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.Collection;\r
import java.util.Comparator;\r
import java.util.HashSet;\r
import java.util.Iterator;\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.Order;\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 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.common.RelationshipBase.Direction;\r
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.location.NamedArea;\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.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
-import eu.etaxonomy.cdm.persistence.query.SelectMode;\r
\r
\r
/**\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
\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
+ this.alternativeSpellingSuggestionParser = alternativeSpellingSuggestionParser; \r
}\r
+ \r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
return (List<TaxonBase>)criteria.list();\r
}\r
\r
- public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode,\r
+ public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
Integer pageSize, Integer pageNumber) {\r
\r
- return getTaxaByName(queryString, matchMode, selectMode, null, pageSize, pageNumber);\r
+ return getTaxaByName(clazz, queryString, matchMode, null, null, pageSize, pageNumber, null);\r
}\r
\r
public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode, \r
Boolean accepted, Integer pageSize, Integer pageNumber) {\r
\r
if (accepted == true) {\r
- return getTaxaByName(queryString, matchMode, SelectMode.TAXA, pageSize, pageNumber);\r
+ return getTaxaByName(Taxon.class, queryString, matchMode, pageSize, pageNumber);\r
} else {\r
- return getTaxaByName(queryString, matchMode, SelectMode.SYNONYMS, pageSize, pageNumber);\r
+ return getTaxaByName(Synonym.class, queryString, matchMode, pageSize, pageNumber);\r
}\r
}\r
\r
\r
- public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode,\r
- ReferenceBase sec, Integer pageSize, Integer pageNumber) {\r
+ public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ ReferenceBase sec, Set<NamedArea> namedAreas, Integer pageSize, \r
+ Integer pageNumber, List<String> propertyPaths) {\r
+ \r
+ \r
+ boolean doCount = false;\r
+ \r
+ Query query = prepareTaxaByName(clazz, queryString, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
\r
- Criteria criteria = null;\r
- Class<?> clazz = selectMode.criteria();\r
- criteria = getSession().createCriteria(clazz);\r
+ List<TaxonBase> results = query.list();\r
\r
- criteria.setFetchMode( "name", FetchMode.JOIN );\r
- criteria.createAlias("name", "name");\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
\r
- if (queryString != null) {\r
- String hqlQueryString = matchMode.queryStringFrom(queryString);\r
- if (matchMode == MatchMode.EXACT) {\r
- criteria.add(Restrictions.eq("name.nameCache", hqlQueryString));\r
+ return results;\r
+ \r
+ }\r
+\r
+ /**\r
+ * @param clazz\r
+ * @param queryString\r
+ * @param matchMode\r
+ * @param namedAreas\r
+ * @param pageSize\r
+ * @param pageNumber\r
+ * @param doCount\r
+ * @return\r
+ * \r
+ * FIXME implement taxontree restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}\r
+ */\r
+ private Query prepareTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount) {\r
+ \r
+ \r
+ //TODO ? checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec)");\r
+\r
+ String hqlQueryString = matchMode.queryStringFrom(queryString);\r
+ \r
+ String matchOperator;\r
+ if (matchMode == MatchMode.EXACT) {\r
+ matchOperator = "=";\r
+ } else {\r
+ matchOperator = "like";\r
+ }\r
+ \r
+ String selectWhat = (doCount ? "count(distinct t)": "distinct t");\r
+ \r
+ String hql = "";\r
+ Set<NamedArea> areasExpanded = new HashSet<NamedArea>();\r
+ if(namedAreas != null && namedAreas.size() > 0){\r
+ // expand areas\r
+ List<NamedArea> childAreas;\r
+ Query areaQuery = getSession().createQuery("select childArea from NamedArea as childArea left join childArea.partOf as parentArea where parentArea = :area");\r
+ expandNamedAreas(namedAreas, areasExpanded, areaQuery);\r
+ \r
+ if(clazz.equals(Taxon.class)){\r
+ hql = "select " + selectWhat + " from Distribution e join e.inDescription d join d.taxon t join t.name n "+\r
+ " where e.area in (:namedAreas) AND n.nameCache " + matchOperator + " :queryString"; \r
} else {\r
- criteria.add(Restrictions.ilike("name.nameCache", hqlQueryString));\r
+ //FIXME implement\r
+ logger.warn("find synonyms by area not jet implemented");\r
+ hql = "select " + selectWhat + " from Distribution e join e.inDescription d join d.taxon t join t.name n "+\r
+ " where e.area in (:namedAreas) AND n.nameCache " + matchOperator + " :queryString"; \r
}\r
+ } else {\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" \r
+ + " where t.name.nameCache " + matchOperator + " :queryString";\r
}\r
\r
- if (sec != null && sec.getId() != 0) {\r
- criteria.add(Restrictions.eq("sec", sec ) );\r
+ if(!doCount){\r
+ hql += " order by t.titleCache"; //" order by t.name.nameCache";\r
}\r
\r
- criteria.addOrder(Order.asc("name.nameCache"));\r
- \r
- if(pageSize != null) {\r
- criteria.setMaxResults(pageSize);\r
+ Query query = getSession().createQuery(hql);\r
+ \r
+ query.setParameter("queryString", hqlQueryString);\r
+ if(areasExpanded.size() > 0){\r
+ query.setParameterList("namedAreas", areasExpanded);\r
+ }\r
+ \r
+ if(pageSize != null && !doCount) {\r
+ query.setMaxResults(pageSize);\r
if(pageNumber != null) {\r
- criteria.setFirstResult(pageNumber * pageSize);\r
+ query.setFirstResult(pageNumber * pageSize);\r
}\r
}\r
-\r
- List<TaxonBase> results = criteria.list();\r
- return results;\r
- \r
+ return query;\r
}\r
\r
- public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode) {\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.util.Set)\r
+ */\r
+ public long countTaxaByName(Class<? extends TaxonBase> clazz, String queryString, MatchMode matchMode,\r
+ ReferenceBase sec, Set<NamedArea> namedAreas) {\r
+ \r
+ boolean doCount = true;\r
+ Query query = prepareTaxaByName(clazz, queryString, matchMode, namedAreas, null, null, doCount);\r
+ Object result = query.uniqueResult();\r
+ return (Long) result;\r
\r
- return countTaxaByName(queryString, matchMode, selectMode, null);\r
}\r
\r
- public Integer countTaxaByName(String queryString, \r
- MatchMode matchMode, SelectMode selectMode, ReferenceBase sec) {\r
-\r
- Criteria criteria = null;\r
- Class<?> clazz = selectMode.criteria();\r
- criteria = getSession().createCriteria(clazz);\r
-\r
- criteria.setFetchMode( "name", FetchMode.JOIN );\r
- criteria.createAlias("name", "name");\r
-\r
- if (queryString != null) {\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
+ * @param namedAreas\r
+ * @param areasExpanded\r
+ * @param areaQuery\r
+ */\r
+ private void expandNamedAreas(Collection<NamedArea> namedAreas, Set<NamedArea> areasExpanded, Query areaQuery) {\r
+ List<NamedArea> childAreas;\r
+ for(NamedArea a : namedAreas){\r
+ areasExpanded.add(a);\r
+ areaQuery.setParameter("area", a);\r
+ childAreas = areaQuery.list();\r
+ if(childAreas.size() > 0){\r
+ areasExpanded.addAll(childAreas);\r
+ expandNamedAreas(childAreas, areasExpanded, areaQuery);\r
}\r
}\r
-\r
- if (sec != null && sec.getId() != 0) {\r
- criteria.add(Restrictions.eq("sec", sec ) );\r
- }\r
-\r
- criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
- return (Integer)criteria.uniqueResult();\r
-\r
}\r
\r
- public Integer countTaxaByName(String queryString, MatchMode matchMode, Boolean accepted) {\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
+// /* (non-Javadoc)\r
+// * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode)\r
+// */\r
+// public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode) { \r
+// return countTaxaByName(queryString, matchMode, selectMode, null);\r
+// }\r
\r
- criteria.setFetchMode( "name", FetchMode.JOIN );\r
- criteria.createAlias("name", "name");\r
- \r
- if (matchMode == MatchMode.EXACT) {\r
- criteria.add(Restrictions.eq("name.nameCache", matchMode.queryStringFrom(queryString)));\r
- } else {\r
- criteria.add(Restrictions.ilike("name.nameCache", matchMode.queryStringFrom(queryString)));\r
- }\r
- \r
- criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));\r
- return (Integer)criteria.uniqueResult();\r
- }\r
+// /* (non-Javadoc)\r
+// * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#countTaxaByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, eu.etaxonomy.cdm.persistence.query.SelectMode, eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
+// */\r
+// public Integer countTaxaByName(String queryString, \r
+// MatchMode matchMode, SelectMode selectMode, ReferenceBase sec) {\r
+//\r
+// Long count = countTaxaByName(queryString, matchMode, selectMode, sec, null);\r
+// return count.intValue();\r
+//\r
+// }\r
+ \r
+// public Integer countTaxaByName(String queryString, MatchMode matchMode, Boolean accepted) {\r
+// \r
+// SelectMode selectMode = (accepted ? SelectMode.TAXA : SelectMode.SYNONYMS);\r
+// Long count = countTaxaByName(queryString, matchMode, selectMode, null, null);\r
+// return count.intValue();\r
+// }\r
\r
\r
public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page) {\r
return result;\r
}\r
\r
- public int countRelatedTaxa(Taxon taxon, TaxonRelationshipType type) {\r
+ public int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Direction direction) {\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
+ query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon");\r
} else {\r
- query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship.relatedTo = :relatedTo and taxonRelationship.type = :type");\r
+ query = getSession().createQuery("select count(taxonRelationship) from TaxonRelationship taxonRelationship where taxonRelationship."+direction+" = :relatedTaxon and taxonRelationship.type = :type");\r
query.setParameter("type",type);\r
}\r
- \r
- query.setParameter("relatedTo", taxon);\r
+ query.setParameter("relatedTaxon", 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.add(AuditEntity.relatedId(direction.toString()).eq(taxon.getId()));\r
query.addProjection(AuditEntity.id().count("id"));\r
\r
if(type != null) {\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
+// public int countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
+// \r
+// SelectMode selectMode = (accepted ? SelectMode.TAXA : SelectMode.SYNONYMS);\r
+// Long count = countTaxaByName(queryString, MatchMode.ANYWHERE, selectMode , sec, null);\r
+// \r
+// return count.intValue();\r
+// }\r
\r
- public int countTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {\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
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
+ public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {\r
AuditEvent auditEvent = getAuditEventFromContext();\r
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {\r
Criteria criteria = getSession().createCriteria(TaxonRelationship.class);\r
BGBM BDI Projects / cdmlib.git / blobdiff