// $Id$
/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* European Distributed Institute of Taxonomy
* http://www.e-taxonomy.eu
-*
+*
* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.UUID;
import org.apache.log4j.Logger;
import org.hibernate.criterion.Criterion;
import org.springframework.transaction.annotation.Transactional;
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
+import eu.etaxonomy.cdm.api.service.dto.FindByIdentifierDTO;
import eu.etaxonomy.cdm.api.service.pager.Pager;
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.ISourceable;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.LSID;
-import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
import eu.etaxonomy.cdm.model.media.Rights;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
import eu.etaxonomy.cdm.persistence.dao.hibernate.HibernateBeanInitializer;
import eu.etaxonomy.cdm.persistence.dao.initializer.AutoPropertyInitializer;
+import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
import eu.etaxonomy.cdm.persistence.query.MatchMode;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
import eu.etaxonomy.cdm.strategy.merge.IMergeStrategy;
import eu.etaxonomy.cdm.strategy.merge.MergeException;
-public abstract class IdentifiableServiceBase<T extends IdentifiableEntity,DAO extends IIdentifiableDao<T>> extends AnnotatableServiceBase<T,DAO>
+public abstract class IdentifiableServiceBase<T extends IdentifiableEntity,DAO extends IIdentifiableDao<T>> extends AnnotatableServiceBase<T,DAO>
implements IIdentifiableEntityService<T>{
-
-// @Autowired
-// protected ICommonService commonService;
-
+
protected static final int UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE = 1000;
protected static final Logger logger = Logger.getLogger(IdentifiableServiceBase.class);
+ @Override
@Transactional(readOnly = true)
public Pager<Rights> getRights(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = dao.countRights(t);
-
+
List<Rights> results = new ArrayList<Rights>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
- results = dao.getRights(t, pageSize, pageNumber,propertyPaths);
+ results = dao.getRights(t, pageSize, pageNumber,propertyPaths);
}
-
+
return new DefaultPagerImpl<Rights>(pageNumber, numberOfResults, pageSize, results);
}
-
+
+ @Override
@Transactional(readOnly = true)
public Pager<IdentifiableSource> getSources(T t, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = dao.countSources(t);
-
- List<IdentifiableSource> results = new ArrayList<IdentifiableSource>();
- if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
- results = dao.getSources(t, pageSize, pageNumber,propertyPaths);
- }
-
- return new DefaultPagerImpl<IdentifiableSource>(pageNumber, numberOfResults, pageSize, results);
+
+ List<IdentifiableSource> results = new ArrayList<IdentifiableSource>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = dao.getSources(t, pageSize, pageNumber,propertyPaths);
+ }
+
+ return new DefaultPagerImpl<IdentifiableSource>(pageNumber, numberOfResults, pageSize, results);
}
-
+
@Transactional(readOnly = false)
+ @Override
public T replace(T x, T y) {
return dao.replace(x, y);
}
/**
* FIXME Candidate for harmonization
* Given that this method is strongly typed, and generic, could we not simply expose it as
- * List<T> findByTitle(String title) as it is somewhat less cumbersome. Admittedly, I don't
+ * List<T> findByTitle(String title) as it is somewhat less cumbersome. Admittedly, I don't
* understand what is going on with the configurators etc. so maybe there is a good reason for
- * the design of this method.
+ * the design of this method.
* @param title
* @return
*/
protected List<T> findCdmObjectsByTitle(String title){
return ((IIdentifiableDao)dao).findByTitle(title);
}
-
+
@Transactional(readOnly = true)
protected List<T> findCdmObjectsByTitle(String title, Class<T> clazz){
return ((IIdentifiableDao)dao).findByTitleAndClass(title, clazz);
protected List<T> findCdmObjectsByTitle(String title, CdmBase sessionObject){
return ((IIdentifiableDao)dao).findByTitle(title, sessionObject);
}
-
+
/*
* TODO - Migrated from CommonServiceBase
* (non-Javadoc)
* @see eu.etaxonomy.cdm.api.service.ICommonService#getSourcedObjectById(java.lang.String, java.lang.String)
*/
@Transactional(readOnly = true)
+ @Override
public ISourceable getSourcedObjectByIdInSource(Class clazz, String idInSource, String idNamespace) {
ISourceable result = null;
}
return result;
}
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getUuidAndTitleCache()
- */
+
@Transactional(readOnly = true)
+ @Override
public List<UuidAndTitleCache<T>> getUuidAndTitleCache() {
return dao.getUuidAndTitleCache();
}\r
-
+
@Transactional(readOnly = true)\r
+ @Override
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) {\r
Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);\r
- \r
+\r
List<T> results = new ArrayList<T>();\r
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)\r
- results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths); \r
+ results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);\r
}\r
- \r
+\r
return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);\r
}
-
+
@Transactional(readOnly = true)
+ @Override
public Pager<T> findByTitle(IIdentifiableEntityServiceConfigurator<T> config){
return findByTitle(config.getClazz(), config.getTitleSearchStringSqlized(), config.getMatchMode(), config.getCriteria(), config.getPageSize(), config.getPageNumber(), config.getOrderHints(), config.getPropertyPaths());
}
-
+
@Transactional(readOnly = true)
+ @Override
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) {
Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
-
+
List<T> results = new ArrayList<T>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
- results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
+ results = dao.findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
}
return results;
}
-
+
@Transactional(readOnly = true)
+ @Override
public Pager<T> findTitleCache(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, MatchMode matchMode){
long numberOfResults = dao.countTitleCache(clazz, queryString, matchMode);
-
+
List<T> results = new ArrayList<T>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
results = dao.findTitleCache(clazz, queryString, pageSize, pageNumber, orderHints, matchMode);
}
int r = 0;
r += numberOfResults;
-
+
return new DefaultPagerImpl<T>(pageNumber, r , pageSize, results);
}
@Transactional(readOnly = true)
+ @Override
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) {
Integer numberOfResults = dao.countByReferenceTitle(clazz, queryString, matchmode, criteria);
-
+
List<T> results = new ArrayList<T>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
- results = dao.findByReferenceTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
+ results = dao.findByReferenceTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
}
return results;
}
-
+
@Transactional(readOnly = true)
+ @Override
public T find(LSID lsid) {
return dao.find(lsid);
}
-
+
@Transactional(readOnly = true)
+ @Override
public Pager<T> search(Class<? extends T> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
Integer numberOfResults = dao.count(clazz,queryString);
-
+
List<T> results = new ArrayList<T>();
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
- results = dao.search(clazz,queryString, pageSize, pageNumber, orderHints, propertyPaths);
+ results = dao.search(clazz,queryString, pageSize, pageNumber, orderHints, propertyPaths);
}
-
+
return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);
}
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache()
- */
@Override
@Transactional(readOnly = false)
public void updateTitleCache() {
updateTitleCache(null, null, null, null);
}
-
- @Transactional(readOnly = false) //TODO check transactional behaviour, e.g. what happens with the session if count is very large
+
+ @Transactional(readOnly = false) //TODO check transactional behaviour, e.g. what happens with the session if count is very large
protected <S extends T > void updateTitleCacheImpl(Class<S> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<T> cacheStrategy, IProgressMonitor monitor) {
if (stepSize == null){
stepSize = UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE;
if (monitor == null){
monitor = DefaultProgressMonitor.NewInstance();
}
-
+
int count = dao.count(clazz);
monitor.beginTask("update titles", count);
int worked = 0;
// not sure if such strict ordering is necessary here, but for safety reasons I do it
ArrayList<OrderHint> orderHints = new ArrayList<OrderHint>();
orderHints.add( new OrderHint("id", OrderHint.SortOrder.ASCENDING));
-
-
+
+
Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> oldAutoInit = switchOfAutoinitializer();
List<S> list = this.list(clazz, stepSize, i, orderHints, null);
switchOnOldAutoInitializer(oldAutoInit);
-
+
List<T> entitiesToUpdate = new ArrayList<T>();
for (T entity : list){
+ HibernateProxyHelper.deproxy(entity, clazz);
if (entity.isProtectedTitleCache() == false){
updateTitleCacheForSingleEntity(cacheStrategy, entitiesToUpdate, entity);
}
/**
* Removes all auto initializers from the bean initializer
- *
+ *
* @see #switchOnOldAutoInitializer(Map)
- * @return
+ * @return
*/
protected Map<Class<? extends CdmBase>, AutoPropertyInitializer<CdmBase>> switchOfAutoinitializer() {
HibernateBeanInitializer initializer = (HibernateBeanInitializer)this.appContext.getBean("defaultBeanInitializer");
private void updateTitleCacheForSingleEntity(
IIdentifiableEntityCacheStrategy<T> cacheStrategy,
List<T> entitiesToUpdate, T entity) {
-
+
assert (entity.isProtectedTitleCache() == false );
-
+
//exclude recursive inreferences
if (entity.isInstanceOf(Reference.class)){
Reference<?> ref = CdmBase.deproxy(entity, Reference.class);
return;
}
}
-
-
+
+
//define the correct cache strategy
IIdentifiableEntityCacheStrategy entityCacheStrategy = cacheStrategy;
if (entityCacheStrategy == null){
entityCacheStrategy = entity.getCacheStrategy();
- //FIXME find out why the wrong cache strategy is loaded here, see #1876
+ //FIXME find out why the wrong cache strategy is loaded here, see #1876
if (entity instanceof Reference){
- entityCacheStrategy = ReferenceFactory.newReference(((Reference)entity).getType()).getCacheStrategy();
+ entityCacheStrategy = ReferenceFactory.newReference(((Reference<?>)entity).getType()).getCacheStrategy();
}
}
entity.setCacheStrategy(entityCacheStrategy);
-
-
+
+
//old titleCache
entity.setProtectedTitleCache(true);
String oldTitleCache = entity.getTitleCache();
entity.setTitleCache(oldTitleCache, false); //before we had entity.setProtectedTitleCache(false) but this deleted the titleCache itself
-
+
//NonViralNames and Reference have more caches //TODO handle in NameService
String oldNameCache = null;
String oldFullTitleCache = null;
String oldAbbrevTitleCache = null;
if (entity instanceof NonViralName ){
- NonViralName<?> nvn = (NonViralName) entity;
- if (!nvn.isProtectedNameCache()){
- nvn.setProtectedNameCache(true);
- oldNameCache = nvn.getNameCache();
- nvn.setProtectedNameCache(false);
- }
- if (!nvn.isProtectedFullTitleCache()){
- nvn.setProtectedFullTitleCache(true);
- oldFullTitleCache = nvn.getFullTitleCache();
- nvn.setProtectedFullTitleCache(false);
+
+ try{
+ NonViralName<?> nvn = (NonViralName) entity;
+ if (!nvn.isProtectedNameCache()){
+ nvn.setProtectedNameCache(true);
+ oldNameCache = nvn.getNameCache();
+ nvn.setProtectedNameCache(false);
+ }
+ if (!nvn.isProtectedFullTitleCache()){
+ nvn.setProtectedFullTitleCache(true);
+ oldFullTitleCache = nvn.getFullTitleCache();
+ nvn.setProtectedFullTitleCache(false);
+ }
+ }catch(ClassCastException e){
+ System.out.println("entity: " + entity.getTitleCache());
}
+
}else if (entity instanceof Reference){
Reference<?> ref = (Reference<?>) entity;
if (!ref.isProtectedAbbrevTitleCache()){
ref.setProtectedAbbrevTitleCache(false);
}
}
- setOtherCachesNull(entity); //TODO find better solution
-
- String newTitleCache = entityCacheStrategy.getTitleCache(entity);
- if (oldTitleCache == null || oldTitleCache != null && ! oldTitleCache.equals(newTitleCache) ){
+ setOtherCachesNull(entity);
+ String newTitleCache= null;
+ NonViralName<?> nvn = null;//TODO find better solution
+ try{
+ if (entity instanceof NonViralName){
+ nvn = (NonViralName) entity;
+ newTitleCache = entityCacheStrategy.getTitleCache(nvn);
+ } else{
+ newTitleCache = entityCacheStrategy.getTitleCache(entity);
+ }
+ }catch (ClassCastException e){
+ nvn = HibernateProxyHelper.deproxy(entity, NonViralName.class);
+ newTitleCache = entityCacheStrategy.getTitleCache(nvn);
+ //System.out.println("titleCache: " +entity.getTitleCache());
+ }
+
+ if ( oldTitleCache == null || oldTitleCache != null && ! oldTitleCache.equals(newTitleCache) ){
entity.setTitleCache(null, false);
String newCache = entity.getTitleCache();
if (newCache == null){
if (oldTitleCache == null){
logger.info("oldTitleCache should never be null");
}
- if (entity instanceof NonViralName){
- NonViralName<?> nvn = (NonViralName) entity;
+ if (nvn != null){
+ //NonViralName<?> nvn = (NonViralName) entity;
nvn.getNameCache();
nvn.getFullTitleCache();
}
ref.getAbbrevTitleCache();
}
entitiesToUpdate.add(entity);
- }else if (entity instanceof NonViralName){
- NonViralName<?> nvn = (NonViralName) entity;
+ }else if (nvn != null){
+ //NonViralName<?> nvn = (NonViralName) entity;
String newNameCache = nvn.getNameCache();
String newFullTitleCache = nvn.getFullTitleCache();
- if (oldNameCache == null || (oldNameCache != null && !oldNameCache.equals(newNameCache))){
+ if ((oldNameCache == null && !nvn.isProtectedNameCache()) || (oldNameCache != null && !oldNameCache.equals(newNameCache))){
entitiesToUpdate.add(entity);
- }else if (oldFullTitleCache == null || (oldFullTitleCache != null && !oldFullTitleCache.equals(newFullTitleCache))){
+ }else if ((oldFullTitleCache == null && !nvn.isProtectedFullTitleCache()) || (oldFullTitleCache != null && !oldFullTitleCache.equals(newFullTitleCache))){
entitiesToUpdate.add(entity);
}
}else if (entity instanceof Reference){
Reference<?> ref = (Reference<?>) entity;
String newAbbrevTitleCache = ref.getAbbrevTitleCache();
- if (oldAbbrevTitleCache == null || (oldAbbrevTitleCache != null && !oldAbbrevTitleCache.equals(newAbbrevTitleCache))){
+ if ( (oldAbbrevTitleCache == null && !ref.isProtectedAbbrevTitleCache() ) || (oldAbbrevTitleCache != null && !oldAbbrevTitleCache.equals(newAbbrevTitleCache))){
entitiesToUpdate.add(entity);
}
}
+
+
}
-
-
+
+
/**
* Needs override if not only the title cache should be set to null to
protected void setOtherCachesNull(T entity) {
return;
}
-
-
+
+
private class DeduplicateState{
String lastTitleCache;
Integer pageSize = 50;
int nPages = 3;
int startPage = 0;
boolean isCompleted = false;
- int result;
+ int result;
}
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#deduplicate(java.lang.Class, eu.etaxonomy.cdm.strategy.match.IMatchStrategy, eu.etaxonomy.cdm.strategy.merge.IMergeStrategy)
- */
+
@Override
@Transactional(readOnly = false)
public int deduplicate(Class<? extends T> clazz, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
DeduplicateState dedupState = new DeduplicateState();
-
+
if (clazz == null){
logger.warn("Deduplication clazz must not be null!");
return 0;
matchStrategy = DefaultMatchStrategy.NewInstance(matchableClass);
}
List<T> nextGroup = new ArrayList<T>();
-
+
int result = 0;
// double countTotal = count(clazz);
-//
-// Number countPagesN = Math.ceil(countTotal/dedupState.pageSize.doubleValue()) ;
+//
+// Number countPagesN = Math.ceil(countTotal/dedupState.pageSize.doubleValue()) ;
// int countPages = countPagesN.intValue();
-//
-
+//
+
List<OrderHint> orderHints = Arrays.asList(new OrderHint[]{new OrderHint("titleCache", SortOrder.ASCENDING)});
-
+
while (! dedupState.isCompleted){
//get x page sizes
List<T> objectList = getPages(clazz, dedupState, orderHints);
int finishedPages = nUnEqualPages / dedupState.pageSize;
dedupState.startPage = finishedPages;
}
-
+
result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
return result;
}
dedupState.result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
nextGroup = new ArrayList<T>();
nextGroup.add(object);
- nUnEqual++;
+ nUnEqual++;
}
dedupState.lastTitleCache = currentTitleCache;
}
}
T firstObject = group.get(i);
T secondObject = group.get(j);
-
+
try {
if (matchStrategy.invoke((IMatchable)firstObject, (IMatchable)secondObject)){
commonService.merge((IMergable)firstObject, (IMergable)secondObject, mergeStrategy);
}
}
return result;
- }
-
- public Integer countByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria){
+ }
+
+ @Transactional(readOnly = true)
+ @Override
+ public Integer countByTitle(Class<? extends T> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria){
Integer numberOfResults = dao.countByTitle(clazz, queryString, matchmode, criteria);
-
+
return numberOfResults;
- }
-
+ }
+
@Transactional(readOnly = true)
+ @Override
public Integer countByTitle(IIdentifiableEntityServiceConfigurator<T> config){
return countByTitle(config.getClazz(), config.getTitleSearchStringSqlized(),
config.getMatchMode(), config.getCriteria());
-
+
+ }
+
+ @Override
+ @Transactional(readOnly = true)
+ public <S extends T> Pager<FindByIdentifierDTO<S>> findByIdentifier(
+ Class<S> clazz, String identifier, DefinedTerm identifierType, MatchMode matchmode,
+ boolean includeEntity, Integer pageSize,
+ Integer pageNumber, List<String> propertyPaths) {
+
+ Integer numberOfResults = dao.countByIdentifier(clazz, identifier, identifierType, matchmode);
+ List<Object[]> daoResults = new ArrayList<Object[]>();
+ if(numberOfResults > 0) { // no point checking again
+ daoResults = dao.findByIdentifier(clazz, identifier, identifierType,
+ matchmode, includeEntity, pageSize, pageNumber, propertyPaths);
+ }
+
+ List<FindByIdentifierDTO<S>> result = new ArrayList<FindByIdentifierDTO<S>>();
+ for (Object[] daoObj : daoResults){
+ if (includeEntity){
+ result.add(new FindByIdentifierDTO<S>((DefinedTerm)daoObj[0], (String)daoObj[1], (S)daoObj[2]));
+ }else{
+ result.add(new FindByIdentifierDTO<S>((DefinedTerm)daoObj[0], (String)daoObj[1], (UUID)daoObj[2], (String)daoObj[3]));
+ }
+ }
+ return new DefaultPagerImpl<FindByIdentifierDTO<S>>(pageNumber, numberOfResults, pageSize, result);
}
-
-
}\r