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.MultilanguageTextFieldBridge;\r
import eu.etaxonomy.cdm.model.CdmBaseType;\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.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
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
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
- \r
- if(configurator.getPageSize() == null ){\r
+\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
}\r
return results;\r
}\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
*/\r
@Override\r
public DeleteResult deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config, Classification classification) {\r
- \r
+\r
if (config == null){\r
config = new TaxonDeletionConfigurator();\r
}\r
" which also describes specimens or abservations";\r
//throw new ReferencedObjectUndeletableException(message);\r
}\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
+\r
+ nameResult = nameService.delete(name, config.getNameDeletionConfig());\r
+\r
+ }\r
+\r
+\r
\r
if (nameResult.isError()){\r
//result.setError();\r
return result;\r
}\r
\r
- \r
+\r
}\r
return result;\r
// else{\r
\r
}\r
\r
+ @Transactional(readOnly = false)\r
+ @Override\r
+ public DeleteResult deleteSynonym(UUID synonymUuid, UUID taxonUuid, SynonymDeletionConfigurator config) {\r
+ Synonym synonym = HibernateProxyHelper.deproxy(dao.load(synonymUuid), Synonym.class);\r
+ Taxon taxon = HibernateProxyHelper.deproxy(dao.load(taxonUuid), Taxon.class);\r
+ return deleteSynonym(synonym, taxon, config);\r
+ }\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List)\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
@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
if (!(ref instanceof TaxonNameBase)){\r
if (!config.isDeleteSynonymRelations() && (ref instanceof SynonymRelationship)){\r
message = "The Taxon can't be deleted as long as it has synonyms.";\r
- \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
- \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
- \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
- \r
+\r
} else{\r
message = "The Taxon can't be deleted as long as it belongs to a taxon node.";\r
- \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
- \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
- \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
- \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
- \r
+\r
}\r
\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
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff