nearly complete support for running Vitro from an arbitrary SPARQL endpoint

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

@@ -135,6 +135,12 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         		        QueryFactory.create(getStatements), dataset)
         		                .execConstruct();
         	} finally {
+        	    if (dataset == null) {
+        	        throw new RuntimeException("dataset is null");
+        	    } else if (dataset.getLock() == null) {
+        	        throw new RuntimeException("dataset lock is null");
+        	    }
+        	    
         		dataset.getLock().leaveCriticalSection();
         		w.close();
         	}

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

@@ -21,13 +21,12 @@ import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.shared.LockMRSW;
 import com.hp.hpl.jena.sparql.core.DatasetGraph;
 import com.hp.hpl.jena.sparql.core.Quad;
 import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
 import com.hp.hpl.jena.sparql.util.Context;
-import com.hp.hpl.jena.sparql.util.NodeFactory;
 import com.hp.hpl.jena.util.iterator.SingletonIterator;
 import com.hp.hpl.jena.util.iterator.WrappedIterator;
 
@@ -35,6 +34,7 @@ public class SparqlDatasetGraph implements DatasetGraph {
 
     private String endpointURI;
     private Repository repository;
+    private Lock lock = new LockMRSW();
     
     public SparqlDatasetGraph(String endpointURI) {
         this.endpointURI = endpointURI;
@@ -171,8 +171,7 @@ public class SparqlDatasetGraph implements DatasetGraph {
 
     @Override
     public Lock getLock() {
-        // TODO Auto-generated method stub
+        return lock;
-        return null;
     }
 
     @Override

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

@@ -204,13 +204,13 @@ public class WebappDaoFactorySDBPrep implements Filter {
         //datasource.addNamedModel("fake:fake", m);
         //dataset = datasource;            
         
-        WebappDaoFactory wadf = new WebappDaoFactoryJena(oms, config);
+        //WebappDaoFactory wadf = new WebappDaoFactoryJena(oms, config);
-        //wadf = new WebappDaoFactorySDB(oms, dataset, config);
+        WebappDaoFactory wadf = new WebappDaoFactorySDB(oms, dataset, config);
         vreq.setWebappDaoFactory(wadf);
         vreq.setFullWebappDaoFactory(wadf);
         vreq.setUnfilteredWebappDaoFactory(wadf);
         vreq.setWebappDaoFactory(wadf);
-        vreq.setAssertionsWebappDaoFactory(wadf);
+        //vreq.setAssertionsWebappDaoFactory(wadf);
         vreq.setDataset(dataset);
         vreq.setJenaOntModel(om);
         vreq.setOntModelSelector(oms);

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

@@ -156,13 +156,14 @@ public class WebappDaoFactorySparqlPrep implements Filter {
 				//datasource.addNamedModel("fake:fake", m);
 				//dataset = datasource;			
 				
+				vreq.setAssertionsWebappDaoFactory(wadf);
+				
 				wadf = new WebappDaoFactoryJena(oms, config);
 				//wadf = new WebappDaoFactorySDB(oms, dataset, config);
 				vreq.setWebappDaoFactory(wadf);
 				vreq.setFullWebappDaoFactory(wadf);
 				vreq.setUnfilteredWebappDaoFactory(wadf);
 				vreq.setWebappDaoFactory(wadf);
-				vreq.setAssertionsWebappDaoFactory(wadf);
 				vreq.setDataset(dataset);
 				vreq.setJenaOntModel(om);
 				vreq.setOntModelSelector(oms);

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupSparql2.java

@@ -249,16 +249,17 @@ public class JenaDataSourceSetupSparql2 extends JenaDataSourceSetupBase
             applicationMetadataModel.getBaseModel().register(
                     new ModelSynchronizer(applicationMetadataModelDB));
             
-            if (isFirstStartup()) {
+            if (applicationMetadataModel.size()== 0 /* isFirstStartup() */) {
                 applicationMetadataModel.add(
                         InitialJenaModelUtils.loadInitialModel(
                                 ctx, getDefaultNamespace(ctx)));
                 
-            } else if (applicationMetadataModelDB.size() == 0) {
-                repairAppMetadataModel(
-                        applicationMetadataModel, aboxAssertions, 
-                        aboxInferences);
             }
+//            else if (applicationMetadataModelDB.size() == 0) {
+//                repairAppMetadataModel(
+//                        applicationMetadataModel, aboxAssertions, 
+//                        aboxInferences);
+//            }
             
             baseOms.setApplicationMetadataModel(applicationMetadataModel);
             inferenceOms.setApplicationMetadataModel(

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

@@ -45,13 +45,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
     @Override
     public void contextInitialized(ServletContextEvent sce) {
         
-        // temporary scaffolding in the rdfapi dev branch
-        // TODO remove me
-        if (ConfigurationProperties.getBean(sce).getProperty(
-                "VitroConnection.DataSource.endpointURI") != null) {
-            return;
-        }
-        
         try {    
             // set up Pellet reasoning for the TBox