org.alfresco.repo.node.index.AbstractReindexComponent.java Source code

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/*
 * #%L
 * Alfresco Repository
 * %%
 * Copyright (C) 2005 - 2016 Alfresco Software Limited
 * %%
 * This file is part of the Alfresco software. 
 * If the software was purchased under a paid Alfresco license, the terms of 
 * the paid license agreement will prevail.  Otherwise, the software is 
 * provided under the following open source license terms:
 * 
 * Alfresco is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * Alfresco is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with Alfresco. If not, see <http://www.gnu.org/licenses/>.
 * #L%
 */
package org.alfresco.repo.node.index;

import java.io.PrintWriter;
import java.io.Serializable;
import java.io.StringWriter;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.locks.ReentrantReadWriteLock;
import java.util.concurrent.locks.ReentrantReadWriteLock.WriteLock;

import org.alfresco.error.AlfrescoRuntimeException;
import org.alfresco.model.ContentModel;
import org.alfresco.repo.domain.node.NodeDAO;
import org.alfresco.repo.domain.node.Transaction;
import org.alfresco.repo.search.Indexer;
import org.alfresco.repo.search.impl.lucene.LuceneResultSetRow;
import org.alfresco.repo.search.impl.lucene.fts.FullTextSearchIndexer;
import org.alfresco.repo.security.authentication.AuthenticationComponent;
import org.alfresco.repo.security.authentication.AuthenticationUtil;
import org.alfresco.repo.tenant.TenantService;
import org.alfresco.repo.transaction.AlfrescoTransactionSupport;
import org.alfresco.repo.transaction.AlfrescoTransactionSupport.TxnReadState;
import org.alfresco.repo.transaction.RetryingTransactionHelper.RetryingTransactionCallback;
import org.alfresco.repo.transaction.TransactionListenerAdapter;
import org.alfresco.repo.transaction.TransactionServiceImpl;
import org.alfresco.service.cmr.repository.ChildAssociationRef;
import org.alfresco.service.cmr.repository.InvalidNodeRefException;
import org.alfresco.service.cmr.repository.NodeRef;
import org.alfresco.service.cmr.repository.NodeRef.Status;
import org.alfresco.service.cmr.repository.NodeService;
import org.alfresco.service.cmr.repository.StoreRef;
import org.alfresco.service.cmr.repository.datatype.DefaultTypeConverter;
import org.alfresco.service.cmr.search.ResultSet;
import org.alfresco.service.cmr.search.ResultSetRow;
import org.alfresco.service.cmr.search.SearchParameters;
import org.alfresco.service.cmr.search.SearchService;
import org.alfresco.util.ParameterCheck;
import org.alfresco.util.PropertyCheck;
import org.alfresco.util.SearchLanguageConversion;
import org.alfresco.util.VmShutdownListener;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.lucene.document.Document;
import org.apache.lucene.document.Field;
import org.springframework.dao.ConcurrencyFailureException;

/**
 * Abstract helper for reindexing.
 * 
 * @see #reindexImpl()
 * @see #getIndexerWriteLock()
 * @see #isShuttingDown()
 * 
 * @author Derek Hulley
 */
public abstract class AbstractReindexComponent implements IndexRecovery {
    private static Log logger = LogFactory.getLog(AbstractReindexComponent.class);
    private static Log loggerOnThread = LogFactory.getLog(AbstractReindexComponent.class.getName() + ".threads");

    /** kept to notify the thread that it should quit */
    private static VmShutdownListener vmShutdownListener = new VmShutdownListener("IndexRecovery");

    /** provides transactions to atomically index each missed transaction */
    protected TransactionServiceImpl transactionService;
    /** the component to index the node hierarchy */
    protected Indexer indexer;
    /** the FTS indexer that we will prompt to pick up on any un-indexed text */
    protected FullTextSearchIndexer ftsIndexer;
    /** the component providing searches of the indexed nodes */
    protected SearchService searcher;
    /** the component giving direct access to <b>store</b> instances */
    protected NodeService nodeService;
    /** the component giving direct access to <b>transaction</b> instances */
    protected NodeDAO nodeDAO;
    /** the component that holds the reindex worker threads */
    private ThreadPoolExecutor threadPoolExecutor;

    private TenantService tenantService;
    private Set<String> storeProtocolsToIgnore = new HashSet<String>(7);
    private Set<StoreRef> storesToIgnore = new HashSet<StoreRef>(7);

    private volatile boolean shutdown;
    private final WriteLock indexerWriteLock;

    public AbstractReindexComponent() {
        shutdown = false;
        ReentrantReadWriteLock readWriteLock = new ReentrantReadWriteLock();
        indexerWriteLock = readWriteLock.writeLock();
    }

    /**
     * Convenience method to get a common write lock.  This can be used to avoid
     * concurrent access to the work methods.
     */
    protected WriteLock getIndexerWriteLock() {
        return indexerWriteLock;
    }

    /**
     * Programmatically notify a reindex thread to terminate
     * 
     * @param shutdown true to shutdown, false to reset
     */
    public void setShutdown(boolean shutdown) {
        this.shutdown = shutdown;
    }

    /**
     * 
     * @return Returns true if the VM shutdown hook has been triggered, or the instance
     *      was programmatically {@link #shutdown shut down}
     */
    protected boolean isShuttingDown() {
        return shutdown || vmShutdownListener.isVmShuttingDown();
    }

    /**
     * No longer required
     */
    public void setAuthenticationComponent(AuthenticationComponent authenticationComponent) {
        logger.warn("Bean property 'authenticationComponent' is no longer required on 'AbstractReindexComponent'.");
    }

    /**
     * Set the low-level transaction component to use
     * 
     * @param transactionService provide transactions to index each missed transaction
     */
    public void setTransactionService(TransactionServiceImpl transactionService) {
        this.transactionService = transactionService;
    }

    /**
     * @param indexer the indexer that will be index
     */
    public void setIndexer(Indexer indexer) {
        this.indexer = indexer;
    }

    /**
     * @param ftsIndexer the FTS background indexer
     */
    public void setFtsIndexer(FullTextSearchIndexer ftsIndexer) {
        this.ftsIndexer = ftsIndexer;
    }

    /**
     * @param searcher component providing index searches
     */
    public void setSearcher(SearchService searcher) {
        this.searcher = searcher;
    }

    /**
     * @param nodeService provides information about nodes for indexing
     */
    public void setNodeService(NodeService nodeService) {
        this.nodeService = nodeService;
    }

    /**
     * @param nodeDAO provides access to transaction-related queries
     */
    public void setNodeDAO(NodeDAO nodeDAO) {
        this.nodeDAO = nodeDAO;
    }

    /**
     * Set the thread pool to use when doing asynchronous reindexing.  Use <tt>null</tt>
     * to have the calling thread do the indexing.
     * 
     * @param threadPoolExecutor        a pre-configured thread pool for the reindex work
     * 
     * @since 2.1.4
     */
    public void setThreadPoolExecutor(ThreadPoolExecutor threadPoolExecutor) {
        this.threadPoolExecutor = threadPoolExecutor;
    }

    public void setTenantService(TenantService tenantService) {
        this.tenantService = tenantService;
    }

    /**
     * @param storeProtocolsToIgnore    a list of store protocols that will be ignored
     *                                  by the index check code e.g. 'deleted' in 'deleted://MyStore'
     * @since 3.4
     */
    public void setStoreProtocolsToIgnore(List<String> storeProtocolsToIgnore) {
        for (String storeProtocolToIgnore : storeProtocolsToIgnore) {
            this.storeProtocolsToIgnore.add(storeProtocolToIgnore);
        }
    }

    /**
     * @param storesToIgnore            a list of store references that will be ignored
     *                                  by the index check code e.g. 'test://TestOne'
     */
    public void setStoresToIgnore(List<String> storesToIgnore) {
        for (String storeToIgnore : storesToIgnore) {
            StoreRef storeRef = new StoreRef(storeToIgnore);
            this.storesToIgnore.add(storeRef);
        }
    }

    /**
     * Find out if a store is ignored by the indexing code
     * 
     * @param storeRef                  the store to check
     * @return                          Returns <tt>true</tt> if the store reference provided is not indexed
     */
    public boolean isIgnorableStore(StoreRef storeRef) {
        storeRef = tenantService.getBaseName(storeRef); // Convert to tenant-safe check
        return storesToIgnore.contains(storeRef) || storeProtocolsToIgnore.contains(storeRef.getProtocol());
    }

    /**
     * Determines if calls to {@link #reindexImpl()} should be wrapped in a transaction or not.
     * The default is <b>true</b>.
     * 
     * @return      Returns <tt>true</tt> if an existing transaction is required for reindexing.
     */
    protected boolean requireTransaction() {
        return true;
    }

    /**
     * Perform the actual work.  This method will be called as the system user
     * and within an existing transaction.  This thread will only ever be accessed
     * by a single thread per instance.
     *
     */
    protected abstract void reindexImpl();

    /**
     * To allow for possible 'read committed' behaviour in some databases, where a node that previously existed during a
     * transaction can disappear from existence, we treat InvalidNodeRefExceptions as concurrency conditions.
     */
    protected <T2> T2 doInRetryingTransaction(final RetryingTransactionCallback<T2> callback,
            boolean isReadThrough) {
        return transactionService.getRetryingTransactionHelper()
                .doInTransaction(new RetryingTransactionCallback<T2>() {
                    @Override
                    public T2 execute() throws Throwable {
                        try {
                            return callback.execute();
                        } catch (InvalidNodeRefException e) {
                            // Turn InvalidNodeRefExceptions into retryable exceptions.
                            throw new ConcurrencyFailureException(
                                    "Possible cache integrity issue during reindexing", e);
                        }

                    }
                }, true, isReadThrough);
    }

    /**
     * If this object is currently busy, then it just nothing
     */
    public final void reindex() {
        PropertyCheck.mandatory(this, "ftsIndexer", this.ftsIndexer);
        PropertyCheck.mandatory(this, "indexer", this.indexer);
        PropertyCheck.mandatory(this, "searcher", this.searcher);
        PropertyCheck.mandatory(this, "nodeService", this.nodeService);
        PropertyCheck.mandatory(this, "nodeDaoService", this.nodeDAO);
        PropertyCheck.mandatory(this, "transactionComponent", this.transactionService);
        PropertyCheck.mandatory(this, "storesToIgnore", this.storesToIgnore);
        PropertyCheck.mandatory(this, "storeProtocolsToIgnore", this.storeProtocolsToIgnore);

        if (indexerWriteLock.tryLock()) {
            try {
                // started
                if (logger.isDebugEnabled()) {
                    logger.debug("Reindex work started: " + this);
                }

                AuthenticationUtil.pushAuthentication();
                // authenticate as the system user
                AuthenticationUtil.setRunAsUserSystem();
                RetryingTransactionCallback<Object> reindexWork = new RetryingTransactionCallback<Object>() {
                    public Object execute() throws Exception {
                        reindexImpl();
                        return null;
                    }
                };
                if (requireTransaction()) {
                    doInRetryingTransaction(reindexWork, false);
                } else {
                    reindexWork.execute();
                }
            } catch (Throwable e) {
                throw new AlfrescoRuntimeException("Reindex failure for " + this.getClass().getName(), e);
            } finally {
                try {
                    indexerWriteLock.unlock();
                } catch (Throwable e) {
                }
                AuthenticationUtil.popAuthentication();
            }
            // done
            if (logger.isDebugEnabled()) {
                logger.debug("Reindex work completed: " + this);
            }
        } else {
            if (logger.isDebugEnabled()) {
                logger.debug("Bypassed reindex work - already busy: " + this);
            }
        }
    }

    public enum InIndex {
        YES, NO, INDETERMINATE;
    }

    private static final String KEY_STORE_REFS = "StoreRefCacheMethodInterceptor.StoreRefs";

    @SuppressWarnings("unchecked")
    /**
     * Helper method that caches ADM store references to prevent repeated and unnecessary calls to the
     * NodeService for this list.
     */
    private Set<StoreRef> getAdmStoreRefs() {
        Set<StoreRef> storeRefs = (Set<StoreRef>) AlfrescoTransactionSupport.getResource(KEY_STORE_REFS);
        if (storeRefs != null) {
            return storeRefs;
        } else {
            storeRefs = new HashSet<StoreRef>(nodeService.getStores());
            Iterator<StoreRef> storeRefsIterator = storeRefs.iterator();
            while (storeRefsIterator.hasNext()) {
                // Remove stores to ignore
                StoreRef storeRef = storeRefsIterator.next();
                if (isIgnorableStore(storeRef)) {
                    storeRefsIterator.remove();
                }
            }

            // Bind it in
            AlfrescoTransactionSupport.bindResource(KEY_STORE_REFS, storeRefs);
        }
        return storeRefs;
    }

    /**
     * Determines if a given transaction is definitely in the index or not.
     * 
     * @param txn       a specific transaction
     * @return          Returns <tt>true</tt> if the transaction is definitely in the index
     */
    @SuppressWarnings("unchecked")
    public InIndex isTxnPresentInIndex(final Transaction txn) {
        if (txn == null) {
            return InIndex.YES;
        }

        final Long txnId = txn.getId();
        if (logger.isTraceEnabled()) {
            logger.trace("Checking for transaction in index: " + txnId);
        }

        // Let's scan the changes for this transaction, and group together changes for applicable stores
        List<NodeRef.Status> nodeStatuses = nodeDAO.getTxnChanges(txnId);
        Set<StoreRef> admStoreRefs = getAdmStoreRefs();
        Map<StoreRef, List<NodeRef.Status>> storeStatusMap = new HashMap<StoreRef, List<Status>>(
                admStoreRefs.size() * 2);
        for (NodeRef.Status nodeStatus : nodeStatuses) {
            StoreRef storeRef = nodeStatus.getNodeRef().getStoreRef();
            if (admStoreRefs.contains(storeRef)) {
                List<NodeRef.Status> storeStatuses = storeStatusMap.get(storeRef);
                if (storeStatuses == null) {
                    storeStatuses = new LinkedList<Status>();
                    storeStatusMap.put(storeRef, storeStatuses);
                }
                storeStatuses.add(nodeStatus);
            }
        }

        // Default decision is indeterminate, unless all established to be in index (YES) or one established to be missing (NO)
        InIndex result = InIndex.INDETERMINATE;

        // Check if the txn ID is present in every applicable store's index
        for (Map.Entry<StoreRef, List<NodeRef.Status>> entry : storeStatusMap.entrySet()) {
            List<NodeRef.Status> storeStatuses = entry.getValue();
            if (storeStatuses.isEmpty()) {
                // Nothing to check
                continue;
            }
            StoreRef storeRef = entry.getKey();

            // Establish the number of deletes and updates for this storeRef
            List<NodeRef> deletedNodes = new LinkedList<NodeRef>();
            boolean hasUpdates = false;
            for (NodeRef.Status nodeStatus : storeStatuses) {
                if (nodeStatus.isDeleted()) {
                    deletedNodes.add(nodeStatus.getNodeRef());
                } else {
                    if (!hasUpdates) {
                        Serializable serIsIndexed = nodeService.getProperty(nodeStatus.getNodeRef(),
                                ContentModel.PROP_IS_INDEXED);
                        if (serIsIndexed == null) {
                            hasUpdates = true;
                        } else {
                            Boolean isIndexed = DefaultTypeConverter.INSTANCE.convert(Boolean.class, serIsIndexed);
                            if (isIndexed == null) {
                                hasUpdates = true;
                            } else {
                                if (isIndexed.booleanValue()) {
                                    hasUpdates = true;
                                } else {
                                    // Still do not know if there is anything to check .... 
                                }
                            }
                        }
                    }
                }
            }

            // There were deleted nodes. Check that all the deleted nodes (including containers) were removed from the
            // index - otherwise it is out of date. If all nodes have been removed from the index then the result is that the index is OK
            // ETWOTWO-1387
            // ALF-1989 - even if the nodes have not been found it is no good to use for AUTO index checking
            if (!deletedNodes.isEmpty() && !haveNodesBeenRemovedFromIndex(storeRef, deletedNodes, txn)) {
                result = InIndex.NO;
                break;
            }
            if (hasUpdates) {
                // Check the index
                if (isTxnIdPresentInIndex(storeRef, txn)) {
                    result = InIndex.YES;
                }
                // There were updates, but there is no sign in the indexes
                else {
                    result = InIndex.NO;
                    break;
                }
            }
        }

        // done
        if (logger.isDebugEnabled()) {
            if (result == InIndex.NO) {
                logger.debug("Transaction " + txnId + " not present in indexes");

                logger.debug(nodeStatuses.size() + " nodes in DB transaction");
                for (NodeRef.Status nodeStatus : nodeStatuses) {
                    NodeRef nodeRef = nodeStatus.getNodeRef();
                    if (nodeStatus.isDeleted()) {
                        logger.debug("  DELETED TX " + nodeStatus.getChangeTxnId() + ": " + nodeRef);
                    } else {
                        logger.debug("  UPDATED / MOVED TX " + nodeStatus.getChangeTxnId() + ": " + nodeRef);
                        logger.debug("    " + nodeService.getProperties(nodeRef));
                    }
                    ResultSet results = null;
                    SearchParameters sp = new SearchParameters();
                    sp.setLanguage(SearchService.LANGUAGE_LUCENE);
                    sp.addStore(nodeRef.getStoreRef());
                    try {
                        sp.setQuery("ID:" + SearchLanguageConversion.escapeLuceneQuery(nodeRef.toString()));

                        results = searcher.query(sp);
                        for (ResultSetRow row : results) {
                            StringBuilder builder = new StringBuilder(1024).append("  STILL INDEXED: {");
                            Document lrsDoc = ((LuceneResultSetRow) row).getDocument();
                            Iterator<Field> fields = ((List<Field>) lrsDoc.getFields()).iterator();
                            if (fields.hasNext()) {
                                Field field = fields.next();
                                builder.append(field.name()).append("=").append(field.stringValue());
                                while (fields.hasNext()) {
                                    field = fields.next();
                                    builder.append(", ").append(field.name()).append("=")
                                            .append(field.stringValue());
                                }
                            }
                            builder.append("}");
                            logger.debug(builder.toString());
                        }
                    } finally {
                        if (results != null) {
                            results.close();
                        }
                    }
                    try {
                        sp.setQuery("FTSREF:" + SearchLanguageConversion.escapeLuceneQuery(nodeRef.toString()));

                        results = searcher.query(sp);
                        for (ResultSetRow row : results) {
                            StringBuilder builder = new StringBuilder(1024).append("  FTSREF: {");
                            Document lrsDoc = ((LuceneResultSetRow) row).getDocument();
                            Iterator<Field> fields = ((List<Field>) lrsDoc.getFields()).iterator();
                            if (fields.hasNext()) {
                                Field field = fields.next();
                                builder.append(field.name()).append("=").append(field.stringValue());
                                while (fields.hasNext()) {
                                    field = fields.next();
                                    builder.append(", ").append(field.name()).append("=")
                                            .append(field.stringValue());
                                }
                            }
                            builder.append("}");
                            logger.debug(builder.toString());
                        }
                    } finally {
                        if (results != null) {
                            results.close();
                        }
                    }
                }
            } else {
                if (logger.isTraceEnabled()) {
                    logger.trace("Transaction " + txnId + " present in indexes: " + result);
                }
            }
        }
        return result;
    }

    public InIndex isTxnPresentInIndex(final Transaction txn, final boolean readThrough) {
        return doInRetryingTransaction(new RetryingTransactionCallback<InIndex>() {
            @Override
            public InIndex execute() throws Throwable {
                return isTxnPresentInIndex(txn);
            }
        }, readThrough);
    }

    /**
     * @return                  Returns true if the given transaction is present in the index
     */
    private boolean isTxnIdPresentInIndex(StoreRef storeRef, Transaction txn) {
        long txnId = txn.getId();
        String changeTxnId = txn.getChangeTxnId();
        // do the most update check, which is most common
        ResultSet results = null;
        try {
            SearchParameters sp = new SearchParameters();
            sp.addStore(storeRef);
            // search for it in the index, sorting with youngest first, fetching only 1
            sp.setLanguage(SearchService.LANGUAGE_LUCENE);
            sp.setQuery("TX:" + SearchLanguageConversion.escapeLuceneQuery(changeTxnId));
            sp.setLimit(1);

            results = searcher.query(sp);

            if (results.length() > 0) {
                if (logger.isTraceEnabled()) {
                    logger.trace("Index has results for txn " + txnId + " for store " + storeRef);
                }
                return true; // there were updates/creates and results for the txn were found
            } else {
                if (logger.isTraceEnabled()) {
                    logger.trace("Transaction " + txnId + " not in index for store " + storeRef
                            + ".  Possibly out of date.");
                }
                return false;
            }
        } finally {
            if (results != null) {
                results.close();
            }
        }
    }

    private boolean haveNodesBeenRemovedFromIndex(final StoreRef storeRef, List<NodeRef> nodeRefs,
            final Transaction txn) {
        final Long txnId = txn.getId();
        // there have been deletes, so we have to ensure that none of the nodes deleted are present in the index
        boolean foundNodeRef = false;
        for (NodeRef nodeRef : nodeRefs) {
            if (logger.isTraceEnabled()) {
                logger.trace(

                        "Searching for node in index: \n" + "   node: " + nodeRef + "\n" + "   txn: " + txnId);
            }
            // we know that these are all deletions
            ResultSet results = null;
            try {
                SearchParameters sp = new SearchParameters();
                sp.addStore(storeRef);
                // search for it in the index, sorting with youngest first, fetching only 1
                sp.setLanguage(SearchService.LANGUAGE_LUCENE);
                sp.setQuery("ID:" + SearchLanguageConversion.escapeLuceneQuery(nodeRef.toString()));
                sp.setLimit(1);

                results = searcher.query(sp);

                if (results.length() > 0) {
                    foundNodeRef = true;
                    break;
                }
            } finally {
                if (results != null) {
                    results.close();
                }
            }
        }
        if (foundNodeRef) {
            if (logger.isDebugEnabled()) {
                logger.debug(" --> Node found (Index out of date)");
            }
        } else {
            // No nodes found
            if (logger.isTraceEnabled()) {
                logger.trace(" --> Node not found (OK)");
            }
        }
        return !foundNodeRef;
    }

    /**
     * Marker exception to neatly handle VM-driven termination of a reindex
     * 
     * @author Derek Hulley
     * @since 2.1.4
     */
    public static class ReindexTerminatedException extends RuntimeException {
        private static final long serialVersionUID = -7928720932368892814L;
    }

    /**
     * Callback to notify caller whenever a node has been indexed
     * 
     * @author Derek Hulley
     * @since 2.1.4
     */
    protected interface ReindexNodeCallback {
        void reindexedNode(NodeRef nodeRef);
    }

    protected void reindexTransaction(Long txnId, boolean isFull) {
        reindexTransaction(txnId, null, isFull);
    }

    /**
     * Perform a full reindexing of the given transaction on the current thread.
     * The calling thread must be in the context of a read-only transaction.
     * 
     * @param txnId         the transaction identifier
     * @param callback      the callback to notify of each node indexed
     * 
     * @throws ReindexTerminatedException if the VM is shutdown during the reindex
     */
    protected void reindexTransaction(final long txnId, final ReindexNodeCallback callback, final boolean isFull) {
        ParameterCheck.mandatory("txnId", txnId);
        if (logger.isDebugEnabled()) {
            logger.debug("Reindexing transaction: " + txnId);
        }
        if (AlfrescoTransactionSupport.getTransactionReadState() != TxnReadState.TXN_READ_ONLY) {
            throw new AlfrescoRuntimeException(
                    "Reindex work must be done in the context of a read-only transaction");
        }

        // The indexer will 'read through' to the latest database changes for the rest of this transaction
        indexer.setReadThrough(true);

        // Compile the complete set of transaction changes - we need to 'read through' here too
        final Collection<ChildAssociationRef> deletedNodes = new LinkedList<ChildAssociationRef>();
        final Collection<NodeRef> updatedNodes = new LinkedList<NodeRef>();
        final Collection<ChildAssociationRef> createdNodes = new LinkedList<ChildAssociationRef>();
        final Collection<ChildAssociationRef> deletedParents = new LinkedList<ChildAssociationRef>();
        final Collection<ChildAssociationRef> addedParents = new LinkedList<ChildAssociationRef>();

        doInRetryingTransaction(new RetryingTransactionCallback<Void>() {
            @Override
            public Void execute() throws Throwable {
                // process the node references pertinent to the transaction
                List<NodeRef.Status> nodeStatuses = nodeDAO.getTxnChanges(txnId);
                int nodeCount = 0;
                for (NodeRef.Status nodeStatus : nodeStatuses) {
                    NodeRef nodeRef = nodeStatus.getNodeRef();
                    if (isFull) {
                        if (!nodeStatus.isDeleted()) {
                            createdNodes
                                    .add(new ChildAssociationRef(ContentModel.ASSOC_CHILDREN, null, null, nodeRef));
                        }
                    } else if (nodeStatus.isDeleted()) // node deleted
                    {
                        // only the child node ref is relevant
                        deletedNodes.add(new ChildAssociationRef(ContentModel.ASSOC_CHILDREN, null, null, nodeRef));
                    } else {
                        // Do a DB / index comparision to determine indexing operations required
                        indexer.detectNodeChanges(nodeRef, searcher, addedParents, deletedParents, createdNodes,
                                updatedNodes);
                    }

                    // Check for VM shutdown every 100 nodes
                    if (++nodeCount % 100 == 0 && isShuttingDown()) {
                        // We can't fail gracefully and run the risk of committing a half-baked transaction
                        logger.info("Reindexing of transaction " + txnId + " terminated by VM shutdown.");
                        throw new ReindexTerminatedException();
                    }
                }
                return null;
            }
        }, true);

        int nodeCount = 0;
        for (ChildAssociationRef deletedNode : deletedNodes) {
            if (logger.isDebugEnabled()) {
                logger.debug("DELETE: " + deletedNode.getChildRef());
            }
            indexer.deleteNode(deletedNode);

            // Make the callback
            if (callback != null) {
                callback.reindexedNode(deletedNode.getChildRef());
            }
            // Check for VM shutdown every 100 nodes
            if (++nodeCount % 100 == 0 && isShuttingDown()) {
                // We can't fail gracefully and run the risk of committing a half-baked transaction
                logger.info("Reindexing of transaction " + txnId + " terminated by VM shutdown.");
                throw new ReindexTerminatedException();
            }
        }
        for (NodeRef updatedNode : updatedNodes) {
            if (logger.isDebugEnabled()) {
                logger.debug("UPDATE: " + updatedNode);
            }
            indexer.updateNode(updatedNode);

            // Make the callback
            if (callback != null) {
                callback.reindexedNode(updatedNode);
            }
            // Check for VM shutdown every 100 nodes
            if (++nodeCount % 100 == 0 && isShuttingDown()) {
                // We can't fail gracefully and run the risk of committing a half-baked transaction
                logger.info("Reindexing of transaction " + txnId + " terminated by VM shutdown.");
                throw new ReindexTerminatedException();
            }
        }
        for (ChildAssociationRef createdNode : createdNodes) {
            if (logger.isDebugEnabled()) {
                logger.debug("CREATE: " + createdNode.getChildRef());
            }
            indexer.createNode(createdNode);

            // Make the callback
            if (callback != null) {
                callback.reindexedNode(createdNode.getChildRef());
            }
            // Check for VM shutdown every 100 nodes
            if (++nodeCount % 100 == 0 && isShuttingDown()) {
                // We can't fail gracefully and run the risk of committing a half-baked transaction
                logger.info("Reindexing of transaction " + txnId + " terminated by VM shutdown.");
                throw new ReindexTerminatedException();
            }
        }
        for (ChildAssociationRef deletedParent : deletedParents) {
            if (logger.isDebugEnabled()) {
                logger.debug("UNLINK: " + deletedParent);
            }
            indexer.deleteChildRelationship(deletedParent);

            // Make the callback
            if (callback != null) {
                callback.reindexedNode(deletedParent.getChildRef());
            }
            // Check for VM shutdown every 100 nodes
            if (++nodeCount % 100 == 0 && isShuttingDown()) {
                // We can't fail gracefully and run the risk of committing a half-baked transaction
                logger.info("Reindexing of transaction " + txnId + " terminated by VM shutdown.");
                throw new ReindexTerminatedException();
            }
        }
        for (ChildAssociationRef addedParent : addedParents) {
            if (logger.isDebugEnabled()) {
                logger.debug("LINK: " + addedParents);
            }
            indexer.createChildRelationship(addedParent);

            // Make the callback
            if (callback != null) {
                callback.reindexedNode(addedParent.getChildRef());
            }
            // Check for VM shutdown every 100 nodes
            if (++nodeCount % 100 == 0 && isShuttingDown()) {
                // We can't fail gracefully and run the risk of committing a half-baked transaction
                logger.info("Reindexing of transaction " + txnId + " terminated by VM shutdown.");
                throw new ReindexTerminatedException();
            }
        }
        // done
    }

    private static final AtomicInteger ID_GENERATOR = new AtomicInteger();

    /**
     * Runnable that does reindex work for a given transaction but waits on a queue before
     * triggering the commit phase.
     * <p>
     * This class uses <code>Object</code>'s default equality and hashcode generation.
     * 
     * @author Derek Hulley
     * @since 2.1.4
     */
    private class ReindexWorkerRunnable extends TransactionListenerAdapter
            implements Runnable, ReindexNodeCallback {
        private final int id;
        private final int uidHashCode;
        private final List<Long> txnIds;
        private long lastIndexedTimestamp;
        private boolean atHeadOfQueue;
        private boolean isFull;

        private ReindexWorkerRunnable(List<Long> txnIds, boolean isFull) {
            this.id = ID_GENERATOR.addAndGet(1);
            if (ID_GENERATOR.get() > 1000) {
                ID_GENERATOR.set(0);
            }
            this.uidHashCode = id * 13 + 11;
            this.txnIds = txnIds;
            this.isFull = isFull;
            this.atHeadOfQueue = false;
            recordTimestamp();
        }

        @Override
        public String toString() {
            StringBuilder sb = new StringBuilder(128);
            sb.append("ReindexWorkerRunnable").append("[id=").append(id).append("[txnIds=").append(txnIds)
                    .append("]");
            return sb.toString();
        }

        @Override
        public boolean equals(Object obj) {
            if (!(obj instanceof ReindexWorkerRunnable)) {
                return false;
            }
            ReindexWorkerRunnable that = (ReindexWorkerRunnable) obj;
            return this.id == that.id;
        }

        @Override
        public int hashCode() {
            return uidHashCode;
        }

        /**
         * @return      the time that the last node was indexed (nanoseconds)
         */
        public synchronized long getLastIndexedTimestamp() {
            return lastIndexedTimestamp;
        }

        private synchronized void recordTimestamp() {
            this.lastIndexedTimestamp = System.nanoTime();
        }

        private synchronized boolean isAtHeadOfQueue() {
            return atHeadOfQueue;
        }

        private synchronized void waitForHeadOfQueue() {
            try {
                wait(100L);
            } catch (InterruptedException e) {
            }
        }

        public synchronized void setAtHeadOfQueue() {
            this.notifyAll();
            this.atHeadOfQueue = true;
        }

        public void run() {
            RetryingTransactionCallback<Object> reindexCallback = new RetryingTransactionCallback<Object>() {
                public Object execute() throws Throwable {
                    // The first thing is to ensure that beforeCommit will be called
                    AlfrescoTransactionSupport.bindListener(ReindexWorkerRunnable.this);
                    // Now reindex
                    for (Long txnId : txnIds) {
                        if (loggerOnThread.isDebugEnabled()) {
                            String msg = String.format("   -> Reindexer %5d reindexing %10d", id,
                                    txnId.longValue());
                            loggerOnThread.debug(msg);
                        }
                        reindexTransaction(txnId, ReindexWorkerRunnable.this, isFull);
                    }
                    // Done
                    return null;
                }
            };
            // Timestamp for when we start
            recordTimestamp();
            try {
                if (loggerOnThread.isDebugEnabled()) {
                    int txnIdsSize = txnIds.size();
                    String msg = String.format("Reindexer %5d starting [%10d, %10d] on %s.", id,
                            (txnIdsSize == 0 ? -1 : txnIds.get(0)),
                            (txnIdsSize == 0 ? -1 : txnIds.get(txnIdsSize - 1)), Thread.currentThread().getName());
                    loggerOnThread.debug(msg);
                }
                // Do the work
                doInRetryingTransaction(reindexCallback, true);
            } catch (ReindexTerminatedException e) {
                // This is OK
                String msg = String.format("Reindexer %5d terminated: %s.", id, e.getMessage());
                loggerOnThread.warn(msg);
                loggerOnThread.warn(getStackTrace(e));
            } catch (Throwable e) {
                String msg = String.format("Reindexer %5d failed with error: %s.", id, e.getMessage());
                loggerOnThread.error(msg);
                loggerOnThread.warn(getStackTrace(e));
            } finally {
                // Triple check that we get the queue state right
                removeFromQueueAndProdHead();
            }
        }

        public String getStackTrace(Throwable t) {
            StringWriter sw = new StringWriter();
            PrintWriter pw = new PrintWriter(sw, true);
            t.printStackTrace(pw);
            pw.flush();
            sw.flush();
            return sw.toString();
        }

        public synchronized void reindexedNode(NodeRef nodeRef) {
            recordTimestamp();
        }

        /**
         * Removes this instance from the queue and notifies the HEAD
         */
        private void removeFromQueueAndProdHead() {
            try {
                reindexThreadLock.writeLock().lock();
                // Remove self from head of queue
                reindexThreadQueue.remove(this);
            } finally {
                reindexThreadLock.writeLock().unlock();
            }
            // Now notify the new head object
            ReindexWorkerRunnable newPeek = peekHeadReindexWorker();
            if (newPeek != null) {
                newPeek.setAtHeadOfQueue();
            }
            if (loggerOnThread.isDebugEnabled()) {
                String msg = String.format("Reindexer %5d removed from queue.  Current HEAD is %s.", id, newPeek);
                loggerOnThread.debug(msg);
            }
        }

        @Override
        public void beforeCommit(boolean readOnly) {
            // Do whatever reindexing work we can in parallel before final queue serialization
            indexer.flushPending();

            // Do the queue ordering in the prepare phase so we don't deadlock with throttling!
            handleQueue();
        }

        @Override
        public void afterCommit() {
            // Lucene can now get on with the commit.  We didn't have ordering at this level
            // and the IndexInfo locks are handled by Lucene.  So we let the thread go and
            // the other worker threads can get on with it.
            // Record the fact that the thread is on the final straight.  From here on, no
            // more work notifications will be possible so the timestamp needs to spoof it.
            recordTimestamp();
        }

        @Override
        public void afterRollback() {
            handleQueue();

            // Lucene can now get on with the commit.  We didn't have ordering at this level
            // and the IndexInfo locks are handled by Lucene.  So we let the thread go and
            // the other worker threads can get on with it.
            // Record the fact that the thread is on the final straight.  From here on, no
            // more work notifications will be possible so the timestamp needs to spoof it.
            recordTimestamp();
        }

        /**
         * Lucene will do its final commit once this has been allowed to proceed.
         */
        private void handleQueue() {
            while (true) {
                // Quick check to see if we're at the head of the queue
                ReindexWorkerRunnable peek = peekHeadReindexWorker();
                // Release the current queue head to finish (this might be this instance)
                if (peek != null) {
                    peek.setAtHeadOfQueue();
                }
                // Check kill switch
                if (peek == null || isAtHeadOfQueue()) {
                    // Going to close
                    break;
                } else {
                    // This thread is not at the head of the queue so just wait
                    // until someone notifies us to carry on
                    waitForHeadOfQueue();
                    // Loop again
                }
            }
        }
    }

    /**
     * FIFO queue to control the ordering of transaction commits.  Synchronization around this object is
     * controlled by the read-write lock.
     */
    private LinkedBlockingQueue<ReindexWorkerRunnable> reindexThreadQueue = new LinkedBlockingQueue<ReindexWorkerRunnable>();
    private ReentrantReadWriteLock reindexThreadLock = new ReentrantReadWriteLock(true);

    /**
     * Read-safe method to peek at the head of the queue
     */
    private ReindexWorkerRunnable peekHeadReindexWorker() {
        try {
            reindexThreadLock.readLock().lock();
            return reindexThreadQueue.peek();
        } finally {
            reindexThreadLock.readLock().unlock();
        }
    }

    /**
     * Performs indexing off the current thread, which may return quickly if there are threads immediately
     * available in the thread pool.
     * <p>
     * Commits are guaranteed to occur in the order in which this reindex jobs are added to the queue.
     *
     * @see #reindexTransaction(Long, boolean)
     * @see #waitForAsynchronousReindexing()
     * @since 2.1.4
     */
    protected void reindexTransactionAsynchronously(final List<Long> txnIds, final boolean isFull) {
        // Bypass if there is no thread pool
        if (threadPoolExecutor == null || threadPoolExecutor.getMaximumPoolSize() < 2) {
            if (loggerOnThread.isDebugEnabled()) {
                String msg = String.format("Reindexing inline: %s.", txnIds.toString());
                loggerOnThread.debug(msg);
            }
            RetryingTransactionCallback<Object> reindexCallback = new RetryingTransactionCallback<Object>() {
                public Object execute() throws Throwable {
                    for (Long txnId : txnIds) {
                        if (loggerOnThread.isDebugEnabled()) {
                            String msg = String.format("Reindex %10d.", txnId.longValue());
                            loggerOnThread.debug(msg);
                        }
                        reindexTransaction(txnId, null, isFull);
                    }
                    return null;
                }
            };
            doInRetryingTransaction(reindexCallback, true);
            return;
        }

        ReindexWorkerRunnable runnable = new ReindexWorkerRunnable(txnIds, isFull);
        try {
            reindexThreadLock.writeLock().lock();
            // Add the runnable to the queue to ensure ordering
            reindexThreadQueue.add(runnable);
        } finally {
            reindexThreadLock.writeLock().unlock();
        }
        // Ship it to a thread.
        // We don't do this in the lock - but the situation should be avoided by having the blocking
        // queue size less than the maximum pool size
        threadPoolExecutor.execute(runnable);
    }

    /**
     * Wait for all asynchronous indexing to finish before returning.  This is useful if the calling thread
     * wants to ensure that all reindex work has finished before continuing.
     */
    protected synchronized void waitForAsynchronousReindexing() {
        ReindexWorkerRunnable lastRunnable = null;
        long lastTimestamp = Long.MAX_VALUE;

        ReindexWorkerRunnable currentRunnable = peekHeadReindexWorker();
        while (currentRunnable != null && !isShuttingDown()) {
            // Notify the runnable that it is at the head of the queue
            currentRunnable.setAtHeadOfQueue();
            // Give the thread chance to commit
            synchronized (this) {
                try {
                    wait(100);
                } catch (InterruptedException e) {
                }
            }

            long currentTimestamp = currentRunnable.getLastIndexedTimestamp();
            // The head of the queue holds proceedings, so it can't be allowed to continue forever
            // Allow 60s of inactivity.  We don't anticipate more than a few milliseconds between
            // timestamp advances for the reindex threads so this checking is just for emergencies
            // to prevent the queue from getting locked up.
            if (lastRunnable == currentRunnable) {
                if (currentTimestamp - lastTimestamp > 600E9) {

                    try {
                        reindexThreadLock.writeLock().lock();
                        // Double check
                        ReindexWorkerRunnable checkCurrentRunnable = reindexThreadQueue.peek();
                        if (lastRunnable != checkCurrentRunnable) {
                            // It's moved on - just in time
                        } else {
                            loggerOnThread.warn("Detected reindex thread inactivity: " + currentRunnable);
                            //reindexThreadQueue.remove(currentRunnable);
                            //currentRunnable.kill();
                        }
                        // Reset
                        lastRunnable = null;
                        lastTimestamp = Long.MAX_VALUE;
                        // Peek at the queue and check again
                        currentRunnable = reindexThreadQueue.peek();
                    } finally {
                        reindexThreadLock.writeLock().unlock();
                    }
                    continue;
                }
                // Swap timestamps
                lastRunnable = currentRunnable;
                lastTimestamp = currentTimestamp;
            } else {
                // Swap timestamps
                lastRunnable = currentRunnable;
                lastTimestamp = currentTimestamp;
            }
            currentRunnable = peekHeadReindexWorker();
        }
    }
}