdmBase cdmBase : relatedObjects) {
// check for type designation
if (cdmBase.isInstanceOf(SpecimenTypeDesignation.class) && !specimenDeleteConfigurator.isDeleteFromTypeDesignation()) {
deleteResult.setAbort();
- deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is a type specimen."));
+ deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is a type specimen."));
deleteResult.addRelatedObject(cdmBase);
break;
}
// check for IndividualsAssociations
else if (cdmBase.isInstanceOf(IndividualsAssociation.class) && !specimenDeleteConfigurator.isDeleteFromIndividualsAssociation()) {
deleteResult.setAbort();
- deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still associated via IndividualsAssociations"));
+ deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is still associated via IndividualsAssociations"));
deleteResult.addRelatedObject(cdmBase);
break;
}
- // check for specimen/taxon description
- else if((cdmBase.isInstanceOf(SpecimenDescription.class) || cdmBase.isInstanceOf(TaxonDescription.class))
+ // check for taxon description
+ else if(cdmBase.isInstanceOf(TaxonDescription.class)
+ && HibernateProxyHelper.deproxy(cdmBase, TaxonDescription.class).getDescribedSpecimenOrObservation().equals(specimen)
&& !specimenDeleteConfigurator.isDeleteFromDescription()){
deleteResult.setAbort();
- deleteResult.addException(new ReferencedObjectUndeletableException("Specimen is still used in a Description."));
+ deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation is still used as \"Described Specimen\" in a taxon description."));
deleteResult.addRelatedObject(cdmBase);
break;
}
if(!specimenDeleteConfigurator.isDeleteChildren()){
//if children should not be deleted then it is undeletable
deleteResult.setAbort();
- deleteResult.addException(new ReferencedObjectUndeletableException("Derivative still has child derivatives."));
+ deleteResult.addException(new ReferencedObjectUndeletableException("Specimen or obeservation still has child derivatives."));
deleteResult.addRelatedObject(cdmBase);
break;
}
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
DeleteResult childResult = new DeleteResult();
for (DerivedUnit derivedUnit : derivatives) {
- childResult.includeResult(isDeletable(derivedUnit, specimenDeleteConfigurator));
+ childResult.includeResult(isDeletable(derivedUnit.getUuid(), specimenDeleteConfigurator));
}
if (!childResult.isOk()) {
deleteResult.setAbort();
}
}
// check for amplification
- else if (cdmBase.isInstanceOf(AmplificationResult.class) && !specimenDeleteConfigurator.isDeleteMolecularData()) {
+ else if (cdmBase.isInstanceOf(AmplificationResult.class)
+ && !specimenDeleteConfigurator.isDeleteMolecularData()
+ && !specimenDeleteConfigurator.isDeleteChildren()) {
deleteResult.setAbort();
deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in amplification results."));
deleteResult.addRelatedObject(cdmBase);
break;
}
// check for sequence
- else if (cdmBase.isInstanceOf(Sequence.class) && !specimenDeleteConfigurator.isDeleteMolecularData()) {
+ else if (cdmBase.isInstanceOf(Sequence.class)
+ && !specimenDeleteConfigurator.isDeleteMolecularData()
+ && !specimenDeleteConfigurator.isDeleteChildren()) {
deleteResult.setAbort();
deleteResult.addException(new ReferencedObjectUndeletableException("DnaSample is used in sequences."));
deleteResult.addRelatedObject(cdmBase);
/**
* {@inheritDoc}
*/
+ @Transactional(readOnly = false)
@Override
public DeleteResult delete(UUID specimenUuid, SpecimenDeleteConfigurator config) {
return delete(load(specimenUuid), config);
}
+
+ @Transactional(readOnly = false)
@Override
public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config) {
specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
+ DeleteResult deleteResult = isDeletable(specimen.getUuid(), config);
+ if (!deleteResult.isOk()) {
+ return deleteResult;
+ }
+
if (config.isDeleteChildren()) {
Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
//clone to avoid concurrent modification
//can happen if the child is deleted and deleted its own derivedFrom event
- Set<DerivationEvent> derivationEventsClone = new HashSet<DerivationEvent>(derivationEvents);
+ Set<DerivationEvent> derivationEventsClone = new HashSet<>(derivationEvents);
for (DerivationEvent derivationEvent : derivationEventsClone) {
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
- for (DerivedUnit derivedUnit : derivatives) {
- delete(derivedUnit, config);
+ Iterator<DerivedUnit> it = derivatives.iterator();
+ Set<DerivedUnit> derivativesToDelete = new HashSet<>();
+ while (it.hasNext()) {
+ DerivedUnit unit = it.next();
+ derivativesToDelete.add(unit);
+ }
+ for (DerivedUnit unit:derivativesToDelete){
+ deleteResult.includeResult(delete(unit, config));
}
}
}
- DeleteResult deleteResult = isDeletable(specimen, config);
- if (!deleteResult.isOk()) {
- return deleteResult;
- }
+
+
// check related objects
Set<CdmBase> relatedObjects = deleteResult.getRelatedObjects();
if (relatedObject.isInstanceOf(SpecimenTypeDesignation.class)) {
SpecimenTypeDesignation designation = HibernateProxyHelper.deproxy(relatedObject, SpecimenTypeDesignation.class);
designation.setTypeSpecimen(null);
- List<TaxonNameBase> typifiedNames = new ArrayList<TaxonNameBase>();
+ List<TaxonName> typifiedNames = new ArrayList<>();
typifiedNames.addAll(designation.getTypifiedNames());
- for (TaxonNameBase taxonNameBase : typifiedNames) {
- taxonNameBase.removeTypeDesignation(designation);
+ for (TaxonName taxonName : typifiedNames) {
+ taxonName.removeTypeDesignation(designation);
}
}
// delete IndividualsAssociation
association.setAssociatedSpecimenOrObservation(null);
association.getInDescription().removeElement(association);
}
- // check for taxon description
+ // check for "described specimen" (deprecated)
if (relatedObject.isInstanceOf(TaxonDescription.class)) {
- TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
- taxonDescription.setDescribedSpecimenOrObservation(null);
+ TaxonDescription description = HibernateProxyHelper.deproxy(relatedObject, TaxonDescription.class);
+ description.setDescribedSpecimenOrObservation(null);
}
// check for specimen description
if (relatedObject.isInstanceOf(SpecimenDescription.class)) {
SpecimenDescription specimenDescription = HibernateProxyHelper.deproxy(relatedObject, SpecimenDescription.class);
- // check if specimen is "described" specimen
- if (specimenDescription.getDescribedSpecimenOrObservation().equals(specimen)) {
- specimenDescription.setDescribedSpecimenOrObservation(null);
- }
+ specimenDescription.setDescribedSpecimenOrObservation(null);
// check if description is a description of the given specimen
if (specimen.getDescriptions().contains(specimenDescription)) {
specimen.removeDescription(specimenDescription);
}
- DeleteResult descriptionDelete = descriptionService.isDeletable(specimenDescription, null);
+ DeleteResult descriptionDelete = descriptionService.isDeletable(specimenDescription.getUuid(), null);
if (descriptionDelete.isOk()){
descriptionService.delete(specimenDescription);
}
specimenOrObservationBase.removeDerivationEvent(derivationEvent);
deleteResult.addUpdatedObject(specimenOrObservationBase);
}
+ // if derivationEvent has no derivates anymore, delete it
+ eventService.delete(derivationEvent);
}
}
else{
}
}
}
+ if (specimen instanceof FieldUnit){
+ FieldUnit fieldUnit = HibernateProxyHelper.deproxy(specimen, FieldUnit.class);
+ GatheringEvent event = fieldUnit.getGatheringEvent();
+ fieldUnit.setGatheringEvent(null);
+ if (event != null){
+ DeleteResult result = eventService.isDeletable(event.getUuid(), null);
+ if (result.isOk()){
+ eventService.delete(event);
+ }
+ }
+ }
deleteResult.includeResult(delete(specimen));
+
return deleteResult;
}
return dao.listIndividualsAssociations(specimen, null, null, null, null);
}
- /**
- * {@inheritDoc}
- */
@Override
public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start,
List<OrderHint> orderHints, List<String> propertyPaths) {
- Collection<TaxonBase<?>> associatedTaxa = new HashSet<TaxonBase<?>>();
+ Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
//individuals associations
- for (IndividualsAssociation individualsAssociation : listIndividualsAssociations(specimen, limit, start, orderHints, propertyPaths)) {
- if(individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)){
- TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
- if(taxonDescription.getTaxon()!=null){
- associatedTaxa.add(taxonDescription.getTaxon());
- }
- }
- }
+ associatedTaxa.addAll(listIndividualsAssociationTaxa(specimen, limit, start, orderHints, propertyPaths));
//type designation
- Collection<SpecimenTypeDesignation> typeDesignations = new HashSet<SpecimenTypeDesignation>();
- for (SpecimenTypeDesignation typeDesignation : listTypeDesignations(specimen, limit, start, orderHints, propertyPaths)) {
- if(typeDesignation.getTypeSpecimen().equals(specimen)){
- Set<TaxonNameBase> typifiedNames = typeDesignation.getTypifiedNames();
- for (TaxonNameBase taxonNameBase : typifiedNames) {
- associatedTaxa.addAll(taxonNameBase.getTaxa());
- }
- }
+ if(specimen.isInstanceOf(DerivedUnit.class)){
+ associatedTaxa.addAll(listTypeDesignationTaxa(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class), limit, start, orderHints, propertyPaths));
}
//determinations
- Collection<DeterminationEvent> determinationEvents = new HashSet<DeterminationEvent>();
+ associatedTaxa.addAll(listDeterminedTaxa(specimen, limit, start, orderHints, propertyPaths));
+
+ return associatedTaxa;
+ }
+
+
+ @Override
+ public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start,
+ List<OrderHint> orderHints, List<String> propertyPaths) {
+ Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
for (DeterminationEvent determinationEvent : listDeterminationEvents(specimen, limit, start, orderHints, propertyPaths)) {
if(determinationEvent.getIdentifiedUnit().equals(specimen)){
if(determinationEvent.getTaxon()!=null){
associatedTaxa.add(determinationEvent.getTaxon());
}
if(determinationEvent.getTaxonName()!=null){
- associatedTaxa.addAll(determinationEvent.getTaxonName().getTaxonBases());
+ associatedTaxa.addAll((Collection)determinationEvent.getTaxonName().getTaxonBases());
}
}
}
+ return associatedTaxa;
+ }
+ @Override
+ public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, Integer limit, Integer start,
+ List<OrderHint> orderHints, List<String> propertyPaths) {
+ Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
+ for (SpecimenTypeDesignation typeDesignation : listTypeDesignations(specimen, limit, start, orderHints, propertyPaths)) {
+ if(typeDesignation.getTypeSpecimen().equals(specimen)){
+ Set<TaxonName> typifiedNames = typeDesignation.getTypifiedNames();
+ for (TaxonName taxonName : typifiedNames) {
+ associatedTaxa.addAll(taxonName.getTaxa());
+ }
+ }
+ }
+ return associatedTaxa;
+ }
+
+ @Override
+ public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start,
+ List<OrderHint> orderHints, List<String> propertyPaths) {
+ Collection<TaxonBase<?>> associatedTaxa = new HashSet<>();
+ for (IndividualsAssociation individualsAssociation : listIndividualsAssociations(specimen, limit, start, orderHints, propertyPaths)) {
+ if(individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class)){
+ TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
+ if(taxonDescription.getTaxon()!=null){
+ associatedTaxa.add(taxonDescription.getTaxon());
+ }
+ }
+ }
return associatedTaxa;
}
}
@Override
- public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen,
+ public Map<DerivedUnit, Collection<SpecimenTypeDesignation>> listTypeDesignations(
+ Collection<DerivedUnit> specimens, Integer limit, Integer start,
+ List<OrderHint> orderHints, List<String> propertyPaths) {
+ Map<DerivedUnit, Collection<SpecimenTypeDesignation>> typeDesignationMap = new HashMap<>();
+ for (DerivedUnit specimen : specimens) {
+ Collection<SpecimenTypeDesignation> typeDesignations = listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
+ typeDesignationMap.put(specimen, typeDesignations);
+ }
+ return typeDesignationMap;
+ }
+
+ @Override
+ public Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen,
Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
return dao.listTypeDesignations(specimen, limit, start, orderHints, propertyPaths);
}
if (specimen != null) {
return specimen.characterData();
}else{
- return new ArrayList<DescriptionElementBase>();
+ return new ArrayList<>();
}
}
}
+ @Override
+ public Integer countByTitle(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
+ if (config instanceof FindOccurrencesConfigurator) {
+ FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
+ Taxon taxon = null;
+ if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
+ TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
+ if(taxonBase.isInstanceOf(Taxon.class)){
+ taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
+ }
+ }
+ TaxonName taxonName = null;
+ if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
+ taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
+ }
+ return dao.countOccurrences(occurrenceConfig.getClazz(),
+ occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
+ occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
+ occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
+ }
+ else{
+ return dao.countByTitle(config.getTitleSearchString());
+ }
+
+ }
+
@Override
public Pager<SpecimenOrObservationBase> findByTitle(
IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config) {
if (config instanceof FindOccurrencesConfigurator) {
FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
- List<SpecimenOrObservationBase> occurrences = new ArrayList<SpecimenOrObservationBase>();
+ List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
Taxon taxon = null;
if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
}
}
- TaxonNameBase taxonName = null;
+ TaxonName taxonName = null;
if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
}
occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(),
occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null,
occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths()));
+ //filter out (un-)assigned specimens
+ if(taxon==null && taxonName==null){
+ AssignmentStatus assignmentStatus = occurrenceConfig.getAssignmentStatus();
+ List<SpecimenOrObservationBase<?>> specimenWithAssociations = new ArrayList<>();
+ if(!assignmentStatus.equals(AssignmentStatus.ALL_SPECIMENS)){
+ for (SpecimenOrObservationBase specimenOrObservationBase : occurrences) {
+ Collection<TaxonBase<?>> associatedTaxa = listAssociatedTaxa(specimenOrObservationBase, null, null, null, null);
+ if(!associatedTaxa.isEmpty()){
+ specimenWithAssociations.add(specimenOrObservationBase);
+ }
+ }
+ }
+ if(assignmentStatus.equals(AssignmentStatus.UNASSIGNED_SPECIMENS)){
+ occurrences.removeAll(specimenWithAssociations);
+ }
+ if(assignmentStatus.equals(AssignmentStatus.ASSIGNED_SPECIMENS)){
+ occurrences = new ArrayList<>(specimenWithAssociations);
+ }
+ }
// indirectly associated specimens
- List<SpecimenOrObservationBase> indirectlyAssociatedOccurrences = new ArrayList<SpecimenOrObservationBase>(occurrences);
if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens()){
+ List<SpecimenOrObservationBase> indirectlyAssociatedOccurrences = new ArrayList<>(occurrences);
for (SpecimenOrObservationBase specimen : occurrences) {
List<SpecimenOrObservationBase<?>> allHierarchyDerivates = getAllHierarchyDerivatives(specimen);
for (SpecimenOrObservationBase<?> specimenOrObservationBase : allHierarchyDerivates) {
@Override
public List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen){
- List<SpecimenOrObservationBase<?>> allHierarchyDerivatives = new ArrayList<SpecimenOrObservationBase<?>>();
+ List<SpecimenOrObservationBase<?>> allHierarchyDerivatives = new ArrayList<>();
Collection<FieldUnit> fieldUnits = getFieldUnits(specimen.getUuid());
if(fieldUnits.isEmpty()){
allHierarchyDerivatives.add(specimen);
return allHierarchyDerivatives;
}
+ @Override
+ public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid){
+ return getAllChildDerivatives(load(specimenUuid));
+ }
+
@Override
public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen){
- List<DerivedUnit> childDerivate = new ArrayList<DerivedUnit>();
+ if (specimen == null){
+ return null;
+ }
+ List<DerivedUnit> childDerivate = new ArrayList<>();
Set<DerivationEvent> derivationEvents = specimen.getDerivationEvents();
for (DerivationEvent derivationEvent : derivationEvents) {
Set<DerivedUnit> derivatives = derivationEvent.getDerivatives();
for (DerivedUnit derivedUnit : derivatives) {
childDerivate.add(derivedUnit);
- childDerivate.addAll(getAllChildDerivatives(derivedUnit));
+ childDerivate.addAll(getAllChildDerivatives(derivedUnit.getUuid()));
}
}
return childDerivate;
@Override
public int countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config){
- if (config instanceof FindOccurrencesConfigurator) {
- FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
- Taxon taxon = null;
- if(occurrenceConfig.getAssociatedTaxonUuid()!=null){
- TaxonBase taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
- if(taxonBase.isInstanceOf(Taxon.class)){
- taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
- }
- }
- TaxonNameBase taxonName = null;
- if(occurrenceConfig.getAssociatedTaxonNameUuid()!=null){
- taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
- }
- // indirectly associated specimens
- if(occurrenceConfig.isRetrieveIndirectlyAssociatedSpecimens()){
- return findByTitle(config).getRecords().size();
- }
- return dao.countOccurrences(occurrenceConfig.getClazz(), occurrenceConfig.getTitleSearchString(),
- occurrenceConfig.getSignificantIdentifier(), occurrenceConfig.getSpecimenType(), taxon, taxonName,
- occurrenceConfig.getMatchMode(), null, null, occurrenceConfig.getOrderHints(),
- occurrenceConfig.getPropertyPaths());
- }
- return super.countByTitle(config);
+ return countByTitle(config);
}
}
BGBM BDI Projects / cdmlib.git / blobdiff