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/**
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* Copyright (C) 2011 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service.search;
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import java.io.IOException;
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import java.lang.management.ManagementFactory;
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import java.lang.management.MemoryMXBean;
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import java.lang.management.MemoryUsage;
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import java.lang.reflect.Field;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.apache.lucene.index.IndexReader;
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import org.apache.lucene.index.IndexWriterConfig;
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import org.apache.lucene.search.spell.Dictionary;
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import org.apache.lucene.search.spell.LuceneDictionary;
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import org.apache.lucene.search.spell.SpellChecker;
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import org.apache.lucene.store.Directory;
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import org.hibernate.CacheMode;
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import org.hibernate.FlushMode;
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import org.hibernate.ObjectNotFoundException;
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import org.hibernate.ScrollMode;
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import org.hibernate.ScrollableResults;
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import org.hibernate.Session;
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import org.hibernate.search.FullTextSession;
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import org.hibernate.search.Search;
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import org.hibernate.search.SearchFactory;
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import org.hibernate.search.batchindexing.MassIndexerProgressMonitor;
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import org.hibernate.search.indexes.spi.DirectoryBasedIndexManager;
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import org.hibernate.search.indexes.spi.IndexManager;
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import org.hibernate.search.spi.SearchIntegrator;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.orm.hibernate5.HibernateTransactionManager;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.NullProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.RestServiceProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.SubProgressMonitor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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/**
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* @author Andreas Kohlbecker
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* @date Dec 15, 2011
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*
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*/
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@Component
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@Transactional
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public class CdmMassIndexer implements ICdmMassIndexer {
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private final Set<Class<? extends CdmBase>> indexedClasses = new HashSet<Class<? extends CdmBase>>();
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public static final Logger logger = Logger.getLogger(CdmMassIndexer.class);
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/*
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* flag to enable old hibernate search 3.1 mode
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*/
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private static final boolean HS_31_MODE = false;
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public HibernateTransactionManager transactionManager;
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@Autowired
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public void setTransactionManager(PlatformTransactionManager transactionManager) {
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this.transactionManager = (HibernateTransactionManager)transactionManager;
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}
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protected Session getSession(){
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Session session = transactionManager.getSessionFactory().getCurrentSession();
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return session;
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}
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/**
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* reindex method based on hibernate search 3.1
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*
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* @param type
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* @param monitor
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*/
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protected <T extends CdmBase>void reindex_31(Class<T> type, IProgressMonitor monitor) {
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//TODO set the application in maintenance mode: making
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// queries to the index is not recommended when a MassIndexer is busy.
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// fullTextSession.createIndexer().startAndWait();
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FullTextSession fullTextSession = Search.getFullTextSession(getSession());
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fullTextSession.setFlushMode(FlushMode.MANUAL);
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fullTextSession.setCacheMode(CacheMode.IGNORE);
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logger.info("start indexing " + type.getName());
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monitor.subTask("indexing " + type.getSimpleName());
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Long countResult = countEntities(type);
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int batchSize = sweetestBatchSize(type);
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int numOfBatches = calculateNumOfBatches(countResult, batchSize);
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SubProgressMonitor subMonitor = new SubProgressMonitor(monitor, 1);
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subMonitor.beginTask("Indexing " + type.getSimpleName(), numOfBatches);
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// Scrollable results will avoid loading too many objects in memory
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ScrollableResults results = fullTextSession.createCriteria(type).setFetchSize(batchSize).scroll(ScrollMode.FORWARD_ONLY);
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long index = 0;
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int batchesWorked = 0;
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try {
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while (results.next()) {
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index++;
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fullTextSession.index(results.get(0)); // index each element
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if (index % batchSize == 0 || index == countResult) {
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batchesWorked++;
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try {
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fullTextSession.flushToIndexes(); // apply changes to indexes
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} catch(ObjectNotFoundException e){
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// TODO report this issue to progress monitor once it can report on errors
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logger.error("possibly invalid data, thus skipping this batch and continuing with next one", e);
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} finally {
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fullTextSession.clear(); // clear since the queue is processed
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getSession().clear(); // clear session to free memory
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subMonitor.worked(1);
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logger.info("\tbatch " + batchesWorked + "/" + numOfBatches + " processed");
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}
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}
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}
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} catch (RuntimeException e) {
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//TODO better means to notify that the process has been stopped, using the STOPPED_WORK_INDICATOR is only a hack
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monitor.worked(RestServiceProgressMonitor.STOPPED_WORK_INDICATOR);
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monitor.done();
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throw e;
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}
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logger.info("end indexing " + type.getName());
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subMonitor.done();
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}
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/**
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*
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*
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* @param type
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* @param monitor
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*/
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protected <T extends CdmBase> void createDictionary(Class<T> type, IProgressMonitor monitor) {
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String indexName = null;
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if(type.isAnnotationPresent(org.hibernate.search.annotations.Indexed.class)) {
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indexName = type.getAnnotation(org.hibernate.search.annotations.Indexed.class).index();
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} else {
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//TODO:give some indication that this class is infact not indexed
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return;
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}
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SearchFactory searchFactory = Search.getFullTextSession(getSession()).getSearchFactory();
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IndexManager indexManager = obtainIndexManager(searchFactory, indexName);
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IndexReader indexReader = searchFactory.getIndexReaderAccessor().open(type);
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List<String> idFields = getIndexedDeclaredFields(type);
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monitor.subTask("creating dictionary " + type.getSimpleName());
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SubProgressMonitor subMonitor = new SubProgressMonitor(monitor, 1);
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subMonitor.beginTask("Creating dictionary " + type.getSimpleName(), 1);
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Directory directory = ((DirectoryBasedIndexManager) indexManager).getDirectoryProvider().getDirectory();
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SpellChecker spellChecker = null;
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try {
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spellChecker = new SpellChecker(directory);
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Iterator<String> itr = idFields.iterator();
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while(itr.hasNext()) {
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String indexedField = itr.next();
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logger.info("creating dictionary for field " + indexedField);
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Dictionary dictionary = new LuceneDictionary(indexReader, indexedField);
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IndexWriterConfig iwc = new IndexWriterConfig(searchFactory.getAnalyzer(type));
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spellChecker.indexDictionary(dictionary, iwc, true);
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}
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subMonitor.internalWorked(1);
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} catch (IOException e) {
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logger.error("IOException when creating dictionary", e);
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//TODO better means to notify that the process has been stopped, using the STOPPED_WORK_INDICATOR is only a hack
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monitor.worked(RestServiceProgressMonitor.STOPPED_WORK_INDICATOR);
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monitor.done();
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} catch (RuntimeException e) {
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logger.error("RuntimeException when creating dictionary", e);
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//TODO better means to notify that the process has been stopped, using the STOPPED_WORK_INDICATOR is only a hack
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monitor.worked(RestServiceProgressMonitor.STOPPED_WORK_INDICATOR);
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monitor.done();
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} finally {
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searchFactory.getIndexReaderAccessor().close(indexReader);
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}
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if (spellChecker != null) {
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try {
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logger.info("closing spellchecker ");
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spellChecker.close();
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} catch (IOException e) {
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logger.error("IOException when closing spellchecker", e);
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}
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}
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logger.info("end creating dictionary " + type.getName());
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subMonitor.done();
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}
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private IndexManager obtainIndexManager(SearchFactory searchFactory, String indexName){
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SearchIntegrator searchIntegrator = searchFactory.unwrap(SearchIntegrator.class );
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IndexManager indexManager = searchIntegrator.getIndexManager(indexName);
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return indexManager;
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}
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private int sweetestBatchSize(Class<? extends CdmBase> type){
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Runtime.getRuntime().gc();
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long freeMemoryMB;
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MemoryMXBean memoryMXBean = ManagementFactory.getMemoryMXBean();
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if(memoryMXBean != null){
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logger.debug("NonHeapMemoryUsage: "+memoryMXBean.getHeapMemoryUsage());
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MemoryUsage memusage = memoryMXBean.getHeapMemoryUsage();
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freeMemoryMB =( memusage.getMax() - memusage.getUsed()) / (1024 * 1024);
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} else {
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// will be smaller than the actual free mem since Runtime does not
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// know about Committed heap mem
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freeMemoryMB = Runtime.getRuntime().freeMemory() / (1024 * 1024);
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}
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// TODO check for min free:
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// < 600MB => ERROR may fail with out of memory
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// < 750MB => WARNING may be slow
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if(freeMemoryMB < 600) {
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logger.error("The available free heap space appears to be too small (<600MB), the mass indexer may run out of memory!");
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}
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if(freeMemoryMB < 750) {
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logger.warn("The available free heap space appears to be small (<750MB), the mass indexer could be slow!");
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}
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double factor = 0.769; // default
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if(DescriptionElementBase.class.isAssignableFrom(type)) {
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factor = 0.025;
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}
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int batchSize = (int) Math.floor( factor * freeMemoryMB);
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logger.info("calculated batch size sweet spot for indexing " + type.getSimpleName()
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+ " with " + freeMemoryMB + "MB free mem is " + batchSize);
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return batchSize;
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}
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/**
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* @param countResult
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* @return
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*/
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private int calculateNumOfBatches(Long countResult, int batchSize) {
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Long numOfBatches = countResult > 0 ? ((countResult-1)/batchSize)+1 : 0;
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return numOfBatches.intValue();
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}
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/**
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* @param type
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* @return
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*/
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private <T> Long countEntities(Class<T> type) {
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Object countResultObj = getSession().createQuery("select count(*) from " + type.getName()).uniqueResult();
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Long countResult = (Long)countResultObj;
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return countResult;
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}
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protected <T extends CdmBase>void purge(Class<T> type, IProgressMonitor monitor) {
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FullTextSession fullTextSession = Search.getFullTextSession(getSession());
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logger.info("purging " + type.getName());
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fullTextSession.purgeAll(type);
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// TODO
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// toggle on/off flag doSpellIndex introduced for debugging, see ticket:
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// #3721 (CdmMassIndexer.purge throwing errors due to LockObtainFailedException)
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// remove once this is fixed
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boolean doSpellIndex = false;
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if(doSpellIndex){
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SearchFactory searchFactory = fullTextSession.getSearchFactory();
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IndexManager indexManager = obtainIndexManager(searchFactory, type.getName());
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if(indexManager == null){
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logger.info("No IndexManager found for " + type.getName() + ", thus nothing to purge");
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return;
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}
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Directory directory = ((DirectoryBasedIndexManager) indexManager).getDirectoryProvider().getDirectory();
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SpellChecker spellChecker = null;
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try {
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spellChecker = new SpellChecker(directory);
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spellChecker.clearIndex();
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} catch (IOException e) {
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logger.error("IOException when creating dictionary", e);
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//TODO better means to notify that the process has been stopped, using the STOPPED_WORK_INDICATOR is only a hack
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monitor.worked(RestServiceProgressMonitor.STOPPED_WORK_INDICATOR);
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monitor.done();
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}
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if (spellChecker != null) {
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try {
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logger.info("closing spellchecker ");
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spellChecker.close();
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} catch (IOException e) {
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logger.error("IOException when closing spellchecker", e);
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}
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}
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}
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}
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320
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321
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@Override
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public void reindex(Collection<Class<? extends CdmBase>> types, IProgressMonitor monitor){
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323
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324
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if(monitor == null){
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monitor = new NullProgressMonitor();
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}
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327
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if(types == null){
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types = indexedClasses();
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}
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330
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331
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if(HS_31_MODE) {
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332
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333
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}
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334
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335
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monitor.setTaskName("CdmMassIndexer");
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336
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int steps = types.size() + (HS_31_MODE ? 1 /* +1 for optimize */ : 0);
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monitor.beginTask("Reindexing " + types.size() + " classes", steps);
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338
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339
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boolean optimize = true;
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340
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341
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long start = System.currentTimeMillis();
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342
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for(Class<? extends CdmBase> type : types){
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343
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long perTypeStart = System.currentTimeMillis();
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344
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345
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if(HS_31_MODE) {
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346
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// TODO remove this mode and all related code once the old reindex method is vanished
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347
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reindex_31(type, monitor);
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348
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} else {
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349
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reindex_55(type, monitor);
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350
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optimize = false;
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351
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}
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352
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353
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354
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logger.info("Indexing of " + type.getSimpleName() + " in " + ((System.currentTimeMillis() - perTypeStart) / 1000) + "s");
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355
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}
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356
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357
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if(HS_31_MODE) {
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358
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monitor.subTask("Optimizing Index");
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359
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SubProgressMonitor subMonitor = new SubProgressMonitor(monitor, 1);
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360
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subMonitor.beginTask("Optimizing Index",1);
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361
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optimize();
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362
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logger.info("end index optimization");
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363
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subMonitor.worked(1);
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subMonitor.done();
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365
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}
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366
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logger.info("reindexing completed in " + ((System.currentTimeMillis() - start) / 1000) + "s");
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367
|
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368
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//monitor.worked(1);
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369
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monitor.done();
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370
|
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371
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}
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372
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|
373
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/**
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374
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* new reindex method which benefits from
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375
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* the mass indexer available in hibernate search 5.5
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376
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*
|
377
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* @param type
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378
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* @param monitor
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379
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* @throws InterruptedException
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380
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*/
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381
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protected void reindex_55(Class<? extends CdmBase> type, IProgressMonitor monitor) {
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382
|
|
383
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FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
384
|
|
385
|
|
386
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logger.info("start indexing " + type.getName());
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387
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monitor.subTask("indexing " + type.getSimpleName());
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388
|
|
389
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Long countResult = countEntities(type);
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390
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int batchSize = sweetestBatchSize(type);
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391
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int numOfBatches = calculateNumOfBatches(countResult * 2, batchSize); // each entity is worked two times 1. document added, 2. document build
|
392
|
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393
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SubProgressMonitor subMonitor = new SubProgressMonitor(monitor, 1);
|
394
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subMonitor.beginTask("Indexing " + type.getSimpleName(), numOfBatches);
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395
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|
396
|
|
397
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MassIndexerProgressMonitor indexerMonitorWrapper = new MassIndexerProgressMonitorWrapper(subMonitor, batchSize);
|
398
|
|
399
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try {
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400
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fullTextSession
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401
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.createIndexer(type)
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402
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.batchSizeToLoadObjects(batchSize)
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403
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.cacheMode(CacheMode.IGNORE)
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404
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.threadsToLoadObjects(4) // optimize http://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/#search-batchindexing-threadsandconnections
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405
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.idFetchSize(150) //TODO optimize
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406
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.progressMonitor(indexerMonitorWrapper)
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407
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.startAndWait();
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408
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} catch (InterruptedException ie) {
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409
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logger.info("Mass indexer has been interrupted");
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410
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subMonitor.isCanceled();
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411
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}
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412
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}
|
413
|
|
414
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@Override
|
415
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public void createDictionary(IProgressMonitor monitor) {
|
416
|
if(monitor == null){
|
417
|
monitor = new NullProgressMonitor();
|
418
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}
|
419
|
|
420
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monitor.setTaskName("CdmMassIndexer_Dictionary");
|
421
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int steps = dictionaryClasses().length; // +1 for optimize
|
422
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monitor.beginTask("Creating Dictionary " + dictionaryClasses().length + " classes", steps);
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423
|
|
424
|
for(Class type : dictionaryClasses()){
|
425
|
createDictionary(type, monitor);
|
426
|
}
|
427
|
|
428
|
monitor.done();
|
429
|
|
430
|
}
|
431
|
protected void optimize() {
|
432
|
|
433
|
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
434
|
fullTextSession.getSearchFactory().optimize();
|
435
|
fullTextSession.flushToIndexes();
|
436
|
fullTextSession.clear();
|
437
|
}
|
438
|
|
439
|
@Override
|
440
|
public void purge(IProgressMonitor monitor){
|
441
|
|
442
|
if(monitor == null){
|
443
|
monitor = new NullProgressMonitor();
|
444
|
}
|
445
|
|
446
|
monitor.setTaskName("CdmMassIndexer");
|
447
|
int steps = indexedClasses().size() + 1; // +1 for optimize
|
448
|
monitor.beginTask("Purging " + indexedClasses().size() + " classes", steps);
|
449
|
|
450
|
for(Class<? extends CdmBase> type : indexedClasses()){
|
451
|
purge(type, monitor);
|
452
|
monitor.worked(1);
|
453
|
}
|
454
|
// need to flush to the index before optimizing
|
455
|
// the purge method is not doing the flushing by itself
|
456
|
FullTextSession fullTextSession = Search.getFullTextSession(getSession());
|
457
|
fullTextSession.flushToIndexes();
|
458
|
|
459
|
// optimize
|
460
|
optimize();
|
461
|
monitor.worked(1);
|
462
|
|
463
|
// done
|
464
|
monitor.done();
|
465
|
}
|
466
|
|
467
|
|
468
|
/**
|
469
|
* Returns a list of declared indexable fields within a class through reflection.
|
470
|
*
|
471
|
* @param clazz
|
472
|
* @return
|
473
|
*/
|
474
|
private List<String> getIndexedDeclaredFields(Class clazz) {
|
475
|
List<String> idFields = new ArrayList<String>();
|
476
|
if(clazz.isAnnotationPresent(org.hibernate.search.annotations.Indexed.class)) {
|
477
|
Field[] declaredFields = clazz.getDeclaredFields();
|
478
|
for(int i=0;i<declaredFields.length;i++ ) {
|
479
|
logger.info("checking field " + declaredFields[i].getName());
|
480
|
if(declaredFields[i].isAnnotationPresent(org.hibernate.search.annotations.Field.class) ||
|
481
|
declaredFields[i].isAnnotationPresent(org.hibernate.search.annotations.Fields.class)) {
|
482
|
idFields.add(declaredFields[i].getName());
|
483
|
logger.info("adding field " + declaredFields[i].getName());
|
484
|
}
|
485
|
}
|
486
|
}
|
487
|
return idFields;
|
488
|
}
|
489
|
/**
|
490
|
* @return
|
491
|
*/
|
492
|
@Override
|
493
|
public Set<Class<? extends CdmBase>> indexedClasses() {
|
494
|
// if no indexed classes have been 'manually' set then
|
495
|
// the default is the full list
|
496
|
if(indexedClasses.size() == 0) {
|
497
|
indexedClasses.add(DescriptionElementBase.class);
|
498
|
indexedClasses.add(TaxonBase.class);
|
499
|
indexedClasses.add(Classification.class);
|
500
|
indexedClasses.add(TaxonName.class);
|
501
|
indexedClasses.add(SpecimenOrObservationBase.class);
|
502
|
indexedClasses.add(TaxonRelationship.class);
|
503
|
}
|
504
|
return indexedClasses;
|
505
|
}
|
506
|
|
507
|
/**
|
508
|
* @return
|
509
|
*/
|
510
|
@Override
|
511
|
public Class[] dictionaryClasses() {
|
512
|
return new Class[] {
|
513
|
TaxonName.class
|
514
|
};
|
515
|
}
|
516
|
|
517
|
}
|