/ - Diff - EDIT - EDIT Project Management

     	private static final String[] table_list = {
     //			"Address",
     			"Agent",
     			"AgentBase",
     //			"Agent_Agent",
     //			"Agent_Annotation",
     //			"Agent_DefinedTermBase",
-...
     		Map<String, List<CdmBase>> tables_ = new HashMap<String, List<CdmBase>>(table_list.length);
     		List<String> tableRows = new ArrayList<String>(MAX_ROWS);
     		//List<Agent> agents = appCtr.getAgentService().getAllAgents(MAX_ROWS, 0);
     		try {
-...
     	    		logger.debug("Retrieving table '" + table_list[i] + "'");
     	    		System.out.println("Retrieving table '" + table_list[i] + "'");
     				List<CdmBase> rows = new ArrayList<CdmBase>(MAX_ROWS);
     				List<CdmBase> rows = new ArrayList<>(MAX_ROWS);
     				rows = appCtr.getMainService().rows(table_list[i], MAX_ROWS, 0);
     //				rows = appCtr.getCommonService().count (table_list[i], MAX_ROWS, 0);
         			tables_.put(table_list[i], rows);
-...
         private Map<String, List<String>> retrieveAllTables___(Source source) {
     		Map<String, List<String>> tables = new HashMap<String, List<String>>(table_list.length);
     		List<String> tableRows = new ArrayList<String>(MAX_ROWS);
     		Map<String, List<String>> tables = new HashMap<>(table_list.length);
     		try {
     			//get data from database
     			for (int i = 0; i < table_list.length; i++) {
     				List<String> rows = new ArrayList<String>(MAX_ROWS);
     				List<String> rows = new ArrayList<>(MAX_ROWS);
     //					Session session = factory.getCurrentSession();
-...
     //		Source source = bmiConfig.getSource();
     //		ResultSet rs = berlinModelSource.getResultSet();
     		Map<String, List<String>> tables = new HashMap<String, List<String>>(table_list.length);
     		List<String> tableRows = new ArrayList<String>(MAX_ROWS);
     		Map<String, List<String>> tables = new HashMap<>(table_list.length);
     		try {
     			//get data from database
-...
     				//ResultSet rs = berlinModelSource.getResultSet();
     				//ResultSet rs = source.getResultSet(strQuery) ;
     				ResultSet rs = source.getResultSet(strQuery) ;
     				List<String> rows = new ArrayList<String>(MAX_ROWS);
     				List<String> rows = new ArrayList<>(MAX_ROWS);
     				while (rs.next()) {
     					rows.add(rs.toString());
-...
         private Map<String, List<String>> retrieveAllTables(CdmApplicationController appCtr) {
     		Map<String, List<String>> tables = new HashMap<String, List<String>>(table_list.length);
     		Map<String, List<String>> tables = new HashMap<>(table_list.length);
     		List<String> agentTableContent = new ArrayList<String>(MAX_ROWS);
     		List<String> agentTableContent = new ArrayList<>(MAX_ROWS);
     		List<? extends AgentBase> agents = appCtr.getAgentService().list(null,MAX_ROWS, 0,null,null);
     		for (AgentBase agent: agents ) {
     			//TODO: Want the entire row as string not just toString() of the object.
-...
     		//List<Annotation> annotations = appCtr.getTermService().getAllAnnotations(MAX_ROWS, 0);
     		List<String> definedTermBaseTableContent = new ArrayList<String>(MAX_ROWS);
     		List<String> definedTermBaseTableContent = new ArrayList<>(MAX_ROWS);
     		List<DefinedTermBase> definedTermBases = appCtr.getTermService().list(null,MAX_ROWS, 0,null,null);
     		for (DefinedTermBase definedTermBase: definedTermBases ) {
     			definedTermBaseTableContent.add(definedTermBase.toString());
-...
+    	}
         	private void doCompareDatabases(Map<String, List<CdmBase>> tablesDbOne, Map<String, List<CdmBase>> tablesDbTwo) {
     //        public void doCompareDatabases(Map<String, List<String>> tablesDbOne, Map<String, List<String>> tablesDbTwo) {
     		logger.debug("# Tables in DB 1: " + tablesDbOne.size());
     		logger.debug("# Tables in DB 2: " + tablesDbTwo.size());
-...
     			logger.info("Comparing table '" + tableName + "'");
     //			List<String> dbOneTableRows = new ArrayList<String>();
     //			List<String> dbTwoTableRows = new ArrayList<String>();
     			List<CdmBase> dbOneTableRows = new ArrayList<CdmBase>();
     			List<CdmBase> dbTwoTableRows = new ArrayList<CdmBase>();
     			List<CdmBase> dbOneTableRows = new ArrayList<>();
     			List<CdmBase> dbTwoTableRows = new ArrayList<>();
     			dbOneTableRows = tablesDbOne.get(tableName);
     			dbTwoTableRows = tablesDbTwo.get(tableName);
-...
     			logger.error("Error creating application controller");
     			e.printStackTrace();
     			System.exit(1);
     			return;
+    		}
     		try {
-...
     	    	TransactionStatus txStatTwo = appCtrTwo.startTransaction(true);
     			for (int i = 0; i < table_list.length; i++) {
     				List<CdmBase> rowsDbOne = new ArrayList<CdmBase>(MAX_ROWS);
     				List<CdmBase> rowsDbTwo = new ArrayList<CdmBase>(MAX_ROWS);
     				rowsDbOne = appCtrOne.getMainService().rows(table_list[i], MAX_ROWS, 0);
     				rowsDbTwo = appCtrTwo.getMainService().rows(table_list[i], MAX_ROWS, 0);
     				List<CdmBase> rowsDbOne = new ArrayList<>(MAX_ROWS);
     				List<CdmBase> rowsDbTwo = new ArrayList<>(MAX_ROWS);
     //				rowsDbOne = appCtrOne.getCommonService().count(table_list[i], MAX_ROWS, 0);
     //				rowsDbTwo = appCtrTwo.getCommonService().count(table_list[i], MAX_ROWS, 0);
     				compareTables(table_list[i], rowsDbOne, rowsDbTwo);
+    			}
     	    	appCtrTwo.commitTransaction(txStatTwo);

          */
         public List<Object[]> group(Class<? extends T> clazz,Integer limit, Integer start, List<Grouping> groups, List<String> propertyPaths);
         public List<T> rows(String tableName, int limit, int start) throws DataAccessException;
         /**
          * @param id
          * @return

cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/AnnotatableDaoImpl.java
101	101	}
102	102	}
103	103
104		List<Annotation> results = query.list();
	104	@SuppressWarnings("unchecked")
	105	List<Annotation> results = query.list();
105	106	defaultBeanInitializer.initializeAll(results, propertyPaths);
106	107	return results;
107	108	}

      * FIXME CdmEntityDaoBase is abstract, can it be annotated with @Repository?
      */
     @Repository
     public abstract class CdmEntityDaoBase<T extends CdmBase> extends DaoBase implements ICdmEntityDao<T> {
     public abstract class CdmEntityDaoBase<T extends CdmBase>
                 extends DaoBase
                 implements ICdmEntityDao<T> {
         private static final Logger logger = Logger.getLogger(CdmEntityDaoBase.class);
-...
             return list(type,limit,start,null,null);
+        }
         @Override
         public List<T> rows(String tableName, int limit, int start) {
             Query query = getSession().createQuery("from " + tableName + " order by uuid");
             query.setFirstResult(start);
             query.setMaxResults(limit);
             @SuppressWarnings("unchecked")
     		List<T> result = query.list();
             return result;
+        }
         @Override
         public Class<T> getType() {
             return type;

+        }
         /**
          * Null save method which compiles a order by clause from the given list of OrderHints
          * Null save method which compiles an order by clause from the given list of OrderHints
+         *
          * @param orderHints can be NULL
          * @return a StringBuffer holding the hql orderby clause
-...
             StringBuffer orderString = new StringBuffer();
             StringBuffer aliasPrefix = new StringBuffer();
             aliasPrefix.append(" ");
             StringBuffer aliasPrefix = new StringBuffer(" ");
             if(aliasName != null && !aliasName.isEmpty()){
                 aliasPrefix.append(aliasName).append(".");
+            }
             if(orderHints != null && !orderHints.isEmpty()) {
                 orderString.append(" order by");
                 orderString.append(" ORDER BY ");
                 for(OrderHint orderHint : orderHints) {
                     orderString.append(aliasPrefix).append(orderHint.toHql());
+                }

             inner.setProjection(Projections.distinct(Projections.id()));
             @SuppressWarnings("unchecked")
             List<Object> intermediateResult = inner.list();
             if(intermediateResult.isEmpty()) {
                 return new ArrayList<DescriptionBase>();
                 return new ArrayList<>();
+            }
             Integer[] resultIds = new Integer[intermediateResult.size()];
-...
             addOrder(criteria,orderHints);
             @SuppressWarnings("unchecked")
             List<Object> intermediateResult = criteria.list();
             if(intermediateResult.isEmpty()) {
                 return new ArrayList<TaxonDescription>();
                 return new ArrayList<>();
+            }
             Integer[] resultIds = new Integer[intermediateResult.size()];
-...
             criteria.add(Restrictions.in("id", resultIds));
             addOrder(criteria,orderHints);
             @SuppressWarnings("unchecked")
             List<TaxonDescription> results = criteria.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
-...
                     crit.setFirstResult(pageNumber * pageSize);
+                }
+            }
             @SuppressWarnings("unchecked")
             List<CommonTaxonName> results = crit.list();
             return results;
+        }
-...
         @Override
         public DescriptionBase find(LSID lsid) {
             DescriptionBase descriptionBase = super.find(lsid);
             DescriptionBase<?> descriptionBase = super.find(lsid);
             if(descriptionBase != null) {
                 List<String> propertyPaths = new ArrayList<String>();
                 List<String> propertyPaths = new ArrayList<>();
                 propertyPaths.add("createdBy");
                 propertyPaths.add("updatedBy");
                 propertyPaths.add("taxon");
-...
                     setPagingParameter(query, pageSize, pageNumber);
                     @SuppressWarnings("unchecked")
                     List<Media> results = query.list();
                     defaultBeanInitializer.initializeAll(results, propertyPaths);
-...
+                }
+        }
         /* (non-Javadoc)
          * @see eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao#countTaxonDescriptionMedia(java.util.UUID, java.lang.Boolean, java.util.Set)
          */
         @Override
         public int countTaxonDescriptionMedia(UUID taxonUuid,
                 Boolean limitToGalleries, Set<MarkerType> markerTypes) {
-...
+        }
         /* (non-Javadoc)
          * @see eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao#listNamedAreasInUse(java.lang.Integer, java.lang.Integer, java.util.List)
          */
         @SuppressWarnings("unchecked")
         @Override
         public List<TermDto> listNamedAreasInUse(boolean includeAllParents, Integer pageSize, Integer pageNumber) {
-...
             List<Object[]> parentResults = new ArrayList<Object[]>();
             if(!areasInUse.isEmpty()) {
                 Set<Object> allAreaIds = new HashSet<Object>(areasInUse.size());
                 Set<Object> allAreaIds = new HashSet<>(areasInUse.size());
                 if(includeAllParents) {
                     // find all parent nodes
-...
                     List<Object[]> allAreasResult = query.list();
                     Map<Object, Object> allAreasMap = ArrayUtils.toMap(allAreasResult.toArray());
                     Set<Object> parents = new HashSet<Object>();
                     Set<Object> parents = new HashSet<>();
                     for(Object[] leaf : areasInUse) {
                         allAreaIds.add(leaf[0]);
-...
          * @return
          */
         private List<TermDto> termDtoListFrom(List<Object[]> results) {
             Map<UUID, TermDto> dtoMap = new HashMap<UUID, TermDto>(results.size());
             Map<UUID, TermDto> dtoMap = new HashMap<>(results.size());
             for (Object[] elements : results) {
                 UUID uuid = (UUID)elements[0];
                 if(dtoMap.containsKey(uuid)){
-...
                     dtoMap.put(uuid, new TermDto(uuid, representations, (UUID)elements[2], (UUID)elements[3], (Integer)elements[4]));
+                }
+            }
             return new ArrayList<TermDto>(dtoMap.values());
             return new ArrayList<>(dtoMap.values());
+        }

cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/description/DescriptionElementDaoImpl.java
94	94	}
95	95	}
96	96
	97	@SuppressWarnings("unchecked")
97	98	List<Media> results = query.list();
98	99	defaultBeanInitializer.initializeAll(results, propertyPaths);
99	100	return results;
...	...
148	149	}
149	150	}
150	151
	152	@SuppressWarnings("unchecked")
151	153	List<DescriptionElementBase> results = fullTextQuery.list();
152	154	defaultBeanInitializer.initializeAll(results, propertyPaths);
153	155	return results;
...	...
160	162	@Override
161	163	public void purgeIndex() {
162	164	FullTextSession fullTextSession = Search.getFullTextSession(getSession());
163		for(Class clazz : indexedClasses) {
164		fullTextSession.purgeAll(type); // remove all description element base from indexes
	165	for(Class<? extends DescriptionElementBase> clazz : indexedClasses) {
	166	fullTextSession.purgeAll(type); // remove all description element base from indexes
165	167	}
166	168	fullTextSession.flushToIndexes();
167	169	}
...	...
182	184	public void optimizeIndex() {
183	185	FullTextSession fullTextSession = Search.getFullTextSession(getSession());
184	186	SearchFactory searchFactory = fullTextSession.getSearchFactory();
185		for(Class clazz : indexedClasses) {
	187	for(Class<? extends DescriptionElementBase> clazz : indexedClasses) {
186	188	searchFactory.optimize(clazz); // optimize the indices ()
187	189	}
188	190	fullTextSession.flushToIndexes();

+    	}
     	@Override
     	public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
     	public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(
     	        Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
     		checkNotInPriorView("DescriptiveDataSetDao.getTaxonFeatureDescriptionElementMap(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,	List<String> propertyPaths)");
     		Map<UuidAndTitleCache, Map<UUID, Set<T>>> result = new HashMap<>();
     		try {
-...
                     T data = (T)listEntry[4];
     				Map<UUID, Set<T>> taxonMap = result.get(taxon);
     				if (taxonMap == null){
     					taxonMap = new HashMap<UUID, Set<T>>();
     					taxonMap = new HashMap<>();
     					result.put(taxon, taxonMap);
+    				}
     				Set<T> featureSet = taxonMap.get(featureUuid);
     				if (featureSet == null){
     					featureSet = new HashSet<T>();
     					featureSet = new HashSet<>();
     					taxonMap.put(featureUuid, featureSet);
     				}else{
     					if (logger.isDebugEnabled()){logger.debug("feature set already exists");}

+        }
         @Override
         public List<HybridRelationship> getHybridNames(INonViralName name, HybridRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
         public List<HybridRelationship> getHybridNames(INonViralName name, HybridRelationshipType type,
                 Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
             AuditEvent auditEvent = getAuditEventFromContext();
             if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
                 Criteria criteria = getSession().createCriteria(HybridRelationship.class);
-...
                 addOrder(criteria, orderHints);
                 @SuppressWarnings("unchecked")
                 List<HybridRelationship> results = criteria.list();
                 defaultBeanInitializer.initializeAll(results, propertyPaths);
                 return results;
-...
+                    }
+                }
                 @SuppressWarnings("unchecked")
                 List<HybridRelationship> results =  query.getResultList();
                 defaultBeanInitializer.initializeAll(results, propertyPaths);
                 return results;
-...
+                }
                 addOrder(criteria, orderHints);
                 @SuppressWarnings("unchecked")
                 List<NameRelationship> results = criteria.list();
                 defaultBeanInitializer.initializeAll(results, propertyPaths);
                 return results;
-...
+                    }
+                }
                 @SuppressWarnings("unchecked")
                 List<NameRelationship> results = query.getResultList();
                 defaultBeanInitializer.initializeAll(results, propertyPaths);
                 return results;
-...
                     query.setFirstResult(0);
+                }
+            }
             return query.list();
             @SuppressWarnings("unchecked")
             List<Integer> result = query.list();
             return result;
+        }
         @Override
-...
                     query.setFirstResult(0);
+                }
+            }
             return defaultBeanInitializer.initializeAll((List<T>)query.list(), propertyPaths);
             @SuppressWarnings("unchecked")
             List<T> result = defaultBeanInitializer.initializeAll((List<T>)query.list(), propertyPaths);
             return result;
+        }
         private <T extends TypeDesignationBase> Query getTypeDesignationQuery(String select, TaxonName name,
-...
                     criteria.setFirstResult(0);
+                }
+            }
             @SuppressWarnings("unchecked")
             List<TaxonName> results = criteria.list();
             return results;
+        }
-...
                 addOrder(criteria, orderHints);
                 @SuppressWarnings("unchecked")
                 List<TaxonName> results = criteria.list();
                 defaultBeanInitializer.initializeAll(results, propertyPaths);
                 return results;
-...
+                    }
+                }
                 @SuppressWarnings("unchecked")
                 List<TaxonName> results = query.getResultList();
                 defaultBeanInitializer.initializeAll(results, propertyPaths);
                 return results;
-...
+                }
+            }
             @SuppressWarnings("unchecked")
             List<? extends TaxonName> results = crit.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
-...
                 // for some reason the HQL .class discriminator didn't work here so I created this preliminary
                 // implementation for now. Should be cleaned in future.
                 List<RelationshipBase> result = new ArrayList<RelationshipBase>();
                 List<RelationshipBase> result = new ArrayList<>();
                 int nameRelSize = countAllRelationships(NameRelationship.class);
                 if (nameRelSize > start){
-...
                 return result;
             } else {
                 AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(RelationshipBase.class,auditEvent.getRevisionNumber());
                 return query.getResultList();
                 @SuppressWarnings("unchecked")
                 List<RelationshipBase> result = query.getResultList();
                 return result;
+            }
+        }
-...
             if(result.size() == 0){
                 return null;
             }else{
                 List<UuidAndTitleCache> list = new ArrayList<UuidAndTitleCache>(result.size());
                 List<UuidAndTitleCache> list = new ArrayList<>(result.size());
                 for (Object object : result){
-...
         public UUID delete (TaxonName persistentObject){
             Set<TaxonBase> taxonBases = persistentObject.getTaxonBases();
             if (persistentObject == null){
                 logger.warn(type.getName() + " was 'null'");
                 return null;
+            }
             getSession().saveOrUpdate(persistentObject);
             UUID persUuid = persistentObject.getUuid();
            // persistentObject = this.load(persUuid);
             UUID homotypicalGroupUUID = persistentObject.getHomotypicalGroup().getUuid();
             for (TaxonBase taxonBase: taxonBases){
             for (TaxonBase<?> taxonBase: taxonBases){
                 taxonDao.delete(taxonBase);
+            }
             HomotypicalGroup homotypicalGroup = homotypicalGroupDao.load(homotypicalGroupUUID);
-...
                     homotypicalGroup.getTypifiedNames().remove(persistentObject);
                     homotypicalGroupDao.saveOrUpdate(homotypicalGroup);
+                }
+            }
             getSession().delete(persistentObject);
-...
         	SQLQuery query = getSession().createSQLQuery(sql);
         	List result = query.list();
         	String hqlQueryStringSelect = "SELECT * ";
-...
         	Query hqlQuery = getSession().createQuery(hqlQueryStringFrom);
         	List hqlResult = hqlQuery.list();
         	List<?> hqlResult = hqlQuery.list();
     		List<HashMap<String,String>> nameRecords = new ArrayList();
     		HashMap<String,String> nameRecord = new HashMap<String,String>();
     		List<HashMap<String,String>> nameRecords = new ArrayList<>();
     		HashMap<String,String> nameRecord = new HashMap<>();
     		Taxon accTaxon = null;
     		Synonym syn = null;
     		TaxonNode familyNode = null;
     		for(Object object : hqlResult)
+             {
     		for(Object object : hqlResult){
     			Object[] row = (Object[])object;
     			nameRecord = new HashMap<String,String>();
     			TaxonBase taxonBase = (TaxonBase)row[0];
     			nameRecord = new HashMap<>();
     			TaxonBase<?> taxonBase = (TaxonBase<?>)row[0];
     			if (taxonBase instanceof Taxon){
     			    accTaxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
     			} else{

      * @since 01.09.2008
      */
     @Repository
     public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase<SpecimenOrObservationBase> implements IOccurrenceDao {
     public class OccurrenceDaoHibernateImpl
               extends IdentifiableDaoBase<SpecimenOrObservationBase>
               implements IOccurrenceDao {
         @SuppressWarnings("unused")
         private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);
-...
                 projectionList.add(Projections.property("titleCache"));
                 criteria.setProjection(projectionList);
                 @SuppressWarnings("unchecked")
                 List<Object[]> result = criteria.list();
                 List<UuidAndTitleCache<SpecimenOrObservationBase>> uuidAndTitleCacheList = new ArrayList<>();
                 for(Object[] object : result){
                     uuidAndTitleCacheList.add(new UuidAndTitleCache<SpecimenOrObservationBase>((UUID) object[0],(Integer) object[1], (String) object[2]));
                     uuidAndTitleCacheList.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));
+                }
                 return uuidAndTitleCacheList;
+            }
-...
         @Override
         public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {
             List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<UuidAndTitleCache<DerivedUnit>>();
             List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<>();
             Session session = getSession();
             Query query;
             if (pattern != null){
-...
                query.setMaxResults(limit);
+            }
             @SuppressWarnings("unchecked")
             List<Object[]> result = query.list();
             for(Object[] object : result){
-...
             Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where dtype = " + FieldUnit.class.getSimpleName());
             @SuppressWarnings("unchecked")
             List<Object[]> result = query.list();
             for(Object[] object : result){
-...
         @Override
         public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,
                 TaxonName associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
             Set<SpecimenOrObservationBase> setOfAll = new HashSet<SpecimenOrObservationBase>();
             Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();
             // A Taxon name may be referenced by the DeterminationEvent of the SpecimenOrObservationBase
             List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxonName, null, 0, null, null);
-...
+            }
             @SuppressWarnings("unchecked")
             List<T> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
-...
+            }
             List<SpecimenNodeWrapper> list = new ArrayList<>();
             @SuppressWarnings("unchecked")
             List<Object[]> result = query.list();
             for(Object[] object : result){
                 list.add(new SpecimenNodeWrapper(
                         new UuidAndTitleCache<SpecimenOrObservationBase>(
                         new UuidAndTitleCache<>(
                                 (UUID) object[0],
                                 (Integer) object[1],
                                 (String) object[2]),
-...
                 return Collections.emptyList();
+            }
             List<UuidAndTitleCache<SpecimenOrObservationBase>> list = new ArrayList<>();
             @SuppressWarnings("unchecked")
             List<Object[]> result = query.list();
             for(Object[] object : result){
                 list.add(new UuidAndTitleCache<SpecimenOrObservationBase>((UUID) object[0],(Integer) object[1], (String) object[2]));
                 list.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));
+            }
             return list;
+        }
-...
             if(query==null){
                 return Collections.emptyList();
+            }
             @SuppressWarnings("unchecked")
             List<T> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
-...
         @Override
         public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
             String queryString = "FROM SpecimenOrObservationBase specimens WHERE specimens.recordBasis = :type";
             String queryString = "FROM SpecimenOrObservationBase specimens "
                     + " WHERE specimens.recordBasis = :type ";
             if(orderHints != null && orderHints.size() > 0){
                 queryString += " order by ";
                 String orderStr = "";
                 for(OrderHint orderHint : orderHints){
                     if(orderStr.length() > 0){
                         orderStr += ", ";
+                    }
                     queryString += "specimens." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
+                }
                 queryString += orderStr;
+            }
             queryString += orderByClause(orderHints, "specimens");
             Query query = getSession().createQuery(queryString);
             query.setParameter("type", type);
-...
                 query.setMaxResults(limit);
+            }
             List results = query.list();
             @SuppressWarnings({ "unchecked", "rawtypes" })
             List<SpecimenOrObservationBase> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
+        }
         @Override
         public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
             String queryString = "FROM DeterminationEvent determination WHERE determination.identifiedUnit = :specimen";
             String queryString = "FROM DeterminationEvent determination "
                     + " WHERE determination.identifiedUnit = :specimen";
             if(orderHints != null && orderHints.size() > 0){
                 queryString += " order by ";
                 String orderStr = "";
                 for(OrderHint orderHint : orderHints){
                     if(orderStr.length() > 0){
                         orderStr += ", ";
+                    }
                     queryString += "determination." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
+                }
                 queryString += orderStr;
+            }
             queryString += orderByClause(orderHints, "determination");
             Query query = getSession().createQuery(queryString);
             query.setParameter("specimen", specimen);
-...
                 query.setMaxResults(limit);
+            }
             List results = query.list();
             @SuppressWarnings("unchecked")
             List<DeterminationEvent> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
+        }
         @Override
         public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
             String queryString = "FROM SpecimenTypeDesignation designations WHERE designations.typeSpecimen = :specimen";
             String queryString = "FROM SpecimenTypeDesignation designations "
                     + " WHERE designations.typeSpecimen = :specimen";
             if(orderHints != null && orderHints.size() > 0){
                 queryString += " ORDER BY ";
                 String orderStr = "";
                 for(OrderHint orderHint : orderHints){
                     if(orderStr.length() > 0){
                         orderStr += ", ";
+                    }
                     queryString += "designations." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
+                }
                 queryString += orderStr;
+            }
             queryString += orderByClause(orderHints, "designations");
             Query query = getSession().createQuery(queryString);
             query.setParameter("specimen", specimen);
-...
             //DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements
             String queryString = "FROM IndividualsAssociation associations WHERE associations.associatedSpecimenOrObservation = :specimen";
             if(orderHints != null && orderHints.size() > 0){
                 queryString += " order by ";
                 String orderStr = "";
                 for(OrderHint orderHint : orderHints){
                     if(orderStr.length() > 0){
                         orderStr += ", ";
+                    }
                     queryString += "associations." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
+                }
                 queryString += orderStr;
+            }
             queryString += orderByClause(orderHints, "associations");
             Query query = getSession().createQuery(queryString);
             query.setParameter("specimen", specimen);
-...
                 query.setMaxResults(limit);
+            }
             List results = query.list();
             @SuppressWarnings("unchecked")
             List<IndividualsAssociation> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
+        }
-...
         @Override
         public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
             //DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements
             String queryString = "FROM DescriptionBase descriptions WHERE descriptions.describedSpecimenOrObservation = :specimen";
             String queryString = "FROM DescriptionBase descriptions "
                     + " WHERE descriptions.describedSpecimenOrObservation = :specimen";
             if(orderHints != null && orderHints.size() > 0){
                 queryString += " order by ";
                 String orderStr = "";
                 for(OrderHint orderHint : orderHints){
                     if(orderStr.length() > 0){
                         orderStr += ", ";
+                    }
                     queryString += "descriptions." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
+                }
                 queryString += orderStr;
+            }
             queryString += orderByClause(orderHints, "descriptions");
             Query query = getSession().createQuery(queryString);
             query.setParameter("specimen", specimen);
-...
                 query.setMaxResults(limit);
+            }
             List results = query.list();
             @SuppressWarnings("unchecked")
             List<DescriptionBase<?>> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
+        }
-...
          */
         @Override
         public List<FieldUnit> getFieldUnitsForGatheringEvent(UUID gatheringEventUuid, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
             String queryString = "FROM SpecimenOrObservationBase s WHERE s.gatheringEvent.uuid = :gatheringEventUuid";
             String queryString = "FROM SpecimenOrObservationBase sob "
                     + "WHERE sob.gatheringEvent.uuid = :gatheringEventUuid";
             if(orderHints != null && orderHints.size() > 0){
                 queryString += " order by ";
                 String orderStr = "";
                 for(OrderHint orderHint : orderHints){
                     if(orderStr.length() > 0){
                         orderStr += ", ";
+                    }
                     queryString += "descriptions." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
+                }
                 queryString += orderStr;
+            }
             queryString += orderByClause(orderHints, "sob");
             Query query = getSession().createQuery(queryString);
             query.setParameter("gatheringEventUuid", gatheringEventUuid);
-...
                 query.setMaxResults(limit);
+            }
             List results = query.list();
             @SuppressWarnings("unchecked")
             List<FieldUnit> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
+        }
-...
             String queryString = "SELECT dnaSample FROM DnaSample dnaSample join dnaSample.sequences sequence WHERE sequence.geneticAccessionNumber LIKE :accessionNumberString";
             Query query = getSession().createQuery(queryString);
             query.setParameter("accessionNumberString", accessionNumberString);
             List results = query.list();
             @SuppressWarnings("unchecked")
             List<DerivedUnit> results = query.list();
             defaultBeanInitializer.initializeAll(results, propertyPaths);
             return results;
+        }

     import eu.etaxonomy.cdm.model.reference.IReport;
     import eu.etaxonomy.cdm.model.reference.IThesis;
     import eu.etaxonomy.cdm.model.reference.Reference;
     import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
     import eu.etaxonomy.cdm.model.reference.ReferenceType;
     import eu.etaxonomy.cdm.model.taxon.TaxonBase;
     import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
-...
     		 */
     		//TODO implement search in nameDescriptions
     		Set<Reference> referenceSet = new HashSet<Reference>();
     		Set<Reference> referenceSet = new HashSet<>();
     		referenceSet.add(reference);
     		if(includeSubordinateReferences){
     			referenceSet.addAll(getSubordinateReferences(reference));
-...
     		return taxonBaseList;
+    	}
         /* (non-Javadoc)
          * @see eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao#getUuidAndAbbrevTitleCache(java.lang.Integer, java.lang.String)
          */
         @Override
         public List<UuidAndTitleCache<Reference>> getUuidAndAbbrevTitleCache(Integer limit, String pattern, ReferenceType refType) {
             Session session = getSession();
             Reference ref = ReferenceFactory.newArticle();
             Query query = null;
             if (pattern != null){
-...
+        }
         /* (non-Javadoc)
          * @see eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao#getUuidAndAbbrevTitleCache(java.lang.Integer, java.lang.String)
          */
         @Override
         public List<UuidAndTitleCache<Reference>> getUuidAndAbbrevTitleCacheForAuthor(Integer limit, String pattern, ReferenceType refType) {
             Session session = getSession();
             Reference ref = ReferenceFactory.newArticle();
             Query query = null;
             if (pattern != null){

+                    }
+                }
                 @SuppressWarnings("unchecked")
                 List<TaxonRelationship> result = query.getResultList();
                 defaultBeanInitializer.initializeAll(result, propertyPaths);
-...
                 // and we can't live without this functionality in CATE as it screws up the whole
                 // taxon tree thing
                 if(orderHints != null && !orderHints.isEmpty()) {
                     SortedSet<TaxonRelationship> sortedList = new TreeSet<TaxonRelationship>(new TaxonRelationshipFromTaxonComparator());
                     SortedSet<TaxonRelationship> sortedList = new TreeSet<>(new TaxonRelationshipFromTaxonComparator());
                     sortedList.addAll(result);
                     return new ArrayList<TaxonRelationship>(sortedList);
                     return new ArrayList<>(sortedList);
+                }
                 return result;

cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/query/OrderHint.java
146	146	*
147	147	* http://opensource.atlassian.com/projects/hibernate/browse/HHH-879
148	148	*/
149		Order order;
150	149
151	150	String[] assocObjs = getPropertyName().split("\\.");
152	151	String path = "";

                 HttpServletResponse response) throws IOException {
             logger.info("doGetFieldUnits() - " + request.getRequestURI());
             ModelAndView mv = new ModelAndView();
             TaxonBase<?> taxonBase = service.load(uuid);
             taxonBase = checkExistsAndAccess(taxonBase, NO_UNPUBLISHED, response);

cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java
331	331	private List<List<Synonym>> removeUnpublishedSynonyms(List<List<Synonym>> synonymyGroups) {
332	332	List<List<Synonym>> result = new ArrayList<>();
333	333	boolean isHomotypicToAccepted = true;
	334
334	335	for (List<Synonym> oldList : synonymyGroups){
335	336	List<Synonym> newList = new ArrayList<>();
336	337	for (Synonym oldSyn : oldList){

     import eu.etaxonomy.cdm.api.service.ICommonService;
     import eu.etaxonomy.cdm.api.service.IDatabaseService;
     import eu.etaxonomy.cdm.api.service.IDescriptionService;
     import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
     import eu.etaxonomy.cdm.api.service.IEntityConstraintViolationService;
     import eu.etaxonomy.cdm.api.service.IEntityValidationService;
     import eu.etaxonomy.cdm.api.service.IEventBaseService;
-...
     import eu.etaxonomy.cdm.api.service.IReferenceService;
     import eu.etaxonomy.cdm.api.service.IRegistrationService;
     import eu.etaxonomy.cdm.api.service.IRightsService;
     import eu.etaxonomy.cdm.api.service.IService;
     import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
     import eu.etaxonomy.cdm.api.service.ITaxonService;
     import eu.etaxonomy.cdm.api.service.ITermService;
     import eu.etaxonomy.cdm.api.service.IUserService;
     import eu.etaxonomy.cdm.api.service.IVocabularyService;
     import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
     import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;
     import eu.etaxonomy.cdm.api.service.molecular.IPrimerService;
     import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
-...
     		return configuration.getEntityConstraintViolationService();
+    	}
     	@Override
     	public final IService<CdmBase> getMainService(){
     		return configuration.getMainService();
+    	}
     	@Override
     	public final IDescriptiveDataSetService getDescriptiveDataSetService(){
     		return configuration.getDescriptiveDataSetService();

     import eu.etaxonomy.cdm.api.service.IReferenceService;
     import eu.etaxonomy.cdm.api.service.IRegistrationService;
     import eu.etaxonomy.cdm.api.service.IRightsService;
     import eu.etaxonomy.cdm.api.service.IService;
     import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
     import eu.etaxonomy.cdm.api.service.ITaxonService;
     import eu.etaxonomy.cdm.api.service.ITermService;
-...
     import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;
     import eu.etaxonomy.cdm.api.service.molecular.IPrimerService;
     import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
     import eu.etaxonomy.cdm.model.common.CdmBase;
     import eu.etaxonomy.cdm.persistence.hibernate.permission.ICdmPermissionEvaluator;
     /**
-...
     	@Autowired
         private SessionFactory factory;
     	//	@Autowired
     	//@Qualifier("mainService")
     	private IService<CdmBase> mainService;
     	@Autowired
     	private IDescriptiveDataSetService descriptiveDataSetService;
-...
     		return this.grantedAuthorityService;
+    	}
     	@Override
     	public IService<CdmBase> getMainService(){
     		return this.mainService;
+    	}
     	@Override
     	public PlatformTransactionManager getTransactionManager(){
     		return this.transactionManager;

     import eu.etaxonomy.cdm.api.service.ICommonService;
     import eu.etaxonomy.cdm.api.service.IDatabaseService;
     import eu.etaxonomy.cdm.api.service.IDescriptionService;
     import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
     import eu.etaxonomy.cdm.api.service.IEntityConstraintViolationService;
     import eu.etaxonomy.cdm.api.service.IEntityValidationService;
     import eu.etaxonomy.cdm.api.service.IEventBaseService;
-...
     import eu.etaxonomy.cdm.api.service.IReferenceService;
     import eu.etaxonomy.cdm.api.service.IRegistrationService;
     import eu.etaxonomy.cdm.api.service.IRightsService;
     import eu.etaxonomy.cdm.api.service.IService;
     import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
     import eu.etaxonomy.cdm.api.service.ITaxonService;
     import eu.etaxonomy.cdm.api.service.ITermService;
     import eu.etaxonomy.cdm.api.service.IUserService;
     import eu.etaxonomy.cdm.api.service.IVocabularyService;
     import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
     import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;
     import eu.etaxonomy.cdm.api.service.molecular.IPrimerService;
     import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
     import eu.etaxonomy.cdm.model.common.CdmBase;
     import eu.etaxonomy.cdm.persistence.hibernate.permission.CdmPermissionEvaluator;
     import eu.etaxonomy.cdm.persistence.hibernate.permission.ICdmPermissionEvaluator;
-...
     	public IGrantedAuthorityService getGrantedAuthorityService();
     	/**
     	 * @return
     	 */
     	public IService<CdmBase> getMainService();
     	/**
     	 * @return
     	 */

     import org.hibernate.LockOptions;
     import org.hibernate.Session;
     import org.hibernate.event.spi.MergeEvent;
     import eu.etaxonomy.cdm.api.service.pager.Pager;
     import eu.etaxonomy.cdm.model.common.ICdmBase;
     import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
     import eu.etaxonomy.cdm.persistence.dto.MergeResult;
     import eu.etaxonomy.cdm.persistence.hibernate.PostMergeEntityListener;
     import eu.etaxonomy.cdm.persistence.query.Grouping;
     import eu.etaxonomy.cdm.persistence.query.OrderHint;
-...
          */
         public UUID refresh(T persistentObject);
         public List<T> rows(String tableName, int limit, int start);
         /**
          * Save a collection containing new entities (persists the entities)
          * @param newInstances the new entities to be persisted

     	public Pager<Rights> getRights(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
             Integer numberOfResults = dao.countRights(t);
     		List<Rights> results = new ArrayList<Rights>();
     		List<Rights> results = new ArrayList<>();
     		if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
     			results = dao.getRights(t, pageSize, pageNumber,propertyPaths);
+    		}

cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
767	767
768	768	for (Taxon taxon : taxa) {
769	769	List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
770		for (SpecimenOrObservationBase o : perTaxonOccurrences) {
	770	for (SpecimenOrObservationBase<?> o : perTaxonOccurrences) {
771	771	occurrenceIds.add(o.getId());
772	772	}
773	773	}
774	774	occurrences = (List<T>) dao.loadList(occurrenceIds, propertyPaths);
775	775
776		return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
	776	return new DefaultPagerImpl<T>(pageNumber, Long.valueOf(occurrenceIds.size()), pageSize, occurrences);
777	777
778	778	}
779	779

     import eu.etaxonomy.cdm.persistence.query.Grouping;
     import eu.etaxonomy.cdm.persistence.query.OrderHint;
     public abstract class ServiceBase<T extends CdmBase, DAO extends ICdmEntityDao<T>> implements IService<T>, ApplicationContextAware {
     public abstract class ServiceBase<T extends CdmBase, DAO extends ICdmEntityDao<T>>
                 implements IService<T>, ApplicationContextAware {
         @SuppressWarnings("unused")
         private static final Logger logger = Logger.getLogger(ServiceBase.class);
-...
             return dao.refresh(persistentObject);
+        }
         /**
          * FIXME Candidate for harmonization
          * is this method used, and if so, should it be exposed in the service layer?
          * it seems a bit incongruous that we use an ORM to hide the fact that there is a
          * database, then expose a method that talks about "rows" . . .
          */
         @Override
         @Transactional(readOnly = true)
         public List<T> rows(String tableName, int limit, int start) {
             return dao.rows(tableName, limit, start);
+        }
         @Override
         @Transactional(readOnly = false)
         public Map<UUID, T> save(Collection<T> newInstances) {

         /**
          * recursively collect related taxa for the given <code>taxon</code> . The returned list will also include the
          * Recursively collect related taxa for the given <code>taxon</code> . The returned list will also include the
          *  <code>taxon</code> supplied as parameter.
+         *
          * @param taxon

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Revision 11d3d7eb

Added by Andreas Müller almost 6 years ago