VIVO-82 Use ModelAccess to get or set the BaseOntModel

a.k.a the Base Full model, or AssertionsModel

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/VitroRequest.java

@@ -191,11 +191,7 @@ public class VitroRequest extends HttpServletRequestWrapper {
     
     
     public OntModel getAssertionsOntModel() {
-    	OntModel jenaOntModel = (OntModel)_req.getSession().getAttribute( JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME );
+        return ModelAccess.on(getSession()).getBaseOntModel();
-    	if ( jenaOntModel == null ) {
-    		jenaOntModel = (OntModel)_req.getSession().getServletContext().getAttribute( JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME );
-    	}
-    	return jenaOntModel;    	
     }
     
     public OntModel getInferenceOntModel() {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/RefactorOperationController.java

@@ -7,7 +7,6 @@ import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
 
 import javax.servlet.RequestDispatcher;
 import javax.servlet.http.HttpServletRequest;
@@ -40,7 +39,6 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.InvalidPropertyURIException;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.util.ResourceUtils;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 import com.hp.hpl.jena.vocabulary.RDF;
 
@@ -50,6 +48,7 @@ import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup;
@@ -74,7 +73,7 @@ public class RefactorOperationController extends BaseEditController {
         request.setAttribute("title","Check Datatype Properties");
         request.setAttribute("css", "<link rel=\"stylesheet\" type=\"text/css\" href=\""+vreq.getAppBean().getThemeDir()+"css/edit.css\"/>");
         
-		OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
+        OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
 		ontModel.enterCriticalSection(Lock.WRITE);
 		ArrayList<String> results = new ArrayList<String>();
 				
@@ -330,7 +329,7 @@ public class RefactorOperationController extends BaseEditController {
 	private void doMovePropertyStatements(VitroRequest request, HttpServletResponse response, EditProcessObject epo) {
 		String userURI = LoginStatusBean.getBean(request).getUserURI();
 		
-		OntModel ontModel = ModelContext.getBaseOntModel(getServletContext());
+		OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
 		
 		Model tempRetractModel = ModelFactory.createDefaultModel();
 		Model tempAddModel = ModelFactory.createDefaultModel();
@@ -414,7 +413,7 @@ public class RefactorOperationController extends BaseEditController {
 	private void doMoveInstances(VitroRequest request, HttpServletResponse response, EditProcessObject epo) {
 		String userURI = LoginStatusBean.getBean(request).getUserURI();
 		
-		OntModel ontModel = ModelContext.getBaseOntModel(getServletContext());
+		OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
 		
 		String oldClassURIStr = (String) epo.getAttribute("VClassURI");
 		String newClassURIStr = (String) request.getParameter("NewVClassURI");

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaAdminActions.java

@@ -94,7 +94,7 @@ public class JenaAdminActions extends BaseEditController {
      * @param response
      */
     private void outputTbox(HttpServletResponse response) {
-        OntModel memoryModel = (OntModel) getServletContext().getAttribute("baseOntModel");
+        OntModel memoryModel = ModelAccess.on(getServletContext()).getBaseOntModel();
         try {
         	OntModel tempOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
         	Property DescriptionProp = ResourceFactory.createProperty(VitroVocabulary.DESCRIPTION_ANNOT);
@@ -306,7 +306,7 @@ public class JenaAdminActions extends BaseEditController {
         if (actionStr.equals("output")) {
             OntModel memoryModel = null;
 	    if (request.getParameter("assertionsOnly") != null) {
-	    	memoryModel = (OntModel) getServletContext().getAttribute("baseOntModel");
+	        memoryModel = ModelAccess.on(getServletContext()).getBaseOntModel();
 	    	System.out.println("baseOntModel");
 	    } else if (request.getParameter("inferences") != null) {
 	    	memoryModel = (OntModel) getServletContext().getAttribute("inferenceOntModel");
@@ -375,7 +375,7 @@ public class JenaAdminActions extends BaseEditController {
             ClosableIterator ooIt = persistentModel.listObjects();
             clean(oIt,persistentModel);
         } else if (actionStr.equals("outputTaxonomy")) {
-        	OntModel ontModel = (OntModel) getServletContext().getAttribute("baseOntModel");
+            OntModel ontModel = ModelAccess.on(getServletContext()).getBaseOntModel();
         	Model taxonomyModel = extractTaxonomy(ontModel);
         	try {
         		taxonomyModel.write(response.getOutputStream());

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaExportController.java

@@ -283,7 +283,6 @@ public class JenaExportController extends BaseEditController {
 		}
 	}
 	
-	static final String ASSERTIONS_ONT_MODEL_ATTR = "baseOntModel";
 	static final String INFERENCES_ONT_MODEL_ATTR = "inferenceOntModel";
 	static final String FULL_GRAPH = "?g";
 	static final String ASSERTIONS_GRAPH = "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>";

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java

@@ -661,8 +661,7 @@ public class JenaIngestController extends BaseEditController {
               /*
                * get baseOnt and infOnt models
                */
-              OntModel baseOntModel = ModelContext.getBaseOntModel(
+              OntModel baseOntModel = ModelAccess.on(getServletContext()).getBaseOntModel();
-                      getServletContext());
               OntModel tboxOntModel = ModelContext.getUnionOntModelSelector(
                       getServletContext()).getTBoxModel();
               
@@ -1314,12 +1313,7 @@ public class JenaIngestController extends BaseEditController {
         if ("vitro:jenaOntModel".equals(name)) {
             return ModelAccess.on(request.getSession()).getJenaOntModel();
         } else if ("vitro:baseOntModel".equals(name)) {
-            Object sessionOntModel = request.getSession().getAttribute("baseOntModel");
+            return ModelAccess.on(request.getSession()).getBaseOntModel();
-            if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
-                return (OntModel) sessionOntModel;
-            } else {
-                return (OntModel) context.getAttribute("baseOntModel");
-            }
         } else if ("vitro:inferenceOntModel".equals(name)) {
             Object sessionOntModel = request.getSession().getAttribute("inferenceOntModel");
             if (sessionOntModel != null && sessionOntModel instanceof OntModel) {

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/ModelAccess.java

@@ -106,18 +106,14 @@ public class ModelAccess {
 		return getOntModel(ModelID.UNION_FULL);
 	}
 
-
+	public void setBaseOntModel(OntModel m) {
-	// /** Is this the same as Assertions model? */
+		setOntModel(ModelID.BASE_FULL, m);
-	// // public OntModel getBaseOntModel() {
+	}
-	// // throw new RuntimeException(
+	
-	// // "ModelAccess.getBaseOntModel not implemented.");
+	public OntModel getBaseOntModel() {
-	// // }
+		return getOntModel(ModelID.BASE_FULL);
-	//
+	}
-	// public OntModel getAssertionsOntModel() {
+	
-	// throw new RuntimeException(
-	// "ModelAccess.getAssertionsOntModel not implemented.");
-	// }
-	//
 	// public OntModel getDisplayTboxOntModel() {
 	// throw new RuntimeException(
 	// "ModelAccess.getDisplayTboxOntModel not implemented.");
@@ -233,14 +229,6 @@ public class ModelAccess {
 	 * 		ctx.setAttribute(INFERENCE_ONT_MODEL_SELECTOR, oms); 
 	 * 	}
 	 * 	
-	 * 	public static OntModel getBaseOntModel(ServletContext ctx) {
-	 * 		return (OntModel) ctx.getAttribute(BASE_ONT_MODEL);
-	 * 	}
-	 * 	
-	 * 	public static void setBaseOntModel(OntModel ontModel, ServletContext ctx) {
-	 * 		ctx.setAttribute(BASE_ONT_MODEL, ontModel);
-	 * 	}
-	 * 	
 	 * 	public static OntModel getInferenceOntModel(ServletContext ctx) {
 	 * 		return (OntModel) ctx.getAttribute(INFERENCE_ONT_MODEL);
 	 * 	}

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

@@ -54,7 +54,6 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 	public static final boolean KEEP_ONLY_IF_TRUE = true; //used for updatePropertyBooleanValue()
     public static final boolean KEEP_ONLY_IF_FALSE = false; //used for updatePropertyBooleanValue()
     
-    public static final String ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME = "baseOntModel";
     public static final String INFERENCE_ONT_MODEL_ATTRIBUTE_NAME = "inferenceOntModel";
     
     protected static final Log log = LogFactory.getLog(JenaBaseDao.class.getName());

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

@@ -22,7 +22,6 @@ public class ModelContext {
 	private static final String BASE_ONT_MODEL_SELECTOR = "baseOntModelSelector";
 	private static final String INFERENCE_ONT_MODEL_SELECTOR = "inferenceOntModelSelector";
 	
-	private static final String BASE_ONT_MODEL = "baseOntModel";
 	private static final String INFERENCE_ONT_MODEL = "inferenceOntModel";
 
 	public ModelContext() {}
@@ -59,14 +58,6 @@ public class ModelContext {
 		ctx.setAttribute(INFERENCE_ONT_MODEL_SELECTOR, oms); 
 	}
 	
-	public static OntModel getBaseOntModel(ServletContext ctx) {
-		return (OntModel) ctx.getAttribute(BASE_ONT_MODEL);
-	}
-	
-	public static void setBaseOntModel(OntModel ontModel, ServletContext ctx) {
-		ctx.setAttribute(BASE_ONT_MODEL, ontModel);
-	}
-	
 	public static OntModel getInferenceOntModel(ServletContext ctx) {
 		return (OntModel) ctx.getAttribute(INFERENCE_ONT_MODEL);
 	}

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

@@ -314,12 +314,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 			if ("vitro:jenaOntModel".equals(modelName)) {
 	    		return ModelAccess.on(request.getSession()).getJenaOntModel();
 			} else if ("vitro:baseOntModel".equals(modelName)) {
-				Object sessionOntModel = request.getSession().getAttribute("baseOntModel");
+		        return ModelAccess.on(request.getSession()).getBaseOntModel();
-				if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
-					return (OntModel) sessionOntModel;
-				} else {
-					return (OntModel) request.getSession().getServletContext().getAttribute("baseOntModel");
-				}
 			} else if ("vitro:inferenceOntModel".equals(modelName)) {
 				Object sessionOntModel = request.getSession().getAttribute("inferenceOntModel");
 				if (sessionOntModel != null && sessionOntModel instanceof OntModel) {

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

@@ -119,12 +119,7 @@ public class VitroJenaSpecialModelMaker implements ModelMaker {
 			if ("vitro:jenaOntModel".equals(modelName)) {
 				return ModelAccess.on(request.getSession()).getJenaOntModel();
 			} else if ("vitro:baseOntModel".equals(modelName)) {
-				Object sessionOntModel = request.getSession().getAttribute("baseOntModel");
+		        return ModelAccess.on(request.getSession()).getBaseOntModel();
-				if (sessionOntModel != null && sessionOntModel instanceof OntModel) {
-					return (OntModel) sessionOntModel;
-				} else {
-					return (OntModel) request.getSession().getServletContext().getAttribute("baseOntModel");
-				}
 			} else if ("vitro:inferenceOntModel".equals(modelName)) {
 				Object sessionOntModel = request.getSession().getAttribute("inferenceOntModel");
 				if (sessionOntModel != null && sessionOntModel instanceof OntModel) {

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

@@ -22,6 +22,7 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 import com.hp.hpl.jena.vocabulary.RDF;
 
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
 
 /**
@@ -42,14 +43,7 @@ public class AssembleModelsSetup implements ServletContextListener {
 	private String SYNTAX = "N3";
 	
 	public void contextInitialized(ServletContextEvent sce) {
-	    
+		OntModel jenaOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
-		OntModel jenaOntModel = null;
-		try {
-			jenaOntModel = (OntModel) sce.getServletContext().getAttribute("baseOntModel");
-		} catch (Exception e) {
-			log.error("No baseOntModel found to which to attach assembled models");
-			return;
-		}
 		// read assemblers out of assemblers directory
 		Set pathSet = sce.getServletContext().getResourcePaths(ASSEMBLERS_DIR_PATH);
 		for (String path : (Set<String>)pathSet) {

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

@@ -90,8 +90,20 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
         OntModel baseFullModel = createCombinedBulkUpdatingModel(baseABoxModel, baseTBoxModel);
         OntModel inferenceFullModel = createCombinedModel(inferenceABoxModel, inferenceTBoxModel);
         OntModel unionFullModel = ModelFactory.createOntologyModel(DB_ONT_MODEL_SPEC, dataset.getDefaultModel());
+
+        ModelAccess.on(ctx).setOntModel(ModelID.APPLICATION_METADATA, applicationMetadataModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.USER_ACCOUNTS, userAccountsModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.DISPLAY, displayModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.BASE_ABOX, baseABoxModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.BASE_TBOX, baseTBoxModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.BASE_FULL, baseFullModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.INFERRED_ABOX, inferenceABoxModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.INFERRED_TBOX, inferenceTBoxModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.INFERRED_FULL, inferenceFullModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.UNION_ABOX, unionABoxModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.UNION_TBOX, unionTBoxModel);
+        ModelAccess.on(ctx).setOntModel(ModelID.UNION_FULL, unionFullModel);
         
-        ModelContext.setBaseOntModel(baseFullModel, ctx);
         ModelContext.setInferenceOntModel(inferenceFullModel, ctx);
         
         checkForNamespaceMismatch( applicationMetadataModel, ctx );
@@ -127,8 +139,6 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
 
 		log.info("Setting up DAO factories");
 		
-		ModelAccess.on(ctx).setJenaOntModel(unionFullModel);
-        
         WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
         config.setDefaultNamespace(getDefaultNamespace(ctx));
         

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

@@ -28,6 +28,7 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.util.ResourceUtils;
 
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 public class RunSparqlConstructs implements ServletContextListener {
@@ -46,7 +47,7 @@ public class RunSparqlConstructs implements ServletContextListener {
 			String namespace = (wadf != null && wadf.getDefaultNamespace() != null) 
 				? wadf.getDefaultNamespace() : DEFAULT_DEFAULT_NAMESPACE;
 			
-			OntModel baseOntModel = (OntModel) sce.getServletContext().getAttribute("baseOntModel");
+		    OntModel baseOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
 			Model anonModel = ModelFactory.createDefaultModel();
 			Model namedModel = ModelFactory.createDefaultModel();