\r
import java.io.IOException;\r
import java.util.ArrayList;\r
+import java.util.EnumSet;\r
import java.util.HashMap;\r
import java.util.HashSet;\r
+import java.util.Iterator;\r
import java.util.List;\r
import java.util.Map;\r
import java.util.Set;\r
import org.apache.lucene.index.CorruptIndexException;\r
import org.apache.lucene.queryParser.ParseException;\r
import org.apache.lucene.search.BooleanClause.Occur;\r
+import org.apache.lucene.search.BooleanFilter;\r
import org.apache.lucene.search.BooleanQuery;\r
+import org.apache.lucene.search.DocIdSet;\r
import org.apache.lucene.search.Query;\r
+import org.apache.lucene.search.QueryWrapperFilter;\r
import org.apache.lucene.search.SortField;\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.api.service.config.MatchingTaxonConfigurator;\r
-import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator;\r
+import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;\r
import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;\r
+import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator.ChildHandling;\r
import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;\r
import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;\r
import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;\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.api.service.search.ISearchResultBuilder;\r
import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearch;\r
+import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;\r
import eu.etaxonomy.cdm.api.service.search.LuceneSearch;\r
import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;\r
import eu.etaxonomy.cdm.api.service.search.QueryFactory;\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.CommonTaxonName;\r
import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
+import eu.etaxonomy.cdm.model.description.Distribution;\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.PresenceAbsenceTermBase;\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.location.NamedArea;\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.Amplification;\r
import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
import eu.etaxonomy.cdm.model.molecular.Sequence;\r
+import eu.etaxonomy.cdm.model.molecular.SingleRead;\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.DerivedUnit;\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.TaxonNode;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
-import eu.etaxonomy.cdm.persistence.dao.AbstractBeanInitializer;\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.initializer.AbstractBeanInitializer;\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
*\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
\r
@Autowired\r
private INameService nameService;\r
+ \r
+ @Autowired\r
+ private ITaxonNodeService nodeService;\r
+ \r
\r
@Autowired\r
private ICdmGenericDao genericDao;\r
@Autowired\r
private AbstractBeanInitializer beanInitializer;\r
\r
+ @Autowired\r
+ private ILuceneIndexToolProvider luceneIndexToolProvider;\r
+\r
/**\r
* Constructor\r
*/\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)\r
*/\r
- //TODO correct delete handling still needs to be implemented / checked\r
+ \r
@Override\r
@Transactional(readOnly = false)\r
public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws HomotypicalGroupChangeException{\r
-\r
+ \r
TaxonNameBase<?,?> acceptedName = acceptedTaxon.getName();\r
TaxonNameBase<?,?> synonymName = synonym.getName();\r
HomotypicalGroup synonymHomotypicGroup = synonymName.getHomotypicalGroup();\r
}\r
\r
//synonym.getName().removeTaxonBase(synonym);\r
- //TODO correct delete handling still needs to be implemented / checked\r
+ \r
if (deleteSynonym){\r
// deleteSynonym(synonym, taxon, false);\r
try {\r
this.dao.flush();\r
- this.delete(synonym);\r
+ this.deleteSynonym(synonym, acceptedTaxon, new SynonymDeletionConfigurator());\r
\r
} catch (Exception e) {\r
logger.info("Can't delete old synonym from database");\r
* @return an List which is not specifically ordered\r
*/\r
@Override\r
- public List<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,\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 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
Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,\r
Boolean includeTaxonNameDescriptions, List<String> propertyPath) {\r
\r
- List<Taxon> taxa = new ArrayList<Taxon>();\r
+ Set<Taxon> taxa = new HashSet<Taxon>();\r
List<Media> taxonMedia = new ArrayList<Media>();\r
\r
if (limitToGalleries == null) {\r
}\r
for (SpecimenOrObservationBase occurrence : specimensOrObservations) {\r
\r
- taxonMedia.addAll(occurrence.getMedia());\r
+// direct media removed from specimen #3597\r
+// taxonMedia.addAll(occurrence.getMedia());\r
\r
// SpecimenDescriptions\r
Set<SpecimenDescription> specimenDescriptions = occurrence.getSpecimenDescriptions();\r
}\r
\r
// Collection\r
- if (occurrence instanceof DerivedUnitBase) {\r
- if (((DerivedUnitBase) occurrence).getCollection() != null){\r
- taxonMedia.addAll(((DerivedUnitBase) occurrence).getCollection().getMedia());\r
+ //TODO why may collections have media attached? #\r
+ if (occurrence.isInstanceOf(DerivedUnit.class)) {\r
+ DerivedUnit derivedUnit = CdmBase.deproxy(occurrence, DerivedUnit.class);\r
+ if (derivedUnit.getCollection() != null){\r
+ taxonMedia.addAll(derivedUnit.getCollection().getMedia());\r
}\r
}\r
\r
- // Chromatograms\r
- if (occurrence instanceof DnaSample) {\r
- Set<Sequence> sequences = ((DnaSample) occurrence).getSequences();\r
+ // pherograms & gelPhotos\r
+ if (occurrence.isInstanceOf(DnaSample.class)) {\r
+ DnaSample dnaSample = CdmBase.deproxy(occurrence, DnaSample.class);\r
+ Set<Sequence> sequences = dnaSample.getSequences();\r
+ //we do show only those gelPhotos which lead to a consensus sequence\r
for (Sequence sequence : sequences) {\r
- taxonMedia.addAll(sequence.getChromatograms());\r
+ Set<Media> dnaRelatedMedia = new HashSet<Media>();\r
+ for (SingleRead singleRead : sequence.getSingleReads()){\r
+ Amplification amplification = singleRead.getAmplification();\r
+ dnaRelatedMedia.add(amplification.getGelPhoto());\r
+ dnaRelatedMedia.add(singleRead.getPherogram());\r
+ dnaRelatedMedia.remove(null);\r
+ }\r
+ taxonMedia.addAll(dnaRelatedMedia);\r
}\r
}\r
\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteTaxon(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator)\r
*/\r
@Override\r
- public void deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config) throws ReferencedObjectUndeletableException {\r
+ public UUID deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config, Classification classification) throws DataChangeNoRollbackException {\r
if (config == null){\r
config = new TaxonDeletionConfigurator();\r
}\r
\r
- // TaxonNode\r
- if (! config.isDeleteTaxonNodes()){\r
- if (taxon.getTaxonNodes().size() > 0){\r
- String message = "Taxon can't be deleted as it is used in a classification node. Remove taxon from all classifications prior to deletion.";\r
- throw new ReferencedObjectUndeletableException(message);\r
- }\r
- }\r
-\r
-\r
// SynonymRelationShip\r
if (config.isDeleteSynonymRelations()){\r
boolean removeSynonymNameFromHomotypicalGroup = false;\r
if (config.isDeleteSynonymsIfPossible()){\r
//TODO which value\r
boolean newHomotypicGroupIfNeeded = true;\r
- deleteSynonym(synonym, taxon, config.isDeleteNameIfPossible(), newHomotypicGroupIfNeeded);\r
+ SynonymDeletionConfigurator synConfig = new SynonymDeletionConfigurator();\r
+ \r
+ deleteSynonym(synonym, taxon, synConfig);\r
}else{\r
deleteSynonymRelationships(synonym, taxon);\r
}\r
String message = "Taxon can't be deleted as it is related to another taxon. Remove taxon from all relations to other taxa prior to deletion.";\r
throw new ReferencedObjectUndeletableException(message);\r
}\r
+ } else{\r
+ for (TaxonRelationship taxRel: taxon.getTaxonRelations()){\r
+ \r
+ \r
+ \r
+ if (config.isDeleteMisappliedNamesAndInvalidDesignations()){\r
+ if (taxRel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR()) || taxRel.getType().equals(TaxonRelationshipType.INVALID_DESIGNATION_FOR())){\r
+ if (taxon.equals(taxRel.getToTaxon())){\r
+ this.deleteTaxon(taxRel.getFromTaxon(), config, classification);\r
+ }\r
+ }\r
+ }\r
+ taxon.removeTaxonRelation(taxRel);\r
+ /*if (taxFrom.equals(taxon)){\r
+ try{\r
+ this.deleteTaxon(taxTo, taxConf, classification);\r
+ } catch(DataChangeNoRollbackException e){\r
+ logger.debug("A related taxon will not be deleted." + e.getMessage());\r
+ }\r
+ } else {\r
+ try{\r
+ this.deleteTaxon(taxFrom, taxConf, classification);\r
+ } catch(DataChangeNoRollbackException e){\r
+ logger.debug("A related taxon will not be deleted." + e.getMessage());\r
+ }\r
+ \r
+ }*/\r
+ }\r
}\r
\r
\r
+ \r
+ \r
// TaxonDescription\r
+ if (config.isDeleteDescriptions()){\r
Set<TaxonDescription> descriptions = taxon.getDescriptions();\r
\r
for (TaxonDescription desc: descriptions){\r
- if (config.isDeleteDescriptions()){\r
- //TODO use description delete configurator ?\r
- //FIXME check if description is ALWAYS deletable\r
- descriptionService.delete(desc);\r
- }else{\r
- if (desc.getDescribedSpecimenOrObservations().size()>0){\r
- String message = "Taxon can't be deleted as it is used in a TaxonDescription" +\r
- " which also describes specimens or abservations";\r
- throw new ReferencedObjectUndeletableException(message);\r
- }\r
- }\r
+ //TODO use description delete configurator ?\r
+ //FIXME check if description is ALWAYS deletable\r
+ if (desc.getDescribedSpecimenOrObservation() != null){\r
+ String message = "Taxon can't be deleted as it is used in a TaxonDescription" +\r
+ " which also describes specimens or abservations";\r
+ throw new ReferencedObjectUndeletableException(message);\r
}\r
+ descriptionService.delete(desc);\r
+ taxon.removeDescription(desc);\r
+ }\r
+ }\r
\r
\r
- //check references with only reverse mapping\r
- Set<CdmBase> referencingObjects = genericDao.getReferencingObjects(taxon);\r
- for (CdmBase referencingObject : referencingObjects){\r
- //IIdentificationKeys (Media, Polytomous, MultiAccess)\r
- if (HibernateProxyHelper.isInstanceOf(referencingObject, IIdentificationKey.class)){\r
- String message = "Taxon can't be deleted as it is used in an identification key. Remove from identification key prior to deleting this name";\r
- message = String.format(message, CdmBase.deproxy(referencingObject, DerivedUnitBase.class).getTitleCache());\r
- throw new ReferencedObjectUndeletableException(message);\r
- }\r
-\r
-\r
- //PolytomousKeyNode\r
- if (referencingObject.isInstanceOf(PolytomousKeyNode.class)){\r
- String message = "Taxon can't be deleted as it is used in polytomous key node";\r
- throw new ReferencedObjectUndeletableException(message);\r
- }\r
-\r
- //TaxonInteraction\r
- if (referencingObject.isInstanceOf(TaxonInteraction.class)){\r
- String message = "Taxon can't be deleted as it is used in taxonInteraction#taxon2";\r
+ //check references with only reverse mapping\r
+ String message = checkForReferences(taxon);\r
+ if (message != null){\r
+ throw new ReferencedObjectUndeletableException(message.toString());\r
+ }\r
+ \r
+ if (! config.isDeleteTaxonNodes() || (!config.isDeleteInAllClassifications() && classification == null )){\r
+ if (taxon.getTaxonNodes().size() > 0){\r
+ message = "Taxon can't be deleted as it is used in a classification node. Remove taxon from all classifications prior to deletion or define a classification where it should be deleted or adapt the taxon deletion configurator.";\r
throw new ReferencedObjectUndeletableException(message);\r
}\r
+ }else{\r
+ if (taxon.getTaxonNodes().size() != 0){\r
+ Set<TaxonNode> nodes = taxon.getTaxonNodes();\r
+ Iterator<TaxonNode> iterator = nodes.iterator();\r
+ TaxonNode node = null;\r
+ boolean deleteChildren;\r
+ if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)){\r
+ deleteChildren = true;\r
+ }else {\r
+ deleteChildren = false;\r
+ }\r
+ boolean success = true;\r
+ if (!config.isDeleteInAllClassifications() && !(classification == null)){\r
+ while (iterator.hasNext()){\r
+ node = iterator.next();\r
+ if (node.getClassification().equals(classification)){\r
+ break;\r
+ }\r
+ node = null;\r
+ }\r
+ if (node != null){\r
+ success =taxon.removeTaxonNode(node, deleteChildren);\r
+ } else {\r
+ message = "Taxon is not used in defined classification";\r
+ throw new DataChangeNoRollbackException(message);\r
+ }\r
+ } else if (config.isDeleteInAllClassifications()){\r
+ List<TaxonNode> nodesList = new ArrayList<TaxonNode>();\r
+ nodesList.addAll(taxon.getTaxonNodes());\r
+ \r
+ for (TaxonNode taxonNode: nodesList){\r
+ if(deleteChildren){\r
+ Object[] childNodes = taxonNode.getChildNodes().toArray();\r
+ for (Object childNode: childNodes){\r
+ TaxonNode childNodeCast = (TaxonNode) childNode;\r
+ deleteTaxon(childNodeCast.getTaxon(), config, classification);\r
+ \r
+ }\r
+ \r
+ /*for (TaxonNode childNode: taxonNode.getChildNodes()){\r
+ deleteTaxon(childNode.getTaxon(), config, classification);\r
+ \r
+ }*/\r
+ //taxon.removeTaxonNode(taxonNode);\r
+ } else{\r
+ Object[] childNodes = taxonNode.getChildNodes().toArray();\r
+ for (Object childNode: childNodes){\r
+ TaxonNode childNodeCast = (TaxonNode) childNode;\r
+ taxonNode.getParent().addChildNode(childNodeCast, childNodeCast.getReference(), childNodeCast.getMicroReference());\r
+ }\r
+ \r
+ //taxon.removeTaxonNode(taxonNode);\r
+ }\r
+ }\r
+ \r
+ \r
+ \r
+ nodeService.deleteTaxonNodes(nodesList);\r
+ \r
+ }\r
+ if (!success){\r
+ message = "The taxon node could not be deleted.";\r
+ throw new DataChangeNoRollbackException(message);\r
+ }\r
+ }\r
}\r
-\r
-\r
//TaxonNameBase\r
if (config.isDeleteNameIfPossible()){\r
try {\r
- nameService.delete(taxon.getName(), config.getNameDeletionConfig());\r
+ \r
+ //TaxonNameBase name = nameService.find(taxon.getName().getUuid());\r
+ TaxonNameBase name = (TaxonNameBase)HibernateProxyHelper.deproxy(taxon.getName());\r
+ //check whether taxon will be deleted or not\r
+ if (taxon.getTaxonNodes() == null || taxon.getTaxonNodes().size()== 0){\r
+ taxon = (Taxon) HibernateProxyHelper.deproxy(taxon);\r
+ name.removeTaxonBase(taxon);\r
+ nameService.save(name);\r
+ nameService.delete(name, config.getNameDeletionConfig());\r
+ }\r
} catch (ReferencedObjectUndeletableException e) {\r
//do nothing\r
if (logger.isDebugEnabled()){logger.debug("Name could not be deleted");}\r
+ \r
}\r
}\r
-\r
+ \r
+// TaxonDescription\r
+ /* Set<TaxonDescription> descriptions = taxon.getDescriptions();\r
+\r
+ for (TaxonDescription desc: descriptions){\r
+ if (config.isDeleteDescriptions()){\r
+ //TODO use description delete configurator ?\r
+ //FIXME check if description is ALWAYS deletable\r
+ taxon.removeDescription(desc);\r
+ descriptionService.delete(desc);\r
+ }else{\r
+ if (desc.getDescribedSpecimenOrObservations().size()>0){\r
+ String message = "Taxon can't be deleted as it is used in a TaxonDescription" +\r
+ " which also describes specimens or observations";\r
+ throw new ReferencedObjectUndeletableException(message);\r
}\r
+ }\r
+ }*/\r
+ \r
+ \r
+\r
+ if (taxon.getTaxonNodes() == null || taxon.getTaxonNodes().size()== 0){\r
+ dao.delete(taxon);\r
+ return taxon.getUuid();\r
+ } else{\r
+ message = "Taxon can't be deleted as it is used in another Taxonnode";\r
+ throw new ReferencedObjectUndeletableException(message);\r
+ }\r
+ \r
+\r
+ }\r
+ \r
+ private String checkForReferences(Taxon taxon){\r
+ Set<CdmBase> referencingObjects = genericDao.getReferencingObjects(taxon);\r
+ for (CdmBase referencingObject : referencingObjects){\r
+ //IIdentificationKeys (Media, Polytomous, MultiAccess)\r
+ if (HibernateProxyHelper.isInstanceOf(referencingObject, IIdentificationKey.class)){\r
+ String message = "Taxon" + taxon.getTitleCache() + "can't be deleted as it is used in an identification key. Remove from identification key prior to deleting this name";\r
+ \r
+ return message;\r
+ }\r
+\r
\r
+ //PolytomousKeyNode\r
+ if (referencingObject.isInstanceOf(PolytomousKeyNode.class)){\r
+ String message = "Taxon" + taxon.getTitleCache() + " can't be deleted as it is used in polytomous key node";\r
+ return message;\r
+ }\r
+\r
+ //TaxonInteraction\r
+ if (referencingObject.isInstanceOf(TaxonInteraction.class)){\r
+ String message = "Taxon can't be deleted as it is used in taxonInteraction#taxon2";\r
+ return message;\r
+ }\r
+ }\r
+ referencingObjects = null;\r
+ return null;\r
+ }\r
+ \r
+ @Transactional(readOnly = false)\r
+ public UUID delete(Synonym syn){\r
+ UUID result = syn.getUuid();\r
+ this.deleteSynonym(syn, null);\r
+ return result;\r
+ }\r
+ \r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)\r
*/\r
@Transactional(readOnly = false)\r
@Override\r
- public void deleteSynonym(Synonym synonym, Taxon taxon, boolean removeNameIfPossible,boolean newHomotypicGroupIfNeeded) {\r
+ public void deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config) {\r
+ deleteSynonym(synonym, null, config);\r
+ \r
+ }\r
+ \r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)\r
+ */\r
+ @Transactional(readOnly = false)\r
+ @Override\r
+ public void deleteSynonym(Synonym synonym, Taxon taxon, SynonymDeletionConfigurator config) {\r
if (synonym == null){\r
return;\r
}\r
+ if (config == null){\r
+ config = new SynonymDeletionConfigurator();\r
+ }\r
synonym = CdmBase.deproxy(dao.merge(synonym), Synonym.class);\r
\r
//remove synonymRelationship\r
}\r
for (Taxon relatedTaxon : taxonSet){\r
// dao.deleteSynonymRelationships(synonym, relatedTaxon);\r
- relatedTaxon.removeSynonym(synonym, newHomotypicGroupIfNeeded);\r
+ relatedTaxon.removeSynonym(synonym, config.isNewHomotypicGroupIfNeeded());\r
}\r
this.saveOrUpdate(synonym);\r
\r
//TODO remove name from homotypical group?\r
\r
//remove synonym (if necessary)\r
+ \r
+ \r
if (synonym.getSynonymRelations().isEmpty()){\r
TaxonNameBase<?,?> name = synonym.getName();\r
synonym.setName(null);\r
dao.delete(synonym);\r
\r
//remove name if possible (and required)\r
- if (name != null && removeNameIfPossible){\r
+ if (name != null && config.isDeleteNameIfPossible()){\r
try{\r
- nameService.delete(name, new NameDeletionConfigurator());\r
- }catch (DataChangeNoRollbackException ex){\r
+ nameService.delete(name, config.getNameDeletionConfig());\r
+ }catch (ReferencedObjectUndeletableException ex){\r
+ System.err.println("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
} catch (Exception e){\r
logger.error(e);\r
+ e.printStackTrace();\r
}\r
\r
return bestCandidate;\r
List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(\r
topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);\r
\r
- int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupedHitCount : 0;\r
+ int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;\r
+ return new DefaultPagerImpl<SearchResult<TaxonBase>>(pageNumber, totalHits, pageSize, searchResults);\r
+ }\r
+\r
+ @Override\r
+ public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTermBase<?>> statusFilter,\r
+ Classification classification,\r
+ Integer pageSize, Integer pageNumber,\r
+ List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, ParseException {\r
+\r
+ LuceneSearch luceneSearch = prepareByDistributionSearch(areaFilter, statusFilter, classification);\r
+\r
+ // --- execute search\r
+ TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);\r
+\r
+ Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();\r
+ idFieldMap.put(CdmBaseType.TAXON, "id");\r
+\r
+ // --- initialize taxa, thighlight matches ....\r
+ ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());\r
+ List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(\r
+ topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);\r
+\r
+ int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;\r
return new DefaultPagerImpl<SearchResult<TaxonBase>>(pageNumber, totalHits, pageSize, searchResults);\r
}\r
\r
BooleanQuery finalQuery = new BooleanQuery();\r
BooleanQuery textQuery = new BooleanQuery();\r
\r
- LuceneSearch luceneSearch = new LuceneSearch(getSession(), TaxonBase.class);\r
- QueryFactory queryFactory = new QueryFactory(luceneSearch);\r
+ LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, TaxonBase.class);\r
+ QueryFactory taxonBaseQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(TaxonBase.class);\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
- luceneSearch.setClazz(clazz);\r
+ luceneSearch.setCdmTypRestriction(clazz);\r
\r
- textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
- textQuery.add(queryFactory.newDefinedTermQuery("name.rank", queryString, languages), Occur.SHOULD);\r
+ textQuery.add(taxonBaseQueryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
+ textQuery.add(taxonBaseQueryFactory.newDefinedTermQuery("name.rank", queryString, languages), Occur.SHOULD);\r
\r
finalQuery.add(textQuery, Occur.MUST);\r
\r
if(classification != null){\r
- finalQuery.add(queryFactory.newEntityIdQuery("taxonNodes.classification.id", classification), Occur.MUST);\r
+ finalQuery.add(taxonBaseQueryFactory.newEntityIdQuery("taxonNodes.classification.id", classification), Occur.MUST);\r
+ }\r
+ luceneSearch.setQuery(finalQuery);\r
+\r
+ if(highlightFragments){\r
+ luceneSearch.setHighlightFields(taxonBaseQueryFactory.getTextFieldNamesAsArray());\r
+ }\r
+ return luceneSearch;\r
+ }\r
+\r
+ /**\r
+ * Uses org.apache.lucene.search.join.JoinUtil for query time joining, alternatively\r
+ * the BlockJoinQuery could be used. The latter might be more memory save but has the\r
+ * drawback of requiring to do the join an indexing time.\r
+ * see http://dev.e-taxonomy.eu/trac/wiki/LuceneNotes#JoinsinLucene for more information on this.\r
+ *\r
+ * Joins TaxonRelationShip with Taxon depending on the direction of the given edge:\r
+ * <ul>\r
+ * <li>direct, everted: {@link Direction.relatedTo}: TaxonRelationShip.relatedTo.id --> Taxon.id </li>\r
+ * <li>inverse: {@link Direction.relatedFrom}: TaxonRelationShip.relatedFrom.id --> Taxon.id </li>\r
+ * <ul>\r
+ *\r
+ * @param queryString\r
+ * @param classification\r
+ * @param languages\r
+ * @param highlightFragments\r
+ * @return\r
+ * @throws IOException\r
+ */\r
+ protected LuceneSearch prepareFindByTaxonRelationFullTextSearch(TaxonRelationshipEdge edge, String queryString, Classification classification, List<Language> languages,\r
+ boolean highlightFragments) throws IOException {\r
+\r
+ String fromField;\r
+ String queryTermField;\r
+ String toField = "id"; // TaxonBase.uuid\r
+\r
+ if(edge.isBidirectional()){\r
+ throw new RuntimeException("Bidirectional joining not supported!");\r
+ }\r
+ if(edge.isEvers()){\r
+ fromField = "relatedFrom.id";\r
+ queryTermField = "relatedFrom.titleCache";\r
+ } else if(edge.isInvers()) {\r
+ fromField = "relatedTo.id";\r
+ queryTermField = "relatedTo.titleCache";\r
+ } else {\r
+ throw new RuntimeException("Invalid direction: " + edge.getDirections());\r
+ }\r
+\r
+ BooleanQuery finalQuery = new BooleanQuery();\r
+\r
+ LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, TaxonBase.class);\r
+ QueryFactory taxonBaseQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(TaxonBase.class);\r
+\r
+ BooleanQuery joinFromQuery = new BooleanQuery();\r
+ joinFromQuery.add(taxonBaseQueryFactory.newTermQuery(queryTermField, queryString), Occur.MUST);\r
+ joinFromQuery.add(taxonBaseQueryFactory.newEntityIdQuery("type.id", edge.getTaxonRelationshipType()), Occur.MUST);\r
+ Query joinQuery = taxonBaseQueryFactory.newJoinQuery(fromField, toField, joinFromQuery, TaxonRelationship.class);\r
+\r
+ SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};\r
+ luceneSearch.setSortFields(sortFields);\r
+\r
+ finalQuery.add(joinQuery, Occur.MUST);\r
+\r
+ if(classification != null){\r
+ finalQuery.add(taxonBaseQueryFactory.newEntityIdQuery("taxonNodes.classification.id", classification), Occur.MUST);\r
}\r
luceneSearch.setQuery(finalQuery);\r
\r
if(highlightFragments){\r
- luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());\r
+ luceneSearch.setHighlightFields(taxonBaseQueryFactory.getTextFieldNamesAsArray());\r
+ }\r
+ return luceneSearch;\r
+ }\r
+\r
+\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNamesByFullText(java.util.EnumSet, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, java.util.Set, java.util.List, boolean, java.lang.Integer, java.lang.Integer, java.util.List, java.util.Map)\r
+ */\r
+ @Override\r
+ public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(\r
+ EnumSet<TaxaAndNamesSearchMode> searchModes, String queryString, Classification classification,\r
+ Set<NamedArea> namedAreas, Set<PresenceAbsenceTermBase<?>> distributionStatus, List<Language> languages,\r
+ boolean highlightFragments, Integer pageSize,\r
+ Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)\r
+ throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException {\r
+\r
+ // FIXME: allow taxonomic ordering\r
+ // hql equivalent: order by t.name.genusOrUninomial, case when t.name.specificEpithet like '\"%\"' then 1 else 0 end, t.name.specificEpithet, t.name.rank desc, t.name.nameCache";\r
+ // this require building a special sort column by a special classBridge\r
+ if(highlightFragments){\r
+ logger.warn("findTaxaAndNamesByFullText() : fragment highlighting is " +\r
+ "currently not fully supported by this method and thus " +\r
+ "may not work with common names and misapplied names.");\r
+ }\r
+\r
+ // convert sets to lists\r
+ List<NamedArea> namedAreaList = null;\r
+ List<PresenceAbsenceTermBase<?>>distributionStatusList = null;\r
+ if(namedAreas != null){\r
+ namedAreaList = new ArrayList<NamedArea>(namedAreas.size());\r
+ namedAreaList.addAll(namedAreas);\r
+ }\r
+ if(distributionStatus != null){\r
+ distributionStatusList = new ArrayList<PresenceAbsenceTermBase<?>>(distributionStatus.size());\r
+ distributionStatusList.addAll(distributionStatus);\r
+ }\r
+\r
+ // set default if parameter is null\r
+ if(searchModes == null){\r
+ searchModes = EnumSet.of(TaxaAndNamesSearchMode.doTaxa);\r
+ }\r
+\r
+ boolean addDistributionFilter = namedAreas != null && namedAreas.size() > 0;\r
+\r
+ List<LuceneSearch> luceneSearches = new ArrayList<LuceneSearch>();\r
+ Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();\r
+\r
+ /*\r
+ ======== filtering by distribution , HOWTO ========\r
+\r
+ - http://www.javaranch.com/journal/2009/02/filtering-a-lucene-search.html\r
+ - http://stackoverflow.com/questions/17709256/lucene-solr-using-complex-filters -> QueryWrapperFilter\r
+ add Filter to search as http://lucene.apache.org/core/3_6_0/api/all/org/apache/lucene/search/Filter.html\r
+ which will be put into a FilteredQuersy in the end ?\r
+\r
+\r
+ 3. how does it work in spatial?\r
+ see\r
+ - http://www.nsshutdown.com/projects/lucene/whitepaper/locallucene_v2.html\r
+ - http://www.infoq.com/articles/LuceneSpatialSupport\r
+ - http://www.mhaller.de/archives/156-Spatial-search-with-Lucene.html\r
+ ------------------------------------------------------------------------\r
+\r
+ filter strategies:\r
+ A) use a separate distribution filter per index sub-query/search:\r
+ - byTaxonSyonym (query TaxaonBase):\r
+ use a join area filter (Distribution -> TaxonBase)\r
+ - byCommonName (query DescriptionElementBase): use an area filter on\r
+ DescriptionElementBase !!! PROBLEM !!!\r
+ This cannot work since the distributions are different entities than the\r
+ common names and thus these are different lucene documents.\r
+ - byMisaplliedNames (join query TaxonRelationship -> TaxaonBase):\r
+ use a join area filter (Distribution -> TaxonBase)\r
+\r
+ B) use a common distribution filter for all index sub-query/searches:\r
+ - use a common join area filter (Distribution -> TaxonBase)\r
+ - also implement the byCommonName as join query (CommonName -> TaxonBase)\r
+ PROBLEM in this case: we are losing the fragment highlighting for the\r
+ common names, since the returned documents are always TaxonBases\r
+ */\r
+\r
+ /* The QueryFactory for creating filter queries on Distributions should\r
+ * The query factory used for the common names query cannot be reused\r
+ * for this case, since we want to only record the text fields which are\r
+ * actually used in the primary query\r
+ */\r
+ QueryFactory distributionFilterQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(Distribution.class);\r
+\r
+ BooleanFilter multiIndexByAreaFilter = new BooleanFilter();\r
+\r
+\r
+ // search for taxa or synonyms\r
+ if(searchModes.contains(TaxaAndNamesSearchMode.doTaxa) || searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {\r
+ Class taxonBaseSubclass = TaxonBase.class;\r
+ if(searchModes.contains(TaxaAndNamesSearchMode.doTaxa) && !searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)){\r
+ taxonBaseSubclass = Taxon.class;\r
+ } else if (!searchModes.contains(TaxaAndNamesSearchMode.doTaxa) && searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {\r
+ taxonBaseSubclass = Synonym.class;\r
+ }\r
+ luceneSearches.add(prepareFindByFullTextSearch(taxonBaseSubclass, queryString, classification, languages, highlightFragments));\r
+ idFieldMap.put(CdmBaseType.TAXON, "id");\r
+ /* A) does not work!!!!\r
+ if(addDistributionFilter){\r
+ // in this case we need a filter which uses a join query\r
+ // to get the TaxonBase documents for the DescriptionElementBase documents\r
+ // which are matching the areas in question\r
+ Query taxonAreaJoinQuery = createByDistributionJoinQuery(\r
+ namedAreaList,\r
+ distributionStatusList,\r
+ distributionFilterQueryFactory\r
+ );\r
+ multiIndexByAreaFilter.add(new QueryWrapperFilter(taxonAreaJoinQuery), Occur.SHOULD);\r
+ }\r
+ */\r
+ if(addDistributionFilter && searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)){\r
+ // add additional area filter for synonyms\r
+ String fromField = "inDescription.taxon.id"; // in DescriptionElementBase index\r
+ String toField = "accTaxon.id"; // id in TaxonBase index\r
+\r
+ BooleanQuery byDistributionQuery = createByDistributionQuery(namedAreaList, distributionStatusList, distributionFilterQueryFactory);\r
+\r
+ Query taxonAreaJoinQuery = distributionFilterQueryFactory.newJoinQuery(fromField, toField, byDistributionQuery, Distribution.class);\r
+ multiIndexByAreaFilter.add(new QueryWrapperFilter(taxonAreaJoinQuery), Occur.SHOULD);\r
+\r
+ }\r
+ }\r
+\r
+ // search by CommonTaxonName\r
+ if(searchModes.contains(TaxaAndNamesSearchMode.doTaxaByCommonNames)) {\r
+ // B)\r
+ QueryFactory descriptionElementQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(DescriptionElementBase.class);\r
+ Query byCommonNameJoinQuery = descriptionElementQueryFactory.newJoinQuery(\r
+ "inDescription.taxon.id",\r
+ "id",\r
+ QueryFactory.addTypeRestriction(\r
+ createByDescriptionElementFullTextQuery(queryString, classification, null, languages, descriptionElementQueryFactory)\r
+ , CommonTaxonName.class\r
+ ),\r
+ CommonTaxonName.class);\r
+ logger.debug("byCommonNameJoinQuery: " + byCommonNameJoinQuery.toString());\r
+ LuceneSearch byCommonNameSearch = new LuceneSearch(luceneIndexToolProvider, GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, Taxon.class);\r
+ byCommonNameSearch.setCdmTypRestriction(Taxon.class);\r
+ byCommonNameSearch.setQuery(byCommonNameJoinQuery);\r
+ idFieldMap.put(CdmBaseType.TAXON, "id");\r
+\r
+ luceneSearches.add(byCommonNameSearch);\r
+\r
+ /* A) does not work!!!!\r
+ luceneSearches.add(\r
+ prepareByDescriptionElementFullTextSearch(CommonTaxonName.class,\r
+ queryString, classification, null, languages, highlightFragments)\r
+ );\r
+ idFieldMap.put(CdmBaseType.DESCRIPTION_ELEMENT, "inDescription.taxon.id");\r
+ if(addDistributionFilter){\r
+ // in this case we are able to use DescriptionElementBase documents\r
+ // which are matching the areas in question directly\r
+ BooleanQuery byDistributionQuery = createByDistributionQuery(\r
+ namedAreaList,\r
+ distributionStatusList,\r
+ distributionFilterQueryFactory\r
+ );\r
+ multiIndexByAreaFilter.add(new QueryWrapperFilter(byDistributionQuery), Occur.SHOULD);\r
+ } */\r
+ }\r
+\r
+ // search by misapplied names\r
+ if(searchModes.contains(TaxaAndNamesSearchMode.doMisappliedNames)) {\r
+ // NOTE:\r
+ // prepareFindByTaxonRelationFullTextSearch() is making use of JoinUtil.createJoinQuery()\r
+ // which allows doing query time joins\r
+ // finds the misapplied name (Taxon B) which is an misapplication for\r
+ // a related Taxon A.\r
+ //\r
+ luceneSearches.add(prepareFindByTaxonRelationFullTextSearch(\r
+ new TaxonRelationshipEdge(TaxonRelationshipType.MISAPPLIED_NAME_FOR(), Direction.relatedTo),\r
+ queryString, classification, languages, highlightFragments));\r
+ idFieldMap.put(CdmBaseType.TAXON, "id");\r
+\r
+ if(addDistributionFilter){\r
+ String fromField = "inDescription.taxon.id"; // in DescriptionElementBase index\r
+\r
+ /*\r
+ * Here i was facing wired and nasty bug which took me bugging be really for hours until I found this solution.\r
+ * Maybe this is a but in java itself java.\r
+ *\r
+ * When the string toField is constructed by using the expression TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString()\r
+ * directly:\r
+ *\r
+ * String toField = "relation." + TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString() +".to.id";\r
+ *\r
+ * The byDistributionQuery fails, however when the uuid is first stored in another string variable the query\r
+ * will execute as expected:\r
+ *\r
+ * String misappliedNameForUuid = TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString();\r
+ * String toField = "relation." + misappliedNameForUuid +".to.id";\r
+ *\r
+ * Comparing both strings by the String.equals method returns true, so both String are identical.\r
+ *\r
+ * The bug occurs when running eu.etaxonomy.cdm.api.service.TaxonServiceSearchTest in eclipse and in maven and seems to to be\r
+ * dependent from a specific jvm (openjdk6 6b27-1.12.6-1ubuntu0.13.04.2, openjdk7 7u25-2.3.10-1ubuntu0.13.04.2, oracle jdk1.7.0_25 tested)\r
+ * The bug is persistent after a reboot of the development computer.\r
+ */\r
+// String misappliedNameForUuid = TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString();\r
+// String toField = "relation." + misappliedNameForUuid +".to.id";\r
+ String toField = "relation.1ed87175-59dd-437e-959e-0d71583d8417.to.id";\r
+// System.out.println("relation.1ed87175-59dd-437e-959e-0d71583d8417.to.id".equals("relation." + misappliedNameForUuid +".to.id") ? " > identical" : " > different");\r
+// System.out.println("relation.1ed87175-59dd-437e-959e-0d71583d8417.to.id".equals("relation." + TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString() +".to.id") ? " > identical" : " > different");\r
+\r
+ BooleanQuery byDistributionQuery = createByDistributionQuery(namedAreaList, distributionStatusList, distributionFilterQueryFactory);\r
+ Query taxonAreaJoinQuery = distributionFilterQueryFactory.newJoinQuery(fromField, toField, byDistributionQuery, Distribution.class);\r
+ QueryWrapperFilter filter = new QueryWrapperFilter(taxonAreaJoinQuery);\r
+\r
+// debug code for bug described above\r
+ DocIdSet filterMatchSet = filter.getDocIdSet(luceneIndexToolProvider.getIndexReaderFor(Taxon.class));\r
+// System.err.println(DocIdBitSetPrinter.docsAsString(filterMatchSet, 100));\r
+\r
+ multiIndexByAreaFilter.add(filter, Occur.SHOULD);\r
+ }\r
+ }\r
+\r
+ LuceneMultiSearch multiSearch = new LuceneMultiSearch(luceneIndexToolProvider,\r
+ luceneSearches.toArray(new LuceneSearch[luceneSearches.size()]));\r
+\r
+\r
+ if(addDistributionFilter){\r
+\r
+ // B)\r
+ // in this case we need a filter which uses a join query\r
+ // to get the TaxonBase documents for the DescriptionElementBase documents\r
+ // which are matching the areas in question\r
+ //\r
+ // for toTaxa, doByCommonName\r
+ Query taxonAreaJoinQuery = createByDistributionJoinQuery(\r
+ namedAreaList,\r
+ distributionStatusList,\r
+ distributionFilterQueryFactory\r
+ );\r
+ multiIndexByAreaFilter.add(new QueryWrapperFilter(taxonAreaJoinQuery), Occur.SHOULD);\r
+ }\r
+\r
+ if (addDistributionFilter){\r
+ multiSearch.setFilter(multiIndexByAreaFilter);\r
}\r
+ // --- execute search\r
+ TopGroupsWithMaxScore topDocsResultSet = multiSearch.executeSearch(pageSize, pageNumber);\r
+\r
+ // --- initialize taxa, highlight matches ....\r
+ ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(multiSearch, multiSearch.getQuery());\r
+\r
+\r
+ List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(\r
+ topDocsResultSet, multiSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);\r
+\r
+ int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;\r
+ return new DefaultPagerImpl<SearchResult<TaxonBase>>(pageNumber, totalHits, pageSize, searchResults);\r
+ }\r
+\r
+ /**\r
+ * @param namedAreaList at least one area must be in the list\r
+ * @param distributionStatusList optional\r
+ * @return\r
+ * @throws IOException\r
+ */\r
+ protected Query createByDistributionJoinQuery(\r
+ List<NamedArea> namedAreaList,\r
+ List<PresenceAbsenceTermBase<?>> distributionStatusList,\r
+ QueryFactory queryFactory\r
+ ) throws IOException {\r
+\r
+ String fromField = "inDescription.taxon.id"; // in DescriptionElementBase index\r
+ String toField = "id"; // id in TaxonBase index\r
+\r
+ BooleanQuery byDistributionQuery = createByDistributionQuery(namedAreaList, distributionStatusList, queryFactory);\r
+\r
+ Query taxonAreaJoinQuery = queryFactory.newJoinQuery(fromField, toField, byDistributionQuery, Distribution.class);\r
+\r
+ return taxonAreaJoinQuery;\r
+ }\r
+\r
+ /**\r
+ * @param namedAreaList\r
+ * @param distributionStatusList\r
+ * @param queryFactory\r
+ * @return\r
+ */\r
+ private BooleanQuery createByDistributionQuery(List<NamedArea> namedAreaList,\r
+ List<PresenceAbsenceTermBase<?>> distributionStatusList, QueryFactory queryFactory) {\r
+ BooleanQuery areaQuery = new BooleanQuery();\r
+ // area field from Distribution\r
+ areaQuery.add(queryFactory.newEntityIdsQuery("area.id", namedAreaList), Occur.MUST);\r
+\r
+ // status field from Distribution\r
+ if(distributionStatusList != null && distributionStatusList.size() > 0){\r
+ areaQuery.add(queryFactory.newEntityIdsQuery("status.id", distributionStatusList), Occur.MUST);\r
+ }\r
+\r
+ logger.debug("createByDistributionQuery() query: " + areaQuery.toString());\r
+ return areaQuery;\r
+ }\r
+\r
+ /**\r
+ * This method has been primarily created for testing the area join query but might\r
+ * also be useful in other situations\r
+ *\r
+ * @param namedAreaList\r
+ * @param distributionStatusList\r
+ * @param classification\r
+ * @param highlightFragments\r
+ * @return\r
+ * @throws IOException\r
+ */\r
+ protected LuceneSearch prepareByDistributionSearch(\r
+ List<NamedArea> namedAreaList, List<PresenceAbsenceTermBase<?>> distributionStatusList,\r
+ Classification classification) throws IOException {\r
+\r
+ BooleanQuery finalQuery = new BooleanQuery();\r
+\r
+ LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, Taxon.class);\r
+\r
+ // FIXME is this query factory using the wrong type?\r
+ QueryFactory taxonQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(Taxon.class);\r
+\r
+ SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};\r
+ luceneSearch.setSortFields(sortFields);\r
+\r
+\r
+ Query byAreaQuery = createByDistributionJoinQuery(namedAreaList, distributionStatusList, taxonQueryFactory);\r
+\r
+ finalQuery.add(byAreaQuery, Occur.MUST);\r
+\r
+ if(classification != null){\r
+ finalQuery.add(taxonQueryFactory.newEntityIdQuery("taxonNodes.classification.id", classification), Occur.MUST);\r
+ }\r
+\r
+ logger.info("prepareByAreaSearch() query: " + finalQuery.toString());\r
+ luceneSearch.setQuery(finalQuery);\r
+\r
return luceneSearch;\r
}\r
\r
\r
+\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findByDescriptionElementFullText(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, java.util.List, java.util.List, boolean, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\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
+ Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException {\r
\r
LuceneSearch luceneSearchByDescriptionElement = prepareByDescriptionElementFullTextSearch(null, queryString, classification, null, languages, highlightFragments);\r
LuceneSearch luceneSearchByTaxonBase = prepareFindByFullTextSearch(null, queryString, classification, languages, highlightFragments);\r
\r
- LuceneMultiSearch multiSearch = new LuceneMultiSearch(luceneSearchByDescriptionElement, luceneSearchByTaxonBase);\r
+ LuceneMultiSearch multiSearch = new LuceneMultiSearch(luceneIndexToolProvider, luceneSearchByDescriptionElement, luceneSearchByTaxonBase);\r
\r
// --- execute search\r
TopGroupsWithMaxScore topDocsResultSet = multiSearch.executeSearch(pageSize, pageNumber);\r
List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(\r
topDocsResultSet, multiSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);\r
\r
- int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupedHitCount : 0;\r
+ int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;\r
return new DefaultPagerImpl<SearchResult<TaxonBase>>(pageNumber, totalHits, pageSize, searchResults);\r
\r
}\r
* @param directorySelectClass\r
* @return\r
*/\r
- protected LuceneSearch prepareByDescriptionElementFullTextSearch(Class<? extends CdmBase> clazz, String queryString, Classification classification, List<Feature> features,\r
+ protected LuceneSearch prepareByDescriptionElementFullTextSearch(Class<? extends CdmBase> clazz,\r
+ String queryString, Classification classification, List<Feature> features,\r
List<Language> languages, boolean highlightFragments) {\r
- BooleanQuery finalQuery = new BooleanQuery();\r
- BooleanQuery textQuery = new BooleanQuery();\r
\r
- LuceneSearch luceneSearch = new LuceneSearch(getSession(), DescriptionElementBase.class);\r
- QueryFactory queryFactory = new QueryFactory(luceneSearch);\r
+ LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, DescriptionElementBase.class);\r
+ QueryFactory descriptionElementQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(DescriptionElementBase.class);\r
+\r
+ SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("inDescription.taxon.titleCache__sort", SortField.STRING, false)};\r
+\r
+ BooleanQuery finalQuery = createByDescriptionElementFullTextQuery(queryString, classification, features,\r
+ languages, descriptionElementQueryFactory);\r
\r
- SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("inDescription.taxon.titleCache__sort", false)};\r
luceneSearch.setSortFields(sortFields);\r
+ luceneSearch.setCdmTypRestriction(clazz);\r
+ luceneSearch.setQuery(finalQuery);\r
+ if(highlightFragments){\r
+ luceneSearch.setHighlightFields(descriptionElementQueryFactory.getTextFieldNamesAsArray());\r
+ }\r
\r
- // ---- search criteria\r
- luceneSearch.setClazz(clazz);\r
- textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
+ return luceneSearch;\r
+ }\r
+\r
+ /**\r
+ * @param queryString\r
+ * @param classification\r
+ * @param features\r
+ * @param languages\r
+ * @param descriptionElementQueryFactory\r
+ * @return\r
+ */\r
+ private BooleanQuery createByDescriptionElementFullTextQuery(String queryString, Classification classification,\r
+ List<Feature> features, List<Language> languages, QueryFactory descriptionElementQueryFactory) {\r
+ BooleanQuery finalQuery = new BooleanQuery();\r
+ BooleanQuery textQuery = new BooleanQuery();\r
+ textQuery.add(descriptionElementQueryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
\r
// common name\r
Query nameQuery;\r
if(languages == null || languages.size() == 0){\r
- nameQuery = queryFactory.newTermQuery("name", queryString);\r
+ nameQuery = descriptionElementQueryFactory.newTermQuery("name", queryString);\r
} else {\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(descriptionElementQueryFactory.newTermQuery("language.uuid", lang.getUuid().toString(), false), Occur.SHOULD);\r
}\r
- ((BooleanQuery) nameQuery).add(queryFactory.newTermQuery("name", queryString), Occur.MUST);\r
+ ((BooleanQuery) nameQuery).add(descriptionElementQueryFactory.newTermQuery("name", queryString), Occur.MUST);\r
((BooleanQuery) nameQuery).add(languageSubQuery, Occur.MUST);\r
}\r
textQuery.add(nameQuery, Occur.SHOULD);\r
\r
\r
// text field from TextData\r
- textQuery.add(queryFactory.newMultilanguageTextQuery("text", queryString, languages), Occur.SHOULD);\r
+ textQuery.add(descriptionElementQueryFactory.newMultilanguageTextQuery("text", queryString, languages), Occur.SHOULD);\r
\r
// --- TermBase fields - by representation ----\r
// state field from CategoricalData\r
- textQuery.add(queryFactory.newDefinedTermQuery("states.state", queryString, languages), Occur.SHOULD);\r
+ textQuery.add(descriptionElementQueryFactory.newDefinedTermQuery("stateData.state", queryString, languages), Occur.SHOULD);\r
\r
// state field from CategoricalData\r
- textQuery.add(queryFactory.newDefinedTermQuery("states.modifyingText", queryString, languages), Occur.SHOULD);\r
+ textQuery.add(descriptionElementQueryFactory.newDefinedTermQuery("stateData.modifyingText", queryString, languages), Occur.SHOULD);\r
\r
// area field from Distribution\r
- textQuery.add(queryFactory.newDefinedTermQuery("area", queryString, languages), Occur.SHOULD);\r
+ textQuery.add(descriptionElementQueryFactory.newDefinedTermQuery("area", queryString, languages), Occur.SHOULD);\r
\r
// status field from Distribution\r
- textQuery.add(queryFactory.newDefinedTermQuery("status", queryString, languages), Occur.SHOULD);\r
+ textQuery.add(descriptionElementQueryFactory.newDefinedTermQuery("status", queryString, languages), Occur.SHOULD);\r
\r
finalQuery.add(textQuery, Occur.MUST);\r
// --- classification ----\r
\r
if(classification != null){\r
- finalQuery.add(queryFactory.newEntityIdQuery("inDescription.taxon.taxonNodes.classification.id", classification), Occur.MUST);\r
+ finalQuery.add(descriptionElementQueryFactory.newEntityIdQuery("inDescription.taxon.taxonNodes.classification.id", classification), Occur.MUST);\r
}\r
\r
// --- IdentifieableEntity fields - by uuid\r
if(features != null && features.size() > 0 ){\r
- finalQuery.add(queryFactory.newEntityUuidQuery("feature.uuid", features), Occur.MUST);\r
+ finalQuery.add(descriptionElementQueryFactory.newEntityUuidsQuery("feature.uuid", features), Occur.MUST);\r
}\r
\r
// the description must be associated with a taxon\r
- finalQuery.add(queryFactory.newIsNotNullQuery("inDescription.taxon.id"), Occur.MUST);\r
-\r
- luceneSearch.setQuery(finalQuery);\r
+ finalQuery.add(descriptionElementQueryFactory.newIsNotNullQuery("inDescription.taxon.id"), Occur.MUST);\r
\r
- if(highlightFragments){\r
- luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());\r
- }\r
- return luceneSearch;\r
+ logger.info("prepareByDescriptionElementFullTextSearch() query: " + finalQuery.toString());\r
+ return finalQuery;\r
}\r
\r
/**\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
if (!node.isTopmostNode()){\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
- //TODO:Remove\r
- System.out.println("The synonym has no sec reference because it is a misapplied name! Take the sec reference of taxon" + taxon.getSec());\r
- sourceReference = taxon.getSec();\r
+ logger.warn("The synonym has no sec reference because it is a misapplied name! Take the sec reference of taxon" + taxon.getSec());\r
+ sourceReference = taxon.getSec();\r
}\r
\r
synName = syn.getName();\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
BGBM BDI Projects / cdmlib.git / blobdiff