working on memory leak NIHVIVO-2782

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

@@ -13,6 +13,7 @@ import org.apache.commons.logging.LogFactory;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.rdf.model.Model;
@@ -74,9 +75,12 @@ public class ObjectPropertyStatementDaoSDB extends
         	DatasetWrapper w = dwf.getDatasetWrapper();
         	Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);
+        	QueryExecution qexec = null;
         	try {
-        		m = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
+        		qexec = QueryExecutionFactory.create(QueryFactory.create(query), dataset);
+        		m = qexec.execConstruct();
         	} finally {
+        	    if(qexec != null) qexec.close();
         		dataset.getLock().leaveCriticalSection();
         		w.close();
         	}

webapp/src/edu/cornell/mannlib/vitro/webapp/filters/VitroRequestPrep.java

@@ -133,6 +133,11 @@ public class VitroRequestPrep implements Filter {
     	//This will replace the WebappDaoFactory with a different version if menu management parameter is found
     	wdf = checkForSpecialWDF(vreq, wdf);
     	
+    	// request.setAttribute("aboxModel", setspeicalABoxModel)
+    	// request.setAttribute("tboxModel", speicalTboxModel)
+    	// request.setAttribute("infModel", speicalInfModel) (maybe?)
+    	// request.setAttribute("displayModel", displayModel) 
+    	
         VitroFilters filters = null;
 		        
         filters = getFiltersFromContextFilterFactory(req, wdf);

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

@@ -146,6 +146,7 @@ public class IndexBuilder extends Thread {
             }
         }
         
+        indexer.abortIndexingAndCleanUp();
         
         if(log != null )//may be null on shutdown 
             log.info("Stopping IndexBuilder thread");

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/CalculateParameters.java

@@ -36,6 +36,7 @@ import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
 
 public class CalculateParameters implements DocumentModifier {
 
+    private boolean shutdown = false;
 	private Dataset dataset;
     public static int totalInd=1;
     protected Map<String,Float> betaMap = new Hashtable<String,Float>();
@@ -91,10 +92,10 @@ public class CalculateParameters implements DocumentModifier {
 		Resource uriResource = ResourceFactory.createResource(uri);
 		initialBinding.add("uri", uriResource);
 		dataset.getLock().enterCriticalSection(Lock.READ);		
-
+		QueryExecution qexec=null;
 		try{
 			query = QueryFactory.create(betaQuery,Syntax.syntaxARQ);
-			QueryExecution qexec = QueryExecutionFactory.create(query,dataset,initialBinding);
+			qexec = QueryExecutionFactory.create(query,dataset,initialBinding);
 			ResultSet results = qexec.execSelect();
 			List<String> resultVars = results.getResultVars();
 			if(resultVars!=null && resultVars.size()!=0){
@@ -102,8 +103,11 @@ public class CalculateParameters implements DocumentModifier {
 				Conn = Integer.parseInt(soln.getLiteral(resultVars.get(0)).getLexicalForm());
 			}
 		}catch(Throwable t){
-			log.error(t,t);
+		    if( ! shutdown )
+		        log.error(t,t);
 		}finally{
+		    if( qexec != null ) 
+		        qexec.close();		    
 			dataset.getLock().leaveCriticalSection();
 		}
 
@@ -238,7 +242,8 @@ public class CalculateParameters implements DocumentModifier {
     						}	
     					}
     			}catch(Exception e){
-    				log.error("Error found in getAdjacentNodes method of SearchQueryHandler");
+    			    if( ! shutdown )
+    			        log.error("Error found in getAdjacentNodes method of SearchQueryHandler");
     			}finally{
     				qexec.close();
     			}	
@@ -260,7 +265,8 @@ public class CalculateParameters implements DocumentModifier {
     		
     	}
     	catch(Throwable t){
-    		log.error(t,t);
+    	    if( ! shutdown )
+    	        log.error(t,t);
     	}finally{
     		dataset.getLock().leaveCriticalSection();
     		adjacentNodes = null;
@@ -285,16 +291,19 @@ public class CalculateParameters implements DocumentModifier {
         
         for(String term: fieldsToAddBetaTo){
             SolrInputField f = doc.getField( term );
-            f.setBoost( getBeta(uri) + phi + IndividualToSolrDocument.NAME_BOOST);
+            float orgBoost = f.getBoost();
+            f.setBoost( getBeta(uri) + phi + orgBoost );
         }
         
         for(String term: fieldsToMultiplyBetaBy){
             SolrInputField f = doc.getField( term );
-            f.addValue(info.toString(),getBeta(uri)*phi*IndividualToSolrDocument.ALL_TEXT_BOOST);
+            //f.addValue(info.toString(),getBeta(uri)*phi*IndividualToSolrDocument.ALL_TEXT_BOOST);
         }
         
-        SolrInputField f = doc.getField(VitroSearchTermNames.targetInfo);
+
-        f.addValue(adjInfo[1],f.getBoost());
+        //SolrInputField f = doc.getField(VitroSearchTermNames.targetInfo);
+        //f.addValue(adjInfo[1],f.getBoost());
+
         doc.setDocumentBoost(getBeta(uri)*phi*IndividualToSolrDocument.ALL_TEXT_BOOST);           
 
         log.debug("Parameter calculation is done");
@@ -304,6 +313,9 @@ public class CalculateParameters implements DocumentModifier {
 		betaMap.clear();
 	}
 	
+	public void shutdown(){
+        shutdown=true;
+    }
 }
 
 class TotalInd implements Runnable{
@@ -321,10 +333,11 @@ class TotalInd implements Runnable{
 	        Query query;
 	    	QuerySolution soln = null;
 			dataset.getLock().enterCriticalSection(Lock.READ);
+			QueryExecution qexec = null;
 			
 			try{
 				query = QueryFactory.create(totalCountQuery,Syntax.syntaxARQ);
-				QueryExecution qexec = QueryExecutionFactory.create(query,dataset);
+				qexec = QueryExecutionFactory.create(query,dataset);
 				ResultSet results = qexec.execSelect();
 				List<String> resultVars = results.getResultVars();
 				
@@ -337,8 +350,12 @@ class TotalInd implements Runnable{
 			}catch(Throwable t){
 				log.error(t,t);
 			}finally{
+			    if( qexec != null ) 
+			        qexec.close();
 				dataset.getLock().leaveCriticalSection();
 			}
 		
 	}
+	
+	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/ContextNodeFields.java

@@ -35,6 +35,7 @@ import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
 public class ContextNodeFields implements DocumentModifier{
     private Model model;
     
+    private boolean shutdown = false;
     private static ExecutorService threadPool = null;
     private static final int THREAD_POOL_SIZE = 10;	 
     
@@ -134,7 +135,8 @@ public class ContextNodeFields implements DocumentModifier{
                     }
                 }
             }catch(Throwable t){
-                log.error(t,t);
+                if( ! shutdown )
+                    log.error(t,t);
             } finally{
                 qExec.close();
             } 
@@ -437,4 +439,7 @@ public class ContextNodeFields implements DocumentModifier{
         }	    
 	}
 
+	public void shutdown(){
+	    shutdown=true;	
+	}
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/DocumentModifier.java

@@ -12,4 +12,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 public interface DocumentModifier {
     public void modifyDocument(Individual individual, SolrInputDocument doc, StringBuffer addUri);
     
+    //called to inform the DocumentModifier that the system is shutting down
+    public void shutdown();
+   
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/IndividualToSolrDocument.java

@@ -315,6 +315,17 @@ public class IndividualToSolrDocument {
         return ent;
     }
     
+    public void shutdown(){
+        for(DocumentModifier dm: documentModifiers){
+            try{
+                dm.shutdown();
+            }catch(Exception e){
+                if( log != null)
+                    log.debug(e,e);
+            }
+        }
+    }
+    
     private void fillContextNodes(){
     	IndividualToSolrDocument.contextNodeClassNames.add("Role");
         IndividualToSolrDocument.contextNodeClassNames.add("AttendeeRole");

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/SolrIndexer.java

@@ -158,32 +158,51 @@ public class SolrIndexer implements IndexerIface {
     
     @Override
     public void abortIndexingAndCleanUp() {
-        endIndexing();        
+        try{
+            server.commit();            
+        }catch(SolrServerException e){
+            if( log != null)
+                log.debug("could not commit to solr server, " +
+                		"this should not be a problem since solr will do autocommit");
+        } catch (IOException e) {
+            if( log != null)
+                log.debug("could not commit to solr server, " +
+                        "this should not be a problem since solr will do autocommit");
+        }
+        try{
+            individualToSolrDoc.shutdown();
+        }catch(Exception e){
+            if( log != null)
+                log.warn(e,e);
+        }
     }
    
+    
     @Override
     public synchronized void endIndexing() {
         try {
-           UpdateResponse res = server.commit();
+            UpdateResponse res = server.commit();
-           log.debug("Response after committing to server: "+ res );
+            log.debug("Response after committing to server: "+ res );
-        } catch (SolrServerException e) {
+         } catch (SolrServerException e) {
-            log.error("Could not commit to solr server", e);
+             log.error("Could not commit to solr server", e);
-        } catch(IOException e){
+         } catch(IOException e){
-        	log.error("Could not commit to solr server", e);
+             log.error("Could not commit to solr server", e);
-        }finally{
+         }finally{
-        	if(!individualToSolrDoc.documentModifiers.isEmpty()){
+             if(!individualToSolrDoc.documentModifiers.isEmpty()){
-        		if(individualToSolrDoc.documentModifiers.get(0) instanceof CalculateParameters){
+                 if(individualToSolrDoc.documentModifiers.get(0) instanceof CalculateParameters){
-        			CalculateParameters c = (CalculateParameters) individualToSolrDoc.documentModifiers.get(0);
+                     CalculateParameters c = (CalculateParameters) individualToSolrDoc.documentModifiers.get(0);
-        			c.clearMap();
+                     c.clearMap();
-        			log.info("BetaMap cleared");
+                     log.info("BetaMap cleared");
-        		}
+                 }
-        	}
+             }
-        }
+         }
+        
         try {
             server.optimize();
         } catch (Exception e) {
             log.error("Could not optimize solr server", e);
         }
+        
         indexing = false;
         notifyAll();
     }
@@ -215,8 +234,4 @@ public class SolrIndexer implements IndexerIface {
         return false;
     }
 
-    
-   
-   
-
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/ObjectPropertyTemplateModel.java

@@ -563,7 +563,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         return TYPE;
     }
 
-    public String getTemplate() {
+    public String Template() {
         return config.templateName;
     }