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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.util.ArrayList;
  14 import java.util.Arrays;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.hibernate.criterion.Criterion;
  21 import org.springframework.beans.factory.annotation.Autowired;
  22 import org.springframework.transaction.annotation.Propagation;
  23 import org.springframework.transaction.annotation.Transactional;
  24
  25 import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
  26 import eu.etaxonomy.cdm.api.service.pager.Pager;
  27 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  28 import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
  29 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.common.ISourceable;
  32 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  33 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  34 import eu.etaxonomy.cdm.model.common.LSID;
  35 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  36 import eu.etaxonomy.cdm.model.media.Rights;
  37 import eu.etaxonomy.cdm.model.name.NonViralName;
  38 import eu.etaxonomy.cdm.model.reference.Reference;
  39 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  40 import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
  41 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  42 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  43 import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
  44 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  45 import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;
  46 import eu.etaxonomy.cdm.strategy.match.IMatchStrategy;
  47 import eu.etaxonomy.cdm.strategy.match.IMatchable;
  48 import eu.etaxonomy.cdm.strategy.match.MatchException;
  49 import eu.etaxonomy.cdm.strategy.merge.IMergable;
  50 import eu.etaxonomy.cdm.strategy.merge.IMergeStrategy;
  51 import eu.etaxonomy.cdm.strategy.merge.MergeException;
  52
  53 public abstract class IdentifiableServiceBase<T extends IdentifiableEntity,DAO extends IIdentifiableDao<T>> extends AnnotatableServiceBase<T,DAO>
  54                                                 implements IIdentifiableEntityService<T>{
  55
  56     @Autowired
  57     protected ICommonService commonService;
  58
  59
  60         protected static final int UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE = 1000;
  61         protected static final  Logger logger = Logger.getLogger(IdentifiableServiceBase.class);
  62
  63         @Transactional(readOnly = true)
  64         public Pager<Rights> getRights(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
  65         Integer numberOfResults = dao.countRights(t);
  66
  67                 List<Rights> results = new ArrayList<Rights>();
  68                 if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
  69                         results = dao.getRights(t, pageSize, pageNumber,propertyPaths);
  70                 }
  71
  72                 return new DefaultPagerImpl<Rights>(pageNumber, numberOfResults, pageSize, results);
  73         }
  74
  75         @Transactional(readOnly = true)
  76         public Pager<IdentifiableSource> getSources(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
  77                  Integer numberOfResults = dao.countSources(t);
  78
  79                         List<IdentifiableSource> results = new ArrayList<IdentifiableSource>();
  80                         if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
  81                                 results = dao.getSources(t, pageSize, pageNumber,propertyPaths);
  82                         }
  83
  84                         return new DefaultPagerImpl<IdentifiableSource>(pageNumber, numberOfResults, pageSize, results);
  85         }
  86
  87
  88         @Transactional(readOnly = false)
  89         public T replace(T x, T y) {
  90                 return dao.replace(x, y);
  91         }
  92         /**
  93          * FIXME Candidate for harmonization
  94          * Given that this method is strongly typed, and generic, could we not simply expose it as
  95          * List<T> findByTitle(String title) as it is somewhat less cumbersome. Admittedly, I don't
  96          * understand what is going on with the configurators etc. so maybe there is a good reason for
  97          * the design of this method.
  98          * @param title
  99          * @return
 100          */
 101         @Transactional(readOnly = true)
 102         protected List<T> findCdmObjectsByTitle(String title){
 103                 return ((IIdentifiableDao)dao).findByTitle(title);
 104         }
 105
 106         @Transactional(readOnly = true)
 107         protected List<T> findCdmObjectsByTitle(String title, Class<T> clazz){
 108                 return ((IIdentifiableDao)dao).findByTitleAndClass(title, clazz);
 109         }
 110         @Transactional(readOnly = true)
 111         protected List<T> findCdmObjectsByTitle(String title, CdmBase sessionObject){
 112                 return ((IIdentifiableDao)dao).findByTitle(title, sessionObject);
 113         }
 114
 115         /*
 116          * TODO - Migrated from CommonServiceBase
 117          *  (non-Javadoc)
 118          * @see eu.etaxonomy.cdm.api.service.ICommonService#getSourcedObjectById(java.lang.String, java.lang.String)
 119          */
 120         @Transactional(readOnly = true)
 121         public ISourceable getSourcedObjectByIdInSource(Class clazz, String idInSource, String idNamespace) {
 122                 ISourceable result = null;
 123
 124                 List<T> list = dao.findOriginalSourceByIdInSource(idInSource, idNamespace);
 125                 if (! list.isEmpty()){
 126                         result = list.get(0);
 127                 }
 128                 return result;
 129         }
 130
 131         /* (non-Javadoc)
 132          * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getUuidAndTitleCache()
 133          */
 134         @Transactional(readOnly = true)
 135         public List<UuidAndTitleCache<T>> getUuidAndTitleCache() {
 136                 return dao.getUuidAndTitleCache();
 137         }
 138
 139         @Transactional(readOnly = true)
 140         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) {
 141                  Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 142
 143                  List<T> results = new ArrayList<T>();
 144                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 145                                 results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
 146                  }
 147
 148                   return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);
 149         }
 150
 151         @Transactional(readOnly = true)
 152         public Pager<T> findByTitle(IIdentifiableEntityServiceConfigurator<T> config){
 153                 return findByTitle(config.getClazz(), config.getTitleSearchStringSqlized(), config.getMatchMode(), config.getCriteria(), config.getPageSize(), config.getPageNumber(), config.getOrderHints(), config.getPropertyPaths());
 154         }
 155
 156         @Transactional(readOnly = true)
 157         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) {
 158                  Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 159
 160                  List<T> results = new ArrayList<T>();
 161                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 162                                 results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
 163                  }
 164                  return results;
 165         }
 166
 167         @Transactional(readOnly = true)
 168         public Pager<T> findTitleCache(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, MatchMode matchMode){
 169                 long numberOfResults = dao.countTitleCache(clazz, queryString, matchMode);
 170
 171                  List<T> results = new ArrayList<T>();
 172                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 173                                 results = dao.findTitleCache(clazz, queryString, pageSize, pageNumber, orderHints, matchMode);
 174                  }
 175                  int r = 0;
 176                  r += numberOfResults;
 177
 178                   return new DefaultPagerImpl<T>(pageNumber, r , pageSize, results);
 179         }
 180
 181         @Transactional(readOnly = true)
 182         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) {
 183                  Integer numberOfResults = dao.countByReferenceTitle(clazz, queryString, matchmode, criteria);
 184
 185                  List<T> results = new ArrayList<T>();
 186                  if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 187                                 results = dao.findByReferenceTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
 188                  }
 189                  return results;
 190         }
 191
 192         @Transactional(readOnly = true)
 193         public T find(LSID lsid) {
 194                 return dao.find(lsid);
 195         }
 196
 197         @Transactional(readOnly = true)
 198         public Pager<T> search(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 199         Integer numberOfResults = dao.count(clazz,queryString);
 200
 201                 List<T> results = new ArrayList<T>();
 202                 if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 203                         results = dao.search(clazz,queryString, pageSize, pageNumber, orderHints, propertyPaths);
 204                 }
 205
 206                 return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);
 207         }
 208
 209
 210         /* (non-Javadoc)
 211          * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache()
 212          */
 213         @Override
 214         @Transactional(readOnly = false)
 215         public void updateTitleCache() {
 216                 updateTitleCache(null, null, null, null);
 217         }
 218
 219         @Transactional(readOnly = false)  //TODO check transactional behaviour, e.g. what happens with the session if count is very large
 220         protected void updateTitleCacheImpl(Class<? extends T> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<T> cacheStrategy, IProgressMonitor monitor) {
 221                 if (stepSize == null){
 222                         stepSize = UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE;
 223                 }
 224                 if (monitor == null){
 225                         monitor = DefaultProgressMonitor.NewInstance();
 226                 }
 227
 228                 int count = dao.count(clazz);
 229                 monitor.beginTask("update titles", count);
 230                 int worked = 0;
 231                 for(int i = 0 ; i < count ; i = i + stepSize){
 232                         // not sure if such strict ordering is necessary here, but for safety reasons I do it
 233                         ArrayList<OrderHint> orderHints = new ArrayList<OrderHint>();
 234                         orderHints.add( new OrderHint("id", OrderHint.SortOrder.ASCENDING));
 235                         List<T> list = this.list(clazz, stepSize, i, orderHints, null);
 236                         List<T> entitiesToUpdate = new ArrayList<T>();
 237                         for (T entity : list){
 238                                 if (entity.isProtectedTitleCache() == false){
 239                                         updateTitleCacheForSingleEntity(cacheStrategy, entitiesToUpdate, entity);
 240                                 }
 241                                 worked++;
 242                         }
 243                         for (T entity: entitiesToUpdate){
 244                                 if (entity.getTitleCache() != null){
 245                                         System.err.println(entity.getTitleCache());
 246                                 }else{
 247                                         System.err.println("no titleCache" + ((NonViralName)entity).getNameCache());
 248                                 }
 249
 250                         }
 251                         saveOrUpdate(entitiesToUpdate);
 252                         monitor.worked(list.size());
 253                         if (monitor.isCanceled()){
 254                                 monitor.done();
 255                                 return;
 256                         }
 257                 }
 258                 monitor.done();
 259         }
 260
 261         /**
 262          * @param cacheStrategy
 263          * @param entitiesToUpdate
 264          * @param entity
 265          */
 266         private void updateTitleCacheForSingleEntity(
 267                         IIdentifiableEntityCacheStrategy<T> cacheStrategy,
 268                         List<T> entitiesToUpdate, T entity) {
 269                 //exclude recursive inreferences
 270                 if (entity.isInstanceOf(Reference.class)){
 271                         Reference ref = CdmBase.deproxy(entity, Reference.class);
 272                         if (ref.getInReference() != null && ref.getInReference().equals(ref)){
 273                                 return;
 274                         }
 275                 }
 276
 277
 278                 IIdentifiableEntityCacheStrategy entityCacheStrategy = cacheStrategy;
 279                 if (entityCacheStrategy == null){
 280                         entityCacheStrategy = entity.getCacheStrategy();
 281                         //FIXME find out why the wrong cache strategy is loaded here, see #1876
 282                         if (entity instanceof Reference){
 283                                 entityCacheStrategy = ReferenceFactory.newReference(((Reference)entity).getType()).getCacheStrategy();
 284                         }
 285                 }
 286                 entity.setCacheStrategy(entityCacheStrategy);
 287                 entity.setProtectedTitleCache(true);
 288                 String titleCache = entity.getTitleCache();
 289                 entity.setProtectedTitleCache(false);
 290                 String nameCache = null;
 291                 if (entity instanceof NonViralName ){
 292                         NonViralName nvn = (NonViralName) entity;
 293                         if (!nvn.isProtectedNameCache()){
 294                                 nvn.setProtectedNameCache(true);
 295                                 nameCache = nvn.getNameCache();
 296                                 nvn.setProtectedNameCache(false);
 297                         }
 298
 299
 300                 }
 301                 setOtherCachesNull(entity); //TODO find better solution
 302                 String newTitleCache = entityCacheStrategy.getTitleCache(entity);
 303                 if (titleCache == null || titleCache != null && ! titleCache.equals(newTitleCache) ){
 304                         entity.setTitleCache(null, false);
 305                         entity.getTitleCache();
 306                         if (entity instanceof NonViralName){
 307                                 NonViralName nvn = (NonViralName) entity;
 308                                 String newnameCache = nvn.getNameCache();
 309                         }
 310                         entitiesToUpdate.add(entity);
 311                 }else if (entity instanceof NonViralName){
 312                         NonViralName nvn = (NonViralName) entity;
 313                         String newnameCache = nvn.getNameCache();
 314                         if (nameCache == null || (nameCache != null && !nameCache.equals(newnameCache))){
 315                                 entitiesToUpdate.add(entity);
 316                         }
 317                 }
 318         }
 319
 320
 321
 322         /**
 323          * Needs override if not only the title cache should be set to null to
 324          * generate the correct new title cache
 325          */
 326         protected void setOtherCachesNull(T entity) {
 327                 return;
 328         }
 329
 330
 331
 332         private class DeduplicateState{
 333                 String lastTitleCache;
 334                 Integer pageSize = 50;
 335                 int nPages = 3;
 336                 int startPage = 0;
 337                 boolean isCompleted = false;
 338                 int result;
 339         }
 340
 341         /* (non-Javadoc)
 342          * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#deduplicate(java.lang.Class, eu.etaxonomy.cdm.strategy.match.IMatchStrategy, eu.etaxonomy.cdm.strategy.merge.IMergeStrategy)
 343          */
 344         @Override
 345         @Transactional(propagation = Propagation.SUPPORTS, readOnly = false)
 346         public int deduplicate(Class<? extends T> clazz, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 347                 DeduplicateState dedupState = new DeduplicateState();
 348
 349                 if (clazz == null){
 350                         logger.warn("Deduplication clazz must not be null!");
 351                         return 0;
 352                 }
 353                 if (! ( IMatchable.class.isAssignableFrom(clazz) && IMergable.class.isAssignableFrom(clazz) )  ){
 354                         logger.warn("Deduplication implemented only for classes implementing IMatchable and IMergeable. No deduplication performed!");
 355                         return 0;
 356                 }
 357                 Class matchableClass = clazz;
 358                 if (matchStrategy == null){
 359                         matchStrategy = DefaultMatchStrategy.NewInstance(matchableClass);
 360                 }
 361                 List<T> nextGroup = new ArrayList<T>();
 362
 363                 int result = 0;
 364 //              double countTotal = count(clazz);
 365 //
 366 //              Number countPagesN = Math.ceil(countTotal/dedupState.pageSize.doubleValue()) ;
 367 //              int countPages = countPagesN.intValue();
 368 //
 369
 370                 List<OrderHint> orderHints = Arrays.asList(new OrderHint[]{new OrderHint("titleCache", SortOrder.ASCENDING)});
 371
 372                 while (! dedupState.isCompleted){
 373                         //get x page sizes
 374                         List<T> objectList = getPages(clazz, dedupState, orderHints);
 375                         //after each page check if any changes took place
 376                         int nUnEqualPages = handleAllPages(objectList, dedupState, nextGroup, matchStrategy, mergeStrategy);
 377                         nUnEqualPages = nUnEqualPages + dedupState.pageSize * dedupState.startPage;
 378                         //refresh start page counter
 379                         int finishedPages = nUnEqualPages / dedupState.pageSize;
 380                         dedupState.startPage = finishedPages;
 381                 }
 382
 383                 result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 384                 return result;
 385         }
 386
 387
 388         private int handleAllPages(List<T> objectList, DeduplicateState dedupState, List<T> nextGroup, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 389                 int nUnEqual = 0;
 390                 for (T object : objectList){
 391                         String currentTitleCache = object.getTitleCache();
 392                         if (currentTitleCache != null && currentTitleCache.equals(dedupState.lastTitleCache)){
 393                                 //=titleCache
 394                                 nextGroup.add(object);
 395                         }else{
 396                                 //<> titleCache
 397                                 dedupState.result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 398                                 nextGroup = new ArrayList<T>();
 399                                 nextGroup.add(object);
 400                                 nUnEqual++;
 401                         }
 402                         dedupState.lastTitleCache = currentTitleCache;
 403                 }
 404                 handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 405                 return nUnEqual;
 406         }
 407
 408         private List<T> getPages(Class<? extends T> clazz, DeduplicateState dedupState, List<OrderHint> orderHints) {
 409                 List<T> result = new ArrayList<T>();
 410                 for (int pageNo = dedupState.startPage; pageNo < dedupState.startPage + dedupState.nPages; pageNo++){
 411                         List<T> objectList = listByTitle(clazz, null, null, null, dedupState.pageSize, pageNo, orderHints, null);
 412                         result.addAll(objectList);
 413                 }
 414                 if (result.size()< dedupState.nPages * dedupState.pageSize ){
 415                         dedupState.isCompleted = true;
 416                 }
 417                 return result;
 418         }
 419
 420         private int handleLastGroup(List<T> group, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 421                 int result = 0;
 422                 int size = group.size();
 423                 Set<Integer> exclude = new HashSet<Integer>();  //set to collect all objects, that have been merged already
 424                 for (int i = 0; i < size - 1; i++){
 425                         if (exclude.contains(i)){
 426                                 continue;
 427                         }
 428                         for (int j = i + 1; j < size; j++){
 429                                 if (exclude.contains(j)){
 430                                         continue;
 431                                 }
 432                                 T firstObject = group.get(i);
 433                                 T secondObject = group.get(j);
 434
 435                                 try {
 436                                         if (matchStrategy.invoke((IMatchable)firstObject, (IMatchable)secondObject)){
 437                                                 commonService.merge((IMergable)firstObject, (IMergable)secondObject, mergeStrategy);
 438                                                 exclude.add(j);
 439                                                 result++;
 440                                         }
 441                                 } catch (MatchException e) {
 442                                         logger.warn("MatchException when trying to match " + firstObject.getTitleCache());
 443                                         e.printStackTrace();
 444                                 } catch (MergeException e) {
 445                                         logger.warn("MergeException when trying to merge " + firstObject.getTitleCache());
 446                                         e.printStackTrace();
 447                                 }
 448                         }
 449                 }
 450                 return result;
 451         }
 452
 453          public Integer countByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria){
 454                  Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 455
 456                  return numberOfResults;
 457          }
 458
 459         @Transactional(readOnly = true)
 460         public Integer countByTitle(IIdentifiableEntityServiceConfigurator<T> config){
 461                 return countByTitle(config.getClazz(), config.getTitleSearchStringSqlized(),
 462                                 config.getMatchMode(), config.getCriteria());
 463
 464         }
 465
 466 }
 467