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                                         IIdentifiableEntityCacheStrategy entityCacheStrategy = cacheStrategy;
 240                                         if (entityCacheStrategy == null){
 241                                                 entityCacheStrategy = entity.getCacheStrategy();
 242                                                 //FIXME find out why the wrong cache strategy is loaded here, see #1876
 243                                                 if (entity instanceof Reference){
 244                                                         entityCacheStrategy = ReferenceFactory.newReference(((Reference)entity).getType()).getCacheStrategy();
 245                                                 }
 246                                         }
 247                                         entity.setCacheStrategy(entityCacheStrategy);
 248                                         entity.setProtectedTitleCache(true);
 249                                         String titleCache = entity.getTitleCache();
 250                                         entity.setProtectedTitleCache(false);
 251                                         String nameCache = null;
 252                                         if (entity instanceof NonViralName ){
 253                                                 NonViralName nvn = (NonViralName) entity;
 254                                                 if (!nvn.isProtectedNameCache()){
 255                                                         nvn.setProtectedNameCache(true);
 256                                                         nameCache = nvn.getNameCache();
 257                                                         nvn.setProtectedNameCache(false);
 258                                                 }
 259
 260
 261                                         }
 262                                         setOtherCachesNull(entity); //TODO find better solution
 263                                         String newTitleCache = entityCacheStrategy.getTitleCache(entity);
 264                                         if (titleCache == null || titleCache != null && ! titleCache.equals(newTitleCache) ){
 265                                                 entity.setTitleCache(null, false);
 266                                                 entity.getTitleCache();
 267                                                 if (entity instanceof NonViralName){
 268                                                         NonViralName nvn = (NonViralName) entity;
 269                                                         String newnameCache = nvn.getNameCache();
 270                                                 }
 271                                                 entitiesToUpdate.add(entity);
 272                                         }else if (entity instanceof NonViralName){
 273                                                 NonViralName nvn = (NonViralName) entity;
 274                                                 String newnameCache = nvn.getNameCache();
 275                                                 if (nameCache == null || (nameCache != null && !nameCache.equals(newnameCache))){
 276                                                         entitiesToUpdate.add(entity);
 277                                                 }
 278                                         }
 279
 280                                 }
 281                         }
 282                         for (T entity: entitiesToUpdate){
 283                                 if (entity.getTitleCache() != null){
 284                                         System.err.println(entity.getTitleCache());
 285                                 }else{
 286                                         System.err.println("no titleCache" + ((NonViralName)entity).getNameCache());
 287                                 }
 288
 289                         }
 290                         saveOrUpdate(entitiesToUpdate);
 291                         monitor.worked(worked++);
 292                         if (monitor.isCanceled()){
 293                                 monitor.done();
 294                                 return;
 295                         }
 296                 }
 297                 monitor.done();
 298         }
 299
 300
 301
 302         /**
 303          * Needs override if not only the title cache should be set to null to
 304          * generate the correct new title cache
 305          */
 306         protected void setOtherCachesNull(T entity) {
 307                 return;
 308         }
 309
 310
 311
 312         private class DeduplicateState{
 313                 String lastTitleCache;
 314                 Integer pageSize = 50;
 315                 int nPages = 3;
 316                 int startPage = 0;
 317                 boolean isCompleted = false;
 318                 int result;
 319         }
 320
 321         /* (non-Javadoc)
 322          * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#deduplicate(java.lang.Class, eu.etaxonomy.cdm.strategy.match.IMatchStrategy, eu.etaxonomy.cdm.strategy.merge.IMergeStrategy)
 323          */
 324         @Override
 325         @Transactional(propagation = Propagation.SUPPORTS, readOnly = false)
 326         public int deduplicate(Class<? extends T> clazz, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 327                 DeduplicateState dedupState = new DeduplicateState();
 328
 329                 if (clazz == null){
 330                         logger.warn("Deduplication clazz must not be null!");
 331                         return 0;
 332                 }
 333                 if (! ( IMatchable.class.isAssignableFrom(clazz) && IMergable.class.isAssignableFrom(clazz) )  ){
 334                         logger.warn("Deduplication implemented only for classes implementing IMatchable and IMergeable. No deduplication performed!");
 335                         return 0;
 336                 }
 337                 Class matchableClass = clazz;
 338                 if (matchStrategy == null){
 339                         matchStrategy = DefaultMatchStrategy.NewInstance(matchableClass);
 340                 }
 341                 List<T> nextGroup = new ArrayList<T>();
 342
 343                 int result = 0;
 344 //              double countTotal = count(clazz);
 345 //
 346 //              Number countPagesN = Math.ceil(countTotal/dedupState.pageSize.doubleValue()) ;
 347 //              int countPages = countPagesN.intValue();
 348 //
 349
 350                 List<OrderHint> orderHints = Arrays.asList(new OrderHint[]{new OrderHint("titleCache", SortOrder.ASCENDING)});
 351
 352                 while (! dedupState.isCompleted){
 353                         //get x page sizes
 354                         List<T> objectList = getPages(clazz, dedupState, orderHints);
 355                         //after each page check if any changes took place
 356                         int nUnEqualPages = handleAllPages(objectList, dedupState, nextGroup, matchStrategy, mergeStrategy);
 357                         nUnEqualPages = nUnEqualPages + dedupState.pageSize * dedupState.startPage;
 358                         //refresh start page counter
 359                         int finishedPages = nUnEqualPages / dedupState.pageSize;
 360                         dedupState.startPage = finishedPages;
 361                 }
 362
 363                 result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 364                 return result;
 365         }
 366
 367
 368         private int handleAllPages(List<T> objectList, DeduplicateState dedupState, List<T> nextGroup, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 369                 int nUnEqual = 0;
 370                 for (T object : objectList){
 371                         String currentTitleCache = object.getTitleCache();
 372                         if (currentTitleCache != null && currentTitleCache.equals(dedupState.lastTitleCache)){
 373                                 //=titleCache
 374                                 nextGroup.add(object);
 375                         }else{
 376                                 //<> titleCache
 377                                 dedupState.result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 378                                 nextGroup = new ArrayList<T>();
 379                                 nextGroup.add(object);
 380                                 nUnEqual++;
 381                         }
 382                         dedupState.lastTitleCache = currentTitleCache;
 383                 }
 384                 handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
 385                 return nUnEqual;
 386         }
 387
 388         private List<T> getPages(Class<? extends T> clazz, DeduplicateState dedupState, List<OrderHint> orderHints) {
 389                 List<T> result = new ArrayList<T>();
 390                 for (int pageNo = dedupState.startPage; pageNo < dedupState.startPage + dedupState.nPages; pageNo++){
 391                         List<T> objectList = listByTitle(clazz, null, null, null, dedupState.pageSize, pageNo, orderHints, null);
 392                         result.addAll(objectList);
 393                 }
 394                 if (result.size()< dedupState.nPages * dedupState.pageSize ){
 395                         dedupState.isCompleted = true;
 396                 }
 397                 return result;
 398         }
 399
 400         private int handleLastGroup(List<T> group, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
 401                 int result = 0;
 402                 int size = group.size();
 403                 Set<Integer> exclude = new HashSet<Integer>();  //set to collect all objects, that have been merged already
 404                 for (int i = 0; i < size - 1; i++){
 405                         if (exclude.contains(i)){
 406                                 continue;
 407                         }
 408                         for (int j = i + 1; j < size; j++){
 409                                 if (exclude.contains(j)){
 410                                         continue;
 411                                 }
 412                                 T firstObject = group.get(i);
 413                                 T secondObject = group.get(j);
 414
 415                                 try {
 416                                         if (matchStrategy.invoke((IMatchable)firstObject, (IMatchable)secondObject)){
 417                                                 commonService.merge((IMergable)firstObject, (IMergable)secondObject, mergeStrategy);
 418                                                 exclude.add(j);
 419                                                 result++;
 420                                         }
 421                                 } catch (MatchException e) {
 422                                         logger.warn("MatchException when trying to match " + firstObject.getTitleCache());
 423                                         e.printStackTrace();
 424                                 } catch (MergeException e) {
 425                                         logger.warn("MergeException when trying to merge " + firstObject.getTitleCache());
 426                                         e.printStackTrace();
 427                                 }
 428                         }
 429                 }
 430                 return result;
 431         }
 432
 433          public Integer countByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria){
 434                  Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
 435
 436                  return numberOfResults;
 437          }
 438
 439         @Transactional(readOnly = true)
 440         public Integer countByTitle(IIdentifiableEntityServiceConfigurator<T> config){
 441                 return countByTitle(config.getClazz(), config.getTitleSearchStringSqlized(),
 442                                 config.getMatchMode(), config.getCriteria());
 443
 444         }
 445
 446 }
 447