/**\r
* Copyright (C) 2008 EDIT\r
-* European Distributed Institute of Taxonomy \r
+* European Distributed Institute of Taxonomy\r
* http://www.e-taxonomy.eu\r
*/\r
\r
package eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence;\r
\r
import java.util.ArrayList;\r
+import java.util.Collection;\r
+import java.util.Collections;\r
import java.util.HashSet;\r
import java.util.List;\r
import java.util.Set;\r
import org.hibernate.Hibernate;\r
import org.hibernate.Query;\r
import org.hibernate.Session;\r
+import org.hibernate.criterion.Disjunction;\r
+import org.hibernate.criterion.ProjectionList;\r
import org.hibernate.criterion.Projections;\r
import org.hibernate.criterion.Restrictions;\r
import org.hibernate.envers.query.AuditEntity;\r
import org.springframework.beans.factory.annotation.Autowired;\r
import org.springframework.stereotype.Repository;\r
\r
-import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;\r
+import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;\r
+import eu.etaxonomy.cdm.model.location.Point;\r
import eu.etaxonomy.cdm.model.media.Media;\r
import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;\r
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;\r
+import eu.etaxonomy.cdm.model.name.TaxonName;\r
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;\r
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
+import eu.etaxonomy.cdm.model.taxon.Synonym;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
import eu.etaxonomy.cdm.model.view.AuditEvent;\r
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;\r
import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;\r
import eu.etaxonomy.cdm.persistence.dao.name.IHomotypicalGroupDao;\r
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;\r
import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;\r
+import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;\r
+import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;\r
+import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
import eu.etaxonomy.cdm.persistence.query.OrderHint;\r
\r
/**\r
* @author a.babadshanjan\r
- * @created 01.09.2008\r
+ * @since 01.09.2008\r
*/\r
@Repository\r
-public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase<SpecimenOrObservationBase> implements IOccurrenceDao {\r
- \r
- @SuppressWarnings("unused")\r
- private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);\r
- \r
- @Autowired\r
- private IDescriptionDao descriptionDao;\r
- \r
- @Autowired\r
- private ITaxonNameDao taxonNameDao;\r
- \r
- @Autowired\r
- private IHomotypicalGroupDao homotypicalGroupDao;\r
-\r
- public OccurrenceDaoHibernateImpl() {\r
- super(SpecimenOrObservationBase.class);\r
- indexedClasses = new Class[7];\r
- indexedClasses[0] = FieldUnit.class;\r
- indexedClasses[1] = DerivedUnit.class;\r
- indexedClasses[5] = DnaSample.class;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#countDerivationEvents(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)\r
- */\r
- @Override\r
- public int countDerivationEvents(SpecimenOrObservationBase occurence) {\r
- checkNotInPriorView("OccurrenceDaoHibernateImpl.countDerivationEvents(SpecimenOrObservationBase occurence)");\r
- Query query = getSession().createQuery("select count(distinct derivationEvent) from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");\r
- query.setParameter("occurence", occurence);\r
- \r
- return ((Long)query.uniqueResult()).intValue();\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)\r
- */\r
- @Override\r
- public int countDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase) {\r
- AuditEvent auditEvent = getAuditEventFromContext();\r
- if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
- Criteria criteria = getSession().createCriteria(DeterminationEvent.class);\r
+public class OccurrenceDaoHibernateImpl\r
+ extends IdentifiableDaoBase<SpecimenOrObservationBase>\r
+ implements IOccurrenceDao {\r
+\r
+ private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);\r
+\r
+ @Autowired\r
+ private IDescriptionDao descriptionDao;\r
+\r
+ @Autowired\r
+ private ITaxonNameDao taxonNameDao;\r
+\r
+ @Autowired\r
+ private IHomotypicalGroupDao homotypicalGroupDao;\r
+\r
+ public OccurrenceDaoHibernateImpl() {\r
+ super(SpecimenOrObservationBase.class);\r
+ indexedClasses = new Class[7];\r
+ indexedClasses[0] = FieldUnit.class;\r
+ indexedClasses[1] = DerivedUnit.class;\r
+ indexedClasses[5] = DnaSample.class;\r
+ }\r
+\r
+ @Override\r
+ public long countDerivationEvents(SpecimenOrObservationBase occurence) {\r
+ checkNotInPriorView("OccurrenceDaoHibernateImpl.countDerivationEvents(SpecimenOrObservationBase occurence)");\r
+ Query query = getSession().createQuery("select count(distinct derivationEvent) from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");\r
+ query.setParameter("occurence", occurence);\r
+\r
+ return (Long)query.uniqueResult();\r
+ }\r
+\r
+ @Override\r
+ public long countDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getCriteria(DeterminationEvent.class);\r
if(occurrence != null) {\r
- criteria.add(Restrictions.eq("identifiedUnit",occurrence));\r
+ criteria.add(Restrictions.eq("identifiedUnit",occurrence));\r
}\r
- \r
+\r
if(taxonBase != null) {\r
- criteria.add(Restrictions.eq("taxon",taxonBase));\r
+ criteria.add(Restrictions.eq("taxon",taxonBase));\r
}\r
- \r
+\r
criteria.setProjection(Projections.rowCount());\r
- return ((Number)criteria.uniqueResult()).intValue();\r
- } else {\r
- AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());\r
- \r
- if(occurrence != null) {\r
- query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));\r
- }\r
- \r
- if(taxonBase != null) {\r
- query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));\r
- }\r
- query.addProjection(AuditEntity.id().count("id"));\r
-\r
- return ((Long)query.getSingleResult()).intValue();\r
- }\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#countMedia(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase)\r
- */\r
- @Override\r
- public int countMedia(SpecimenOrObservationBase occurence) {\r
- checkNotInPriorView("OccurrenceDaoHibernateImpl.countMedia(SpecimenOrObservationBase occurence)");\r
- Query query = getSession().createQuery("select count(media) from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");\r
- query.setParameter("occurence", occurence);\r
- \r
- return ((Long)query.uniqueResult()).intValue();\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#getDerivationEvents(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List)\r
- */\r
- @Override\r
- public List<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {\r
- checkNotInPriorView("OccurrenceDaoHibernateImpl.getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber)");\r
- Query query = getSession().createQuery("select distinct derivationEvent from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");\r
- query.setParameter("occurence", occurence);\r
- \r
- if(pageSize != null) {\r
- query.setMaxResults(pageSize);\r
- if(pageNumber != null) {\r
- query.setFirstResult(pageNumber * pageSize);\r
- } else {\r
- query.setFirstResult(0);\r
- }\r
- }\r
- \r
- List<DerivationEvent> result = (List<DerivationEvent>)query.list();\r
- defaultBeanInitializer.initializeAll(result, propertyPaths);\r
- return result;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#getDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase, java.lang.Integer, java.lang.Integer, java.util.List)\r
- */\r
- @Override\r
- public List<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {\r
- AuditEvent auditEvent = getAuditEventFromContext();\r
- if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
- Criteria criteria = getSession().createCriteria(DeterminationEvent.class);\r
- if(occurrence != null) {\r
- criteria.add(Restrictions.eq("identifiedUnit",occurrence));\r
+ return (Long)criteria.uniqueResult();\r
+ } else {\r
+ AuditQuery query = makeAuditQuery(DeterminationEvent.class,auditEvent);\r
+\r
+ if(occurrence != null) {\r
+ query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));\r
+ }\r
+\r
+ if(taxonBase != null) {\r
+ query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));\r
+ }\r
+ query.addProjection(AuditEntity.id().count());\r
+\r
+ return (Long)query.getSingleResult();\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public long countMedia(SpecimenOrObservationBase occurence) {\r
+ checkNotInPriorView("OccurrenceDaoHibernateImpl.countMedia(SpecimenOrObservationBase occurence)");\r
+ Query query = getSession().createQuery("SELECT count(media) FROM SpecimenOrObservationBase occurence JOIN occurence.media media WHERE occurence = :occurence");\r
+ query.setParameter("occurence", occurence);\r
+\r
+ return (Long)query.uniqueResult();\r
+ }\r
+\r
+ @Override\r
+ public List<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {\r
+ checkNotInPriorView("OccurrenceDaoHibernateImpl.getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber)");\r
+ Query query = getSession().createQuery("SELECT DISTINCT derivationEvent FROM DerivationEvent derivationEvent JOIN derivationEvent.originals occurence WHERE occurence = :occurence");\r
+ query.setParameter("occurence", occurence);\r
+\r
+ addPageSizeAndNumber(query, pageSize, pageNumber);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<DerivationEvent> result = query.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public List<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence,\r
+ TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(DeterminationEvent.class);\r
+ if(occurrence != null) {\r
+ criteria.add(Restrictions.eq("identifiedUnit",occurrence));\r
+ }\r
+\r
+ if(taxonBase != null) {\r
+ criteria.add(Restrictions.eq("taxon",taxonBase));\r
+ }\r
+\r
+ addPageSizeAndNumber(criteria, pageSize, pageNumber);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<DeterminationEvent> result = criteria.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ return result;\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());\r
+ if(occurrence != null) {\r
+ query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));\r
}\r
- \r
+\r
if(taxonBase != null) {\r
- criteria.add(Restrictions.eq("taxon",taxonBase));\r
+ query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));\r
}\r
+ addPageSizeAndNumber(query, pageSize, pageNumber);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<DeterminationEvent> result = query.getResultList();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ return result;\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public List<Media> getMedia(SpecimenOrObservationBase occurence,\r
+ Integer pageSize, Integer pageNumber, List<String> propertyPaths) {\r
+ checkNotInPriorView("OccurrenceDaoHibernateImpl.getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");\r
+ Query query = getSession().createQuery(\r
+ " SELECT media "\r
+ + " FROM SpecimenOrObservationBase occurence "\r
+ + " JOIN occurence.media media "\r
+ + " WHERE occurence = :occurence");\r
+ query.setParameter("occurence", occurence);\r
+\r
+ addPageSizeAndNumber(query, pageSize, pageNumber);\r
\r
- if(pageSize != null) {\r
- criteria.setMaxResults(pageSize);\r
- if(pageNumber != null) {\r
- criteria.setFirstResult(pageNumber * pageSize);\r
- } else {\r
- criteria.setFirstResult(0);\r
- }\r
- }\r
- List<DeterminationEvent> result = (List<DeterminationEvent>)criteria.list();\r
- defaultBeanInitializer.initializeAll(result, propertyPaths); \r
- return result;\r
- } else {\r
- AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());\r
- if(occurrence != null) {\r
- query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));\r
- }\r
- \r
- if(taxonBase != null) {\r
- query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));\r
- }\r
- if(pageSize != null) {\r
- query.setMaxResults(pageSize);\r
- if(pageNumber != null) {\r
- query.setFirstResult(pageNumber * pageSize);\r
- } else {\r
- query.setFirstResult(0);\r
- }\r
- }\r
- List<DeterminationEvent> result = (List<DeterminationEvent>)query.getResultList();\r
- defaultBeanInitializer.initializeAll(result, propertyPaths); \r
- return result;\r
- }\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#getMedia(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List)\r
- */\r
- @Override\r
- public List<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {\r
- checkNotInPriorView("OccurrenceDaoHibernateImpl.getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");\r
- Query query = getSession().createQuery("select media from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");\r
- query.setParameter("occurence", occurence);\r
- \r
- if(pageSize != null) {\r
- query.setMaxResults(pageSize);\r
- if(pageNumber != null) {\r
- query.setFirstResult(pageNumber * pageSize);\r
- } else {\r
- query.setFirstResult(0);\r
- }\r
- }\r
- \r
- List<Media> results = (List<Media>)query.list();\r
- defaultBeanInitializer.initializeAll(results, propertyPaths); \r
- return results;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase#rebuildIndex()\r
- */\r
- @Override\r
- public void rebuildIndex() {\r
+ @SuppressWarnings("unchecked")\r
+ List<Media> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ @Override\r
+ public void rebuildIndex() {\r
FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
- \r
- for(SpecimenOrObservationBase occurrence : list(null,null)) { // re-index all taxon base\r
-\r
- for(DeterminationEvent determination : (Set<DeterminationEvent>)occurrence.getDeterminations()) {\r
- Hibernate.initialize(determination.getActor());\r
- Hibernate.initialize(determination.getTaxon());\r
- }\r
- Hibernate.initialize(occurrence.getDefinition());\r
- if(occurrence instanceof DerivedUnit) {\r
- DerivedUnit derivedUnit = (DerivedUnit) occurrence;\r
- Hibernate.initialize(derivedUnit.getCollection());\r
- if(derivedUnit.getCollection() != null) {\r
- Hibernate.initialize(derivedUnit.getCollection().getSuperCollection());\r
- Hibernate.initialize(derivedUnit.getCollection().getInstitute());\r
- }\r
- Hibernate.initialize(derivedUnit.getStoredUnder());\r
- SpecimenOrObservationBase original = derivedUnit.getOriginalUnit();\r
- if(original != null && original.isInstanceOf(FieldUnit.class)) {\r
- FieldUnit fieldUnit = original.deproxy(original, FieldUnit.class);\r
- Hibernate.initialize(fieldUnit.getGatheringEvent());\r
- if(fieldUnit.getGatheringEvent() != null) {\r
- Hibernate.initialize(fieldUnit.getGatheringEvent().getActor());\r
- }\r
- }\r
- }\r
- fullTextSession.index(occurrence);\r
- }\r
- fullTextSession.flushToIndexes();\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#count(java.lang.Class, eu.etaxonomy.cdm.model.taxon.TaxonBase)\r
- */\r
- @Override\r
- public int count(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs) {\r
-\r
- Criteria criteria = null;\r
- if(clazz == null) {\r
- criteria = getSession().createCriteria(type);\r
- } else {\r
- criteria = getSession().createCriteria(clazz);\r
- }\r
- \r
- criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));\r
- criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
- return ((Number)criteria.uniqueResult()).intValue();\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#list(java.lang.Class, eu.etaxonomy.cdm.model.taxon.TaxonBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)\r
- */\r
- @Override\r
- public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
- Criteria criteria = null;\r
- if(clazz == null) {\r
- criteria = getSession().createCriteria(type); \r
- } else {\r
- criteria = getSession().createCriteria(clazz); \r
- } \r
- \r
- criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));\r
- \r
- if(limit != null) {\r
- if(start != null) {\r
- criteria.setFirstResult(start);\r
- } else {\r
- criteria.setFirstResult(0);\r
- }\r
- criteria.setMaxResults(limit);\r
- }\r
- \r
- addOrder(criteria,orderHints);\r
- \r
- List<SpecimenOrObservationBase> results = (List<SpecimenOrObservationBase>)criteria.list();\r
- defaultBeanInitializer.initializeAll(results, propertyPaths);\r
- return results; \r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#getDerivedUnitUuidAndTitleCache()\r
- */\r
- @Override\r
- public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {\r
- List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<UuidAndTitleCache<DerivedUnit>>();\r
- Session session = getSession();\r
- \r
- Query query = session.createQuery("select uuid, titleCache from " + type.getSimpleName() + " where NOT dtype = " + FieldUnit.class.getSimpleName());\r
- \r
- List<Object[]> result = query.list();\r
- \r
- for(Object[] object : result){\r
- list.add(new UuidAndTitleCache<DerivedUnit>(DerivedUnit.class, (UUID) object[0], (String) object[1]));\r
- }\r
- \r
- return list;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#getFieldUnitUuidAndTitleCache()\r
- */\r
- @Override\r
- public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {\r
- List<UuidAndTitleCache<FieldUnit>> list = new ArrayList<UuidAndTitleCache<FieldUnit>>();\r
- Session session = getSession();\r
- \r
- Query query = session.createQuery("select uuid, titleCache from " + type.getSimpleName() + " where dtype = " + FieldUnit.class.getSimpleName());\r
- \r
- List<Object[]> result = query.list();\r
- \r
- for(Object[] object : result){\r
- list.add(new UuidAndTitleCache<FieldUnit>(FieldUnit.class, (UUID) object[0], (String) object[1]));\r
- }\r
- \r
- return list;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao#listByAnyAssociation(java.lang.Class, eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)\r
- */\r
- @Override\r
- public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type,\r
- Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
- \r
- Set<SpecimenOrObservationBase> setOfAll = new HashSet<SpecimenOrObservationBase>();\r
- \r
- // A Taxon may be referenced by the DeterminationEvent of the SpecimenOrObservationBase\r
- List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxon, null, 0, null, null);\r
- setOfAll.addAll(byDetermination);\r
- \r
- // The IndividualsAssociation elements in a TaxonDescription contain DerivedUnits \r
- List<IndividualsAssociation> byIndividualsAssociation = descriptionDao.getDescriptionElementForTaxon(\r
- associatedTaxon, null, IndividualsAssociation.class, null, 0, null);\r
- for(IndividualsAssociation individualsAssociation : byIndividualsAssociation){\r
- setOfAll.add(individualsAssociation.getAssociatedSpecimenOrObservation());\r
- }\r
- \r
- // SpecimenTypeDesignations may be associated with the TaxonName.\r
- List<SpecimenTypeDesignation> bySpecimenTypeDesignation = taxonNameDao.getTypeDesignations(associatedTaxon.getName(), \r
- SpecimenTypeDesignation.class, null, null, 0, null);\r
- for (SpecimenTypeDesignation specimenTypeDesignation : bySpecimenTypeDesignation) {\r
- setOfAll.add(specimenTypeDesignation.getTypeSpecimen());\r
- }\r
- \r
- // SpecimenTypeDesignations may be associated with any HomotypicalGroup related to the specific Taxon.\r
- for(HomotypicalGroup homotypicalGroup : associatedTaxon.getHomotypicSynonymyGroups()) {\r
- List<SpecimenTypeDesignation> byHomotypicalGroup = homotypicalGroupDao.getTypeDesignations(homotypicalGroup, SpecimenTypeDesignation.class, null, null, 0, null);\r
- for (SpecimenTypeDesignation specimenTypeDesignation : byHomotypicalGroup) {\r
- setOfAll.add(specimenTypeDesignation.getTypeSpecimen());\r
- }\r
- }\r
- \r
- if(setOfAll.size() == 0){\r
- // no need querying the data base\r
- return new ArrayList<T>();\r
- }\r
- \r
- String queryString = \r
- "select sob " +\r
- " from SpecimenOrObservationBase sob" +\r
- " where sob in (:setOfAll)";\r
- \r
- if(type != null){\r
- queryString += " and sob.class = :type";\r
- }\r
- \r
- if(orderHints != null && orderHints.size() > 0){\r
- queryString += " order by ";\r
- String orderStr = "";\r
- for(OrderHint orderHint : orderHints){\r
- if(orderStr.length() > 0){\r
- orderStr += ", ";\r
- }\r
- queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();\r
- }\r
- queryString += orderStr;\r
- }\r
- \r
- Query query = getSession().createQuery(queryString);\r
- query.setParameterList("setOfAll", setOfAll);\r
- \r
- if(type != null){\r
- query.setParameter("type", type.getSimpleName());\r
- }\r
- \r
- if(limit != null) {\r
- if(start != null) {\r
- query.setFirstResult(start);\r
- } else {\r
- query.setFirstResult(0);\r
- }\r
- query.setMaxResults(limit);\r
- }\r
- \r
- \r
- List<T> results = (List<T>) query.list();\r
- defaultBeanInitializer.initializeAll(results, propertyPaths);\r
- return results;\r
- }\r
-}
\ No newline at end of file
+\r
+ for(SpecimenOrObservationBase<?> occurrence : list(null,null)) { // re-index all taxon base\r
+\r
+ for(DeterminationEvent determination : occurrence.getDeterminations()) {\r
+ Hibernate.initialize(determination.getActor());\r
+ Hibernate.initialize(determination.getTaxon());\r
+ }\r
+ Hibernate.initialize(occurrence.getDefinition());\r
+ if(occurrence instanceof DerivedUnit) {\r
+ DerivedUnit derivedUnit = (DerivedUnit) occurrence;\r
+ Hibernate.initialize(derivedUnit.getCollection());\r
+ if(derivedUnit.getCollection() != null) {\r
+ Hibernate.initialize(derivedUnit.getCollection().getSuperCollection());\r
+ Hibernate.initialize(derivedUnit.getCollection().getInstitute());\r
+ }\r
+ Hibernate.initialize(derivedUnit.getStoredUnder());\r
+ SpecimenOrObservationBase<?> original = derivedUnit.getOriginalUnit();\r
+ if(original != null && original.isInstanceOf(FieldUnit.class)) {\r
+ FieldUnit fieldUnit = CdmBase.deproxy(original, FieldUnit.class);\r
+ Hibernate.initialize(fieldUnit.getGatheringEvent());\r
+ if(fieldUnit.getGatheringEvent() != null) {\r
+ Hibernate.initialize(fieldUnit.getGatheringEvent().getActor());\r
+ }\r
+ }\r
+ }\r
+ fullTextSession.index(occurrence);\r
+ }\r
+ fullTextSession.flushToIndexes();\r
+ }\r
+\r
+ @Override\r
+ public long count(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs) {\r
+\r
+ Criteria criteria = getCriteria(clazz);\r
+\r
+ criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));\r
+ criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
+ return (Long)criteria.uniqueResult();\r
+ }\r
+\r
+ @Override\r
+ public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs,\r
+ Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ Criteria criteria = getCriteria(clazz);\r
+\r
+ criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));\r
+\r
+ addPageSizeAndNumber(criteria, pageSize, pageNumber);\r
+ addOrder(criteria,orderHints);\r
+\r
+ @SuppressWarnings({ "unchecked", "rawtypes" })\r
+ List<SpecimenOrObservationBase> results = criteria.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ @Override\r
+ public long count(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs) {\r
+\r
+ Criteria criteria = getCriteria(clazz);\r
+\r
+ criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));\r
+ criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
+ return (Long)criteria.uniqueResult();\r
+ }\r
+\r
+\r
+ @Override\r
+ public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs,\r
+ Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+\r
+ Criteria criteria = getCriteria(clazz);\r
+\r
+ criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));\r
+\r
+ addPageSizeAndNumber(criteria, pageSize, pageNumber);\r
+ addOrder(criteria,orderHints);\r
+\r
+ @SuppressWarnings({ "unchecked", "rawtypes" })\r
+ List<SpecimenOrObservationBase> results = criteria.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> findOccurrencesUuidAndTitleCache(\r
+ Class<T> clazz, String queryString, String significantIdentifier, SpecimenOrObservationType recordBasis,\r
+ Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,\r
+ List<OrderHint> orderHints) {\r
+ Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,\r
+ associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, null);\r
+ if(criteria!=null){\r
+ ProjectionList projectionList = Projections.projectionList();\r
+ projectionList.add(Projections.property("uuid"));\r
+ projectionList.add(Projections.property("id"));\r
+ projectionList.add(Projections.property("titleCache"));\r
+ criteria.setProjection(projectionList);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<Object[]> result = criteria.list();\r
+ List<UuidAndTitleCache<SpecimenOrObservationBase>> uuidAndTitleCacheList = new ArrayList<>();\r
+ for(Object[] object : result){\r
+ uuidAndTitleCacheList.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));\r
+ }\r
+ return uuidAndTitleCacheList;\r
+ }else{\r
+ return Collections.emptyList();\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> List<T> findOccurrences(Class<T> clazz, String queryString,\r
+ String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,\r
+ MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+\r
+ Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,\r
+ associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);\r
+ if(criteria!=null){\r
+ @SuppressWarnings("unchecked")\r
+ List<T> results = criteria.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }else{\r
+ return Collections.emptyList();\r
+ }\r
+ }\r
+\r
+ private <T extends SpecimenOrObservationBase> Criteria createFindOccurrenceCriteria(Class<T> clazz, String queryString,\r
+ String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon,\r
+ TaxonName associatedTaxonName, MatchMode matchmode, Integer limit,\r
+ Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ Criteria criteria = null;\r
+\r
+ if(clazz == null) {\r
+ criteria = getSession().createCriteria(type);\r
+ } else {\r
+ criteria = getSession().createCriteria(clazz);\r
+ }\r
+\r
+ //queryString\r
+ if (queryString != null) {\r
+ if(matchmode == null) {\r
+ matchmode = MatchMode.ANYWHERE;\r
+ criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));\r
+ } else if(matchmode == MatchMode.BEGINNING) {\r
+ criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.START));\r
+ } else if(matchmode == MatchMode.END) {\r
+ criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.END));\r
+ } else if(matchmode == MatchMode.EXACT) {\r
+ criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.EXACT));\r
+ } else {\r
+ criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.ANYWHERE));\r
+ }\r
+ }\r
+\r
+ //significant identifier\r
+ if (significantIdentifier != null) {\r
+ criteria.add(Restrictions.or(Restrictions.ilike("accessionNumber", significantIdentifier),\r
+ Restrictions.ilike("catalogNumber", significantIdentifier), Restrictions.ilike("barcode", significantIdentifier)));\r
+ }\r
+\r
+ //recordBasis/SpecimenOrObservationType\r
+ Set<SpecimenOrObservationType> typeAndSubtypes = new HashSet<>();\r
+ if(recordBasis==null){\r
+ //add all types\r
+ SpecimenOrObservationType[] values = SpecimenOrObservationType.values();\r
+ for (SpecimenOrObservationType specimenOrObservationType : values) {\r
+ typeAndSubtypes.add(specimenOrObservationType);\r
+ }\r
+ }\r
+ else{\r
+ typeAndSubtypes = recordBasis.getGeneralizationOf(true);\r
+ typeAndSubtypes.add(recordBasis);\r
+ }\r
+ criteria.add(Restrictions.in("recordBasis", typeAndSubtypes));\r
+\r
+ Set<UUID> associationUuids = new HashSet<>();\r
+ //taxon associations\r
+ if(associatedTaxon!=null){\r
+ List<UuidAndTitleCache<SpecimenOrObservationBase>> associatedTaxaList = listUuidAndTitleCacheByAssociatedTaxon(clazz, associatedTaxon, limit, start, orderHints);\r
+ if(associatedTaxaList!=null){\r
+ for (UuidAndTitleCache<SpecimenOrObservationBase> uuidAndTitleCache : associatedTaxaList) {\r
+ associationUuids.add(uuidAndTitleCache.getUuid());\r
+ }\r
+ }\r
+ }\r
+ //taxon name associations\r
+ else if(associatedTaxonName!=null){\r
+ List<? extends SpecimenOrObservationBase> associatedTaxaList = listByAssociatedTaxonName(clazz, associatedTaxonName, limit, start, orderHints, propertyPaths);\r
+ if(associatedTaxaList!=null){\r
+ for (SpecimenOrObservationBase<?> specimenOrObservationBase : associatedTaxaList) {\r
+ associationUuids.add(specimenOrObservationBase.getUuid());\r
+ }\r
+ }\r
+ }\r
+ if(associatedTaxon!=null || associatedTaxonName!=null){\r
+ if(!associationUuids.isEmpty()){\r
+ criteria.add(Restrictions.in("uuid", associationUuids));\r
+ }\r
+ else{\r
+ return null;\r
+ }\r
+ }\r
+ if(limit != null) {\r
+ if(start != null) {\r
+ criteria.setFirstResult(start);\r
+ } else {\r
+ criteria.setFirstResult(0);\r
+ }\r
+ criteria.setMaxResults(limit);\r
+ }\r
+\r
+ if(orderHints!=null){\r
+ addOrder(criteria,orderHints);\r
+ }\r
+ return criteria;\r
+ }\r
+\r
+\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> long countOccurrences(Class<T> clazz, String queryString,\r
+ String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,\r
+ MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+\r
+ Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,\r
+ associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);\r
+\r
+ if(criteria!=null){\r
+ criteria.setProjection(Projections.rowCount());\r
+ return (Long)criteria.uniqueResult();\r
+ }else{\r
+ return 0;\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {\r
+ List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<>();\r
+ Session session = getSession();\r
+ String hql = "SELECT uuid, id, titleCache "\r
+ + " FROM " + type.getSimpleName()\r
+ + " WHERE NOT dtype = " + FieldUnit.class.getSimpleName();\r
+ Query query;\r
+ if (pattern != null){\r
+ pattern = pattern.replace("*", "%");\r
+ pattern = pattern.replace("?", "_");\r
+ pattern = pattern + "%";\r
+ query = session.createQuery(hql +" AND titleCache like :pattern");\r
+ query.setParameter("pattern", pattern);\r
+ } else {\r
+ query = session.createQuery(hql);\r
+ }\r
+ if (limit != null){\r
+ query.setMaxResults(limit);\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<Object[]> result = query.list();\r
+\r
+ for(Object[] object : result){\r
+ list.add(new UuidAndTitleCache<DerivedUnit>(DerivedUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));\r
+ }\r
+\r
+ return list;\r
+ }\r
+\r
+ @Override\r
+ public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {\r
+ List<UuidAndTitleCache<FieldUnit>> list = new ArrayList<>();\r
+ Session session = getSession();\r
+\r
+ Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where dtype = " + FieldUnit.class.getSimpleName());\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<Object[]> result = query.list();\r
+\r
+ for(Object[] object : result){\r
+ list.add(new UuidAndTitleCache<FieldUnit>(FieldUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));\r
+ }\r
+\r
+ return list;\r
+ }\r
+\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,\r
+ TaxonName associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+\r
+ @SuppressWarnings("rawtypes")\r
+ Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();\r
+\r
+ // A Taxon name may be referenced by the DeterminationEvent of the SpecimenOrObservationBase\r
+ @SuppressWarnings("rawtypes")\r
+ List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxonName, null, 0, null, null);\r
+ setOfAll.addAll(byDetermination);\r
+\r
+ if(setOfAll.size() == 0){\r
+ // no need querying the data base\r
+ return new ArrayList<T>();\r
+ }\r
+\r
+ String queryString =\r
+ "SELECT sob " +\r
+ " FROM SpecimenOrObservationBase sob" +\r
+ " WHERE sob in (:setOfAll)";\r
+\r
+ if(type != null && !type.equals(SpecimenOrObservationBase.class)){\r
+ queryString += " AND sob.class = :type";\r
+ }\r
+ queryString += orderByClause("sob", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameterList("setOfAll", setOfAll);\r
+\r
+ if(type != null && !type.equals(SpecimenOrObservationBase.class)){\r
+ query.setParameter("type", type.getSimpleName());\r
+ }\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<T> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ private List<SpecimenNodeWrapper> querySpecimen(Query query, List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start){\r
+ query.setParameterList("taxonNodeUuids", taxonNodeUuids);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ List<SpecimenNodeWrapper> list = new ArrayList<>();\r
+ @SuppressWarnings("unchecked")\r
+ List<Object[]> result = query.list();\r
+ for(Object[] object : result){\r
+ SpecimenNodeWrapper wrapper = new SpecimenNodeWrapper(\r
+ new UuidAndTitleCache<>(\r
+ (UUID) object[0],\r
+ (Integer) object[1],\r
+ (String) object[2]),\r
+ (SpecimenOrObservationType)object[3],\r
+ new TaxonNodeDto((TaxonNode)object[4]));\r
+ if(object.length>5) {\r
+ wrapper.setTaxonDescriptionUuid((UUID)object[5]);\r
+ }\r
+ list.add(wrapper);\r
+ }\r
+ return list;\r
+ }\r
+\r
+ private List<SpecimenNodeWrapper> queryIndividualAssociatedSpecimen(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start){\r
+ String queryString = "SELECT "\r
+ + "de.associatedSpecimenOrObservation.uuid, "\r
+ + "de.associatedSpecimenOrObservation.id, "\r
+ + "de.associatedSpecimenOrObservation.titleCache, "\r
+ + "de.associatedSpecimenOrObservation.recordBasis, "\r
+ + "tn, "\r
+ + "d.uuid "\r
+ + "FROM DescriptionElementBase AS de "\r
+ + "LEFT JOIN de.inDescription AS d "\r
+ + "LEFT JOIN d.taxon AS t "\r
+ + "JOIN t.taxonNodes AS tn "\r
+ + "WHERE d.class = 'TaxonDescription' "\r
+ + "AND tn.uuid in (:taxonNodeUuids) "\r
+ ;\r
+ Query query = getSession().createQuery(queryString);\r
+ return querySpecimen(query, taxonNodeUuids, limit, start);\r
+ }\r
+\r
+ private List<SpecimenNodeWrapper> queryTypeSpecimen(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start){\r
+ String queryString = "SELECT "\r
+ + "td.typeSpecimen.uuid, "\r
+ + "td.typeSpecimen.id, "\r
+ + "td.typeSpecimen.titleCache, "\r
+ + "td.typeSpecimen.recordBasis, "\r
+ + "tn "\r
+ + "FROM SpecimenTypeDesignation AS td "\r
+ + "LEFT JOIN td.typifiedNames AS tn "\r
+ + "LEFT JOIN tn.taxonBases AS t "\r
+ + "JOIN t.taxonNodes AS tn "\r
+ + "WHERE tn.uuid in (:taxonNodeUuids) "\r
+ ;\r
+ Query query = getSession().createQuery(queryString);\r
+ return querySpecimen(query, taxonNodeUuids, limit, start);\r
+ }\r
+\r
+ private List<SpecimenNodeWrapper> queryTaxonDeterminations(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start){\r
+ String queryString = "SELECT "\r
+ + "det.identifiedUnit.uuid, "\r
+ + "det.identifiedUnit.id, "\r
+ + "det.identifiedUnit.titleCache, "\r
+ + "det.identifiedUnit.recordBasis, "\r
+ + "tn "\r
+ + "FROM DeterminationEvent AS det "\r
+ + "LEFT JOIN det.taxon AS t "\r
+ + "JOIN t.taxonNodes AS tn "\r
+ + "WHERE tn.uuid in (:taxonNodeUuids) "\r
+ ;\r
+ Query query = getSession().createQuery(queryString);\r
+ return querySpecimen(query, taxonNodeUuids, limit, start);\r
+ }\r
+\r
+ private List<SpecimenNodeWrapper> queryTaxonNameDeterminations(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start){\r
+ String queryString = "SELECT "\r
+ + "det.identifiedUnit.uuid, "\r
+ + "det.identifiedUnit.id, "\r
+ + "det.identifiedUnit.titleCache, "\r
+ + "det.identifiedUnit.recordBasis, "\r
+ + "tn "\r
+ + "FROM DeterminationEvent AS det "\r
+ + "LEFT JOIN det.taxonName AS n "\r
+ + "LEFT JOIN n.taxonBases AS t "\r
+ + "JOIN t.taxonNodes AS tn "\r
+ + "WHERE tn.uuid in (:taxonNodeUuids) "\r
+ ;\r
+ Query query = getSession().createQuery(queryString);\r
+ return querySpecimen(query, taxonNodeUuids, limit, start);\r
+ }\r
+\r
+ @Override\r
+ public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start){\r
+\r
+ Set<SpecimenNodeWrapper> testSet = new HashSet();\r
+\r
+ testSet.addAll(queryIndividualAssociatedSpecimen(taxonNodeUuids, limit, start));\r
+ testSet.addAll(queryTaxonDeterminations(taxonNodeUuids, limit, start));\r
+ testSet.addAll(queryTaxonNameDeterminations(taxonNodeUuids, limit, start));\r
+ testSet.addAll(queryTypeSpecimen(taxonNodeUuids, limit, start));\r
+\r
+ Collection<SpecimenNodeWrapper> wrappers = new HashSet<>();\r
+ wrappers.addAll(testSet);\r
+ return wrappers;\r
+ }\r
+\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> listUuidAndTitleCacheByAssociatedTaxon(Class<T> clazz, Taxon associatedTaxon,\r
+ Integer limit, Integer start, List<OrderHint> orderHints){\r
+ Query query = createSpecimenQuery("sob.uuid, sob.id, sob.titleCache", clazz, associatedTaxon, limit, start, orderHints);\r
+ if(query==null){\r
+ return Collections.emptyList();\r
+ }\r
+ List<UuidAndTitleCache<SpecimenOrObservationBase>> list = new ArrayList<>();\r
+ @SuppressWarnings("unchecked")\r
+ List<Object[]> result = query.list();\r
+ for(Object[] object : result){\r
+ list.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));\r
+ }\r
+ return list;\r
+ }\r
+\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> clazz,\r
+ Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ Query query = createSpecimenQuery("sob", clazz, associatedTaxon, limit, start, orderHints);\r
+ if(query==null){\r
+ return Collections.emptyList();\r
+ }\r
+ @SuppressWarnings("unchecked")\r
+ List<T> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ private <T extends SpecimenOrObservationBase> Query createSpecimenQuery(String select, Class<T> clazz,\r
+ Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints){\r
+// Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();\r
+ Set<Integer> setOfAllIds = new HashSet<>();\r
+\r
+ Criteria criteria = null;\r
+ if(clazz == null) {\r
+ criteria = getSession().createCriteria(type, "specimen");\r
+ } else {\r
+ criteria = getSession().createCriteria(clazz, "specimen");\r
+ }\r
+\r
+ Disjunction determinationOr = Restrictions.disjunction();\r
+\r
+ // A Taxon may be referenced by the DeterminationEvent of the SpecimenOrObservationBase\r
+ Criteria determinationsCriteria = criteria.createCriteria("determinations");\r
+\r
+ determinationOr.add(Restrictions.eq("taxon", associatedTaxon));\r
+ //check also for synonyms\r
+ for (Synonym synonym : associatedTaxon.getSynonyms()) {\r
+ determinationOr.add(Restrictions.eq("taxon", synonym));\r
+ }\r
+\r
+ //check also for name determinations\r
+ determinationOr.add(Restrictions.eq("taxonName", associatedTaxon.getName()));\r
+ for (TaxonName synonymName : associatedTaxon.getSynonymNames()) {\r
+ determinationOr.add(Restrictions.eq("taxonName", synonymName));\r
+ }\r
+\r
+ determinationsCriteria.add(determinationOr);\r
+\r
+ if(limit != null) {\r
+ if(start != null) {\r
+ criteria.setFirstResult(start);\r
+ } else {\r
+ criteria.setFirstResult(0);\r
+ }\r
+ criteria.setMaxResults(limit);\r
+ }\r
+ criteria.setProjection(Projections.property("id"));\r
+\r
+ addOrder(criteria,orderHints);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<Integer> detResults = criteria.list();\r
+ setOfAllIds.addAll(detResults);\r
+\r
+ // The IndividualsAssociation elements in a TaxonDescription contain DerivedUnits\r
+ setOfAllIds.addAll(descriptionDao.getIndividualAssociationSpecimenIDs(\r
+ associatedTaxon.getUuid(), null, null, 0, null));\r
+\r
+\r
+ // SpecimenTypeDesignations may be associated with the TaxonName.\r
+ setOfAllIds.addAll(taxonNameDao.getTypeSpecimenIdsForTaxonName(\r
+ associatedTaxon.getName(), null, null, null));\r
+\r
+ // SpecimenTypeDesignations may be associated with any HomotypicalGroup related to the specific Taxon.\r
+ //TODO adapt to set of ids\r
+ for(HomotypicalGroup homotypicalGroup : associatedTaxon.getHomotypicSynonymyGroups()) {\r
+ List<SpecimenTypeDesignation> byHomotypicalGroup = homotypicalGroupDao.getTypeDesignations(homotypicalGroup, SpecimenTypeDesignation.class, null, null, 0, null);\r
+ for (SpecimenTypeDesignation specimenTypeDesignation : byHomotypicalGroup) {\r
+ if (specimenTypeDesignation.getTypeSpecimen() != null){\r
+ setOfAllIds.add(specimenTypeDesignation.getTypeSpecimen().getId());\r
+ }\r
+ }\r
+ }\r
+\r
+ if(setOfAllIds.size() == 0){\r
+ // no need querying the data base\r
+ return null;\r
+ }\r
+\r
+ String queryString =\r
+ "select "+select+\r
+ " from SpecimenOrObservationBase sob" +\r
+ " where sob.id in (:setOfAllIds)";\r
+\r
+ if(clazz != null && !clazz.equals(SpecimenOrObservationBase.class)){\r
+ queryString += " and sob.class = :type ";\r
+ }\r
+\r
+ if(orderHints != null && orderHints.size() > 0){\r
+ queryString += " order by ";\r
+ String orderStr = "";\r
+ for(OrderHint orderHint : orderHints){\r
+ if(orderStr.length() > 0){\r
+ orderStr += ", ";\r
+ }\r
+ queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();\r
+ }\r
+ queryString += orderStr;\r
+ }\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameterList("setOfAllIds", setOfAllIds);\r
+\r
+ if(clazz != null && !clazz.equals(SpecimenOrObservationBase.class)){\r
+ query.setParameter("type", clazz.getSimpleName());\r
+ }\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ return query;\r
+ }\r
+\r
+ @Override\r
+ public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ String queryString = "FROM SpecimenOrObservationBase specimens "\r
+ + " WHERE specimens.recordBasis = :type ";\r
+\r
+ queryString += orderByClause("specimens", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("type", type);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings({ "unchecked", "rawtypes" })\r
+ List<SpecimenOrObservationBase> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+\r
+ @Override\r
+ public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ String queryString = "FROM DeterminationEvent determination "\r
+ + " WHERE determination.identifiedUnit = :specimen";\r
+\r
+ queryString += orderByClause("determination", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("specimen", specimen);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<DeterminationEvent> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ @Override\r
+ public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ String queryString = "FROM SpecimenTypeDesignation designations "\r
+ + " WHERE designations.typeSpecimen = :specimen";\r
+\r
+ queryString += orderByClause("designations", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("specimen", specimen);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<SpecimenTypeDesignation> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+\r
+ @Override\r
+ public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ //DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements\r
+ String queryString = "FROM IndividualsAssociation associations WHERE associations.associatedSpecimenOrObservation = :specimen";\r
+\r
+ queryString += orderByClause("associations", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("specimen", specimen);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<IndividualsAssociation> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ @Override\r
+ public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ //DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements\r
+ String queryString = "FROM DescriptionBase descriptions "\r
+ + " WHERE descriptions.describedSpecimenOrObservation = :specimen";\r
+\r
+ queryString += orderByClause("descriptions", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("specimen", specimen);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<DescriptionBase<?>> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ /**\r
+ * {@inheritDoc}\r
+ */\r
+ @Override\r
+ public List<FieldUnit> findFieldUnitsForGatheringEvent(UUID gatheringEventUuid, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ String queryString = "FROM SpecimenOrObservationBase sob "\r
+ + "WHERE sob.gatheringEvent.uuid = :gatheringEventUuid";\r
+\r
+ queryString += orderByClause("sob", orderHints);\r
+\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("gatheringEventUuid", gatheringEventUuid);\r
+\r
+ addLimitAndStart(query, limit, start);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ List<FieldUnit> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ /**\r
+ *\r
+ * {@inheritDoc}\r
+ */\r
+ @Override\r
+ public DnaSample findByGeneticAccessionNumber(String accessionNumberString, List<String> propertyPaths) {\r
+ String queryString = "SELECT dnaSample FROM DnaSample as dnaSample join dnaSample.sequences as sequences WITH sequences.geneticAccessionNumber LIKE :accessionNumberString";\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("accessionNumberString", accessionNumberString);\r
+ @SuppressWarnings("unchecked")\r
+ List<DnaSample> dnaSamples = query.list();\r
+ defaultBeanInitializer.initializeAll(dnaSamples, propertyPaths);\r
+\r
+\r
+ if (dnaSamples.isEmpty()){\r
+ logger.debug("there is no dnaSample for genetic accession number " + accessionNumberString + " this should not happen.");\r
+ return null;\r
+ }else if (dnaSamples.size() == 1){\r
+ return dnaSamples.get(0);\r
+ } else{\r
+ logger.debug("there are more than one dnaSample for genetic accession number " + accessionNumberString + " this should not happen.");\r
+ return null;\r
+ }\r
+\r
+\r
+ }\r
+\r
+ /**\r
+ *\r
+ * {@inheritDoc}\r
+ */\r
+ @Override\r
+ public long countByGeneticAccessionNumber(String accessionNumberString) {\r
+ String queryString = "SELECT count(dnaSample) FROM DnaSample dnaSample JOIN dnaSample.sequences sequence WHERE sequence.geneticAccessionNumber LIKE :accessionNumberString";\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("accessionNumberString", accessionNumberString);\r
+ @SuppressWarnings("unchecked")\r
+ List<DerivedUnit> dnaSamples = query.list();\r
+ long result = (long)query.uniqueResult();\r
+\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * @param dnaSamples\r
+ * @param results\r
+ */\r
+ private void extractDeterminedOriginals(List<DerivedUnit> samples, List<DerivedUnit> results) {\r
+ for (DerivedUnit sample:samples){\r
+ if (sample.getDeterminations() != null && !sample.getDeterminations().isEmpty()){\r
+ results.add(sample);\r
+ }else{\r
+ if (sample instanceof DerivedUnit){\r
+ Set<SpecimenOrObservationBase> originals = sample.getDerivedFrom().getOriginals();\r
+ List<DerivedUnit> originalDerivedUnits = new ArrayList();\r
+ for (SpecimenOrObservationBase original:originals){\r
+ if (original instanceof DerivedUnit){\r
+ originalDerivedUnits.add((DerivedUnit)original);\r
+ }\r
+ }\r
+ if(!originalDerivedUnits.isEmpty()){\r
+ extractDeterminedOriginals(originalDerivedUnits, results);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * {@inheritDoc}\r
+ */\r
+ @Override\r
+ public List<SpecimenOrObservationBase> findOriginalsForDerivedUnit(UUID derivedUnitUuid, List<String> propertyPaths) {\r
+ String queryString = "SELECT DISTINCT o FROM DerivedUnit du"\r
+ + " JOIN du.derivedFrom.originals o WHERE du.uuid LIKE :derivedUnitUuid";\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameter("derivedUnitUuid", derivedUnitUuid);\r
+ @SuppressWarnings("unchecked")\r
+ List<SpecimenOrObservationBase> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+\r
+ /**\r
+ * {@inheritDoc}\r
+ */\r
+ @Override\r
+ public List<Point> findPointsForFieldUnitList(List<UUID> fieldUnitUuids) {\r
+ String queryString = "SELECT DISTINCT fu.gatheringEvent.exactLocation FROM FieldUnit fu"\r
+ + " WHERE fu.uuid IN (:fieldUnitUuids)";\r
+ Query query = getSession().createQuery(queryString);\r
+ query.setParameterList("fieldUnitUuids", fieldUnitUuids);\r
+ @SuppressWarnings("unchecked")\r
+ List<Point> results = query.list();\r
+\r
+ return results;\r
+ }\r
+\r
+}
BGBM BDI Projects / cdmlib.git / blobdiff