\r
import javax.persistence.EntityNotFoundException;\r
\r
+import org.apache.commons.lang.StringUtils;\r
import org.apache.log4j.Logger;\r
import org.apache.lucene.index.CorruptIndexException;\r
import org.apache.lucene.queryParser.ParseException;\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.dto.FindByIdentifierDTO;\r
import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO;\r
import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;\r
import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;\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.Annotation;\r
+import eu.etaxonomy.cdm.model.common.AnnotationType;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.DefinedTerm;\r
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
import eu.etaxonomy.cdm.model.common.IdentifiableSource;\r
import eu.etaxonomy.cdm.model.common.Language;\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.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.PresenceAbsenceTerm;\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.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.AmplificationResult;\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.persistence.dao.occurrence.IOccurrenceDao;\r
import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;\r
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;\r
+import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;\r
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;\r
import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
import eu.etaxonomy.cdm.persistence.query.OrderHint;\r
return taxonRelTypeVocabulary;\r
}\r
\r
-\r
-\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
+ public UpdateResult swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){\r
+ UpdateResult result = new UpdateResult();\r
TaxonNameBase<?,?> synonymName = synonym.getName();\r
synonymName.removeTaxonBase(synonym);\r
TaxonNameBase<?,?> taxonName = acceptedTaxon.getName();\r
\r
synonym.setName(taxonName);\r
acceptedTaxon.setName(synonymName);\r
+ result.addUpdatedObject(acceptedTaxon);\r
+ result.addUpdatedObject(synonym);\r
+ return result;\r
\r
// the accepted taxon needs a new uuid because the concept has changed\r
// FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"\r
}\r
\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
-\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
return newAcceptedTaxon;\r
}\r
\r
+ @Override\r
+ @Transactional(readOnly = false)\r
+ public Taxon changeSynonymToAcceptedTaxon(UUID synonymUuid,\r
+ UUID acceptedTaxonUuid,\r
+ boolean deleteSynonym,\r
+ boolean copyCitationInfo,\r
+ Reference citation,\r
+ String microCitation) throws HomotypicalGroupChangeException {\r
+ Synonym synonym = CdmBase.deproxy(dao.load(synonymUuid), Synonym.class);\r
+ Taxon acceptedTaxon = CdmBase.deproxy(dao.load(acceptedTaxonUuid), Taxon.class);\r
+ return changeSynonymToAcceptedTaxon(synonym, acceptedTaxon, deleteSynonym, copyCitationInfo, citation, microCitation);\r
+ }\r
+\r
+ @Override\r
+ @Transactional(readOnly = false)\r
+ public UpdateResult changeSynonymToRelatedTaxon(UUID synonymUuid,\r
+ UUID toTaxonUuid,\r
+ TaxonRelationshipType taxonRelationshipType,\r
+ Reference citation,\r
+ String microcitation){\r
+\r
+ UpdateResult result = new UpdateResult();\r
+ Taxon toTaxon = (Taxon) dao.load(toTaxonUuid);\r
+ Synonym synonym = (Synonym) dao.load(synonymUuid);\r
+ Taxon relatedTaxon = changeSynonymToRelatedTaxon(synonym, toTaxon, taxonRelationshipType, citation, microcitation);\r
+ result.setCdmEntity(relatedTaxon);\r
+ result.addUpdatedObject(relatedTaxon);\r
+ result.addUpdatedObject(toTaxon);\r
+ return result;\r
+ }\r
\r
@Override\r
+ @Transactional(readOnly = false)\r
public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){\r
\r
// Get name from synonym\r
return fromTaxon;\r
}\r
\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#changeHomotypicalGroupOfSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)\r
- */\r
@Transactional(readOnly = false)\r
@Override\r
public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,\r
\r
\r
// Switch groups\r
- oldHomotypicalGroup.removeTypifiedName(synonymName);\r
+ oldHomotypicalGroup.removeTypifiedName(synonymName, false);\r
newHomotypicalGroup.addTypifiedName(synonymName);\r
\r
//remove existing basionym relationships\r
\r
}\r
\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)\r
- */\r
@Override\r
@Transactional(readOnly = false)\r
public void updateTitleCache(Class<? extends TaxonBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy, IProgressMonitor monitor) {\r
this.dao = dao;\r
}\r
\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
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);\r
}\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
return results;\r
}\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
return results;\r
}\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
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);\r
}\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
return results;\r
}\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
\r
\r
- /**\r
- * @param taxon\r
- * @param includeRelationships\r
- * @param maxDepth\r
- * @param limit\r
- * @param starts\r
- * @param propertyPaths\r
- * @return an List which is not specifically ordered\r
- */\r
@Override\r
public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,\r
Integer limit, Integer start, List<String> propertyPaths) {\r
return taxa;\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
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);\r
}\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
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);\r
}\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<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){\r
List<List<Synonym>> result = new ArrayList<List<Synonym>>();\r
\r
}\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
}\r
\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
}\r
\r
@Override\r
- public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator){\r
+ public List<UuidAndTitleCache<IdentifiableEntity>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator){\r
\r
- List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();\r
-// Class<? extends TaxonBase> clazz = null;\r
-// if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {\r
-// clazz = TaxonBase.class;\r
-// //propertyPath.addAll(configurator.getTaxonPropertyPath());\r
-// //propertyPath.addAll(configurator.getSynonymPropertyPath());\r
-// } else if(configurator.isDoTaxa()) {\r
-// clazz = Taxon.class;\r
-// //propertyPath = configurator.getTaxonPropertyPath();\r
-// } else if (configurator.isDoSynonyms()) {\r
-// clazz = Synonym.class;\r
-// //propertyPath = configurator.getSynonymPropertyPath();\r
-// }\r
+ List<UuidAndTitleCache<IdentifiableEntity>> results = new ArrayList<UuidAndTitleCache<IdentifiableEntity>>();\r
\r
\r
- result = dao.getTaxaByNameForEditor(configurator.isDoTaxa(), configurator.isDoSynonyms(), configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());\r
- return result;\r
+ if (configurator.isDoSynonyms() || configurator.isDoTaxa() || configurator.isDoNamesWithoutTaxa()){\r
+ results = dao.getTaxaByNameForEditor(configurator.isDoTaxa(), configurator.isDoSynonyms(), configurator.isDoNamesWithoutTaxa(), configurator.isDoMisappliedNames(),configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());\r
+ }\r
+ if (configurator.isDoTaxaByCommonNames()) {\r
+ //if(configurator.getPageSize() == null ){\r
+ List<UuidAndTitleCache<IdentifiableEntity>> commonNameResults = dao.getTaxaByCommonNameForEditor(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());\r
+ if(commonNameResults != null){\r
+ results.addAll(commonNameResults);\r
+ }\r
+ // }\r
+ }\r
+ return results;\r
}\r
\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
return dao.getUuidAndTitleCache();\r
}\r
\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
return medRep;\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxonDescriptionMedia(eu.etaxonomy.cdm.model.taxon.Taxon, boolean)\r
- */\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
-\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
+ // logger.setLevel(Level.TRACE);\r
+// Logger.getLogger("org.hibernate.SQL").setLevel(Level.TRACE);\r
+\r
logger.trace("listMedia() - START");\r
\r
Set<Taxon> taxa = new HashSet<Taxon>();\r
for (Sequence sequence : sequences) {\r
Set<Media> dnaRelatedMedia = new HashSet<Media>();\r
for (SingleRead singleRead : sequence.getSingleReads()){\r
- Amplification amplification = singleRead.getAmplification();\r
+ AmplificationResult amplification = singleRead.getAmplificationResult();\r
dnaRelatedMedia.add(amplification.getGelPhoto());\r
dnaRelatedMedia.add(singleRead.getPherogram());\r
dnaRelatedMedia.remove(null);\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
\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
\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
\r
-\r
-\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
\r
-\r
- /* (non-Javadoc)\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 DeleteResult deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config, Classification classification) {\r
- DeleteResult result = new DeleteResult();\r
+ @Transactional(readOnly = false)\r
+ public DeleteResult deleteTaxon(UUID taxonUUID, TaxonDeletionConfigurator config, UUID classificationUuid) {\r
+\r
if (config == null){\r
config = new TaxonDeletionConfigurator();\r
}\r
+ Taxon taxon = (Taxon)dao.load(taxonUUID);\r
+ Classification classification = HibernateProxyHelper.deproxy(classificationDao.load(classificationUuid), Classification.class);\r
+ DeleteResult result = isDeletable(taxon, config);\r
\r
- List<String> referencedObjects = isDeletable(taxon, config);\r
-\r
- if (referencedObjects.isEmpty()){\r
+ if (result.isOk()){\r
// --- DeleteSynonymRelations\r
if (config.isDeleteSynonymRelations()){\r
boolean removeSynonymNameFromHomotypicalGroup = false;\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
+ this.deleteTaxon(taxRel.getFromTaxon().getUuid(), config, classificationUuid);\r
}\r
}\r
}\r
//throw new ReferencedObjectUndeletableException(message);\r
}\r
removeDescriptions.add(desc);\r
- descriptionService.delete(desc);\r
+\r
\r
}\r
for (TaxonDescription desc: removeDescriptions){\r
taxon.removeDescription(desc);\r
+ descriptionService.delete(desc);\r
}\r
}\r
\r
//check whether taxon will be deleted or not\r
if ((taxon.getTaxonNodes() == null || taxon.getTaxonNodes().size()== 0) && name != null ){\r
taxon = (Taxon) HibernateProxyHelper.deproxy(taxon);\r
- name.removeTaxonBase(taxon);\r
- nameService.saveOrUpdate(name);\r
+ //name.removeTaxonBase(taxon);\r
+ //nameService.saveOrUpdate(name);\r
+ taxon.setName(null);\r
+ //dao.delete(taxon);\r
DeleteResult nameResult = new DeleteResult();\r
\r
- nameResult = nameService.delete(name, config.getNameDeletionConfig());\r
+ //remove name if possible (and required)\r
+ if (name != null && config.isDeleteNameIfPossible()){\r
+ nameResult = nameService.delete(name.getUuid(), config.getNameDeletionConfig());\r
+ }\r
\r
- if (nameResult.isError()){\r
+ if (nameResult.isError() || nameResult.isAbort()){\r
//result.setError();\r
result.addRelatedObject(name);\r
result.addExceptions(nameResult.getExceptions());\r
result.addException(new Exception("The Taxon can't be deleted."));\r
\r
}\r
- }else {\r
- List<Exception> exceptions = new ArrayList<Exception>();\r
- for (String message: referencedObjects){\r
- ReferencedObjectUndeletableException exception = new ReferencedObjectUndeletableException(message);\r
- exceptions.add(exception);\r
- }\r
- result.addExceptions(exceptions);\r
- result.setError();\r
-\r
}\r
+// }else {\r
+// List<Exception> exceptions = new ArrayList<Exception>();\r
+// for (String message: referencedObjects){\r
+// ReferencedObjectUndeletableException exception = new ReferencedObjectUndeletableException(message);\r
+// exceptions.add(exception);\r
+// }\r
+// result.addExceptions(exceptions);\r
+// result.setError();\r
+//\r
+// }\r
return result;\r
\r
}\r
return result;\r
}\r
\r
+ @Override\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
+ public DeleteResult delete(UUID synUUID){\r
+ DeleteResult result = new DeleteResult();\r
+ Synonym syn = (Synonym)dao.load(synUUID);\r
\r
+ return this.deleteSynonym(syn, null);\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
+ @Transactional(readOnly = false)\r
public DeleteResult deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config) {\r
return deleteSynonym(synonym, null, config);\r
\r
}\r
\r
+ @Override\r
+ @Transactional(readOnly = false)\r
+ public DeleteResult deleteSynonym(UUID synonymUuid, SynonymDeletionConfigurator config) {\r
+ return deleteSynonym((Synonym)dao.load(synonymUuid), config);\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 DeleteResult deleteSynonym(Synonym synonym, Taxon taxon, SynonymDeletionConfigurator config) {\r
if (config == null){\r
config = new SynonymDeletionConfigurator();\r
}\r
- List<String> messages = isDeletable(synonym, config);\r
+ result = isDeletable(synonym, config);\r
\r
\r
- if (messages.isEmpty()){\r
+ if (result.isOk()){\r
+\r
synonym = CdmBase.deproxy(dao.merge(synonym), Synonym.class);\r
\r
//remove synonymRelationship\r
taxonSet.addAll(synonym.getAcceptedTaxa());\r
}\r
for (Taxon relatedTaxon : taxonSet){\r
- // dao.deleteSynonymRelationships(synonym, relatedTaxon);\r
- relatedTaxon.removeSynonym(synonym, config.isNewHomotypicGroupIfNeeded());\r
+ relatedTaxon = HibernateProxyHelper.deproxy(relatedTaxon, Taxon.class);\r
+ relatedTaxon.removeSynonym(synonym, false);\r
+ this.saveOrUpdate(relatedTaxon);\r
}\r
this.saveOrUpdate(synonym);\r
\r
\r
//remove synonym (if necessary)\r
\r
- UUID uuid = null;\r
+ result.addUpdatedObject(taxon);\r
if (synonym.getSynonymRelations().isEmpty()){\r
TaxonNameBase<?,?> name = synonym.getName();\r
synonym.setName(null);\r
- uuid = dao.delete(synonym);\r
+ dao.delete(synonym);\r
\r
//remove name if possible (and required)\r
if (name != null && config.isDeleteNameIfPossible()){\r
\r
- nameService.delete(name, config.getNameDeletionConfig());\r
+ DeleteResult nameDeleteresult = nameService.delete(name.getUuid(), config.getNameDeletionConfig());\r
+ if (nameDeleteresult.isAbort()){\r
+ result.addExceptions(nameDeleteresult.getExceptions());\r
+ result.addUpdatedObject(name);\r
+ }\r
\r
}\r
\r
return result;\r
}\r
\r
- return result;\r
- }else{\r
- List<Exception> exceptions = new ArrayList<Exception>();\r
- for (String message :messages){\r
- exceptions.add(new ReferencedObjectUndeletableException(message));\r
- }\r
- result.setError();\r
- result.addExceptions(exceptions);\r
- return result;\r
+\r
}\r
+ return result;\r
+// else{\r
+// List<Exception> exceptions = new ArrayList<Exception>();\r
+// for (String message :messages){\r
+// exceptions.add(new ReferencedObjectUndeletableException(message));\r
+// }\r
+// result.setError();\r
+// result.addExceptions(exceptions);\r
+// return result;\r
+// }\r
\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
}\r
\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
\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
\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
\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
return results;\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingTaxon(java.lang.String)\r
- */\r
@Override\r
public Taxon findBestMatchingTaxon(String taxonName) {\r
MatchingTaxonConfigurator config = MatchingTaxonConfigurator.NewInstance();\r
return findBestMatchingTaxon(config);\r
}\r
\r
-\r
-\r
@Override\r
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config) {\r
\r
return configSecUuid.equals(taxonSecUuid);\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingSynonym(java.lang.String)\r
- */\r
@Override\r
public Synonym findBestMatchingSynonym(String taxonName) {\r
List<TaxonBase> synonymList = dao.findByNameTitleCache(false, true, taxonName, null, MatchMode.EXACT, null, 0, null, null);\r
return null;\r
}\r
\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#moveSynonymToAnotherTaxon(eu.etaxonomy.cdm.model.taxon.SynonymRelationship, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String, boolean)\r
- */\r
@Override\r
- public SynonymRelationship moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation, Taxon newTaxon, boolean moveHomotypicGroup,\r
- SynonymRelationshipType newSynonymRelationshipType, Reference reference, String referenceDetail, boolean keepReference) throws HomotypicalGroupChangeException {\r
-\r
- Synonym synonym = oldSynonymRelation.getSynonym();\r
- Taxon fromTaxon = oldSynonymRelation.getAcceptedTaxon();\r
+ @Transactional(readOnly = false)\r
+ public SynonymRelationship moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation,\r
+ Taxon newTaxon,\r
+ boolean moveHomotypicGroup,\r
+ SynonymRelationshipType newSynonymRelationshipType,\r
+ Reference reference,\r
+ String referenceDetail,\r
+ boolean keepReference) throws HomotypicalGroupChangeException {\r
+\r
+ Synonym synonym = (Synonym) dao.load(oldSynonymRelation.getSynonym().getUuid());\r
+ Taxon fromTaxon = (Taxon) dao.load(oldSynonymRelation.getAcceptedTaxon().getUuid());\r
//TODO what if there is no name ?? Concepts may be cached (e.g. via TCS import)\r
TaxonNameBase<?,?> synonymName = synonym.getName();\r
TaxonNameBase<?,?> fromTaxonName = fromTaxon.getName();\r
if (newRefDetail == null && keepReference){\r
newRefDetail = synRelation.getCitationMicroReference();\r
}\r
+ newTaxon = HibernateProxyHelper.deproxy(newTaxon, Taxon.class);\r
+ fromTaxon = HibernateProxyHelper.deproxy(fromTaxon, Taxon.class);\r
SynonymRelationship newSynRelation = newTaxon.addSynonym(syn, newSynonymRelationshipType, newReference, newRefDetail);\r
fromTaxon.removeSynonymRelation(synRelation, false);\r
//\r
}\r
\r
}\r
+ saveOrUpdate(fromTaxon);\r
saveOrUpdate(newTaxon);\r
//Assert that there is a result\r
if (result == null){\r
return result;\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheTaxon()\r
- */\r
@Override\r
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {\r
return dao.getUuidAndTitleCacheTaxon();\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheSynonym()\r
- */\r
@Override\r
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {\r
return dao.getUuidAndTitleCacheSynonym();\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#findByFullText(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, java.util.List, boolean, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
- */\r
@Override\r
public Pager<SearchResult<TaxonBase>> findByFullText(\r
Class<? extends TaxonBase> clazz, String queryString,\r
}\r
\r
@Override\r
- public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTermBase<?>> statusFilter,\r
+ public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTerm> statusFilter,\r
Classification classification,\r
Integer pageSize, Integer pageNumber,\r
List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, ParseException {\r
// ---- search criteria\r
luceneSearch.setCdmTypRestriction(clazz);\r
\r
- textQuery.add(taxonBaseQueryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
- textQuery.add(taxonBaseQueryFactory.newDefinedTermQuery("name.rank", queryString, languages), Occur.SHOULD);\r
+ if(!queryString.isEmpty() && !queryString.equals("*") && !queryString.equals("?") ) {\r
+ textQuery.add(taxonBaseQueryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
+ textQuery.add(taxonBaseQueryFactory.newDefinedTermQuery("name.rank", queryString, languages), Occur.SHOULD);\r
+ }\r
+\r
+ if(textQuery.getClauses().length > 0) {\r
+ finalQuery.add(textQuery, Occur.MUST);\r
+ }\r
\r
- finalQuery.add(textQuery, Occur.MUST);\r
\r
if(classification != null){\r
finalQuery.add(taxonBaseQueryFactory.newEntityIdQuery("taxonNodes.classification.id", classification), Occur.MUST);\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
+ Set<NamedArea> namedAreas, Set<PresenceAbsenceTerm> 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
// convert sets to lists\r
List<NamedArea> namedAreaList = null;\r
- List<PresenceAbsenceTermBase<?>>distributionStatusList = null;\r
+ List<PresenceAbsenceTerm>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 = new ArrayList<PresenceAbsenceTerm>(distributionStatus.size());\r
distributionStatusList.addAll(distributionStatus);\r
}\r
\r
*/\r
protected Query createByDistributionJoinQuery(\r
List<NamedArea> namedAreaList,\r
- List<PresenceAbsenceTermBase<?>> distributionStatusList,\r
+ List<PresenceAbsenceTerm> distributionStatusList,\r
QueryFactory queryFactory\r
) throws IOException {\r
\r
* @return\r
*/\r
private BooleanQuery createByDistributionQuery(List<NamedArea> namedAreaList,\r
- List<PresenceAbsenceTermBase<?>> distributionStatusList, QueryFactory queryFactory) {\r
+ List<PresenceAbsenceTerm> distributionStatusList, QueryFactory queryFactory) {\r
BooleanQuery areaQuery = new BooleanQuery();\r
// area field from Distribution\r
areaQuery.add(queryFactory.newEntityIdsQuery("area.id", namedAreaList), Occur.MUST);\r
* @throws IOException\r
*/\r
protected LuceneSearch prepareByDistributionSearch(\r
- List<NamedArea> namedAreaList, List<PresenceAbsenceTermBase<?>> distributionStatusList,\r
+ List<NamedArea> namedAreaList, List<PresenceAbsenceTerm> distributionStatusList,\r
Classification classification) throws IOException {\r
\r
BooleanQuery finalQuery = new BooleanQuery();\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>> findByDescriptionElementFullText(\r
Class<? extends DescriptionElementBase> clazz, String queryString,\r
}\r
\r
@Override\r
+ @Transactional(readOnly = false)\r
+ public UpdateResult changeRelatedTaxonToSynonym(UUID fromTaxonUuid,\r
+ UUID toTaxonUuid,\r
+ TaxonRelationshipType oldRelationshipType,\r
+ SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException {\r
+ UpdateResult result = new UpdateResult();\r
+ Taxon fromTaxon = (Taxon) dao.load(fromTaxonUuid);\r
+ Taxon toTaxon = (Taxon) dao.load(toTaxonUuid);\r
+ Synonym synonym = changeRelatedTaxonToSynonym(fromTaxon, toTaxon, oldRelationshipType, synonymRelationshipType);\r
+ result.setCdmEntity(synonym);\r
+ result.addUpdatedObject(fromTaxon);\r
+ result.addUpdatedObject(toTaxon);\r
+ result.addUpdatedObject(synonym);\r
+\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ @Transactional(readOnly = false)\r
public Synonym changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon, TaxonRelationshipType oldRelationshipType,\r
SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException {\r
// Create new synonym using concept name\r
//TODO: configurator and classification\r
TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();\r
config.setDeleteNameIfPossible(false);\r
- this.deleteTaxon(fromTaxon, config, null);\r
+ this.deleteTaxon(fromTaxon.getUuid(), config, null);\r
return synonymRelationship.getSynonym();\r
\r
}\r
+\r
@Override\r
- public List<String> isDeletable(TaxonBase taxonBase, DeleteConfiguratorBase config){\r
- List<String> result = new ArrayList<String>();\r
+ public DeleteResult isDeletable(TaxonBase taxonBase, DeleteConfiguratorBase config){\r
+ DeleteResult result = new DeleteResult();\r
Set<CdmBase> references = commonService.getReferencingObjectsForDeletion(taxonBase);\r
if (taxonBase instanceof Taxon){\r
TaxonDeletionConfigurator taxonConfig = (TaxonDeletionConfigurator) config;\r
return result;\r
}\r
\r
- private List<String> isDeletableForSynonym(Set<CdmBase> references, SynonymDeletionConfigurator config){\r
+ private DeleteResult isDeletableForSynonym(Set<CdmBase> references, SynonymDeletionConfigurator config){\r
String message;\r
- List<String> result = new ArrayList<String>();\r
+ DeleteResult result = new DeleteResult();\r
for (CdmBase ref: references){\r
if (!(ref instanceof SynonymRelationship || ref instanceof Taxon || ref instanceof TaxonNameBase )){\r
message = "The Synonym can't be deleted as long as it is referenced by " + ref.getClass().getSimpleName() + " with id "+ ref.getId();\r
- result.add(message);\r
+ result.addException(new ReferencedObjectUndeletableException(message));\r
+ result.addRelatedObject(ref);\r
+ result.setAbort();\r
}\r
}\r
\r
return result;\r
}\r
- private List<String> isDeletableForTaxon(Set<CdmBase> references, TaxonDeletionConfigurator config){\r
- String message;\r
- List<String> result = new ArrayList<String>();\r
+\r
+ private DeleteResult isDeletableForTaxon(Set<CdmBase> references, TaxonDeletionConfigurator config){\r
+ String message = null;\r
+ DeleteResult result = new DeleteResult();\r
for (CdmBase ref: references){\r
if (!(ref instanceof TaxonNameBase)){\r
+ message = null;\r
if (!config.isDeleteSynonymRelations() && (ref instanceof SynonymRelationship)){\r
message = "The Taxon can't be deleted as long as it has synonyms.";\r
- result.add(message);\r
+\r
}\r
if (!config.isDeleteDescriptions() && (ref instanceof DescriptionBase)){\r
message = "The Taxon can't be deleted as long as it has factual data.";\r
- result.add(message);\r
+\r
}\r
\r
if (!config.isDeleteTaxonNodes() && (ref instanceof TaxonNode)){\r
message = "The Taxon can't be deleted as long as it belongs to a taxon node.";\r
- result.add(message);\r
+\r
}\r
if (!config.isDeleteTaxonRelationships() && (ref instanceof TaxonNode)){\r
if (!config.isDeleteMisappliedNamesAndInvalidDesignations() && (((TaxonRelationship)ref).getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())|| ((TaxonRelationship)ref).getType().equals(TaxonRelationshipType.INVALID_DESIGNATION_FOR()))){\r
message = "The Taxon can't be deleted as long as it has misapplied names or invalid designations.";\r
- result.add(message);\r
+\r
} else{\r
message = "The Taxon can't be deleted as long as it belongs to a taxon node.";\r
- result.add(message);\r
+\r
}\r
}\r
if (ref instanceof PolytomousKeyNode){\r
message = "The Taxon can't be deleted as long as it is referenced by a polytomous key node.";\r
- result.add(message);\r
+\r
}\r
\r
if (HibernateProxyHelper.isInstanceOf(ref, IIdentificationKey.class)){\r
message = "Taxon can't be deleted as it is used in an identification key. Remove from identification key prior to deleting this name";\r
- result.add(message);\r
+\r
\r
}\r
\r
//TaxonInteraction\r
if (ref.isInstanceOf(TaxonInteraction.class)){\r
message = "Taxon can't be deleted as it is used in taxonInteraction#taxon2";\r
- result.add(message);\r
+\r
}\r
\r
//TaxonInteraction\r
if (ref.isInstanceOf(DeterminationEvent.class)){\r
message = "Taxon can't be deleted as it is used in a determination event";\r
- result.add(message);\r
+\r
}\r
\r
}\r
-\r
+ if (message != null){\r
+ result.addException(new ReferencedObjectUndeletableException(message));\r
+ result.addRelatedObject(ref);\r
+ result.setAbort();\r
+ }\r
}\r
\r
return result;\r
Set<Taxon> children = new HashSet<Taxon>();\r
if (! config.onlyCongruent){\r
for (TaxonNode node: taxonNodes){\r
- List<TaxonNode> childNodes = nodeService.loadChildNodesOfTaxonNode(node, null, true, false);\r
+ List<TaxonNode> childNodes = nodeService.loadChildNodesOfTaxonNode(node, null, true, null);\r
for (TaxonNode child : childNodes){\r
children.add(child.getTaxon());\r
}\r
}\r
return result;\r
}\r
+\r
@Override\r
public List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config){\r
List<TaxonBase> taxonList = dao.getTaxaByName(true, false, false, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, 0, config.getPropertyPath());\r
return taxonList;\r
}\r
\r
+ @Override\r
+ @Transactional(readOnly = true)\r
+ public <S extends TaxonBase> Pager<FindByIdentifierDTO<S>> findByIdentifier(\r
+ Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,\r
+ MatchMode matchmode, boolean includeEntity, Integer pageSize,\r
+ Integer pageNumber, List<String> propertyPaths) {\r
+ if (subtreeFilter == null){\r
+ return findByIdentifier(clazz, identifier, identifierType, matchmode, includeEntity, pageSize, pageNumber, propertyPaths);\r
+ }\r
+\r
+ Integer numberOfResults = dao.countByIdentifier(clazz, identifier, identifierType, subtreeFilter, matchmode);\r
+ List<Object[]> daoResults = new ArrayList<Object[]>();\r
+ if(numberOfResults > 0) { // no point checking again\r
+ daoResults = dao.findByIdentifier(clazz, identifier, identifierType, subtreeFilter,\r
+ matchmode, includeEntity, pageSize, pageNumber, propertyPaths);\r
+ }\r
+\r
+ List<FindByIdentifierDTO<S>> result = new ArrayList<FindByIdentifierDTO<S>>();\r
+ for (Object[] daoObj : daoResults){\r
+ if (includeEntity){\r
+ result.add(new FindByIdentifierDTO<S>((DefinedTerm)daoObj[0], (String)daoObj[1], (S)daoObj[2]));\r
+ }else{\r
+ result.add(new FindByIdentifierDTO<S>((DefinedTerm)daoObj[0], (String)daoObj[1], (UUID)daoObj[2], (String)daoObj[3]));\r
+ }\r
+ }\r
+ return new DefaultPagerImpl<FindByIdentifierDTO<S>>(pageNumber, numberOfResults, pageSize, result);\r
+ }\r
+\r
+ @Override\r
+ @Transactional(readOnly = false)\r
+ public UpdateResult moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation, UUID newTaxonUUID, boolean moveHomotypicGroup,\r
+ SynonymRelationshipType newSynonymRelationshipType, Reference reference, String referenceDetail, boolean keepReference) throws HomotypicalGroupChangeException {\r
+\r
+ UpdateResult result = new UpdateResult();\r
+ Taxon newTaxon = (Taxon) dao.load(newTaxonUUID);\r
+ SynonymRelationship sr = moveSynonymToAnotherTaxon(oldSynonymRelation, newTaxon, moveHomotypicGroup, newSynonymRelationshipType, reference, referenceDetail, keepReference);\r
+ result.setCdmEntity(sr);\r
+ result.addUpdatedObject(sr);\r
+ result.addUpdatedObject(newTaxon);\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public UpdateResult moveFactualDateToAnotherTaxon(UUID fromTaxonUuid, UUID toTaxonUuid){\r
+ UpdateResult result = new UpdateResult();\r
+\r
+ Taxon fromTaxon = (Taxon)dao.load(fromTaxonUuid);\r
+ Taxon toTaxon = (Taxon) dao.load(toTaxonUuid);\r
+ for(TaxonDescription description : fromTaxon.getDescriptions()){\r
+ //reload to avoid session conflicts\r
+ description = HibernateProxyHelper.deproxy(description, TaxonDescription.class);\r
+\r
+ String moveMessage = String.format("Description moved from %s", fromTaxon);\r
+ if(description.isProtectedTitleCache()){\r
+ String separator = "";\r
+ if(!StringUtils.isBlank(description.getTitleCache())){\r
+ separator = " - ";\r
+ }\r
+ description.setTitleCache(description.getTitleCache() + separator + moveMessage, true);\r
+ }\r
+ Annotation annotation = Annotation.NewInstance(moveMessage, Language.getDefaultLanguage());\r
+ annotation.setAnnotationType(AnnotationType.TECHNICAL());\r
+ description.addAnnotation(annotation);\r
+ toTaxon.addDescription(description);\r
+ dao.saveOrUpdate(toTaxon);\r
+ dao.saveOrUpdate(fromTaxon);\r
+ result.addUpdatedObject(toTaxon);\r
+ result.addUpdatedObject(fromTaxon);\r
+\r
+ }\r
+\r
+\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public DeleteResult deleteSynonym(UUID synonymUuid, UUID taxonUuid,\r
+ SynonymDeletionConfigurator config) {\r
+ TaxonBase base = this.load(synonymUuid);\r
+ Synonym syn = HibernateProxyHelper.deproxy(base, Synonym.class);\r
+ base = this.load(taxonUuid);\r
+ Taxon taxon = HibernateProxyHelper.deproxy(base, Taxon.class);\r
+\r
+ return this.deleteSynonym(syn, taxon, config);\r
+ }\r
+\r
+ @Override\r
+ @Transactional(readOnly = false)\r
+ public UpdateResult swapSynonymAndAcceptedTaxon(UUID synonymUUid,\r
+ UUID acceptedTaxonUuid) {\r
+ TaxonBase base = this.load(synonymUUid);\r
+ Synonym syn = HibernateProxyHelper.deproxy(base, Synonym.class);\r
+ base = this.load(acceptedTaxonUuid);\r
+ Taxon taxon = HibernateProxyHelper.deproxy(base, Taxon.class);\r
+\r
+ return this.swapSynonymAndAcceptedTaxon(syn, taxon);\r
+ }\r
+\r
+\r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff