/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy \r
-* http://www.e-taxonomy.eu\r
-* \r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
+ * Copyright (C) 2007 EDIT\r
+ * European Distributed Institute of Taxonomy \r
+ * http://www.e-taxonomy.eu\r
+ * \r
+ * The contents of this file are subject to the Mozilla Public License Version 1.1\r
+ * See LICENSE.TXT at the top of this package for the full license terms.\r
+ */\r
package eu.etaxonomy.cdm.persistence.dao.hibernate.taxon;\r
\r
+import java.lang.reflect.Field;\r
+import java.lang.reflect.InvocationTargetException;\r
+import java.lang.reflect.Method;\r
+import java.util.ArrayList;\r
+import java.util.Collections;\r
+import java.util.Comparator;\r
+import java.util.HashSet;\r
+import java.util.Iterator;\r
import java.util.List;\r
+import java.util.Set;\r
+import java.util.SortedSet;\r
+import java.util.TreeSet;\r
+import java.util.UUID;\r
+\r
import org.apache.log4j.Logger;\r
+import org.apache.lucene.analysis.SimpleAnalyzer;\r
+import org.apache.lucene.queryParser.ParseException;\r
+import org.apache.lucene.queryParser.QueryParser;\r
+import org.apache.lucene.search.Sort;\r
+import org.apache.lucene.search.SortField;\r
import org.hibernate.Criteria;\r
+import org.hibernate.FetchMode;\r
+import org.hibernate.Hibernate;\r
+import org.hibernate.LazyInitializationException;\r
+import org.hibernate.Query;\r
+import org.hibernate.Transaction;\r
+import org.hibernate.criterion.Criterion;\r
+import org.hibernate.criterion.Projections;\r
import org.hibernate.criterion.Restrictions;\r
+import org.hibernate.envers.query.AuditEntity;\r
+import org.hibernate.envers.query.AuditQuery;\r
+import org.hibernate.search.FullTextQuery;\r
+import org.hibernate.search.FullTextSession;\r
+import org.hibernate.search.Search;\r
+import org.hibernate.search.SearchFactory;\r
+import org.springframework.beans.factory.annotation.Autowired;\r
+import org.springframework.beans.factory.annotation.Qualifier;\r
+import org.springframework.dao.DataAccessException;\r
import org.springframework.stereotype.Repository;\r
+import org.springframework.util.ReflectionUtils;\r
+\r
+import eu.etaxonomy.cdm.model.common.Annotation;\r
+import eu.etaxonomy.cdm.model.common.Extension;\r
+import eu.etaxonomy.cdm.model.common.Marker;\r
+import eu.etaxonomy.cdm.model.common.OriginalSource;\r
+import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
+import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.media.Rights;\r
+import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;\r
+import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
+import eu.etaxonomy.cdm.model.occurrence.Collection;\r
+import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
+import eu.etaxonomy.cdm.model.taxon.Synonym;\r
+import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;\r
+import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
+import eu.etaxonomy.cdm.model.view.AuditEvent;\r
+import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;\r
+import eu.etaxonomy.cdm.persistence.dao.QueryParseException;\r
+import eu.etaxonomy.cdm.persistence.dao.common.ISearchableDao;\r
+import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;\r
+import eu.etaxonomy.cdm.persistence.dao.hibernate.AlternativeSpellingSuggestionParser;\r
+import eu.etaxonomy.cdm.persistence.dao.hibernate.HibernateBeanInitializer;\r
import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;\r
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;\r
+import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
+import eu.etaxonomy.cdm.persistence.query.OrderHint;\r
+\r
\r
/**\r
* @author a.mueller\r
- *\r
+ * @created 24.11.2008\r
+ * @version 1.0\r
*/\r
@Repository\r
-public class TaxonDaoHibernateImpl extends IdentifiableDaoBase<TaxonBase> implements ITaxonDao {\r
- static Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);\r
+@Qualifier("taxonDaoHibernateImpl")\r
+public class TaxonDaoHibernateImpl extends IdentifiableDaoBase<TaxonBase> implements ITaxonDao { \r
+ private AlternativeSpellingSuggestionParser<TaxonBase> alternativeSpellingSuggestionParser;\r
+ \r
+ \r
+ @SuppressWarnings("unused")\r
+ private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);\r
+ \r
+ private String defaultField = "name.titleCache";\r
+ private Class<? extends TaxonBase> indexedClasses[]; \r
\r
public TaxonDaoHibernateImpl() {\r
super(TaxonBase.class);\r
+ indexedClasses = new Class[2];\r
+ indexedClasses[0] = Taxon.class;\r
+ indexedClasses[1] = Synonym.class;\r
+ }\r
+ \r
+ @Autowired(required = false) //TODO switched of because it caused problems when starting CdmApplicationController\r
+ public void setAlternativeSpellingSuggestionParser(AlternativeSpellingSuggestionParser<TaxonBase> alternativeSpellingSuggestionParser) {\r
+ this.alternativeSpellingSuggestionParser = alternativeSpellingSuggestionParser;\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
+ */\r
public List<Taxon> getRootTaxa(ReferenceBase sec) {\r
+ return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true, false);\r
+ }\r
+ \r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.ReferenceBase, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)\r
+ */\r
+ public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.getRootTaxa(Rank rank, ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications)");\r
+ if (onlyWithChildren == null){\r
+ onlyWithChildren = true;\r
+ }\r
+ if (withMisapplications == null){\r
+ withMisapplications = true;\r
+ }\r
+ if (cdmFetch == null){\r
+ cdmFetch = CdmFetch.NO_FETCH();\r
+ }\r
+\r
Criteria crit = getSession().createCriteria(Taxon.class);\r
- crit.add(Restrictions.isNull("taxonomicParentCache"));\r
+ \r
+ crit.setFetchMode("name", FetchMode.JOIN);\r
+ crit.createAlias("name", "name");\r
+ \r
+ if (rank != null) {\r
+ crit.add(Restrictions.eq("name.rank", rank));\r
+ }else{\r
+ crit.add(Restrictions.isNull("taxonomicParentCache"));\r
+ }\r
+\r
if (sec != null){\r
crit.add(Restrictions.eq("sec", sec) );\r
}\r
- List<Taxon> results = crit.list();\r
+\r
+ if (! cdmFetch.includes(CdmFetch.FETCH_CHILDTAXA())){\r
+ logger.info("Not fetching child taxa");\r
+ //TODO overwrite LAZY (SELECT) does not work (bug in hibernate?)\r
+ crit.setFetchMode("relationsToThisTaxon.fromTaxon", FetchMode.LAZY);\r
+ }\r
+\r
+ List<Taxon> results = new ArrayList<Taxon>();\r
+ List<Taxon> taxa = crit.list();\r
+ for(Taxon taxon : taxa){\r
+ \r
+ \r
+ //childTaxa\r
+ //TODO create restriction instead\r
+ // (a) not using cache fields\r
+ /*Hibernate.initialize(taxon.getRelationsFromThisTaxon());\r
+ if (onlyWithChildren == false || taxon.getRelationsFromThisTaxon().size() > 0){\r
+ if (withMisapplications == true || ! taxon.isMisappliedName()){\r
+ defaultBeanInitializer.initialize(taxon, propertyPaths);\r
+ results.add(taxon);\r
+ }\r
+ }*/\r
+ // (b) using cache fields\r
+ if (onlyWithChildren == false || taxon.hasTaxonomicChildren()){\r
+ if (withMisapplications == true || ! taxon.isMisappliedName()){\r
+ defaultBeanInitializer.initialize(taxon, propertyPaths);\r
+ results.add(taxon);\r
+ }\r
+ }\r
+ }\r
return results;\r
}\r
\r
- public List<TaxonBase> getTaxaByName(String name, ReferenceBase sec) {\r
- Criteria crit = getSession().createCriteria(Taxon.class);\r
- if (sec != null){\r
- crit.add(Restrictions.eq("sec", sec ) );\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, eu.etaxonomy.cdm.persistence.fetch.CdmFetch, java.lang.Boolean, java.lang.Boolean)\r
+ */\r
+ public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {\r
+ return getRootTaxa(null, sec, cdmFetch, onlyWithChildren, withMisapplications, null);\r
+ }\r
+ \r
+\r
+ public List<TaxonBase> getTaxaByName(String queryString, ReferenceBase sec) {\r
+ \r
+ return getTaxaByName(queryString, true, sec);\r
+ }\r
+\r
+ public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.getTaxaByName(String name, ReferenceBase sec)");\r
+ \r
+ Criteria criteria = null;\r
+ if (accepted == true) {\r
+ criteria = getSession().createCriteria(Taxon.class);\r
+ } else {\r
+ criteria = getSession().createCriteria(Synonym.class);\r
}\r
- crit.createCriteria("name").add(Restrictions.eq("titleCache", name));\r
- List<TaxonBase> results = crit.list();\r
- return results;\r
+ \r
+ criteria.setFetchMode( "name", FetchMode.JOIN );\r
+ criteria.createAlias("name", "name");\r
+ \r
+ if (sec != null && sec.getId() != 0) {\r
+ criteria.add(Restrictions.eq("sec", sec ) );\r
+ }\r
+\r
+ // FIXME: sec restriction caused problems in cich image import: results was empty\r
+ \r
+ if (queryString != null) {\r
+ criteria.add(Restrictions.ilike("name.nameCache", queryString));\r
+ }\r
+\r
+ return (List<TaxonBase>)criteria.list();\r
}\r
\r
- public List<TaxonBase> getAllTaxa(Integer pagesize, Integer page) {\r
- Criteria crit = getSession().createCriteria(TaxonBase.class);\r
- List<TaxonBase> results = crit.list();\r
- // TODO add page & pagesize criteria\r
+ public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode, \r
+ Boolean accepted, Integer pageSize, Integer pageNumber) {\r
+ \r
+ Criteria criteria = null;\r
+ if (accepted == true) {\r
+ criteria = getSession().createCriteria(Taxon.class);\r
+ } else {\r
+ criteria = getSession().createCriteria(Synonym.class);\r
+ }\r
+\r
+ criteria.setFetchMode( "name", FetchMode.JOIN );\r
+ criteria.createAlias("name", "name");\r
+ \r
+ String hqlQueryString = matchMode.queryStringFrom(queryString);\r
+ if (matchMode == MatchMode.EXACT) {\r
+ criteria.add(Restrictions.eq("name.nameCache", hqlQueryString));\r
+ } else {\r
+ criteria.add(Restrictions.ilike("name.nameCache", hqlQueryString));\r
+ }\r
+ \r
+ if(pageSize != null) {\r
+ criteria.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ criteria.setFirstResult(pageNumber * pageSize);\r
+ }\r
+ }\r
+\r
+ List<TaxonBase> results = criteria.list();\r
return results;\r
}\r
\r
-}
\ No newline at end of file
+ public Integer countTaxaByName(String queryString, MatchMode matchMode, \r
+ Boolean accepted) {\r
+ //TODO improve performance\r
+ List<TaxonBase> restultSet = getTaxaByName(queryString, matchMode, accepted, null, null);\r
+ return restultSet.size();\r
+ }\r
+ \r
+\r
+ public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page) {\r
+ return super.list(pagesize, page);\r
+ }\r
+\r
+ public List<Synonym> getAllSynonyms(Integer limit, Integer start) {\r
+ return super.list(Synonym.class, limit, start);\r
+ }\r
+\r
+ public List<Taxon> getAllTaxa(Integer limit, Integer start) {\r
+ return super.list(Taxon.class, limit, start);\r
+ }\r
+\r
+ public List<RelationshipBase> getAllRelationships(Integer limit, Integer start) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(RelationshipBase.class);\r
+ return (List<RelationshipBase>)criteria.list();\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(RelationshipBase.class,auditEvent.getRevisionNumber());\r
+ return (List<RelationshipBase>)query.getResultList();\r
+ }\r
+ }\r
+ \r
+ /** Sets the taxonomic parent to null. Does not handle taxonomic relationships. */\r
+// private boolean nullifyTaxonomicParent(Taxon taxon) {\r
+//\r
+// try {\r
+// Method nullifyTaxonomicParent = taxon.getClass().getMethod("nullifyTaxonomicParent");\r
+// nullifyTaxonomicParent.invoke(taxon);\r
+// } catch (NoSuchMethodException ex) {\r
+// logger.error("NoSuchMethod: " + ex.getMessage());\r
+// return false;\r
+// } catch (IllegalArgumentException ex) {\r
+// logger.error("IllegalArgumentException: " + ex.getMessage());\r
+// return false;\r
+// } catch (IllegalAccessException ex) {\r
+// logger.error("IllegalAccessException: " + ex.getMessage());\r
+// return false;\r
+// } catch (InvocationTargetException ex) {\r
+// logger.error("IllegalAccessException: " + ex.getMessage());\r
+// return false;\r
+// }\r
+// return true;\r
+// }\r
+ \r
+ @Override\r
+ public UUID delete(TaxonBase taxonBase) throws DataAccessException{\r
+ if (taxonBase == null){\r
+ logger.warn("TaxonBase was 'null'");\r
+ return null;\r
+ }\r
+ \r
+ // Merge the object in if it is detached\r
+ //\r
+ // I think this is preferable to catching lazy initialization errors \r
+ // as that solution only swallows and hides the exception, but doesn't \r
+ // actually solve it.\r
+ getSession().merge(taxonBase);\r
+ \r
+ for(Iterator<Annotation> iterator = taxonBase.getAnnotations().iterator(); iterator.hasNext();) {\r
+ Annotation annotation = iterator.next();\r
+ annotation.setAnnotatedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(annotation);\r
+ }\r
+ \r
+ for(Iterator<Marker> iterator = taxonBase.getMarkers().iterator(); iterator.hasNext();) {\r
+ Marker marker = iterator.next();\r
+ marker.setMarkedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(marker);\r
+ }\r
+ \r
+ for(Iterator<Extension> iterator = taxonBase.getExtensions().iterator(); iterator.hasNext();) {\r
+ Extension extension = iterator.next();\r
+ extension.setExtendedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(extension);\r
+ }\r
+ \r
+ for(Iterator<OriginalSource> iterator = taxonBase.getSources().iterator(); iterator.hasNext();) {\r
+ OriginalSource source = iterator.next();\r
+ source.setSourcedObj(null);\r
+ iterator.remove();\r
+ getSession().delete(source);\r
+ }\r
+\r
+ for(Iterator<Rights> iterator = taxonBase.getRights().iterator(); iterator.hasNext();) {\r
+ Rights rights = iterator.next();\r
+ iterator.remove();\r
+ getSession().delete(rights);\r
+ }\r
+ \r
+ if (taxonBase instanceof Taxon){ // is Taxon\r
+ //taxonRelationships\r
+ Taxon taxon = (Taxon)taxonBase;\r
+ \r
+ for (Iterator<TaxonRelationship> iterator = taxon.getRelationsFromThisTaxon().iterator(); iterator.hasNext();){\r
+ TaxonRelationship relationFromThisTaxon = iterator.next();\r
+ iterator.remove();\r
+ \r
+ // decrease children count of taxonomic parent by one\r
+ if (relationFromThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {\r
+ Taxon toTaxon = relationFromThisTaxon.getToTaxon(); // parent\r
+ if (toTaxon != null) {\r
+ toTaxon.setTaxonomicChildrenCount(toTaxon.getTaxonomicChildrenCount() - 1); \r
+ }\r
+ }\r
+ relationFromThisTaxon.setToTaxon(null);\r
+ relationFromThisTaxon.setFromTaxon(null);\r
+ getSession().delete(relationFromThisTaxon);\r
+ }\r
+ \r
+ for (Iterator<TaxonRelationship> iterator = taxon.getRelationsToThisTaxon().iterator(); iterator.hasNext();){\r
+ TaxonRelationship relationToThisTaxon = iterator.next();\r
+ iterator.remove();\r
+ \r
+ // set parent cache of child to null\r
+ if (relationToThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {\r
+ Taxon fromTaxon = relationToThisTaxon.getFromTaxon(); // child\r
+ if (fromTaxon != null) {\r
+ fromTaxon.nullifyTaxonomicParent();\r
+ }\r
+ }\r
+ relationToThisTaxon.setFromTaxon(null);\r
+ relationToThisTaxon.setToTaxon(null);\r
+ getSession().delete(relationToThisTaxon);\r
+ }\r
+ \r
+ //SynonymRelationships\r
+ for (Iterator<SynonymRelationship> iterator = taxon.getSynonymRelations().iterator(); iterator.hasNext();){\r
+ SynonymRelationship synonymRelation = iterator.next();\r
+ iterator.remove();\r
+ synonymRelation.setAcceptedTaxon(null);\r
+ synonymRelation.setSynonym(null);\r
+ getSession().delete(synonymRelation);\r
+ } \r
+ \r
+ // Descriptions\r
+ for (Iterator<TaxonDescription> iterDesc = taxon.getDescriptions().iterator(); iterDesc.hasNext();) {\r
+ TaxonDescription taxonDescription = iterDesc.next();\r
+ iterDesc.remove();\r
+ //taxonDescription.setTaxon(null);\r
+ Field field = ReflectionUtils.findField(TaxonDescription.class, "taxon", Taxon.class);\r
+ ReflectionUtils.makeAccessible(field);\r
+ ReflectionUtils.setField(field, taxonDescription, null);\r
+ for (Iterator<DescriptionElementBase> iterDescElem = \r
+ taxonDescription.getElements().iterator(); iterDescElem.hasNext();) {\r
+ DescriptionElementBase descriptionElement = iterDescElem.next();\r
+ iterDescElem.remove();\r
+ getSession().delete(descriptionElement);\r
+ }\r
+ getSession().delete(taxonDescription);\r
+ }\r
+ \r
+ taxon.nullifyTaxonomicParent();\r
+\r
+ } else { //is Synonym\r
+ Synonym synonym = (Synonym)taxonBase;\r
+ for (Iterator<SynonymRelationship> iterator = synonym.getSynonymRelations().iterator(); iterator.hasNext();){\r
+ SynonymRelationship synonymRelation = iterator.next();\r
+ iterator.remove();\r
+ synonymRelation.setAcceptedTaxon(null);\r
+ synonymRelation.setSynonym(null);\r
+ } ;\r
+ }\r
+ return super.delete(taxonBase);\r
+ }\r
+\r
+\r
+ // TODO add generic return type !!\r
+ public List findByName(String queryString, MatchMode matchMode, int page, int pagesize, boolean onlyAcccepted) {\r
+ ArrayList<Criterion> criteria = new ArrayList<Criterion>();\r
+ //TODO ... Restrictions.eq(propertyName, value)\r
+ return super.findByTitle(queryString, matchMode, page, pagesize, criteria);\r
+\r
+ }\r
+\r
+ public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted)");\r
+ Criteria crit = getSession().createCriteria(type);\r
+ crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));\r
+ crit.setProjection(Projections.rowCount());\r
+ int result = ((Integer)crit.list().get(0)).intValue();\r
+ return result;\r
+ }\r
+\r
+\r
+ public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countMatchesByName(String queryString, ITitledDao.MATCH_MODE matchMode, boolean onlyAcccepted, List<Criterion> criteria)");\r
+ Criteria crit = getSession().createCriteria(type);\r
+ crit.add(Restrictions.ilike("titleCache", matchMode.queryStringFrom(queryString)));\r
+ if(criteria != null){\r
+ for (Criterion criterion : criteria) {\r
+ crit.add(criterion);\r
+ }\r
+ }\r
+ crit.setProjection(Projections.rowCount());\r
+ int result = ((Integer)crit.list().get(0)).intValue();\r
+ return result;\r
+ }\r
+\r
+ public int countRelatedTaxa(Taxon taxon, TaxonRelationshipType type) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Query query = null;\r
+ \r
+ if(type == null) {\r
+ query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo");\r
+ } else {\r
+ query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo and taxonRelationship.type = :type");\r
+ query.setParameter("type",type);\r
+ }\r
+ \r
+ query.setParameter("relatedTo", taxon);\r
+ \r
+ return ((Long)query.uniqueResult()).intValue();\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ query.addProjection(AuditEntity.id().count("id"));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\r
+ \r
+ return ((Long)query.getSingleResult()).intValue();\r
+ }\r
+ }\r
+\r
+ public int countSynonyms(Taxon taxon, SynonymRelationshipType type) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Query query = null;\r
+\r
+ if(type == null) {\r
+ query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo");\r
+ } else {\r
+ query = getSession().createQuery("select count(synonymRelationship) from SynonymRelationship synonymRelationship where synonymRelationship.relatedTo = :relatedTo and synonymRelationship.type = :type");\r
+ query.setParameter("type",type);\r
+ }\r
+\r
+ query.setParameter("relatedTo", taxon);\r
+\r
+ return ((Long)query.uniqueResult()).intValue();\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ query.addProjection(AuditEntity.id().count("id"));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\r
+ \r
+ return ((Long)query.getSingleResult()).intValue();\r
+ }\r
+ }\r
+\r
+ public int count(Class<? extends TaxonBase> clazz, String queryString) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.count(String queryString, Boolean accepted)");\r
+ QueryParser queryParser = new QueryParser(defaultField, new SimpleAnalyzer());\r
+ \r
+ try {\r
+ org.apache.lucene.search.Query query = queryParser.parse(queryString);\r
+ \r
+ FullTextSession fullTextSession = Search.getFullTextSession(this.getSession());\r
+ org.hibernate.search.FullTextQuery fullTextQuery = null;\r
+ \r
+ if(clazz == null) {\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, type);\r
+ } else {\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, clazz);\r
+ }\r
+ \r
+ Integer result = fullTextQuery.getResultSize();\r
+ return result;\r
+\r
+ } catch (ParseException e) {\r
+ throw new QueryParseException(e, queryString);\r
+ }\r
+ }\r
+ \r
+ public int countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec)");\r
+ Criteria criteria = null;\r
+ \r
+ if (accepted == true) {\r
+ criteria = getSession().createCriteria(Taxon.class);\r
+ } else {\r
+ criteria = getSession().createCriteria(Synonym.class);\r
+ }\r
+ \r
+ criteria.setFetchMode( "name", FetchMode.JOIN );\r
+ criteria.createAlias("name", "name");\r
+\r
+ if (sec != null){\r
+ if(sec.getId() == 0){\r
+ getSession().save(sec);\r
+ }\r
+ criteria.add(Restrictions.eq("sec", sec ) );\r
+ }\r
+ if (queryString != null) {\r
+ criteria.add(Restrictions.ilike("name.nameCache", queryString));\r
+ }\r
+ criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
+ \r
+ return (Integer)criteria.uniqueResult();\r
+ }\r
+\r
+ public int countTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank)");\r
+ Criteria criteria = null;\r
+ \r
+ if(clazz == null) {\r
+ criteria = getSession().createCriteria(TaxonBase.class);\r
+ } else {\r
+ criteria = getSession().createCriteria(clazz); \r
+ }\r
+ \r
+ criteria.setFetchMode( "name", FetchMode.JOIN );\r
+ criteria.createAlias("name", "name");\r
+ \r
+ if(genusOrUninomial != null) {\r
+ criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));\r
+ }\r
+ \r
+ if(infraGenericEpithet != null) {\r
+ criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));\r
+ }\r
+ \r
+ if(specificEpithet != null) {\r
+ criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));\r
+ }\r
+ \r
+ if(infraSpecificEpithet != null) {\r
+ criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));\r
+ }\r
+ \r
+ if(rank != null) {\r
+ criteria.add(Restrictions.eq("name.rank", rank));\r
+ }\r
+ \r
+ criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
+ \r
+ return (Integer)criteria.uniqueResult();\r
+ }\r
+\r
+ public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber)");\r
+ Criteria criteria = null;\r
+ \r
+ if(clazz == null) {\r
+ criteria = getSession().createCriteria(TaxonBase.class);\r
+ } else {\r
+ criteria = getSession().createCriteria(clazz);\r
+ }\r
+ \r
+ criteria.setFetchMode( "name", FetchMode.JOIN );\r
+ criteria.createAlias("name", "name");\r
+ \r
+ if(genusOrUninomial == null) {\r
+ criteria.add(Restrictions.isNull("name.genusOrUninomial"));\r
+ } else if(!genusOrUninomial.equals("*")) {\r
+ criteria.add(Restrictions.eq("name.genusOrUninomial", genusOrUninomial));\r
+ }\r
+ \r
+ if(infraGenericEpithet == null) {\r
+ criteria.add(Restrictions.isNull("name.infraGenericEpithet"));\r
+ } else if(!infraGenericEpithet.equals("*")) {\r
+ criteria.add(Restrictions.eq("name.infraGenericEpithet", infraGenericEpithet));\r
+ } \r
+ \r
+ if(specificEpithet == null) {\r
+ criteria.add(Restrictions.isNull("name.specificEpithet"));\r
+ } else if(!specificEpithet.equals("*")) {\r
+ criteria.add(Restrictions.eq("name.specificEpithet", specificEpithet));\r
+ \r
+ }\r
+ \r
+ if(infraSpecificEpithet == null) {\r
+ criteria.add(Restrictions.isNull("name.infraSpecificEpithet"));\r
+ } else if(!infraSpecificEpithet.equals("*")) {\r
+ criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));\r
+ }\r
+ \r
+ if(rank != null) {\r
+ criteria.add(Restrictions.eq("name.rank", rank));\r
+ }\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
+ \r
+ return (List<TaxonBase>)criteria.list();\r
+ }\r
+\r
+ public List<TaxonRelationship> getRelatedTaxa(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(TaxonRelationship.class);\r
+ \r
+ criteria.add(Restrictions.eq("relatedTo", taxon));\r
+ if(type != null) {\r
+ criteria.add(Restrictions.eq("type", type));\r
+ } \r
+ \r
+ addOrder(criteria,orderHints);\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
+ \r
+ List<TaxonRelationship> result = (List<TaxonRelationship>)criteria.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ return result;\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\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<TaxonRelationship> result = (List<TaxonRelationship>)query.getResultList();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ // Ugly, but for now, there is no way to sort on a related entity property in Envers,\r
+ // and we can't live without this functionality in CATE as it screws up the whole \r
+ // taxon tree thing\r
+ if(orderHints != null && !orderHints.isEmpty()) {\r
+ SortedSet<TaxonRelationship> sortedList = new TreeSet<TaxonRelationship>(new TaxonRelationshipFromTaxonComparator());\r
+ sortedList.addAll(result);\r
+ return new ArrayList<TaxonRelationship>(sortedList);\r
+ }\r
+ \r
+ return result;\r
+ }\r
+ }\r
+ \r
+ class TaxonRelationshipFromTaxonComparator implements Comparator<TaxonRelationship> {\r
+\r
+ public int compare(TaxonRelationship o1, TaxonRelationship o2) {\r
+ return o1.getFromTaxon().getTitleCache().compareTo(o2.getFromTaxon().getTitleCache());\r
+ }\r
+ \r
+ }\r
+\r
+ public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ AuditEvent auditEvent = getAuditEventFromContext();\r
+ if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
+ Criteria criteria = getSession().createCriteria(SynonymRelationship.class);\r
+ \r
+ criteria.add(Restrictions.eq("relatedTo", taxon));\r
+ if(type != null) {\r
+ criteria.add(Restrictions.eq("type", type));\r
+ } \r
+ \r
+ addOrder(criteria,orderHints);\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
+ \r
+ List<SynonymRelationship> result = (List<SynonymRelationship>)criteria.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ return result;\r
+ } else {\r
+ AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(SynonymRelationship.class,auditEvent.getRevisionNumber());\r
+ query.add(AuditEntity.relatedId("relatedTo").eq(taxon.getId()));\r
+ \r
+ if(type != null) {\r
+ query.add(AuditEntity.relatedId("type").eq(type.getId()));\r
+ }\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<SynonymRelationship> result = (List<SynonymRelationship>)query.getResultList();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ \r
+ return result;\r
+ }\r
+ }\r
+\r
+ public List<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString,Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.searchTaxa(String queryString, Boolean accepted, Integer pageSize, Integer pageNumber)");\r
+ QueryParser queryParser = new QueryParser(defaultField, new SimpleAnalyzer());\r
+ List<TaxonBase> results = new ArrayList<TaxonBase>();\r
+ \r
+ try {\r
+ org.apache.lucene.search.Query query = queryParser.parse(queryString);\r
+ \r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
+ org.hibernate.search.FullTextQuery fullTextQuery = null;\r
+ \r
+ if(clazz == null) {\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, TaxonBase.class);\r
+ } else {\r
+ fullTextQuery = fullTextSession.createFullTextQuery(query, clazz);\r
+ }\r
+ \r
+ addOrder(fullTextQuery,orderHints);\r
+ \r
+ if(pageSize != null) {\r
+ fullTextQuery.setMaxResults(pageSize);\r
+ if(pageNumber != null) {\r
+ fullTextQuery.setFirstResult(pageNumber * pageSize);\r
+ } else {\r
+ fullTextQuery.setFirstResult(0);\r
+ }\r
+ }\r
+ \r
+ List<TaxonBase> result = (List<TaxonBase>)fullTextQuery.list();\r
+ defaultBeanInitializer.initializeAll(result, propertyPaths);\r
+ return result;\r
+\r
+ } catch (ParseException e) {\r
+ throw new QueryParseException(e, queryString);\r
+ }\r
+ }\r
+ \r
+ public void purgeIndex() {\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
+ for(Class clazz : indexedClasses) {\r
+ fullTextSession.purgeAll(clazz); // remove all taxon base from indexes\r
+ }\r
+ fullTextSession.flushToIndexes();\r
+ }\r
+\r
+ public void rebuildIndex() {\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
+ \r
+ for(TaxonBase taxonBase : list(null,null)) { // re-index all taxon base\r
+ Hibernate.initialize(taxonBase.getName());\r
+ fullTextSession.index(taxonBase);\r
+ }\r
+ fullTextSession.flushToIndexes();\r
+ }\r
+ \r
+ public void optimizeIndex() {\r
+ FullTextSession fullTextSession = Search.getFullTextSession(getSession());\r
+ SearchFactory searchFactory = fullTextSession.getSearchFactory();\r
+ for(Class clazz : indexedClasses) {\r
+ searchFactory.optimize(clazz); // optimize the indices ()\r
+ }\r
+ fullTextSession.flushToIndexes();\r
+ }\r
+\r
+ public String suggestQuery(String queryString) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.suggestQuery(String queryString)");\r
+ String alternativeQueryString = null;\r
+ if (alternativeSpellingSuggestionParser != null) {\r
+ try {\r
+\r
+ alternativeSpellingSuggestionParser.parse(queryString);\r
+ org.apache.lucene.search.Query alternativeQuery = alternativeSpellingSuggestionParser.suggest(queryString);\r
+ if (alternativeQuery != null) {\r
+ alternativeQueryString = alternativeQuery\r
+ .toString("name.titleCache");\r
+ }\r
+\r
+ } catch (ParseException e) {\r
+ throw new QueryParseException(e, queryString);\r
+ }\r
+ }\r
+ return alternativeQueryString;\r
+ }\r
+}\r
BGBM BDI Projects / cdmlib.git / blobdiff