import org.apache.lucene.search.BooleanClause.Occur;\r
import org.apache.lucene.search.BooleanQuery;\r
import org.apache.lucene.search.SortField;\r
+import org.hibernate.TransientObjectException;\r
import org.hibernate.search.spatial.impl.Rectangle;\r
import org.springframework.beans.factory.annotation.Autowired;\r
import org.springframework.stereotype.Service;\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;\r
+import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO;\r
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;\r
import eu.etaxonomy.cdm.api.service.pager.Pager;\r
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;\r
import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;\r
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;\r
import eu.etaxonomy.cdm.model.location.Country;\r
import eu.etaxonomy.cdm.model.media.Media;\r
+import eu.etaxonomy.cdm.model.media.MediaRepresentation;\r
+import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;\r
import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
import eu.etaxonomy.cdm.model.molecular.Sequence;\r
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;\r
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;\r
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
@Autowired\r
private ITaxonService taxonService;\r
\r
+ @Autowired\r
+ private ISequenceService sequenceService;\r
+\r
@Autowired\r
private AbstractBeanInitializer beanInitializer;\r
\r
return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)\r
+ */\r
+ @Override\r
+ public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {\r
+ return dao.countDeterminations(occurence, taxonbase);\r
+ }\r
+\r
@Override\r
public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {\r
Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);\r
return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listByAnyAssociation(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
+ */\r
+ @Override\r
+ public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,\r
+ Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();\r
+\r
+ List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();\r
+ for(SpecimenOrObservationBase<?> specimen:records){\r
+ fieldUnits.addAll(getFieldUnits(specimen.getUuid()));\r
+ }\r
+ return fieldUnits;\r
+ }\r
+\r
+ @Override\r
+ public Collection<DerivateHierarchyDTO> listDerivateHierarchyDTOsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,\r
+ Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ Collection<FieldUnit> fieldUnits = listFieldUnitsByAssociatedTaxon(includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);\r
+\r
+ Collection<DerivateHierarchyDTO> derivateHierarchyDTOs = new ArrayList<DerivateHierarchyDTO>();\r
+ for(FieldUnit fieldUnit:fieldUnits){\r
+ derivateHierarchyDTOs.add(assembleDerivateHierarchyDTO(fieldUnit, associatedTaxon));\r
+ }\r
+ return derivateHierarchyDTOs;\r
+ }\r
+\r
+ private DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, Taxon associatedTaxon){\r
+ DerivateHierarchyDTO dto = new DerivateHierarchyDTO();\r
+ // TaxonNameBase name = associatedTaxon.getName();\r
+ // name = HibernateProxyHelper.deproxy(name, TaxonNameBase.class);\r
+ // dto.setType(!name.getTypeDesignations().isEmpty());\r
+ dto.setFieldUnit(fieldUnit);\r
+\r
+ if(fieldUnit.getGatheringEvent()!=null){\r
+ GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();\r
+ dto.setCountry(gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getDescription():"");\r
+ dto.setDate(gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate().toString("yyyy-MM-dd"):"");\r
+ dto.setCollection((gatheringEvent.getActor()!=null?gatheringEvent.getActor():"") + fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():"");\r
+ }\r
+\r
+ dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());\r
+ //get derivatives\r
+ Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();\r
+ getDerivedUnitsFor(fieldUnit, derivedUnits);\r
+\r
+ for (DerivedUnit derivedUnit : derivedUnits) {\r
+ if(derivedUnit instanceof DnaSample){//.getRecordBasis()==SpecimenOrObservationType.DnaSample){\r
+ dto.setHasDna(true);\r
+\r
+ DnaSample dna = (DnaSample)derivedUnit;\r
+ if(dna.getBankNumber()!=null){\r
+ dto.getMolecularData().add(dna.getBankNumber());\r
+ }\r
+ }\r
+ if(derivedUnit instanceof MediaSpecimen){\r
+ dto.setHasDna(true);\r
+\r
+ MediaSpecimen media = (MediaSpecimen)derivedUnit;\r
+ String mediaUriString = getMediaUriString(media);\r
+ if(media.getKindOfUnit()!=null){\r
+ if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){\r
+ dto.setHasSpecimenScan(true);\r
+ if(mediaUriString!=null){\r
+ dto.getSpecimenScans().add(mediaUriString);\r
+ }\r
+ }\r
+ if(media.getKindOfUnit().getUuid().equals(UUID.fromString("detailImageUUid"))){\r
+ dto.setHasDetailImage(true);\r
+ if(mediaUriString!=null){\r
+ dto.getDetailImages().add(mediaUriString);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return dto;\r
+ }\r
+\r
+private String getMediaUriString(MediaSpecimen mediaSpecimen){\r
+ String mediaUri = null;\r
+ Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();\r
+ if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){\r
+ Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();\r
+ if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){\r
+ MediaRepresentationPart part = mediaRepresentationParts.iterator().next();\r
+ if(part.getUri()!=null){\r
+ mediaUri = part.getUri().toASCIIString();\r
+ }\r
+ }\r
+ }\r
+ return mediaUri;\r
+}\r
+\r
+ private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){\r
+ for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){\r
+ for(DerivedUnit derivative:derivationEvent.getDerivatives()){\r
+ derivedUnits.add(derivative);\r
+ getDerivedUnitsFor(derivative, derivedUnits);\r
+ }\r
+ }\r
+ }\r
+\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.IOccurrenceService#pageByAssociatedTaxon(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
//from which this DerivedUnit was derived until all FieldUnits are found.\r
\r
//FIXME: use HQL queries to increase performance\r
+ SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);\r
+// specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);\r
Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();\r
- SpecimenOrObservationBase derivedUnit = load(derivedUnitUuid);\r
- if(derivedUnit instanceof DerivedUnit){\r
- getFieldUnits((DerivedUnit) derivedUnit, fieldUnits);\r
+\r
+ if(specimen instanceof FieldUnit){\r
+ fieldUnits.add((FieldUnit) specimen);\r
+ }\r
+ else if(specimen instanceof DerivedUnit){\r
+ getFieldUnits((DerivedUnit) specimen, fieldUnits);\r
}\r
return fieldUnits;\r
}\r
*/\r
@Override\r
public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {\r
+ //reload specimens to avoid session conflicts\r
+ from = (DnaSample) load(from.getUuid());\r
+ to = (DnaSample) load(to.getUuid());\r
+ sequence = sequenceService.load(sequence.getUuid());\r
+\r
+ if(from==null || to==null || sequence==null){\r
+ throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +\r
+ "Operation was move "+sequence+ " from "+from+" to "+to);\r
+ }\r
from.removeSequence(sequence);\r
saveOrUpdate(from);\r
to.addSequence(sequence);\r
*/\r
@Override\r
public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {\r
+ //reload specimens to avoid session conflicts\r
+ from = load(from.getUuid());\r
+ to = load(to.getUuid());\r
+ derivate = (DerivedUnit) load(derivate.getUuid());\r
+\r
+ if(from==null || to==null || derivate==null){\r
+ throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +\r
+ "Operation was move "+derivate+ " from "+from+" to "+to);\r
+ }\r
+\r
SpecimenOrObservationType derivateType = derivate.getRecordBasis();\r
SpecimenOrObservationType toType = to.getRecordBasis();\r
//check if type is a sub derivate type\r
if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works\r
+ || derivateType==SpecimenOrObservationType.Media //moving media always works\r
|| (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type\r
//remove derivation event from parent specimen of dragged object\r
DerivationEvent eventToRemove = null;\r
BGBM BDI Projects / cdmlib.git / blobdiff