various and sundry small DAO improvements

webapp/src/edu/cornell/mannlib/vedit/controller/OperationController.java

@@ -441,14 +441,14 @@ public class OperationController extends BaseEditController {
             } catch (InvocationTargetException e) {
                 log.error(this.getClass().getName()+" encountered exception performing two-stage update");
                 Throwable innerE = e.getTargetException();
-                log.error(innerE);
+                log.error(innerE, innerE);
                 if (innerE.getMessage()!=null) {
-                	log.error(innerE.getMessage());
+                	//log.error(innerE.getMessage());
                 	epo.setAttribute("globalErrorMsg",innerE.getMessage());
                 }
                 return FAILURE;
             } catch (IllegalAccessException iae) {
-            	log.error(iae);
+            	log.error(iae, iae);
             	epo.setAttribute("globalErrorMessage", "Illegal access - see error logs.");
             	return FAILURE;
             }
@@ -459,15 +459,15 @@ public class OperationController extends BaseEditController {
             	log.error(this.getClass().getName()+" encountered exception performing edit action");
                 Throwable innerE = e.getTargetException();
                 //innerE.printStackTrace();
-                log.error(innerE);
+                log.error(innerE, innerE);
                 if (innerE.getMessage()!=null) {
                     //System.out.println(innerE.getMessage());
-                	log.error(innerE.getMessage());
+                	//log.error(innerE.getMessage());
                 	epo.setAttribute("globalErrorMsg",innerE.getMessage());
                 }
                 return FAILURE;
             } catch (IllegalAccessException iae) {
-            	log.error(iae);
+            	log.error(iae, iae);
             	epo.setAttribute("globalErrorMessage", "Illegal access - see error logs.");
             	return FAILURE;
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ObjectPropertyStatement.java

@@ -7,10 +7,6 @@ public interface ObjectPropertyStatement {
 
     public String toString();
 
-    public boolean isSubjectOriented();
-
-    public void setSubjectOriented(boolean subjectOriented);
-
     public String getSubjectURI();
 
     public void setSubjectURI(String subjectURI);

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ObjectPropertyStatementImpl.java

@@ -18,9 +18,7 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
 
     private String propertyURI = null;
     private ObjectProperty property = null;
-    private String qualifier = null;
     private boolean subjectOriented = true; //is the range the item of interest?  
-    private String description = null;  //generated desc based on subjectOriented during sql query.  
     
    public ObjectPropertyStatementImpl() { }
 
@@ -37,23 +35,7 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
            String prop = (getProperty()!=null)?getProperty().getDomainPublic():"by propURI"+getPropertyURI();
            String ran = (getObject()!= null)?getObject().getName():"objectURI:"+getObjectURI();
            String dom = (getSubject()!= null)?getSubject().getName():"subjectURI:"+getSubjectURI();
-           String orent = (isSubjectOriented() )?"subject oriented":"object oriented";
+           return "Object Property Statements: "+dom+" "+prop+" to "+ran+" ";
-           return "Object Property Statements: "+dom+" "+prop+" to "+ran+" "+orent;
-    }
-
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#isSubjectOriented()
-     */
-    public boolean isSubjectOriented() {
-        return subjectOriented;
-    }
-
-
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#setSubjectOriented(boolean)
-     */
-    public void setSubjectOriented(boolean subjectOriented) {
-        this.subjectOriented = subjectOriented;
     }
 
     /* (non-Javadoc)
@@ -100,6 +82,11 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
      */
     public void setSubject(Individual subject) {
         this.subject = subject;
+        if (subject == null || subject.isAnonymous()) {
+            setSubjectURI(null);    
+        } else {
+            setSubjectURI(subject.getURI());
+        }
     }
 
 
@@ -136,6 +123,11 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
      */
     public void setObject(Individual object) {
         this.object = object;
+        if (object == null || object.isAnonymous()) {
+            setObjectURI(null);    
+        } else {
+            setObjectURI(object.getURI());
+        }
     }
 
 

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/VClass.java

@@ -133,8 +133,14 @@ public class VClass extends BaseResourceBean implements Comparable<VClass>
      * Sorts alphabetically by name
      */
     public int compareTo (VClass o1) {
-        Collator collator = Collator.getInstance();
+        if (this.getName() == null) {
-        return collator.compare(this.getName(),o1.getName());
+            return 1;
+        } else if (o1.getName() == null) {
+            return -1;
+        } else {
+            Collator collator = Collator.getInstance();
+            return collator.compare(this.getName(),o1.getName());
+        }
     }
 
     /**

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

@@ -39,7 +39,7 @@ public interface WebappDaoFactory {
     
     public Set<String> getNonuserNamespaces();
     
-    public String[] getPreferredLanguages();
+    public List<String> getPreferredLanguages();
     
     /**
      * BJL23 2008-05-20: Putting this here for lack of a more logical place.  

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

@@ -2,30 +2,29 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao;
 
+import java.util.Arrays;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
 public class WebappDaoFactoryConfig {
 	
-	private String[] preferredLanguages;
+	private List<String> preferredLanguages;
 	private String defaultNamespace;
 	private Set<String> nonUserNamespaces;
 	
 	public WebappDaoFactoryConfig() {
-        preferredLanguages = new String[3];
+	    preferredLanguages = Arrays.asList("en-US", "en", "EN");
-        preferredLanguages[0] = "en-US";
-        preferredLanguages[1] = "en";
-        preferredLanguages[2] = "EN";
 		defaultNamespace = "http://vitro.mannlib.cornell.edu/ns/default#";
 		nonUserNamespaces = new HashSet<String>();
 		nonUserNamespaces.add(VitroVocabulary.vitroURI);
 	}
 	
-	public String[] getPreferredLanguages() {
+	public List<String> getPreferredLanguages() {
 		return this.preferredLanguages;
 	}
 	
-	public void setPreferredLanguages(String[] pl) {
+	public void setPreferredLanguages(List<String> pl) {
 		this.preferredLanguages = pl;
 	}
 	

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/ObjectPropertyStatementFiltering.java

@@ -56,10 +56,6 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         return innerStmt.getSubjectURI();
     }
 
-    public boolean isSubjectOriented() {
-        return innerStmt.isSubjectOriented();
-    }
-
     public void setObject(Individual object) {
         innerStmt.setObject(object);
     }
@@ -80,10 +76,6 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         innerStmt.setSubject(subject);
     }
 
-    public void setSubjectOriented(boolean subjectOriented) {
-        innerStmt.setSubjectOriented(subjectOriented);
-    }
-
     public void setSubjectURI(String subjectURI) {
         innerStmt.setSubjectURI(subjectURI);
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/WebappDaoFactoryFiltering.java

@@ -101,7 +101,7 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
     	return innerWebappDaoFactory.getNonuserNamespaces();
     }
     
-    public String[] getPreferredLanguages() {
+    public List<String> getPreferredLanguages() {
     	return innerWebappDaoFactory.getPreferredLanguages();
     }
     

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

@@ -187,9 +187,10 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		        continue;
     		    }
     		    if (uri != null && !uri.equals(currRes.getURI())) {
-    		        Individual ent = makeIndividual(uri, label);
+    		        try {
-    		        if (ent != null) {
+    		            ents.add(makeIndividual(uri, label));
-    		            ents.add(ent);
+    		        } catch (IndividualNotFoundException e) {
+    		            // don't add
     		        }
     	            uri = currRes.getURI();
     	            label = null;
@@ -201,9 +202,10 @@ public class IndividualDaoSDB extends IndividualDaoJena {
                     label = labelLit.getLexicalForm();
                 }
                 if (!rs.hasNext()) {
-                    Individual ent = makeIndividual(uri, label);
+                    try {
-                    if (ent != null) {
+                        ents.add(makeIndividual(uri, label));
-                        ents.add(ent);
+                    } catch (IndividualNotFoundException e) {
+                        // don't add   
                     }
                 }
     		}
@@ -237,8 +239,12 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		    if (currRes.isAnon()) {
     		        continue;
     		    }
-    		    filteredIndividualList.add(
+    		    try {
-    		    		makeIndividual(currRes.getURI(), null));
+    		        filteredIndividualList.add(
+    		    	    	makeIndividual(currRes.getURI(), null));
+    		    } catch (IndividualNotFoundException e) {
+    		        // don't add
+    		    }
     		}
        	} finally {
     		dataset.getLock().leaveCriticalSection();
@@ -247,7 +253,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
        	return filteredIndividualList;
     }
     
-    private Individual makeIndividual(String uri, String label) {
+    private Individual makeIndividual(String uri, String label) throws IndividualNotFoundException {
         Individual ent = new IndividualSDB(uri, 
                 this.dwf, datasetMode, getWebappDaoFactory(), 
                 SKIP_INITIALIZATION);

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

@@ -109,7 +109,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             DatasetWrapperFactory datasetWrapperFactory, 
             SDBDatasetMode datasetMode,
             WebappDaoFactoryJena wadf,
-            boolean skipInitialization) {
+            boolean skipInitialization) throws IndividualNotFoundException {
     	this.individualURI = individualURI;
     	this.datasetMode = datasetMode;
     	this.dwf = datasetWrapperFactory;
@@ -176,7 +176,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     public IndividualSDB(String individualURI, 
             DatasetWrapperFactory datasetWrapperFactory,
             SDBDatasetMode datasetMode,
-            WebappDaoFactoryJena wadf) {
+            WebappDaoFactoryJena wadf) throws IndividualNotFoundException {
         this(individualURI, 
              datasetWrapperFactory, 
              datasetMode, 
@@ -184,7 +184,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
              !SKIP_INITIALIZATION);
     }
     
-    public class IndividualNotFoundException extends RuntimeException {}
+    public class IndividualNotFoundException extends Exception {}
     
     private void setUpURIParts(OntResource ind) {
         if (ind != null) {
@@ -464,8 +464,24 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     			if (!s.getSubject().canAs(OntResource.class) || !s.getObject().canAs(OntResource.class)) {
     			    continue;	
     			}
-    			Individual subj = new IndividualSDB(((OntResource) s.getSubject().as(OntResource.class)).getURI(), this.dwf, datasetMode, webappDaoFactory);
+    			Individual subj = null;
-    			Individual obj = new IndividualSDB(((OntResource) s.getObject().as(OntResource.class)).getURI(), this.dwf, datasetMode, webappDaoFactory);
+    			try {
+    			    subj = new IndividualSDB(
+    			            ((OntResource) s.getSubject().as(OntResource.class))
+    			                    .getURI(), 
+    			                            this.dwf, datasetMode, webappDaoFactory);
+    			} catch (IndividualNotFoundException e) {
+    			    // leave null subject
+    			}
+    			Individual obj = null;
+    			try {
+    			    obj = new IndividualSDB(
+    			            ((OntResource) s.getObject().as(OntResource.class))
+    			                    .getURI(), 
+    			                            this.dwf, datasetMode, webappDaoFactory);
+    			} catch (IndividualNotFoundException e) {
+    			    // leave null object
+    			}
     			ObjectProperty op = webappDaoFactory.getObjectPropertyDao().getObjectPropertyByURI(s.getPredicate().getURI());
     			// We don't want to filter out statements simply because we 
     			// can't find a type for the property, so we'll just make a 
@@ -517,15 +533,19 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    while (values.hasNext()) {
     	    	result = values.next();
     	    	RDFNode value = result.get("object");
-    	    	if (value.canAs(OntResource.class)) {
+    	    	try {
-        	    	relatedIndividuals.add(
+        	    	if (value.canAs(OntResource.class)) {
-        	    		new IndividualSDB(
+            	    	relatedIndividuals.add(
-        	    		        ((OntResource) value.as(OntResource.class))
+            	    		new IndividualSDB(
-        	    		                .getURI(), 
+            	    		        ((OntResource) value.as(OntResource.class))
-        	    		                this.dwf, 
+            	    		                .getURI(), 
-        	    		                datasetMode, 
+            	    		                this.dwf, 
-        	    		                webappDaoFactory) );  
+            	    		                datasetMode, 
-        	    } 
+            	    		                webappDaoFactory) );  
+            	    } 
+    	    	} catch (IndividualNotFoundException e) {
+    	    	    // don't add to the list
+    	    	}
     	    }
     	} finally {
     		dataset.getLock().leaveCriticalSection();
@@ -555,9 +575,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             		QuerySolution result = results.next();
             		RDFNode value = result.get("object");
             	    if (value != null && value.canAs(OntResource.class)) {
-            	    	return new IndividualSDB(
+            	        try {
-            	    	        ((OntResource) value.as(OntResource.class)).getURI(), 
+                	    	return new IndividualSDB(
-            	    	                dwf, datasetMode, webappDaoFactory);  
+                	    	        ((OntResource) value.as(OntResource.class)).getURI(), 
+                	    	                dwf, datasetMode, webappDaoFactory);
+            	        } catch (IndividualNotFoundException e) {
+            	            return null;
+            	        }
             	    } 
         	    }
         		return null;

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

@@ -80,7 +80,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 
     protected String DEFAULT_NAMESPACE;
     protected Set<String> NONUSER_NAMESPACES;
-    protected String[] PREFERRED_LANGUAGES;
+    protected List<String> PREFERRED_LANGUAGES;
 
     /* ******************* constructor ************************* */
     
@@ -501,7 +501,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
                 }
             }
         } catch (Exception e) {
-            log.error("Error in updatePropertyDateValue");
+            log.error("Error in updatePropertyDateValue", e);
         }
     }
     
@@ -552,8 +552,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
                 }
             }
         } catch (Exception e) {
-            log.error("Error in updatePropertyDateTimeValue");
+            log.error("Error in updatePropertyDateTimeValue", e);
-            log.error(e, e);
         }
     }
 
@@ -767,7 +766,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     		if (label.isLiteral()) {
     			Literal labelLit = ((Literal)label);
     			String labelLanguage = labelLit.getLanguage();
-    			if ( (labelLanguage==null) && (lang==null) ) {
+    			if ( (labelLanguage == null) && (lang == null || lang.isEmpty()) ) {
     				return labelLit;
     			}
     			if ( (lang != null) && (lang.equals(labelLanguage)) ) {
@@ -857,6 +856,10 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     	Literal label = null;
 	    List<RDFNode> labels = r.listPropertyValues(p).toList();
 	    
+	    if (labels.size() == 0) {
+	        return null;
+	    }
+
 	    // Sort by lexical value to guarantee consistent results
 	    Collections.sort(labels, new Comparator<RDFNode>() {
 	        public int compare(RDFNode left, RDFNode right) {
@@ -871,8 +874,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 	        }
 	    });
 	    
-	    for (int i=0; i<PREFERRED_LANGUAGES.length; i++) {
+	    for (String lang : PREFERRED_LANGUAGES) {
-	    	String lang = PREFERRED_LANGUAGES[i];
 	    	label = getLabel(lang,labels);
 	    	if (label != null) {
 	    		break;
@@ -880,12 +882,21 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 	    }
         if ( label == null && alsoTryNoLang ) {
         	label = getLabel("", labels);
+        	// accept any label as a last resort
+        	if (label == null) {
+        	    for (RDFNode labelNode : labels) {
+        	      if (labelNode instanceof Literal) {
+        	          label = ((Literal) labelNode);
+        	          break;
+        	      }
+        	    }
+        	}
         }
 	    return label;
     }
 
     protected String getDefaultLanguage() {
-        return PREFERRED_LANGUAGES[0];
+        return PREFERRED_LANGUAGES.get(0);
     }
     
     /**

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

@@ -132,7 +132,7 @@ public class OntologyDaoJena extends JenaBaseDao implements OntologyDao {
             try {
                 com.hp.hpl.jena.ontology.Ontology o = ontModel.createOntology(adjustOntologyURI(ontology.getURI()));
                 if (ontology.getName() != null && ontology.getName().length()>0) {
-                    o.setLabel(ontology.getName(), PREFERRED_LANGUAGES[0]);
+                    o.setLabel(ontology.getName(), getDefaultLanguage());
                 }
                 if (ontology.getPrefix() != null && ontology.getPrefix().length()>0) {
                     addPropertyStringValue(o,ONTOLOGY_PREFIX_ANNOT,ontology.getPrefix(),ontModel);

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

@@ -9,6 +9,9 @@ import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
 import com.hp.hpl.jena.ontology.AnnotationProperty;
 import com.hp.hpl.jena.ontology.CardinalityRestriction;
@@ -59,6 +62,8 @@ 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);
+    
     public VClassDaoJena(WebappDaoFactoryJena wadf) {
         super(wadf);
     }
@@ -446,11 +451,12 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         List<VClass> classes = new ArrayList<VClass>();
         getOntModel().enterCriticalSection(Lock.READ);
         try {
-            ClosableIterator<OntClass> classIt = getOntModel().listClasses();
+            ClosableIterator<Individual> classIt = getOntModel().listIndividuals(OWL.Class);
             try {
                 while (classIt.hasNext()) {
                     try {
-                        OntClass cls = classIt.next();
+                        Individual classInd = classIt.next();
+                        OntClass cls = (OntClass) classInd.as(OntClass.class);
                         if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
                             classes.add(new VClassJena(cls,getWebappDaoFactory()));
                         }
@@ -481,11 +487,15 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 	 */
     private Iterator<OntClass> smarterListHierarchyRootClasses(OntModel ontModel, String ontologyURI) {
     	List<OntClass> rootClassList = new ArrayList<OntClass>();
-    	ClosableIterator ci = ontModel.listClasses();
+    	ClosableIterator<Individual> ci = ontModel.listIndividuals(OWL.Class);
     	try {
-	    	for (ClosableIterator i = ci ; i.hasNext(); ) {
+	    	for (ClosableIterator<Individual> i = ci ; i.hasNext(); ) {
 	    		try {
-		    		OntClass ontClass = (OntClass) i.next();
+	    		    Individual classInd = i.next();
+//	    		    if (!classInd.canAs(OntClass.class)) {
+//	    		        continue;
+//	    		    }
+		    		OntClass ontClass = (OntClass) classInd.as(OntClass.class);
 	    			boolean isRoot = true;
 	    			for (Iterator<RDFNode> j = ontClass.listPropertyValues(RDFS.subClassOf); j.hasNext(); ) {
 	    				Resource res = (Resource) j.next();
@@ -510,7 +520,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 	    				rootClassList.add(ontClass);
 	    			}
 	    		} catch (ClassCastException cce) {
-					log.error(cce);
+					log.error(cce, cce);
 				}
 	    	}
     	} finally {

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

@@ -233,7 +233,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         return config.getDefaultNamespace();
     }
     
-    public String[] getPreferredLanguages() {
+    public List<String> getPreferredLanguages() {
     	return config.getPreferredLanguages();
     }
     

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/filtering/IndividualFilteringByStatementTest.java

@@ -638,18 +638,6 @@ public class IndividualFilteringByStatementTest extends AbstractTestClass {
 		// Un-implemented methods
 		// ----------------------------------------------------------------------
 
-		@Override
-		public boolean isSubjectOriented() {
-			throw new RuntimeException(
-					"ObjectPropertyStatement.isSubjectOriented() not implemented.");
-		}
-
-		@Override
-		public void setSubjectOriented(boolean subjectOriented) {
-			throw new RuntimeException(
-					"ObjectPropertyStatement.setSubjectOriented() not implemented.");
-		}
-
 		@Override
 		public void setSubjectURI(String subjectURI) {
 			throw new RuntimeException(

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/ObjectPropertyStatementDaoStub.java

@@ -55,16 +55,6 @@ public class ObjectPropertyStatementDaoStub implements
 					.getObjectURI());
 		}
 
-		@Override
-		public boolean isSubjectOriented() {
-			return false;
-		}
-
-		@Override
-		public void setSubjectOriented(boolean subjectOriented) {
-			throw new UnsupportedOperationException();
-		}
-
 		@Override
 		public String getSubjectURI() {
 			return s;

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactoryStub.java

@@ -169,7 +169,7 @@ return this.objectPropertyStatementDao;	}
 	}
 
 	@Override
-	public String[] getPreferredLanguages() {
+	public List<String> getPreferredLanguages() {
 		throw new RuntimeException(
 				"WebappDaoFactory.getPreferredLanguages() not implemented.");
 	}