NIHVIVO-1570 changes to support SPARQL queries with GRAPH filtering in non-SDB Jena implementation

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

@@ -64,11 +64,10 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     protected static final String dataPropertyQueryString = 
         PREFIXES + "\n" +
         "SELECT DISTINCT ?property WHERE { \n" +
-        //"   GRAPH ?g {\n" + 
+        "   GRAPH ?g { ?subject ?property ?object } \n" + 
-        "       ?subject ?property ?object . \n" +        
+        "   GRAPH ?h { ?property rdf:type owl:DatatypeProperty } \n" +
-        "       ?property rdf:type owl:DatatypeProperty . \n" +
         propertyFilters +
-        //"   }\n" +
+        "   }\n" +
         "}";
     
     static protected Query dataPropertyQuery;
@@ -93,8 +92,9 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
         }
     }
 
-    public DataPropertyDaoJena(WebappDaoFactoryJena wadf) {
+    public DataPropertyDaoJena(DatasetWrapperFactory dwf, 
-        super(wadf);
+                               WebappDaoFactoryJena wadf) {
+        super(dwf, wadf);
     }
 
     public void deleteDataProperty(DataProperty dtp) {

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

@@ -10,6 +10,7 @@ import com.hp.hpl.jena.datatypes.TypeMapper;
 import com.hp.hpl.jena.ontology.DatatypeProperty;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntResource;
+import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -39,11 +40,13 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent;
 public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPropertyStatementDao
 {
 
+    private DatasetWrapperFactory dwf;
+    
     protected static final String dataPropertyValueQueryString = 
         "SELECT ?value WHERE { \n" +
-        //"   GRAPH ?g {\n" + 
+        "   GRAPH ?g {\n" + 
         "       ?subject ?property ?value . \n" +        
-        //"   }\n" +
+        "   }\n" +
         "}";
     
     static protected Query dataPropertyValueQuery;
@@ -56,8 +59,10 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         }             
     }
     
-    public DataPropertyStatementDaoJena(WebappDaoFactoryJena wadf) {
+    public DataPropertyStatementDaoJena(DatasetWrapperFactory dwf, 
+                                        WebappDaoFactoryJena wadf) {
         super(wadf);
+        this.dwf = dwf;
     }
 
     public void deleteDataPropertyStatement(DataPropertyStatement dataPropertyStmt) {
@@ -296,16 +301,27 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         bindings.add("property", ResourceFactory.createResource(propertyUri));
 
         // Run the SPARQL query to get the properties
-        QueryExecution qexec = QueryExecutionFactory.create(dataPropertyValueQuery, getOntModelSelector().getFullModel(), bindings);
+        List<DataPropertyStatement> statements = 
+                new ArrayList<DataPropertyStatement>();
+        DatasetWrapper w = dwf.getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+        dataset.getLock().enterCriticalSection(Lock.READ);
+        try {
+            QueryExecution qexec = QueryExecutionFactory.create(
+                    dataPropertyValueQuery, dataset, bindings);
             ResultSet results = qexec.execSelect(); 
     
-        List<DataPropertyStatement> statements = new ArrayList<DataPropertyStatement>();
             while (results.hasNext()) {
                 QuerySolution sol = results.next();
                 Literal value = sol.getLiteral("value");
-            DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri, propertyUri, value.getLexicalForm());
+                DataPropertyStatement dps = new DataPropertyStatementImpl(
+                        subjectUri, propertyUri, value.getLexicalForm());
                 statements.add(dps);
             }
+        } finally {
+            dataset.getLock().leaveCriticalSection();
+            w.close();
+        }
         return statements;  
     }
 }

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

@@ -38,7 +38,7 @@ public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
 	private DatasetWrapperFactory dwf;
 	
 	public DataPropertyStatementDaoSDB(DatasetWrapperFactory datasetWrapperFactory, WebappDaoFactoryJena wadf) {
-		super (wadf);
+		super (datasetWrapperFactory, wadf);
 		this.dwf = datasetWrapperFactory;
 	}
 	

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

@@ -55,11 +55,10 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     protected static final String objectPropertyQueryString = 
         PREFIXES + "\n" +
         "SELECT DISTINCT ?property WHERE { \n" +
-        //"   GRAPH ?g {\n" + 
+        "   GRAPH ?g { ?subject ?property ?object } \n" + 
-        "       ?subject ?property ?object . \n" +
+        "   GRAPH ?h { ?property rdf:type owl:ObjectProperty } \n" +
-        "       ?property rdf:type owl:ObjectProperty . \n" +
         propertyFilters +
-        //"   }\n" +
+        "   }\n" +
         "}";
 
     static protected Query objectPropertyQuery;
@@ -90,8 +89,9 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     
     Map<ObjectProperty, String> customListViewConfigFileMap = null;
     
-    public ObjectPropertyDaoJena(WebappDaoFactoryJena wadf) {
+    public ObjectPropertyDaoJena(DatasetWrapperFactory dwf, 
-        super(wadf);
+                                 WebappDaoFactoryJena wadf) {
+        super(dwf, wadf);
     }
 
     @Override

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

@@ -11,6 +11,7 @@ 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.Dataset;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -38,8 +39,12 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
 
     protected static final Log log = LogFactory.getLog(ObjectPropertyStatementDaoJena.class);
     
-    public ObjectPropertyStatementDaoJena(WebappDaoFactoryJena wadf) {
+    private DatasetWrapperFactory dwf;
+    
+    public ObjectPropertyStatementDaoJena(DatasetWrapperFactory dwf,
+                                          WebappDaoFactoryJena wadf) {
         super(wadf);
+        this.dwf = dwf;
     }
 
     @Override
@@ -72,7 +77,7 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         else {
         	Map<String, ObjectProperty> uriToObjectProperty = new HashMap<String,ObjectProperty>();
         	
-        	ObjectPropertyDaoJena opDaoJena = new ObjectPropertyDaoJena(getWebappDaoFactory());
+        	ObjectPropertyDaoJena opDaoJena = new ObjectPropertyDaoJena(dwf, getWebappDaoFactory());
         	
         	OntModel ontModel = getOntModelSelector().getABoxModel();
         	ontModel.enterCriticalSection(Lock.READ);
@@ -266,14 +271,25 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         bindings.add("property", ResourceFactory.createResource(propertyUri));
 
         // Run the SPARQL query to get the properties
-        QueryExecution qexec = QueryExecutionFactory.create(query, getOntModelSelector().getFullModel(), bindings);
-        ResultSet results = qexec.execSelect();
         List<Map<String, String>> list = new ArrayList<Map<String, String>>();
+        DatasetWrapper w = dwf.getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+        dataset.getLock().enterCriticalSection(Lock.READ);
+        try {
+            
+            QueryExecution qexec = QueryExecutionFactory.create(
+                    query, dataset, bindings);
+            ResultSet results = qexec.execSelect();
         
             while (results.hasNext()) {
                 QuerySolution soln = results.nextSolution();
                 list.add(QueryUtils.querySolutionToStringValueMap(soln));
             }
+            
+        } finally {
+            dataset.getLock().leaveCriticalSection();
+            w.close();
+        }
         return list;
     }
  

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

@@ -34,10 +34,10 @@ public class ObjectPropertyStatementDaoSDB extends
 	private DatasetWrapperFactory dwf;
 	
 	public ObjectPropertyStatementDaoSDB(
-	            DatasetWrapperFactory datasetWrapperFactory, 
+	            DatasetWrapperFactory dwf, 
 	            WebappDaoFactoryJena wadf) {
-		super (wadf);
+		super (dwf, wadf);
-		this.dwf = datasetWrapperFactory;
+		this.dwf = dwf;
 	}
 	
 	@Override

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

@@ -15,6 +15,7 @@ import org.apache.commons.logging.LogFactory;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -69,8 +70,12 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         }
     }
     
-    public PropertyDaoJena(WebappDaoFactoryJena wadf) {
+    private DatasetWrapperFactory dwf;
+    
+    public PropertyDaoJena(DatasetWrapperFactory dwf, 
+                           WebappDaoFactoryJena wadf) {
         super(wadf);
+        this.dwf = dwf;
     }
     
     @Override
@@ -410,10 +415,21 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         log.debug("SPARQL query:\n" + query.toString());
         // Bind the subject's uri to the ?subject query term
         QuerySolutionMap subjectBinding = new QuerySolutionMap();
-        subjectBinding.add("subject", ResourceFactory.createResource(subjectUri));
+        subjectBinding.add("subject", 
+                ResourceFactory.createResource(subjectUri));
 
         // Run the SPARQL query to get the properties        
-        QueryExecution qexec = QueryExecutionFactory.create(query, getOntModelSelector().getFullModel(), subjectBinding);
+        DatasetWrapper w = dwf.getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+        dataset.getLock().enterCriticalSection(Lock.READ);
+        try {
+            QueryExecution qexec = QueryExecutionFactory.create(
+                    query, dataset, subjectBinding);
             return qexec.execSelect();
+        } finally {
+            dataset.getLock().leaveCriticalSection();
+            w.close();
         }
     }
+    
+}

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

@@ -0,0 +1,17 @@
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import com.hp.hpl.jena.query.Dataset;
+
+public class StaticDatasetFactory implements DatasetWrapperFactory {
+    
+    private Dataset _dataset;
+    
+    public StaticDatasetFactory (Dataset dataset) {
+        _dataset = dataset;
+    }
+    
+    public DatasetWrapper getDatasetWrapper() {
+        return new DatasetWrapper(_dataset);
+    }
+    
+}

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

@@ -16,6 +16,9 @@ import com.hp.hpl.jena.iri.Violation;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntResource;
+import com.hp.hpl.jena.query.DataSource;
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.DatasetFactory;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -59,6 +62,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class WebappDaoFactoryJena implements WebappDaoFactory {
 
@@ -99,6 +103,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
 	
 	private Map<String,String> properties = new HashMap<String,String>();
 	
+	private DatasetWrapperFactory dwf;
+
     // for temporary use to construct URIs for the things that still use integer IDs.
     // As these objects get changed to support getURI(), this should become unnecessary.
 
@@ -114,7 +120,12 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         this.flag2ClassLabelMap = base.flag2ClassLabelMap;
     }
 
-    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, String defaultNamespace, HashSet<String> nonuserNamespaces, String[] preferredLanguages, String userURI){
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
+                                OntModelSelector inferenceOntModelSelector,
+                                String defaultNamespace, 
+                                HashSet<String> nonuserNamespaces, 
+                                String[] preferredLanguages, 
+                                String userURI){
     	
         this.ontModelSelector = ontModelSelector;
         
@@ -162,14 +173,43 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         if (languageUniversalsModel.size()>0) {
         	this.ontModelSelector.getTBoxModel().addSubModel(languageUniversalsModel);
         }
+        DataSource dataset = DatasetFactory.create();
+        
+        dataset.addNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL, 
+                ontModelSelector.getFullModel());
+        if (inferenceOntModelSelector != null) {
+            dataset.addNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL, 
+                    inferenceOntModelSelector.getFullModel());
+        }
+        this.dwf = new StaticDatasetFactory(dataset);
+        
+        
+        
+    } 
+    
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
+            String defaultNamespace, 
+            HashSet<String> nonuserNamespaces, 
+            String[] preferredLanguages, 
+            String userURI){
+        this(ontModelSelector, 
+             null, 
+             defaultNamespace,
+             nonuserNamespaces, 
+             preferredLanguages, 
+             userURI);
     }
 
     public WebappDaoFactoryJena(OntModelSelector ontModelSelector, String defaultNamespace, HashSet<String> nonuserNamespaces, String[] preferredLanguages){
         this(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages, null);
     }
     
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, OntModelSelector inferenceOntModelSelector, String defaultNamespace, HashSet<String> nonuserNamespaces, String[] preferredLanguages){
+        this(ontModelSelector, inferenceOntModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages, null);
+    }
+
     public WebappDaoFactoryJena(OntModelSelector ontModelSelector) {
-        this(ontModelSelector, null, null, null, null);
+        this(ontModelSelector, null, null, null, null, null);
     }
 
     public WebappDaoFactoryJena(OntModel ontModel, String defaultNamespace, HashSet<String> nonuserNamespaces, String[] preferredLanguages, String userURI){
@@ -181,7 +221,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     }
 
     public WebappDaoFactoryJena(OntModel ontModel) {
-        this(new SimpleOntModelSelector(ontModel), null, null, null, null);
+        this(new SimpleOntModelSelector(ontModel), null, null, null, null, null);
     }
     
     public OntModelSelector getOntModelSelector() {
@@ -493,7 +533,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     DataPropertyStatementDao dataPropertyStatementDao = null;
     public DataPropertyStatementDao getDataPropertyStatementDao() {
         if( dataPropertyStatementDao == null )
-            dataPropertyStatementDao = new DataPropertyStatementDaoJena(this);
+            dataPropertyStatementDao = new DataPropertyStatementDaoJena(
+                    dwf, this);
         return dataPropertyStatementDao;
     }
 
@@ -507,7 +548,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     DataPropertyDao dataPropertyDao = null;
     public DataPropertyDao getDataPropertyDao() {
         if( dataPropertyDao == null )
-            dataPropertyDao = new DataPropertyDaoJena(this);
+            dataPropertyDao = new DataPropertyDaoJena(dwf, this);
         return dataPropertyDao;
     }
 
@@ -528,7 +569,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     ObjectPropertyStatementDao objectPropertyStatementDao = null;
     public ObjectPropertyStatementDao getObjectPropertyStatementDao() {
         if( objectPropertyStatementDao == null )
-            objectPropertyStatementDao = new ObjectPropertyStatementDaoJena(this);
+            objectPropertyStatementDao = new ObjectPropertyStatementDaoJena(
+                    dwf, this);
         return objectPropertyStatementDao;
     }
 
@@ -542,7 +584,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     private ObjectPropertyDao objectPropertyDao = null;
     public ObjectPropertyDao getObjectPropertyDao() {
         if( objectPropertyDao == null )
-            objectPropertyDao = new ObjectPropertyDaoJena(this);
+            objectPropertyDao = new ObjectPropertyDaoJena(dwf, this);
         return objectPropertyDao;
     }
 
@@ -595,4 +637,5 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     public DisplayModelDao getDisplayModelDao(){
         return new DisplayModelDaoJena( this );
     }
+   
 }

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

@@ -97,20 +97,6 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 			return vClassDao = new VClassDaoSDB(dwf, this);
 	}
 	
-	private class StaticDatasetFactory implements DatasetWrapperFactory {
-	 
-	    private Dataset _dataset;
-	    
-	    public StaticDatasetFactory (Dataset dataset) {
-	        _dataset = dataset;
-	    }
-	    
-	    public DatasetWrapper getDatasetWrapper() {
-	        return new DatasetWrapper(_dataset);
-	    }
-	    
-	}
-	
 	private class ReconnectingDatasetFactory implements DatasetWrapperFactory {
 	    
 	    private BasicDataSource _bds;

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

@@ -87,17 +87,20 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         	checkForNamespaceMismatch( memModel, defaultNamespace );
         	
             sce.getServletContext().setAttribute("baseOntModel", memModel);
-            WebappDaoFactory baseWadf = new WebappDaoFactoryJena(baseOms, defaultNamespace, null, null);
+            WebappDaoFactory baseWadf = new WebappDaoFactoryJena(
+                    baseOms, defaultNamespace, null, null);
             sce.getServletContext().setAttribute("assertionsWebappDaoFactory",baseWadf);
             sce.getServletContext().setAttribute("baseOntModelSelector", baseOms);
             
             sce.getServletContext().setAttribute("inferenceOntModel", inferenceModel);
-            WebappDaoFactory infWadf = new WebappDaoFactoryJena(inferenceOms, defaultNamespace, null, null);
+            WebappDaoFactory infWadf = new WebappDaoFactoryJena(
+                    inferenceOms, defaultNamespace, null, null);
             sce.getServletContext().setAttribute("deductionsWebappDaoFactory", infWadf);
             sce.getServletContext().setAttribute("inferenceOntModelSelector", inferenceOms);
             
             sce.getServletContext().setAttribute("jenaOntModel", unionModel);  
-            WebappDaoFactory wadf = new WebappDaoFactoryJena(unionOms, defaultNamespace, null, null);
+            WebappDaoFactory wadf = new WebappDaoFactoryJena(
+                    baseOms, inferenceOms,  defaultNamespace, null, null);
             sce.getServletContext().setAttribute("webappDaoFactory",wadf);
             sce.getServletContext().setAttribute("unionOntModelSelector", unionOms);
             

webapp/web/config/listViewConfig-default.xml

@@ -23,9 +23,9 @@
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  
           
         SELECT ?object ?name ?moniker {
-            ?subject ?property ?object .
+            GRAPH ?g1 { ?subject ?property ?object }
-            OPTIONAL { ?object rdfs:label ?name . }
+            OPTIONAL { GRAPH ?g2 { ?object rdfs:label ?name } }
-            OPTIONAL { ?object vitro:moniker ?moniker . }
+            OPTIONAL { GRAPH ?g3 { ?object vitro:moniker ?moniker } }
         }       
     </query>