import org.apache.lucene.search.BooleanQuery;\r
import org.apache.lucene.search.Query;\r
import org.apache.lucene.search.SortField;\r
-import org.apache.lucene.search.TopDocs;\r
-import org.apache.lucene.search.grouping.TopGroups;\r
import org.springframework.beans.factory.annotation.Autowired;\r
import org.springframework.stereotype.Service;\r
-import org.springframework.transaction.annotation.Propagation;\r
import org.springframework.transaction.annotation.Transactional;\r
\r
import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;\r
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;\r
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
import eu.etaxonomy.cdm.hibernate.search.DefinedTermBaseClassBridge;\r
+import eu.etaxonomy.cdm.hibernate.search.GroupByTaxonClassBridge;\r
import eu.etaxonomy.cdm.hibernate.search.MultilanguageTextFieldBridge;\r
import eu.etaxonomy.cdm.model.CdmBaseType;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
import eu.etaxonomy.cdm.model.common.IdentifiableSource;\r
import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\r
+import eu.etaxonomy.cdm.model.common.OriginalSourceType;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;\r
import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;\r
+import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
import eu.etaxonomy.cdm.model.description.IIdentificationKey;\r
import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;\r
+import eu.etaxonomy.cdm.model.description.SpecimenDescription;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
import eu.etaxonomy.cdm.model.description.TaxonInteraction;\r
+import eu.etaxonomy.cdm.model.description.TaxonNameDescription;\r
import eu.etaxonomy.cdm.model.media.Media;\r
import eu.etaxonomy.cdm.model.media.MediaRepresentation;\r
import eu.etaxonomy.cdm.model.media.MediaUtils;\r
+import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
+import eu.etaxonomy.cdm.model.molecular.Sequence;\r
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.taxon.Classification;\r
import eu.etaxonomy.cdm.model.taxon.Synonym;\r
import eu.etaxonomy.cdm.persistence.dao.common.ICdmGenericDao;\r
import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;\r
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;\r
+import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;\r
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;\r
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;\r
import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
*\r
*/\r
@Service\r
-@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)\r
+@Transactional(readOnly = true)\r
public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService{\r
private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);\r
\r
@Autowired\r
private IOrderedTermVocabularyDao orderedVocabularyDao;\r
\r
+ @Autowired\r
+ private IOccurrenceDao occurrenceDao;\r
+\r
@Autowired\r
private AbstractBeanInitializer beanInitializer;\r
\r
* FIXME Candidate for harmonization\r
* rename searchByName ?\r
*/\r
+ @Override\r
public List<TaxonBase> searchTaxaByName(String name, Reference sec) {\r
return dao.getTaxaByName(name, sec);\r
}\r
* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllSynonyms(int, int)\r
*/\r
+ @Override\r
public List<Synonym> getAllSynonyms(int limit, int start) {\r
return dao.getAllSynonyms(limit, start);\r
}\r
* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllTaxa(int, int)\r
*/\r
+ @Override\r
public List<Taxon> getAllTaxa(int limit, int start) {\r
return dao.getAllTaxa(limit, start);\r
}\r
* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean)\r
*/\r
+ @Override\r
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren) {\r
if (cdmFetch == null){\r
cdmFetch = CdmFetch.NO_FETCH();\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, boolean, boolean)\r
*/\r
+ @Override\r
public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,boolean withMisapplications, List<String> propertyPaths) {\r
return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths);\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllRelationships(int, int)\r
*/\r
+ @Override\r
public List<RelationshipBase> getAllRelationships(int limit, int start){\r
return dao.getAllRelationships(limit, start);\r
}\r
* FIXME Candidate for harmonization\r
* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ?\r
*/\r
+ @Override\r
@Deprecated\r
public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {\r
\r
* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)\r
*/\r
+ @Override\r
@Transactional(readOnly = false)\r
public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){\r
\r
}\r
\r
\r
+ @Override\r
public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){\r
\r
// Get name from synonym\r
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);\r
}\r
\r
+ @Override\r
@Autowired\r
protected void setDao(ITaxonDao dao) {\r
this.dao = dao;\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)\r
*/\r
+ @Override\r
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {\r
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)\r
*/\r
+ @Override\r
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {\r
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
*/\r
+ @Override\r
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){\r
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
*/\r
+ @Override\r
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
*/\r
+ @Override\r
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){\r
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
*/\r
+ @Override\r
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);\r
\r
* @param propertyPaths\r
* @return an List which is not specifically ordered\r
*/\r
- public List<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,\r
+ @Override\r
+ public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,\r
Integer limit, Integer start, List<String> propertyPaths) {\r
\r
- List<Taxon> relatedTaxa = collectRelatedTaxa(taxon, includeRelationships, new ArrayList<Taxon>(), maxDepth);\r
+ Set<Taxon> relatedTaxa = collectRelatedTaxa(taxon, includeRelationships, new HashSet<Taxon>(), maxDepth);\r
relatedTaxa.remove(taxon);\r
beanInitializer.initializeAll(relatedTaxa, propertyPaths);\r
return relatedTaxa;\r
* @param taxon\r
* @param includeRelationships\r
* @param taxa\r
- * @param maxDepth\r
+ * @param maxDepth can be <code>null</code> for infinite depth\r
* @return\r
*/\r
- private List<Taxon> collectRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, List<Taxon> taxa, Integer maxDepth) {\r
+ private Set<Taxon> collectRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Set<Taxon> taxa, Integer maxDepth) {\r
\r
if(taxa.isEmpty()) {\r
taxa.add(taxon);\r
}\r
\r
- maxDepth--;\r
- logger.debug("collecting related taxa for " + taxon + " with maxDepth=" + maxDepth);\r
+ if(maxDepth != null) {\r
+ maxDepth--;\r
+ }\r
+ if(logger.isDebugEnabled()){\r
+ logger.debug("collecting related taxa for " + taxon + " with maxDepth=" + maxDepth);\r
+ }\r
List<TaxonRelationship> taxonRelationships = dao.getTaxonRelationships(taxon, null, null, null, null, null, null);\r
- for(TaxonRelationship taxRel : taxonRelationships) {\r
+ for (TaxonRelationship taxRel : taxonRelationships) {\r
+\r
+ // skip invalid data\r
+ if (taxRel.getToTaxon() == null || taxRel.getFromTaxon() == null || taxRel.getType() == null) {\r
+ continue;\r
+ }\r
// filter by includeRelationships\r
for (TaxonRelationshipEdge relationshipEdgeFilter : includeRelationships) {\r
if ( relationshipEdgeFilter.getTaxonRelationshipType().equals(taxRel.getType()) ) {\r
if (relationshipEdgeFilter.getDirections().contains(Direction.relatedTo) && !taxa.contains(taxRel.getToTaxon())) {\r
- logger.debug("adding toTaxon for " + taxRel.getType());\r
+ if(logger.isDebugEnabled()){\r
+ logger.debug(maxDepth + ": " + taxon.getTitleCache() + " --[" + taxRel.getType().getLabel() + "]--> " + taxRel.getToTaxon().getTitleCache());\r
+ }\r
taxa.add(taxRel.getToTaxon());\r
- if(maxDepth > 0) {\r
- taxa.addAll(collectRelatedTaxa(taxon, includeRelationships, taxa, maxDepth));\r
+ if(maxDepth == null || maxDepth > 0) {\r
+ taxa.addAll(collectRelatedTaxa(taxRel.getToTaxon(), includeRelationships, taxa, maxDepth));\r
}\r
}\r
if(relationshipEdgeFilter.getDirections().contains(Direction.relatedFrom) && !taxa.contains(taxRel.getFromTaxon())) {\r
taxa.add(taxRel.getFromTaxon());\r
- logger.debug("adding fromTaxon for " + taxRel.getType());\r
- if(maxDepth > 0) {\r
- taxa.addAll(collectRelatedTaxa(taxon, includeRelationships, taxa, maxDepth));\r
+ if(logger.isDebugEnabled()){\r
+ logger.debug(maxDepth + ": " +taxRel.getFromTaxon().getTitleCache() + " --[" + taxRel.getType().getLabel() + "]--> " + taxon.getTitleCache() );\r
+ }\r
+ if(maxDepth == null || maxDepth > 0) {\r
+ taxa.addAll(collectRelatedTaxa(taxRel.getFromTaxon(), includeRelationships, taxa, maxDepth));\r
}\r
}\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
*/\r
+ @Override\r
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
Integer numberOfResults = dao.countSynonyms(taxon, type);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
*/\r
+ @Override\r
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
Integer numberOfResults = dao.countSynonyms(synonym, type);\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHomotypicSynonymsByHomotypicGroup(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)\r
*/\r
+ @Override\r
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){\r
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);\r
return t.getHomotypicSynonymsByHomotypicGroup();\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHeterotypicSynonymyGroups(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)\r
*/\r
+ @Override\r
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){\r
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);\r
List<HomotypicalGroup> homotypicalGroups = t.getHeterotypicSynonymyGroups();\r
return heterotypicSynonymyGroups;\r
}\r
\r
+ @Override\r
public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator){\r
\r
List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)\r
*/\r
+ @Override\r
public Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator) {\r
\r
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllMedia(eu.etaxonomy.cdm.model.taxon.Taxon, int, int, int, java.lang.String[])\r
*/\r
+ @Override\r
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){\r
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>();\r
taxon = (Taxon)dao.load(taxon.getUuid());\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxonDescriptionMedia(eu.etaxonomy.cdm.model.taxon.Taxon, boolean)\r
*/\r
- public List<Media> listTaxonDescriptionMedia(Taxon taxon, boolean limitToGalleries, List<String> propertyPath){\r
-\r
- Pager<TaxonDescription> p =\r
- descriptionService.getTaxonDescriptions(taxon, null, null, null, null, propertyPath);\r
+ @Override\r
+ public List<Media> listTaxonDescriptionMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, List<String> propertyPath){\r
+ return listMedia(taxon, includeRelationships, limitToGalleries, true, false, false, propertyPath);\r
+ }\r
\r
- // pars the media and quality parameters\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#listMedia(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.Set, boolean, java.util.List)\r
+ */\r
+ @Override\r
+ public List<Media> listMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,\r
+ Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,\r
+ Boolean includeTaxonNameDescriptions, List<String> propertyPath) {\r
\r
- // collect all media of the given taxon\r
+ Set<Taxon> taxa = new HashSet<Taxon>();\r
List<Media> taxonMedia = new ArrayList<Media>();\r
- List<Media> taxonGalleryMedia = new ArrayList<Media>();\r
- for(TaxonDescription desc : p.getRecords()){\r
\r
- if(desc.isImageGallery()){\r
- for(DescriptionElementBase element : desc.getElements()){\r
- for(Media media : element.getMedia()){\r
- taxonGalleryMedia.add(media);\r
+ if (limitToGalleries == null) {\r
+ limitToGalleries = false;\r
+ }\r
+\r
+ // --- resolve related taxa\r
+ if (includeRelationships != null) {\r
+ taxa = listRelatedTaxa(taxon, includeRelationships, null, null, null, null);\r
+ }\r
+\r
+ taxa.add((Taxon) dao.load(taxon.getUuid()));\r
+\r
+ if(includeTaxonDescriptions != null && includeTaxonDescriptions){\r
+ List<TaxonDescription> taxonDescriptions = new ArrayList<TaxonDescription>();\r
+ // --- TaxonDescriptions\r
+ for (Taxon t : taxa) {\r
+ taxonDescriptions.addAll(descriptionService.listTaxonDescriptions(t, null, null, null, null, propertyPath));\r
+ }\r
+ for (TaxonDescription taxonDescription : taxonDescriptions) {\r
+ if (!limitToGalleries || taxonDescription.isImageGallery()) {\r
+ for (DescriptionElementBase element : taxonDescription.getElements()) {\r
+ for (Media media : element.getMedia()) {\r
+ taxonMedia.add(media);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if(includeOccurrences != null && includeOccurrences) {\r
+ Set<SpecimenOrObservationBase> specimensOrObservations = new HashSet<SpecimenOrObservationBase>();\r
+ // --- Specimens\r
+ for (Taxon t : taxa) {\r
+ specimensOrObservations.addAll(occurrenceDao.listByAssociatedTaxon(null, t, null, null, null, null));\r
+ }\r
+ for (SpecimenOrObservationBase occurrence : specimensOrObservations) {\r
+\r
+ taxonMedia.addAll(occurrence.getMedia());\r
+\r
+ // SpecimenDescriptions\r
+ Set<SpecimenDescription> specimenDescriptions = occurrence.getSpecimenDescriptions();\r
+ for (DescriptionBase specimenDescription : specimenDescriptions) {\r
+ if (!limitToGalleries || specimenDescription.isImageGallery()) {\r
+ Set<DescriptionElementBase> elements = specimenDescription.getElements();\r
+ for (DescriptionElementBase element : elements) {\r
+ for (Media media : element.getMedia()) {\r
+ taxonMedia.add(media);\r
+ }\r
+ }\r
}\r
}\r
- } else if(!limitToGalleries){\r
- for(DescriptionElementBase element : desc.getElements()){\r
- for(Media media : element.getMedia()){\r
- taxonMedia.add(media);\r
+\r
+ // Collection\r
+ if (occurrence instanceof DerivedUnitBase) {\r
+ if (((DerivedUnitBase) occurrence).getCollection() != null){\r
+ taxonMedia.addAll(((DerivedUnitBase) occurrence).getCollection().getMedia());\r
}\r
}\r
+\r
+ // Chromatograms\r
+ if (occurrence instanceof DnaSample) {\r
+ Set<Sequence> sequences = ((DnaSample) occurrence).getSequences();\r
+ for (Sequence sequence : sequences) {\r
+ taxonMedia.addAll(sequence.getChromatograms());\r
+ }\r
+ }\r
+\r
}\r
+ }\r
\r
+ if(includeTaxonNameDescriptions != null && includeTaxonNameDescriptions) {\r
+ // --- TaxonNameDescription\r
+ Set<TaxonNameDescription> nameDescriptions = new HashSet<TaxonNameDescription>();\r
+ for (Taxon t : taxa) {\r
+ nameDescriptions .addAll(t.getName().getDescriptions());\r
+ }\r
+ for(TaxonNameDescription nameDescription: nameDescriptions){\r
+ if (!limitToGalleries || nameDescription.isImageGallery()) {\r
+ Set<DescriptionElementBase> elements = nameDescription.getElements();\r
+ for (DescriptionElementBase element : elements) {\r
+ for (Media media : element.getMedia()) {\r
+ taxonMedia.add(media);\r
+ }\r
+ }\r
+ }\r
+ }\r
}\r
\r
- taxonGalleryMedia.addAll(taxonMedia);\r
- return taxonGalleryMedia;\r
+ beanInitializer.initializeAll(taxonMedia, propertyPath);\r
+ return taxonMedia;\r
}\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByID(java.util.Set)\r
*/\r
+ @Override\r
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {\r
return this.dao.listByIds(listOfIDs, null, null, null, null);\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxonByUuid(UUID uuid, List<String> propertyPaths)\r
*/\r
+ @Override\r
public TaxonBase findTaxonByUuid(UUID uuid, List<String> propertyPaths){\r
return this.dao.findByUuid(uuid, null ,propertyPaths);\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#countAllRelationships()\r
*/\r
+ @Override\r
public int countAllRelationships() {\r
return this.dao.countAllRelationships();\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNames(java.util.List)\r
*/\r
+ @Override\r
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {\r
return this.dao.findIdenticalTaxonNames(propertyPath);\r
}\r
try{\r
nameService.delete(name, new NameDeletionConfigurator());\r
}catch (DataChangeNoRollbackException ex){\r
- if (logger.isDebugEnabled())logger.debug("Name wasn't deleted as it is referenced");\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Name wasn't deleted as it is referenced");\r
+ }\r
}\r
}\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List)\r
*/\r
+ @Override\r
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {\r
\r
return this.dao.findIdenticalNamesNew(propertyPath);\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getPhylumName(eu.etaxonomy.cdm.model.name.TaxonNameBase)\r
*/\r
+ @Override\r
public String getPhylumName(TaxonNameBase name){\r
return this.dao.getPhylumName(name);\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)\r
*/\r
+ @Override\r
public long deleteSynonymRelationships(Synonym syn, Taxon taxon) {\r
return dao.deleteSynonymRelationships(syn, taxon);\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym)\r
*/\r
+ @Override\r
public long deleteSynonymRelationships(Synonym syn) {\r
return dao.deleteSynonymRelationships(syn, null);\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listSynonymRelationships(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction)\r
*/\r
+ @Override\r
public List<SynonymRelationship> listSynonymRelationships(\r
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,\r
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {\r
LuceneSearch luceneSearch = new LuceneSearch(getSession(), TaxonBase.class);\r
QueryFactory queryFactory = new QueryFactory(luceneSearch);\r
\r
- SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", false)};\r
+ SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};\r
luceneSearch.setSortFields(sortFields);\r
\r
// ---- search criteria\r
}\r
\r
\r
+ @Override\r
public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,\r
Classification classification, List<Language> languages, boolean highlightFragments,\r
Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {\r
BooleanQuery finalQuery = new BooleanQuery();\r
BooleanQuery textQuery = new BooleanQuery();\r
\r
- LuceneSearch luceneSearch = new LuceneSearch(getSession(), DescriptionElementBase.class);\r
+ LuceneSearch luceneSearch = new LuceneSearch(getSession(), GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, DescriptionElementBase.class);\r
QueryFactory queryFactory = new QueryFactory(luceneSearch);\r
\r
- SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("inDescription.taxon.titleCache__sort", false)};\r
+ SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("inDescription.taxon.titleCache__sort", SortField.STRING, false)};\r
luceneSearch.setSortFields(sortFields);\r
\r
// ---- search criteria\r
nameQuery = new BooleanQuery();\r
BooleanQuery languageSubQuery = new BooleanQuery();\r
for(Language lang : languages){\r
- languageSubQuery.add(queryFactory.newTermQuery("language.uuid", lang.getUuid().toString()), Occur.SHOULD);\r
+ languageSubQuery.add(queryFactory.newTermQuery("language.uuid", lang.getUuid().toString(), false), Occur.SHOULD);\r
}\r
((BooleanQuery) nameQuery).add(queryFactory.newTermQuery("name", queryString), Occur.MUST);\r
((BooleanQuery) nameQuery).add(languageSubQuery, Occur.MUST);\r
// the description must be associated with a taxon\r
finalQuery.add(queryFactory.newIsNotNullQuery("inDescription.taxon.id"), Occur.MUST);\r
\r
+ logger.info("prepareByDescriptionElementFullTextSearch() query: " + finalQuery.toString());\r
luceneSearch.setQuery(finalQuery);\r
\r
if(highlightFragments){\r
return stringBuilder;\r
}\r
\r
+ @Override\r
public List<Synonym> createInferredSynonyms(Taxon taxon, Classification classification, SynonymRelationshipType type, boolean doWithMisappliedNames){\r
List <Synonym> inferredSynonyms = new ArrayList<Synonym>();\r
List<Synonym> inferredSynonymsToBeRemoved = new ArrayList<Synonym>();\r
HashMap <UUID, ZoologicalName> zooHashMap = new HashMap<UUID, ZoologicalName>();\r
\r
\r
- UUID uuid= taxon.getName().getUuid();\r
- ZoologicalName taxonName = getZoologicalName(uuid, zooHashMap);\r
+ UUID nameUuid= taxon.getName().getUuid();\r
+ ZoologicalName taxonName = getZoologicalName(nameUuid, zooHashMap);\r
String epithetOfTaxon = null;\r
String infragenericEpithetOfTaxon = null;\r
String infraspecificEpithetOfTaxon = null;\r
\r
if (node.getClassification().equals(classification)){\r
if (!node.isTopmostNode()){\r
- TaxonNode parent = (TaxonNode)node.getParent();\r
+ TaxonNode parent = node.getParent();\r
parent = (TaxonNode)HibernateProxyHelper.deproxy(parent);\r
- TaxonNameBase parentName = parent.getTaxon().getName();\r
+ TaxonNameBase<?,?> parentName = parent.getTaxon().getName();\r
ZoologicalName zooParentName = HibernateProxyHelper.deproxy(parentName, ZoologicalName.class);\r
Taxon parentTaxon = (Taxon)HibernateProxyHelper.deproxy(parent.getTaxon());\r
Rank rankOfTaxon = taxonName.getRank();\r
\r
\r
if (type.equals(SynonymRelationshipType.INFERRED_EPITHET_OF())){\r
- Set<String> genusNames = new HashSet<String>();\r
+\r
\r
for (SynonymRelationship synonymRelationOfParent:synonymRelationshipsOfParent){\r
Synonym syn = synonymRelationOfParent.getSynonym();\r
String idInSourceSyn= getIdInSource(syn);\r
\r
if (idInSourceParent != null && idInSourceSyn != null) {\r
- IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSourceSyn + "; " + idInSourceParent, POTENTIAL_COMBINATION_NAMESPACE, sourceReference, null);\r
+ IdentifiableSource originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, idInSourceSyn + "; " + idInSourceParent, POTENTIAL_COMBINATION_NAMESPACE, sourceReference, null);\r
inferredSynName.addSource(originalSource);\r
- originalSource = IdentifiableSource.NewInstance(idInSourceSyn + "; " + idInSourceParent, POTENTIAL_COMBINATION_NAMESPACE, sourceReference, null);\r
+ originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, idInSourceSyn + "; " + idInSourceParent, POTENTIAL_COMBINATION_NAMESPACE, sourceReference, null);\r
potentialCombination.addSource(originalSource);\r
}\r
\r
\r
// Add the original source\r
if (idInSourceSyn != null && idInSourceTaxon != null) {\r
- IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
+ IdentifiableSource originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, \r
+ idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
inferredGenus.addSource(originalSource);\r
\r
- originalSource = IdentifiableSource.NewInstance(idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
+ originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, \r
+ idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
inferredSynName.addSource(originalSource);\r
originalSource = null;\r
\r
}else{\r
logger.error("There is an idInSource missing: " + idInSourceSyn + " of Synonym or " + idInSourceTaxon + " of Taxon");\r
- IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
+ IdentifiableSource originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, \r
+ idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
inferredGenus.addSource(originalSource);\r
\r
- originalSource = IdentifiableSource.NewInstance(idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
+ originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, \r
+ idInSourceSyn + "; " + idInSourceTaxon, INFERRED_GENUS_NAMESPACE, sourceReference, null);\r
inferredSynName.addSource(originalSource);\r
originalSource = null;\r
}\r
TaxonNameBase parentName, TaxonBase syn) {\r
\r
Synonym inferredEpithet;\r
- TaxonNameBase synName;\r
+ TaxonNameBase<?,?> synName;\r
ZoologicalName inferredSynName;\r
HibernateProxyHelper.deproxy(syn);\r
\r
String idInSourceSyn = getIdInSource(syn);\r
String idInSourceTaxon = getIdInSource(taxon);\r
// Determine the sourceReference\r
- Reference sourceReference = syn.getSec();\r
+ Reference<?> sourceReference = syn.getSec();\r
\r
if (sourceReference == null){\r
logger.warn("The synonym has no sec reference because it is a misapplied name! Take the sec reference of taxon");\r
}*/\r
String taxonId = idInSourceTaxon+ "; " + idInSourceSyn;\r
\r
- IdentifiableSource originalSource;\r
- originalSource = IdentifiableSource.NewInstance(taxonId, INFERRED_EPITHET_NAMESPACE, sourceReference, null);\r
+\r
+ IdentifiableSource originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, \r
+ taxonId, INFERRED_EPITHET_NAMESPACE, sourceReference, null);\r
\r
inferredEpithet.addSource(originalSource);\r
\r
- originalSource = IdentifiableSource.NewInstance(taxonId, INFERRED_EPITHET_NAMESPACE, sourceReference, null);\r
+ originalSource = IdentifiableSource.NewInstance(OriginalSourceType.Transformation, \r
+ taxonId, INFERRED_EPITHET_NAMESPACE, sourceReference, null);\r
\r
inferredSynName.addSource(originalSource);\r
\r
return citation;\r
}\r
\r
+ @Override\r
public List<Synonym> createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames){\r
List <Synonym> inferredSynonyms = new ArrayList<Synonym>();\r
\r
return inferredSynonyms;\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#listClassifications(eu.etaxonomy.cdm.model.taxon.TaxonBase, java.lang.Integer, java.lang.Integer, java.util.List)\r
+ */\r
+ @Override\r
+ public List<Classification> listClassifications(TaxonBase taxonBase, Integer limit, Integer start, List<String> propertyPaths) {\r
+\r
+ // TODO quickly implemented, create according dao !!!!\r
+ Set<TaxonNode> nodes = new HashSet<TaxonNode>();\r
+ Set<Classification> classifications = new HashSet<Classification>();\r
+ List<Classification> list = new ArrayList<Classification>();\r
+\r
+ if (taxonBase == null) {\r
+ return list;\r
+ }\r
+\r
+ taxonBase = load(taxonBase.getUuid());\r
+\r
+ if (taxonBase instanceof Taxon) {\r
+ nodes.addAll(((Taxon)taxonBase).getTaxonNodes());\r
+ } else {\r
+ for (Taxon taxon : ((Synonym)taxonBase).getAcceptedTaxa() ) {\r
+ nodes.addAll(taxon.getTaxonNodes());\r
+ }\r
+ }\r
+ for (TaxonNode node : nodes) {\r
+ classifications.add(node.getClassification());\r
+ }\r
+ list.addAll(classifications);\r
+ return list;\r
+ }\r
+\r
+\r
+\r
\r
\r
\r
BGBM BDI Projects / cdmlib.git / blobdiff