import eu.etaxonomy.cdm.model.common.LSID;\r
import eu.etaxonomy.cdm.model.common.OriginalSourceBase;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
-import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;\r
+import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;\r
import eu.etaxonomy.cdm.model.location.NamedArea;\r
import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.name.TaxonNameComparator;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.taxon.Classification;\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.TaxonNode;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;\r
import eu.etaxonomy.cdm.model.view.AuditEvent;\r
import eu.etaxonomy.cdm.persistence.dao.QueryParseException;\r
import eu.etaxonomy.cdm.persistence.dao.hibernate.AlternativeSpellingSuggestionParser;\r
\r
\r
/* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference)\r
*/\r
- public List<Taxon> getRootTaxa(ReferenceBase sec) {\r
+ public List<Taxon> getRootTaxa(Reference 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
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, 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
+ public List<Taxon> getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications)");\r
if (onlyWithChildren == null){\r
onlyWithChildren = true;\r
}\r
}\r
\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
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, 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
+ public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {\r
return getRootTaxa(null, sec, cdmFetch, onlyWithChildren, withMisapplications, null);\r
}\r
\r
/*\r
* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)\r
*/\r
- public List<TaxonBase> getTaxaByName(String queryString, ReferenceBase sec) {\r
+ public List<TaxonBase> getTaxaByName(String queryString, Reference sec) {\r
\r
return getTaxaByName(queryString, true, sec);\r
}\r
\r
/*\r
* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, java.lang.Boolean, eu.etaxonomy.cdm.model.reference.ReferenceBase)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.String, java.lang.Boolean, eu.etaxonomy.cdm.model.reference.Reference)\r
*/\r
- public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, ReferenceBase sec) {\r
- checkNotInPriorView("TaxonDaoHibernateImpl.getTaxaByName(String name, ReferenceBase sec)");\r
+ public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, Reference sec) {\r
+ checkNotInPriorView("TaxonDaoHibernateImpl.getTaxaByName(String name, Reference sec)");\r
\r
Criteria criteria = null;\r
if (accepted == true) {\r
\r
/*\r
* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.TaxonomicTree, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)\r
*/\r
- public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, TaxonomicTree taxonomicTree,\r
+ public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, Classification classification,\r
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, \r
Integer pageNumber, List<String> propertyPaths) {\r
\r
boolean doCount = false;\r
- Query query = prepareTaxaByName(clazz, queryString, taxonomicTree, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
+ \r
+ Query query = prepareTaxaByName(clazz, "nameCache", queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
+ \r
if (query != null){\r
List<TaxonBase> results = query.list();\r
- //results.addAll (prepareTaxaByCommonName(queryString, taxonomicTree, matchMode, namedAreas, pageSize, pageNumber, doCount).list());\r
+ \r
defaultBeanInitializer.initializeAll(results, propertyPaths);\r
//TaxonComparatorSearch comp = new TaxonComparatorSearch();\r
//Collections.sort(results, comp);\r
return results;\r
}\r
+ \r
return new ArrayList<TaxonBase>();\r
\r
}\r
\r
/*\r
* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByCommonName(java.lang.String, eu.etaxonomy.cdm.model.taxon.TaxonomicTree, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByName(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)\r
*/\r
- public List<TaxonBase> getTaxaByCommonName(String queryString, TaxonomicTree taxonomicTree,\r
+ //new search for the editor, for performance issues the return values are only uuid and titleCache, to avoid the initialisation of all objects\r
+ @SuppressWarnings("unchecked")\r
+ public List<UuidAndTitleCache<TaxonBase>> getTaxaByNameForEditor(Class<? extends TaxonBase> clazz, String queryString, Classification classification,\r
+ MatchMode matchMode, Set<NamedArea> namedAreas) {\r
+ long zstVorher;\r
+ long zstNachher;\r
+ \r
+ boolean doCount = false;\r
+ Query query = prepareTaxaByNameForEditor(clazz, "nameCache", queryString, classification, matchMode, namedAreas, doCount);\r
+ \r
+ \r
+ if (query != null){\r
+ List<Object[]> results = query.list();\r
+ \r
+ List<UuidAndTitleCache<TaxonBase>> resultObjects = new ArrayList<UuidAndTitleCache<TaxonBase>>();\r
+ Object[] result;\r
+ for(int i = 0; i<results.size();i++){\r
+ result = results.get(i);\r
+ \r
+ //unterscheiden von taxa und synonymen\r
+ if (clazz.equals(Taxon.class)){\r
+ resultObjects.add( new UuidAndTitleCache(Taxon.class, (UUID) result[0], (String)result[1]));\r
+ }else if (clazz.equals(Synonym.class)){\r
+ resultObjects.add( new UuidAndTitleCache(Synonym.class, (UUID) result[0], (String)result[1]));\r
+ } else{\r
+ if (result[2].equals("synonym")) {\r
+ resultObjects.add( new UuidAndTitleCache(Synonym.class, (UUID) result[0], (String)result[1]));\r
+ }\r
+ else {\r
+ resultObjects.add( new UuidAndTitleCache(Taxon.class, (UUID) result[0], (String)result[1]));\r
+ }\r
+ }\r
+ }\r
+ \r
+ return resultObjects;\r
+ \r
+ }\r
+ return new ArrayList<UuidAndTitleCache<TaxonBase>>();\r
+ \r
+ }\r
+ \r
+ /*\r
+ * (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getTaxaByCommonName(java.lang.String, eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)\r
+ */\r
+ public List<TaxonBase> getTaxaByCommonName(String queryString, Classification classification,\r
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, \r
Integer pageNumber, List<String> propertyPaths) {\r
boolean doCount = false; \r
- Query query = prepareTaxaByCommonName(queryString, taxonomicTree, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
+ Query query = prepareTaxaByCommonName(queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
if (query != null){\r
List<TaxonBase> results = query.list();\r
defaultBeanInitializer.initializeAll(results, propertyPaths);\r
\r
}\r
\r
-\r
/**\r
* @param clazz\r
+ * @param searchField the field in TaxonNameBase to be searched through usually either <code>nameCache</code> or <code>titleCache</code>\r
* @param queryString\r
- * @param taxonomicTree TODO\r
+ * @param classification TODO\r
* @param matchMode\r
* @param namedAreas\r
* @param pageSize\r
* @param doCount\r
* @return\r
* \r
- * FIXME implement taxontree restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}\r
+ *\r
*/\r
- private Query prepareTaxaByName(Class<? extends TaxonBase> clazz, String queryString, TaxonomicTree taxonomicTree,\r
- MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount) {\r
-\r
- //TODO ? checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(String queryString, Boolean accepted, ReferenceBase sec)");\r
-\r
+ private Query prepareTaxaByNameForEditor(Class<? extends TaxonBase> clazz, String searchField, String queryString, Classification classification,\r
+ MatchMode matchMode, Set<NamedArea> namedAreas, boolean doCount) {\r
+ return prepareQuery(clazz, searchField, queryString, classification,\r
+ matchMode, namedAreas, doCount, true);\r
+ }\r
+ \r
+ /**\r
+ * @param clazz\r
+ * @param searchField\r
+ * @param queryString\r
+ * @param classification\r
+ * @param matchMode\r
+ * @param namedAreas\r
+ * @param doCount\r
+ * @param doNotReturnFullEntities\r
+ * if set true the seach method will not return synonym and taxon\r
+ * entities but an array containing the uuid, titleCache, and the\r
+ * DTYPE in lowercase letters.\r
+ * @return\r
+ */\r
+ private Query prepareQuery(Class<? extends TaxonBase> clazz, String searchField, String queryString, Classification classification,\r
+ MatchMode matchMode, Set<NamedArea> namedAreas, boolean doCount, boolean doNotReturnFullEntities){\r
+ \r
String hqlQueryString = matchMode.queryStringFrom(queryString);\r
+ String selectWhat;\r
+ if (doNotReturnFullEntities){\r
+ selectWhat = "t.uuid, t.titleCache ";\r
+ }else {\r
+ selectWhat = (doCount ? "count(t)": "t");\r
+ }\r
+ \r
+ String hql = "";\r
+ Set<NamedArea> areasExpanded = new HashSet<NamedArea>();\r
+ if(namedAreas != null && namedAreas.size() > 0){\r
+ // expand areas and restrict by distribution area\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
+ boolean doAreaRestriction = areasExpanded.size() > 0;\r
+ \r
+ Set<UUID> namedAreasUuids = new HashSet<UUID>();\r
+ for (NamedArea area:areasExpanded){\r
+ namedAreasUuids.add(area.getUuid());\r
+ }\r
\r
- String matchOperator;\r
- if (matchMode == MatchMode.EXACT) {\r
- matchOperator = "=";\r
+ String taxonSubselect = null;\r
+ String synonymSubselect = null;\r
+ \r
+ if(classification != null){\r
+ \r
+ if(doAreaRestriction){\r
+ \r
+ taxonSubselect = "select t.id from" +\r
+ " Distribution e" +\r
+ " join e.inDescription d" +\r
+ " join d.taxon t" +\r
+ " join t.name n " +\r
+ " join t.taxonNodes as tn "+\r
+ " where" +\r
+ " e.area.uuid in (:namedAreasUuids) AND" +\r
+ " tn.classification = :classification" +\r
+ " AND n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ \r
+ \r
+ synonymSubselect = "select s.id from" +\r
+ " Distribution e" +\r
+ " join e.inDescription d" +\r
+ " join d.taxon t" + // the taxa\r
+ " join t.taxonNodes as tn "+\r
+ " join t.synonymRelations sr" +\r
+ " join sr.relatedFrom s" + // the synonyms\r
+ " join s.name sn"+ \r
+ " where" +\r
+ " e.area.uuid in (:namedAreasUuids) AND" +\r
+ " tn.classification = :classification" +\r
+ " AND sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ \r
+ } else {\r
+ \r
+ taxonSubselect = "select t.id from" +\r
+ " Taxon t" +\r
+ " join t.name n " +\r
+ " join t.taxonNodes as tn "+\r
+ " where" +\r
+ " tn.classification = :classification" +\r
+ " AND n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ \r
+ synonymSubselect = "select s.id from" +\r
+ " Taxon t" + // the taxa\r
+ " join t.taxonNodes as tn "+\r
+ " join t.synonymRelations sr" +\r
+ " join sr.relatedFrom s" + // the synonyms\r
+ " join s.name sn"+ \r
+ " where" +\r
+ " tn.classification = :classification" +\r
+ " AND sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ } \r
} else {\r
- matchOperator = "like";\r
+ \r
+ if(doAreaRestriction){\r
+ \r
+ taxonSubselect = "select t.id from " +\r
+ " Distribution e" +\r
+ " join e.inDescription d" +\r
+ " join d.taxon t" +\r
+ " join t.name n "+\r
+ " where" +\r
+ (doAreaRestriction ? " e.area.uuid in (:namedAreasUuids) AND" : "") +\r
+ " n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ \r
+ synonymSubselect = "select s.id from" +\r
+ " Distribution e" +\r
+ " join e.inDescription d" +\r
+ " join d.taxon t" + // the taxa\r
+ " join t.synonymRelations sr" +\r
+ " join sr.relatedFrom s" + // the synonyms\r
+ " join s.name sn"+ \r
+ " where" +\r
+ (doAreaRestriction ? " e.area.uuid in (:namedAreasUuids) AND" : "") +\r
+ " sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ \r
+ } else {\r
+ \r
+ taxonSubselect = "select t.id from " +\r
+ " Taxon t" +\r
+ " join t.name n "+\r
+ " where" +\r
+ " n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+\r
+ synonymSubselect = "select s.id from" +\r
+ " Taxon t" + // the taxa\r
+ " join t.synonymRelations sr" +\r
+ " join sr.relatedFrom s" + // the synonyms\r
+ " join s.name sn"+ \r
+ " where" +\r
+ " sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
+ }\r
+ \r
}\r
\r
+ Query subTaxon = null;\r
+ Query subSynonym = null;\r
+ if(clazz.equals(Taxon.class)){\r
+ // find Taxa\r
+ subTaxon = getSession().createQuery(taxonSubselect).setParameter("queryString", hqlQueryString);\r
+ //subTaxon = getSession().createQuery(taxonSubselect);\r
+ \r
+ if(doAreaRestriction){\r
+ subTaxon.setParameterList("namedAreasUuids", namedAreasUuids);\r
+ } \r
+ if(classification != null){\r
+ subTaxon.setParameter("classification", classification);\r
+ }\r
+ } else if(clazz.equals(Synonym.class)){\r
+ // find synonyms\r
+ subSynonym = getSession().createQuery(synonymSubselect).setParameter("queryString", hqlQueryString);\r
+ \r
+ if(doAreaRestriction){\r
+ subSynonym.setParameterList("namedAreasUuids", namedAreasUuids);\r
+ } \r
+ if(classification != null){\r
+ subSynonym.setParameter("classification", classification);\r
+ }\r
+ } else {\r
+ // find taxa and synonyms\r
+ subSynonym = getSession().createQuery(synonymSubselect).setParameter("queryString", hqlQueryString);\r
+ subTaxon = getSession().createQuery(taxonSubselect).setParameter("queryString", hqlQueryString);\r
+ if(doAreaRestriction){\r
+ subTaxon.setParameterList("namedAreasUuids", namedAreasUuids);\r
+ subSynonym.setParameterList("namedAreasUuids", namedAreasUuids);\r
+ }\r
+ if(classification != null){\r
+ subTaxon.setParameter("classification", classification);\r
+ subSynonym.setParameter("classification", classification);\r
+ }\r
+ }\r
+ \r
+ List<Integer> taxa = new ArrayList<Integer>();\r
+ List<Integer> synonyms = new ArrayList<Integer>();\r
+ if(clazz.equals(Taxon.class)){\r
+ taxa = subTaxon.list();\r
+ \r
+ }else if (clazz.equals(Synonym.class)){\r
+ synonyms = subSynonym.list();\r
+ }else {\r
+ taxa = subTaxon.list();\r
+ synonyms = subSynonym.list();\r
+ }\r
+ if(clazz.equals(Taxon.class)){\r
+ if (taxa.size()>0){\r
+ if (doNotReturnFullEntities){\r
+ hql = "select " + selectWhat + ", 'taxon' from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa)";\r
+ }else{\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa)";\r
+ }\r
+ }else{\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t";\r
+ }\r
+ } else if(clazz.equals(Synonym.class) ){\r
+ if (synonyms.size()>0){\r
+ if (doNotReturnFullEntities){\r
+ hql = "select " + selectWhat + ", 'synonym' from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)";\r
+ }else{\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)"; \r
+ }\r
+ }else{\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t";\r
+ }\r
+ } else {\r
+ \r
+ if(synonyms.size()>0 && taxa.size()>0){\r
+ if (doNotReturnFullEntities && !doCount ){\r
+ // in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:\r
+ hql = "select " + selectWhat + ", case when t.id in (:taxa) then 'taxon' else 'synonym' end" + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) OR t.id in (:synonyms)";\r
+ }else{\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) OR t.id in (:synonyms)";\r
+ }\r
+ }else if (synonyms.size()>0 ){\r
+ if (doNotReturnFullEntities && !doCount ){\r
+ // in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:\r
+ hql = "select " + selectWhat + ", 'synonym' from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)"; \r
+ } else {\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:synonyms)"; \r
+ }\r
+ } else if (taxa.size()>0 ){\r
+ if (doNotReturnFullEntities && !doCount ){\r
+ // in doNotReturnFullEntities mode it is nesscary to also return the type of the matching entities:\r
+ hql = "select " + selectWhat + ", 'taxon' from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) ";\r
+ } else {\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t" + " where t.id in (:taxa) ";\r
+ }\r
+ } else{\r
+ hql = "select " + selectWhat + " from " + clazz.getSimpleName() + " t";\r
+ }\r
+ }\r
+ \r
+ if (hql == "") return null;\r
+ if(!doCount){\r
+ hql += " order by t.name.genusOrUninomial, case when t.name.specificEpithet like '\"%\"' then 1 else 0 end, t.name.specificEpithet, t.name.rank desc, t.name.nameCache";\r
+ }\r
+ \r
+ Query query = getSession().createQuery(hql);\r
+ \r
+ if(clazz.equals(Taxon.class) && taxa.size()>0){\r
+ //find taxa\r
+ query.setParameterList("taxa", taxa );\r
+ } else if(clazz.equals(Synonym.class) && synonyms.size()>0){\r
+ // find synonyms\r
+ query.setParameterList("synonyms", synonyms);\r
+ \r
+ \r
+ } else {\r
+ // find taxa and synonyms\r
+ if (taxa.size()>0){\r
+ query.setParameterList("taxa", taxa);\r
+ }\r
+ if (synonyms.size()>0){\r
+ query.setParameterList("synonyms",synonyms);\r
+ }\r
+ if (taxa.size()== 0 && synonyms.size() == 0){\r
+ return null;\r
+ }\r
+ }\r
+ return query;\r
+ \r
+ }\r
+ \r
+ \r
+ /**\r
+ * @param clazz\r
+ * @param searchField the field in TaxonNameBase to be searched through usually either <code>nameCache</code> or <code>titleCache</code>\r
+ * @param queryString\r
+ * @param classification TODO\r
+ * @param matchMode\r
+ * @param namedAreas\r
+ * @param pageSize\r
+ * @param pageNumber\r
+ * @param doCount\r
+ * @return\r
+ * \r
+ * FIXME implement classification restriction & implement test: see {@link TaxonDaoHibernateImplTest#testCountTaxaByName()}\r
+ */\r
+ private Query prepareTaxaByName(Class<? extends TaxonBase> clazz, String searchField, String queryString, Classification classification,\r
+ MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount) {\r
+\r
+ //TODO ? checkNotInPriorView("TaxonDaoHibernateImpl.countTaxaByName(String queryString, Boolean accepted, Reference sec)");\r
+\r
+ /*String hqlQueryString = matchMode.queryStringFrom(queryString);\r
+ \r
String selectWhat = (doCount ? "count(t)": "t");\r
\r
String hql = "";\r
String taxonSubselect = null;\r
String synonymSubselect = null;\r
\r
- if(taxonomicTree != null){\r
+ if(classification != null){\r
\r
if(doAreaRestriction){\r
\r
" join t.taxonNodes as tn "+\r
" where" +\r
" e.area.uuid in (:namedAreasUuids) AND" +\r
- " tn.taxonomicTree = :taxonomicTree" +\r
- " AND n.nameCache " + matchOperator + " :queryString";\r
+ " tn.classification = :classification" +\r
+ " AND n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
\r
\r
synonymSubselect = "select s.id from" +\r
" join s.name sn"+ \r
" where" +\r
" e.area.uuid in (:namedAreasUuids) AND" +\r
- " tn.taxonomicTree = :taxonomicTree" +\r
- " AND sn.nameCache " + matchOperator + " :queryString";\r
+ " tn.classification = :classification" +\r
+ " AND sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
\r
} else {\r
\r
" join t.name n " +\r
" join t.taxonNodes as tn "+\r
" where" +\r
- " tn.taxonomicTree = :taxonomicTree" +\r
- " AND n.nameCache " + matchOperator + " :queryString";\r
+ " tn.classification = :classification" +\r
+ " AND n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
\r
synonymSubselect = "select s.id from" +\r
" Taxon t" + // the taxa\r
" join sr.relatedFrom s" + // the synonyms\r
" join s.name sn"+ \r
" where" +\r
- " tn.taxonomicTree = :taxonomicTree" +\r
- " AND sn.nameCache " + matchOperator + " :queryString";\r
+ " tn.classification = :classification" +\r
+ " AND sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
} \r
} else {\r
\r
" join t.name n "+\r
" where" +\r
(doAreaRestriction ? " e.area.uuid in (:namedAreasUuids) AND" : "") +\r
- " n.nameCache " + matchOperator + " :queryString";\r
+ " n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
\r
synonymSubselect = "select s.id from" +\r
" Distribution e" +\r
" join s.name sn"+ \r
" where" +\r
(doAreaRestriction ? " e.area.uuid in (:namedAreasUuids) AND" : "") +\r
- " sn.nameCache " + matchOperator + " :queryString";\r
+ " sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
\r
} else {\r
\r
" Taxon t" +\r
" join t.name n "+\r
" where" +\r
- " n.nameCache " + matchOperator + " :queryString";\r
+ " n." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
\r
synonymSubselect = "select s.id from" +\r
" Taxon t" + // the taxa\r
" join sr.relatedFrom s" + // the synonyms\r
" join s.name sn"+ \r
" where" +\r
- " sn.nameCache " + matchOperator + " :queryString";\r
+ " sn." + searchField + " " + matchMode.getMatchOperator() + " :queryString";\r
}\r
\r
\r
\r
\r
\r
- // TODO mysql needs optimization: see http://www.xaprb.com/blog/2006/04/30/how-to-optimize-subqueries-and-joins-in-mysql/#commen\r
+ \r
Query subTaxon = null;\r
Query subSynonym = null;\r
if(clazz.equals(Taxon.class)){\r
if(doAreaRestriction){\r
subTaxon.setParameterList("namedAreasUuids", namedAreasUuids);\r
} \r
- if(taxonomicTree != null){\r
- subTaxon.setParameter("taxonomicTree", taxonomicTree);\r
+ if(classification != null){\r
+ subTaxon.setParameter("classification", classification);\r
}\r
} else if(clazz.equals(Synonym.class)){\r
// find synonyms\r
if(doAreaRestriction){\r
subSynonym.setParameterList("namedAreasUuids", namedAreasUuids);\r
} \r
- if(taxonomicTree != null){\r
- subSynonym.setParameter("taxonomicTree", taxonomicTree);\r
+ if(classification != null){\r
+ subSynonym.setParameter("classification", classification);\r
}\r
} else {\r
// find taxa and synonyms\r
subTaxon.setParameterList("namedAreasUuids", namedAreasUuids);\r
subSynonym.setParameterList("namedAreasUuids", namedAreasUuids);\r
}\r
- if(taxonomicTree != null){\r
- subTaxon.setParameter("taxonomicTree", taxonomicTree);\r
- subSynonym.setParameter("taxonomicTree", taxonomicTree);\r
+ if(classification != null){\r
+ subTaxon.setParameter("classification", classification);\r
+ subSynonym.setParameter("classification", classification);\r
}\r
}\r
\r
if (taxa.size()== 0 && synonyms.size() == 0){\r
return null;\r
}\r
- }\r
- \r
+ }*/\r
+ Query query = prepareQuery(clazz, searchField, queryString, classification,\r
+ matchMode, namedAreas, doCount, false);\r
\r
if(pageSize != null && !doCount) {\r
query.setMaxResults(pageSize);\r
return query;\r
}\r
\r
- private Query prepareTaxaByCommonName(String queryString, TaxonomicTree taxonomicTree,\r
+ private Query prepareTaxaByCommonName(String queryString, Classification classification,\r
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, boolean doCount){\r
- \r
- String matchOperator;\r
- if (matchMode == MatchMode.EXACT) {\r
- matchOperator = "=";\r
- } else {\r
- matchOperator = "like";\r
- }\r
- \r
+ \r
String hql= "from Taxon t " +\r
"join t.descriptions d "+\r
"join d.descriptionElements e " +\r
"join e.feature f " +\r
- "where f.supportsCommonTaxonName = true and e.name "+matchOperator+" :queryString";//and ls.text like 'common%'";\r
+ "where f.supportsCommonTaxonName = true and e.name "+matchMode.getMatchOperator()+" :queryString";//and ls.text like 'common%'";\r
\r
Query query = getSession().createQuery(hql);\r
\r
}\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, java.util.Set)\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.Reference, java.util.Set)\r
*/\r
- public long countTaxaByName(Class<? extends TaxonBase> clazz, String queryString, TaxonomicTree taxonomicTree,\r
+ public long countTaxaByName(Class<? extends TaxonBase> clazz, String queryString, Classification classification,\r
MatchMode matchMode, Set<NamedArea> namedAreas) {\r
\r
boolean doCount = true;\r
- Query query = prepareTaxaByName(clazz, queryString, taxonomicTree, matchMode, namedAreas, null, null, doCount);\r
+ Query query = prepareTaxaByName(clazz, "nameCache", queryString, classification, matchMode, namedAreas, null, null, doCount);\r
if (query != null) {\r
return (Long)query.uniqueResult();\r
+ }else{\r
+ return 0;\r
}\r
- return 0;\r
- \r
}\r
\r
/**\r
// }\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
+// * @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.Reference)\r
// */\r
// public Integer countTaxaByName(String queryString, \r
-// MatchMode matchMode, SelectMode selectMode, ReferenceBase sec) {\r
+// MatchMode matchMode, SelectMode selectMode, Reference sec) {\r
//\r
// Long count = countTaxaByName(queryString, matchMode, selectMode, sec, null);\r
// return count.intValue();\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
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#findByName(java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, int, int, boolean)\r
+ */\r
+ public List<TaxonBase> findByNameTitleCache(Class<? extends TaxonBase>clazz, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths) {\r
+ \r
+ boolean doCount = false;\r
+ Query query = prepareTaxaByName(clazz, "titleCache", queryString, classification, matchMode, namedAreas, pageSize, pageNumber, doCount);\r
+ if (query != null){\r
+ List<TaxonBase> results = query.list();\r
+ defaultBeanInitializer.initializeAll(results, propertyPaths);\r
+ return results;\r
+ }\r
+ return new ArrayList<TaxonBase>();\r
\r
}\r
\r
\r
/*\r
* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheOfAcceptedTaxa(eu.etaxonomy.cdm.model.taxon.TaxonomicTree)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheOfAcceptedTaxa(eu.etaxonomy.cdm.model.taxon.Classification)\r
*/\r
- public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByTaxonomicTree(TaxonomicTree taxonomicTree) {\r
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification) {\r
\r
- int taxonomicTreeId = taxonomicTree.getId();\r
+ int classificationId = classification.getId();\r
\r
- String queryString = "SELECT nodes.uuid, taxa.titleCache FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.taxonomictree_id = " + taxonomicTreeId;\r
+ String queryString = "SELECT nodes.uuid, taxa.titleCache FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.classification_id = " + classificationId;\r
\r
List<Object[]> result = getSession().createSQLQuery(queryString).list();\r
\r
}\r
\r
public List<TaxonBase> getTaxaByCommonName(String queryString,\r
- TaxonomicTree taxonomicTree, MatchMode matchMode,\r
+ Classification classification, MatchMode matchMode,\r
Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber) {\r
// TODO Auto-generated method stub\r
return null;\r
}\r
\r
\r
- public List<Synonym> createAllInferredSynonyms(Taxon taxon, TaxonomicTree tree){\r
+ public List<Synonym> createAllInferredSynonyms(Taxon taxon, Classification tree){\r
List <Synonym> inferredSynonyms = new ArrayList<Synonym>();\r
\r
inferredSynonyms.addAll(createInferredSynonyms(taxon, tree, SynonymRelationshipType.INFERRED_EPITHET_OF()));\r
return taxonName;\r
}\r
\r
- public List<Synonym> createInferredSynonyms(Taxon taxon, TaxonomicTree tree, SynonymRelationshipType type){\r
+ public List<Synonym> createInferredSynonyms(Taxon taxon, Classification tree, SynonymRelationshipType type){\r
List <Synonym> inferredSynonyms = new ArrayList<Synonym>();\r
List<Synonym> inferredSynonymsToBeRemoved = new ArrayList<Synonym>();\r
\r
List<String> taxonNames = new ArrayList<String>();\r
\r
for (TaxonNode node: nodes){\r
- HashMap<String, String> synonymsGenus = new HashMap<String, String>();\r
+ HashMap<String, String> synonymsGenus = new HashMap<String, String>(); // Changed this to be able to store the idInSource to a genusName\r
List<String> synonymsEpithet = new ArrayList<String>();\r
\r
- if (node.getTaxonomicTree().equals(tree)){\r
+ if (node.getClassification().equals(tree)){\r
if (!node.isTopmostNode()){\r
TaxonNode parent = (TaxonNode)node.getParent();\r
parent = (TaxonNode)HibernateProxyHelper.deproxy(parent);\r
// Determine the idInSource\r
String idInSource = getIdInSource(syn);\r
\r
+ // Determine the sourceReference\r
+ Reference sourceReference = syn.getSec();\r
+ \r
synName = syn.getName();\r
ZoologicalName zooName = getZoologicalName(synName.getUuid(), zooHashMap);\r
String synGenusName = zooName.getGenusOrUninomial();\r
- if (!synonymsGenus.containsKey(synGenusName)){\r
+ if (synGenusName != null && !synonymsGenus.containsKey(synGenusName)){\r
synonymsGenus.put(synGenusName, idInSource);\r
}\r
inferredSynName = ZoologicalName.NewInstance(Rank.SPECIES());\r
+ \r
+ // DEBUG\r
+ if (epithetOfTaxon == null) {\r
+ logger.error("This specificEpithet is NULL");\r
+ }\r
+ \r
inferredSynName.setSpecificEpithet(epithetOfTaxon);\r
inferredSynName.setGenusOrUninomial(synGenusName);\r
inferredEpithet = Synonym.NewInstance(inferredSynName, null);\r
+ \r
+ // Set the sourceReference\r
+ inferredEpithet.setSec(sourceReference);\r
\r
// Add the original source\r
if (idInSource != null) {\r
IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSource, "InferredEpithetOf", syn.getSec(), null);\r
\r
// Add the citation\r
- ReferenceBase citation = getCitation(syn);\r
+ Reference citation = getCitation(syn);\r
if (citation != null) {\r
originalSource.setCitation(citation);\r
inferredEpithet.addSource(originalSource);\r
taxon.addSynonym(inferredEpithet, SynonymRelationshipType.INFERRED_GENUS_OF());\r
inferredSynonyms.add(inferredEpithet);\r
inferredSynName.generateTitle();\r
- zooHashMap.put(inferredSynName.getUuid(), inferredSynName); // I guess this needs to be added here?\r
+ zooHashMap.put(inferredSynName.getUuid(), inferredSynName);\r
taxonNames.add(inferredSynName.getNameCache());\r
}\r
\r
\r
// Determine the idInSource\r
String idInSource = getIdInSource(syn);\r
+ \r
+ // Determine the sourceReference\r
+ Reference sourceReference = syn.getSec();\r
\r
synName = syn.getName();\r
ZoologicalName zooName = getZoologicalName(synName.getUuid(), zooHashMap);\r
String speciesEpithetName = zooName.getSpecificEpithet();\r
- if (!synonymsEpithet.contains(speciesEpithetName)){\r
+ if (synonymsEpithet != null && !synonymsEpithet.contains(speciesEpithetName)){\r
synonymsEpithet.add(speciesEpithetName);\r
}\r
inferredSynName = ZoologicalName.NewInstance(Rank.SPECIES());\r
inferredSynName.setGenusOrUninomial(genusOfTaxon);\r
inferredGenus = Synonym.NewInstance(inferredSynName, null);\r
\r
+ // Set the sourceReference\r
+ inferredGenus.setSec(sourceReference);\r
+ \r
// Add the original source\r
if (idInSource != null) {\r
IdentifiableSource originalSource = IdentifiableSource.NewInstance(idInSource, "InferredGenusOf", syn.getSec(), null);\r
\r
// Add the citation\r
- ReferenceBase citation = getCitation(syn);\r
+ Reference citation = getCitation(syn);\r
if (citation != null) {\r
originalSource.setCitation(citation);\r
inferredGenus.addSource(originalSource);\r
taxon.addSynonym(inferredGenus, SynonymRelationshipType.INFERRED_EPITHET_OF());\r
inferredSynonyms.add(inferredGenus);\r
inferredSynName.generateTitle();\r
- zooHashMap.put(inferredSynName.getUuid(), inferredSynName); // I guess this needs to be added here?\r
+ zooHashMap.put(inferredSynName.getUuid(), inferredSynName);\r
taxonNames.add(inferredSynName.getNameCache());\r
}\r
\r
\r
}else if (type.equals(SynonymRelationshipType.POTENTIAL_COMBINATION_OF())){\r
\r
- ReferenceBase sourceReference = null; // TODO: Determination of sourceReference is redundant\r
+ Reference sourceReference = null; // TODO: Determination of sourceReference is redundant\r
\r
for (SynonymRelationship synonymRelationOfGenus:synonymRelationshipsOfGenus){\r
TaxonNameBase synName;\r
\r
ZoologicalName zooName = getZoologicalName(synName.getUuid(), zooHashMap);\r
String synGenusName = zooName.getGenusOrUninomial();\r
- if (!synonymsGenus.containsKey(synGenusName)){\r
+ if (synGenusName != null && !synonymsGenus.containsKey(synGenusName)){\r
synonymsGenus.put(synGenusName, idInSource);\r
}\r
}\r
\r
ZoologicalName zooName = getZoologicalName(syn.getName().getUuid(), zooHashMap);\r
String epithetName = zooName.getSpecificEpithet();\r
- if (!synonymsEpithet.contains(epithetName)){\r
+ if (epithetName != null && !synonymsEpithet.contains(epithetName)){\r
synonymsEpithet.add(epithetName);\r
}\r
}\r
inferredSynName.setGenusOrUninomial(genusName);\r
potentialCombination = Synonym.NewInstance(inferredSynName, null);\r
\r
+ // Set the sourceReference\r
+ potentialCombination.setSec(sourceReference);\r
+ \r
// Add the original source\r
String idInSource = synonymsGenus.get(genusName);\r
if (idInSource != null) {\r
}\r
\r
/**\r
- * Returns the idInSource for a given Synonym.\r
+ * Returns the citation for a given Synonym.\r
* @param syn\r
*/\r
- private ReferenceBase getCitation(Synonym syn) {\r
- ReferenceBase citation = null;\r
+ private Reference getCitation(Synonym syn) {\r
+ Reference citation = null;\r
Set<IdentifiableSource> sources = syn.getSources();\r
if (sources.size() == 1) {\r
IdentifiableSource source = sources.iterator().next();\r
//TODO: mal nur mit UUID probieren (ohne fetch all properties), vielleicht geht das schneller?\r
public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPaths){\r
Query query=getSession().createQuery("select tmb2 from ZoologicalName tmb, ZoologicalName tmb2 fetch all properties where tmb.id != tmb2.id and tmb.nameCache = tmb2.nameCache");\r
- System.err.println("query: " + query.getQueryString());\r
List<UUID> zooNames = query.list();\r
- System.err.println("number of identical names"+zooNames.size());\r
- \r
- \r
+ \r
return zooNames;\r
\r
}\r
\r
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPaths) {\r
\r
- //hole alle TaxonNames, die es mindestens zweimal gibt.\r
- \r
- \r
- \r
Query query=getSession().createQuery("select tmb2 from ZoologicalName tmb, ZoologicalName tmb2 fetch all properties where tmb.id != tmb2.id and tmb.nameCache = tmb2.nameCache");\r
- System.err.println("query: " + query.getQueryString());\r
+ \r
List<TaxonNameBase> zooNames = query.list();\r
- System.err.println("number of identical names"+zooNames.size());\r
\r
TaxonNameComparator taxComp = new TaxonNameComparator();\r
Collections.sort(zooNames, taxComp);\r
- System.err.println("list is sorted");\r
+ \r
for (TaxonNameBase taxonNameBase: zooNames){\r
defaultBeanInitializer.initialize(taxonNameBase, propertyPaths);\r
}\r
public List<TaxonNameBase> findIdenticalNamesNew(List<String> propertyPaths){\r
\r
//Hole die beiden Source_ids von "Fauna Europaea" und "Erms" und in sources der names darf jeweils nur das entgegengesetzte auftreten (i member of tmb.taxonBases)\r
- Query query = getSession().createQuery("Select id from ReferenceBase where titleCache like 'Fauna Europaea database'");\r
+ Query query = getSession().createQuery("Select id from Reference where titleCache like 'Fauna Europaea database'");\r
List<String> secRefFauna = query.list();\r
- query = getSession().createQuery("Select id from ReferenceBase where titleCache like 'ERMS'");\r
+ query = getSession().createQuery("Select id from Reference where titleCache like 'ERMS'");\r
List<String> secRefErms = query.list();\r
//Query query = getSession().createQuery("select tmb2.nameCache from ZoologicalName tmb, TaxonBase tb1, ZoologicalName tmb2, TaxonBase tb2 where tmb.id != tmb2.id and tb1.name = tmb and tb2.name = tmb2 and tmb.nameCache = tmb2.nameCache and tb1.sec != tb2.sec");\r
//Get all names of fauna europaea\r
identicalNames.add(nameFauna);\r
}\r
}\r
- System.err.println("number of identical names: " + identicalNames.size());\r
+ \r
\r
query = getSession().createQuery("from ZoologicalName zn where zn.nameCache IN (:identicalNames)");\r
query.setParameterList("identicalNames", identicalNames);\r
TaxonNameBase temp = result.get(0);\r
\r
Iterator<OriginalSourceBase> sources = temp.getSources().iterator();\r
- System.err.println(temp.getSources().size());\r
- if (sources.hasNext()){\r
- System.err.println("funktioniert..."+ sources.next().getIdInSource());\r
- //sources.next().getIdInSource();\r
- }\r
+ \r
TaxonNameComparator taxComp = new TaxonNameComparator();\r
Collections.sort(result, taxComp);\r
defaultBeanInitializer.initializeAll(result, propertyPaths);\r
\r
\r
public long countTaxaByCommonName(String searchString,\r
- TaxonomicTree taxonomicTree, MatchMode matchMode,\r
+ Classification classification, MatchMode matchMode,\r
Set<NamedArea> namedAreas) {\r
boolean doCount = true;\r
- Query query = prepareTaxaByCommonName(searchString, taxonomicTree, matchMode, namedAreas, null, null, doCount);\r
+ Query query = prepareTaxaByCommonName(searchString, classification, matchMode, namedAreas, null, null, doCount);\r
if (query != null && !query.list().isEmpty()) {\r
Object o = query.uniqueResult();\r
if(o != null) {\r
}\r
\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getUuidAndTitleCacheTaxon()\r
+ */\r
+ @Override\r
+ public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {\r
+ String queryString = String.format("select uuid, titleCache from %s where DTYPE = '%s'", type.getSimpleName(), Taxon.class.getSimpleName());\r
+ Query query = getSession().createQuery(queryString);\r
+ \r
+ List<UuidAndTitleCache<TaxonBase>> result = getUuidAndTitleCache(query);\r
+ \r
+ return result;\r
+ }\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao#getUuidAndTitleCacheSynonym()\r
+ */\r
+ @Override\r
+ public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {\r
+ String queryString = String.format("select uuid, titleCache from %s where DTYPE = '%s'", type.getSimpleName(), Synonym.class.getSimpleName());\r
+ Query query = getSession().createQuery(queryString);\r
+ \r
+ List<UuidAndTitleCache<TaxonBase>> result = getUuidAndTitleCache(query);\r
+ \r
+ return result;\r
+ }\r
+\r
+\r
\r
\r
\r
BGBM BDI Projects / cdmlib.git / blobdiff