Changing the models that the SearchReindexingListener listens to. NIHVIVO-2076

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ModelContext.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
 import javax.servlet.ServletContext;
 
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.ModelChangedListener;
 
 public class ModelContext {
 	
@@ -75,4 +76,26 @@ public class ModelContext {
 		ctx.setAttribute(INFERENCE_ONT_MODEL, ontModel);
 	}
 	
+	/**
+	 * Register a listener to the models needed to get changes to:
+	 *   class membership
+	 *   inferred class membership
+	 *   class group membership,   
+	 *   object properties,
+	 *   data properties,
+	 *   inferred object properties,
+	 *   rdfs:label annotations
+	 * This listener does not need:
+	 *   other annotations
+	 *   change to TBox  
+	 */
+	public static void registerListenerForChanges(ServletContext ctx, ModelChangedListener ml){
+	    ModelContext.getJenaOntModel(ctx).register(ml);
+        ModelContext.getBaseOntModel(ctx).register(ml);
+        ModelContext.getInferenceOntModel(ctx).register(ml);
+        ModelContext.getUnionOntModelSelector(ctx).getABoxModel().register(ml);
+        ModelContext.getBaseOntModelSelector(ctx).getABoxModel().register(ml);
+        ModelContext.getInferenceOntModelSelector(ctx).getABoxModel().register(ml);
+	}
+	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SearchReindexingListener.java

@@ -2,9 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -34,16 +32,32 @@ public class SearchReindexingListener implements ModelChangedListener {
 
 	private synchronized void addChange(Statement stmt){	    
 		if( stmt == null ) return;
+		if( log.isDebugEnabled() ){
+		    String sub="unknown";
+		    String pred = "unknown";
+		    String obj ="unknown";
+		    
+		    if( stmt.getSubject().isURIResource() ){           
+	            sub =  stmt.getSubject().getURI();
+	        }	                
+		    if( stmt.getPredicate() != null ){
+		        pred = stmt.getPredicate().getURI();
+		    }
+	        if( stmt.getObject().isURIResource() ){          
+	            obj =  ((Resource) (stmt.getPredicate().as(Resource.class))).getURI();
+	        }else{
+	            obj = stmt.getObject().toString();
+	        }
+	        log.debug("changed statement: sub='" + sub + "' pred='" + pred +"' obj='" + obj + "'");
+        }
+		
 		if( stmt.getSubject().isURIResource() ){			
-			//changedUris.add( stmt.getSubject().getURI());
 			indexBuilder.addToChangedUris(stmt.getSubject().getURI());
 			log.debug("subject: " + stmt.getSubject().getURI());
 		}
 				
 		if( stmt.getObject().isURIResource() ){
-			//changedUris.add( ((Resource) stmt.getObject().as(Resource.class)).getURI() );
 			indexBuilder.addToChangedUris(((Resource) stmt.getObject()).getURI());			
-			log.debug("object: " + ((Resource) stmt.getObject().as(Resource.class)).getURI());
 		}	
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassGroupCache.java

@@ -70,12 +70,14 @@ public class VClassGroupCache{
         }
         
         VClassGroupCacheChangeListener bccl = new VClassGroupCacheChangeListener(this);
-        ModelContext.getJenaOntModel(context).register(bccl);
+        ModelContext.registerListenerForChanges(context, bccl);
-        ModelContext.getBaseOntModel(context).register(bccl);
+//        
-        ModelContext.getInferenceOntModel(context).register(bccl);
+//        ModelContext.getJenaOntModel(context).register(bccl);
-        ModelContext.getUnionOntModelSelector(context).getABoxModel().register(bccl);
+//        ModelContext.getBaseOntModel(context).register(bccl);
-        ModelContext.getBaseOntModelSelector(context).getABoxModel().register(bccl);
+//        ModelContext.getInferenceOntModel(context).register(bccl);
-        ModelContext.getInferenceOntModelSelector(context).getABoxModel().register(bccl);
+//        ModelContext.getUnionOntModelSelector(context).getABoxModel().register(bccl);
+//        ModelContext.getBaseOntModelSelector(context).getABoxModel().register(bccl);
+//        ModelContext.getInferenceOntModelSelector(context).getABoxModel().register(bccl);
        
         _rebuildQueue.add(REBUILD_EVERY_PORTAL);
         _cacheRebuildThread = new RebuildGroupCacheThread(this);

webapp/src/edu/cornell/mannlib/vitro/webapp/search/indexing/IndexBuilder.java

@@ -26,38 +26,31 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 
 /**
  * The IndexBuilder is used to rebuild or update a search index.
+ * There should only be one IndexBuilder in a vitro web application.
  * It uses an implementation of a back-end through an object that
  * implements IndexerIface.  An example of a back-end is LuceneIndexer.
  *
  * See the class SearchReindexingListener for an example of how a model change
  * listener can use an IndexBuilder to keep the full text index in sncy with 
- * updates to a model.
+ * updates to a model. It calls IndexBuilder.addToChangedUris().
  *
- * There should be an IndexBuilder in the servlet context, try:
- *
-    IndexBuilder builder = (IndexBuilder)getServletContext().getAttribute(IndexBuilder.class.getName());
-    if( request.getParameter("update") != null )
-        builder.doUpdateIndex();
-
  * @author bdc34
  *
  */
-public class IndexBuilder {
+public class IndexBuilder extends Thread {
     private List<ObjectSourceIface> sourceList = new LinkedList<ObjectSourceIface>();
     private IndexerIface indexer = null;
     private ServletContext context = null;       
     
-    private long lastRun = 0;
+    /* changedUris should only be accessed from synchronized blocks */
-     
     private HashSet<String> changedUris = null;
     
     private List<Individual> updatedInds = null;
     private List<Individual> deletedInds = null;    
     
-    private IndexBuilderThread indexingThread = null;
-    
-    //shared with IndexBuilderThread
     private boolean reindexRequested = false;    
+    protected boolean stopRequested = false;
+    protected long reindexInterval = 1000 * 60 /* msec */ ;        
     
     public static final boolean UPDATE_DOCS = false;
     public static final boolean NEW_DOCS = true;
@@ -67,13 +60,18 @@ public class IndexBuilder {
     public IndexBuilder(ServletContext context,
                 IndexerIface indexer,
                 List /*ObjectSourceIface*/ sources){
+        super("IndexBuilder");
         this.indexer = indexer;
         this.sourceList = sources;
         this.context = context;    
         
         this.changedUris = new HashSet<String>();    
-        this.indexingThread = new IndexBuilderThread(this); 
+        this.start();
-        this.indexingThread.start();
+    }
+    
+    protected IndexBuilder(){
+        //for testing only
+        this( null, null, Collections.emptyList());        
     }
     
     public void addObjectSource(ObjectSourceIface osi) {    	
@@ -89,24 +87,20 @@ public class IndexBuilder {
         return sourceList;
     }
 
-    public void doIndexRebuild() throws IndexingException {
+    public synchronized void doIndexRebuild() throws IndexingException {
-    	//set up full index rebuild
+    	//set flag for full index rebuild
-    	setReindexRequested( true );    	
+    	this.reindexRequested = true; 	
-    	//wake up indexing thread
+    	//wake up     						
-    	synchronized (this.indexingThread) {					
+    	this.notifyAll();    	
-    		this.indexingThread.notifyAll();
-    	}
     }
 
     /** 
      * This will re-index Individuals that changed because of modtime or because they
      * were added with addChangedUris(). 
      */
-    public void doUpdateIndex() {        	    
+    public synchronized void doUpdateIndex() {        	    
-    	//wake up thread
+    	//wake up thread and it will attempt to index anything in changedUris
-    	synchronized (this.indexingThread) {					
+        this.notifyAll();    	    	   
-    		this.indexingThread.notifyAll();
-    	}    	    
     }
    
     public synchronized void addToChangedUris(String uri){
@@ -125,79 +119,47 @@ public class IndexBuilder {
 		return isReindexRequested() || ! changedUris.isEmpty() ;
 	}
 	
-	public void killIndexingThread() {
+	public synchronized void stopIndexingThread() {
-		this.indexingThread.kill();		
+	    stopRequested = true;
+	    this.notifyAll();		
 	}
+	
+    @Override
+    public void run() {
+        while(! stopRequested ){                        
+            try{
+                if( !stopRequested && isReindexRequested() ){
+                    log.debug("full re-index requested");
+                    indexRebuild();
+                }else if( !stopRequested && isThereWorkToDo() ){                       
+                    Thread.sleep(250); //wait a bit to let a bit more work to come into the queue
+                    log.debug("work found for IndexBuilder, starting update");
+                    updatedIndex();
+                }else if( !stopRequested && ! isThereWorkToDo() ){
+                    log.debug("there is no indexing working to do, waiting for work");              
+                    synchronized (this) { this.wait(reindexInterval); }                         
+                }
+            } catch (InterruptedException e) {
+                log.debug("woken up",e);
+            }catch(Throwable e){
+                log.error(e,e);
+            }
+        }
+        log.info("Stopping IndexBuilder thread");
+    }
+
+  
 	/* ******************** non-public methods ************************* */
-	
-	private synchronized void setReindexRequested(boolean reindexRequested) {
-		this.reindexRequested = reindexRequested;
-	}
-	
     private synchronized Collection<String> getAndEmptyChangedUris(){
     	Collection<String> out = changedUris;     	    
     	changedUris = new HashSet<String>();
     	return out;
     }
     
-    protected void indexRebuild() throws IndexingException {    	
-        log.info("Rebuild of search index is starting.");
-
-        Iterator<ObjectSourceIface> sources = sourceList.iterator();
-        List listOfIterators = new LinkedList();
-        while(sources.hasNext()){
-            Object obj = sources.next();
-             if( obj != null && obj instanceof ObjectSourceIface )
-                 listOfIterators.add((((ObjectSourceIface) obj)
-                        .getAllOfThisTypeIterator()));
-             else
-                 log.warn("\tskipping object of class "
-                         + obj.getClass().getName() + "\n"
-                         + "\tIt doesn not implement ObjectSourceIface.\n");
-        }
-        
-        //clear out changed uris since we are doing a full index rebuild
-        getAndEmptyChangedUris();
-        
-        if( listOfIterators.size() == 0){ log.warn("Warning: no ObjectSources found.");}
-                
-        setReindexRequested(false);
-        doBuild( listOfIterators, Collections.EMPTY_LIST, true, NEW_DOCS );
-        log.info("Rebuild of search index is complete.");
-    }
-    
-    protected void updatedIndex() throws IndexingException{
-    	log.debug("Starting updateIndex()");
-		long since = indexer.getModified() - 60000;
-			    		
-	    Iterator<ObjectSourceIface> sources = sourceList.iterator();
-	    
-	    List<Iterator<Individual>> listOfIterators = 
-	        new LinkedList<Iterator<Individual>>();
-	    
-	    while (sources.hasNext()) {
-	        Object obj = sources.next();
-	        if (obj != null && obj instanceof ObjectSourceIface)
-	            listOfIterators.add((((ObjectSourceIface) obj)
-	                    .getUpdatedSinceIterator(since)));
-	        else
-	            log.warn("\tskipping object of class "
-	                    + obj.getClass().getName() + "\n"
-	                    + "\tIt doesn not implement " + "ObjectSourceIface.\n");
-	    }
-	                 
-	    buildAddAndDeleteLists( getAndEmptyChangedUris());                   
-	    listOfIterators.add( (new IndexBuilder.BuilderObjectSource(updatedInds)).getUpdatedSinceIterator(0) );
-	    
-	    doBuild( listOfIterators, deletedInds, false,  UPDATE_DOCS );
-	    log.debug("Ending updateIndex()");
-    }
-    
 	/**
-	 * Sets updatedUris and deletedUris.
+	 * Sets updatedUris and deletedUris lists.
-	 * @param changedUris
 	 */
-	private void buildAddAndDeleteLists( Collection<String> uris){	    
+	private void makeAddAndDeleteLists( Collection<String> uris){	    
 		/* clear updateInds and deletedUris.  This is the only method that should set these. */
 		this.updatedInds = new ArrayList<Individual>();
 		this.deletedInds = new ArrayList<Individual>();
@@ -218,8 +180,160 @@ public class IndexBuilder {
 	    this.updatedInds = addDepResourceClasses(updatedInds);	            	
 	}	
   
+    protected void indexRebuild() throws IndexingException {
+        log.info("Rebuild of search index is starting.");
 
+        Iterator<ObjectSourceIface> sources = sourceList.iterator();
+        List listOfIterators = new LinkedList();
+        while (sources.hasNext()) {
+            Object obj = sources.next();
+            if (obj != null && obj instanceof ObjectSourceIface)
+                listOfIterators.add((((ObjectSourceIface) obj)
+                        .getAllOfThisTypeIterator()));
+            else
+                log.warn("\tskipping object of class "
+                        + obj.getClass().getName() + "\n"
+                        + "\tIt doesn not implement ObjectSourceIface.\n");
+        }
 
+        // clear out changed uris since we are doing a full index rebuild
+        getAndEmptyChangedUris();
+
+        if (listOfIterators.size() == 0) 
+            log.warn("Warning: no ObjectSources found.");        
+
+        doBuild(listOfIterators, Collections.EMPTY_LIST );
+        if( log != null )  //log might be null if system is shutting down.
+            log.info("Rebuild of search index is complete.");
+    }
+      
+    protected void updatedIndex() throws IndexingException{
+        log.debug("Starting updateIndex()");
+        long since = indexer.getModified() - 60000;
+                        
+        Iterator<ObjectSourceIface> sources = sourceList.iterator();        
+        List<Iterator<Individual>> listOfIterators = 
+            new LinkedList<Iterator<Individual>>();
+        
+        while (sources.hasNext()) {
+            Object obj = sources.next();
+            if (obj != null && obj instanceof ObjectSourceIface)
+                listOfIterators.add((((ObjectSourceIface) obj)
+                        .getUpdatedSinceIterator(since)));
+            else
+                log.warn("\tskipping object of class "
+                        + obj.getClass().getName() + "\n"
+                        + "\tIt doesn not implement " + "ObjectSourceIface.\n");
+        }
+                     
+        makeAddAndDeleteLists( getAndEmptyChangedUris());                   
+        listOfIterators.add( (new IndexBuilder.BuilderObjectSource(updatedInds)).getUpdatedSinceIterator(0) );
+        
+        doBuild( listOfIterators, deletedInds );
+        log.debug("Ending updateIndex()");
+    }
+    
+    /**
+     * For each sourceIterator, get all of the objects and attempt to
+     * index them.
+     *
+     * This takes a list of source Iterators and, for each of these,
+     * calls indexForSource.
+     *
+     * @param sourceIterators
+     * @param newDocs true if we know that the document is new. Set
+     * to false if we want to attempt to remove the object from the index before
+     * attempting to index it.  If an object is not on the list but you set this
+     * to false, and a check is made before adding, it will work fine; but
+     * checking if an object is on the index is slow.
+     */
+    private void doBuild(List<Iterator<Individual>> sourceIterators, Collection<Individual> deletes ){
+        boolean aborted = false;
+        boolean newDocs = reindexRequested;
+        boolean forceNewIndex = reindexRequested;
+        
+        try {
+            if( reindexRequested )
+                indexer.prepareForRebuild();
+            
+            indexer.startIndexing();
+            reindexRequested = false;
+            
+            if( ! forceNewIndex ){                
+                for(Individual deleteMe : deletes ){
+                    indexer.removeFromIndex(deleteMe);
+                }
+            }            
+
+            //get an iterator for all of the sources of indexable objects
+            Iterator sourceIters = sourceIterators.iterator();
+            Object obj = null;
+            while (sourceIters.hasNext()) {
+                obj = sourceIters.next();
+                if (obj == null || !(obj instanceof Iterator)) {
+                    log.warn("skipping object of class " + obj.getClass().getName() 
+                            + "It doesn not implement Iterator.");
+                    continue;
+                }
+                indexForSource((Iterator)obj, newDocs);
+            }
+        } catch (AbortIndexing abort){
+            if( log != null)
+                log.debug("aborting the indexing because thread stop was requested");
+            aborted = true;                            
+        } catch (Exception e) {
+            log.error(e,e);
+        }
+        
+        if( aborted && forceNewIndex ){
+            indexer.abortIndexingAndCleanUp();
+        }else{
+            indexer.endIndexing();
+        }
+        
+    }
+    
+    /**
+     * Use the back end indexer to index each object that the Iterator returns.
+     * @throws AbortIndexing 
+     */
+    private void indexForSource(Iterator<Individual> individuals , boolean newDocs) throws AbortIndexing{     
+        long starttime = System.currentTimeMillis();         
+        long count = 0;
+        while(individuals.hasNext()){
+            if( stopRequested )
+                throw new AbortIndexing();
+            
+            Individual ind = null;
+            try{
+                ind = individuals.next();                                
+                indexer.index(ind, newDocs);                         
+            }catch(Throwable ex){
+                if( stopRequested || log == null){//log might be null if system is shutting down.
+                    throw new AbortIndexing();
+                }
+                String uri = ind!=null?ind.getURI():"null";
+                log.warn("Error indexing individual " + uri + " " + ex.getMessage());
+            }
+            count++;
+            if( log.isDebugEnabled() ){            
+                if( (count % 100 ) == 0 && count > 0 ){
+                    long dt = (System.currentTimeMillis() - starttime);
+                    log.debug("individuals indexed: " + count + " in " + dt + " msec " +
+                             " time pre individual = " + (dt / count) + " msec" );                          
+                }                
+            }                
+        }
+        
+        log.info( 
+             "individuals indexed: " + count + " in " + (System.currentTimeMillis() - starttime) + " msec" +
+              (count!=0?(" time per individual = " + (System.currentTimeMillis() - starttime)/ count + " msec"):"")
+        );
+    }        
+    
+    /**
+     * For a list of individuals, this builds a list of dependent resources and returns it.  
+     */
     private List<Individual> addDepResourceClasses(List<Individual> inds) {
         WebappDaoFactory wdf = (WebappDaoFactory)context.getAttribute("webappDaoFactory");
         VClassDao vClassDao = wdf.getVClassDao();
@@ -256,107 +370,12 @@ public class IndexBuilder {
         return inds;
     }    
     
-    /**
+    /* maybe ObjectSourceIface should be replaced with just an iterator. */
-     * For each sourceIterator, get all of the objects and attempt to
-     * index them.
-     *
-     * This takes a list of source Iterators and, for each of these,
-     * calls indexForSource.
-     *
-     * @param sourceIterators
-     * @param newDocs true if we know that the document is new. Set
-     * to false if we want to attempt to remove the object from the index before
-     * attempting to index it.  If an object is not on the list but you set this
-     * to false, and a check is made before adding, it will work fine; but
-     * checking if an object is on the index is slow.
-     */
-    private void doBuild(List sourceIterators, Collection<Individual> deletes, boolean forceNewIndex, boolean newDocs ){
-        try {
-            if( forceNewIndex )
-                indexer.prepareForRebuild();
-            
-            indexer.startIndexing();
-
-            if( ! forceNewIndex ){                
-            	for(Individual deleteMe : deletes ){
-            		indexer.removeFromIndex(deleteMe);
-            	}
-            }            
-
-            //get an iterator for all of the sources of indexable objects
-            Iterator sourceIters = sourceIterators.iterator();
-            Object obj = null;
-            while (sourceIters.hasNext()) {
-                obj = sourceIters.next();
-                if (obj == null || !(obj instanceof Iterator)) {
-                    log.warn("\tskipping object of class "
-                            + obj.getClass().getName() + "\n"
-                            + "\tIt doesn not implement "
-                            + "Iterator.\n");
-                    continue;
-                }
-                indexForSource((Iterator)obj, newDocs);
-            }
-        } catch (IndexingException ex) {
-            log.error(ex,ex);
-        } catch (Exception e) {
-            log.error(e,e);
-        } finally {
-            indexer.endIndexing();
-        }
-    }
-    
-    /**
-     * Use the back end indexer to index each object that the Iterator returns.
-     * @param items
-     * @return
-     */
-    private void indexForSource(Iterator<Individual> individuals , boolean newDocs){
-        if( individuals == null ) return;
-     
-        long starttime = System.currentTimeMillis();         
-        long count = 0;
-        while(individuals.hasNext()){            
-            indexItem(individuals.next(), newDocs);
-            count++;
-            if( log.isDebugEnabled() ){            
-                if( (count % 100 ) == 0 && count > 0 ){
-                    long dt = (System.currentTimeMillis() - starttime);
-                    log.debug("individuals indexed: " + count + " in " + dt + " msec " +
-                             " time pre individual = " + (dt / count) + " msec" );                          
-                }                
-            }                
-        }
-        
-        log.info( 
-             "individuals indexed: " + count + " in " + (System.currentTimeMillis() - starttime) + " msec" +
-        	  (count!=0?(" time per individual = " + (System.currentTimeMillis() - starttime)/ count + " msec"):"")
-        );
-    }
-    
-    /**
-     * Use the backend indexer to index a single item.
-     * @param item
-     * @return
-     */
-    private void indexItem( Individual ind, boolean newDoc){
-        try{
-        	if( ind != null ){        	       
-        		indexer.index(ind, newDoc);
-        	}        	
-        }catch(Throwable ex){            
-            log.warn("IndexBuilder.indexItem() Error indexing "
-                    + ind + "\n" +ex);
-        }
-        return ;
-    } 
-    
     private class BuilderObjectSource implements ObjectSourceIface {
         private final List<Individual> individuals; 
         public BuilderObjectSource( List<Individual>  individuals){
             this.individuals=individuals;
         }        
-		
         public Iterator getAllOfThisTypeIterator() {
             return new Iterator(){
                 final Iterator it = individuals.iterator();
@@ -372,13 +391,10 @@ public class IndexBuilder {
                 public void remove() { /* not implemented */}               
             };
         }        
-		
         public Iterator getUpdatedSinceIterator(long msSinceEpoc) {
             return getAllOfThisTypeIterator();
         }
     }
     
-	
+    private class AbortIndexing extends Exception { }    
-
-
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/indexing/IndexBuilderThread.java

@@ -1,72 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.search.indexing;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * Thread that executes the methods in IndexBuilder.  
- * 
- * @author bdc34
- *
- */
-public class IndexBuilderThread extends Thread{
-	private IndexBuilder indexBuilder;
-	protected boolean stopRequested = false;
-	protected long reindexInterval = 1000 * 60 /* msec */ ;
-	
-	private static final Log log = LogFactory.getLog(IndexBuilderThread.class.getName());
-	
-	public IndexBuilderThread(IndexBuilder ib){
-		super("IndexBuilderThread");
-		if( ib == null )
-		    log.error("IndexBuilderThread needs an IndexBuilder, search is not configured.");
-		this.indexBuilder = ib;
-	}
-	
-	@Override
-	public void run() {
-		while(true){
-			if( stopRequested ){
-				log.info("Stopping IndexBuilderThread ");		
-				return;
-			}
-			
-			if( indexBuilder == null )
-			    log.warn("IndexBuilderThread needs a IndexBuilder, search may not be configured.");
-			
-			try{
-				if( indexBuilder != null && indexBuilder.isReindexRequested() ){
-					log.debug("full re-index requested");
-					indexBuilder.indexRebuild();
-				}else{
-					if( indexBuilder != null && indexBuilder.isThereWorkToDo() ){						
-						Thread.sleep(250); //wait a bit to let a bit more work to come into the queue
-						log.debug("work found for IndexBuilder, starting update");
-						indexBuilder.updatedIndex();
-					}
-				}
-			}catch (Throwable e) {
-				log.error(e,e);
-			}
-			
-			if( indexBuilder != null && ! indexBuilder.isThereWorkToDo() ){
-				log.debug("there is no indexing working to do, going to sleep");
-				try {
-					synchronized (this) {
-						this.wait(reindexInterval);	
-					}			
-				} catch (InterruptedException e) {
-					log.debug(" woken up",e);
-				}
-			}
-		}
-	}
-
-	public synchronized void kill(){
-		log.debug("Attempting to kill IndexBuilderThread ");
-		stopRequested = true;
-		this.notifyAll();
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/search/indexing/IndexerIface.java

@@ -54,4 +54,10 @@ public interface IndexerIface {
     public void endIndexing();
 
     public long getModified();
+    
+    /**
+     * Ends the indexing and removes any temporary files.
+     * This may be called instead of endIndexing()
+     */
+    public void abortIndexingAndCleanUp();
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneIndexer.java

@@ -456,4 +456,21 @@ public class LuceneIndexer implements IndexerIface {
         //if it is clear it out but don't rebuild.
         return false;
     }
+
+    @Override
+    public synchronized void abortIndexingAndCleanUp() {
+        if( ! indexing )
+            log.error("abortIndexingAndCleanUp() should only be called if LuceneIndexer is indexing.");
+        else if( ! fullRebuild )
+            log.error("abortIndexingAndCleanUp() should only be called if LuceneIndexer to end an aborted full index rebuild");
+        else{
+            closeWriter();
+            File offLineDir = new File(currentOffLineDir);
+            boolean deleted = deleteDir(offLineDir);
+            //log might be null if system is shutting down.
+            if( ! deleted ){
+                System.out.println("Could not clean up temp indexing dir " + currentOffLineDir);
+            }
+        }                
+    }    
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneSetup.java

@@ -134,17 +134,12 @@ public class LuceneSetup implements javax.servlet.ServletContextListener {
 			// set up listeners so search index builder is notified of changes to model
 			ServletContext ctx = sce.getServletContext();
 			SearchReindexingListener srl = new SearchReindexingListener(builder);
-			ModelContext.getBaseOntModel(ctx).getBaseModel().register(srl);
+			ModelContext.registerListenerForChanges(ctx, srl);
-			ModelContext.getJenaOntModel(ctx).getBaseModel().register(srl);
-			ModelContext.getInferenceOntModel(ctx).register(srl);
-			ModelContext.getUnionOntModelSelector(ctx).getABoxModel()
-			        .getBaseModel().register(srl);
 									
 			if( (Boolean)sce.getServletContext().getAttribute(INDEX_REBUILD_REQUESTED_AT_STARTUP) instanceof Boolean &&
 				(Boolean)sce.getServletContext().getAttribute(INDEX_REBUILD_REQUESTED_AT_STARTUP) ){
 			    log.info("Rebuild of lucene index required before startup.");
 				builder.doIndexRebuild();												
-				Thread.currentThread().sleep(500);				
 				int n = 0;
 				while( builder.isReindexRequested() || builder.isIndexing() ){
 				    n++;
@@ -169,7 +164,7 @@ public class LuceneSetup implements javax.servlet.ServletContextListener {
 		log.debug("**** Running " + this.getClass().getName() + ".contextDestroyed()");
 		IndexBuilder builder = (IndexBuilder) sce.getServletContext().getAttribute(IndexBuilder.class.getName());
 		if( builder != null){		    		
-		    builder.killIndexingThread();
+		    builder.stopIndexingThread();
 		}
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneSetupCJK.java

@@ -25,8 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilterUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SearchReindexingListener;
-import edu.cornell.mannlib.vitro.webapp.search.beans.Searcher;
 import edu.cornell.mannlib.vitro.webapp.search.indexing.IndexBuilder;
 
 /**
@@ -108,8 +108,7 @@ public class LuceneSetupCJK implements javax.servlet.ServletContextListener {
             OntModel baseOntModel = (OntModel)sce.getServletContext().getAttribute("baseOntModel");
             OntModel jenaOntModel = (OntModel)sce.getServletContext().getAttribute("jenaOntModel");
             SearchReindexingListener srl = new SearchReindexingListener( builder );
-            baseOntModel.getBaseModel().register(srl);
+            ModelContext.registerListenerForChanges(sce.getServletContext(), srl);
-        	jenaOntModel.getBaseModel().register(srl);
         	
             }catch(Exception ex){
                 log.error("Could not setup lucene full text search." , ex);
@@ -125,7 +124,7 @@ public class LuceneSetupCJK implements javax.servlet.ServletContextListener {
         	
             log.info("**** Running "+this.getClass().getName()+".contextDestroyed()");
             IndexBuilder builder = (IndexBuilder)sce.getServletContext().getAttribute(IndexBuilder.class.getName());
-        	builder.killIndexingThread();
+        	builder.stopIndexingThread();
         }
 
         /**

webapp/test/edu/cornell/mannlib/vitro/webapp/search/indexing/IndexBuilderThreadTest.java

@@ -14,20 +14,24 @@ public class IndexBuilderThreadTest extends AbstractTestClass {
 	
 	@Test
 	public void testStoppingTheThread(){	 
-		setLoggerLevel(IndexBuilderThread.class, Level.OFF);
+	    setLoggerLevel(IndexBuilder.class, Level.OFF);
-		IndexBuilderThread ibt = new IndexBuilderThread(null);
+	    
-		ibt.start();
+		IndexBuilder ib = new IndexBuilder();		
+		Assert.assertNotSame(Thread.State.NEW, ib.getState() );
+		Assert.assertNotSame(Thread.State.TERMINATED, ib.getState() );
+		
 		try {
 			Thread.sleep(100);
 		} catch (InterruptedException e) {
 			Assert.fail(e.getMessage());
 		}
-		ibt.kill();
+		ib.stopIndexingThread();
 		try {
 			Thread.sleep(100);
 		} catch (InterruptedException e) {
 			Assert.fail(e.getMessage());
 		}
-		Assert.assertFalse(ibt.isAlive());
+		Assert.assertFalse(ib.isAlive());
+		Assert.assertSame(Thread.State.TERMINATED, ib.getState() );
 	}
 }