// $Id$
/**
* 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 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.model.reference.ReferenceFactory;
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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>{
-
+
protected static final int UPDATE_TITLE_CACHE_DEFAULT_STEP_SIZE = 1000;
protected static final Logger logger = Logger.getLogger(IdentifiableServiceBase.class);
@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);
+ 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) {
/**
* 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)
}
return result;
}
-
+
@Transactional(readOnly = true)
@Override
public List<UuidAndTitleCache<T>> getUuidAndTitleCache() {
return dao.getUuidAndTitleCache();
- }\r
-
- @Transactional(readOnly = true)\r
+ }
+
+ @Transactional(readOnly = true)
@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
- 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
- }\r
- \r
- return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);\r
+ 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) {
+ 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);
+ }
+
+ return new DefaultPagerImpl<T>(pageNumber, numberOfResults, pageSize, results);
}
-
+
@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);
}
@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);
}
-
+
@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);
/**
* 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");
* @param entitiesToUpdate
* @param entity
*/
+ @SuppressWarnings("unchecked")
private void updateTitleCacheForSingleEntity(
IIdentifiableEntityCacheStrategy<T> cacheStrategy,
List<T> entitiesToUpdate, T entity) {
-
- assert (entity.isProtectedTitleCache() == false );
-
+
+ //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();
}
}
- 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
-
+ entity.setCacheStrategy(entityCacheStrategy);
//NonViralNames and Reference have more caches //TODO handle in NameService
String oldNameCache = null;
String oldFullTitleCache = null;
String oldAbbrevTitleCache = null;
if (entity instanceof NonViralName ){
-
+
try{
NonViralName<?> nvn = (NonViralName) entity;
if (!nvn.isProtectedNameCache()){
}catch(ClassCastException e){
System.out.println("entity: " + entity.getTitleCache());
}
-
+
}else if (entity instanceof Reference){
Reference<?> ref = (Reference<?>) entity;
if (!ref.isProtectedAbbrevTitleCache()){
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){
logger.warn("newCache should never be null");
}
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;
}
-
+
@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;
- }
-
+ }
+
@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,
+ 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]));
+ 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
+}
BGBM BDI Projects / cdmlib.git / blobdiff