improvements to superclass methods in VClassDaoJena to support VIVO-60

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

@@ -12,6 +12,7 @@ public class WebappDaoFactoryConfig {
 	private List<String> preferredLanguages;
 	private String defaultNamespace;
 	private Set<String> nonUserNamespaces;
+	private boolean isUnderlyingStoreReasoned = false;
 	
 	public WebappDaoFactoryConfig() {
 	    preferredLanguages = Arrays.asList("en-US", "en", "EN");
@@ -44,4 +45,12 @@ public class WebappDaoFactoryConfig {
 		this.nonUserNamespaces = nonUserNamespaces;
 	}
 	
+	public void setUnderlyingStoreReasoned(boolean isReasoned) {
+	    this.isUnderlyingStoreReasoned = isReasoned;
+	}
+	
+	public boolean isUnderlyingStoreReasoned() {
+	    return this.isUnderlyingStoreReasoned;
+	}
+	
 }

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

@@ -310,7 +310,6 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
             ResultSet rs = qe.execSelect();
             if (rs.hasNext()) {
                 QuerySolution qsoln = rs.nextSolution();
-                log.debug(qsoln);
                 Resource groupRes = qsoln.getResource("group");
                 if (groupRes != null) {
                     op.setGroupURI(groupRes.getURI());

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

@@ -503,7 +503,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
     	List<VClass> allTypes = ind.getVClasses(false); // include indirect types
         
         Set<String> allSuperclassURIs = new HashSet<String>();
-       
+        
         for (VClass type : allTypes) {
             String classURI = type.getURI();
             if (classURI != null) {
@@ -718,7 +718,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	                            : (op.getRange() == null && foundRanges[1] != null)
 	                            ? foundRanges[1]
 	                                    : op.getRange();
-	                            propInsts.add(getPropInstForPropertyAndRange(op, rangeRes, applicableProperties));	
+	                            propInsts.add(getPropInstForPropertyAndRange(op, rangeRes, applicableProperties));
 	            List<String> additionalFauxSubpropertyRangeURIs = getAdditionalFauxSubpropertyRangeURIsForPropertyURI(propertyURI);
 	            for (String rangeURI : additionalFauxSubpropertyRangeURIs) {
 	                if (getWebappDaoFactory().getVClassDao().isSubClassOf(rangeURI, rangeRes.getURI())) {

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

@@ -66,15 +66,21 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
 public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 
     protected static final Log log = LogFactory.getLog(VClassDaoJena.class);
+    private boolean isUnderlyingStoreReasoned = false;
 
-    public VClassDaoJena(WebappDaoFactoryJena wadf) {
+    public VClassDaoJena(WebappDaoFactoryJena wadf, boolean isUnderlyingStoreReasoned) {
         super(wadf);
+        this.isUnderlyingStoreReasoned = isUnderlyingStoreReasoned;
     }
 
     @Override
     protected OntModel getOntModel() {
         return getOntModelSelector().getTBoxModel();
     }
+    
+    protected boolean isUnderlyingStoreReasoned() {
+        return this.isUnderlyingStoreReasoned;
+    }
 
     /* ************************************************** */
 
@@ -412,14 +418,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 
         List<String> superclassURIs = null;
 
-        //String infersTypes = getWebappDaoFactory().getProperties().get("infersTypes");
+        if (isUnderlyingStoreReasoned()) {	
-        //if ("true".equalsIgnoreCase(infersTypes)) {
-
-        PelletListener pl = getWebappDaoFactory().getPelletListener();
-        if (pl != null && pl.isConsistent() && !pl.isInErrorState() && !pl.isReasoning()) {	
             superclassURIs = new ArrayList<String>();
-            OntClass cls = getOntClass(getOntModel(),classURI);
+            Resource cls = ResourceFactory.createResource(classURI);
-            StmtIterator superClassIt = getOntModel().listStatements(cls,RDFS.subClassOf,(RDFNode)null);
+            StmtIterator superClassIt = getOntModel().listStatements(
+                    cls, RDFS.subClassOf, (RDFNode)null);
             while (superClassIt.hasNext()) {
                 Statement stmt = superClassIt.nextStatement();
                 if (stmt.getObject().canAs(OntResource.class)) {
@@ -766,12 +769,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                     }
                     if (superVclass != null) {
                         vClasses.add(superVclass);                                                                       
-                        String isInferencing = getWebappDaoFactory().getProperties().get("infersTypes");
 						// if this model infers types based on the taxonomy, adding the subclasses will only
 						// waste time for no benefit
-						PelletListener pl = getWebappDaoFactory().getPelletListener();
+						if (!isUnderlyingStoreReasoned()) {
-						if (pl == null || !pl.isConsistent() || pl.isInErrorState() || pl.isReasoning() 
-								|| isInferencing == null || "false".equalsIgnoreCase(isInferencing)) {
                         	Iterator classURIs = getAllSubClassURIs(getClassURIStr(superclass)).iterator();
                         	while (classURIs.hasNext()) {
                             	String classURI = (String) classURIs.next();

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

@@ -35,8 +35,8 @@ public class VClassDaoSDB extends VClassDaoJena {
 	
     public VClassDaoSDB(DatasetWrapperFactory datasetWrapperFactory, 
                         SDBDatasetMode datasetMode,
-                        WebappDaoFactoryJena wadf) {
+                        WebappDaoFactoryJena wadf, boolean isUnderlyingStoreReasoned) {
-        super(wadf);
+        super(wadf, isUnderlyingStoreReasoned);
         this.dwf = datasetWrapperFactory;
         this.datasetMode = datasetMode;
     }

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

@@ -376,7 +376,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     protected VClassDao vClassDao = null;
     public VClassDao getVClassDao() {
         if( vClassDao == null )
-            vClassDao = new VClassDaoJena(this);
+            vClassDao = new VClassDaoJena(this, config.isUnderlyingStoreReasoned());
         return vClassDao;
     }
 

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

@@ -91,7 +91,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (vClassDao != null) 
 			return vClassDao;
 		else
-			return vClassDao = new VClassDaoSDB(dwf, datasetMode, this);
+			return vClassDao = new VClassDaoSDB(dwf, datasetMode, this, config.isUnderlyingStoreReasoned());
 	}
 	
 	public WebappDaoFactory getUserAwareDaoFactory(String userURI) {

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

@@ -138,7 +138,7 @@ public class RequestModelsPrep implements Filter {
 		Dataset dataset = new RDFServiceDataset(rdfService);
 		vreq.setDataset(dataset);
 
-		WebappDaoFactoryConfig config = createWadfConfig(langs);
+		WebappDaoFactoryConfig config = createWadfConfig(langs, req);
 		
 		WebappDaoFactory assertions = new WebappDaoFactorySDB(rdfService,
 				ModelAccess.on(ctx).getBaseOntModelSelector(), config,
@@ -175,10 +175,11 @@ public class RequestModelsPrep implements Filter {
 		ModelAccess.on(vreq).setWebappDaoFactory(filteredWadf);
 	}
 
-	private WebappDaoFactoryConfig createWadfConfig(List<String> langs) {
+	private WebappDaoFactoryConfig createWadfConfig(List<String> langs, HttpServletRequest req) {
 		WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
 		config.setDefaultNamespace(defaultNamespace);
 		config.setPreferredLanguages(langs);
+		config.setUnderlyingStoreReasoned(isStoreReasoned(req));
 		return config;
 	}
 
@@ -212,6 +213,12 @@ public class RequestModelsPrep implements Filter {
 			ModelAccess.on(req).setOntModel(id, aware);
 		}
 	}
+	
+	private boolean isStoreReasoned(ServletRequest req) {
+	    String isStoreReasoned = ConfigurationProperties.getBean(req).getProperty(
+	            "VitroConnection.DataSource.isStoreReasoned", "true");
+	    return ("true".equals(isStoreReasoned));
+	}
 
 	@Override
 	public void destroy() {

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

@@ -86,7 +86,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         }
         
         populatedObjectPropertyList.addAll(additions);
-                
+        
         propertyList.addAll(populatedObjectPropertyList);
 
         // If editing this page, merge in object properties applicable to the individual that are currently
@@ -95,7 +95,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         if (editing) {
             mergeAllPossibleObjectProperties(populatedObjectPropertyList, propertyList);
         }
-
+        
         // Now do much the same with data properties: get the list of populated data properties, then add in placeholders for missing ones 
         // rjy7 Currently we are getting the list of properties in one sparql query, then doing a separate query
         // to get values for each property. This could be optimized by doing a single query to get a map of properties to 
@@ -105,11 +105,11 @@ public class GroupedPropertyList extends BaseTemplateModel {
         List<DataProperty> populatedDataPropertyList = subject
                 .getPopulatedDataPropertyList();
         propertyList.addAll(populatedDataPropertyList);
-
+        
         if (editing) {
             mergeAllPossibleDataProperties(propertyList);
         }
-
+        
         sort(propertyList);
 
         // Put the list into groups