cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IdentifiableServiceBase.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.api.service;
  11
  12 import java.util.ArrayList;
  13 import java.util.Arrays;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.log4j.Logger;
  22 import org.hibernate.criterion.Criterion;
  23 import org.springframework.transaction.annotation.Transactional;
  24
  25 import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
  26 import eu.etaxonomy.cdm.api.service.dto.IdentifiedEntityDTO;
  27 import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
  28 import eu.etaxonomy.cdm.api.service.pager.Pager;
  29 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  30 import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
  31 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  32 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  33 import eu.etaxonomy.cdm.model.common.CdmBase;
  34 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  35 import eu.etaxonomy.cdm.model.common.ISourceable;
  36 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  37 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  38 import eu.etaxonomy.cdm.model.common.LSID;
  39 import eu.etaxonomy.cdm.model.common.MarkerType;
  40 import eu.etaxonomy.cdm.model.media.Rights;
  41 import eu.etaxonomy.cdm.model.name.INonViralName;
  42 import eu.etaxonomy.cdm.model.name.NonViralName;
  43 import eu.etaxonomy.cdm.model.reference.Reference;
  44 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  45 import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
  46 import eu.etaxonomy.cdm.persistence.dao.hibernate.HibernateBeanInitializer;
  47 import eu.etaxonomy.cdm.persistence.dao.initializer.AutoPropertyInitializer;
  48 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  49 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  50 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  51 import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
  52 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  53 import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;
  54 import eu.etaxonomy.cdm.strategy.match.IMatchStrategy;
  55 import eu.etaxonomy.cdm.strategy.match.IMatchable;
  56 import eu.etaxonomy.cdm.strategy.match.MatchException;
  57 import eu.etaxonomy.cdm.strategy.merge.IMergable;
  58 import eu.etaxonomy.cdm.strategy.merge.IMergeStrategy;
  59 import eu.etaxonomy.cdm.strategy.merge.MergeException;
  60
  61 public abstract class IdentifiableServiceBase<T extends IdentifiableEntity, DAO extends IIdentifiableDao<T>> extends AnnotatableServiceBase<T,DAO>
  62                                                 implements IIdentifiableEntityService<T>{
  63
  64
  65         protected static final int UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE = 1000;
  66         protected static final  Logger logger = Logger.getLogger(IdentifiableServiceBase.class);
  67
  68         @Override
  69         @Transactional(readOnly = true)
  70         public Pager<Rights> getRights(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
  71         Integer numberOfResults = dao.countRights(t);
  72
  73                 List<Rights> results = new ArrayList<Rights>();
  74                 if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
  75                         results = dao.getRights(t, pageSize, pageNumber,propertyPaths);
  76                 }
  77
  78                 return new DefaultPagerImpl<Rights>(pageNumber, numberOfResults, pageSize, results);
  79         }
  80
  81         @Override
  82         @Transactional(readOnly = true)
  83         public Pager<IdentifiableSource> getSources(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
  84                  Integer numberOfResults = dao.countSources(t);
  85
  86                  List<IdentifiableSource> results = new ArrayList<IdentifiableSource>();
  87                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
  88                          results = dao.getSources(t, pageSize, pageNumber,propertyPaths);
  89                  }
  90
  91                  return new DefaultPagerImpl<IdentifiableSource>(pageNumber, numberOfResults, pageSize, results);
  92         }
  93
  94
  95         @Transactional(readOnly = false)
  96         @Override
  97         public T replace(T x, T y) {
  98                 return dao.replace(x, y);
  99         }
 100         /**
 101          * FIXME Candidate for harmonization
 102          * Given that this method is strongly typed, and generic, could we not simply expose it as
 103          * List<T> findByTitle(String title) as it is somewhat less cumbersome. Admittedly, I don't
 104          * understand what is going on with the configurators etc. so maybe there is a good reason for
 105          * the design of this method.
 106          * @param title
 107          * @return
 108          */
 109         @Transactional(readOnly = true)
 110         protected List<T> findCdmObjectsByTitle(String title){
 111                 return ((IIdentifiableDao)dao).findByTitle(title);
 112         }
 113
 114         @Transactional(readOnly = true)
 115         protected List<T> findCdmObjectsByTitle(String title, Class<T> clazz){
 116                 return ((IIdentifiableDao)dao).findByTitleAndClass(title, clazz);
 117         }
 118         @Transactional(readOnly = true)
 119         protected List<T> findCdmObjectsByTitle(String title, CdmBase sessionObject){
 120                 return ((IIdentifiableDao)dao).findByTitle(title, sessionObject);
 121         }
 122
 123         /*
 124          * TODO - Migrated from CommonServiceBase
 125          *  (non-Javadoc)
 126          * @see eu.etaxonomy.cdm.api.service.ICommonService#getSourcedObjectById(java.lang.String, java.lang.String)
 127          */
 128         @Transactional(readOnly = true)
 129         @Override
 130         public ISourceable getSourcedObjectByIdInSource(Class clazz, String idInSource, String idNamespace) {
 131                 ISourceable result = null;
 132
 133                 List<T> list = dao.findOriginalSourceByIdInSource(idInSource, idNamespace);
 134                 if (! list.isEmpty()){
 135                         result = list.get(0);
 136                 }
 137                 return result;
 138         }
 139
 140         @Transactional(readOnly = true)
 141         @Override
 142         public List<UuidAndTitleCache<T>> getUuidAndTitleCache(Integer limit, String pattern) {
 143                 return dao.getUuidAndTitleCache(limit, pattern);
 144         }
 145
 146     @Transactional(readOnly = true)
 147     @Override
 148     public <S extends T> List<UuidAndTitleCache<S>> getUuidAndTitleCache(Class<S> clazz,Integer limit, String pattern) {
 149         return dao.getUuidAndTitleCache(clazz, limit, pattern);
 150     }
 151
 152     @Transactional(readOnly = true)
 153     @Override
 154     public String getTitleCache(UUID uuid, boolean refresh){
 155         return dao.getTitleCache(uuid, refresh);
 156     }
 157
 158         @Transactional(readOnly = true)
 159         @Override
 160         public Pager<T> findByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 161                  long numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 162
 163                  List<T> results = new ArrayList<T>();
 164                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 165                                 results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
 166                  }
 167
 168                   return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);
 169         }
 170
 171         @Transactional(readOnly = true)
 172         @Override
 173         public Pager<T> findByTitle(IIdentifiableEntityServiceConfigurator<T> config){
 174                 return findByTitle(config.getClazz(), config.getTitleSearchStringSqlized(), config.getMatchMode(), config.getCriteria(), config.getPageSize(), config.getPageNumber(), config.getOrderHints(), config.getPropertyPaths());
 175         }
 176
 177         @Transactional(readOnly = true)
 178         @Override
 179         public List<T> listByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 180                  long numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 181
 182                  List<T> results = new ArrayList<T>();
 183                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 184                                 results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
 185                  }
 186                  return results;
 187         }
 188
 189         @Transactional(readOnly = true)
 190         @Override
 191         public Pager<T> findTitleCache(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, MatchMode matchMode){
 192                 long numberOfResults = dao.countTitleCache(clazz, queryString, matchMode);
 193
 194                  List<T> results = new ArrayList<T>();
 195                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 196                                 results = dao.findTitleCache(clazz, queryString, pageSize, pageNumber, orderHints, matchMode);
 197                  }
 198                  long r = 0;
 199                  r += numberOfResults;
 200
 201                   return new DefaultPagerImpl<T>(pageNumber, r , pageSize, results);
 202         }
 203
 204         @Transactional(readOnly = true)
 205         @Override
 206         public List<T> listByReferenceTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 207                  long numberOfResults = dao.countByReferenceTitle(clazz, queryString, matchmode, criteria);
 208
 209                  List<T> results = new ArrayList<T>();
 210                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 211                                 results = dao.findByReferenceTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
 212                  }
 213                  return results;
 214         }
 215
 216         @Transactional(readOnly = true)
 217         @Override
 218         public T find(LSID lsid) {
 219                 return dao.find(lsid);
 220         }
 221
 222         @Transactional(readOnly = true)
 223         @Override
 224         public Pager<T> search(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 225         Integer numberOfResults = dao.count(clazz,queryString);
 226
 227                 List<T> results = new ArrayList<T>();
 228                 if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 229                         results = dao.search(clazz,queryString, pageSize, pageNumber, orderHints, propertyPaths);
 230                 }
 231
 232                 return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);
 233         }
 234
 235         @Override
 236         @Transactional(readOnly = false)
 237         public void updateTitleCache() {
 238                 updateTitleCache(null, null, null, null);
 239         }
 240
 241         @Transactional(readOnly = false)  //TODO check transactional behaviour, e.g. what happens with the session if count is very large
 242         protected <S extends T > void updateTitleCacheImpl(Class<S> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<T> cacheStrategy, IProgressMonitor monitor) {
 243                 if (stepSize == null){
 244                         stepSize = UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE;
 245                 }
 246                 if (monitor == null){
 247                         monitor = DefaultProgressMonitor.NewInstance();
 248                 }
 249
 250                 int count = dao.count(clazz);
 251                 monitor.beginTask("update titles", count);
 252                 int worked = 0;
 253                 for(int i = 0 ; i < count ; i = i + stepSize){
 254                         // not sure if such strict ordering is necessary here, but for safety reasons I do it
 255                         ArrayList<OrderHint> orderHints = new ArrayList<OrderHint>();
 256                         orderHints.add( new OrderHint("id", OrderHint.SortOrder.ASCENDING));
 257
 258
 259                         Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> oldAutoInit = switchOfAutoinitializer();
 260                         List<S> list = this.list(clazz, stepSize, i, orderHints, null);
 261                         switchOnOldAutoInitializer(oldAutoInit);
 262
 263                         List<T> entitiesToUpdate = new ArrayList<T>();
 264                         for (T entity : list){
 265                                 HibernateProxyHelper.deproxy(entity, clazz);
 266                                 if (entity.isProtectedTitleCache() == false){
 267                                         updateTitleCacheForSingleEntity(cacheStrategy, entitiesToUpdate, entity);
 268                                 }
 269                                 worked++;
 270                         }
 271                         for (T entity: entitiesToUpdate){
 272                                 if (entity.getTitleCache() != null){
 273                                         //System.err.println(entity.getTitleCache());
 274                                 }else{
 275                                     //System.err.println("no titleCache" + ((TaxonNameBase<?,?>)entity).getNameCache());
 276                                 }
 277                         }
 278                         saveOrUpdate(entitiesToUpdate);
 279                         monitor.worked(list.size());
 280                         if (monitor.isCanceled()){
 281                                 monitor.done();
 282                                 return;
 283                         }
 284                 }
 285                 monitor.done();
 286         }
 287
 288         /**
 289          * Brings back all auto initializers to the bean initializer
 290          * @see #switchOfAutoinitializer()
 291          * @param oldAutoInit
 292          */
 293         protected void switchOnOldAutoInitializer(
 294                         Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> oldAutoInit) {
 295                 HibernateBeanInitializer initializer = (HibernateBeanInitializer)this.appContext.getBean("defaultBeanInitializer");
 296                 initializer.setBeanAutoInitializers(oldAutoInit);
 297         }
 298
 299         /**
 300          * Removes all auto initializers from the bean initializer
 301          *
 302          * @see #switchOnOldAutoInitializer(Map)
 303          * @return
 304          */
 305         protected Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> switchOfAutoinitializer() {
 306                 HibernateBeanInitializer initializer = (HibernateBeanInitializer)this.appContext.getBean("defaultBeanInitializer");
 307                 Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> oldAutoInitializers = initializer.getBeanAutoInitializers();
 308                 Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> map = new HashMap<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>>();
 309                 initializer.setBeanAutoInitializers(map);
 310                 return oldAutoInitializers;
 311         }
 312
 313         /**
 314          * @param cacheStrategy
 315          * @param entitiesToUpdate
 316          * @param entity
 317          */
 318         /**
 319          * @param cacheStrategy
 320          * @param entitiesToUpdate
 321          * @param entity
 322          */
 323         @SuppressWarnings("unchecked")
 324         private void updateTitleCacheForSingleEntity(
 325                         IIdentifiableEntityCacheStrategy<T> cacheStrategy,
 326                         List<T> entitiesToUpdate,
 327                         T entity) {
 328
 329                 //assert (entity.isProtectedTitleCache() == false );
 330
 331                 //exclude recursive inreferences
 332                 if (entity.isInstanceOf(Reference.class)){
 333                         Reference ref = CdmBase.deproxy(entity, Reference.class);
 334                         if (ref.getInReference() != null && ref.getInReference().equals(ref)){
 335                                 return;
 336                         }
 337                 }
 338
 339
 340                 //define the correct cache strategy
 341                 IIdentifiableEntityCacheStrategy entityCacheStrategy = cacheStrategy;
 342                 if (entityCacheStrategy == null){
 343                         entityCacheStrategy = entity.getCacheStrategy();
 344                         //FIXME find out why the wrong cache strategy is loaded here, see #1876
 345                         if (entity instanceof Reference){
 346                                 entityCacheStrategy = ReferenceFactory.newReference(((Reference)entity).getType()).getCacheStrategy();
 347                         }
 348                 }
 349
 350
 351                 //old titleCache
 352                 entity.setProtectedTitleCache(true);
 353
 354                 String oldTitleCache = entity.getTitleCache();
 355                 entity.setTitleCache(oldTitleCache, false);   //before we had entity.setProtectedTitleCache(false) but this deleted the titleCache itself
 356                 entity.setCacheStrategy(entityCacheStrategy);
 357                 //NonViralNames and Reference have more caches //TODO handle in NameService
 358                 String oldNameCache = null;
 359                 String oldFullTitleCache = null;
 360                 String oldAbbrevTitleCache = null;
 361                 if (entity instanceof NonViralName ){
 362
 363                         try{
 364                                 INonViralName nvn = (INonViralName) entity;
 365                                 if (!nvn.isProtectedNameCache()){
 366                                     nvn.setProtectedNameCache(true);
 367                                         oldNameCache = nvn.getNameCache();
 368                                         nvn.setProtectedNameCache(false);
 369                                 }
 370                                 if (!nvn.isProtectedFullTitleCache()){
 371                                     nvn.setProtectedFullTitleCache(true);
 372                                         oldFullTitleCache = nvn.getFullTitleCache();
 373                                         nvn.setProtectedFullTitleCache(false);
 374                                 }
 375                         }catch(ClassCastException e){
 376                                 System.out.println("entity: " + entity.getTitleCache());
 377                         }
 378
 379                 }else if (entity instanceof Reference){
 380                         Reference ref = (Reference) entity;
 381                         if (!ref.isProtectedAbbrevTitleCache()){
 382                                 ref.setProtectedAbbrevTitleCache(true);
 383                                 oldAbbrevTitleCache = ref.getAbbrevTitleCache();
 384                                 ref.setProtectedAbbrevTitleCache(false);
 385                         }
 386                 }
 387                 setOtherCachesNull(entity);
 388                 String newTitleCache= null;
 389                 INonViralName nvn = null; //TODO find better solution
 390                 try{
 391                         if (entity instanceof NonViralName){
 392                                 nvn = (INonViralName) entity;
 393                                 newTitleCache = entityCacheStrategy.getTitleCache(nvn);
 394                         } else{
 395                                  newTitleCache = entityCacheStrategy.getTitleCache(entity);
 396                         }
 397                 }catch (ClassCastException e){
 398                         nvn = HibernateProxyHelper.deproxy(entity, NonViralName.class);
 399                         newTitleCache = entityCacheStrategy.getTitleCache(nvn);
 400                         //System.out.println("titleCache: " +entity.getTitleCache());
 401                 }
 402
 403                 if ( oldTitleCache == null   || ! oldTitleCache.equals(newTitleCache) ){
 404                         entity.setTitleCache(null, false);
 405                         String newCache = entity.getTitleCache();
 406
 407                         if (newCache == null){
 408                                 logger.warn("newCache should never be null");
 409                         }
 410                         if (oldTitleCache == null){
 411                                 logger.info("oldTitleCache should never be null");
 412                         }
 413                         if (nvn != null){
 414                                 nvn.getNameCache();
 415                                 nvn.getFullTitleCache();
 416                         }
 417                         if (entity instanceof Reference){
 418                                 Reference ref = (Reference) entity;
 419                                 ref.getAbbrevTitleCache();
 420                         }
 421                         entitiesToUpdate.add(entity);
 422                 }else if (nvn != null){
 423                         String newNameCache = nvn.getNameCache();
 424                         String newFullTitleCache = nvn.getFullTitleCache();
 425                         if ((oldNameCache == null && !nvn.isProtectedNameCache()) || (oldNameCache != null && !oldNameCache.equals(newNameCache))){
 426                                 entitiesToUpdate.add(entity);
 427                         }else if ((oldFullTitleCache == null && !nvn.isProtectedFullTitleCache()) || (oldFullTitleCache != null && !oldFullTitleCache.equals(newFullTitleCache))){
 428                                 entitiesToUpdate.add(entity);
 429                         }
 430                 }else if (entity instanceof Reference){
 431                         Reference ref = (Reference) entity;
 432                         String newAbbrevTitleCache = ref.getAbbrevTitleCache();
 433                         if ( (oldAbbrevTitleCache == null && !ref.isProtectedAbbrevTitleCache() ) || (oldAbbrevTitleCache != null && !oldAbbrevTitleCache.equals(newAbbrevTitleCache))){
 434                                 entitiesToUpdate.add(entity);
 435                         }
 436                 }
 437
 438
 439         }
 440
 441
 442
 443         /**
 444          * Needs override if not only the title cache should be set to null to
 445          * generate the correct new title cache
 446          */
 447         protected void setOtherCachesNull(T entity) {
 448                 return;
 449         }
 450
 451
 452
 453         private class DeduplicateState{
 454                 String lastTitleCache;
 455                 Integer pageSize = 50;
 456                 int nPages = 3;
 457                 int startPage = 0;
 458                 boolean isCompleted = false;
 459                 int result;
 460         }
 461
 462         @Override
 463         @Transactional(readOnly = false)
 464         public int deduplicate(Class<? extends T> clazz, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 465                 DeduplicateState dedupState = new DeduplicateState();
 466
 467                 if (clazz == null){
 468                         logger.warn("Deduplication clazz must not be null!");
 469                         return 0;
 470                 }
 471                 if (! ( IMatchable.class.isAssignableFrom(clazz) && IMergable.class.isAssignableFrom(clazz) )  ){
 472                         logger.warn("Deduplication implemented only for classes implementing IMatchable and IMergeable. No deduplication performed!");
 473                         return 0;
 474                 }
 475                 Class matchableClass = clazz;
 476                 if (matchStrategy == null){
 477                         matchStrategy = DefaultMatchStrategy.NewInstance(matchableClass);
 478                 }
 479                 List<T> nextGroup = new ArrayList<T>();
 480
 481                 int result = 0;
 482 //              double countTotal = count(clazz);
 483 //
 484 //              Number countPagesN = Math.ceil(countTotal/dedupState.pageSize.doubleValue()) ;
 485 //              int countPages = countPagesN.intValue();
 486 //
 487
 488                 List<OrderHint> orderHints = Arrays.asList(new OrderHint[]{new OrderHint("titleCache", SortOrder.ASCENDING)});
 489
 490                 while (! dedupState.isCompleted){
 491                         //get x page sizes
 492                         List<T> objectList = getPages(clazz, dedupState, orderHints);
 493                         //after each page check if any changes took place
 494                         int nUnEqualPages = handleAllPages(objectList, dedupState, nextGroup, matchStrategy, mergeStrategy);
 495                         nUnEqualPages = nUnEqualPages + dedupState.pageSize * dedupState.startPage;
 496                         //refresh start page counter
 497                         int finishedPages = nUnEqualPages / dedupState.pageSize;
 498                         dedupState.startPage = finishedPages;
 499                 }
 500
 501                 result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 502                 return result;
 503         }
 504
 505
 506         private int handleAllPages(List<T> objectList, DeduplicateState dedupState, List<T> nextGroup, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 507                 int nUnEqual = 0;
 508                 for (T object : objectList){
 509                         String currentTitleCache = object.getTitleCache();
 510                         if (currentTitleCache != null && currentTitleCache.equals(dedupState.lastTitleCache)){
 511                                 //=titleCache
 512                                 nextGroup.add(object);
 513                         }else{
 514                                 //<> titleCache
 515                                 dedupState.result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 516                                 nextGroup = new ArrayList<T>();
 517                                 nextGroup.add(object);
 518                                 nUnEqual++;
 519                         }
 520                         dedupState.lastTitleCache = currentTitleCache;
 521                 }
 522                 handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 523                 return nUnEqual;
 524         }
 525
 526         private List<T> getPages(Class<? extends T> clazz, DeduplicateState dedupState, List<OrderHint> orderHints) {
 527                 List<T> result = new ArrayList<T>();
 528                 for (int pageNo = dedupState.startPage; pageNo < dedupState.startPage + dedupState.nPages; pageNo++){
 529                         List<T> objectList = listByTitle(clazz, null, null, null, dedupState.pageSize, pageNo, orderHints, null);
 530                         result.addAll(objectList);
 531                 }
 532                 if (result.size()< dedupState.nPages * dedupState.pageSize ){
 533                         dedupState.isCompleted = true;
 534                 }
 535                 return result;
 536         }
 537
 538         private int handleLastGroup(List<T> group, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 539                 int result = 0;
 540                 int size = group.size();
 541                 Set<Integer> exclude = new HashSet<Integer>();  //set to collect all objects, that have been merged already
 542                 for (int i = 0; i < size - 1; i++){
 543                         if (exclude.contains(i)){
 544                                 continue;
 545                         }
 546                         for (int j = i + 1; j < size; j++){
 547                                 if (exclude.contains(j)){
 548                                         continue;
 549                                 }
 550                                 T firstObject = group.get(i);
 551                                 T secondObject = group.get(j);
 552
 553                                 try {
 554                                         if (matchStrategy.invoke((IMatchable)firstObject, (IMatchable)secondObject)){
 555                                                 commonService.merge((IMergable)firstObject, (IMergable)secondObject, mergeStrategy);
 556                                                 exclude.add(j);
 557                                                 result++;
 558                                         }
 559                                 } catch (MatchException e) {
 560                                         logger.warn("MatchException when trying to match " + firstObject.getTitleCache());
 561                                         e.printStackTrace();
 562                                 } catch (MergeException e) {
 563                                         logger.warn("MergeException when trying to merge " + firstObject.getTitleCache());
 564                                         e.printStackTrace();
 565                                 }
 566                         }
 567                 }
 568                 return result;
 569         }
 570
 571         @Transactional(readOnly = true)
 572         @Override
 573         public Integer countByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria){
 574                  long numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 575
 576                  return ((Number)numberOfResults).intValue();
 577         }
 578
 579         @Transactional(readOnly = true)
 580         @Override
 581         public Integer countByTitle(IIdentifiableEntityServiceConfigurator<T> config){
 582                 return countByTitle(config.getClazz(), config.getTitleSearchStringSqlized(),
 583                                 config.getMatchMode(), config.getCriteria());
 584
 585         }
 586
 587         @Override
 588         @Transactional(readOnly = true)
 589         public <S extends T> Pager<IdentifiedEntityDTO<S>> findByIdentifier(
 590                         Class<S> clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode,
 591                         boolean includeEntity, Integer pageSize,
 592                         Integer pageNumber,     List<String> propertyPaths) {
 593
 594                 Integer numberOfResults = dao.countByIdentifier(clazz, identifier, identifierType, matchmode);
 595         List<Object[]> daoResults = new ArrayList<Object[]>();
 596         if(numberOfResults > 0) { // no point checking again
 597                 daoResults = dao.findByIdentifier(clazz, identifier, identifierType,
 598                                 matchmode, includeEntity, pageSize, pageNumber, propertyPaths);
 599         }
 600
 601         List<IdentifiedEntityDTO<S>> result = new ArrayList<IdentifiedEntityDTO<S>>();
 602         for (Object[] daoObj : daoResults){
 603                 if (includeEntity){
 604                         result.add(new IdentifiedEntityDTO<S>((DefinedTerm)daoObj[0], (String)daoObj[1], (S)daoObj[2]));
 605                 }else{
 606                         result.add(new IdentifiedEntityDTO<S>((DefinedTerm)daoObj[0], (String)daoObj[1], (UUID)daoObj[2], (String)daoObj[3]));
 607                 }
 608         }
 609                 return new DefaultPagerImpl<IdentifiedEntityDTO<S>>(pageNumber, numberOfResults, pageSize, result);
 610         }
 611
 612     @Override
 613     @Transactional(readOnly = true)
 614     public <S extends T> Pager<MarkedEntityDTO<S>> findByMarker(
 615             Class<S> clazz, MarkerType markerType, Boolean markerValue,
 616             boolean includeEntity, Integer pageSize,
 617             Integer pageNumber, List<String> propertyPaths) {
 618
 619         Long numberOfResults = dao.countByMarker(clazz, markerType, markerValue);
 620         List<Object[]> daoResults = new ArrayList<>();
 621         if(numberOfResults > 0) { // no point checking again
 622             daoResults = dao.findByMarker(clazz, markerType, markerValue, includeEntity,
 623                     pageSize, pageNumber, propertyPaths);
 624         }
 625
 626         List<MarkedEntityDTO<S>> result = new ArrayList<>();
 627         for (Object[] daoObj : daoResults){
 628             if (includeEntity){
 629                 result.add(new MarkedEntityDTO<S>((MarkerType)daoObj[0], (Boolean)daoObj[1], (S)daoObj[2]));
 630             }else{
 631                 result.add(new MarkedEntityDTO<S>((MarkerType)daoObj[0], (Boolean)daoObj[1], (UUID)daoObj[2], (String)daoObj[3]));
 632             }
 633         }
 634         return new DefaultPagerImpl<MarkedEntityDTO<S>>(pageNumber, numberOfResults, pageSize, result);
 635     }
 636 }
 637