package eu.etaxonomy.cdm.api.service;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import org.apache.log4j.Logger;
import org.hibernate.criterion.Criterion;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
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.model.common.CdmBase;
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.model.reference.ReferenceFactory;
import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
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.cache.common.IIdentifiableEntityCacheStrategy;
+import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;
+import eu.etaxonomy.cdm.strategy.match.IMatchStrategy;
+import eu.etaxonomy.cdm.strategy.match.IMatchable;
+import eu.etaxonomy.cdm.strategy.match.MatchException;
+import eu.etaxonomy.cdm.strategy.merge.IMergable;
+import eu.etaxonomy.cdm.strategy.merge.IMergeStrategy;
+import eu.etaxonomy.cdm.strategy.merge.MergeException;
-@Transactional(readOnly = true)
public abstract class IdentifiableServiceBase<T extends IdentifiableEntity,DAO extends IIdentifiableDao<T>> extends AnnotatableServiceBase<T,DAO>
implements IIdentifiableEntityService<T>{
- @SuppressWarnings("unused")
- protected
- static final Logger logger = Logger.getLogger(IdentifiableServiceBase.class);
+
+ @Autowired
+ protected ICommonService commonService;
+ 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
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
results = dao.getRights(t, pageSize, pageNumber,propertyPaths);
}
return new DefaultPagerImpl<Rights>(pageNumber, numberOfResults, pageSize, results);
}
-
+
+ @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
+ 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);
}
- protected List<T> findByTitle(IIdentifiableEntityServiceConfigurator config){
- return ((IIdentifiableDao)dao).findByTitle(config.getTitleSearchString(),
- config.getMatchMode(), 0, -1, null);
- // TODO: Implement parameters pageSize, pageNumber, and criteria
+
+ @Transactional(readOnly = false)
+ public T replace(T x, T y) {
+ return dao.replace(x, y);
}
/**
* FIXME Candidate for harmonization
* @param title
* @return
*/
+ @Transactional(readOnly = true)
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);
}
+ @Transactional(readOnly = true)
protected List<T> findCdmObjectsByTitle(String title, CdmBase sessionObject){
return ((IIdentifiableDao)dao).findByTitle(title, sessionObject);
}
* (non-Javadoc)
* @see eu.etaxonomy.cdm.api.service.ICommonService#getSourcedObjectById(java.lang.String, java.lang.String)
*/
+ @Transactional(readOnly = true)
public ISourceable getSourcedObjectByIdInSource(Class clazz, String idInSource, String idNamespace) {
ISourceable result = null;
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getUuidAndTitleCache()
*/
+ @Transactional(readOnly = true)
public List<UuidAndTitleCache<T>> getUuidAndTitleCache() {
return dao.getUuidAndTitleCache();
}\r
- \r
+
+ @Transactional(readOnly = true)\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) {\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\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
}
+
+ @Transactional(readOnly = true)
+ 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)
+ 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);
+ }
+ return results;
+ }
+
+ @Transactional(readOnly = true)
+ 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)
+ 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);
+ }
+ return results;
+ }
+
+ @Transactional(readOnly = true)
+ public T find(LSID lsid) {
+ return dao.find(lsid);
+ }
+
+ @Transactional(readOnly = true)
+ 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);
+ }
+
+ 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
+ protected void updateTitleCacheImpl(Class<? extends T> 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;
+ for(int i = 0 ; i < count ; i = i + stepSize){
+ // 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));
+ List<T> list = this.list(clazz, stepSize, i, orderHints, null);
+ List<T> entitiesToUpdate = new ArrayList<T>();
+ for (T entity : list){
+ if (entity.isProtectedTitleCache() == false){
+ updateTitleCacheForSingleEntity(cacheStrategy, entitiesToUpdate, entity);
+ }
+ worked++;
+ }
+ for (T entity: entitiesToUpdate){
+ if (entity.getTitleCache() != null){
+ System.err.println(entity.getTitleCache());
+ }else{
+ System.err.println("no titleCache" + ((NonViralName)entity).getNameCache());
+ }
+
+ }
+ saveOrUpdate(entitiesToUpdate);
+ monitor.worked(list.size());
+ if (monitor.isCanceled()){
+ monitor.done();
+ return;
+ }
+ }
+ monitor.done();
+ }
+
+ /**
+ * @param cacheStrategy
+ * @param entitiesToUpdate
+ * @param entity
+ */
+ private void updateTitleCacheForSingleEntity(
+ IIdentifiableEntityCacheStrategy<T> cacheStrategy,
+ List<T> entitiesToUpdate, T entity) {
+ //exclude recursive inreferences
+ if (entity.isInstanceOf(Reference.class)){
+ Reference ref = CdmBase.deproxy(entity, Reference.class);
+ if (ref.getInReference() != null && ref.getInReference().equals(ref)){
+ return;
+ }
+ }
+
+
+ IIdentifiableEntityCacheStrategy entityCacheStrategy = cacheStrategy;
+ if (entityCacheStrategy == null){
+ entityCacheStrategy = entity.getCacheStrategy();
+ //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);
+ entity.setProtectedTitleCache(true);
+ String titleCache = entity.getTitleCache();
+ entity.setProtectedTitleCache(false);
+ String nameCache = null;
+ if (entity instanceof NonViralName ){
+ NonViralName nvn = (NonViralName) entity;
+ if (!nvn.isProtectedNameCache()){
+ nvn.setProtectedNameCache(true);
+ nameCache = nvn.getNameCache();
+ nvn.setProtectedNameCache(false);
+ }
+
+
+ }
+ setOtherCachesNull(entity); //TODO find better solution
+ String newTitleCache = entityCacheStrategy.getTitleCache(entity);
+ if (titleCache == null || titleCache != null && ! titleCache.equals(newTitleCache) ){
+ entity.setTitleCache(null, false);
+ entity.getTitleCache();
+ if (entity instanceof NonViralName){
+ NonViralName nvn = (NonViralName) entity;
+ String newnameCache = nvn.getNameCache();
+ }
+ entitiesToUpdate.add(entity);
+ }else if (entity instanceof NonViralName){
+ NonViralName nvn = (NonViralName) entity;
+ String newnameCache = nvn.getNameCache();
+ if (nameCache == null || (nameCache != null && !nameCache.equals(newnameCache))){
+ entitiesToUpdate.add(entity);
+ }
+ }
+ }
+
+
+
+ /**
+ * Needs override if not only the title cache should be set to null to
+ * generate the correct new title cache
+ */
+ 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;
+ }
+
+ /* (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(propagation = Propagation.SUPPORTS, 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;
+ }
+ if (! ( IMatchable.class.isAssignableFrom(clazz) && IMergable.class.isAssignableFrom(clazz) ) ){
+ logger.warn("Deduplication implemented only for classes implementing IMatchable and IMergeable. No deduplication performed!");
+ return 0;
+ }
+ Class matchableClass = clazz;
+ if (matchStrategy == null){
+ 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()) ;
+// 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);
+ //after each page check if any changes took place
+ int nUnEqualPages = handleAllPages(objectList, dedupState, nextGroup, matchStrategy, mergeStrategy);
+ nUnEqualPages = nUnEqualPages + dedupState.pageSize * dedupState.startPage;
+ //refresh start page counter
+ int finishedPages = nUnEqualPages / dedupState.pageSize;
+ dedupState.startPage = finishedPages;
+ }
+
+ result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
+ return result;
+ }
+
+
+ private int handleAllPages(List<T> objectList, DeduplicateState dedupState, List<T> nextGroup, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
+ int nUnEqual = 0;
+ for (T object : objectList){
+ String currentTitleCache = object.getTitleCache();
+ if (currentTitleCache != null && currentTitleCache.equals(dedupState.lastTitleCache)){
+ //=titleCache
+ nextGroup.add(object);
+ }else{
+ //<> titleCache
+ dedupState.result += handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
+ nextGroup = new ArrayList<T>();
+ nextGroup.add(object);
+ nUnEqual++;
+ }
+ dedupState.lastTitleCache = currentTitleCache;
+ }
+ handleLastGroup(nextGroup, matchStrategy, mergeStrategy);
+ return nUnEqual;
+ }
+
+ private List<T> getPages(Class<? extends T> clazz, DeduplicateState dedupState, List<OrderHint> orderHints) {
+ List<T> result = new ArrayList<T>();
+ for (int pageNo = dedupState.startPage; pageNo < dedupState.startPage + dedupState.nPages; pageNo++){
+ List<T> objectList = listByTitle(clazz, null, null, null, dedupState.pageSize, pageNo, orderHints, null);
+ result.addAll(objectList);
+ }
+ if (result.size()< dedupState.nPages * dedupState.pageSize ){
+ dedupState.isCompleted = true;
+ }
+ return result;
+ }
+
+ private int handleLastGroup(List<T> group, IMatchStrategy matchStrategy, IMergeStrategy mergeStrategy) {
+ int result = 0;
+ int size = group.size();
+ Set<Integer> exclude = new HashSet<Integer>(); //set to collect all objects, that have been merged already
+ for (int i = 0; i < size - 1; i++){
+ if (exclude.contains(i)){
+ continue;
+ }
+ for (int j = i + 1; j < size; j++){
+ if (exclude.contains(j)){
+ continue;
+ }
+ 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);
+ exclude.add(j);
+ result++;
+ }
+ } catch (MatchException e) {
+ logger.warn("MatchException when trying to match " + firstObject.getTitleCache());
+ e.printStackTrace();
+ } catch (MergeException e) {
+ logger.warn("MergeException when trying to merge " + firstObject.getTitleCache());
+ e.printStackTrace();
+ }
+ }
+ }
+ return result;
+ }
+
+ 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)
+ public Integer countByTitle(IIdentifiableEntityServiceConfigurator<T> config){
+ return countByTitle(config.getClazz(), config.getTitleSearchStringSqlized(),
+ config.getMatchMode(), config.getCriteria());
+
+ }
+
}\r
BGBM BDI Projects / cdmlib.git / blobdiff