applying ABox update to all graphs

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -14,6 +14,7 @@ import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -27,7 +28,9 @@ import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 
 /**  
 * Performs knowledge base updates to the abox to align with a new ontology version
@@ -38,7 +41,8 @@ public class ABoxUpdater {
     private final Log log = LogFactory.getLog(ABoxUpdater.class);
 	private OntModel oldTboxModel;
 	private OntModel newTboxModel;
-	private OntModel aboxModel;
+	private Dataset dataset;
+	private RDFService rdfService;
 	private OntModel newTBoxAnnotationsModel;
 	private ChangeLogger logger;  
 	private ChangeRecord record;
@@ -59,14 +63,15 @@ public class ABoxUpdater {
 	 */
 	public ABoxUpdater(OntModel oldTboxModel,
 			           OntModel newTboxModel,
-			           OntModel aboxModel,
+			           RDFService rdfService,
 			           OntModel newAnnotationsModel,
 		               ChangeLogger logger,
 		               ChangeRecord record) {
 		
 		this.oldTboxModel = oldTboxModel;
 		this.newTboxModel = newTboxModel;
-		this.aboxModel = aboxModel;
+		this.dataset = new RDFServiceDataset(rdfService);
+		this.rdfService = rdfService;
 		this.newTBoxAnnotationsModel = newAnnotationsModel;
 		this.logger = logger;
 		this.record = record;
@@ -126,8 +131,15 @@ public class ABoxUpdater {
 	public void renameClass(AtomicOntologyChange change) throws IOException {
 		
 		//logger.log("Processing a class rename from: " + change.getSourceURI() + " to " + change.getDestinationURI());
-		aboxModel.enterCriticalSection(Lock.WRITE);
 	    
+	    Iterator<String> graphIt = dataset.listNames();
+	    while(graphIt.hasNext()) {
+	        String graph = graphIt.next();
+	        if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+	            continue;
+	        }
+	        Model aboxModel = dataset.getNamedModel(graph);
+	        aboxModel.enterCriticalSection(Lock.WRITE);
     		try {
     			
     	       Model additions = ModelFactory.createDefaultModel();
@@ -187,7 +199,7 @@ public class ABoxUpdater {
     		} finally {
     			aboxModel.leaveCriticalSection();
     		}
-		
+	    }
 	}
 
 	/**
@@ -233,16 +245,17 @@ public class ABoxUpdater {
 
 			if (!parentOfAddedClass.equals(OWL.Thing)) {
 				
+			    Iterator<String> graphIt = dataset.listNames();
+	            while(graphIt.hasNext()) {
+	                String graph = graphIt.next();
+	                if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+	                    continue;
+	                }
+			        Model aboxModel = dataset.getNamedModel(graph);
+			            
     				StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
     				
     				int count = stmtIter.toList().size();
-				if (count > 0) {
-					
-					String indList = "";
-					while (stmtIter.hasNext()) {
-						Statement stmt = stmtIter.next();
-						indList += "\n\t" + stmt.getSubject().getURI(); 
-					}
     					
 					if (count > 0) {
 						//TODO - take out the detailed logging after our internal testing is completed.
@@ -250,6 +263,7 @@ public class ABoxUpdater {
 				        		    " and a new subclass of that class has been added: " + addedClass.getURI() + ". " +
 				        		    "Please review " + ((count > 1) ? "these" : "this") + " individual" + ((count > 1) ? "s" : "") + " to see whether " + ((count > 1) ? "they" : "it") + " should be of type: " +  addedClass.getURI() );
 					}
+				
 	            }
 			}			
 		}
@@ -332,6 +346,13 @@ public class ABoxUpdater {
 		}
 		
 		// Remove instances of the deleted class
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
     		aboxModel.enterCriticalSection(Lock.WRITE);
     	    try {
     	       int count = 0;
@@ -352,12 +373,20 @@ public class ABoxUpdater {
     			aboxModel.leaveCriticalSection();
     		}
         }
+	}
 	
 	protected int deleteIndividual(Resource individual) throws IOException {
 
 	    Model retractions = ModelFactory.createDefaultModel();
 	    int refCount = 0;
 	    
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
     		aboxModel.enterCriticalSection(Lock.WRITE);
     	    try {			   
     		   StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null);
@@ -381,6 +410,7 @@ public class ABoxUpdater {
     		} finally {
     			aboxModel.leaveCriticalSection();
     		}
+        }
 		
 		return refCount;
 	}
@@ -439,6 +469,13 @@ public class ABoxUpdater {
 		
 		if (inverseOfAddedProperty != null) {
 			Model additions = ModelFactory.createDefaultModel();
+            Iterator<String> graphIt = dataset.listNames();
+            while(graphIt.hasNext()) {
+                String graph = graphIt.next();
+                if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                    continue;
+                }
+                Model aboxModel = dataset.getNamedModel(graph);
     			aboxModel.enterCriticalSection(Lock.WRITE);
     			
     			try {
@@ -472,6 +509,7 @@ public class ABoxUpdater {
     			}
             }
 		}
+	}
 	
 	private void deleteProperty(AtomicOntologyChange propObj) throws IOException{
 		
@@ -507,6 +545,13 @@ public class ABoxUpdater {
 			}
 		}
 		
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
     		Model deletePropModel = ModelFactory.createDefaultModel();
     		
     		if (replacementProperty == null) {
@@ -528,6 +573,7 @@ public class ABoxUpdater {
     			AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
     			renameProperty(chg);
     		}		
+        }
 		
 	}
 	
@@ -548,6 +594,14 @@ public class ABoxUpdater {
 			return;
 		}
 		
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
+		
     		Model renamePropAddModel = ModelFactory.createDefaultModel();
     		Model renamePropRetractModel = 	ModelFactory.createDefaultModel();
     		
@@ -578,6 +632,7 @@ public class ABoxUpdater {
     					propObj.getDestinationURI() + " instead");		
     		}
         }
+	}
 	
 	public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
        logChange(oldStatement,false);

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java

@@ -24,19 +24,16 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.query.Query;
+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.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.shared.Lock;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
@@ -123,10 +120,10 @@ public class KnowledgeBaseUpdater {
     	updateABox(changes);
     	
     	log.info("performing SPARQL CONSTRUCT additions");
-    	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), readModel, writeModel, ADD);
+    	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
     	
         log.info("performing SPARQL CONSTRUCT retractions");
-        performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), readModel, writeModel, RETRACT);
+        performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
 
 	}
 	
@@ -144,10 +141,11 @@ public class KnowledgeBaseUpdater {
      * @param add (add = true; retract = false)
      */
     private void performSparqlConstructs(String sparqlConstructDir, 
-            OntModel readModel, OntModel writeModel,
+            RDFService rdfService,
             boolean add)   throws IOException {
+        Dataset dataset = new RDFServiceDataset(rdfService);
         File sparqlConstructDirectory = new File(sparqlConstructDir);
-        log.info("Using SPARQL CONSTRUCT director " + sparqlConstructDirectory);
+        log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
         if (!sparqlConstructDirectory.isDirectory()) {
             String logMsg = this.getClass().getName() + 
                     "performSparqlConstructs() expected to find a directory " +
@@ -161,7 +159,6 @@ public class KnowledgeBaseUpdater {
         Collections.sort(sparqlFiles); // queries may depend on being run in a certain order
         JenaIngestUtils jiu = new JenaIngestUtils();
         for (File sparqlFile : sparqlFiles) {			
-            Model anonModel = ModelFactory.createDefaultModel();
             StringBuffer fileContents = new StringBuffer();
             try {
                 BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
@@ -176,16 +173,16 @@ public class KnowledgeBaseUpdater {
                 log.info(logMsg);
                 continue;
             }   
+            Model anonModel = ModelFactory.createDefaultModel();
             try {
                 log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
-                Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
+                
-                readModel.enterCriticalSection(Lock.READ);
+                anonModel = RDFServiceUtils.parseModel(
-                try {
+                        rdfService.sparqlConstructQuery(fileContents.toString(), 
-                    QueryExecution qe = QueryExecutionFactory.create(q,	readModel);
+                                RDFService.ModelSerializationFormat.NTRIPLE), 
-                    long numBefore = anonModel.size();
+                                ModelSerializationFormat.NTRIPLE);
-                    qe.execConstruct(anonModel);
+
-                    long numAfter = anonModel.size();
+                long num = anonModel.size();
-                    long num = numAfter - numBefore;
                 if (num > 0) {
                     String logMsg = (add ? "Added " : "Removed ") + num + 
                             " statement"  + ((num > 1) ? "s" : "") + 
@@ -195,23 +192,34 @@ public class KnowledgeBaseUpdater {
                     logger.log(logMsg);
                     log.info(logMsg);
                 }
-                    qe.close();
+        
-                } finally {
-                    readModel.leaveCriticalSection();
-                }
             } catch (Exception e) {
                 logger.logError(this.getClass().getName() + 
                         ".performSparqlConstructs() unable to execute " +
                         "query at " + sparqlFile + ". Error message is: " + e.getMessage());
                 log.error(e,e);
             }
-            writeModel.enterCriticalSection(Lock.WRITE);
+        
-            try {
             if(!add) {
-                    writeModel.remove(anonModel);
+                StmtIterator sit = anonModel.listStatements();
+                while (sit.hasNext()) {
+                    Statement stmt = sit.nextStatement();
+                    Iterator<String> graphIt = dataset.listNames();
+                    while(graphIt.hasNext()) {
+                        String graph = graphIt.next();
+                        if(!isUpdatableABoxGraph(graph)) {
+                            continue;
+                        }
+                        Model writeModel = dataset.getNamedModel(graph);
+                        if (writeModel.contains(stmt)) {
+                            writeModel.remove(stmt);
+                        }
+                    }
+                }            
                 record.recordRetractions(anonModel);
                 //log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
             } else {
+                Model writeModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL);
                 Model additions = jiu.renameBNodes(
                         anonModel, settings.getDefaultNamespace() + "n", writeModel);
                 Model actualAdditions = ModelFactory.createDefaultModel();
@@ -226,9 +234,7 @@ public class KnowledgeBaseUpdater {
                 //log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
                 record.recordAdditions(actualAdditions);
             }
-            } finally {
+            
-                writeModel.leaveCriticalSection();
-            }
         }
     }
 	
@@ -245,8 +251,8 @@ public class KnowledgeBaseUpdater {
 		
 		OntModel oldTBoxModel = settings.getOldTBoxModel();
 		OntModel newTBoxModel = settings.getNewTBoxModel();
-		OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
+		RDFService rdfService = settings.getRDFService();
-		ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
+		ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, rdfService, settings.getNewTBoxAnnotationsModel(), logger, record);
 		aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
 		aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
 	}
@@ -367,7 +373,9 @@ public class KnowledgeBaseUpdater {
 		}		
 	}
 	
-
+	public static boolean isUpdatableABoxGraph(String graphName) {
+	    return (!graphName.contains("tbox") && !graphName.contains("filegraph"));
+	}
 
 	/**
 	 * A class that allows to access two different ontology change lists,
@@ -434,5 +442,6 @@ public class KnowledgeBaseUpdater {
 		public List<AtomicOntologyChange> getAtomicPropertyChanges() {
 			return atomicPropertyChanges;
 		}		
+		
 	}	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 
 public class UpdateSettings {
 
@@ -37,6 +38,8 @@ public class UpdateSettings {
 	private OntModel newDisplayModelFromFile;
 	private OntModel loadedAtStartupDisplayModel;
 	private OntModel oldDisplayModelVivoListViewConfig;
+	private RDFService rdfService;
+	
 	public String getDataDir() {
 		return dataDir;
 	}
@@ -223,6 +226,13 @@ public class UpdateSettings {
 		return this.oldDisplayModelVivoListViewConfig;
 	}
 	
+	public RDFService getRDFService() {
+	    return this.rdfService;
+	}
+	
+	public void setRDFService(RDFService rdfService) {
+	    this.rdfService = rdfService;
+	}
 	
 	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java

@@ -41,6 +41,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -95,6 +98,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
 			OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "everytime").toString());
 			settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
+			settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
 				
 	        boolean tryMigrateDisplay = true;
 			try {